1: /* $Id: imach.c,v 1.167 2014/12/22 13:50:56 brouard Exp $
2: $State: Exp $
3: $Log: imach.c,v $
4: Revision 1.167 2014/12/22 13:50:56 brouard
5: Summary: Testing uname and compiler version and if compiled 32 or 64
6:
7: Testing on Linux 64
8:
9: Revision 1.166 2014/12/22 11:40:47 brouard
10: *** empty log message ***
11:
12: Revision 1.165 2014/12/16 11:20:36 brouard
13: Summary: After compiling on Visual C
14:
15: * imach.c (Module): Merging 1.61 to 1.162
16:
17: Revision 1.164 2014/12/16 10:52:11 brouard
18: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
19:
20: * imach.c (Module): Merging 1.61 to 1.162
21:
22: Revision 1.163 2014/12/16 10:30:11 brouard
23: * imach.c (Module): Merging 1.61 to 1.162
24:
25: Revision 1.162 2014/09/25 11:43:39 brouard
26: Summary: temporary backup 0.99!
27:
28: Revision 1.1 2014/09/16 11:06:58 brouard
29: Summary: With some code (wrong) for nlopt
30:
31: Author:
32:
33: Revision 1.161 2014/09/15 20:41:41 brouard
34: Summary: Problem with macro SQR on Intel compiler
35:
36: Revision 1.160 2014/09/02 09:24:05 brouard
37: *** empty log message ***
38:
39: Revision 1.159 2014/09/01 10:34:10 brouard
40: Summary: WIN32
41: Author: Brouard
42:
43: Revision 1.158 2014/08/27 17:11:51 brouard
44: *** empty log message ***
45:
46: Revision 1.157 2014/08/27 16:26:55 brouard
47: Summary: Preparing windows Visual studio version
48: Author: Brouard
49:
50: In order to compile on Visual studio, time.h is now correct and time_t
51: and tm struct should be used. difftime should be used but sometimes I
52: just make the differences in raw time format (time(&now).
53: Trying to suppress #ifdef LINUX
54: Add xdg-open for __linux in order to open default browser.
55:
56: Revision 1.156 2014/08/25 20:10:10 brouard
57: *** empty log message ***
58:
59: Revision 1.155 2014/08/25 18:32:34 brouard
60: Summary: New compile, minor changes
61: Author: Brouard
62:
63: Revision 1.154 2014/06/20 17:32:08 brouard
64: Summary: Outputs now all graphs of convergence to period prevalence
65:
66: Revision 1.153 2014/06/20 16:45:46 brouard
67: Summary: If 3 live state, convergence to period prevalence on same graph
68: Author: Brouard
69:
70: Revision 1.152 2014/06/18 17:54:09 brouard
71: Summary: open browser, use gnuplot on same dir than imach if not found in the path
72:
73: Revision 1.151 2014/06/18 16:43:30 brouard
74: *** empty log message ***
75:
76: Revision 1.150 2014/06/18 16:42:35 brouard
77: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
78: Author: brouard
79:
80: Revision 1.149 2014/06/18 15:51:14 brouard
81: Summary: Some fixes in parameter files errors
82: Author: Nicolas Brouard
83:
84: Revision 1.148 2014/06/17 17:38:48 brouard
85: Summary: Nothing new
86: Author: Brouard
87:
88: Just a new packaging for OS/X version 0.98nS
89:
90: Revision 1.147 2014/06/16 10:33:11 brouard
91: *** empty log message ***
92:
93: Revision 1.146 2014/06/16 10:20:28 brouard
94: Summary: Merge
95: Author: Brouard
96:
97: Merge, before building revised version.
98:
99: Revision 1.145 2014/06/10 21:23:15 brouard
100: Summary: Debugging with valgrind
101: Author: Nicolas Brouard
102:
103: Lot of changes in order to output the results with some covariates
104: After the Edimburgh REVES conference 2014, it seems mandatory to
105: improve the code.
106: No more memory valgrind error but a lot has to be done in order to
107: continue the work of splitting the code into subroutines.
108: Also, decodemodel has been improved. Tricode is still not
109: optimal. nbcode should be improved. Documentation has been added in
110: the source code.
111:
112: Revision 1.143 2014/01/26 09:45:38 brouard
113: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
114:
115: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
116: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
117:
118: Revision 1.142 2014/01/26 03:57:36 brouard
119: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
120:
121: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
122:
123: Revision 1.141 2014/01/26 02:42:01 brouard
124: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
125:
126: Revision 1.140 2011/09/02 10:37:54 brouard
127: Summary: times.h is ok with mingw32 now.
128:
129: Revision 1.139 2010/06/14 07:50:17 brouard
130: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
131: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
132:
133: Revision 1.138 2010/04/30 18:19:40 brouard
134: *** empty log message ***
135:
136: Revision 1.137 2010/04/29 18:11:38 brouard
137: (Module): Checking covariates for more complex models
138: than V1+V2. A lot of change to be done. Unstable.
139:
140: Revision 1.136 2010/04/26 20:30:53 brouard
141: (Module): merging some libgsl code. Fixing computation
142: of likelione (using inter/intrapolation if mle = 0) in order to
143: get same likelihood as if mle=1.
144: Some cleaning of code and comments added.
145:
146: Revision 1.135 2009/10/29 15:33:14 brouard
147: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
148:
149: Revision 1.134 2009/10/29 13:18:53 brouard
150: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
151:
152: Revision 1.133 2009/07/06 10:21:25 brouard
153: just nforces
154:
155: Revision 1.132 2009/07/06 08:22:05 brouard
156: Many tings
157:
158: Revision 1.131 2009/06/20 16:22:47 brouard
159: Some dimensions resccaled
160:
161: Revision 1.130 2009/05/26 06:44:34 brouard
162: (Module): Max Covariate is now set to 20 instead of 8. A
163: lot of cleaning with variables initialized to 0. Trying to make
164: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
165:
166: Revision 1.129 2007/08/31 13:49:27 lievre
167: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
168:
169: Revision 1.128 2006/06/30 13:02:05 brouard
170: (Module): Clarifications on computing e.j
171:
172: Revision 1.127 2006/04/28 18:11:50 brouard
173: (Module): Yes the sum of survivors was wrong since
174: imach-114 because nhstepm was no more computed in the age
175: loop. Now we define nhstepma in the age loop.
176: (Module): In order to speed up (in case of numerous covariates) we
177: compute health expectancies (without variances) in a first step
178: and then all the health expectancies with variances or standard
179: deviation (needs data from the Hessian matrices) which slows the
180: computation.
181: In the future we should be able to stop the program is only health
182: expectancies and graph are needed without standard deviations.
183:
184: Revision 1.126 2006/04/28 17:23:28 brouard
185: (Module): Yes the sum of survivors was wrong since
186: imach-114 because nhstepm was no more computed in the age
187: loop. Now we define nhstepma in the age loop.
188: Version 0.98h
189:
190: Revision 1.125 2006/04/04 15:20:31 lievre
191: Errors in calculation of health expectancies. Age was not initialized.
192: Forecasting file added.
193:
194: Revision 1.124 2006/03/22 17:13:53 lievre
195: Parameters are printed with %lf instead of %f (more numbers after the comma).
196: The log-likelihood is printed in the log file
197:
198: Revision 1.123 2006/03/20 10:52:43 brouard
199: * imach.c (Module): <title> changed, corresponds to .htm file
200: name. <head> headers where missing.
201:
202: * imach.c (Module): Weights can have a decimal point as for
203: English (a comma might work with a correct LC_NUMERIC environment,
204: otherwise the weight is truncated).
205: Modification of warning when the covariates values are not 0 or
206: 1.
207: Version 0.98g
208:
209: Revision 1.122 2006/03/20 09:45:41 brouard
210: (Module): Weights can have a decimal point as for
211: English (a comma might work with a correct LC_NUMERIC environment,
212: otherwise the weight is truncated).
213: Modification of warning when the covariates values are not 0 or
214: 1.
215: Version 0.98g
216:
217: Revision 1.121 2006/03/16 17:45:01 lievre
218: * imach.c (Module): Comments concerning covariates added
219:
220: * imach.c (Module): refinements in the computation of lli if
221: status=-2 in order to have more reliable computation if stepm is
222: not 1 month. Version 0.98f
223:
224: Revision 1.120 2006/03/16 15:10:38 lievre
225: (Module): refinements in the computation of lli if
226: status=-2 in order to have more reliable computation if stepm is
227: not 1 month. Version 0.98f
228:
229: Revision 1.119 2006/03/15 17:42:26 brouard
230: (Module): Bug if status = -2, the loglikelihood was
231: computed as likelihood omitting the logarithm. Version O.98e
232:
233: Revision 1.118 2006/03/14 18:20:07 brouard
234: (Module): varevsij Comments added explaining the second
235: table of variances if popbased=1 .
236: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
237: (Module): Function pstamp added
238: (Module): Version 0.98d
239:
240: Revision 1.117 2006/03/14 17:16:22 brouard
241: (Module): varevsij Comments added explaining the second
242: table of variances if popbased=1 .
243: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
244: (Module): Function pstamp added
245: (Module): Version 0.98d
246:
247: Revision 1.116 2006/03/06 10:29:27 brouard
248: (Module): Variance-covariance wrong links and
249: varian-covariance of ej. is needed (Saito).
250:
251: Revision 1.115 2006/02/27 12:17:45 brouard
252: (Module): One freematrix added in mlikeli! 0.98c
253:
254: Revision 1.114 2006/02/26 12:57:58 brouard
255: (Module): Some improvements in processing parameter
256: filename with strsep.
257:
258: Revision 1.113 2006/02/24 14:20:24 brouard
259: (Module): Memory leaks checks with valgrind and:
260: datafile was not closed, some imatrix were not freed and on matrix
261: allocation too.
262:
263: Revision 1.112 2006/01/30 09:55:26 brouard
264: (Module): Back to gnuplot.exe instead of wgnuplot.exe
265:
266: Revision 1.111 2006/01/25 20:38:18 brouard
267: (Module): Lots of cleaning and bugs added (Gompertz)
268: (Module): Comments can be added in data file. Missing date values
269: can be a simple dot '.'.
270:
271: Revision 1.110 2006/01/25 00:51:50 brouard
272: (Module): Lots of cleaning and bugs added (Gompertz)
273:
274: Revision 1.109 2006/01/24 19:37:15 brouard
275: (Module): Comments (lines starting with a #) are allowed in data.
276:
277: Revision 1.108 2006/01/19 18:05:42 lievre
278: Gnuplot problem appeared...
279: To be fixed
280:
281: Revision 1.107 2006/01/19 16:20:37 brouard
282: Test existence of gnuplot in imach path
283:
284: Revision 1.106 2006/01/19 13:24:36 brouard
285: Some cleaning and links added in html output
286:
287: Revision 1.105 2006/01/05 20:23:19 lievre
288: *** empty log message ***
289:
290: Revision 1.104 2005/09/30 16:11:43 lievre
291: (Module): sump fixed, loop imx fixed, and simplifications.
292: (Module): If the status is missing at the last wave but we know
293: that the person is alive, then we can code his/her status as -2
294: (instead of missing=-1 in earlier versions) and his/her
295: contributions to the likelihood is 1 - Prob of dying from last
296: health status (= 1-p13= p11+p12 in the easiest case of somebody in
297: the healthy state at last known wave). Version is 0.98
298:
299: Revision 1.103 2005/09/30 15:54:49 lievre
300: (Module): sump fixed, loop imx fixed, and simplifications.
301:
302: Revision 1.102 2004/09/15 17:31:30 brouard
303: Add the possibility to read data file including tab characters.
304:
305: Revision 1.101 2004/09/15 10:38:38 brouard
306: Fix on curr_time
307:
308: Revision 1.100 2004/07/12 18:29:06 brouard
309: Add version for Mac OS X. Just define UNIX in Makefile
310:
311: Revision 1.99 2004/06/05 08:57:40 brouard
312: *** empty log message ***
313:
314: Revision 1.98 2004/05/16 15:05:56 brouard
315: New version 0.97 . First attempt to estimate force of mortality
316: directly from the data i.e. without the need of knowing the health
317: state at each age, but using a Gompertz model: log u =a + b*age .
318: This is the basic analysis of mortality and should be done before any
319: other analysis, in order to test if the mortality estimated from the
320: cross-longitudinal survey is different from the mortality estimated
321: from other sources like vital statistic data.
322:
323: The same imach parameter file can be used but the option for mle should be -3.
324:
325: Agnès, who wrote this part of the code, tried to keep most of the
326: former routines in order to include the new code within the former code.
327:
328: The output is very simple: only an estimate of the intercept and of
329: the slope with 95% confident intervals.
330:
331: Current limitations:
332: A) Even if you enter covariates, i.e. with the
333: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
334: B) There is no computation of Life Expectancy nor Life Table.
335:
336: Revision 1.97 2004/02/20 13:25:42 lievre
337: Version 0.96d. Population forecasting command line is (temporarily)
338: suppressed.
339:
340: Revision 1.96 2003/07/15 15:38:55 brouard
341: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
342: rewritten within the same printf. Workaround: many printfs.
343:
344: Revision 1.95 2003/07/08 07:54:34 brouard
345: * imach.c (Repository):
346: (Repository): Using imachwizard code to output a more meaningful covariance
347: matrix (cov(a12,c31) instead of numbers.
348:
349: Revision 1.94 2003/06/27 13:00:02 brouard
350: Just cleaning
351:
352: Revision 1.93 2003/06/25 16:33:55 brouard
353: (Module): On windows (cygwin) function asctime_r doesn't
354: exist so I changed back to asctime which exists.
355: (Module): Version 0.96b
356:
357: Revision 1.92 2003/06/25 16:30:45 brouard
358: (Module): On windows (cygwin) function asctime_r doesn't
359: exist so I changed back to asctime which exists.
360:
361: Revision 1.91 2003/06/25 15:30:29 brouard
362: * imach.c (Repository): Duplicated warning errors corrected.
363: (Repository): Elapsed time after each iteration is now output. It
364: helps to forecast when convergence will be reached. Elapsed time
365: is stamped in powell. We created a new html file for the graphs
366: concerning matrix of covariance. It has extension -cov.htm.
367:
368: Revision 1.90 2003/06/24 12:34:15 brouard
369: (Module): Some bugs corrected for windows. Also, when
370: mle=-1 a template is output in file "or"mypar.txt with the design
371: of the covariance matrix to be input.
372:
373: Revision 1.89 2003/06/24 12:30:52 brouard
374: (Module): Some bugs corrected for windows. Also, when
375: mle=-1 a template is output in file "or"mypar.txt with the design
376: of the covariance matrix to be input.
377:
378: Revision 1.88 2003/06/23 17:54:56 brouard
379: * 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.
380:
381: Revision 1.87 2003/06/18 12:26:01 brouard
382: Version 0.96
383:
384: Revision 1.86 2003/06/17 20:04:08 brouard
385: (Module): Change position of html and gnuplot routines and added
386: routine fileappend.
387:
388: Revision 1.85 2003/06/17 13:12:43 brouard
389: * imach.c (Repository): Check when date of death was earlier that
390: current date of interview. It may happen when the death was just
391: prior to the death. In this case, dh was negative and likelihood
392: was wrong (infinity). We still send an "Error" but patch by
393: assuming that the date of death was just one stepm after the
394: interview.
395: (Repository): Because some people have very long ID (first column)
396: we changed int to long in num[] and we added a new lvector for
397: memory allocation. But we also truncated to 8 characters (left
398: truncation)
399: (Repository): No more line truncation errors.
400:
401: Revision 1.84 2003/06/13 21:44:43 brouard
402: * imach.c (Repository): Replace "freqsummary" at a correct
403: place. It differs from routine "prevalence" which may be called
404: many times. Probs is memory consuming and must be used with
405: parcimony.
406: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
407:
408: Revision 1.83 2003/06/10 13:39:11 lievre
409: *** empty log message ***
410:
411: Revision 1.82 2003/06/05 15:57:20 brouard
412: Add log in imach.c and fullversion number is now printed.
413:
414: */
415: /*
416: Interpolated Markov Chain
417:
418: Short summary of the programme:
419:
420: This program computes Healthy Life Expectancies from
421: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
422: first survey ("cross") where individuals from different ages are
423: interviewed on their health status or degree of disability (in the
424: case of a health survey which is our main interest) -2- at least a
425: second wave of interviews ("longitudinal") which measure each change
426: (if any) in individual health status. Health expectancies are
427: computed from the time spent in each health state according to a
428: model. More health states you consider, more time is necessary to reach the
429: Maximum Likelihood of the parameters involved in the model. The
430: simplest model is the multinomial logistic model where pij is the
431: probability to be observed in state j at the second wave
432: conditional to be observed in state i at the first wave. Therefore
433: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
434: 'age' is age and 'sex' is a covariate. If you want to have a more
435: complex model than "constant and age", you should modify the program
436: where the markup *Covariates have to be included here again* invites
437: you to do it. More covariates you add, slower the
438: convergence.
439:
440: The advantage of this computer programme, compared to a simple
441: multinomial logistic model, is clear when the delay between waves is not
442: identical for each individual. Also, if a individual missed an
443: intermediate interview, the information is lost, but taken into
444: account using an interpolation or extrapolation.
445:
446: hPijx is the probability to be observed in state i at age x+h
447: conditional to the observed state i at age x. The delay 'h' can be
448: split into an exact number (nh*stepm) of unobserved intermediate
449: states. This elementary transition (by month, quarter,
450: semester or year) is modelled as a multinomial logistic. The hPx
451: matrix is simply the matrix product of nh*stepm elementary matrices
452: and the contribution of each individual to the likelihood is simply
453: hPijx.
454:
455: Also this programme outputs the covariance matrix of the parameters but also
456: of the life expectancies. It also computes the period (stable) prevalence.
457:
458: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
459: Institut national d'études démographiques, Paris.
460: This software have been partly granted by Euro-REVES, a concerted action
461: from the European Union.
462: It is copyrighted identically to a GNU software product, ie programme and
463: software can be distributed freely for non commercial use. Latest version
464: can be accessed at http://euroreves.ined.fr/imach .
465:
466: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
467: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
468:
469: **********************************************************************/
470: /*
471: main
472: read parameterfile
473: read datafile
474: concatwav
475: freqsummary
476: if (mle >= 1)
477: mlikeli
478: print results files
479: if mle==1
480: computes hessian
481: read end of parameter file: agemin, agemax, bage, fage, estepm
482: begin-prev-date,...
483: open gnuplot file
484: open html file
485: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
486: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
487: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
488: freexexit2 possible for memory heap.
489:
490: h Pij x | pij_nom ficrestpij
491: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
492: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
493: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
494:
495: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
496: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
497: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
498: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
499: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
500:
501: forecasting if prevfcast==1 prevforecast call prevalence()
502: health expectancies
503: Variance-covariance of DFLE
504: prevalence()
505: movingaverage()
506: varevsij()
507: if popbased==1 varevsij(,popbased)
508: total life expectancies
509: Variance of period (stable) prevalence
510: end
511: */
512:
513: #define POWELL /* Instead of NLOPT */
514:
515: #include <math.h>
516: #include <stdio.h>
517: #include <stdlib.h>
518: #include <string.h>
519:
520: #ifdef _WIN32
521: #include <io.h>
522: #else
523: #include <unistd.h>
524: #endif
525:
526: #include <limits.h>
527: #include <sys/types.h>
528: #include <sys/utsname.h>
529: #include <sys/stat.h>
530: #include <errno.h>
531: /* extern int errno; */
532:
533: /* #ifdef LINUX */
534: /* #include <time.h> */
535: /* #include "timeval.h" */
536: /* #else */
537: /* #include <sys/time.h> */
538: /* #endif */
539:
540: #include <time.h>
541:
542: #ifdef GSL
543: #include <gsl/gsl_errno.h>
544: #include <gsl/gsl_multimin.h>
545: #endif
546:
547:
548: #ifdef NLOPT
549: #include <nlopt.h>
550: typedef struct {
551: double (* function)(double [] );
552: } myfunc_data ;
553: #endif
554:
555: /* #include <libintl.h> */
556: /* #define _(String) gettext (String) */
557:
558: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
559:
560: #define GNUPLOTPROGRAM "gnuplot"
561: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
562: #define FILENAMELENGTH 132
563:
564: #define GLOCK_ERROR_NOPATH -1 /* empty path */
565: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
566:
567: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
568: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
569:
570: #define NINTERVMAX 8
571: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
572: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
573: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
574: #define codtabm(h,k) 1 & (h-1) >> (k-1) ;
575: #define MAXN 20000
576: #define YEARM 12. /**< Number of months per year */
577: #define AGESUP 130
578: #define AGEBASE 40
579: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
580: #ifdef _WIN32
581: #define DIRSEPARATOR '\\'
582: #define CHARSEPARATOR "\\"
583: #define ODIRSEPARATOR '/'
584: #else
585: #define DIRSEPARATOR '/'
586: #define CHARSEPARATOR "/"
587: #define ODIRSEPARATOR '\\'
588: #endif
589:
590: /* $Id: imach.c,v 1.167 2014/12/22 13:50:56 brouard Exp $ */
591: /* $State: Exp $ */
592:
593: char version[]="Imach version 0.99, September 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
594: char fullversion[]="$Revision: 1.167 $ $Date: 2014/12/22 13:50:56 $";
595: char strstart[80];
596: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
597: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
598: int nvar=0, nforce=0; /* Number of variables, number of forces */
599: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
600: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
601: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
602: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
603: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
604: int cptcovprodnoage=0; /**< Number of covariate products without age */
605: int cptcoveff=0; /* Total number of covariates to vary for printing results */
606: int cptcov=0; /* Working variable */
607: int npar=NPARMAX;
608: int nlstate=2; /* Number of live states */
609: int ndeath=1; /* Number of dead states */
610: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
611: int popbased=0;
612:
613: int *wav; /* Number of waves for this individuual 0 is possible */
614: int maxwav=0; /* Maxim number of waves */
615: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
616: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
617: int gipmx=0, gsw=0; /* Global variables on the number of contributions
618: to the likelihood and the sum of weights (done by funcone)*/
619: int mle=1, weightopt=0;
620: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
621: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
622: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
623: * wave mi and wave mi+1 is not an exact multiple of stepm. */
624: int countcallfunc=0; /* Count the number of calls to func */
625: double jmean=1; /* Mean space between 2 waves */
626: double **matprod2(); /* test */
627: double **oldm, **newm, **savm; /* Working pointers to matrices */
628: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
629: /*FILE *fic ; */ /* Used in readdata only */
630: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
631: FILE *ficlog, *ficrespow;
632: int globpr=0; /* Global variable for printing or not */
633: double fretone; /* Only one call to likelihood */
634: long ipmx=0; /* Number of contributions */
635: double sw; /* Sum of weights */
636: char filerespow[FILENAMELENGTH];
637: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
638: FILE *ficresilk;
639: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
640: FILE *ficresprobmorprev;
641: FILE *fichtm, *fichtmcov; /* Html File */
642: FILE *ficreseij;
643: char filerese[FILENAMELENGTH];
644: FILE *ficresstdeij;
645: char fileresstde[FILENAMELENGTH];
646: FILE *ficrescveij;
647: char filerescve[FILENAMELENGTH];
648: FILE *ficresvij;
649: char fileresv[FILENAMELENGTH];
650: FILE *ficresvpl;
651: char fileresvpl[FILENAMELENGTH];
652: char title[MAXLINE];
653: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
654: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
655: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
656: char command[FILENAMELENGTH];
657: int outcmd=0;
658:
659: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
660:
661: char filelog[FILENAMELENGTH]; /* Log file */
662: char filerest[FILENAMELENGTH];
663: char fileregp[FILENAMELENGTH];
664: char popfile[FILENAMELENGTH];
665:
666: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
667:
668: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
669: /* struct timezone tzp; */
670: /* extern int gettimeofday(); */
671: struct tm tml, *gmtime(), *localtime();
672:
673: extern time_t time();
674:
675: struct tm start_time, end_time, curr_time, last_time, forecast_time;
676: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
677: struct tm tm;
678:
679: char strcurr[80], strfor[80];
680:
681: char *endptr;
682: long lval;
683: double dval;
684:
685: #define NR_END 1
686: #define FREE_ARG char*
687: #define FTOL 1.0e-10
688:
689: #define NRANSI
690: #define ITMAX 200
691:
692: #define TOL 2.0e-4
693:
694: #define CGOLD 0.3819660
695: #define ZEPS 1.0e-10
696: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
697:
698: #define GOLD 1.618034
699: #define GLIMIT 100.0
700: #define TINY 1.0e-20
701:
702: static double maxarg1,maxarg2;
703: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
704: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
705:
706: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
707: #define rint(a) floor(a+0.5)
708: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
709: /* #define mytinydouble 1.0e-16 */
710: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
711: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
712: /* static double dsqrarg; */
713: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
714: static double sqrarg;
715: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
716: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
717: int agegomp= AGEGOMP;
718:
719: int imx;
720: int stepm=1;
721: /* Stepm, step in month: minimum step interpolation*/
722:
723: int estepm;
724: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
725:
726: int m,nb;
727: long *num;
728: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
729: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
730: double **pmmij, ***probs;
731: double *ageexmed,*agecens;
732: double dateintmean=0;
733:
734: double *weight;
735: int **s; /* Status */
736: double *agedc;
737: double **covar; /**< covar[j,i], value of jth covariate for individual i,
738: * covar=matrix(0,NCOVMAX,1,n);
739: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
740: double idx;
741: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
742: int *Ndum; /** Freq of modality (tricode */
743: int **codtab; /**< codtab=imatrix(1,100,1,10); */
744: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
745: double *lsurv, *lpop, *tpop;
746:
747: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
748: double ftolhess; /**< Tolerance for computing hessian */
749:
750: /**************** split *************************/
751: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
752: {
753: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
754: the name of the file (name), its extension only (ext) and its first part of the name (finame)
755: */
756: char *ss; /* pointer */
757: int l1, l2; /* length counters */
758:
759: l1 = strlen(path ); /* length of path */
760: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
761: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
762: if ( ss == NULL ) { /* no directory, so determine current directory */
763: strcpy( name, path ); /* we got the fullname name because no directory */
764: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
765: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
766: /* get current working directory */
767: /* extern char* getcwd ( char *buf , int len);*/
768: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
769: return( GLOCK_ERROR_GETCWD );
770: }
771: /* got dirc from getcwd*/
772: printf(" DIRC = %s \n",dirc);
773: } else { /* strip direcotry from path */
774: ss++; /* after this, the filename */
775: l2 = strlen( ss ); /* length of filename */
776: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
777: strcpy( name, ss ); /* save file name */
778: strncpy( dirc, path, l1 - l2 ); /* now the directory */
779: dirc[l1-l2] = 0; /* add zero */
780: printf(" DIRC2 = %s \n",dirc);
781: }
782: /* We add a separator at the end of dirc if not exists */
783: l1 = strlen( dirc ); /* length of directory */
784: if( dirc[l1-1] != DIRSEPARATOR ){
785: dirc[l1] = DIRSEPARATOR;
786: dirc[l1+1] = 0;
787: printf(" DIRC3 = %s \n",dirc);
788: }
789: ss = strrchr( name, '.' ); /* find last / */
790: if (ss >0){
791: ss++;
792: strcpy(ext,ss); /* save extension */
793: l1= strlen( name);
794: l2= strlen(ss)+1;
795: strncpy( finame, name, l1-l2);
796: finame[l1-l2]= 0;
797: }
798:
799: return( 0 ); /* we're done */
800: }
801:
802:
803: /******************************************/
804:
805: void replace_back_to_slash(char *s, char*t)
806: {
807: int i;
808: int lg=0;
809: i=0;
810: lg=strlen(t);
811: for(i=0; i<= lg; i++) {
812: (s[i] = t[i]);
813: if (t[i]== '\\') s[i]='/';
814: }
815: }
816:
817: char *trimbb(char *out, char *in)
818: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
819: char *s;
820: s=out;
821: while (*in != '\0'){
822: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
823: in++;
824: }
825: *out++ = *in++;
826: }
827: *out='\0';
828: return s;
829: }
830:
831: char *cutl(char *blocc, char *alocc, char *in, char occ)
832: {
833: /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ'
834: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
835: gives blocc="abcdef2ghi" and alocc="j".
