1: /* $Id: imach.c,v 1.169 2014/12/22 23:08:31 brouard Exp $
2: $State: Exp $
3: $Log: imach.c,v $
4: Revision 1.169 2014/12/22 23:08:31 brouard
5: Summary: 0.98p
6:
7: Outputs some informations on compiler used, OS etc. Testing on different platforms.
8:
9: Revision 1.168 2014/12/22 15:17:42 brouard
10: Summary: udate
11:
12: Revision 1.167 2014/12/22 13:50:56 brouard
13: Summary: Testing uname and compiler version and if compiled 32 or 64
14:
15: Testing on Linux 64
16:
17: Revision 1.166 2014/12/22 11:40:47 brouard
18: *** empty log message ***
19:
20: Revision 1.165 2014/12/16 11:20:36 brouard
21: Summary: After compiling on Visual C
22:
23: * imach.c (Module): Merging 1.61 to 1.162
24:
25: Revision 1.164 2014/12/16 10:52:11 brouard
26: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
27:
28: * imach.c (Module): Merging 1.61 to 1.162
29:
30: Revision 1.163 2014/12/16 10:30:11 brouard
31: * imach.c (Module): Merging 1.61 to 1.162
32:
33: Revision 1.162 2014/09/25 11:43:39 brouard
34: Summary: temporary backup 0.99!
35:
36: Revision 1.1 2014/09/16 11:06:58 brouard
37: Summary: With some code (wrong) for nlopt
38:
39: Author:
40:
41: Revision 1.161 2014/09/15 20:41:41 brouard
42: Summary: Problem with macro SQR on Intel compiler
43:
44: Revision 1.160 2014/09/02 09:24:05 brouard
45: *** empty log message ***
46:
47: Revision 1.159 2014/09/01 10:34:10 brouard
48: Summary: WIN32
49: Author: Brouard
50:
51: Revision 1.158 2014/08/27 17:11:51 brouard
52: *** empty log message ***
53:
54: Revision 1.157 2014/08/27 16:26:55 brouard
55: Summary: Preparing windows Visual studio version
56: Author: Brouard
57:
58: In order to compile on Visual studio, time.h is now correct and time_t
59: and tm struct should be used. difftime should be used but sometimes I
60: just make the differences in raw time format (time(&now).
61: Trying to suppress #ifdef LINUX
62: Add xdg-open for __linux in order to open default browser.
63:
64: Revision 1.156 2014/08/25 20:10:10 brouard
65: *** empty log message ***
66:
67: Revision 1.155 2014/08/25 18:32:34 brouard
68: Summary: New compile, minor changes
69: Author: Brouard
70:
71: Revision 1.154 2014/06/20 17:32:08 brouard
72: Summary: Outputs now all graphs of convergence to period prevalence
73:
74: Revision 1.153 2014/06/20 16:45:46 brouard
75: Summary: If 3 live state, convergence to period prevalence on same graph
76: Author: Brouard
77:
78: Revision 1.152 2014/06/18 17:54:09 brouard
79: Summary: open browser, use gnuplot on same dir than imach if not found in the path
80:
81: Revision 1.151 2014/06/18 16:43:30 brouard
82: *** empty log message ***
83:
84: Revision 1.150 2014/06/18 16:42:35 brouard
85: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
86: Author: brouard
87:
88: Revision 1.149 2014/06/18 15:51:14 brouard
89: Summary: Some fixes in parameter files errors
90: Author: Nicolas Brouard
91:
92: Revision 1.148 2014/06/17 17:38:48 brouard
93: Summary: Nothing new
94: Author: Brouard
95:
96: Just a new packaging for OS/X version 0.98nS
97:
98: Revision 1.147 2014/06/16 10:33:11 brouard
99: *** empty log message ***
100:
101: Revision 1.146 2014/06/16 10:20:28 brouard
102: Summary: Merge
103: Author: Brouard
104:
105: Merge, before building revised version.
106:
107: Revision 1.145 2014/06/10 21:23:15 brouard
108: Summary: Debugging with valgrind
109: Author: Nicolas Brouard
110:
111: Lot of changes in order to output the results with some covariates
112: After the Edimburgh REVES conference 2014, it seems mandatory to
113: improve the code.
114: No more memory valgrind error but a lot has to be done in order to
115: continue the work of splitting the code into subroutines.
116: Also, decodemodel has been improved. Tricode is still not
117: optimal. nbcode should be improved. Documentation has been added in
118: the source code.
119:
120: Revision 1.143 2014/01/26 09:45:38 brouard
121: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
122:
123: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
124: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
125:
126: Revision 1.142 2014/01/26 03:57:36 brouard
127: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
128:
129: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
130:
131: Revision 1.141 2014/01/26 02:42:01 brouard
132: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
133:
134: Revision 1.140 2011/09/02 10:37:54 brouard
135: Summary: times.h is ok with mingw32 now.
136:
137: Revision 1.139 2010/06/14 07:50:17 brouard
138: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
139: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
140:
141: Revision 1.138 2010/04/30 18:19:40 brouard
142: *** empty log message ***
143:
144: Revision 1.137 2010/04/29 18:11:38 brouard
145: (Module): Checking covariates for more complex models
146: than V1+V2. A lot of change to be done. Unstable.
147:
148: Revision 1.136 2010/04/26 20:30:53 brouard
149: (Module): merging some libgsl code. Fixing computation
150: of likelione (using inter/intrapolation if mle = 0) in order to
151: get same likelihood as if mle=1.
152: Some cleaning of code and comments added.
153:
154: Revision 1.135 2009/10/29 15:33:14 brouard
155: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
156:
157: Revision 1.134 2009/10/29 13:18:53 brouard
158: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
159:
160: Revision 1.133 2009/07/06 10:21:25 brouard
161: just nforces
162:
163: Revision 1.132 2009/07/06 08:22:05 brouard
164: Many tings
165:
166: Revision 1.131 2009/06/20 16:22:47 brouard
167: Some dimensions resccaled
168:
169: Revision 1.130 2009/05/26 06:44:34 brouard
170: (Module): Max Covariate is now set to 20 instead of 8. A
171: lot of cleaning with variables initialized to 0. Trying to make
172: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
173:
174: Revision 1.129 2007/08/31 13:49:27 lievre
175: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
176:
177: Revision 1.128 2006/06/30 13:02:05 brouard
178: (Module): Clarifications on computing e.j
179:
180: Revision 1.127 2006/04/28 18:11:50 brouard
181: (Module): Yes the sum of survivors was wrong since
182: imach-114 because nhstepm was no more computed in the age
183: loop. Now we define nhstepma in the age loop.
184: (Module): In order to speed up (in case of numerous covariates) we
185: compute health expectancies (without variances) in a first step
186: and then all the health expectancies with variances or standard
187: deviation (needs data from the Hessian matrices) which slows the
188: computation.
189: In the future we should be able to stop the program is only health
190: expectancies and graph are needed without standard deviations.
191:
192: Revision 1.126 2006/04/28 17:23:28 brouard
193: (Module): Yes the sum of survivors was wrong since
194: imach-114 because nhstepm was no more computed in the age
195: loop. Now we define nhstepma in the age loop.
196: Version 0.98h
197:
198: Revision 1.125 2006/04/04 15:20:31 lievre
199: Errors in calculation of health expectancies. Age was not initialized.
200: Forecasting file added.
201:
202: Revision 1.124 2006/03/22 17:13:53 lievre
203: Parameters are printed with %lf instead of %f (more numbers after the comma).
204: The log-likelihood is printed in the log file
205:
206: Revision 1.123 2006/03/20 10:52:43 brouard
207: * imach.c (Module): <title> changed, corresponds to .htm file
208: name. <head> headers where missing.
209:
210: * imach.c (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 1.122 2006/03/20 09:45:41 brouard
218: (Module): Weights can have a decimal point as for
219: English (a comma might work with a correct LC_NUMERIC environment,
220: otherwise the weight is truncated).
221: Modification of warning when the covariates values are not 0 or
222: 1.
223: Version 0.98g
224:
225: Revision 1.121 2006/03/16 17:45:01 lievre
226: * imach.c (Module): Comments concerning covariates added
227:
228: * imach.c (Module): refinements in the computation of lli if
229: status=-2 in order to have more reliable computation if stepm is
230: not 1 month. Version 0.98f
231:
232: Revision 1.120 2006/03/16 15:10:38 lievre
233: (Module): refinements in the computation of lli if
234: status=-2 in order to have more reliable computation if stepm is
235: not 1 month. Version 0.98f
236:
237: Revision 1.119 2006/03/15 17:42:26 brouard
238: (Module): Bug if status = -2, the loglikelihood was
239: computed as likelihood omitting the logarithm. Version O.98e
240:
241: Revision 1.118 2006/03/14 18:20:07 brouard
242: (Module): varevsij Comments added explaining the second
243: table of variances if popbased=1 .
244: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
245: (Module): Function pstamp added
246: (Module): Version 0.98d
247:
248: Revision 1.117 2006/03/14 17:16:22 brouard
249: (Module): varevsij Comments added explaining the second
250: table of variances if popbased=1 .
251: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
252: (Module): Function pstamp added
253: (Module): Version 0.98d
254:
255: Revision 1.116 2006/03/06 10:29:27 brouard
256: (Module): Variance-covariance wrong links and
257: varian-covariance of ej. is needed (Saito).
258:
259: Revision 1.115 2006/02/27 12:17:45 brouard
260: (Module): One freematrix added in mlikeli! 0.98c
261:
262: Revision 1.114 2006/02/26 12:57:58 brouard
263: (Module): Some improvements in processing parameter
264: filename with strsep.
265:
266: Revision 1.113 2006/02/24 14:20:24 brouard
267: (Module): Memory leaks checks with valgrind and:
268: datafile was not closed, some imatrix were not freed and on matrix
269: allocation too.
270:
271: Revision 1.112 2006/01/30 09:55:26 brouard
272: (Module): Back to gnuplot.exe instead of wgnuplot.exe
273:
274: Revision 1.111 2006/01/25 20:38:18 brouard
275: (Module): Lots of cleaning and bugs added (Gompertz)
276: (Module): Comments can be added in data file. Missing date values
277: can be a simple dot '.'.
278:
279: Revision 1.110 2006/01/25 00:51:50 brouard
280: (Module): Lots of cleaning and bugs added (Gompertz)
281:
282: Revision 1.109 2006/01/24 19:37:15 brouard
283: (Module): Comments (lines starting with a #) are allowed in data.
284:
285: Revision 1.108 2006/01/19 18:05:42 lievre
286: Gnuplot problem appeared...
287: To be fixed
288:
289: Revision 1.107 2006/01/19 16:20:37 brouard
290: Test existence of gnuplot in imach path
291:
292: Revision 1.106 2006/01/19 13:24:36 brouard
293: Some cleaning and links added in html output
294:
295: Revision 1.105 2006/01/05 20:23:19 lievre
296: *** empty log message ***
297:
298: Revision 1.104 2005/09/30 16:11:43 lievre
299: (Module): sump fixed, loop imx fixed, and simplifications.