836: If occ is not found blocc is null and alocc is equal to in. Returns blocc
837: */
838: char *s, *t;
839: t=in;s=in;
840: while ((*in != occ) && (*in != '\0')){
841: *alocc++ = *in++;
842: }
843: if( *in == occ){
844: *(alocc)='\0';
845: s=++in;
846: }
847:
848: if (s == t) {/* occ not found */
849: *(alocc-(in-s))='\0';
850: in=s;
851: }
852: while ( *in != '\0'){
853: *blocc++ = *in++;
854: }
855:
856: *blocc='\0';
857: return t;
858: }
859: char *cutv(char *blocc, char *alocc, char *in, char occ)
860: {
861: /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
862: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
863: gives blocc="abcdef2ghi" and alocc="j".
864: If occ is not found blocc is null and alocc is equal to in. Returns alocc
865: */
866: char *s, *t;
867: t=in;s=in;
868: while (*in != '\0'){
869: while( *in == occ){
870: *blocc++ = *in++;
871: s=in;
872: }
873: *blocc++ = *in++;
874: }
875: if (s == t) /* occ not found */
876: *(blocc-(in-s))='\0';
877: else
878: *(blocc-(in-s)-1)='\0';
879: in=s;
880: while ( *in != '\0'){
881: *alocc++ = *in++;
882: }
883:
884: *alocc='\0';
885: return s;
886: }
887:
888: int nbocc(char *s, char occ)
889: {
890: int i,j=0;
891: int lg=20;
892: i=0;
893: lg=strlen(s);
894: for(i=0; i<= lg; i++) {
895: if (s[i] == occ ) j++;
896: }
897: return j;
898: }
899:
900: /* void cutv(char *u,char *v, char*t, char occ) */
901: /* { */
902: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
903: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
904: /* gives u="abcdef2ghi" and v="j" *\/ */
905: /* int i,lg,j,p=0; */
906: /* i=0; */
907: /* lg=strlen(t); */
908: /* for(j=0; j<=lg-1; j++) { */
909: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
910: /* } */
911:
912: /* for(j=0; j<p; j++) { */
913: /* (u[j] = t[j]); */
914: /* } */
915: /* u[p]='\0'; */
916:
917: /* for(j=0; j<= lg; j++) { */
918: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
919: /* } */
920: /* } */
921:
922: #ifdef _WIN32
923: char * strsep(char **pp, const char *delim)
924: {
925: char *p, *q;
926:
927: if ((p = *pp) == NULL)
928: return 0;
929: if ((q = strpbrk (p, delim)) != NULL)
930: {
931: *pp = q + 1;
932: *q = '\0';
933: }
934: else
935: *pp = 0;
936: return p;
937: }
938: #endif
939:
940: /********************** nrerror ********************/
941:
942: void nrerror(char error_text[])
943: {
944: fprintf(stderr,"ERREUR ...\n");
945: fprintf(stderr,"%s\n",error_text);
946: exit(EXIT_FAILURE);
947: }
948: /*********************** vector *******************/
949: double *vector(int nl, int nh)
950: {
951: double *v;
952: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
953: if (!v) nrerror("allocation failure in vector");
954: return v-nl+NR_END;
955: }
956:
957: /************************ free vector ******************/
958: void free_vector(double*v, int nl, int nh)
959: {
960: free((FREE_ARG)(v+nl-NR_END));
961: }
962:
963: /************************ivector *******************************/
964: int *ivector(long nl,long nh)
965: {
966: int *v;
967: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
968: if (!v) nrerror("allocation failure in ivector");
969: return v-nl+NR_END;
970: }
971:
972: /******************free ivector **************************/
973: void free_ivector(int *v, long nl, long nh)
974: {
975: free((FREE_ARG)(v+nl-NR_END));
976: }
977:
978: /************************lvector *******************************/
979: long *lvector(long nl,long nh)
980: {
981: long *v;
982: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
983: if (!v) nrerror("allocation failure in ivector");
984: return v-nl+NR_END;
985: }
986:
987: /******************free lvector **************************/
988: void free_lvector(long *v, long nl, long nh)
989: {
990: free((FREE_ARG)(v+nl-NR_END));
991: }
992:
993: /******************* imatrix *******************************/
994: int **imatrix(long nrl, long nrh, long ncl, long nch)
995: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
996: {
997: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
998: int **m;
999:
1000: /* allocate pointers to rows */
1001: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1002: if (!m) nrerror("allocation failure 1 in matrix()");
1003: m += NR_END;
1004: m -= nrl;
1005:
1006:
1007: /* allocate rows and set pointers to them */
1008: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1009: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1010: m[nrl] += NR_END;
1011: m[nrl] -= ncl;
1012:
1013: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1014:
1015: /* return pointer to array of pointers to rows */
1016: return m;
1017: }
1018:
1019: /****************** free_imatrix *************************/
1020: void free_imatrix(m,nrl,nrh,ncl,nch)
1021: int **m;
1022: long nch,ncl,nrh,nrl;
1023: /* free an int matrix allocated by imatrix() */
1024: {
1025: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1026: free((FREE_ARG) (m+nrl-NR_END));
1027: }
1028:
1029: /******************* matrix *******************************/
1030: double **matrix(long nrl, long nrh, long ncl, long nch)
1031: {
1032: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1033: double **m;
1034:
1035: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1036: if (!m) nrerror("allocation failure 1 in matrix()");
1037: m += NR_END;
1038: m -= nrl;
1039:
1040: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1041: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1042: m[nrl] += NR_END;
1043: m[nrl] -= ncl;
1044:
1045: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1046: return m;
1047: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1048: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1049: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1050: */
1051: }
1052:
1053: /*************************free matrix ************************/
1054: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1055: {
1056: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1057: free((FREE_ARG)(m+nrl-NR_END));
1058: }
1059:
1060: /******************* ma3x *******************************/
1061: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1062: {
1063: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1064: double ***m;
1065:
1066: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1067: if (!m) nrerror("allocation failure 1 in matrix()");
1068: m += NR_END;
1069: m -= nrl;
1070:
1071: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1072: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1073: m[nrl] += NR_END;
1074: m[nrl] -= ncl;
1075:
1076: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1077:
1078: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1079: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1080: m[nrl][ncl] += NR_END;
1081: m[nrl][ncl] -= nll;
1082: for (j=ncl+1; j<=nch; j++)
1083: m[nrl][j]=m[nrl][j-1]+nlay;
1084:
1085: for (i=nrl+1; i<=nrh; i++) {
1086: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1087: for (j=ncl+1; j<=nch; j++)
1088: m[i][j]=m[i][j-1]+nlay;
1089: }
1090: return m;
1091: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1092: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1093: */
1094: }
1095:
1096: /*************************free ma3x ************************/
1097: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1098: {
1099: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1100: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1101: free((FREE_ARG)(m+nrl-NR_END));
1102: }
1103:
1104: /*************** function subdirf ***********/
1105: char *subdirf(char fileres[])
1106: {
1107: /* Caution optionfilefiname is hidden */
1108: strcpy(tmpout,optionfilefiname);
1109: strcat(tmpout,"/"); /* Add to the right */
1110: strcat(tmpout,fileres);
1111: return tmpout;
1112: }
1113:
1114: /*************** function subdirf2 ***********/
1115: char *subdirf2(char fileres[], char *preop)
1116: {
1117:
1118: /* Caution optionfilefiname is hidden */
1119: strcpy(tmpout,optionfilefiname);
1120: strcat(tmpout,"/");
1121: strcat(tmpout,preop);
1122: strcat(tmpout,fileres);
1123: return tmpout;
1124: }
1125:
1126: /*************** function subdirf3 ***********/
1127: char *subdirf3(char fileres[], char *preop, char *preop2)
1128: {
1129:
1130: /* Caution optionfilefiname is hidden */
1131: strcpy(tmpout,optionfilefiname);
1132: strcat(tmpout,"/");
1133: strcat(tmpout,preop);
1134: strcat(tmpout,preop2);
1135: strcat(tmpout,fileres);
1136: return tmpout;
1137: }
1138:
1139: char *asc_diff_time(long time_sec, char ascdiff[])
1140: {
1141: long sec_left, days, hours, minutes;
1142: days = (time_sec) / (60*60*24);
1143: sec_left = (time_sec) % (60*60*24);
1144: hours = (sec_left) / (60*60) ;
1145: sec_left = (sec_left) %(60*60);
1146: minutes = (sec_left) /60;
1147: sec_left = (sec_left) % (60);
1148: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1149: return ascdiff;
1150: }
1151:
1152: /***************** f1dim *************************/
1153: extern int ncom;
1154: extern double *pcom,*xicom;
1155: extern double (*nrfunc)(double []);
1156:
1157: double f1dim(double x)
1158: {
1159: int j;
1160: double f;
1161: double *xt;
1162:
1163: xt=vector(1,ncom);
1164: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1165: f=(*nrfunc)(xt);
1166: free_vector(xt,1,ncom);
1167: return f;
1168: }
1169:
1170: /*****************brent *************************/
1171: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1172: {
1173: int iter;
1174: double a,b,d,etemp;
1175: double fu=0,fv,fw,fx;
1176: double ftemp=0.;
1177: double p,q,r,tol1,tol2,u,v,w,x,xm;
1178: double e=0.0;
1179:
1180: a=(ax < cx ? ax : cx);
1181: b=(ax > cx ? ax : cx);
1182: x=w=v=bx;
1183: fw=fv=fx=(*f)(x);
1184: for (iter=1;iter<=ITMAX;iter++) {
1185: xm=0.5*(a+b);
1186: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1187: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1188: printf(".");fflush(stdout);
1189: fprintf(ficlog,".");fflush(ficlog);
1190: #ifdef DEBUGBRENT
1191: 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);
1192: 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);
1193: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1194: #endif
1195: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1196: *xmin=x;
1197: return fx;
1198: }
1199: ftemp=fu;
1200: if (fabs(e) > tol1) {
1201: r=(x-w)*(fx-fv);
1202: q=(x-v)*(fx-fw);
1203: p=(x-v)*q-(x-w)*r;
1204: q=2.0*(q-r);
1205: if (q > 0.0) p = -p;
1206: q=fabs(q);
1207: etemp=e;
1208: e=d;
1209: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1210: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1211: else {
1212: d=p/q;
1213: u=x+d;
1214: if (u-a < tol2 || b-u < tol2)
1215: d=SIGN(tol1,xm-x);
1216: }
1217: } else {
1218: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1219: }
1220: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1221: fu=(*f)(u);
1222: if (fu <= fx) {
1223: if (u >= x) a=x; else b=x;
1224: SHFT(v,w,x,u)
1225: SHFT(fv,fw,fx,fu)
1226: } else {
1227: if (u < x) a=u; else b=u;
1228: if (fu <= fw || w == x) {
1229: v=w;
1230: w=u;
1231: fv=fw;
1232: fw=fu;
1233: } else if (fu <= fv || v == x || v == w) {
1234: v=u;
1235: fv=fu;
1236: }
1237: }
1238: }
1239: nrerror("Too many iterations in brent");
1240: *xmin=x;
1241: return fx;
1242: }
1243:
1244: /****************** mnbrak ***********************/
1245:
1246: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1247: double (*func)(double))
1248: {
1249: double ulim,u,r,q, dum;
1250: double fu;
1251:
1252: *fa=(*func)(*ax);
1253: *fb=(*func)(*bx);
1254: if (*fb > *fa) {
1255: SHFT(dum,*ax,*bx,dum)
1256: SHFT(dum,*fb,*fa,dum)
1257: }
1258: *cx=(*bx)+GOLD*(*bx-*ax);
1259: *fc=(*func)(*cx);
1260: while (*fb > *fc) { /* Declining fa, fb, fc */
1261: r=(*bx-*ax)*(*fb-*fc);
1262: q=(*bx-*cx)*(*fb-*fa);
1263: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1264: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1265: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
1266: if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
1267: fu=(*func)(u);
1268: #ifdef DEBUG
1269: /* f(x)=A(x-u)**2+f(u) */
1270: double A, fparabu;
1271: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1272: fparabu= *fa - A*(*ax-u)*(*ax-u);
1273: printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
1274: fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
1275: #endif
1276: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1277: fu=(*func)(u);
1278: if (fu < *fc) {
1279: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1280: SHFT(*fb,*fc,fu,(*func)(u))
1281: }
1282: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1283: u=ulim;
1284: fu=(*func)(u);
1285: } else {
1286: u=(*cx)+GOLD*(*cx-*bx);
1287: fu=(*func)(u);
1288: }
1289: SHFT(*ax,*bx,*cx,u)
1290: SHFT(*fa,*fb,*fc,fu)
1291: }
1292: }
1293:
1294: /*************** linmin ************************/
1295: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1296: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1297: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1298: the value of func at the returned location p . This is actually all accomplished by calling the
1299: routines mnbrak and brent .*/
1300: int ncom;
1301: double *pcom,*xicom;
1302: double (*nrfunc)(double []);
1303:
1304: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1305: {
1306: double brent(double ax, double bx, double cx,
1307: double (*f)(double), double tol, double *xmin);
1308: double f1dim(double x);
1309: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1310: double *fc, double (*func)(double));
1311: int j;
1312: double xx,xmin,bx,ax;
1313: double fx,fb,fa;
1314:
1315: ncom=n;
1316: pcom=vector(1,n);
1317: xicom=vector(1,n);
1318: nrfunc=func;
1319: for (j=1;j<=n;j++) {
1320: pcom[j]=p[j];
1321: xicom[j]=xi[j];
1322: }
1323: ax=0.0;
1324: xx=1.0;
1325: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
1326: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
1327: #ifdef DEBUG
1328: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1329: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1330: #endif
1331: for (j=1;j<=n;j++) {
1332: xi[j] *= xmin;
1333: p[j] += xi[j];
1334: }
1335: free_vector(xicom,1,n);
1336: free_vector(pcom,1,n);
1337: }
1338:
1339:
1340: /*************** powell ************************/
1341: /*
1342: Minimization of a function func of n variables. Input consists of an initial starting point
1343: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1344: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1345: such that failure to decrease by more than this amount on one iteration signals doneness. On
1346: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1347: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1348: */
1349: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1350: double (*func)(double []))
1351: {
1352: void linmin(double p[], double xi[], int n, double *fret,
1353: double (*func)(double []));
1354: int i,ibig,j;
1355: double del,t,*pt,*ptt,*xit;
1356: double fp,fptt;
1357: double *xits;
1358: int niterf, itmp;
1359:
1360: pt=vector(1,n);
1361: ptt=vector(1,n);
1362: xit=vector(1,n);
1363: xits=vector(1,n);
1364: *fret=(*func)(p);
1365: for (j=1;j<=n;j++) pt[j]=p[j];
1366: rcurr_time = time(NULL);
1367: for (*iter=1;;++(*iter)) {
1368: fp=(*fret);
1369: ibig=0;
1370: del=0.0;
1371: rlast_time=rcurr_time;
1372: /* (void) gettimeofday(&curr_time,&tzp); */
1373: rcurr_time = time(NULL);
1374: curr_time = *localtime(&rcurr_time);
1375: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1376: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1377: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1378: for (i=1;i<=n;i++) {
1379: printf(" %d %.12f",i, p[i]);
1380: fprintf(ficlog," %d %.12lf",i, p[i]);
1381: fprintf(ficrespow," %.12lf", p[i]);
1382: }
1383: printf("\n");
1384: fprintf(ficlog,"\n");
1385: fprintf(ficrespow,"\n");fflush(ficrespow);
1386: if(*iter <=3){
1387: tml = *localtime(&rcurr_time);
1388: strcpy(strcurr,asctime(&tml));
1389: rforecast_time=rcurr_time;
1390: itmp = strlen(strcurr);
1391: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1392: strcurr[itmp-1]='\0';
1393: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1394: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1395: for(niterf=10;niterf<=30;niterf+=10){
1396: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1397: forecast_time = *localtime(&rforecast_time);
1398: strcpy(strfor,asctime(&forecast_time));
1399: itmp = strlen(strfor);
1400: if(strfor[itmp-1]=='\n')
1401: strfor[itmp-1]='\0';
1402: 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);
1403: 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);
1404: }
1405: }
1406: for (i=1;i<=n;i++) {
1407: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1408: fptt=(*fret);
1409: #ifdef DEBUG
1410: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1411: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1412: #endif
1413: printf("%d",i);fflush(stdout);
1414: fprintf(ficlog,"%d",i);fflush(ficlog);
1415: linmin(p,xit,n,fret,func);
1416: if (fabs(fptt-(*fret)) > del) {
1417: del=fabs(fptt-(*fret));
1418: ibig=i;
1419: }
1420: #ifdef DEBUG
1421: printf("%d %.12e",i,(*fret));
1422: fprintf(ficlog,"%d %.12e",i,(*fret));
1423: for (j=1;j<=n;j++) {
1424: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1425: printf(" x(%d)=%.12e",j,xit[j]);
1426: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1427: }
1428: for(j=1;j<=n;j++) {
1429: printf(" p(%d)=%.12e",j,p[j]);
1430: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1431: }
1432: printf("\n");
1433: fprintf(ficlog,"\n");
1434: #endif
1435: } /* end i */
1436: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1437: #ifdef DEBUG
1438: int k[2],l;
1439: k[0]=1;
1440: k[1]=-1;
1441: printf("Max: %.12e",(*func)(p));
1442: fprintf(ficlog,"Max: %.12e",(*func)(p));
1443: for (j=1;j<=n;j++) {
1444: printf(" %.12e",p[j]);
1445: fprintf(ficlog," %.12e",p[j]);
1446: }
1447: printf("\n");
1448: fprintf(ficlog,"\n");
1449: for(l=0;l<=1;l++) {
1450: for (j=1;j<=n;j++) {
1451: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1452: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1453: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1454: }
1455: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1456: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1457: }
1458: #endif
1459:
1460:
1461: free_vector(xit,1,n);
1462: free_vector(xits,1,n);
1463: free_vector(ptt,1,n);
1464: free_vector(pt,1,n);
1465: return;
1466: }
1467: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1468: for (j=1;j<=n;j++) { /* Computes an extrapolated point */
1469: ptt[j]=2.0*p[j]-pt[j];
1470: xit[j]=p[j]-pt[j];
1471: pt[j]=p[j];
1472: }
1473: fptt=(*func)(ptt);
1474: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1475: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1476: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1477: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1478: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1479: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1480: /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
1481: /* Thus we compare delta(2h) with observed f1-f3 */
1482: /* or best gain on one ancient line 'del' with total */
1483: /* gain f1-f2 = f1 - f2 - 'del' with del */
1484: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1485:
1486: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
1487: t= t- del*SQR(fp-fptt);
1488: printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
1489: fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
1490: #ifdef DEBUG
1491: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1492: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1493: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1494: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1495: printf("tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
1496: fprintf(ficlog, "tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
1497: #endif
1498: if (t < 0.0) { /* Then we use it for last direction */
1499: linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
1500: for (j=1;j<=n;j++) {
1501: xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
1502: xi[j][n]=xit[j]; /* and nth direction by the extrapolated */
1503: }
1504: printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1505: fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction :\n",n,ibig);
1506:
1507: #ifdef DEBUG
1508: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1509: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1510: for(j=1;j<=n;j++){
1511: printf(" %.12e",xit[j]);
1512: fprintf(ficlog," %.12e",xit[j]);
1513: }
1514: printf("\n");
1515: fprintf(ficlog,"\n");
1516: #endif
1517: } /* end of t negative */
1518: } /* end if (fptt < fp) */
1519: }
1520: }
1521:
1522: /**** Prevalence limit (stable or period prevalence) ****************/
1523:
1524: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1525: {
1526: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1527: matrix by transitions matrix until convergence is reached */
1528:
1529: int i, ii,j,k;
1530: double min, max, maxmin, maxmax,sumnew=0.;
1531: /* double **matprod2(); */ /* test */
1532: double **out, cov[NCOVMAX+1], **pmij();
1533: double **newm;
1534: double agefin, delaymax=50 ; /* Max number of years to converge */
1535:
1536: for (ii=1;ii<=nlstate+ndeath;ii++)
1537: for (j=1;j<=nlstate+ndeath;j++){
1538: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1539: }
1540:
1541: cov[1]=1.;
1542:
1543: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1544: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1545: newm=savm;
1546: /* Covariates have to be included here again */
1547: cov[2]=agefin;
1548:
1549: for (k=1; k<=cptcovn;k++) {
1550: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1551: /*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]]);*/
1552: }
1553: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1554: /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
1555: /* cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
1556:
1557: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1558: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1559: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1560: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1561: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1562: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1563:
1564: savm=oldm;
1565: oldm=newm;
1566: maxmax=0.;
1567: for(j=1;j<=nlstate;j++){
1568: min=1.;
1569: max=0.;
1570: for(i=1; i<=nlstate; i++) {
1571: sumnew=0;
1572: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1573: prlim[i][j]= newm[i][j]/(1-sumnew);
1574: /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
1575: max=FMAX(max,prlim[i][j]);
1576: min=FMIN(min,prlim[i][j]);
1577: }
1578: maxmin=max-min;
1579: maxmax=FMAX(maxmax,maxmin);
1580: }
1581: if(maxmax < ftolpl){
1582: return prlim;
1583: }
1584: }
1585: }
1586:
1587: /*************** transition probabilities ***************/
1588:
1589: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1590: {
1591: /* According to parameters values stored in x and the covariate's values stored in cov,
1592: computes the probability to be observed in state j being in state i by appying the
1593: model to the ncovmodel covariates (including constant and age).
1594: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1595: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1596: ncth covariate in the global vector x is given by the formula:
1597: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1598: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1599: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1600: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1601: Outputs ps[i][j] the probability to be observed in j being in j according to
1602: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1603: */
1604: double s1, lnpijopii;
1605: /*double t34;*/
1606: int i,j, nc, ii, jj;
1607:
1608: for(i=1; i<= nlstate; i++){
1609: for(j=1; j<i;j++){
1610: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1611: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1612: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1613: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1614: }
1615: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1616: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1617: }
1618: for(j=i+1; j<=nlstate+ndeath;j++){
1619: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1620: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
1621: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
1622: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1623: }
1624: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1625: }
1626: }
1627:
1628: for(i=1; i<= nlstate; i++){
1629: s1=0;
1630: for(j=1; j<i; j++){
1631: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1632: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1633: }
1634: for(j=i+1; j<=nlstate+ndeath; j++){
1635: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1636: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1637: }
1638: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1639: ps[i][i]=1./(s1+1.);
1640: /* Computing other pijs */
1641: for(j=1; j<i; j++)
1642: ps[i][j]= exp(ps[i][j])*ps[i][i];
1643: for(j=i+1; j<=nlstate+ndeath; j++)
1644: ps[i][j]= exp(ps[i][j])*ps[i][i];
1645: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1646: } /* end i */
1647:
1648: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1649: for(jj=1; jj<= nlstate+ndeath; jj++){
1650: ps[ii][jj]=0;
1651: ps[ii][ii]=1;
1652: }
1653: }
1654:
1655:
1656: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1657: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1658: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
1659: /* } */
1660: /* printf("\n "); */
1661: /* } */
1662: /* printf("\n ");printf("%lf ",cov[2]);*/
1663: /*
1664: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1665: goto end;*/
1666: return ps;
1667: }
1668:
1669: /**************** Product of 2 matrices ******************/
1670:
1671: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1672: {
1673: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1674: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1675: /* in, b, out are matrice of pointers which should have been initialized
1676: before: only the contents of out is modified. The function returns
1677: a pointer to pointers identical to out */
1678: int i, j, k;
1679: for(i=nrl; i<= nrh; i++)
1680: for(k=ncolol; k<=ncoloh; k++){
1681: out[i][k]=0.;
1682: for(j=ncl; j<=nch; j++)
1683: out[i][k] +=in[i][j]*b[j][k];
1684: }
1685: return out;
1686: }
1687:
1688:
1689: /************* Higher Matrix Product ***************/
1690:
1691: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1692: {
1693: /* Computes the transition matrix starting at age 'age' over
1694: 'nhstepm*hstepm*stepm' months (i.e. until
1695: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1696: nhstepm*hstepm matrices.