300: (Module): If the status is missing at the last wave but we know
301: that the person is alive, then we can code his/her status as -2
302: (instead of missing=-1 in earlier versions) and his/her
303: contributions to the likelihood is 1 - Prob of dying from last
304: health status (= 1-p13= p11+p12 in the easiest case of somebody in
305: the healthy state at last known wave). Version is 0.98
306:
307: Revision 1.103 2005/09/30 15:54:49 lievre
308: (Module): sump fixed, loop imx fixed, and simplifications.
309:
310: Revision 1.102 2004/09/15 17:31:30 brouard
311: Add the possibility to read data file including tab characters.
312:
313: Revision 1.101 2004/09/15 10:38:38 brouard
314: Fix on curr_time
315:
316: Revision 1.100 2004/07/12 18:29:06 brouard
317: Add version for Mac OS X. Just define UNIX in Makefile
318:
319: Revision 1.99 2004/06/05 08:57:40 brouard
320: *** empty log message ***
321:
322: Revision 1.98 2004/05/16 15:05:56 brouard
323: New version 0.97 . First attempt to estimate force of mortality
324: directly from the data i.e. without the need of knowing the health
325: state at each age, but using a Gompertz model: log u =a + b*age .
326: This is the basic analysis of mortality and should be done before any
327: other analysis, in order to test if the mortality estimated from the
328: cross-longitudinal survey is different from the mortality estimated
329: from other sources like vital statistic data.
330:
331: The same imach parameter file can be used but the option for mle should be -3.
332:
333: Agnès, who wrote this part of the code, tried to keep most of the
334: former routines in order to include the new code within the former code.
335:
336: The output is very simple: only an estimate of the intercept and of
337: the slope with 95% confident intervals.
338:
339: Current limitations:
340: A) Even if you enter covariates, i.e. with the
341: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
342: B) There is no computation of Life Expectancy nor Life Table.
343:
344: Revision 1.97 2004/02/20 13:25:42 lievre
345: Version 0.96d. Population forecasting command line is (temporarily)
346: suppressed.
347:
348: Revision 1.96 2003/07/15 15:38:55 brouard
349: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
350: rewritten within the same printf. Workaround: many printfs.
351:
352: Revision 1.95 2003/07/08 07:54:34 brouard
353: * imach.c (Repository):
354: (Repository): Using imachwizard code to output a more meaningful covariance
355: matrix (cov(a12,c31) instead of numbers.
356:
357: Revision 1.94 2003/06/27 13:00:02 brouard
358: Just cleaning
359:
360: Revision 1.93 2003/06/25 16:33:55 brouard
361: (Module): On windows (cygwin) function asctime_r doesn't
362: exist so I changed back to asctime which exists.
363: (Module): Version 0.96b
364:
365: Revision 1.92 2003/06/25 16:30:45 brouard
366: (Module): On windows (cygwin) function asctime_r doesn't
367: exist so I changed back to asctime which exists.
368:
369: Revision 1.91 2003/06/25 15:30:29 brouard
370: * imach.c (Repository): Duplicated warning errors corrected.
371: (Repository): Elapsed time after each iteration is now output. It
372: helps to forecast when convergence will be reached. Elapsed time
373: is stamped in powell. We created a new html file for the graphs
374: concerning matrix of covariance. It has extension -cov.htm.
375:
376: Revision 1.90 2003/06/24 12:34:15 brouard
377: (Module): Some bugs corrected for windows. Also, when
378: mle=-1 a template is output in file "or"mypar.txt with the design
379: of the covariance matrix to be input.
380:
381: Revision 1.89 2003/06/24 12:30:52 brouard
382: (Module): Some bugs corrected for windows. Also, when
383: mle=-1 a template is output in file "or"mypar.txt with the design
384: of the covariance matrix to be input.
385:
386: Revision 1.88 2003/06/23 17:54:56 brouard
387: * 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.
388:
389: Revision 1.87 2003/06/18 12:26:01 brouard
390: Version 0.96
391:
392: Revision 1.86 2003/06/17 20:04:08 brouard
393: (Module): Change position of html and gnuplot routines and added
394: routine fileappend.
395:
396: Revision 1.85 2003/06/17 13:12:43 brouard
397: * imach.c (Repository): Check when date of death was earlier that
398: current date of interview. It may happen when the death was just
399: prior to the death. In this case, dh was negative and likelihood
400: was wrong (infinity). We still send an "Error" but patch by
401: assuming that the date of death was just one stepm after the
402: interview.
403: (Repository): Because some people have very long ID (first column)
404: we changed int to long in num[] and we added a new lvector for
405: memory allocation. But we also truncated to 8 characters (left
406: truncation)
407: (Repository): No more line truncation errors.
408:
409: Revision 1.84 2003/06/13 21:44:43 brouard
410: * imach.c (Repository): Replace "freqsummary" at a correct
411: place. It differs from routine "prevalence" which may be called
412: many times. Probs is memory consuming and must be used with
413: parcimony.
414: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
415:
416: Revision 1.83 2003/06/10 13:39:11 lievre
417: *** empty log message ***
418:
419: Revision 1.82 2003/06/05 15:57:20 brouard
420: Add log in imach.c and fullversion number is now printed.
421:
422: */
423: /*
424: Interpolated Markov Chain
425:
426: Short summary of the programme:
427:
428: This program computes Healthy Life Expectancies from
429: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
430: first survey ("cross") where individuals from different ages are
431: interviewed on their health status or degree of disability (in the
432: case of a health survey which is our main interest) -2- at least a
433: second wave of interviews ("longitudinal") which measure each change
434: (if any) in individual health status. Health expectancies are
435: computed from the time spent in each health state according to a
436: model. More health states you consider, more time is necessary to reach the
437: Maximum Likelihood of the parameters involved in the model. The
438: simplest model is the multinomial logistic model where pij is the
439: probability to be observed in state j at the second wave
440: conditional to be observed in state i at the first wave. Therefore
441: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
442: 'age' is age and 'sex' is a covariate. If you want to have a more
443: complex model than "constant and age", you should modify the program
444: where the markup *Covariates have to be included here again* invites
445: you to do it. More covariates you add, slower the
446: convergence.