1697: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1698: (typically every 2 years instead of every month which is too big
1699: for the memory).
1700: Model is determined by parameters x and covariates have to be
1701: included manually here.
1702:
1703: */
1704:
1705: int i, j, d, h, k;
1706: double **out, cov[NCOVMAX+1];
1707: double **newm;
1708:
1709: /* Hstepm could be zero and should return the unit matrix */
1710: for (i=1;i<=nlstate+ndeath;i++)
1711: for (j=1;j<=nlstate+ndeath;j++){
1712: oldm[i][j]=(i==j ? 1.0 : 0.0);
1713: po[i][j][0]=(i==j ? 1.0 : 0.0);
1714: }
1715: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1716: for(h=1; h <=nhstepm; h++){
1717: for(d=1; d <=hstepm; d++){
1718: newm=savm;
1719: /* Covariates have to be included here again */
1720: cov[1]=1.;
1721: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1722: for (k=1; k<=cptcovn;k++)
1723: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1724: for (k=1; k<=cptcovage;k++)
1725: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1726: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1727: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1728:
1729:
1730: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1731: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1732: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1733: pmij(pmmij,cov,ncovmodel,x,nlstate));
1734: savm=oldm;
1735: oldm=newm;
1736: }
1737: for(i=1; i<=nlstate+ndeath; i++)
1738: for(j=1;j<=nlstate+ndeath;j++) {
1739: po[i][j][h]=newm[i][j];
1740: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1741: }
1742: /*printf("h=%d ",h);*/
1743: } /* end h */
1744: /* printf("\n H=%d \n",h); */
1745: return po;
1746: }
1747:
1748: #ifdef NLOPT
1749: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
1750: double fret;
1751: double *xt;
1752: int j;
1753: myfunc_data *d2 = (myfunc_data *) pd;
1754: /* xt = (p1-1); */
1755: xt=vector(1,n);
1756: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
1757:
1758: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
1759: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
1760: printf("Function = %.12lf ",fret);
1761: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
1762: printf("\n");
1763: free_vector(xt,1,n);
1764: return fret;
1765: }
1766: #endif
1767:
1768: /*************** log-likelihood *************/
1769: double func( double *x)
1770: {
1771: int i, ii, j, k, mi, d, kk;
1772: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1773: double **out;
1774: double sw; /* Sum of weights */
1775: double lli; /* Individual log likelihood */
1776: int s1, s2;
1777: double bbh, survp;
1778: long ipmx;
1779: /*extern weight */
1780: /* We are differentiating ll according to initial status */
1781: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1782: /*for(i=1;i<imx;i++)
1783: printf(" %d\n",s[4][i]);
1784: */
1785:
1786: ++countcallfunc;
1787:
1788: cov[1]=1.;
1789:
1790: for(k=1; k<=nlstate; k++) ll[k]=0.;
1791:
1792: if(mle==1){
1793: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1794: /* Computes the values of the ncovmodel covariates of the model
1795: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
1796: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
1797: to be observed in j being in i according to the model.
1798: */
1799: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1800: cov[2+k]=covar[Tvar[k]][i];
1801: }
1802: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1803: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1804: has been calculated etc */
1805: for(mi=1; mi<= wav[i]-1; mi++){
1806: for (ii=1;ii<=nlstate+ndeath;ii++)
1807: for (j=1;j<=nlstate+ndeath;j++){
1808: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1809: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1810: }
1811: for(d=0; d<dh[mi][i]; d++){
1812: newm=savm;
1813: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1814: for (kk=1; kk<=cptcovage;kk++) {
1815: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
1816: }
1817: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1818: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1819: savm=oldm;
1820: oldm=newm;
1821: } /* end mult */
1822:
1823: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1824: /* But now since version 0.9 we anticipate for bias at large stepm.
1825: * If stepm is larger than one month (smallest stepm) and if the exact delay
1826: * (in months) between two waves is not a multiple of stepm, we rounded to
1827: * the nearest (and in case of equal distance, to the lowest) interval but now
1828: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1829: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1830: * probability in order to take into account the bias as a fraction of the way
1831: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1832: * -stepm/2 to stepm/2 .
1833: * For stepm=1 the results are the same as for previous versions of Imach.
1834: * For stepm > 1 the results are less biased than in previous versions.
1835: */
1836: s1=s[mw[mi][i]][i];
1837: s2=s[mw[mi+1][i]][i];
1838: bbh=(double)bh[mi][i]/(double)stepm;
1839: /* bias bh is positive if real duration
1840: * is higher than the multiple of stepm and negative otherwise.
1841: */
1842: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1843: if( s2 > nlstate){
1844: /* i.e. if s2 is a death state and if the date of death is known
1845: then the contribution to the likelihood is the probability to
1846: die between last step unit time and current step unit time,
1847: which is also equal to probability to die before dh
1848: minus probability to die before dh-stepm .
1849: In version up to 0.92 likelihood was computed
1850: as if date of death was unknown. Death was treated as any other
1851: health state: the date of the interview describes the actual state
1852: and not the date of a change in health state. The former idea was
1853: to consider that at each interview the state was recorded
1854: (healthy, disable or death) and IMaCh was corrected; but when we
1855: introduced the exact date of death then we should have modified
1856: the contribution of an exact death to the likelihood. This new
1857: contribution is smaller and very dependent of the step unit
1858: stepm. It is no more the probability to die between last interview
1859: and month of death but the probability to survive from last
1860: interview up to one month before death multiplied by the
1861: probability to die within a month. Thanks to Chris
1862: Jackson for correcting this bug. Former versions increased
1863: mortality artificially. The bad side is that we add another loop
1864: which slows down the processing. The difference can be up to 10%
1865: lower mortality.
1866: */
1867: lli=log(out[s1][s2] - savm[s1][s2]);
1868:
1869:
1870: } else if (s2==-2) {
1871: for (j=1,survp=0. ; j<=nlstate; j++)
1872: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1873: /*survp += out[s1][j]; */
1874: lli= log(survp);
1875: }
1876:
1877: else if (s2==-4) {
1878: for (j=3,survp=0. ; j<=nlstate; j++)
1879: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1880: lli= log(survp);
1881: }
1882:
1883: else if (s2==-5) {
1884: for (j=1,survp=0. ; j<=2; j++)
1885: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1886: lli= log(survp);
1887: }
1888:
1889: else{
1890: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1891: /* 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 */
1892: }
1893: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1894: /*if(lli ==000.0)*/
1895: /*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); */
1896: ipmx +=1;
1897: sw += weight[i];
1898: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1899: } /* end of wave */
1900: } /* end of individual */
1901: } else if(mle==2){
1902: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1903: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1904: for(mi=1; mi<= wav[i]-1; mi++){
1905: for (ii=1;ii<=nlstate+ndeath;ii++)
1906: for (j=1;j<=nlstate+ndeath;j++){
1907: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1908: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1909: }
1910: for(d=0; d<=dh[mi][i]; d++){
1911: newm=savm;
1912: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1913: for (kk=1; kk<=cptcovage;kk++) {
1914: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1915: }
1916: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1917: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1918: savm=oldm;
1919: oldm=newm;
1920: } /* end mult */
1921:
1922: s1=s[mw[mi][i]][i];
1923: s2=s[mw[mi+1][i]][i];
1924: bbh=(double)bh[mi][i]/(double)stepm;
1925: 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 */
1926: ipmx +=1;
1927: sw += weight[i];
1928: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1929: } /* end of wave */
1930: } /* end of individual */
1931: } else if(mle==3){ /* exponential inter-extrapolation */
1932: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1933: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1934: for(mi=1; mi<= wav[i]-1; mi++){
1935: for (ii=1;ii<=nlstate+ndeath;ii++)
1936: for (j=1;j<=nlstate+ndeath;j++){
1937: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1938: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1939: }
1940: for(d=0; d<dh[mi][i]; d++){
1941: newm=savm;
1942: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1943: for (kk=1; kk<=cptcovage;kk++) {
1944: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1945: }
1946: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1947: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1948: savm=oldm;
1949: oldm=newm;
1950: } /* end mult */
1951:
1952: s1=s[mw[mi][i]][i];
1953: s2=s[mw[mi+1][i]][i];
1954: bbh=(double)bh[mi][i]/(double)stepm;
1955: 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 */
1956: ipmx +=1;
1957: sw += weight[i];
1958: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1959: } /* end of wave */
1960: } /* end of individual */
1961: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1962: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1963: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1964: for(mi=1; mi<= wav[i]-1; mi++){
1965: for (ii=1;ii<=nlstate+ndeath;ii++)
1966: for (j=1;j<=nlstate+ndeath;j++){
1967: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1968: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1969: }
1970: for(d=0; d<dh[mi][i]; d++){
1971: newm=savm;
1972: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1973: for (kk=1; kk<=cptcovage;kk++) {
1974: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1975: }
1976:
1977: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1978: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1979: savm=oldm;
1980: oldm=newm;
1981: } /* end mult */
1982:
1983: s1=s[mw[mi][i]][i];
1984: s2=s[mw[mi+1][i]][i];
1985: if( s2 > nlstate){
1986: lli=log(out[s1][s2] - savm[s1][s2]);
1987: }else{
1988: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1989: }
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: } /* end of wave */
1995: } /* end of individual */
1996: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1997: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1998: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1999: for(mi=1; mi<= wav[i]-1; mi++){
2000: for (ii=1;ii<=nlstate+ndeath;ii++)
2001: for (j=1;j<=nlstate+ndeath;j++){
2002: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2003: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2004: }
2005: for(d=0; d<dh[mi][i]; d++){
2006: newm=savm;
2007: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2008: for (kk=1; kk<=cptcovage;kk++) {
2009: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2010: }
2011:
2012: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2013: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2014: savm=oldm;
2015: oldm=newm;
2016: } /* end mult */
2017:
2018: s1=s[mw[mi][i]][i];
2019: s2=s[mw[mi+1][i]][i];
2020: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2021: ipmx +=1;
2022: sw += weight[i];
2023: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2024: /*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]);*/
2025: } /* end of wave */
2026: } /* end of individual */
2027: } /* End of if */
2028: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2029: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2030: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2031: return -l;
2032: }
2033:
2034: /*************** log-likelihood *************/
2035: double funcone( double *x)
2036: {
2037: /* Same as likeli but slower because of a lot of printf and if */
2038: int i, ii, j, k, mi, d, kk;
2039: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
2040: double **out;
2041: double lli; /* Individual log likelihood */
2042: double llt;
2043: int s1, s2;
2044: double bbh, survp;
2045: /*extern weight */
2046: /* We are differentiating ll according to initial status */
2047: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2048: /*for(i=1;i<imx;i++)
2049: printf(" %d\n",s[4][i]);
2050: */
2051: cov[1]=1.;
2052:
2053: for(k=1; k<=nlstate; k++) ll[k]=0.;
2054:
2055: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2056: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2057: for(mi=1; mi<= wav[i]-1; mi++){
2058: for (ii=1;ii<=nlstate+ndeath;ii++)
2059: for (j=1;j<=nlstate+ndeath;j++){
2060: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2061: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2062: }
2063: for(d=0; d<dh[mi][i]; d++){
2064: newm=savm;
2065: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2066: for (kk=1; kk<=cptcovage;kk++) {
2067: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2068: }
2069: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2070: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2071: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2072: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2073: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
2074: savm=oldm;
2075: oldm=newm;
2076: } /* end mult */
2077:
2078: s1=s[mw[mi][i]][i];
2079: s2=s[mw[mi+1][i]][i];
2080: bbh=(double)bh[mi][i]/(double)stepm;
2081: /* bias is positive if real duration
2082: * is higher than the multiple of stepm and negative otherwise.
2083: */
2084: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2085: lli=log(out[s1][s2] - savm[s1][s2]);
2086: } else if (s2==-2) {
2087: for (j=1,survp=0. ; j<=nlstate; j++)
2088: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2089: lli= log(survp);
2090: }else if (mle==1){
2091: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2092: } else if(mle==2){
2093: 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 */
2094: } else if(mle==3){ /* exponential inter-extrapolation */
2095: 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 */
2096: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2097: lli=log(out[s1][s2]); /* Original formula */
2098: } else{ /* mle=0 back to 1 */
2099: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2100: /*lli=log(out[s1][s2]); */ /* Original formula */
2101: } /* End of if */
2102: ipmx +=1;
2103: sw += weight[i];
2104: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2105: /*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]); */
2106: if(globpr){
2107: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
2108: %11.6f %11.6f %11.6f ", \
2109: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
2110: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2111: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2112: llt +=ll[k]*gipmx/gsw;
2113: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2114: }
2115: fprintf(ficresilk," %10.6f\n", -llt);
2116: }
2117: } /* end of wave */
2118: } /* end of individual */
2119: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2120: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2121: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2122: if(globpr==0){ /* First time we count the contributions and weights */
2123: gipmx=ipmx;
2124: gsw=sw;
2125: }
2126: return -l;
2127: }
2128:
2129:
2130: /*************** function likelione ***********/
2131: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2132: {
2133: /* This routine should help understanding what is done with
2134: the selection of individuals/waves and
2135: to check the exact contribution to the likelihood.
2136: Plotting could be done.
2137: */
2138: int k;
2139:
2140: if(*globpri !=0){ /* Just counts and sums, no printings */
2141: strcpy(fileresilk,"ilk");
2142: strcat(fileresilk,fileres);
2143: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2144: printf("Problem with resultfile: %s\n", fileresilk);
2145: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2146: }
2147: 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");
2148: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
2149: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2150: for(k=1; k<=nlstate; k++)
2151: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2152: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2153: }
2154:
2155: *fretone=(*funcone)(p);
2156: if(*globpri !=0){
2157: fclose(ficresilk);
2158: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
2159: fflush(fichtm);
2160: }
2161: return;
2162: }
2163:
2164:
2165: /*********** Maximum Likelihood Estimation ***************/
2166:
2167: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2168: {
2169: int i,j, iter=0;
2170: double **xi;
2171: double fret;
2172: double fretone; /* Only one call to likelihood */
2173: /* char filerespow[FILENAMELENGTH];*/
2174:
2175: #ifdef NLOPT
2176: int creturn;
2177: nlopt_opt opt;
2178: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2179: double *lb;
2180: double minf; /* the minimum objective value, upon return */
2181: double * p1; /* Shifted parameters from 0 instead of 1 */
2182: myfunc_data dinst, *d = &dinst;
2183: #endif
2184:
2185:
2186: xi=matrix(1,npar,1,npar);
2187: for (i=1;i<=npar;i++)
2188: for (j=1;j<=npar;j++)
2189: xi[i][j]=(i==j ? 1.0 : 0.0);
2190: printf("Powell\n"); fprintf(ficlog,"Powell\n");
2191: strcpy(filerespow,"pow");
2192: strcat(filerespow,fileres);
2193: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2194: printf("Problem with resultfile: %s\n", filerespow);
2195: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2196: }
2197: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2198: for (i=1;i<=nlstate;i++)
2199: for(j=1;j<=nlstate+ndeath;j++)
2200: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2201: fprintf(ficrespow,"\n");
2202: #ifdef POWELL
2203: powell(p,xi,npar,ftol,&iter,&fret,func);
2204: #endif
2205:
2206: #ifdef NLOPT
2207: #ifdef NEWUOA
2208: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2209: #else
2210: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2211: #endif
2212: lb=vector(0,npar-1);
2213: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2214: nlopt_set_lower_bounds(opt, lb);
2215: nlopt_set_initial_step1(opt, 0.1);
2216:
2217: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2218: d->function = func;
2219: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2220: nlopt_set_min_objective(opt, myfunc, d);
2221: nlopt_set_xtol_rel(opt, ftol);
2222: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2223: printf("nlopt failed! %d\n",creturn);
2224: }
2225: else {
2226: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2227: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2228: iter=1; /* not equal */
2229: }
2230: nlopt_destroy(opt);
2231: #endif
2232: free_matrix(xi,1,npar,1,npar);
2233: fclose(ficrespow);
2234: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2235: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2236: fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2237:
2238: }
2239:
2240: /**** Computes Hessian and covariance matrix ***/
2241: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
2242: {
2243: double **a,**y,*x,pd;
2244: double **hess;
2245: int i, j;
2246: int *indx;
2247:
2248: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
2249: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
2250: void lubksb(double **a, int npar, int *indx, double b[]) ;
2251: void ludcmp(double **a, int npar, int *indx, double *d) ;
2252: double gompertz(double p[]);
2253: hess=matrix(1,npar,1,npar);
2254:
2255: printf("\nCalculation of the hessian matrix. Wait...\n");
2256: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2257: for (i=1;i<=npar;i++){
2258: printf("%d",i);fflush(stdout);
2259: fprintf(ficlog,"%d",i);fflush(ficlog);
2260:
2261: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2262:
2263: /* printf(" %f ",p[i]);
2264: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2265: }
2266:
2267: for (i=1;i<=npar;i++) {
2268: for (j=1;j<=npar;j++) {
2269: if (j>i) {
2270: printf(".%d%d",i,j);fflush(stdout);
2271: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
2272: hess[i][j]=hessij(p,delti,i,j,func,npar);
2273:
2274: hess[j][i]=hess[i][j];
2275: /*printf(" %lf ",hess[i][j]);*/
2276: }
2277: }
2278: }
2279: printf("\n");
2280: fprintf(ficlog,"\n");
2281:
2282: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2283: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2284:
2285: a=matrix(1,npar,1,npar);
2286: y=matrix(1,npar,1,npar);
2287: x=vector(1,npar);
2288: indx=ivector(1,npar);
2289: for (i=1;i<=npar;i++)
2290: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2291: ludcmp(a,npar,indx,&pd);
2292:
2293: for (j=1;j<=npar;j++) {
2294: for (i=1;i<=npar;i++) x[i]=0;
2295: x[j]=1;
2296: lubksb(a,npar,indx,x);
2297: for (i=1;i<=npar;i++){
2298: matcov[i][j]=x[i];
2299: }
2300: }
2301:
2302: printf("\n#Hessian matrix#\n");
2303: fprintf(ficlog,"\n#Hessian matrix#\n");
2304: for (i=1;i<=npar;i++) {
2305: for (j=1;j<=npar;j++) {
2306: printf("%.3e ",hess[i][j]);
2307: fprintf(ficlog,"%.3e ",hess[i][j]);
2308: }
2309: printf("\n");
2310: fprintf(ficlog,"\n");
2311: }
2312:
2313: /* Recompute Inverse */
2314: for (i=1;i<=npar;i++)
2315: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
2316: ludcmp(a,npar,indx,&pd);
2317:
2318: /* printf("\n#Hessian matrix recomputed#\n");
2319:
2320: for (j=1;j<=npar;j++) {
2321: for (i=1;i<=npar;i++) x[i]=0;
2322: x[j]=1;
2323: lubksb(a,npar,indx,x);
2324: for (i=1;i<=npar;i++){
2325: y[i][j]=x[i];
2326: printf("%.3e ",y[i][j]);
2327: fprintf(ficlog,"%.3e ",y[i][j]);
2328: }
2329: printf("\n");
2330: fprintf(ficlog,"\n");
2331: }
2332: */
2333:
2334: free_matrix(a,1,npar,1,npar);
2335: free_matrix(y,1,npar,1,npar);
2336: free_vector(x,1,npar);
2337: free_ivector(indx,1,npar);
2338: free_matrix(hess,1,npar,1,npar);
2339:
2340:
2341: }
2342:
2343: /*************** hessian matrix ****************/
2344: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2345: {
2346: int i;
2347: int l=1, lmax=20;
2348: double k1,k2;
2349: double p2[MAXPARM+1]; /* identical to x */
2350: double res;
2351: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2352: double fx;
2353: int k=0,kmax=10;
2354: double l1;
2355:
2356: fx=func(x);
2357: for (i=1;i<=npar;i++) p2[i]=x[i];
2358: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
2359: l1=pow(10,l);
2360: delts=delt;
2361: for(k=1 ; k <kmax; k=k+1){
2362: delt = delta*(l1*k);
2363: p2[theta]=x[theta] +delt;
2364: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
2365: p2[theta]=x[theta]-delt;
2366: k2=func(p2)-fx;
2367: /*res= (k1-2.0*fx+k2)/delt/delt; */
2368: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2369:
2370: #ifdef DEBUGHESS
2371: 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);
2372: 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);
2373: #endif
2374: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2375: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2376: k=kmax;
2377: }
2378: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
2379: k=kmax; l=lmax*10;
2380: }
2381: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2382: delts=delt;
2383: }
2384: }
2385: }
2386: delti[theta]=delts;
2387: return res;
2388:
2389: }
2390:
2391: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2392: {
2393: int i;
2394: int l=1, lmax=20;
2395: double k1,k2,k3,k4,res,fx;
2396: double p2[MAXPARM+1];
2397: int k;
2398:
2399: fx=func(x);
2400: for (k=1; k<=2; k++) {
2401: for (i=1;i<=npar;i++) p2[i]=x[i];
2402: p2[thetai]=x[thetai]+delti[thetai]/k;
2403: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2404: k1=func(p2)-fx;
2405:
2406: p2[thetai]=x[thetai]+delti[thetai]/k;
2407: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2408: k2=func(p2)-fx;
2409:
2410: p2[thetai]=x[thetai]-delti[thetai]/k;
2411: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2412: k3=func(p2)-fx;
2413:
2414: p2[thetai]=x[thetai]-delti[thetai]/k;
2415: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2416: k4=func(p2)-fx;
2417: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2418: #ifdef DEBUG
2419: 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);
2420: 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);
2421: #endif
2422: }
2423: return res;
2424: }
2425:
2426: /************** Inverse of matrix **************/
2427: void ludcmp(double **a, int n, int *indx, double *d)
2428: {
2429: int i,imax,j,k;
2430: double big,dum,sum,temp;
2431: double *vv;
2432:
2433: vv=vector(1,n);
2434: *d=1.0;
2435: for (i=1;i<=n;i++) {
2436: big=0.0;
2437: for (j=1;j<=n;j++)
2438: if ((temp=fabs(a[i][j])) > big) big=temp;
2439: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2440: vv[i]=1.0/big;
2441: }
2442: for (j=1;j<=n;j++) {
2443: for (i=1;i<j;i++) {
2444: sum=a[i][j];
2445: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2446: a[i][j]=sum;
2447: }
2448: big=0.0;
2449: for (i=j;i<=n;i++) {
2450: sum=a[i][j];
2451: for (k=1;k<j;k++)
2452: sum -= a[i][k]*a[k][j];
2453: a[i][j]=sum;
2454: if ( (dum=vv[i]*fabs(sum)) >= big) {
2455: big=dum;
2456: imax=i;
2457: }
2458: }
2459: if (j != imax) {
2460: for (k=1;k<=n;k++) {
2461: dum=a[imax][k];
2462: a[imax][k]=a[j][k];
2463: a[j][k]=dum;
2464: }
2465: *d = -(*d);
2466: vv[imax]=vv[j];
2467: }
2468: indx[j]=imax;
2469: if (a[j][j] == 0.0) a[j][j]=TINY;
2470: if (j != n) {
2471: dum=1.0/(a[j][j]);
2472: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2473: }
2474: }
2475: free_vector(vv,1,n); /* Doesn't work */
2476: ;
2477: }
2478:
2479: void lubksb(double **a, int n, int *indx, double b[])
2480: {
2481: int i,ii=0,ip,j;
2482: double sum;
2483:
2484: for (i=1;i<=n;i++) {
2485: ip=indx[i];
2486: sum=b[ip];
2487: b[ip]=b[i];
2488: if (ii)
2489: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2490: else if (sum) ii=i;
2491: b[i]=sum;
2492: }
2493: for (i=n;i>=1;i--) {
2494: sum=b[i];
2495: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2496: b[i]=sum/a[i][i];
2497: }
2498: }
2499:
2500: void pstamp(FILE *fichier)
2501: {
2502: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2503: }
2504:
2505: /************ Frequencies ********************/
2506: 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[])
2507: { /* Some frequencies */
2508:
2509: int i, m, jk, j1, bool, z1,j;
2510: int first;
2511: double ***freq; /* Frequencies */
2512: double *pp, **prop;
2513: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2514: char fileresp[FILENAMELENGTH];
2515:
2516: pp=vector(1,nlstate);
2517: prop=matrix(1,nlstate,iagemin,iagemax+3);
2518: strcpy(fileresp,"p");
2519: strcat(fileresp,fileres);
2520: if((ficresp=fopen(fileresp,"w"))==NULL) {
2521: printf("Problem with prevalence resultfile: %s\n", fileresp);
2522: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2523: exit(0);
2524: }
2525: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2526: j1=0;
2527:
2528: j=cptcoveff;
2529: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2530:
2531: first=1;
2532:
2533: /* for(k1=1; k1<=j ; k1++){ /* Loop on covariates */
2534: /* for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
2535: /* j1++;
2536: */
2537: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
2538: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2539: scanf("%d", i);*/
2540: for (i=-5; i<=nlstate+ndeath; i++)
2541: for (jk=-5; jk<=nlstate+ndeath; jk++)
2542: for(m=iagemin; m <= iagemax+3; m++)
2543: freq[i][jk][m]=0;
2544:
2545: for (i=1; i<=nlstate; i++)
2546: for(m=iagemin; m <= iagemax+3; m++)
2547: prop[i][m]=0;
2548:
2549: dateintsum=0;
2550: k2cpt=0;
2551: for (i=1; i<=imx; i++) {
2552: bool=1;
2553: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
2554: for (z1=1; z1<=cptcoveff; z1++)
2555: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
2556: /* Tests if the value of each of the covariates of i is equal to filter j1 */
2557: bool=0;
2558: /* 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",
2559: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
2560: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
2561: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
2562: }
2563: }
2564:
2565: if (bool==1){
2566: for(m=firstpass; m<=lastpass; m++){
2567: k2=anint[m][i]+(mint[m][i]/12.);
2568: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2569: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2570: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2571: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2572: if (m<lastpass) {
2573: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2574: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2575: }
2576:
2577: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2578: dateintsum=dateintsum+k2;
2579: k2cpt++;
2580: }
2581: /*}*/
2582: }
2583: }
2584: } /* end i */
2585:
2586: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2587: pstamp(ficresp);
2588: if (cptcovn>0) {
2589: fprintf(ficresp, "\n#********** Variable ");
2590: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2591: fprintf(ficresp, "**********\n#");
2592: fprintf(ficlog, "\n#********** Variable ");
2593: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2594: fprintf(ficlog, "**********\n#");
2595: }
2596: for(i=1; i<=nlstate;i++)
2597: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2598: fprintf(ficresp, "\n");
2599:
2600: for(i=iagemin; i <= iagemax+3; i++){
2601: if(i==iagemax+3){
2602: fprintf(ficlog,"Total");
2603: }else{
2604: if(first==1){
2605: first=0;
2606: printf("See log file for details...\n");
2607: }
2608: fprintf(ficlog,"Age %d", i);
2609: }
2610: for(jk=1; jk <=nlstate ; jk++){
2611: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2612: pp[jk] += freq[jk][m][i];
2613: }
2614: for(jk=1; jk <=nlstate ; jk++){
2615: for(m=-1, pos=0; m <=0 ; m++)
2616: pos += freq[jk][m][i];
2617: if(pp[jk]>=1.e-10){
2618: if(first==1){
2619: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2620: }
2621: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2622: }else{
2623: if(first==1)
2624: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2625: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2626: }
2627: }
2628:
2629: for(jk=1; jk <=nlstate ; jk++){
2630: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2631: pp[jk] += freq[jk][m][i];
2632: }
2633: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2634: pos += pp[jk];
2635: posprop += prop[jk][i];
2636: }
2637: for(jk=1; jk <=nlstate ; jk++){
2638: if(pos>=1.e-5){
2639: if(first==1)
2640: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2641: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2642: }else{
2643: if(first==1)
2644: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2645: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2646: }
2647: if( i <= iagemax){
2648: if(pos>=1.e-5){
2649: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2650: /*probs[i][jk][j1]= pp[jk]/pos;*/
2651: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2652: }
2653: else
2654: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2655: }
2656: }
2657:
2658: for(jk=-1; jk <=nlstate+ndeath; jk++)
2659: for(m=-1; m <=nlstate+ndeath; m++)
2660: if(freq[jk][m][i] !=0 ) {
2661: if(first==1)
2662: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2663: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2664: }
2665: if(i <= iagemax)
2666: fprintf(ficresp,"\n");
2667: if(first==1)
2668: printf("Others in log...\n");
2669: fprintf(ficlog,"\n");
2670: }
2671: /*}*/
2672: }
2673: dateintmean=dateintsum/k2cpt;
2674:
2675: fclose(ficresp);
2676: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2677: free_vector(pp,1,nlstate);
2678: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2679: /* End of Freq */
2680: }
2681:
2682: /************ Prevalence ********************/
2683: 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)
2684: {
2685: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2686: in each health status at the date of interview (if between dateprev1 and dateprev2).
2687: We still use firstpass and lastpass as another selection.
2688: */
2689:
2690: int i, m, jk, j1, bool, z1,j;
2691:
2692: double **prop;
2693: double posprop;
2694: double y2; /* in fractional years */
2695: int iagemin, iagemax;
2696: int first; /** to stop verbosity which is redirected to log file */
2697:
2698: iagemin= (int) agemin;
2699: iagemax= (int) agemax;
2700: /*pp=vector(1,nlstate);*/
2701: prop=matrix(1,nlstate,iagemin,iagemax+3);
2702: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2703: j1=0;
2704:
2705: /*j=cptcoveff;*/
2706: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2707:
2708: first=1;
2709: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
2710: /*for(i1=1; i1<=ncodemax[k1];i1++){
2711: j1++;*/
2712:
2713: for (i=1; i<=nlstate; i++)
2714: for(m=iagemin; m <= iagemax+3; m++)
2715: prop[i][m]=0.0;
2716:
2717: for (i=1; i<=imx; i++) { /* Each individual */
2718: bool=1;
2719: if (cptcovn>0) {
2720: for (z1=1; z1<=cptcoveff; z1++)
2721: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2722: bool=0;
2723: }
2724: if (bool==1) {
2725: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2726: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2727: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2728: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2729: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2730: 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);
2731: if (s[m][i]>0 && s[m][i]<=nlstate) {
2732: /*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]]);*/
2733: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2734: prop[s[m][i]][iagemax+3] += weight[i];
2735: }
2736: }
2737: } /* end selection of waves */
2738: }
2739: }
2740: for(i=iagemin; i <= iagemax+3; i++){
2741: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2742: posprop += prop[jk][i];
2743: }
2744:
2745: for(jk=1; jk <=nlstate ; jk++){
2746: if( i <= iagemax){
2747: if(posprop>=1.e-5){
2748: probs[i][jk][j1]= prop[jk][i]/posprop;
2749: } else{
2750: if(first==1){
2751: first=0;
2752: 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]);
2753: }
2754: }
2755: }
2756: }/* end jk */
2757: }/* end i */
2758: /*} *//* end i1 */
2759: } /* end j1 */
2760:
2761: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2762: /*free_vector(pp,1,nlstate);*/
2763: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2764: } /* End of prevalence */
2765:
2766: /************* Waves Concatenation ***************/
2767:
2768: 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)
2769: {
2770: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2771: Death is a valid wave (if date is known).
2772: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2773: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2774: and mw[mi+1][i]. dh depends on stepm.
2775: */
2776:
2777: int i, mi, m;
2778: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2779: double sum=0., jmean=0.;*/
2780: int first;
2781: int j, k=0,jk, ju, jl;
2782: double sum=0.;
2783: first=0;
2784: jmin=100000;
2785: jmax=-1;
2786: jmean=0.;
2787: for(i=1; i<=imx; i++){
2788: mi=0;
2789: m=firstpass;
2790: while(s[m][i] <= nlstate){
2791: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2792: mw[++mi][i]=m;
2793: if(m >=lastpass)
2794: break;
2795: else
2796: m++;
2797: }/* end while */
2798: if (s[m][i] > nlstate){
2799: mi++; /* Death is another wave */
2800: /* if(mi==0) never been interviewed correctly before death */
2801: /* Only death is a correct wave */
2802: mw[mi][i]=m;
2803: }
2804:
2805: wav[i]=mi;
2806: if(mi==0){
2807: nbwarn++;
2808: if(first==0){
2809: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2810: first=1;
2811: }
2812: if(first==1){
2813: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2814: }
2815: } /* end mi==0 */
2816: } /* End individuals */
2817:
2818: for(i=1; i<=imx; i++){
2819: for(mi=1; mi<wav[i];mi++){
2820: if (stepm <=0)
2821: dh[mi][i]=1;
2822: else{
2823: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2824: if (agedc[i] < 2*AGESUP) {
2825: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2826: if(j==0) j=1; /* Survives at least one month after exam */
2827: else if(j<0){
2828: nberr++;
2829: 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]);
2830: j=1; /* Temporary Dangerous patch */
2831: 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);
2832: 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]);
2833: 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);
2834: }
2835: k=k+1;
2836: if (j >= jmax){
2837: jmax=j;
2838: ijmax=i;
2839: }
2840: if (j <= jmin){
2841: jmin=j;
2842: ijmin=i;
2843: }
2844: sum=sum+j;
2845: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2846: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2847: }
2848: }
2849: else{
2850: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2851: /* 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]); */
2852:
2853: k=k+1;
2854: if (j >= jmax) {
2855: jmax=j;
2856: ijmax=i;
2857: }
2858: else if (j <= jmin){
2859: jmin=j;
2860: ijmin=i;
2861: }
2862: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2863: /*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]);*/
2864: if(j<0){
2865: nberr++;
2866: 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]);
2867: 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]);
2868: }
2869: sum=sum+j;
2870: }
2871: jk= j/stepm;
2872: jl= j -jk*stepm;
2873: ju= j -(jk+1)*stepm;
2874: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2875: if(jl==0){
2876: dh[mi][i]=jk;
2877: bh[mi][i]=0;
2878: }else{ /* We want a negative bias in order to only have interpolation ie
2879: * to avoid the price of an extra matrix product in likelihood */
2880: dh[mi][i]=jk+1;
2881: bh[mi][i]=ju;
2882: }
2883: }else{
2884: if(jl <= -ju){
2885: dh[mi][i]=jk;
2886: bh[mi][i]=jl; /* bias is positive if real duration
2887: * is higher than the multiple of stepm and negative otherwise.
2888: */
2889: }
2890: else{
2891: dh[mi][i]=jk+1;
2892: bh[mi][i]=ju;
2893: }
2894: if(dh[mi][i]==0){
2895: dh[mi][i]=1; /* At least one step */
2896: bh[mi][i]=ju; /* At least one step */
2897: /* 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);*/
2898: }
2899: } /* end if mle */
2900: }
2901: } /* end wave */
2902: }
2903: jmean=sum/k;
2904: 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);
2905: 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);
2906: }
2907:
2908: /*********** Tricode ****************************/
2909: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
2910: {
2911: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
2912: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
2913: /* Boring subroutine which should only output nbcode[Tvar[j]][k]
2914: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
2915: /* nbcode[Tvar[j]][1]=
2916: */
2917:
2918: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
2919: int modmaxcovj=0; /* Modality max of covariates j */
2920: int cptcode=0; /* Modality max of covariates j */
2921: int modmincovj=0; /* Modality min of covariates j */
2922:
2923:
2924: cptcoveff=0;
2925:
2926: for (k=-1; k < maxncov; k++) Ndum[k]=0;
2927: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
2928:
2929: /* Loop on covariates without age and products */
2930: for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
2931: for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the
2932: modality of this covariate Vj*/
2933: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
2934: * If product of Vn*Vm, still boolean *:
2935: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
2936: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
2937: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
2938: modality of the nth covariate of individual i. */
2939: if (ij > modmaxcovj)
2940: modmaxcovj=ij;
2941: else if (ij < modmincovj)
2942: modmincovj=ij;
2943: if ((ij < -1) && (ij > NCOVMAX)){
2944: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
2945: exit(1);
2946: }else
2947: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
2948: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
2949: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
2950: /* getting the maximum value of the modality of the covariate
2951: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
2952: female is 1, then modmaxcovj=1.*/
2953: }
2954: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
2955: cptcode=modmaxcovj;
2956: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
2957: /*for (i=0; i<=cptcode; i++) {*/
2958: for (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
2959: printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
2960: if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
2961: ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
2962: }
2963: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
2964: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
2965: } /* Ndum[-1] number of undefined modalities */
2966:
2967: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
2968: /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
2969: /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
2970: modmincovj=3; modmaxcovj = 7;
2971: There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
2972: which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy
2973: variables V1_1 and V1_2.
2974: nbcode[Tvar[j]][ij]=k;
2975: nbcode[Tvar[j]][1]=0;
2976: nbcode[Tvar[j]][2]=1;
2977: nbcode[Tvar[j]][3]=2;
2978: */
2979: ij=1; /* ij is similar to i but can jumps over null modalities */
2980: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
2981: for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
2982: /*recode from 0 */
2983: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
2984: nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode.
2985: k is a modality. If we have model=V1+V1*sex
2986: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
2987: ij++;
2988: }
2989: if (ij > ncodemax[j]) break;
2990: } /* end of loop on */
2991: } /* end of loop on modality */
2992: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
2993:
2994: for (k=-1; k< maxncov; k++) Ndum[k]=0;
2995:
2996: for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
2997: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
2998: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
2999: Ndum[ij]++;
3000: }
3001:
3002: ij=1;
3003: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
3004: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
3005: if((Ndum[i]!=0) && (i<=ncovcol)){
3006: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
3007: Tvaraff[ij]=i; /*For printing (unclear) */
3008: ij++;
3009: }else
3010: Tvaraff[ij]=0;
3011: }
3012: ij--;
3013: cptcoveff=ij; /*Number of total covariates*/
3014:
3015: }
3016:
3017:
3018: /*********** Health Expectancies ****************/
3019:
3020: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
3021:
3022: {
3023: /* Health expectancies, no variances */
3024: int i, j, nhstepm, hstepm, h, nstepm;
3025: int nhstepma, nstepma; /* Decreasing with age */
3026: double age, agelim, hf;
3027: double ***p3mat;
3028: double eip;
3029:
3030: pstamp(ficreseij);
3031: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3032: fprintf(ficreseij,"# Age");
3033: for(i=1; i<=nlstate;i++){
3034: for(j=1; j<=nlstate;j++){
3035: fprintf(ficreseij," e%1d%1d ",i,j);
3036: }
3037: fprintf(ficreseij," e%1d. ",i);
3038: }
3039: fprintf(ficreseij,"\n");
3040:
3041:
3042: if(estepm < stepm){
3043: printf ("Problem %d lower than %d\n",estepm, stepm);
3044: }
3045: else hstepm=estepm;
3046: /* We compute the life expectancy from trapezoids spaced every estepm months
3047: * This is mainly to measure the difference between two models: for example
3048: * if stepm=24 months pijx are given only every 2 years and by summing them
3049: * we are calculating an estimate of the Life Expectancy assuming a linear
3050: * progression in between and thus overestimating or underestimating according
3051: * to the curvature of the survival function. If, for the same date, we
3052: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3053: * to compare the new estimate of Life expectancy with the same linear
3054: * hypothesis. A more precise result, taking into account a more precise
3055: * curvature will be obtained if estepm is as small as stepm. */
3056:
3057: /* For example we decided to compute the life expectancy with the smallest unit */
3058: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3059: nhstepm is the number of hstepm from age to agelim
3060: nstepm is the number of stepm from age to agelin.
3061: Look at hpijx to understand the reason of that which relies in memory size
3062: and note for a fixed period like estepm months */
3063: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3064: survival function given by stepm (the optimization length). Unfortunately it
3065: means that if the survival funtion is printed only each two years of age and if
3066: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3067: results. So we changed our mind and took the option of the best precision.
3068: */
3069: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3070:
3071: agelim=AGESUP;
3072: /* If stepm=6 months */
3073: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3074: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3075:
3076: /* nhstepm age range expressed in number of stepm */
3077: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3078: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3079: /* if (stepm >= YEARM) hstepm=1;*/
3080: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3081: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3082:
3083: for (age=bage; age<=fage; age ++){
3084: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3085: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3086: /* if (stepm >= YEARM) hstepm=1;*/
3087: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3088:
3089: /* If stepm=6 months */
3090: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3091: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3092:
3093: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3094:
3095: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3096:
3097: printf("%d|",(int)age);fflush(stdout);
3098: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3099:
3100: /* Computing expectancies */
3101: for(i=1; i<=nlstate;i++)
3102: for(j=1; j<=nlstate;j++)
3103: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3104: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3105:
3106: /* 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]);*/
3107:
3108: }
3109:
3110: fprintf(ficreseij,"%3.0f",age );
3111: for(i=1; i<=nlstate;i++){
3112: eip=0;
3113: for(j=1; j<=nlstate;j++){
3114: eip +=eij[i][j][(int)age];
3115: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3116: }
3117: fprintf(ficreseij,"%9.4f", eip );
3118: }
3119: fprintf(ficreseij,"\n");
3120:
3121: }
3122: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3123: printf("\n");
3124: fprintf(ficlog,"\n");
3125:
3126: }
3127:
3128: 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[] )
3129:
3130: {
3131: /* Covariances of health expectancies eij and of total life expectancies according
3132: to initial status i, ei. .
3133: */
3134: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3135: int nhstepma, nstepma; /* Decreasing with age */
3136: double age, agelim, hf;
3137: double ***p3matp, ***p3matm, ***varhe;
3138: double **dnewm,**doldm;
3139: double *xp, *xm;
3140: double **gp, **gm;
3141: double ***gradg, ***trgradg;
3142: int theta;
3143:
3144: double eip, vip;
3145:
3146: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
3147: xp=vector(1,npar);
3148: xm=vector(1,npar);
3149: dnewm=matrix(1,nlstate*nlstate,1,npar);
3150: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3151:
3152: pstamp(ficresstdeij);
3153: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3154: fprintf(ficresstdeij,"# Age");
3155: for(i=1; i<=nlstate;i++){
3156: for(j=1; j<=nlstate;j++)
3157: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3158: fprintf(ficresstdeij," e%1d. ",i);
3159: }
3160: fprintf(ficresstdeij,"\n");
3161:
3162: pstamp(ficrescveij);
3163: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3164: fprintf(ficrescveij,"# Age");
3165: for(i=1; i<=nlstate;i++)
3166: for(j=1; j<=nlstate;j++){
3167: cptj= (j-1)*nlstate+i;
3168: for(i2=1; i2<=nlstate;i2++)
3169: for(j2=1; j2<=nlstate;j2++){
3170: cptj2= (j2-1)*nlstate+i2;
3171: if(cptj2 <= cptj)
3172: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3173: }
3174: }
3175: fprintf(ficrescveij,"\n");
3176:
3177: if(estepm < stepm){
3178: printf ("Problem %d lower than %d\n",estepm, stepm);
3179: }
3180: else hstepm=estepm;
3181: /* We compute the life expectancy from trapezoids spaced every estepm months
3182: * This is mainly to measure the difference between two models: for example
3183: * if stepm=24 months pijx are given only every 2 years and by summing them
3184: * we are calculating an estimate of the Life Expectancy assuming a linear
3185: * progression in between and thus overestimating or underestimating according
3186: * to the curvature of the survival function. If, for the same date, we
3187: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3188: * to compare the new estimate of Life expectancy with the same linear
3189: * hypothesis. A more precise result, taking into account a more precise
3190: * curvature will be obtained if estepm is as small as stepm. */
3191:
3192: /* For example we decided to compute the life expectancy with the smallest unit */
3193: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3194: nhstepm is the number of hstepm from age to agelim
3195: nstepm is the number of stepm from age to agelin.
3196: Look at hpijx to understand the reason of that which relies in memory size
3197: and note for a fixed period like estepm months */
3198: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3199: survival function given by stepm (the optimization length). Unfortunately it
3200: means that if the survival funtion is printed only each two years of age and if
3201: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3202: results. So we changed our mind and took the option of the best precision.
3203: */
3204: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3205:
3206: /* If stepm=6 months */
3207: /* nhstepm age range expressed in number of stepm */
3208: agelim=AGESUP;
3209: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3210: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3211: /* if (stepm >= YEARM) hstepm=1;*/
3212: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3213:
3214: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3215: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3216: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3217: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3218: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3219: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3220:
3221: for (age=bage; age<=fage; age ++){
3222: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3223: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3224: /* if (stepm >= YEARM) hstepm=1;*/
3225: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3226:
3227: /* If stepm=6 months */
3228: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3229: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3230:
3231: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3232:
3233: /* Computing Variances of health expectancies */
3234: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3235: decrease memory allocation */
3236: for(theta=1; theta <=npar; theta++){
3237: for(i=1; i<=npar; i++){
3238: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3239: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3240: }
3241: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3242: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3243:
3244: for(j=1; j<= nlstate; j++){
3245: for(i=1; i<=nlstate; i++){
3246: for(h=0; h<=nhstepm-1; h++){
3247: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3248: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3249: }
3250: }
3251: }
3252:
3253: for(ij=1; ij<= nlstate*nlstate; ij++)
3254: for(h=0; h<=nhstepm-1; h++){
3255: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3256: }
3257: }/* End theta */
3258:
3259:
3260: for(h=0; h<=nhstepm-1; h++)
3261: for(j=1; j<=nlstate*nlstate;j++)
3262: for(theta=1; theta <=npar; theta++)
3263: trgradg[h][j][theta]=gradg[h][theta][j];
3264:
3265:
3266: for(ij=1;ij<=nlstate*nlstate;ij++)
3267: for(ji=1;ji<=nlstate*nlstate;ji++)
3268: varhe[ij][ji][(int)age] =0.;
3269:
3270: printf("%d|",(int)age);fflush(stdout);
3271: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3272: for(h=0;h<=nhstepm-1;h++){
3273: for(k=0;k<=nhstepm-1;k++){
3274: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3275: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3276: for(ij=1;ij<=nlstate*nlstate;ij++)
3277: for(ji=1;ji<=nlstate*nlstate;ji++)
3278: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3279: }
3280: }
3281:
3282: /* Computing expectancies */
3283: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3284: for(i=1; i<=nlstate;i++)
3285: for(j=1; j<=nlstate;j++)
3286: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3287: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3288:
3289: /* 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]);*/
3290:
3291: }
3292:
3293: fprintf(ficresstdeij,"%3.0f",age );
3294: for(i=1; i<=nlstate;i++){
3295: eip=0.;
3296: vip=0.;
3297: for(j=1; j<=nlstate;j++){
3298: eip += eij[i][j][(int)age];
3299: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3300: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3301: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3302: }
3303: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3304: }
3305: fprintf(ficresstdeij,"\n");
3306:
3307: fprintf(ficrescveij,"%3.0f",age );
3308: for(i=1; i<=nlstate;i++)
3309: for(j=1; j<=nlstate;j++){
3310: cptj= (j-1)*nlstate+i;
3311: for(i2=1; i2<=nlstate;i2++)
3312: for(j2=1; j2<=nlstate;j2++){
3313: cptj2= (j2-1)*nlstate+i2;
3314: if(cptj2 <= cptj)
3315: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3316: }
3317: }
3318: fprintf(ficrescveij,"\n");
3319:
3320: }
3321: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3322: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3323: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3324: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3325: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3326: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3327: printf("\n");
3328: fprintf(ficlog,"\n");
3329:
3330: free_vector(xm,1,npar);
3331: free_vector(xp,1,npar);
3332: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3333: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3334: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3335: }
3336:
3337: /************ Variance ******************/
3338: 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[])
3339: {
3340: /* Variance of health expectancies */
3341: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3342: /* double **newm;*/
3343: double **dnewm,**doldm;
3344: double **dnewmp,**doldmp;
3345: int i, j, nhstepm, hstepm, h, nstepm ;
3346: int k;
3347: double *xp;
3348: double **gp, **gm; /* for var eij */
3349: double ***gradg, ***trgradg; /*for var eij */
3350: double **gradgp, **trgradgp; /* for var p point j */
3351: double *gpp, *gmp; /* for var p point j */
3352: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3353: double ***p3mat;
3354: double age,agelim, hf;
3355: double ***mobaverage;
3356: int theta;
3357: char digit[4];
3358: char digitp[25];
3359:
3360: char fileresprobmorprev[FILENAMELENGTH];
3361:
3362: if(popbased==1){
3363: if(mobilav!=0)
3364: strcpy(digitp,"-populbased-mobilav-");
3365: else strcpy(digitp,"-populbased-nomobil-");
3366: }
3367: else
3368: strcpy(digitp,"-stablbased-");
3369:
3370: if (mobilav!=0) {
3371: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3372: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3373: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3374: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3375: }
3376: }
3377:
3378: strcpy(fileresprobmorprev,"prmorprev");
3379: sprintf(digit,"%-d",ij);
3380: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3381: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3382: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
3383: strcat(fileresprobmorprev,fileres);
3384: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3385: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3386: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3387: }
3388: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3389:
3390: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3391: pstamp(ficresprobmorprev);
3392: 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);
3393: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3394: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3395: fprintf(ficresprobmorprev," p.%-d SE",j);
3396: for(i=1; i<=nlstate;i++)
3397: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3398: }
3399: fprintf(ficresprobmorprev,"\n");
3400: fprintf(ficgp,"\n# Routine varevsij");
3401: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
3402: 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");
3403: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3404: /* } */
3405: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3406: pstamp(ficresvij);
3407: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3408: if(popbased==1)
3409: 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);
3410: else
3411: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3412: fprintf(ficresvij,"# Age");
3413: for(i=1; i<=nlstate;i++)
3414: for(j=1; j<=nlstate;j++)
3415: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3416: fprintf(ficresvij,"\n");
3417:
3418: xp=vector(1,npar);
3419: dnewm=matrix(1,nlstate,1,npar);
3420: doldm=matrix(1,nlstate,1,nlstate);
3421: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3422: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3423:
3424: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3425: gpp=vector(nlstate+1,nlstate+ndeath);
3426: gmp=vector(nlstate+1,nlstate+ndeath);
3427: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3428:
3429: if(estepm < stepm){
3430: printf ("Problem %d lower than %d\n",estepm, stepm);
3431: }
3432: else hstepm=estepm;
3433: /* For example we decided to compute the life expectancy with the smallest unit */
3434: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3435: nhstepm is the number of hstepm from age to agelim
3436: nstepm is the number of stepm from age to agelin.