447:
448: The advantage of this computer programme, compared to a simple
449: multinomial logistic model, is clear when the delay between waves is not
450: identical for each individual. Also, if a individual missed an
451: intermediate interview, the information is lost, but taken into
452: account using an interpolation or extrapolation.
453:
454: hPijx is the probability to be observed in state i at age x+h
455: conditional to the observed state i at age x. The delay 'h' can be
456: split into an exact number (nh*stepm) of unobserved intermediate
457: states. This elementary transition (by month, quarter,
458: semester or year) is modelled as a multinomial logistic. The hPx
459: matrix is simply the matrix product of nh*stepm elementary matrices
460: and the contribution of each individual to the likelihood is simply
461: hPijx.
462:
463: Also this programme outputs the covariance matrix of the parameters but also
464: of the life expectancies. It also computes the period (stable) prevalence.
465:
466: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
467: Institut national d'études démographiques, Paris.
468: This software have been partly granted by Euro-REVES, a concerted action
469: from the European Union.
470: It is copyrighted identically to a GNU software product, ie programme and
471: software can be distributed freely for non commercial use. Latest version
472: can be accessed at http://euroreves.ined.fr/imach .
473:
474: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
475: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
476:
477: **********************************************************************/
478: /*
479: main
480: read parameterfile
481: read datafile
482: concatwav
483: freqsummary
484: if (mle >= 1)
485: mlikeli
486: print results files
487: if mle==1
488: computes hessian
489: read end of parameter file: agemin, agemax, bage, fage, estepm
490: begin-prev-date,...
491: open gnuplot file
492: open html file
493: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
494: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
495: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
496: freexexit2 possible for memory heap.
497:
498: h Pij x | pij_nom ficrestpij
499: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
500: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
501: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
502:
503: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
504: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
505: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
506: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
507: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
508:
509: forecasting if prevfcast==1 prevforecast call prevalence()
510: health expectancies
511: Variance-covariance of DFLE
512: prevalence()
513: movingaverage()
514: varevsij()
515: if popbased==1 varevsij(,popbased)
516: total life expectancies
517: Variance of period (stable) prevalence
518: end
519: */
520:
521: #define POWELL /* Instead of NLOPT */
522:
523: #include <math.h>
524: #include <stdio.h>
525: #include <stdlib.h>
526: #include <string.h>
527:
528: #ifdef _WIN32
529: #include <io.h>
530: #else
531: #include <unistd.h>
532: #endif
533:
534: #include <limits.h>
535: #include <sys/types.h>
536: #include <sys/utsname.h>
537: #include <sys/stat.h>
538: #include <errno.h>
539: /* extern int errno; */
540:
541: /* #ifdef LINUX */
542: /* #include <time.h> */
543: /* #include "timeval.h" */
544: /* #else */
545: /* #include <sys/time.h> */
546: /* #endif */
547:
548: #include <time.h>
549:
550: #ifdef GSL
551: #include <gsl/gsl_errno.h>
552: #include <gsl/gsl_multimin.h>
553: #endif
554:
555:
556: #ifdef NLOPT
557: #include <nlopt.h>
558: typedef struct {
559: double (* function)(double [] );
560: } myfunc_data ;
561: #endif
562:
563: /* #include <libintl.h> */
564: /* #define _(String) gettext (String) */
565:
566: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
567:
568: #define GNUPLOTPROGRAM "gnuplot"
569: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
570: #define FILENAMELENGTH 132
571:
572: #define GLOCK_ERROR_NOPATH -1 /* empty path */
573: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
574:
575: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
576: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
577:
578: #define NINTERVMAX 8
579: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
580: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
581: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
582: #define codtabm(h,k) 1 & (h-1) >> (k-1) ;
583: #define MAXN 20000
584: #define YEARM 12. /**< Number of months per year */
585: #define AGESUP 130
586: #define AGEBASE 40
587: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
588: #ifdef _WIN32
589: #define DIRSEPARATOR '\\'
590: #define CHARSEPARATOR "\\"
591: #define ODIRSEPARATOR '/'
592: #else
593: #define DIRSEPARATOR '/'
594: #define CHARSEPARATOR "/"
595: #define ODIRSEPARATOR '\\'
596: #endif
597:
598: /* $Id: imach.c,v 1.169 2014/12/22 23:08:31 brouard Exp $ */
599: /* $State: Exp $ */
600:
601: char version[]="Imach version 0.98p, December 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
602: char fullversion[]="$Revision: 1.169 $ $Date: 2014/12/22 23:08:31 $";
603: char strstart[80];
604: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
605: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
606: int nvar=0, nforce=0; /* Number of variables, number of forces */
607: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
608: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
609: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
610: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
611: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
612: int cptcovprodnoage=0; /**< Number of covariate products without age */
613: int cptcoveff=0; /* Total number of covariates to vary for printing results */
614: int cptcov=0; /* Working variable */
615: int npar=NPARMAX;
616: int nlstate=2; /* Number of live states */
617: int ndeath=1; /* Number of dead states */
618: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
619: int popbased=0;
620:
621: int *wav; /* Number of waves for this individuual 0 is possible */
622: int maxwav=0; /* Maxim number of waves */
623: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
624: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
625: int gipmx=0, gsw=0; /* Global variables on the number of contributions
626: to the likelihood and the sum of weights (done by funcone)*/
627: int mle=1, weightopt=0;
628: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
629: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
630: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
631: * wave mi and wave mi+1 is not an exact multiple of stepm. */
632: int countcallfunc=0; /* Count the number of calls to func */
633: double jmean=1; /* Mean space between 2 waves */