3437: Look at function hpijx to understand why (it is linked to memory size questions) */
3438: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3439: survival function given by stepm (the optimization length). Unfortunately it
3440: means that if the survival funtion is printed every two years of age and if
3441: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3442: results. So we changed our mind and took the option of the best precision.
3443: */
3444: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3445: agelim = AGESUP;
3446: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3447: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3448: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3449: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3450: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3451: gp=matrix(0,nhstepm,1,nlstate);
3452: gm=matrix(0,nhstepm,1,nlstate);
3453:
3454:
3455: for(theta=1; theta <=npar; theta++){
3456: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3457: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3458: }
3459: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3460: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3461:
3462: if (popbased==1) {
3463: if(mobilav ==0){
3464: for(i=1; i<=nlstate;i++)
3465: prlim[i][i]=probs[(int)age][i][ij];
3466: }else{ /* mobilav */
3467: for(i=1; i<=nlstate;i++)
3468: prlim[i][i]=mobaverage[(int)age][i][ij];
3469: }
3470: }
3471:
3472: for(j=1; j<= nlstate; j++){
3473: for(h=0; h<=nhstepm; h++){
3474: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3475: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3476: }
3477: }
3478: /* This for computing probability of death (h=1 means
3479: computed over hstepm matrices product = hstepm*stepm months)
3480: as a weighted average of prlim.
3481: */
3482: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3483: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3484: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3485: }
3486: /* end probability of death */
3487:
3488: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3489: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3490: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3491: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3492:
3493: if (popbased==1) {
3494: if(mobilav ==0){
3495: for(i=1; i<=nlstate;i++)
3496: prlim[i][i]=probs[(int)age][i][ij];
3497: }else{ /* mobilav */
3498: for(i=1; i<=nlstate;i++)
3499: prlim[i][i]=mobaverage[(int)age][i][ij];
3500: }
3501: }
3502:
3503: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
3504: for(h=0; h<=nhstepm; h++){
3505: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3506: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3507: }
3508: }
3509: /* This for computing probability of death (h=1 means
3510: computed over hstepm matrices product = hstepm*stepm months)
3511: as a weighted average of prlim.
3512: */
3513: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3514: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3515: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3516: }
3517: /* end probability of death */
3518:
3519: for(j=1; j<= nlstate; j++) /* vareij */
3520: for(h=0; h<=nhstepm; h++){
3521: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3522: }
3523:
3524: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3525: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3526: }
3527:
3528: } /* End theta */
3529:
3530: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3531:
3532: for(h=0; h<=nhstepm; h++) /* veij */
3533: for(j=1; j<=nlstate;j++)
3534: for(theta=1; theta <=npar; theta++)
3535: trgradg[h][j][theta]=gradg[h][theta][j];
3536:
3537: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3538: for(theta=1; theta <=npar; theta++)
3539: trgradgp[j][theta]=gradgp[theta][j];
3540:
3541:
3542: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3543: for(i=1;i<=nlstate;i++)
3544: for(j=1;j<=nlstate;j++)
3545: vareij[i][j][(int)age] =0.;
3546:
3547: for(h=0;h<=nhstepm;h++){
3548: for(k=0;k<=nhstepm;k++){
3549: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3550: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3551: for(i=1;i<=nlstate;i++)
3552: for(j=1;j<=nlstate;j++)
3553: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3554: }
3555: }
3556:
3557: /* pptj */
3558: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3559: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3560: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3561: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3562: varppt[j][i]=doldmp[j][i];
3563: /* end ppptj */
3564: /* x centered again */
3565: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3566: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3567:
3568: if (popbased==1) {
3569: if(mobilav ==0){
3570: for(i=1; i<=nlstate;i++)
3571: prlim[i][i]=probs[(int)age][i][ij];
3572: }else{ /* mobilav */
3573: for(i=1; i<=nlstate;i++)
3574: prlim[i][i]=mobaverage[(int)age][i][ij];
3575: }
3576: }
3577:
3578: /* This for computing probability of death (h=1 means
3579: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3580: as a weighted average of prlim.
3581: */
3582: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3583: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3584: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3585: }
3586: /* end probability of death */
3587:
3588: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3589: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3590: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3591: for(i=1; i<=nlstate;i++){
3592: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3593: }
3594: }
3595: fprintf(ficresprobmorprev,"\n");
3596:
3597: fprintf(ficresvij,"%.0f ",age );
3598: for(i=1; i<=nlstate;i++)
3599: for(j=1; j<=nlstate;j++){
3600: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3601: }
3602: fprintf(ficresvij,"\n");
3603: free_matrix(gp,0,nhstepm,1,nlstate);
3604: free_matrix(gm,0,nhstepm,1,nlstate);
3605: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3606: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3607: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3608: } /* End age */
3609: free_vector(gpp,nlstate+1,nlstate+ndeath);
3610: free_vector(gmp,nlstate+1,nlstate+ndeath);
3611: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3612: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3613: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
3614: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
3615: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
3616: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3617: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3618: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
3619: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
3620: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
3621: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
3622: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3623: 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);
3624: /* 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);
3625: */
3626: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3627: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3628:
3629: free_vector(xp,1,npar);
3630: free_matrix(doldm,1,nlstate,1,nlstate);
3631: free_matrix(dnewm,1,nlstate,1,npar);
3632: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3633: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3634: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3635: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3636: fclose(ficresprobmorprev);
3637: fflush(ficgp);
3638: fflush(fichtm);
3639: } /* end varevsij */
3640:
3641: /************ Variance of prevlim ******************/
3642: 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[])
3643: {
3644: /* Variance of prevalence limit */
3645: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
3646:
3647: double **dnewm,**doldm;
3648: int i, j, nhstepm, hstepm;
3649: double *xp;
3650: double *gp, *gm;
3651: double **gradg, **trgradg;
3652: double age,agelim;
3653: int theta;
3654:
3655: pstamp(ficresvpl);
3656: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3657: fprintf(ficresvpl,"# Age");
3658: for(i=1; i<=nlstate;i++)
3659: fprintf(ficresvpl," %1d-%1d",i,i);
3660: fprintf(ficresvpl,"\n");
3661:
3662: xp=vector(1,npar);
3663: dnewm=matrix(1,nlstate,1,npar);
3664: doldm=matrix(1,nlstate,1,nlstate);
3665:
3666: hstepm=1*YEARM; /* Every year of age */
3667: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3668: agelim = AGESUP;
3669: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3670: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3671: if (stepm >= YEARM) hstepm=1;
3672: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3673: gradg=matrix(1,npar,1,nlstate);
3674: gp=vector(1,nlstate);
3675: gm=vector(1,nlstate);
3676:
3677: for(theta=1; theta <=npar; theta++){
3678: for(i=1; i<=npar; i++){ /* Computes gradient */
3679: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3680: }
3681: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3682: for(i=1;i<=nlstate;i++)
3683: gp[i] = prlim[i][i];
3684:
3685: for(i=1; i<=npar; i++) /* Computes gradient */
3686: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3687: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3688: for(i=1;i<=nlstate;i++)
3689: gm[i] = prlim[i][i];
3690:
3691: for(i=1;i<=nlstate;i++)
3692: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3693: } /* End theta */
3694:
3695: trgradg =matrix(1,nlstate,1,npar);
3696:
3697: for(j=1; j<=nlstate;j++)
3698: for(theta=1; theta <=npar; theta++)
3699: trgradg[j][theta]=gradg[theta][j];
3700:
3701: for(i=1;i<=nlstate;i++)
3702: varpl[i][(int)age] =0.;
3703: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3704: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3705: for(i=1;i<=nlstate;i++)
3706: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3707:
3708: fprintf(ficresvpl,"%.0f ",age );
3709: for(i=1; i<=nlstate;i++)
3710: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3711: fprintf(ficresvpl,"\n");
3712: free_vector(gp,1,nlstate);
3713: free_vector(gm,1,nlstate);
3714: free_matrix(gradg,1,npar,1,nlstate);
3715: free_matrix(trgradg,1,nlstate,1,npar);
3716: } /* End age */
3717:
3718: free_vector(xp,1,npar);
3719: free_matrix(doldm,1,nlstate,1,npar);
3720: free_matrix(dnewm,1,nlstate,1,nlstate);
3721:
3722: }
3723:
3724: /************ Variance of one-step probabilities ******************/
3725: 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[])
3726: {
3727: int i, j=0, k1, l1, tj;
3728: int k2, l2, j1, z1;
3729: int k=0, l;
3730: int first=1, first1, first2;
3731: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3732: double **dnewm,**doldm;
3733: double *xp;
3734: double *gp, *gm;
3735: double **gradg, **trgradg;
3736: double **mu;
3737: double age, cov[NCOVMAX+1];
3738: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3739: int theta;
3740: char fileresprob[FILENAMELENGTH];
3741: char fileresprobcov[FILENAMELENGTH];
3742: char fileresprobcor[FILENAMELENGTH];
3743: double ***varpij;
3744:
3745: strcpy(fileresprob,"prob");
3746: strcat(fileresprob,fileres);
3747: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3748: printf("Problem with resultfile: %s\n", fileresprob);
3749: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3750: }
3751: strcpy(fileresprobcov,"probcov");
3752: strcat(fileresprobcov,fileres);
3753: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3754: printf("Problem with resultfile: %s\n", fileresprobcov);
3755: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3756: }
3757: strcpy(fileresprobcor,"probcor");
3758: strcat(fileresprobcor,fileres);
3759: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3760: printf("Problem with resultfile: %s\n", fileresprobcor);
3761: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3762: }
3763: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3764: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3765: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3766: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3767: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3768: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3769: pstamp(ficresprob);
3770: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3771: fprintf(ficresprob,"# Age");
3772: pstamp(ficresprobcov);
3773: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3774: fprintf(ficresprobcov,"# Age");
3775: pstamp(ficresprobcor);
3776: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3777: fprintf(ficresprobcor,"# Age");
3778:
3779:
3780: for(i=1; i<=nlstate;i++)
3781: for(j=1; j<=(nlstate+ndeath);j++){
3782: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3783: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3784: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3785: }
3786: /* fprintf(ficresprob,"\n");
3787: fprintf(ficresprobcov,"\n");
3788: fprintf(ficresprobcor,"\n");
3789: */
3790: xp=vector(1,npar);
3791: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3792: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3793: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3794: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3795: first=1;
3796: fprintf(ficgp,"\n# Routine varprob");
3797: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3798: fprintf(fichtm,"\n");
3799:
3800: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3801: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3802: file %s<br>\n",optionfilehtmcov);
3803: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3804: and drawn. It helps understanding how is the covariance between two incidences.\
3805: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3806: 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. \
3807: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3808: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3809: standard deviations wide on each axis. <br>\
3810: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3811: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3812: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3813:
3814: cov[1]=1;
3815: /* tj=cptcoveff; */
3816: tj = (int) pow(2,cptcoveff);
3817: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3818: j1=0;
3819: for(j1=1; j1<=tj;j1++){
3820: /*for(i1=1; i1<=ncodemax[t];i1++){ */
3821: /*j1++;*/
3822: if (cptcovn>0) {
3823: fprintf(ficresprob, "\n#********** Variable ");
3824: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3825: fprintf(ficresprob, "**********\n#\n");
3826: fprintf(ficresprobcov, "\n#********** Variable ");
3827: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3828: fprintf(ficresprobcov, "**********\n#\n");
3829:
3830: fprintf(ficgp, "\n#********** Variable ");
3831: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3832: fprintf(ficgp, "**********\n#\n");
3833:
3834:
3835: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
3836: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3837: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
3838:
3839: fprintf(ficresprobcor, "\n#********** Variable ");
3840: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3841: fprintf(ficresprobcor, "**********\n#");
3842: }
3843:
3844: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3845: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3846: gp=vector(1,(nlstate)*(nlstate+ndeath));
3847: gm=vector(1,(nlstate)*(nlstate+ndeath));
3848: for (age=bage; age<=fage; age ++){
3849: cov[2]=age;
3850: for (k=1; k<=cptcovn;k++) {
3851: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
3852: * 1 1 1 1 1
3853: * 2 2 1 1 1
3854: * 3 1 2 1 1
3855: */
3856: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
3857: }
3858: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3859: for (k=1; k<=cptcovprod;k++)
3860: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3861:
3862:
3863: for(theta=1; theta <=npar; theta++){
3864: for(i=1; i<=npar; i++)
3865: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3866:
3867: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3868:
3869: k=0;
3870: for(i=1; i<= (nlstate); i++){
3871: for(j=1; j<=(nlstate+ndeath);j++){
3872: k=k+1;
3873: gp[k]=pmmij[i][j];
3874: }
3875: }
3876:
3877: for(i=1; i<=npar; i++)
3878: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
3879:
3880: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3881: k=0;
3882: for(i=1; i<=(nlstate); i++){
3883: for(j=1; j<=(nlstate+ndeath);j++){
3884: k=k+1;
3885: gm[k]=pmmij[i][j];
3886: }
3887: }
3888:
3889: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3890: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3891: }
3892:
3893: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3894: for(theta=1; theta <=npar; theta++)
3895: trgradg[j][theta]=gradg[theta][j];
3896:
3897: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3898: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3899:
3900: pmij(pmmij,cov,ncovmodel,x,nlstate);
3901:
3902: k=0;
3903: for(i=1; i<=(nlstate); i++){
3904: for(j=1; j<=(nlstate+ndeath);j++){
3905: k=k+1;
3906: mu[k][(int) age]=pmmij[i][j];
3907: }
3908: }
3909: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3910: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3911: varpij[i][j][(int)age] = doldm[i][j];
3912:
3913: /*printf("\n%d ",(int)age);
3914: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3915: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3916: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3917: }*/
3918:
3919: fprintf(ficresprob,"\n%d ",(int)age);
3920: fprintf(ficresprobcov,"\n%d ",(int)age);
3921: fprintf(ficresprobcor,"\n%d ",(int)age);
3922:
3923: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3924: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3925: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3926: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3927: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3928: }
3929: i=0;
3930: for (k=1; k<=(nlstate);k++){
3931: for (l=1; l<=(nlstate+ndeath);l++){
3932: i++;
3933: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3934: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3935: for (j=1; j<=i;j++){
3936: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
3937: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3938: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3939: }
3940: }
3941: }/* end of loop for state */
3942: } /* end of loop for age */
3943: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3944: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3945: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3946: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3947:
3948: /* Confidence intervalle of pij */
3949: /*
3950: fprintf(ficgp,"\nunset parametric;unset label");
3951: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3952: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3953: 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);
3954: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3955: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3956: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3957: */
3958:
3959: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3960: first1=1;first2=2;
3961: for (k2=1; k2<=(nlstate);k2++){
3962: for (l2=1; l2<=(nlstate+ndeath);l2++){
3963: if(l2==k2) continue;
3964: j=(k2-1)*(nlstate+ndeath)+l2;
3965: for (k1=1; k1<=(nlstate);k1++){
3966: for (l1=1; l1<=(nlstate+ndeath);l1++){
3967: if(l1==k1) continue;
3968: i=(k1-1)*(nlstate+ndeath)+l1;
3969: if(i<=j) continue;
3970: for (age=bage; age<=fage; age ++){
3971: if ((int)age %5==0){
3972: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3973: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3974: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3975: mu1=mu[i][(int) age]/stepm*YEARM ;
3976: mu2=mu[j][(int) age]/stepm*YEARM;
3977: c12=cv12/sqrt(v1*v2);
3978: /* Computing eigen value of matrix of covariance */
3979: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3980: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3981: if ((lc2 <0) || (lc1 <0) ){
3982: if(first2==1){
3983: first1=0;
3984: 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);
3985: }
3986: 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);
3987: /* lc1=fabs(lc1); */ /* If we want to have them positive */
3988: /* lc2=fabs(lc2); */
3989: }
3990:
3991: /* Eigen vectors */
3992: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3993: /*v21=sqrt(1.-v11*v11); *//* error */
3994: v21=(lc1-v1)/cv12*v11;
3995: v12=-v21;
3996: v22=v11;
3997: tnalp=v21/v11;
3998: if(first1==1){
3999: first1=0;
4000: 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);
4001: }
4002: 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);
4003: /*printf(fignu*/
4004: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
4005: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
4006: if(first==1){
4007: first=0;
4008: fprintf(ficgp,"\nset parametric;unset label");
4009: 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);
4010: fprintf(ficgp,"\nset ter png small size 320, 240");
4011: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
4012: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
4013: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
4014: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
4015: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4016: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4017: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
4018: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4019: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4020: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4021: 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",\
4022: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4023: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4024: }else{
4025: first=0;
4026: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4027: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4028: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4029: 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",\
4030: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4031: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4032: }/* if first */
4033: } /* age mod 5 */
4034: } /* end loop age */
4035: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4036: first=1;
4037: } /*l12 */
4038: } /* k12 */
4039: } /*l1 */
4040: }/* k1 */
4041: /* } /* loop covariates */
4042: }
4043: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4044: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4045: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4046: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4047: free_vector(xp,1,npar);
4048: fclose(ficresprob);
4049: fclose(ficresprobcov);
4050: fclose(ficresprobcor);
4051: fflush(ficgp);
4052: fflush(fichtmcov);
4053: }
4054:
4055:
4056: /******************* Printing html file ***********/
4057: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
4058: int lastpass, int stepm, int weightopt, char model[],\
4059: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
4060: int popforecast, int estepm ,\
4061: double jprev1, double mprev1,double anprev1, \
4062: double jprev2, double mprev2,double anprev2){
4063: int jj1, k1, i1, cpt;
4064:
4065: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4066: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4067: </ul>");
4068: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
4069: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
4070: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
4071: fprintf(fichtm,"\
4072: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
4073: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
4074: fprintf(fichtm,"\
4075: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
4076: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
4077: fprintf(fichtm,"\
4078: - (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): \
4079: <a href=\"%s\">%s</a> <br>\n",
4080: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
4081: fprintf(fichtm,"\
4082: - Population projections by age and states: \
4083: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
4084:
4085: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4086:
4087: m=pow(2,cptcoveff);
4088: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4089:
4090: jj1=0;
4091: for(k1=1; k1<=m;k1++){
4092: for(i1=1; i1<=ncodemax[k1];i1++){
4093: jj1++;
4094: if (cptcovn > 0) {
4095: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4096: for (cpt=1; cpt<=cptcoveff;cpt++)
4097: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4098: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4099: }
4100: /* Pij */
4101: 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> \
4102: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
4103: /* Quasi-incidences */
4104: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
4105: 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> \
4106: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
4107: /* Period (stable) prevalence in each health state */
4108: for(cpt=1; cpt<=nlstate;cpt++){
4109: fprintf(fichtm,"<br>- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
4110: <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
4111: }
4112: for(cpt=1; cpt<=nlstate;cpt++) {
4113: 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> \
4114: <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
4115: }
4116: } /* end i1 */
4117: }/* End k1 */
4118: fprintf(fichtm,"</ul>");
4119:
4120:
4121: fprintf(fichtm,"\
4122: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
4123: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
4124:
4125: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4126: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
4127: fprintf(fichtm,"\
4128: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4129: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
4130:
4131: fprintf(fichtm,"\
4132: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4133: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
4134: fprintf(fichtm,"\
4135: - 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): \
4136: <a href=\"%s\">%s</a> <br>\n</li>",
4137: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
4138: fprintf(fichtm,"\
4139: - (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): \
4140: <a href=\"%s\">%s</a> <br>\n</li>",
4141: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
4142: fprintf(fichtm,"\
4143: - 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",
4144: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
4145: fprintf(fichtm,"\
4146: - 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",
4147: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
4148: fprintf(fichtm,"\
4149: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
4150: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
4151:
4152: /* if(popforecast==1) fprintf(fichtm,"\n */
4153: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4154: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4155: /* <br>",fileres,fileres,fileres,fileres); */
4156: /* else */
4157: /* 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); */
4158: fflush(fichtm);
4159: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4160:
4161: m=pow(2,cptcoveff);
4162: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4163:
4164: jj1=0;
4165: for(k1=1; k1<=m;k1++){
4166: for(i1=1; i1<=ncodemax[k1];i1++){
4167: jj1++;
4168: if (cptcovn > 0) {
4169: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4170: for (cpt=1; cpt<=cptcoveff;cpt++)
4171: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4172: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4173: }
4174: for(cpt=1; cpt<=nlstate;cpt++) {
4175: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
4176: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
4177: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
4178: }
4179: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
4180: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4181: true period expectancies (those weighted with period prevalences are also\
4182: drawn in addition to the population based expectancies computed using\
4183: observed and cahotic prevalences: %s%d.png<br>\
4184: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
4185: } /* end i1 */
4186: }/* End k1 */
4187: fprintf(fichtm,"</ul>");
4188: fflush(fichtm);
4189: }
4190:
4191: /******************* Gnuplot file **************/
4192: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4193:
4194: char dirfileres[132],optfileres[132];
4195: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
4196: int ng=0;
4197: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4198: /* printf("Problem with file %s",optionfilegnuplot); */
4199: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4200: /* } */
4201:
4202: /*#ifdef windows */
4203: fprintf(ficgp,"cd \"%s\" \n",pathc);
4204: /*#endif */
4205: m=pow(2,cptcoveff);
4206:
4207: strcpy(dirfileres,optionfilefiname);
4208: strcpy(optfileres,"vpl");
4209: /* 1eme*/
4210: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
4211: for (cpt=1; cpt<= nlstate ; cpt ++) {
4212: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
4213: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
4214: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
4215: fprintf(ficgp,"set xlabel \"Age\" \n\
4216: set ylabel \"Probability\" \n\
4217: set ter png small size 320, 240\n\
4218: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
4219:
4220: for (i=1; i<= nlstate ; i ++) {
4221: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
4222: else fprintf(ficgp," \%%*lf (\%%*lf)");
4223: }
4224: 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);
4225: for (i=1; i<= nlstate ; i ++) {
4226: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
4227: else fprintf(ficgp," \%%*lf (\%%*lf)");
4228: }
4229: fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
4230: for (i=1; i<= nlstate ; i ++) {
4231: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
4232: else fprintf(ficgp," \%%*lf (\%%*lf)");
4233: }
4234: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
4235: }
4236: }
4237: /*2 eme*/
4238: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
4239: for (k1=1; k1<= m ; k1 ++) {
4240: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
4241: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
4242:
4243: for (i=1; i<= nlstate+1 ; i ++) {
4244: k=2*i;
4245: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4246: for (j=1; j<= nlstate+1 ; j ++) {
4247: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
4248: else fprintf(ficgp," \%%*lf (\%%*lf)");
4249: }
4250: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
4251: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
4252: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4253: for (j=1; j<= nlstate+1 ; j ++) {
4254: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
4255: else fprintf(ficgp," \%%*lf (\%%*lf)");
4256: }
4257: fprintf(ficgp,"\" t\"\" w l lt 0,");
4258: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4259: for (j=1; j<= nlstate+1 ; j ++) {
4260: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
4261: else fprintf(ficgp," \%%*lf (\%%*lf)");
4262: }
4263: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4264: else fprintf(ficgp,"\" t\"\" w l lt 0,");
4265: }
4266: }
4267:
4268: /*3eme*/
4269:
4270: for (k1=1; k1<= m ; k1 ++) {
4271: for (cpt=1; cpt<= nlstate ; cpt ++) {
4272: /* k=2+nlstate*(2*cpt-2); */
4273: k=2+(nlstate+1)*(cpt-1);
4274: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
4275: fprintf(ficgp,"set ter png small size 320, 240\n\
4276: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
4277: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4278: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4279: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4280: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4281: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4282: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4283:
4284: */
4285: for (i=1; i< nlstate ; i ++) {
4286: 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);
4287: /* 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);*/
4288:
4289: }
4290: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
4291: }
4292: }
4293:
4294: /* CV preval stable (period) */
4295: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
4296: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
4297: k=3;
4298: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
4299: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
4300: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
4301: set ter png small size 320, 240\n\
4302: unset log y\n\
4303: plot [%.f:%.f] ", ageminpar, agemaxpar);
4304: for (i=1; i<= nlstate ; i ++){
4305: if(i==1)
4306: fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
4307: else
4308: fprintf(ficgp,", '' ");
4309: l=(nlstate+ndeath)*(i-1)+1;
4310: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
4311: for (j=1; j<= (nlstate-1) ; j ++)
4312: fprintf(ficgp,"+$%d",k+l+j);
4313: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
4314: } /* nlstate */
4315: fprintf(ficgp,"\n");
4316: } /* end cpt state*/
4317: } /* end covariate */
4318:
4319: /* proba elementaires */
4320: for(i=1,jk=1; i <=nlstate; i++){
4321: for(k=1; k <=(nlstate+ndeath); k++){
4322: if (k != i) {
4323: for(j=1; j <=ncovmodel; j++){
4324: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
4325: jk++;
4326: fprintf(ficgp,"\n");
4327: }
4328: }
4329: }
4330: }
4331: /*goto avoid;*/
4332: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
4333: for(jk=1; jk <=m; jk++) {
4334: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
4335: if (ng==2)
4336: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
4337: else
4338: fprintf(ficgp,"\nset title \"Probability\"\n");
4339: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
4340: i=1;
4341: for(k2=1; k2<=nlstate; k2++) {
4342: k3=i;
4343: for(k=1; k<=(nlstate+ndeath); k++) {
4344: if (k != k2){
4345: if(ng==2)
4346: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
4347: else
4348: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
4349: ij=1;/* To be checked else nbcode[0][0] wrong */
4350: for(j=3; j <=ncovmodel; j++) {
4351: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
4352: /* /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
4353: /* ij++; */
4354: /* } */
4355: /* else */
4356: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4357: }
4358: fprintf(ficgp,")/(1");
4359:
4360: for(k1=1; k1 <=nlstate; k1++){
4361: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
4362: ij=1;
4363: for(j=3; j <=ncovmodel; j++){
4364: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
4365: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
4366: /* ij++; */
4367: /* } */
4368: /* else */
4369: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4370: }
4371: fprintf(ficgp,")");
4372: }
4373: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
4374: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
4375: i=i+ncovmodel;
4376: }
4377: } /* end k */
4378: } /* end k2 */
4379: } /* end jk */
4380: } /* end ng */
4381: /* avoid: */
4382: fflush(ficgp);
4383: } /* end gnuplot */
4384:
4385:
4386: /*************** Moving average **************/
4387: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
4388:
4389: int i, cpt, cptcod;
4390: int modcovmax =1;
4391: int mobilavrange, mob;
4392: double age;
4393:
4394: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
4395: a covariate has 2 modalities */
4396: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
4397:
4398: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
4399: if(mobilav==1) mobilavrange=5; /* default */
4400: else mobilavrange=mobilav;
4401: for (age=bage; age<=fage; age++)
4402: for (i=1; i<=nlstate;i++)
4403: for (cptcod=1;cptcod<=modcovmax;cptcod++)
4404: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
4405: /* We keep the original values on the extreme ages bage, fage and for
4406: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
4407: we use a 5 terms etc. until the borders are no more concerned.
4408: */
4409: for (mob=3;mob <=mobilavrange;mob=mob+2){
4410: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
4411: for (i=1; i<=nlstate;i++){
4412: for (cptcod=1;cptcod<=modcovmax;cptcod++){
4413: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
4414: for (cpt=1;cpt<=(mob-1)/2;cpt++){
4415: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
4416: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
4417: }
4418: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
4419: }
4420: }
4421: }/* end age */
4422: }/* end mob */
4423: }else return -1;
4424: return 0;
4425: }/* End movingaverage */
4426:
4427:
4428: /************** Forecasting ******************/
4429: 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){
4430: /* proj1, year, month, day of starting projection
4431: agemin, agemax range of age
4432: dateprev1 dateprev2 range of dates during which prevalence is computed
4433: anproj2 year of en of projection (same day and month as proj1).
4434: */
4435: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
4436: double agec; /* generic age */
4437: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
4438: double *popeffectif,*popcount;
4439: double ***p3mat;
4440: double ***mobaverage;
4441: char fileresf[FILENAMELENGTH];
4442:
4443: agelim=AGESUP;
4444: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4445:
4446: strcpy(fileresf,"f");
4447: strcat(fileresf,fileres);
4448: if((ficresf=fopen(fileresf,"w"))==NULL) {
4449: printf("Problem with forecast resultfile: %s\n", fileresf);
4450: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
4451: }
4452: printf("Computing forecasting: result on file '%s' \n", fileresf);
4453: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
4454:
4455: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4456:
4457: if (mobilav!=0) {
4458: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4459: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4460: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4461: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4462: }
4463: }
4464:
4465: stepsize=(int) (stepm+YEARM-1)/YEARM;
4466: if (stepm<=12) stepsize=1;
4467: if(estepm < stepm){
4468: printf ("Problem %d lower than %d\n",estepm, stepm);
4469: }
4470: else hstepm=estepm;
4471:
4472: hstepm=hstepm/stepm;
4473: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
4474: fractional in yp1 */
4475: anprojmean=yp;
4476: yp2=modf((yp1*12),&yp);
4477: mprojmean=yp;
4478: yp1=modf((yp2*30.5),&yp);
4479: jprojmean=yp;
4480: if(jprojmean==0) jprojmean=1;
4481: if(mprojmean==0) jprojmean=1;
4482:
4483: i1=cptcoveff;
4484: if (cptcovn < 1){i1=1;}
4485:
4486: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4487:
4488: fprintf(ficresf,"#****** Routine prevforecast **\n");
4489:
4490: /* if (h==(int)(YEARM*yearp)){ */
4491: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4492: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4493: k=k+1;
4494: fprintf(ficresf,"\n#******");
4495: for(j=1;j<=cptcoveff;j++) {
4496: 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]]);
4497: }
4498: fprintf(ficresf,"******\n");
4499: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4500: for(j=1; j<=nlstate+ndeath;j++){
4501: for(i=1; i<=nlstate;i++)
4502: fprintf(ficresf," p%d%d",i,j);
4503: fprintf(ficresf," p.%d",j);
4504: }
4505: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4506: fprintf(ficresf,"\n");
4507: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4508:
4509: for (agec=fage; agec>=(ageminpar-1); agec--){
4510: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4511: nhstepm = nhstepm/hstepm;
4512: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4513: oldm=oldms;savm=savms;
4514: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4515:
4516: for (h=0; h<=nhstepm; h++){
4517: if (h*hstepm/YEARM*stepm ==yearp) {
4518: fprintf(ficresf,"\n");
4519: for(j=1;j<=cptcoveff;j++)
4520: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4521: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4522: }
4523: for(j=1; j<=nlstate+ndeath;j++) {
4524: ppij=0.;
4525: for(i=1; i<=nlstate;i++) {
4526: if (mobilav==1)
4527: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4528: else {
4529: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4530: }
4531: if (h*hstepm/YEARM*stepm== yearp) {
4532: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4533: }
4534: } /* end i */
4535: if (h*hstepm/YEARM*stepm==yearp) {
4536: fprintf(ficresf," %.3f", ppij);
4537: }
4538: }/* end j */
4539: } /* end h */
4540: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4541: } /* end agec */
4542: } /* end yearp */
4543: } /* end cptcod */
4544: } /* end cptcov */
4545:
4546: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4547:
4548: fclose(ficresf);
4549: }
4550:
4551: /************** Forecasting *****not tested NB*************/
4552: 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){
4553:
4554: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4555: int *popage;
4556: double calagedatem, agelim, kk1, kk2;
4557: double *popeffectif,*popcount;
4558: double ***p3mat,***tabpop,***tabpopprev;
4559: double ***mobaverage;
4560: char filerespop[FILENAMELENGTH];
4561:
4562: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4563: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4564: agelim=AGESUP;
4565: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4566:
4567: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4568:
4569:
4570: strcpy(filerespop,"pop");
4571: strcat(filerespop,fileres);
4572: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4573: printf("Problem with forecast resultfile: %s\n", filerespop);
4574: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4575: }
4576: printf("Computing forecasting: result on file '%s' \n", filerespop);
4577: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4578:
4579: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4580:
4581: if (mobilav!=0) {
4582: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4583: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4584: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4585: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4586: }
4587: }
4588:
4589: stepsize=(int) (stepm+YEARM-1)/YEARM;
4590: if (stepm<=12) stepsize=1;
4591:
4592: agelim=AGESUP;
4593:
4594: hstepm=1;
4595: hstepm=hstepm/stepm;
4596:
4597: if (popforecast==1) {
4598: if((ficpop=fopen(popfile,"r"))==NULL) {
4599: printf("Problem with population file : %s\n",popfile);exit(0);
4600: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4601: }
4602: popage=ivector(0,AGESUP);
4603: popeffectif=vector(0,AGESUP);
4604: popcount=vector(0,AGESUP);
4605:
4606: i=1;
4607: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4608:
4609: imx=i;
4610: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4611: }
4612:
4613: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4614: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4615: k=k+1;
4616: fprintf(ficrespop,"\n#******");
4617: for(j=1;j<=cptcoveff;j++) {
4618: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4619: }
4620: fprintf(ficrespop,"******\n");
4621: fprintf(ficrespop,"# Age");
4622: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4623: if (popforecast==1) fprintf(ficrespop," [Population]");
4624:
4625: for (cpt=0; cpt<=0;cpt++) {
4626: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4627:
4628: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4629: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4630: nhstepm = nhstepm/hstepm;
4631:
4632: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4633: oldm=oldms;savm=savms;
4634: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4635:
4636: for (h=0; h<=nhstepm; h++){
4637: if (h==(int) (calagedatem+YEARM*cpt)) {
4638: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4639: }
4640: for(j=1; j<=nlstate+ndeath;j++) {
4641: kk1=0.;kk2=0;
4642: for(i=1; i<=nlstate;i++) {
4643: if (mobilav==1)
4644: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4645: else {
4646: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4647: }
4648: }
4649: if (h==(int)(calagedatem+12*cpt)){
4650: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4651: /*fprintf(ficrespop," %.3f", kk1);
4652: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4653: }
4654: }
4655: for(i=1; i<=nlstate;i++){
4656: kk1=0.;
4657: for(j=1; j<=nlstate;j++){
4658: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4659: }
4660: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
4661: }
4662:
4663: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
4664: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4665: }
4666: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4667: }
4668: }
4669:
4670: /******/
4671:
4672: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4673: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4674: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4675: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4676: nhstepm = nhstepm/hstepm;
4677:
4678: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4679: oldm=oldms;savm=savms;
4680: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4681: for (h=0; h<=nhstepm; h++){
4682: if (h==(int) (calagedatem+YEARM*cpt)) {
4683: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4684: }
4685: for(j=1; j<=nlstate+ndeath;j++) {
4686: kk1=0.;kk2=0;
4687: for(i=1; i<=nlstate;i++) {
4688: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4689: }
4690: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
4691: }
4692: }
4693: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4694: }
4695: }
4696: }
4697: }
4698:
4699: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4700:
4701: if (popforecast==1) {
4702: free_ivector(popage,0,AGESUP);
4703: free_vector(popeffectif,0,AGESUP);
4704: free_vector(popcount,0,AGESUP);
4705: }
4706: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4707: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4708: fclose(ficrespop);
4709: } /* End of popforecast */
4710:
4711: int fileappend(FILE *fichier, char *optionfich)
4712: {
4713: if((fichier=fopen(optionfich,"a"))==NULL) {
4714: printf("Problem with file: %s\n", optionfich);
4715: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4716: return (0);
4717: }
4718: fflush(fichier);
4719: return (1);
4720: }
4721:
4722:
4723: /**************** function prwizard **********************/
4724: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4725: {
4726:
4727: /* Wizard to print covariance matrix template */
4728:
4729: char ca[32], cb[32];
4730: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
4731: int numlinepar;
4732:
4733: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4734: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4735: for(i=1; i <=nlstate; i++){
4736: jj=0;
4737: for(j=1; j <=nlstate+ndeath; j++){
4738: if(j==i) continue;
4739: jj++;
4740: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4741: printf("%1d%1d",i,j);
4742: fprintf(ficparo,"%1d%1d",i,j);
4743: for(k=1; k<=ncovmodel;k++){
4744: /* printf(" %lf",param[i][j][k]); */
4745: /* fprintf(ficparo," %lf",param[i][j][k]); */
4746: printf(" 0.");
4747: fprintf(ficparo," 0.");
4748: }
4749: printf("\n");
4750: fprintf(ficparo,"\n");
4751: }
4752: }
4753: printf("# Scales (for hessian or gradient estimation)\n");
4754: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4755: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4756: for(i=1; i <=nlstate; i++){
4757: jj=0;
4758: for(j=1; j <=nlstate+ndeath; j++){
4759: if(j==i) continue;
4760: jj++;
4761: fprintf(ficparo,"%1d%1d",i,j);
4762: printf("%1d%1d",i,j);
4763: fflush(stdout);
4764: for(k=1; k<=ncovmodel;k++){
4765: /* printf(" %le",delti3[i][j][k]); */
4766: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4767: printf(" 0.");
4768: fprintf(ficparo," 0.");
4769: }
4770: numlinepar++;
4771: printf("\n");
4772: fprintf(ficparo,"\n");
4773: }
4774: }
4775: printf("# Covariance matrix\n");
4776: /* # 121 Var(a12)\n\ */
4777: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4778: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4779: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4780: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4781: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4782: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4783: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4784: fflush(stdout);
4785: fprintf(ficparo,"# Covariance matrix\n");
4786: /* # 121 Var(a12)\n\ */
4787: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4788: /* # ...\n\ */
4789: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4790:
4791: for(itimes=1;itimes<=2;itimes++){
4792: jj=0;
4793: for(i=1; i <=nlstate; i++){
4794: for(j=1; j <=nlstate+ndeath; j++){
4795: if(j==i) continue;
4796: for(k=1; k<=ncovmodel;k++){
4797: jj++;
4798: ca[0]= k+'a'-1;ca[1]='\0';
4799: if(itimes==1){
4800: printf("#%1d%1d%d",i,j,k);
4801: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4802: }else{
4803: printf("%1d%1d%d",i,j,k);
4804: fprintf(ficparo,"%1d%1d%d",i,j,k);
4805: /* printf(" %.5le",matcov[i][j]); */
4806: }
4807: ll=0;
4808: for(li=1;li <=nlstate; li++){
4809: for(lj=1;lj <=nlstate+ndeath; lj++){
4810: if(lj==li) continue;
4811: for(lk=1;lk<=ncovmodel;lk++){
4812: ll++;
4813: if(ll<=jj){
4814: cb[0]= lk +'a'-1;cb[1]='\0';
4815: if(ll<jj){
4816: if(itimes==1){
4817: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4818: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4819: }else{
4820: printf(" 0.");
4821: fprintf(ficparo," 0.");
4822: }
4823: }else{
4824: if(itimes==1){
4825: printf(" Var(%s%1d%1d)",ca,i,j);
4826: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4827: }else{
4828: printf(" 0.");
4829: fprintf(ficparo," 0.");
4830: }
4831: }
4832: }
4833: } /* end lk */
4834: } /* end lj */
4835: } /* end li */
4836: printf("\n");
4837: fprintf(ficparo,"\n");
4838: numlinepar++;
4839: } /* end k*/
4840: } /*end j */
4841: } /* end i */
4842: } /* end itimes */
4843:
4844: } /* end of prwizard */
4845: /******************* Gompertz Likelihood ******************************/
4846: double gompertz(double x[])
4847: {
4848: double A,B,L=0.0,sump=0.,num=0.;
4849: int i,n=0; /* n is the size of the sample */
4850:
4851: for (i=0;i<=imx-1 ; i++) {
4852: sump=sump+weight[i];
4853: /* sump=sump+1;*/
4854: num=num+1;
4855: }
4856:
4857:
4858: /* for (i=0; i<=imx; i++)
4859: 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]);*/
4860:
4861: for (i=1;i<=imx ; i++)
4862: {
4863: if (cens[i] == 1 && wav[i]>1)
4864: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
4865:
4866: if (cens[i] == 0 && wav[i]>1)
4867: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4868: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
4869:
4870: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4871: if (wav[i] > 1 ) { /* ??? */
4872: L=L+A*weight[i];
4873: /* 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]);*/
4874: }
4875: }
4876:
4877: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4878:
4879: return -2*L*num/sump;
4880: }
4881:
4882: #ifdef GSL
4883: /******************* Gompertz_f Likelihood ******************************/
4884: double gompertz_f(const gsl_vector *v, void *params)
4885: {
4886: double A,B,LL=0.0,sump=0.,num=0.;
4887: double *x= (double *) v->data;
4888: int i,n=0; /* n is the size of the sample */
4889:
4890: for (i=0;i<=imx-1 ; i++) {
4891: sump=sump+weight[i];
4892: /* sump=sump+1;*/
4893: num=num+1;
4894: }
4895:
4896:
4897: /* for (i=0; i<=imx; i++)
4898: 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]);*/
4899: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
4900: for (i=1;i<=imx ; i++)
4901: {
4902: if (cens[i] == 1 && wav[i]>1)
4903: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
4904:
4905: if (cens[i] == 0 && wav[i]>1)
4906: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
4907: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
4908:
4909: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4910: if (wav[i] > 1 ) { /* ??? */
4911: LL=LL+A*weight[i];
4912: /* 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]);*/
4913: }
4914: }
4915:
4916: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4917: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
4918:
4919: return -2*LL*num/sump;
4920: }
4921: #endif
4922:
4923: /******************* Printing html file ***********/
4924: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4925: int lastpass, int stepm, int weightopt, char model[],\
4926: int imx, double p[],double **matcov,double agemortsup){
4927: int i,k;
4928:
4929: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4930: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4931: for (i=1;i<=2;i++)
4932: 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]));
4933: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4934: fprintf(fichtm,"</ul>");
4935:
4936: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4937:
4938: 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>");
4939:
4940: for (k=agegomp;k<(agemortsup-2);k++)
4941: 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]);
4942:
4943:
4944: fflush(fichtm);
4945: }
4946:
4947: /******************* Gnuplot file **************/
4948: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4949:
4950: char dirfileres[132],optfileres[132];
4951:
4952: int ng;
4953:
4954:
4955: /*#ifdef windows */
4956: fprintf(ficgp,"cd \"%s\" \n",pathc);
4957: /*#endif */
4958:
4959:
4960: strcpy(dirfileres,optionfilefiname);
4961: strcpy(optfileres,"vpl");
4962: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4963: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
4964: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
4965: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
4966: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4967:
4968: }
4969:
4970: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
4971: {
4972:
4973: /*-------- data file ----------*/
4974: FILE *fic;
4975: char dummy[]=" ";
4976: int i=0, j=0, n=0;
4977: int linei, month, year,iout;
4978: char line[MAXLINE], linetmp[MAXLINE];
4979: char stra[MAXLINE], strb[MAXLINE];
4980: char *stratrunc;
4981: int lstra;
4982:
4983:
4984: if((fic=fopen(datafile,"r"))==NULL) {
4985: printf("Problem while opening datafile: %s\n", datafile);return 1;
4986: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
4987: }
4988:
4989: i=1;
4990: linei=0;
4991: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
4992: linei=linei+1;
4993: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
4994: if(line[j] == '\t')
4995: line[j] = ' ';
4996: }
4997: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
4998: ;
4999: };
5000: line[j+1]=0; /* Trims blanks at end of line */
5001: if(line[0]=='#'){
5002: fprintf(ficlog,"Comment line\n%s\n",line);
5003: printf("Comment line\n%s\n",line);
5004: continue;
5005: }
5006: trimbb(linetmp,line); /* Trims multiple blanks in line */
5007: strcpy(line, linetmp);
5008:
5009:
5010: for (j=maxwav;j>=1;j--){
5011: cutv(stra, strb, line, ' ');
5012: if(strb[0]=='.') { /* Missing status */
5013: lval=-1;
5014: }else{
5015: errno=0;
5016: lval=strtol(strb,&endptr,10);
5017: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
5018: if( strb[0]=='\0' || (*endptr != '\0')){
5019: 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);
5020: 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);
5021: return 1;
5022: }
5023: }
5024: s[j][i]=lval;
5025:
5026: strcpy(line,stra);
5027: cutv(stra, strb,line,' ');
5028: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
5029: }
5030: else if(iout=sscanf(strb,"%s.",dummy) != 0){
5031: month=99;
5032: year=9999;
5033: }else{
5034: 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);
5035: 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);
5036: return 1;
5037: }
5038: anint[j][i]= (double) year;
5039: mint[j][i]= (double)month;
5040: strcpy(line,stra);
5041: } /* ENd Waves */
5042:
5043: cutv(stra, strb,line,' ');
5044: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
5045: }
5046: else if(iout=sscanf(strb,"%s.",dummy) != 0){
5047: month=99;
5048: year=9999;
5049: }else{
5050: 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);
5051: 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);
5052: return 1;
5053: }
5054: andc[i]=(double) year;
5055: moisdc[i]=(double) month;
5056: strcpy(line,stra);
5057:
5058: cutv(stra, strb,line,' ');
5059: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
5060: }
5061: else if(iout=sscanf(strb,"%s.", dummy) != 0){
5062: month=99;
5063: year=9999;
5064: }else{
5065: 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);
5066: 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);
5067: return 1;
5068: }
5069: if (year==9999) {
5070: 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);
5071: 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);
5072: return 1;
5073:
5074: }
5075: annais[i]=(double)(year);
5076: moisnais[i]=(double)(month);
5077: strcpy(line,stra);
5078:
5079: cutv(stra, strb,line,' ');
5080: errno=0;
5081: dval=strtod(strb,&endptr);
5082: if( strb[0]=='\0' || (*endptr != '\0')){
5083: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
5084: 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);
5085: fflush(ficlog);
5086: return 1;
5087: }
5088: weight[i]=dval;
5089: strcpy(line,stra);
5090:
5091: for (j=ncovcol;j>=1;j--){
5092: cutv(stra, strb,line,' ');
5093: if(strb[0]=='.') { /* Missing status */
5094: lval=-1;
5095: }else{
5096: errno=0;
5097: lval=strtol(strb,&endptr,10);
5098: if( strb[0]=='\0' || (*endptr != '\0')){
5099: 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);
5100: 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);
5101: return 1;
5102: }
5103: }
5104: if(lval <-1 || lval >1){
5105: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
5106: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5107: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5108: For example, for multinomial values like 1, 2 and 3,\n \
5109: build V1=0 V2=0 for the reference value (1),\n \
5110: V1=1 V2=0 for (2) \n \
5111: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5112: output of IMaCh is often meaningless.\n \
5113: Exiting.\n",lval,linei, i,line,j);
5114: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
5115: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5116: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5117: For example, for multinomial values like 1, 2 and 3,\n \
5118: build V1=0 V2=0 for the reference value (1),\n \
5119: V1=1 V2=0 for (2) \n \
5120: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5121: output of IMaCh is often meaningless.\n \
5122: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
5123: return 1;
5124: }
5125: covar[j][i]=(double)(lval);
5126: strcpy(line,stra);
5127: }
5128: lstra=strlen(stra);
5129:
5130: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
5131: stratrunc = &(stra[lstra-9]);
5132: num[i]=atol(stratrunc);
5133: }
5134: else
5135: num[i]=atol(stra);
5136: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
5137: 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;}*/
5138:
5139: i=i+1;
5140: } /* End loop reading data */
5141:
5142: *imax=i-1; /* Number of individuals */
5143: fclose(fic);
5144:
5145: return (0);
5146: /* endread: */
5147: printf("Exiting readdata: ");
5148: fclose(fic);
5149: return (1);
5150:
5151:
5152:
5153: }
5154: void removespace(char *str) {
5155: char *p1 = str, *p2 = str;
5156: do
5157: while (*p2 == ' ')
5158: p2++;
5159: while (*p1++ = *p2++);
5160: }
5161:
5162: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
5163: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
5164: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
5165: * - cptcovn or number of covariates k of the models excluding age*products =6
5166: * - cptcovage number of covariates with age*products =2
5167: * - cptcovs number of simple covariates
5168: * - 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
5169: * which is a new column after the 9 (ncovcol) variables.
5170: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
5171: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
5172: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
5173: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
5174: */
5175: {
5176: int i, j, k, ks;
5177: int j1, k1, k2;
5178: char modelsav[80];
5179: char stra[80], strb[80], strc[80], strd[80],stre[80];
5180:
5181: /*removespace(model);*/
5182: if (strlen(model) >1){ /* If there is at least 1 covariate */
5183: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
5184: j=nbocc(model,'+'); /**< j=Number of '+' */
5185: j1=nbocc(model,'*'); /**< j1=Number of '*' */
5186: cptcovs=j+1-j1; /**< Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2 */
5187: cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
5188: /* including age products which are counted in cptcovage.
5189: /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
5190: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
5191: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
5192: strcpy(modelsav,model);
5193: if (strstr(model,"AGE") !=0){
5194: printf("Error. AGE must be in lower case 'age' model=%s ",model);
5195: fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
5196: return 1;
5197: }
5198: if (strstr(model,"v") !=0){
5199: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
5200: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
5201: return 1;
5202: }
5203:
5204: /* Design
5205: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
5206: * < ncovcol=8 >
5207: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
5208: * k= 1 2 3 4 5 6 7 8
5209: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
5210: * covar[k,i], value of kth covariate if not including age for individual i:
5211: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
5212: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
5213: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
5214: * Tage[++cptcovage]=k
5215: * if products, new covar are created after ncovcol with k1
5216: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
5217: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
5218: * 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
5219: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
5220: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
5221: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
5222: * < ncovcol=8 >
5223: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
5224: * k= 1 2 3 4 5 6 7 8 9 10 11 12
5225: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
5226: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5227: * p Tprod[1]@2={ 6, 5}
5228: *p Tvard[1][1]@4= {7, 8, 5, 6}
5229: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
5230: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
5231: *How to reorganize?