634: double **matprod2(); /* test */
635: double **oldm, **newm, **savm; /* Working pointers to matrices */
636: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
637: /*FILE *fic ; */ /* Used in readdata only */
638: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
639: FILE *ficlog, *ficrespow;
640: int globpr=0; /* Global variable for printing or not */
641: double fretone; /* Only one call to likelihood */
642: long ipmx=0; /* Number of contributions */
643: double sw; /* Sum of weights */
644: char filerespow[FILENAMELENGTH];
645: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
646: FILE *ficresilk;
647: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
648: FILE *ficresprobmorprev;
649: FILE *fichtm, *fichtmcov; /* Html File */
650: FILE *ficreseij;
651: char filerese[FILENAMELENGTH];
652: FILE *ficresstdeij;
653: char fileresstde[FILENAMELENGTH];
654: FILE *ficrescveij;
655: char filerescve[FILENAMELENGTH];
656: FILE *ficresvij;
657: char fileresv[FILENAMELENGTH];
658: FILE *ficresvpl;
659: char fileresvpl[FILENAMELENGTH];
660: char title[MAXLINE];
661: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
662: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
663: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
664: char command[FILENAMELENGTH];
665: int outcmd=0;
666:
667: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
668:
669: char filelog[FILENAMELENGTH]; /* Log file */
670: char filerest[FILENAMELENGTH];
671: char fileregp[FILENAMELENGTH];
672: char popfile[FILENAMELENGTH];
673:
674: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
675:
676: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
677: /* struct timezone tzp; */
678: /* extern int gettimeofday(); */
679: struct tm tml, *gmtime(), *localtime();
680:
681: extern time_t time();
682:
683: struct tm start_time, end_time, curr_time, last_time, forecast_time;
684: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
685: struct tm tm;
686:
687: char strcurr[80], strfor[80];
688:
689: char *endptr;
690: long lval;
691: double dval;
692:
693: #define NR_END 1
694: #define FREE_ARG char*
695: #define FTOL 1.0e-10
696:
697: #define NRANSI
698: #define ITMAX 200
699:
700: #define TOL 2.0e-4
701:
702: #define CGOLD 0.3819660
703: #define ZEPS 1.0e-10
704: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
705:
706: #define GOLD 1.618034
707: #define GLIMIT 100.0
708: #define TINY 1.0e-20
709:
710: static double maxarg1,maxarg2;
711: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
712: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
713:
714: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
715: #define rint(a) floor(a+0.5)
716: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
717: /* #define mytinydouble 1.0e-16 */
718: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
719: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
720: /* static double dsqrarg; */
721: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
722: static double sqrarg;
723: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
724: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
725: int agegomp= AGEGOMP;
726:
727: int imx;
728: int stepm=1;
729: /* Stepm, step in month: minimum step interpolation*/
730:
731: int estepm;
732: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
733:
734: int m,nb;
735: long *num;
736: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
737: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
738: double **pmmij, ***probs;
739: double *ageexmed,*agecens;
740: double dateintmean=0;
741:
742: double *weight;
743: int **s; /* Status */
744: double *agedc;
745: double **covar; /**< covar[j,i], value of jth covariate for individual i,
746: * covar=matrix(0,NCOVMAX,1,n);
747: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
748: double idx;
749: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
750: int *Ndum; /** Freq of modality (tricode */
751: int **codtab; /**< codtab=imatrix(1,100,1,10); */
752: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
753: double *lsurv, *lpop, *tpop;
754:
755: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
756: double ftolhess; /**< Tolerance for computing hessian */
757:
758: /**************** split *************************/
759: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
760: {
761: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
762: the name of the file (name), its extension only (ext) and its first part of the name (finame)
763: */
764: char *ss; /* pointer */
765: int l1, l2; /* length counters */
766:
767: l1 = strlen(path ); /* length of path */
768: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
769: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
770: if ( ss == NULL ) { /* no directory, so determine current directory */
771: strcpy( name, path ); /* we got the fullname name because no directory */
772: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
773: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
774: /* get current working directory */
775: /* extern char* getcwd ( char *buf , int len);*/
776: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
777: return( GLOCK_ERROR_GETCWD );
778: }
779: /* got dirc from getcwd*/
780: printf(" DIRC = %s \n",dirc);
781: } else { /* strip direcotry from path */
782: ss++; /* after this, the filename */
783: l2 = strlen( ss ); /* length of filename */
784: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
785: strcpy( name, ss ); /* save file name */
786: strncpy( dirc, path, l1 - l2 ); /* now the directory */
787: dirc[l1-l2] = 0; /* add zero */
788: printf(" DIRC2 = %s \n",dirc);
789: }
790: /* We add a separator at the end of dirc if not exists */
791: l1 = strlen( dirc ); /* length of directory */
792: if( dirc[l1-1] != DIRSEPARATOR ){
793: dirc[l1] = DIRSEPARATOR;
794: dirc[l1+1] = 0;
795: printf(" DIRC3 = %s \n",dirc);
796: }
797: ss = strrchr( name, '.' ); /* find last / */
798: if (ss >0){
799: ss++;
800: strcpy(ext,ss); /* save extension */
801: l1= strlen( name);
802: l2= strlen(ss)+1;
803: strncpy( finame, name, l1-l2);
804: finame[l1-l2]= 0;
805: }
806:
807: return( 0 ); /* we're done */
808: }
809:
810:
811: /******************************************/
812:
813: void replace_back_to_slash(char *s, char*t)
814: {
815: int i;
816: int lg=0;
817: i=0;
818: lg=strlen(t);
819: for(i=0; i<= lg; i++) {
820: (s[i] = t[i]);
821: if (t[i]== '\\') s[i]='/';
822: }
823: }
824:
825: char *trimbb(char *out, char *in)
826: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
827: char *s;
828: s=out;
829: while (*in != '\0'){
830: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
831: in++;
832: }
833: *out++ = *in++;
834: }
835: *out='\0';
836: return s;
837: }
838:
839: char *cutl(char *blocc, char *alocc, char *in, char occ)
840: {
841: /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ'
842: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
843: gives blocc="abcdef2ghi" and alocc="j".