5232: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
5233: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5234: * {2, 1, 4, 8, 5, 6, 3, 7}
5235: * Struct []
5236: */
5237:
5238: /* This loop fills the array Tvar from the string 'model'.*/
5239: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
5240: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
5241: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
5242: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
5243: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
5244: /* k=1 Tvar[1]=2 (from V2) */
5245: /* k=5 Tvar[5] */
5246: /* for (k=1; k<=cptcovn;k++) { */
5247: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
5248: /* } */
5249: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
5250: /*
5251: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
5252: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
5253: Tvar[k]=0;
5254: cptcovage=0;
5255: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
5256: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5257: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
5258: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
5259: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5260: /*scanf("%d",i);*/
5261: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
5262: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
5263: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
5264: /* covar is not filled and then is empty */
5265: cptcovprod--;
5266: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
5267: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
5268: cptcovage++; /* Sums the number of covariates which include age as a product */
5269: Tage[cptcovage]=k; /* Tage[1] = 4 */
5270: /*printf("stre=%s ", stre);*/
5271: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
5272: cptcovprod--;
5273: cutl(stre,strb,strc,'V');
5274: Tvar[k]=atoi(stre);
5275: cptcovage++;
5276: Tage[cptcovage]=k;
5277: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
5278: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
5279: cptcovn++;
5280: cptcovprodnoage++;k1++;
5281: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5282: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
5283: because this model-covariate is a construction we invent a new column
5284: ncovcol + k1
5285: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
5286: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
5287: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
5288: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
5289: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
5290: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
5291: k2=k2+2;
5292: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
5293: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
5294: for (i=1; i<=lastobs;i++){
5295: /* Computes the new covariate which is a product of
5296: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
5297: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
5298: }
5299: } /* End age is not in the model */
5300: } /* End if model includes a product */
5301: else { /* no more sum */
5302: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5303: /* scanf("%d",i);*/
5304: cutl(strd,strc,strb,'V');
5305: ks++; /**< Number of simple covariates */
5306: cptcovn++;
5307: Tvar[k]=atoi(strd);
5308: }
5309: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
5310: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5311: scanf("%d",i);*/
5312: } /* end of loop + */
5313: } /* end model */
5314:
5315: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5316: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5317:
5318: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5319: printf("cptcovprod=%d ", cptcovprod);
5320: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5321:
5322: scanf("%d ",i);*/
5323:
5324:
5325: return (0); /* with covar[new additional covariate if product] and Tage if age */
5326: /*endread:*/
5327: printf("Exiting decodemodel: ");
5328: return (1);
5329: }
5330:
5331: calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
5332: {
5333: int i, m;
5334:
5335: for (i=1; i<=imx; i++) {
5336: for(m=2; (m<= maxwav); m++) {
5337: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5338: anint[m][i]=9999;
5339: s[m][i]=-1;
5340: }
5341: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
5342: *nberr++;
5343: 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);
5344: 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);
5345: s[m][i]=-1;
5346: }
5347: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
5348: *nberr++;
5349: 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]);
5350: 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]);
5351: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5352: }
5353: }
5354: }
5355:
5356: for (i=1; i<=imx; i++) {
5357: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5358: for(m=firstpass; (m<= lastpass); m++){
5359: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5360: if (s[m][i] >= nlstate+1) {
5361: if(agedc[i]>0)
5362: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
5363: agev[m][i]=agedc[i];
5364: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
5365: else {
5366: if ((int)andc[i]!=9999){
5367: nbwarn++;
5368: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5369: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5370: agev[m][i]=-1;
5371: }
5372: }
5373: }
5374: else if(s[m][i] !=9){ /* Standard case, age in fractional
5375: years but with the precision of a month */
5376: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5377: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5378: agev[m][i]=1;
5379: else if(agev[m][i] < *agemin){
5380: *agemin=agev[m][i];
5381: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
5382: }
5383: else if(agev[m][i] >*agemax){
5384: *agemax=agev[m][i];
5385: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
5386: }
5387: /*agev[m][i]=anint[m][i]-annais[i];*/
5388: /* agev[m][i] = age[i]+2*m;*/
5389: }
5390: else { /* =9 */
5391: agev[m][i]=1;
5392: s[m][i]=-1;
5393: }
5394: }
5395: else /*= 0 Unknown */
5396: agev[m][i]=1;
5397: }
5398:
5399: }
5400: for (i=1; i<=imx; i++) {
5401: for(m=firstpass; (m<=lastpass); m++){
5402: if (s[m][i] > (nlstate+ndeath)) {
5403: *nberr++;
5404: 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);
5405: 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);
5406: return 1;
5407: }
5408: }
5409: }
5410:
5411: /*for (i=1; i<=imx; i++){
5412: for (m=firstpass; (m<lastpass); m++){
5413: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5414: }
5415:
5416: }*/
5417:
5418:
5419: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5420: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5421:
5422: return (0);
5423: /* endread:*/
5424: printf("Exiting calandcheckages: ");
5425: return (1);
5426: }
5427:
5428: syscompilerinfo()
5429: {
5430: /* #include "syscompilerinfo.h"*/
5431: #include <gnu/libc-version.h>
5432: #if defined(__GNUC__)
5433: # if defined(__GNUC_PATCHLEVEL__)
5434: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
5435: + __GNUC_MINOR__ * 100 \
5436: + __GNUC_PATCHLEVEL__)
5437: # else
5438: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
5439: + __GNUC_MINOR__ * 100)
5440: # endif
5441: #endif
5442:
5443: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
5444: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
5445: // Windows (x64 and x86)
5446: #elif __unix__ // all unices, not all compilers
5447: // Unix
5448: #elif __linux__
5449: // linux
5450: #elif __APPLE__
5451: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though...
5452: #endif
5453:
5454: /* __MINGW32__ */
5455: /* __CYGWIN__ */
5456: /* __MINGW64__ */
5457: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
5458: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
5459: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
5460: /* _WIN64 // Defined for applications for Win64. */
5461: /* _M_X64 // Defined for compilations that target x64 processors. */
5462: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
5463: #include <stdint.h>
5464: #if UINTPTR_MAX == 0xffffffff
5465: printf("32-bit \n"); /* 32-bit */
5466: #elif UINTPTR_MAX == 0xffffffffffffffff
5467: printf("64-bit \n");/* 64-bit */
5468: #else
5469: printf("wtf-bit \n"); /* wtf */
5470: #endif
5471:
5472: struct utsname sysInfo;
5473:
5474: if (uname(&sysInfo) != -1) {
5475: puts(sysInfo.sysname);
5476: puts(sysInfo.nodename);
5477: puts(sysInfo.release);
5478: puts(sysInfo.version);
5479: puts(sysInfo.machine);
5480: }
5481: else
5482: perror("uname() error");
5483: printf("GNU C version %d\n", __GNUC_VERSION__);
5484: printf("GNU libc version: %s\n", gnu_get_libc_version());
5485:
5486: }
5487:
5488: /***********************************************/
5489: /**************** Main Program *****************/
5490: /***********************************************/
5491:
5492: int main(int argc, char *argv[])
5493: {
5494: #ifdef GSL
5495: const gsl_multimin_fminimizer_type *T;
5496: size_t iteri = 0, it;
5497: int rval = GSL_CONTINUE;
5498: int status = GSL_SUCCESS;
5499: double ssval;
5500: #endif
5501: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
5502: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
5503:
5504: int jj, ll, li, lj, lk;
5505: int numlinepar=0; /* Current linenumber of parameter file */
5506: int itimes;
5507: int NDIM=2;
5508: int vpopbased=0;
5509:
5510: char ca[32], cb[32];
5511: /* FILE *fichtm; *//* Html File */
5512: /* FILE *ficgp;*/ /*Gnuplot File */
5513: struct stat info;
5514: double agedeb;
5515: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
5516:
5517: double fret;
5518: double dum; /* Dummy variable */
5519: double ***p3mat;
5520: double ***mobaverage;
5521:
5522: char line[MAXLINE];
5523: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
5524: char pathr[MAXLINE], pathimach[MAXLINE];
5525: char *tok, *val; /* pathtot */
5526: int firstobs=1, lastobs=10;
5527: int c, h , cpt;
5528: int jl;
5529: int i1, j1, jk, stepsize;
5530: int *tab;
5531: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
5532: int mobilav=0,popforecast=0;
5533: int hstepm, nhstepm;
5534: int agemortsup;
5535: float sumlpop=0.;
5536: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
5537: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
5538:
5539: double bage=0, fage=110, age, agelim, agebase;
5540: double ftolpl=FTOL;
5541: double **prlim;
5542: double ***param; /* Matrix of parameters */
5543: double *p;
5544: double **matcov; /* Matrix of covariance */
5545: double ***delti3; /* Scale */
5546: double *delti; /* Scale */
5547: double ***eij, ***vareij;
5548: double **varpl; /* Variances of prevalence limits by age */
5549: double *epj, vepp;
5550:
5551: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
5552: double **ximort;
5553: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
5554: int *dcwave;
5555:
5556: char z[1]="c";
5557:
5558: /*char *strt;*/
5559: char strtend[80];
5560:
5561:
5562: /* setlocale (LC_ALL, ""); */
5563: /* bindtextdomain (PACKAGE, LOCALEDIR); */
5564: /* textdomain (PACKAGE); */
5565: /* setlocale (LC_CTYPE, ""); */
5566: /* setlocale (LC_MESSAGES, ""); */
5567:
5568: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
5569: rstart_time = time(NULL);
5570: /* (void) gettimeofday(&start_time,&tzp);*/
5571: start_time = *localtime(&rstart_time);
5572: curr_time=start_time;
5573: /*tml = *localtime(&start_time.tm_sec);*/
5574: /* strcpy(strstart,asctime(&tml)); */
5575: strcpy(strstart,asctime(&start_time));
5576:
5577: /* printf("Localtime (at start)=%s",strstart); */
5578: /* tp.tm_sec = tp.tm_sec +86400; */
5579: /* tm = *localtime(&start_time.tm_sec); */
5580: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
5581: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
5582: /* tmg.tm_hour=tmg.tm_hour + 1; */
5583: /* tp.tm_sec = mktime(&tmg); */
5584: /* strt=asctime(&tmg); */
5585: /* printf("Time(after) =%s",strstart); */
5586: /* (void) time (&time_value);
5587: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
5588: * tm = *localtime(&time_value);
5589: * strstart=asctime(&tm);
5590: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
5591: */
5592:
5593: nberr=0; /* Number of errors and warnings */
5594: nbwarn=0;
5595: getcwd(pathcd, size);
5596:
5597: printf("\n%s\n%s",version,fullversion);
5598: if(argc <=1){
5599: printf("\nEnter the parameter file name: ");
5600: fgets(pathr,FILENAMELENGTH,stdin);
5601: i=strlen(pathr);
5602: if(pathr[i-1]=='\n')
5603: pathr[i-1]='\0';
5604: i=strlen(pathr);
5605: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
5606: pathr[i-1]='\0';
5607: for (tok = pathr; tok != NULL; ){
5608: printf("Pathr |%s|\n",pathr);
5609: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
5610: printf("val= |%s| pathr=%s\n",val,pathr);
5611: strcpy (pathtot, val);
5612: if(pathr[0] == '\0') break; /* Dirty */
5613: }
5614: }
5615: else{
5616: strcpy(pathtot,argv[1]);
5617: }
5618: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
5619: /*cygwin_split_path(pathtot,path,optionfile);
5620: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
5621: /* cutv(path,optionfile,pathtot,'\\');*/
5622:
5623: /* Split argv[0], imach program to get pathimach */
5624: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
5625: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5626: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5627: /* strcpy(pathimach,argv[0]); */
5628: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
5629: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
5630: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
5631: chdir(path); /* Can be a relative path */
5632: if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
5633: printf("Current directory %s!\n",pathcd);
5634: strcpy(command,"mkdir ");
5635: strcat(command,optionfilefiname);
5636: if((outcmd=system(command)) != 0){
5637: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
5638: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
5639: /* fclose(ficlog); */
5640: /* exit(1); */
5641: }
5642: /* if((imk=mkdir(optionfilefiname))<0){ */
5643: /* perror("mkdir"); */
5644: /* } */
5645:
5646: /*-------- arguments in the command line --------*/
5647:
5648: /* Log file */
5649: strcat(filelog, optionfilefiname);
5650: strcat(filelog,".log"); /* */
5651: if((ficlog=fopen(filelog,"w"))==NULL) {
5652: printf("Problem with logfile %s\n",filelog);
5653: goto end;
5654: }
5655: fprintf(ficlog,"Log filename:%s\n",filelog);
5656: fprintf(ficlog,"\n%s\n%s",version,fullversion);
5657: fprintf(ficlog,"\nEnter the parameter file name: \n");
5658: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
5659: path=%s \n\
5660: optionfile=%s\n\
5661: optionfilext=%s\n\
5662: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
5663:
5664: syscompilerinfo();
5665:
5666: printf("Local time (at start):%s",strstart);
5667: fprintf(ficlog,"Local time (at start): %s",strstart);
5668: fflush(ficlog);
5669: /* (void) gettimeofday(&curr_time,&tzp); */
5670: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
5671:
5672: /* */
5673: strcpy(fileres,"r");
5674: strcat(fileres, optionfilefiname);
5675: strcat(fileres,".txt"); /* Other files have txt extension */
5676:
5677: /*---------arguments file --------*/
5678:
5679: if((ficpar=fopen(optionfile,"r"))==NULL) {
5680: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
5681: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
5682: fflush(ficlog);
5683: /* goto end; */
5684: exit(70);
5685: }
5686:
5687:
5688:
5689: strcpy(filereso,"o");
5690: strcat(filereso,fileres);
5691: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
5692: printf("Problem with Output resultfile: %s\n", filereso);
5693: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
5694: fflush(ficlog);
5695: goto end;
5696: }
5697:
5698: /* Reads comments: lines beginning with '#' */
5699: numlinepar=0;
5700: while((c=getc(ficpar))=='#' && c!= EOF){
5701: ungetc(c,ficpar);
5702: fgets(line, MAXLINE, ficpar);
5703: numlinepar++;
5704: fputs(line,stdout);
5705: fputs(line,ficparo);
5706: fputs(line,ficlog);
5707: }
5708: ungetc(c,ficpar);
5709:
5710: 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);
5711: numlinepar++;
5712: 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);
5713: 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);
5714: 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);
5715: fflush(ficlog);
5716: while((c=getc(ficpar))=='#' && c!= EOF){
5717: ungetc(c,ficpar);
5718: fgets(line, MAXLINE, ficpar);
5719: numlinepar++;
5720: fputs(line, stdout);
5721: //puts(line);
5722: fputs(line,ficparo);
5723: fputs(line,ficlog);
5724: }
5725: ungetc(c,ficpar);
5726:
5727:
5728: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
5729: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
5730: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
5731: v1+v2*age+v2*v3 makes cptcovn = 3
5732: */
5733: if (strlen(model)>1)
5734: 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*/
5735: else
5736: ncovmodel=2;
5737: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
5738: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
5739: npar= nforce*ncovmodel; /* Number of parameters like aij*/
5740: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
5741: 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);
5742: 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);
5743: fflush(stdout);
5744: fclose (ficlog);
5745: goto end;
5746: }
5747: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5748: delti=delti3[1][1];
5749: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
5750: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
5751: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5752: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5753: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5754: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5755: fclose (ficparo);
5756: fclose (ficlog);
5757: goto end;
5758: exit(0);
5759: }
5760: else if(mle==-3) {
5761: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5762: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5763: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5764: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5765: matcov=matrix(1,npar,1,npar);
5766: }
5767: else{
5768: /* Read guessed parameters */
5769: /* Reads comments: lines beginning with '#' */
5770: while((c=getc(ficpar))=='#' && c!= EOF){
5771: ungetc(c,ficpar);
5772: fgets(line, MAXLINE, ficpar);
5773: numlinepar++;
5774: fputs(line,stdout);
5775: fputs(line,ficparo);
5776: fputs(line,ficlog);
5777: }
5778: ungetc(c,ficpar);
5779:
5780: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5781: for(i=1; i <=nlstate; i++){
5782: j=0;
5783: for(jj=1; jj <=nlstate+ndeath; jj++){
5784: if(jj==i) continue;
5785: j++;
5786: fscanf(ficpar,"%1d%1d",&i1,&j1);
5787: if ((i1 != i) && (j1 != j)){
5788: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
5789: It might be a problem of design; if ncovcol and the model are correct\n \
5790: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
5791: exit(1);
5792: }
5793: fprintf(ficparo,"%1d%1d",i1,j1);
5794: if(mle==1)
5795: printf("%1d%1d",i,j);
5796: fprintf(ficlog,"%1d%1d",i,j);
5797: for(k=1; k<=ncovmodel;k++){
5798: fscanf(ficpar," %lf",¶m[i][j][k]);
5799: if(mle==1){
5800: printf(" %lf",param[i][j][k]);
5801: fprintf(ficlog," %lf",param[i][j][k]);
5802: }
5803: else
5804: fprintf(ficlog," %lf",param[i][j][k]);
5805: fprintf(ficparo," %lf",param[i][j][k]);
5806: }
5807: fscanf(ficpar,"\n");
5808: numlinepar++;
5809: if(mle==1)
5810: printf("\n");
5811: fprintf(ficlog,"\n");
5812: fprintf(ficparo,"\n");
5813: }
5814: }
5815: fflush(ficlog);
5816:
5817: /* Reads scales values */
5818: p=param[1][1];
5819:
5820: /* Reads comments: lines beginning with '#' */
5821: while((c=getc(ficpar))=='#' && c!= EOF){
5822: ungetc(c,ficpar);
5823: fgets(line, MAXLINE, ficpar);
5824: numlinepar++;
5825: fputs(line,stdout);
5826: fputs(line,ficparo);
5827: fputs(line,ficlog);
5828: }
5829: ungetc(c,ficpar);
5830:
5831: for(i=1; i <=nlstate; i++){
5832: for(j=1; j <=nlstate+ndeath-1; j++){
5833: fscanf(ficpar,"%1d%1d",&i1,&j1);
5834: if ( (i1-i) * (j1-j) != 0){
5835: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
5836: exit(1);
5837: }
5838: printf("%1d%1d",i,j);
5839: fprintf(ficparo,"%1d%1d",i1,j1);
5840: fprintf(ficlog,"%1d%1d",i1,j1);
5841: for(k=1; k<=ncovmodel;k++){
5842: fscanf(ficpar,"%le",&delti3[i][j][k]);
5843: printf(" %le",delti3[i][j][k]);
5844: fprintf(ficparo," %le",delti3[i][j][k]);
5845: fprintf(ficlog," %le",delti3[i][j][k]);
5846: }
5847: fscanf(ficpar,"\n");
5848: numlinepar++;
5849: printf("\n");
5850: fprintf(ficparo,"\n");
5851: fprintf(ficlog,"\n");
5852: }
5853: }
5854: fflush(ficlog);
5855:
5856: /* Reads covariance matrix */
5857: delti=delti3[1][1];
5858:
5859:
5860: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
5861:
5862: /* Reads comments: lines beginning with '#' */
5863: while((c=getc(ficpar))=='#' && c!= EOF){
5864: ungetc(c,ficpar);
5865: fgets(line, MAXLINE, ficpar);
5866: numlinepar++;
5867: fputs(line,stdout);
5868: fputs(line,ficparo);
5869: fputs(line,ficlog);
5870: }
5871: ungetc(c,ficpar);
5872:
5873: matcov=matrix(1,npar,1,npar);
5874: for(i=1; i <=npar; i++)
5875: for(j=1; j <=npar; j++) matcov[i][j]=0.;
5876:
5877: for(i=1; i <=npar; i++){
5878: fscanf(ficpar,"%s",str);
5879: if(mle==1)
5880: printf("%s",str);
5881: fprintf(ficlog,"%s",str);
5882: fprintf(ficparo,"%s",str);
5883: for(j=1; j <=i; j++){
5884: fscanf(ficpar," %le",&matcov[i][j]);
5885: if(mle==1){
5886: printf(" %.5le",matcov[i][j]);
5887: }
5888: fprintf(ficlog," %.5le",matcov[i][j]);
5889: fprintf(ficparo," %.5le",matcov[i][j]);
5890: }
5891: fscanf(ficpar,"\n");
5892: numlinepar++;
5893: if(mle==1)
5894: printf("\n");
5895: fprintf(ficlog,"\n");
5896: fprintf(ficparo,"\n");
5897: }
5898: for(i=1; i <=npar; i++)
5899: for(j=i+1;j<=npar;j++)
5900: matcov[i][j]=matcov[j][i];
5901:
5902: if(mle==1)
5903: printf("\n");
5904: fprintf(ficlog,"\n");
5905:
5906: fflush(ficlog);
5907:
5908: /*-------- Rewriting parameter file ----------*/
5909: strcpy(rfileres,"r"); /* "Rparameterfile */
5910: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
5911: strcat(rfileres,"."); /* */
5912: strcat(rfileres,optionfilext); /* Other files have txt extension */
5913: if((ficres =fopen(rfileres,"w"))==NULL) {
5914: printf("Problem writing new parameter file: %s\n", fileres);goto end;
5915: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
5916: }
5917: fprintf(ficres,"#%s\n",version);
5918: } /* End of mle != -3 */
5919:
5920:
5921: n= lastobs;
5922: num=lvector(1,n);
5923: moisnais=vector(1,n);
5924: annais=vector(1,n);
5925: moisdc=vector(1,n);
5926: andc=vector(1,n);
5927: agedc=vector(1,n);
5928: cod=ivector(1,n);
5929: weight=vector(1,n);
5930: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
5931: mint=matrix(1,maxwav,1,n);
5932: anint=matrix(1,maxwav,1,n);
5933: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
5934: tab=ivector(1,NCOVMAX);
5935: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
5936:
5937: /* Reads data from file datafile */
5938: if (readdata(datafile, firstobs, lastobs, &imx)==1)
5939: goto end;
5940:
5941: /* Calculation of the number of parameters from char model */
5942: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
5943: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
5944: k=3 V4 Tvar[k=3]= 4 (from V4)
5945: k=2 V1 Tvar[k=2]= 1 (from V1)
5946: k=1 Tvar[1]=2 (from V2)
5947: */
5948: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
5949: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
5950: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
5951: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
5952: */
5953: /* For model-covariate k tells which data-covariate to use but
5954: because this model-covariate is a construction we invent a new column
5955: ncovcol + k1
5956: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
5957: Tvar[3=V1*V4]=4+1 etc */
5958: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
5959: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
5960: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
5961: */
5962: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
5963: 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
5964: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
5965: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
5966: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
5967: 4 covariates (3 plus signs)
5968: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
5969: */
5970:
5971: if(decodemodel(model, lastobs) == 1)
5972: goto end;
5973:
5974: if((double)(lastobs-imx)/(double)imx > 1.10){
5975: nbwarn++;
5976: 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);
5977: 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);
5978: }
5979: /* if(mle==1){*/
5980: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
5981: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
5982: }
5983:
5984: /*-calculation of age at interview from date of interview and age at death -*/
5985: agev=matrix(1,maxwav,1,imx);
5986:
5987: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
5988: goto end;
5989:
5990:
5991: agegomp=(int)agemin;
5992: free_vector(moisnais,1,n);
5993: free_vector(annais,1,n);
5994: /* free_matrix(mint,1,maxwav,1,n);
5995: free_matrix(anint,1,maxwav,1,n);*/
5996: free_vector(moisdc,1,n);
5997: free_vector(andc,1,n);
5998: /* */
5999:
6000: wav=ivector(1,imx);
6001: dh=imatrix(1,lastpass-firstpass+1,1,imx);
6002: bh=imatrix(1,lastpass-firstpass+1,1,imx);
6003: mw=imatrix(1,lastpass-firstpass+1,1,imx);
6004:
6005: /* Concatenates waves */
6006: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
6007: /* */
6008:
6009: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
6010:
6011: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
6012: ncodemax[1]=1;
6013: Ndum =ivector(-1,NCOVMAX);
6014: if (ncovmodel > 2)
6015: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
6016:
6017: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
6018: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
6019: h=0;
6020:
6021:
6022: /*if (cptcovn > 0) */
6023:
6024:
6025: m=pow(2,cptcoveff);
6026:
6027: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
6028: 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 */
6029: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
6030: for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
6031: h++;
6032: if (h>m)
6033: h=1;
6034: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
6035: * h 1 2 3 4
6036: *______________________________
6037: * 1 i=1 1 i=1 1 i=1 1 i=1 1
6038: * 2 2 1 1 1
6039: * 3 i=2 1 2 1 1
6040: * 4 2 2 1 1
6041: * 5 i=3 1 i=2 1 2 1
6042: * 6 2 1 2 1
6043: * 7 i=4 1 2 2 1
6044: * 8 2 2 2 1
6045: * 9 i=5 1 i=3 1 i=2 1 1
6046: * 10 2 1 1 1
6047: * 11 i=6 1 2 1 1
6048: * 12 2 2 1 1
6049: * 13 i=7 1 i=4 1 2 1
6050: * 14 2 1 2 1
6051: * 15 i=8 1 2 2 1
6052: * 16 2 2 2 1
6053: */
6054: codtab[h][k]=j;
6055: /*codtab[h][Tvar[k]]=j;*/
6056: 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]]);
6057: }
6058: }
6059: }
6060: }
6061: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
6062: codtab[1][2]=1;codtab[2][2]=2; */
6063: /* for(i=1; i <=m ;i++){
6064: for(k=1; k <=cptcovn; k++){
6065: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
6066: }
6067: printf("\n");
6068: }
6069: scanf("%d",i);*/
6070:
6071: free_ivector(Ndum,-1,NCOVMAX);
6072:
6073:
6074:
6075: /*------------ gnuplot -------------*/
6076: strcpy(optionfilegnuplot,optionfilefiname);
6077: if(mle==-3)
6078: strcat(optionfilegnuplot,"-mort");
6079: strcat(optionfilegnuplot,".gp");
6080:
6081: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
6082: printf("Problem with file %s",optionfilegnuplot);
6083: }
6084: else{
6085: fprintf(ficgp,"\n# %s\n", version);
6086: fprintf(ficgp,"# %s\n", optionfilegnuplot);
6087: //fprintf(ficgp,"set missing 'NaNq'\n");
6088: fprintf(ficgp,"set datafile missing 'NaNq'\n");
6089: }
6090: /* fclose(ficgp);*/
6091: /*--------- index.htm --------*/
6092:
6093: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
6094: if(mle==-3)
6095: strcat(optionfilehtm,"-mort");
6096: strcat(optionfilehtm,".htm");
6097: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
6098: printf("Problem with %s \n",optionfilehtm);
6099: exit(0);
6100: }
6101:
6102: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
6103: strcat(optionfilehtmcov,"-cov.htm");
6104: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
6105: printf("Problem with %s \n",optionfilehtmcov), exit(0);
6106: }
6107: else{
6108: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6109: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6110: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
6111: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