844: If occ is not found blocc is null and alocc is equal to in. Returns blocc
845: */
846: char *s, *t;
847: t=in;s=in;
848: while ((*in != occ) && (*in != '\0')){
849: *alocc++ = *in++;
850: }
851: if( *in == occ){
852: *(alocc)='\0';
853: s=++in;
854: }
855:
856: if (s == t) {/* occ not found */
857: *(alocc-(in-s))='\0';
858: in=s;
859: }
860: while ( *in != '\0'){
861: *blocc++ = *in++;
862: }
863:
864: *blocc='\0';
865: return t;
866: }
867: char *cutv(char *blocc, char *alocc, char *in, char occ)
868: {
869: /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
870: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
871: gives blocc="abcdef2ghi" and alocc="j".
872: If occ is not found blocc is null and alocc is equal to in. Returns alocc
873: */
874: char *s, *t;
875: t=in;s=in;
876: while (*in != '\0'){
877: while( *in == occ){
878: *blocc++ = *in++;
879: s=in;
880: }
881: *blocc++ = *in++;
882: }
883: if (s == t) /* occ not found */
884: *(blocc-(in-s))='\0';
885: else
886: *(blocc-(in-s)-1)='\0';
887: in=s;
888: while ( *in != '\0'){
889: *alocc++ = *in++;
890: }
891:
892: *alocc='\0';
893: return s;
894: }
895:
896: int nbocc(char *s, char occ)
897: {
898: int i,j=0;
899: int lg=20;
900: i=0;
901: lg=strlen(s);
902: for(i=0; i<= lg; i++) {
903: if (s[i] == occ ) j++;
904: }
905: return j;
906: }
907:
908: /* void cutv(char *u,char *v, char*t, char occ) */
909: /* { */
910: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
911: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
912: /* gives u="abcdef2ghi" and v="j" *\/ */
913: /* int i,lg,j,p=0; */
914: /* i=0; */
915: /* lg=strlen(t); */
916: /* for(j=0; j<=lg-1; j++) { */
917: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
918: /* } */
919:
920: /* for(j=0; j<p; j++) { */
921: /* (u[j] = t[j]); */
922: /* } */
923: /* u[p]='\0'; */
924:
925: /* for(j=0; j<= lg; j++) { */
926: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
927: /* } */
928: /* } */
929:
930: #ifdef _WIN32
931: char * strsep(char **pp, const char *delim)
932: {
933: char *p, *q;
934:
935: if ((p = *pp) == NULL)
936: return 0;
937: if ((q = strpbrk (p, delim)) != NULL)
938: {
939: *pp = q + 1;
940: *q = '\0';
941: }
942: else
943: *pp = 0;
944: return p;
945: }
946: #endif
947:
948: /********************** nrerror ********************/
949:
950: void nrerror(char error_text[])
951: {
952: fprintf(stderr,"ERREUR ...\n");
953: fprintf(stderr,"%s\n",error_text);
954: exit(EXIT_FAILURE);
955: }
956: /*********************** vector *******************/
957: double *vector(int nl, int nh)
958: {
959: double *v;
960: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
961: if (!v) nrerror("allocation failure in vector");
962: return v-nl+NR_END;
963: }
964:
965: /************************ free vector ******************/
966: void free_vector(double*v, int nl, int nh)
967: {
968: free((FREE_ARG)(v+nl-NR_END));
969: }
970:
971: /************************ivector *******************************/
972: int *ivector(long nl,long nh)
973: {
974: int *v;
975: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
976: if (!v) nrerror("allocation failure in ivector");
977: return v-nl+NR_END;
978: }
979:
980: /******************free ivector **************************/
981: void free_ivector(int *v, long nl, long nh)
982: {
983: free((FREE_ARG)(v+nl-NR_END));
984: }
985:
986: /************************lvector *******************************/
987: long *lvector(long nl,long nh)
988: {
989: long *v;
990: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
991: if (!v) nrerror("allocation failure in ivector");
992: return v-nl+NR_END;
993: }
994:
995: /******************free lvector **************************/
996: void free_lvector(long *v, long nl, long nh)
997: {
998: free((FREE_ARG)(v+nl-NR_END));
999: }
1000:
1001: /******************* imatrix *******************************/
1002: int **imatrix(long nrl, long nrh, long ncl, long nch)
1003: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1004: {
1005: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1006: int **m;
1007:
1008: /* allocate pointers to rows */
1009: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1010: if (!m) nrerror("allocation failure 1 in matrix()");
1011: m += NR_END;
1012: m -= nrl;
1013:
1014:
1015: /* allocate rows and set pointers to them */
1016: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1017: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1018: m[nrl] += NR_END;
1019: m[nrl] -= ncl;
1020:
1021: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1022:
1023: /* return pointer to array of pointers to rows */
1024: return m;
1025: }
1026:
1027: /****************** free_imatrix *************************/
1028: void free_imatrix(m,nrl,nrh,ncl,nch)
1029: int **m;
1030: long nch,ncl,nrh,nrl;
1031: /* free an int matrix allocated by imatrix() */
1032: {
1033: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1034: free((FREE_ARG) (m+nrl-NR_END));
1035: }
1036:
1037: /******************* matrix *******************************/
1038: double **matrix(long nrl, long nrh, long ncl, long nch)
1039: {
1040: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1041: double **m;
1042:
1043: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1044: if (!m) nrerror("allocation failure 1 in matrix()");
1045: m += NR_END;
1046: m -= nrl;
1047:
1048: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1049: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1050: m[nrl] += NR_END;
1051: m[nrl] -= ncl;
1052:
1053: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1054: return m;
1055: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1056: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1057: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1058: */
1059: }
1060:
1061: /*************************free matrix ************************/
1062: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1063: {
1064: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1065: free((FREE_ARG)(m+nrl-NR_END));
1066: }
1067:
1068: /******************* ma3x *******************************/
1069: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1070: {
1071: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1072: double ***m;
1073:
1074: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1075: if (!m) nrerror("allocation failure 1 in matrix()");
1076: m += NR_END;
1077: m -= nrl;
1078:
1079: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1080: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1081: m[nrl] += NR_END;
1082: m[nrl] -= ncl;
1083:
1084: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1085:
1086: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1087: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1088: m[nrl][ncl] += NR_END;
1089: m[nrl][ncl] -= nll;
1090: for (j=ncl+1; j<=nch; j++)
1091: m[nrl][j]=m[nrl][j-1]+nlay;
1092:
1093: for (i=nrl+1; i<=nrh; i++) {
1094: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1095: for (j=ncl+1; j<=nch; j++)
1096: m[i][j]=m[i][j-1]+nlay;
1097: }
1098: return m;
1099: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1100: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1101: */
1102: }
1103:
1104: /*************************free ma3x ************************/
1105: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1106: {
1107: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1108: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1109: free((FREE_ARG)(m+nrl-NR_END));
1110: }
1111:
1112: /*************** function subdirf ***********/
1113: char *subdirf(char fileres[])
1114: {
1115: /* Caution optionfilefiname is hidden */
1116: strcpy(tmpout,optionfilefiname);
1117: strcat(tmpout,"/"); /* Add to the right */
1118: strcat(tmpout,fileres);
1119: return tmpout;
1120: }
1121:
1122: /*************** function subdirf2 ***********/
1123: char *subdirf2(char fileres[], char *preop)
1124: {
1125:
1126: /* Caution optionfilefiname is hidden */
1127: strcpy(tmpout,optionfilefiname);
1128: strcat(tmpout,"/");
1129: strcat(tmpout,preop);
1130: strcat(tmpout,fileres);
1131: return tmpout;
1132: }
1133:
1134: /*************** function subdirf3 ***********/
1135: char *subdirf3(char fileres[], char *preop, char *preop2)
1136: {
1137:
1138: /* Caution optionfilefiname is hidden */
1139: strcpy(tmpout,optionfilefiname);
1140: strcat(tmpout,"/");
1141: strcat(tmpout,preop);
1142: strcat(tmpout,preop2);
1143: strcat(tmpout,fileres);
1144: return tmpout;
1145: }
1146:
1147: char *asc_diff_time(long time_sec, char ascdiff[])
1148: {
1149: long sec_left, days, hours, minutes;
1150: days = (time_sec) / (60*60*24);
1151: sec_left = (time_sec) % (60*60*24);
1152: hours = (sec_left) / (60*60) ;
1153: sec_left = (sec_left) %(60*60);
1154: minutes = (sec_left) /60;
1155: sec_left = (sec_left) % (60);
1156: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1157: return ascdiff;
1158: }
1159:
1160: /***************** f1dim *************************/
1161: extern int ncom;
1162: extern double *pcom,*xicom;
1163: extern double (*nrfunc)(double []);
1164:
1165: double f1dim(double x)
1166: {
1167: int j;
1168: double f;
1169: double *xt;
1170:
1171: xt=vector(1,ncom);
1172: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1173: f=(*nrfunc)(xt);
1174: free_vector(xt,1,ncom);
1175: return f;
1176: }
1177:
1178: /*****************brent *************************/
1179: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1180: {
1181: int iter;
1182: double a,b,d,etemp;
1183: double fu=0,fv,fw,fx;
1184: double ftemp=0.;
1185: double p,q,r,tol1,tol2,u,v,w,x,xm;
1186: double e=0.0;
1187:
1188: a=(ax < cx ? ax : cx);
1189: b=(ax > cx ? ax : cx);
1190: x=w=v=bx;
1191: fw=fv=fx=(*f)(x);
1192: for (iter=1;iter<=ITMAX;iter++) {
1193: xm=0.5*(a+b);
1194: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1195: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1196: printf(".");fflush(stdout);
1197: fprintf(ficlog,".");fflush(ficlog);
1198: #ifdef DEBUGBRENT
1199: 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);
1200: 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);
1201: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1202: #endif
1203: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1204: *xmin=x;
1205: return fx;
1206: }
1207: ftemp=fu;
1208: if (fabs(e) > tol1) {
1209: r=(x-w)*(fx-fv);
1210: q=(x-v)*(fx-fw);
1211: p=(x-v)*q-(x-w)*r;
1212: q=2.0*(q-r);
1213: if (q > 0.0) p = -p;
1214: q=fabs(q);
1215: etemp=e;
1216: e=d;
1217: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1218: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1219: else {
1220: d=p/q;
1221: u=x+d;
1222: if (u-a < tol2 || b-u < tol2)