6112: }
6113:
6114: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6115: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6116: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
6117: \n\
6118: <hr size=\"2\" color=\"#EC5E5E\">\
6119: <ul><li><h4>Parameter files</h4>\n\
6120: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
6121: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
6122: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
6123: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
6124: - Date and time at start: %s</ul>\n",\
6125: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
6126: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
6127: fileres,fileres,\
6128: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
6129: fflush(fichtm);
6130:
6131: strcpy(pathr,path);
6132: strcat(pathr,optionfilefiname);
6133: chdir(optionfilefiname); /* Move to directory named optionfile */
6134:
6135: /* Calculates basic frequencies. Computes observed prevalence at single age
6136: and prints on file fileres'p'. */
6137: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
6138:
6139: fprintf(fichtm,"\n");
6140: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
6141: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
6142: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
6143: imx,agemin,agemax,jmin,jmax,jmean);
6144: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6145: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6146: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6147: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6148: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
6149:
6150:
6151: /* For Powell, parameters are in a vector p[] starting at p[1]
6152: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
6153: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
6154:
6155: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
6156:
6157: if (mle==-3){
6158: ximort=matrix(1,NDIM,1,NDIM);
6159: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
6160: cens=ivector(1,n);
6161: ageexmed=vector(1,n);
6162: agecens=vector(1,n);
6163: dcwave=ivector(1,n);
6164:
6165: for (i=1; i<=imx; i++){
6166: dcwave[i]=-1;
6167: for (m=firstpass; m<=lastpass; m++)
6168: if (s[m][i]>nlstate) {
6169: dcwave[i]=m;
6170: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
6171: break;
6172: }
6173: }
6174:
6175: for (i=1; i<=imx; i++) {
6176: if (wav[i]>0){
6177: ageexmed[i]=agev[mw[1][i]][i];
6178: j=wav[i];
6179: agecens[i]=1.;
6180:
6181: if (ageexmed[i]> 1 && wav[i] > 0){
6182: agecens[i]=agev[mw[j][i]][i];
6183: cens[i]= 1;
6184: }else if (ageexmed[i]< 1)
6185: cens[i]= -1;
6186: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
6187: cens[i]=0 ;
6188: }
6189: else cens[i]=-1;
6190: }
6191:
6192: for (i=1;i<=NDIM;i++) {
6193: for (j=1;j<=NDIM;j++)
6194: ximort[i][j]=(i == j ? 1.0 : 0.0);
6195: }
6196:
6197: /*p[1]=0.0268; p[NDIM]=0.083;*/
6198: /*printf("%lf %lf", p[1], p[2]);*/
6199:
6200:
6201: #ifdef GSL
6202: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
6203: #else
6204: printf("Powell\n"); fprintf(ficlog,"Powell\n");
6205: #endif
6206: strcpy(filerespow,"pow-mort");
6207: strcat(filerespow,fileres);
6208: if((ficrespow=fopen(filerespow,"w"))==NULL) {
6209: printf("Problem with resultfile: %s\n", filerespow);
6210: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
6211: }
6212: #ifdef GSL
6213: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
6214: #else
6215: fprintf(ficrespow,"# Powell\n# iter -2*LL");
6216: #endif
6217: /* for (i=1;i<=nlstate;i++)
6218: for(j=1;j<=nlstate+ndeath;j++)
6219: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
6220: */
6221: fprintf(ficrespow,"\n");
6222: #ifdef GSL
6223: /* gsl starts here */
6224: T = gsl_multimin_fminimizer_nmsimplex;
6225: gsl_multimin_fminimizer *sfm = NULL;
6226: gsl_vector *ss, *x;
6227: gsl_multimin_function minex_func;
6228:
6229: /* Initial vertex size vector */
6230: ss = gsl_vector_alloc (NDIM);
6231:
6232: if (ss == NULL){
6233: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
6234: }
6235: /* Set all step sizes to 1 */
6236: gsl_vector_set_all (ss, 0.001);
6237:
6238: /* Starting point */
6239:
6240: x = gsl_vector_alloc (NDIM);
6241:
6242: if (x == NULL){
6243: gsl_vector_free(ss);
6244: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
6245: }
6246:
6247: /* Initialize method and iterate */
6248: /* p[1]=0.0268; p[NDIM]=0.083; */
6249: /* gsl_vector_set(x, 0, 0.0268); */
6250: /* gsl_vector_set(x, 1, 0.083); */
6251: gsl_vector_set(x, 0, p[1]);
6252: gsl_vector_set(x, 1, p[2]);
6253:
6254: minex_func.f = &gompertz_f;
6255: minex_func.n = NDIM;
6256: minex_func.params = (void *)&p; /* ??? */
6257:
6258: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
6259: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
6260:
6261: printf("Iterations beginning .....\n\n");
6262: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
6263:
6264: iteri=0;
6265: while (rval == GSL_CONTINUE){
6266: iteri++;
6267: status = gsl_multimin_fminimizer_iterate(sfm);
6268:
6269: if (status) printf("error: %s\n", gsl_strerror (status));
6270: fflush(0);
6271:
6272: if (status)
6273: break;
6274:
6275: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
6276: ssval = gsl_multimin_fminimizer_size (sfm);
6277:
6278: if (rval == GSL_SUCCESS)
6279: printf ("converged to a local maximum at\n");
6280:
6281: printf("%5d ", iteri);
6282: for (it = 0; it < NDIM; it++){
6283: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
6284: }
6285: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
6286: }
6287:
6288: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
6289:
6290: gsl_vector_free(x); /* initial values */
6291: gsl_vector_free(ss); /* inital step size */
6292: for (it=0; it<NDIM; it++){
6293: p[it+1]=gsl_vector_get(sfm->x,it);
6294: fprintf(ficrespow," %.12lf", p[it]);
6295: }
6296: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
6297: #endif
6298: #ifdef POWELL
6299: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
6300: #endif
6301: fclose(ficrespow);
6302:
6303: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
6304:
6305: for(i=1; i <=NDIM; i++)
6306: for(j=i+1;j<=NDIM;j++)
6307: matcov[i][j]=matcov[j][i];
6308:
6309: printf("\nCovariance matrix\n ");
6310: for(i=1; i <=NDIM; i++) {
6311: for(j=1;j<=NDIM;j++){
6312: printf("%f ",matcov[i][j]);
6313: }
6314: printf("\n ");
6315: }
6316:
6317: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
6318: for (i=1;i<=NDIM;i++)
6319: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
6320:
6321: lsurv=vector(1,AGESUP);
6322: lpop=vector(1,AGESUP);
6323: tpop=vector(1,AGESUP);
6324: lsurv[agegomp]=100000;
6325:
6326: for (k=agegomp;k<=AGESUP;k++) {
6327: agemortsup=k;
6328: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
6329: }
6330:
6331: for (k=agegomp;k<agemortsup;k++)
6332: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
6333:
6334: for (k=agegomp;k<agemortsup;k++){
6335: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
6336: sumlpop=sumlpop+lpop[k];
6337: }
6338:
6339: tpop[agegomp]=sumlpop;
6340: for (k=agegomp;k<(agemortsup-3);k++){
6341: /* tpop[k+1]=2;*/
6342: tpop[k+1]=tpop[k]-lpop[k];
6343: }
6344:
6345:
6346: printf("\nAge lx qx dx Lx Tx e(x)\n");
6347: for (k=agegomp;k<(agemortsup-2);k++)
6348: 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]);
6349:
6350:
6351: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6352: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6353:
6354: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
6355: stepm, weightopt,\
6356: model,imx,p,matcov,agemortsup);
6357:
6358: free_vector(lsurv,1,AGESUP);
6359: free_vector(lpop,1,AGESUP);
6360: free_vector(tpop,1,AGESUP);
6361: #ifdef GSL
6362: free_ivector(cens,1,n);
6363: free_vector(agecens,1,n);
6364: free_ivector(dcwave,1,n);
6365: free_matrix(ximort,1,NDIM,1,NDIM);
6366: #endif
6367: } /* Endof if mle==-3 */
6368:
6369: else{ /* For mle >=1 */
6370: globpr=0;/* debug */
6371: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6372: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6373: for (k=1; k<=npar;k++)
6374: printf(" %d %8.5f",k,p[k]);
6375: printf("\n");
6376: globpr=1; /* to print the contributions */
6377: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6378: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6379: for (k=1; k<=npar;k++)
6380: printf(" %d %8.5f",k,p[k]);
6381: printf("\n");
6382: if(mle>=1){ /* Could be 1 or 2 */
6383: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
6384: }
6385:
6386: /*--------- results files --------------*/
6387: 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);
6388:
6389:
6390: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6391: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6392: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6393: for(i=1,jk=1; i <=nlstate; i++){
6394: for(k=1; k <=(nlstate+ndeath); k++){
6395: if (k != i) {
6396: printf("%d%d ",i,k);
6397: fprintf(ficlog,"%d%d ",i,k);
6398: fprintf(ficres,"%1d%1d ",i,k);
6399: for(j=1; j <=ncovmodel; j++){
6400: printf("%lf ",p[jk]);
6401: fprintf(ficlog,"%lf ",p[jk]);
6402: fprintf(ficres,"%lf ",p[jk]);
6403: jk++;
6404: }
6405: printf("\n");
6406: fprintf(ficlog,"\n");
6407: fprintf(ficres,"\n");
6408: }
6409: }
6410: }
6411: if(mle!=0){
6412: /* Computing hessian and covariance matrix */
6413: ftolhess=ftol; /* Usually correct */
6414: hesscov(matcov, p, npar, delti, ftolhess, func);
6415: }
6416: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
6417: printf("# Scales (for hessian or gradient estimation)\n");
6418: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
6419: for(i=1,jk=1; i <=nlstate; i++){
6420: for(j=1; j <=nlstate+ndeath; j++){
6421: if (j!=i) {
6422: fprintf(ficres,"%1d%1d",i,j);
6423: printf("%1d%1d",i,j);
6424: fprintf(ficlog,"%1d%1d",i,j);
6425: for(k=1; k<=ncovmodel;k++){
6426: printf(" %.5e",delti[jk]);
6427: fprintf(ficlog," %.5e",delti[jk]);
6428: fprintf(ficres," %.5e",delti[jk]);
6429: jk++;
6430: }
6431: printf("\n");
6432: fprintf(ficlog,"\n");
6433: fprintf(ficres,"\n");
6434: }
6435: }
6436: }
6437:
6438: 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");
6439: if(mle>=1)
6440: 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");
6441: 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");
6442: /* # 121 Var(a12)\n\ */
6443: /* # 122 Cov(b12,a12) Var(b12)\n\ */
6444: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
6445: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
6446: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
6447: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
6448: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
6449: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
6450:
6451:
6452: /* Just to have a covariance matrix which will be more understandable
6453: even is we still don't want to manage dictionary of variables
6454: */
6455: for(itimes=1;itimes<=2;itimes++){
6456: jj=0;
6457: for(i=1; i <=nlstate; i++){
6458: for(j=1; j <=nlstate+ndeath; j++){
6459: if(j==i) continue;
6460: for(k=1; k<=ncovmodel;k++){
6461: jj++;
6462: ca[0]= k+'a'-1;ca[1]='\0';
6463: if(itimes==1){
6464: if(mle>=1)
6465: printf("#%1d%1d%d",i,j,k);
6466: fprintf(ficlog,"#%1d%1d%d",i,j,k);
6467: fprintf(ficres,"#%1d%1d%d",i,j,k);
6468: }else{
6469: if(mle>=1)
6470: printf("%1d%1d%d",i,j,k);
6471: fprintf(ficlog,"%1d%1d%d",i,j,k);
6472: fprintf(ficres,"%1d%1d%d",i,j,k);
6473: }
6474: ll=0;
6475: for(li=1;li <=nlstate; li++){
6476: for(lj=1;lj <=nlstate+ndeath; lj++){
6477: if(lj==li) continue;
6478: for(lk=1;lk<=ncovmodel;lk++){
6479: ll++;
6480: if(ll<=jj){
6481: cb[0]= lk +'a'-1;cb[1]='\0';
6482: if(ll<jj){
6483: if(itimes==1){
6484: if(mle>=1)
6485: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6486: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6487: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6488: }else{
6489: if(mle>=1)
6490: printf(" %.5e",matcov[jj][ll]);
6491: fprintf(ficlog," %.5e",matcov[jj][ll]);
6492: fprintf(ficres," %.5e",matcov[jj][ll]);
6493: }
6494: }else{
6495: if(itimes==1){
6496: if(mle>=1)
6497: printf(" Var(%s%1d%1d)",ca,i,j);
6498: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
6499: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
6500: }else{
6501: if(mle>=1)
6502: printf(" %.5e",matcov[jj][ll]);
6503: fprintf(ficlog," %.5e",matcov[jj][ll]);
6504: fprintf(ficres," %.5e",matcov[jj][ll]);
6505: }
6506: }
6507: }
6508: } /* end lk */
6509: } /* end lj */
6510: } /* end li */
6511: if(mle>=1)
6512: printf("\n");
6513: fprintf(ficlog,"\n");
6514: fprintf(ficres,"\n");
6515: numlinepar++;
6516: } /* end k*/
6517: } /*end j */
6518: } /* end i */
6519: } /* end itimes */
6520:
6521: fflush(ficlog);
6522: fflush(ficres);
6523:
6524: while((c=getc(ficpar))=='#' && c!= EOF){
6525: ungetc(c,ficpar);
6526: fgets(line, MAXLINE, ficpar);
6527: fputs(line,stdout);
6528: fputs(line,ficparo);
6529: }
6530: ungetc(c,ficpar);
6531:
6532: estepm=0;
6533: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
6534: if (estepm==0 || estepm < stepm) estepm=stepm;
6535: if (fage <= 2) {
6536: bage = ageminpar;
6537: fage = agemaxpar;
6538: }
6539:
6540: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
6541: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6542: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6543:
6544: while((c=getc(ficpar))=='#' && c!= EOF){
6545: ungetc(c,ficpar);
6546: fgets(line, MAXLINE, ficpar);
6547: fputs(line,stdout);
6548: fputs(line,ficparo);
6549: }
6550: ungetc(c,ficpar);
6551:
6552: 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);
6553: 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);
6554: 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);
6555: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
6556: 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);
6557:
6558: while((c=getc(ficpar))=='#' && c!= EOF){
6559: ungetc(c,ficpar);
6560: fgets(line, MAXLINE, ficpar);
6561: fputs(line,stdout);
6562: fputs(line,ficparo);
6563: }
6564: ungetc(c,ficpar);
6565:
6566:
6567: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
6568: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
6569:
6570: fscanf(ficpar,"pop_based=%d\n",&popbased);
6571: fprintf(ficparo,"pop_based=%d\n",popbased);
6572: fprintf(ficres,"pop_based=%d\n",popbased);
6573:
6574: while((c=getc(ficpar))=='#' && c!= EOF){
6575: ungetc(c,ficpar);
6576: fgets(line, MAXLINE, ficpar);
6577: fputs(line,stdout);
6578: fputs(line,ficparo);
6579: }
6580: ungetc(c,ficpar);
6581:
6582: 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);
6583: 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);
6584: 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);
6585: 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);
6586: 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);
6587: /* day and month of proj2 are not used but only year anproj2.*/
6588:
6589:
6590:
6591: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
6592: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
6593:
6594: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6595: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6596:
6597: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
6598: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
6599: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
6600:
6601: /*------------ free_vector -------------*/
6602: /* chdir(path); */
6603:
6604: free_ivector(wav,1,imx);
6605: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
6606: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
6607: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
6608: free_lvector(num,1,n);
6609: free_vector(agedc,1,n);
6610: /*free_matrix(covar,0,NCOVMAX,1,n);*/
6611: /*free_matrix(covar,1,NCOVMAX,1,n);*/
6612: fclose(ficparo);
6613: fclose(ficres);
6614:
6615:
6616: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6617: #include "prevlim.h" /* Use ficrespl, ficlog */
6618: fclose(ficrespl);
6619:
6620: #ifdef FREEEXIT2
6621: #include "freeexit2.h"
6622: #endif
6623:
6624: /*------------- h Pij x at various ages ------------*/
6625: #include "hpijx.h"
6626: fclose(ficrespij);
6627:
6628: /*-------------- Variance of one-step probabilities---*/
6629: k=1;
6630: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
6631:
6632:
6633: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6634: for(i=1;i<=AGESUP;i++)
6635: for(j=1;j<=NCOVMAX;j++)
6636: for(k=1;k<=NCOVMAX;k++)
6637: probs[i][j][k]=0.;
6638:
6639: /*---------- Forecasting ------------------*/
6640: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
6641: if(prevfcast==1){
6642: /* if(stepm ==1){*/
6643: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
6644: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
6645: /* } */
6646: /* else{ */
6647: /* erreur=108; */
6648: /* 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); */
6649: /* 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); */
6650: /* } */
6651: }
6652:
6653:
6654: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
6655:
6656: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
6657: /* 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",\
6658: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
6659: */
6660:
6661: if (mobilav!=0) {
6662: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6663: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
6664: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
6665: printf(" Error in movingaverage mobilav=%d\n",mobilav);
6666: }
6667: }
6668:
6669:
6670: /*---------- Health expectancies, no variances ------------*/
6671:
6672: strcpy(filerese,"e");
6673: strcat(filerese,fileres);
6674: if((ficreseij=fopen(filerese,"w"))==NULL) {
6675: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6676: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6677: }
6678: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
6679: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
6680: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6681: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6682:
6683: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6684: fprintf(ficreseij,"\n#****** ");
6685: for(j=1;j<=cptcoveff;j++) {
6686: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6687: }
6688: fprintf(ficreseij,"******\n");
6689:
6690: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6691: oldm=oldms;savm=savms;
6692: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
6693:
6694: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6695: /*}*/
6696: }
6697: fclose(ficreseij);
6698:
6699:
6700: /*---------- Health expectancies and variances ------------*/
6701:
6702:
6703: strcpy(filerest,"t");
6704: strcat(filerest,fileres);
6705: if((ficrest=fopen(filerest,"w"))==NULL) {
6706: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
6707: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
6708: }
6709: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6710: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6711:
6712:
6713: strcpy(fileresstde,"stde");
6714: strcat(fileresstde,fileres);
6715: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
6716: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6717: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6718: }
6719: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6720: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6721:
6722: strcpy(filerescve,"cve");
6723: strcat(filerescve,fileres);
6724: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
6725: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6726: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6727: }
6728: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6729: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6730:
6731: strcpy(fileresv,"v");
6732: strcat(fileresv,fileres);
6733: if((ficresvij=fopen(fileresv,"w"))==NULL) {
6734: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
6735: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
6736: }
6737: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6738: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6739:
6740: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6741: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6742:
6743: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6744: fprintf(ficrest,"\n#****** ");
6745: for(j=1;j<=cptcoveff;j++)
6746: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6747: fprintf(ficrest,"******\n");
6748:
6749: fprintf(ficresstdeij,"\n#****** ");
6750: fprintf(ficrescveij,"\n#****** ");
6751: for(j=1;j<=cptcoveff;j++) {
6752: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6753: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6754: }
6755: fprintf(ficresstdeij,"******\n");
6756: fprintf(ficrescveij,"******\n");
6757:
6758: fprintf(ficresvij,"\n#****** ");
6759: for(j=1;j<=cptcoveff;j++)
6760: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6761: fprintf(ficresvij,"******\n");
6762:
6763: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6764: oldm=oldms;savm=savms;
6765: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
6766: /*
6767: */
6768: /* goto endfree; */
6769:
6770: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6771: pstamp(ficrest);
6772:
6773:
6774: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
6775: oldm=oldms;savm=savms; /* Segmentation fault */
6776: cptcod= 0; /* To be deleted */
6777: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
6778: 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 ");
6779: if(vpopbased==1)
6780: 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);
6781: else
6782: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
6783: fprintf(ficrest,"# Age e.. (std) ");
6784: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
6785: fprintf(ficrest,"\n");
6786:
6787: epj=vector(1,nlstate+1);
6788: for(age=bage; age <=fage ;age++){
6789: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6790: if (vpopbased==1) {
6791: if(mobilav ==0){
6792: for(i=1; i<=nlstate;i++)
6793: prlim[i][i]=probs[(int)age][i][k];
6794: }else{ /* mobilav */
6795: for(i=1; i<=nlstate;i++)
6796: prlim[i][i]=mobaverage[(int)age][i][k];
6797: }
6798: }
6799:
6800: fprintf(ficrest," %4.0f",age);
6801: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
6802: for(i=1, epj[j]=0.;i <=nlstate;i++) {
6803: epj[j] += prlim[i][i]*eij[i][j][(int)age];
6804: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
6805: }
6806: epj[nlstate+1] +=epj[j];
6807: }
6808:
6809: for(i=1, vepp=0.;i <=nlstate;i++)
6810: for(j=1;j <=nlstate;j++)
6811: vepp += vareij[i][j][(int)age];
6812: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
6813: for(j=1;j <=nlstate;j++){
6814: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
6815: }
6816: fprintf(ficrest,"\n");
6817: }
6818: }
6819: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6820: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6821: free_vector(epj,1,nlstate+1);
6822: /*}*/
6823: }
6824: free_vector(weight,1,n);
6825: free_imatrix(Tvard,1,NCOVMAX,1,2);
6826: free_imatrix(s,1,maxwav+1,1,n);
6827: free_matrix(anint,1,maxwav,1,n);
6828: free_matrix(mint,1,maxwav,1,n);
6829: free_ivector(cod,1,n);
6830: free_ivector(tab,1,NCOVMAX);
6831: fclose(ficresstdeij);
6832: fclose(ficrescveij);
6833: fclose(ficresvij);
6834: fclose(ficrest);
6835: fclose(ficpar);
6836:
6837: /*------- Variance of period (stable) prevalence------*/
6838:
6839: strcpy(fileresvpl,"vpl");
6840: strcat(fileresvpl,fileres);
6841: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
6842: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
6843: exit(0);
6844: }
6845: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
6846:
6847: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6848: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6849:
6850: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6851: fprintf(ficresvpl,"\n#****** ");
6852: for(j=1;j<=cptcoveff;j++)
6853: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6854: fprintf(ficresvpl,"******\n");
6855:
6856: varpl=matrix(1,nlstate,(int) bage, (int) fage);
6857: oldm=oldms;savm=savms;
6858: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
6859: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
6860: /*}*/
6861: }
6862:
6863: fclose(ficresvpl);
6864:
6865: /*---------- End : free ----------------*/
6866: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6867: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6868: } /* mle==-3 arrives here for freeing */
6869: /* endfree:*/
6870: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
6871: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
6872: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
6873: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
6874: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
6875: free_matrix(covar,0,NCOVMAX,1,n);
6876: free_matrix(matcov,1,npar,1,npar);
6877: /*free_vector(delti,1,npar);*/
6878: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6879: free_matrix(agev,1,maxwav,1,imx);
6880: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6881:
6882: free_ivector(ncodemax,1,NCOVMAX);
6883: free_ivector(Tvar,1,NCOVMAX);
6884: free_ivector(Tprod,1,NCOVMAX);
6885: free_ivector(Tvaraff,1,NCOVMAX);
6886: free_ivector(Tage,1,NCOVMAX);
6887:
6888: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
6889: free_imatrix(codtab,1,100,1,10);
6890: fflush(fichtm);
6891: fflush(ficgp);
6892:
6893:
6894: if((nberr >0) || (nbwarn>0)){
6895: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
6896: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
6897: }else{
6898: printf("End of Imach\n");
6899: fprintf(ficlog,"End of Imach\n");
6900: }
6901: printf("See log file on %s\n",filelog);
6902: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
6903: /*(void) gettimeofday(&end_time,&tzp);*/
6904: rend_time = time(NULL);
6905: end_time = *localtime(&rend_time);
6906: /* tml = *localtime(&end_time.tm_sec); */
6907: strcpy(strtend,asctime(&end_time));
6908: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
6909: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
6910: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
6911:
6912: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
6913: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
6914: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
6915: /* printf("Total time was %d uSec.\n", total_usecs);*/
6916: /* if(fileappend(fichtm,optionfilehtm)){ */
6917: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6918: fclose(fichtm);
6919: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6920: fclose(fichtmcov);
6921: fclose(ficgp);
6922: fclose(ficlog);
6923: /*------ End -----------*/
6924:
6925:
6926: printf("Before Current directory %s!\n",pathcd);
6927: if(chdir(pathcd) != 0)
6928: printf("Can't move to directory %s!\n",path);
6929: if(getcwd(pathcd,MAXLINE) > 0)
6930: printf("Current directory %s!\n",pathcd);
6931: /*strcat(plotcmd,CHARSEPARATOR);*/
6932: sprintf(plotcmd,"gnuplot");
6933: #ifdef _WIN32
6934: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
6935: #endif
6936: if(!stat(plotcmd,&info)){
6937: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
6938: if(!stat(getenv("GNUPLOTBIN"),&info)){
6939: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
6940: }else
6941: strcpy(pplotcmd,plotcmd);
6942: #ifdef __unix
6943: strcpy(plotcmd,GNUPLOTPROGRAM);
6944: if(!stat(plotcmd,&info)){
6945: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
6946: }else
6947: strcpy(pplotcmd,plotcmd);
6948: #endif
6949: }else
6950: strcpy(pplotcmd,plotcmd);
6951:
6952: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
6953: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
6954:
6955: if((outcmd=system(plotcmd)) != 0){
6956: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
6957: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
6958: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
6959: if((outcmd=system(plotcmd)) != 0)
6960: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
6961: }
6962: printf(" Successful, please wait...");
6963: while (z[0] != 'q') {
6964: /* chdir(path); */
6965: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
6966: scanf("%s",z);
6967: /* if (z[0] == 'c') system("./imach"); */
6968: if (z[0] == 'e') {
6969: #ifdef __APPLE__
6970: sprintf(pplotcmd, "open %s", optionfilehtm);
6971: #elif __linux
6972: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
6973: #else
6974: sprintf(pplotcmd, "%s", optionfilehtm);
6975: #endif
6976: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
6977: system(pplotcmd);
6978: }
6979: else if (z[0] == 'g') system(plotcmd);
6980: else if (z[0] == 'q') exit(0);
6981: }
6982: end:
6983: while (z[0] != 'q') {
6984: printf("\nType q for exiting: ");
6985: scanf("%s",z);
6986: }
6987: }
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