1223: d=SIGN(tol1,xm-x);
1224: }
1225: } else {
1226: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1227: }
1228: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1229: fu=(*f)(u);
1230: if (fu <= fx) {
1231: if (u >= x) a=x; else b=x;
1232: SHFT(v,w,x,u)
1233: SHFT(fv,fw,fx,fu)
1234: } else {
1235: if (u < x) a=u; else b=u;
1236: if (fu <= fw || w == x) {
1237: v=w;
1238: w=u;
1239: fv=fw;
1240: fw=fu;
1241: } else if (fu <= fv || v == x || v == w) {
1242: v=u;
1243: fv=fu;
1244: }
1245: }
1246: }
1247: nrerror("Too many iterations in brent");
1248: *xmin=x;
1249: return fx;
1250: }
1251:
1252: /****************** mnbrak ***********************/
1253:
1254: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1255: double (*func)(double))
1256: {
1257: double ulim,u,r,q, dum;
1258: double fu;
1259:
1260: *fa=(*func)(*ax);
1261: *fb=(*func)(*bx);
1262: if (*fb > *fa) {
1263: SHFT(dum,*ax,*bx,dum)
1264: SHFT(dum,*fb,*fa,dum)
1265: }
1266: *cx=(*bx)+GOLD*(*bx-*ax);
1267: *fc=(*func)(*cx);
1268: while (*fb > *fc) { /* Declining fa, fb, fc */
1269: r=(*bx-*ax)*(*fb-*fc);
1270: q=(*bx-*cx)*(*fb-*fa);
1271: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1272: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1273: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
1274: if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
1275: fu=(*func)(u);
1276: #ifdef DEBUG
1277: /* f(x)=A(x-u)**2+f(u) */
1278: double A, fparabu;
1279: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1280: fparabu= *fa - A*(*ax-u)*(*ax-u);
1281: 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);
1282: 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);
1283: #endif
1284: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1285: fu=(*func)(u);
1286: if (fu < *fc) {
1287: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1288: SHFT(*fb,*fc,fu,(*func)(u))
1289: }
1290: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1291: u=ulim;
1292: fu=(*func)(u);
1293: } else {
1294: u=(*cx)+GOLD*(*cx-*bx);
1295: fu=(*func)(u);
1296: }
1297: SHFT(*ax,*bx,*cx,u)
1298: SHFT(*fa,*fb,*fc,fu)
1299: }
1300: }
1301:
1302: /*************** linmin ************************/
1303: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1304: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1305: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1306: the value of func at the returned location p . This is actually all accomplished by calling the
1307: routines mnbrak and brent .*/
1308: int ncom;
1309: double *pcom,*xicom;
1310: double (*nrfunc)(double []);
1311:
1312: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1313: {
1314: double brent(double ax, double bx, double cx,
1315: double (*f)(double), double tol, double *xmin);
1316: double f1dim(double x);
1317: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1318: double *fc, double (*func)(double));
1319: int j;
1320: double xx,xmin,bx,ax;
1321: double fx,fb,fa;
1322:
1323: ncom=n;
1324: pcom=vector(1,n);
1325: xicom=vector(1,n);
1326: nrfunc=func;
1327: for (j=1;j<=n;j++) {
1328: pcom[j]=p[j];
1329: xicom[j]=xi[j];
1330: }
1331: ax=0.0;
1332: xx=1.0;
1333: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
1334: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
1335: #ifdef DEBUG
1336: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1337: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1338: #endif
1339: for (j=1;j<=n;j++) {
1340: xi[j] *= xmin;
1341: p[j] += xi[j];
1342: }
1343: free_vector(xicom,1,n);
1344: free_vector(pcom,1,n);
1345: }
1346:
1347:
1348: /*************** powell ************************/
1349: /*
1350: Minimization of a function func of n variables. Input consists of an initial starting point
1351: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1352: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1353: such that failure to decrease by more than this amount on one iteration signals doneness. On
1354: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1355: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1356: */
1357: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1358: double (*func)(double []))
1359: {
1360: void linmin(double p[], double xi[], int n, double *fret,
1361: double (*func)(double []));
1362: int i,ibig,j;
1363: double del,t,*pt,*ptt,*xit;
1364: double fp,fptt;
1365: double *xits;
1366: int niterf, itmp;
1367:
1368: pt=vector(1,n);
1369: ptt=vector(1,n);
1370: xit=vector(1,n);
1371: xits=vector(1,n);
1372: *fret=(*func)(p);
1373: for (j=1;j<=n;j++) pt[j]=p[j];
1374: rcurr_time = time(NULL);
1375: for (*iter=1;;++(*iter)) {
1376: fp=(*fret);
1377: ibig=0;
1378: del=0.0;
1379: rlast_time=rcurr_time;
1380: /* (void) gettimeofday(&curr_time,&tzp); */
1381: rcurr_time = time(NULL);
1382: curr_time = *localtime(&rcurr_time);
1383: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1384: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1385: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1386: for (i=1;i<=n;i++) {
1387: printf(" %d %.12f",i, p[i]);
1388: fprintf(ficlog," %d %.12lf",i, p[i]);
1389: fprintf(ficrespow," %.12lf", p[i]);
1390: }
1391: printf("\n");
1392: fprintf(ficlog,"\n");
1393: fprintf(ficrespow,"\n");fflush(ficrespow);
1394: if(*iter <=3){
1395: tml = *localtime(&rcurr_time);
1396: strcpy(strcurr,asctime(&tml));
1397: rforecast_time=rcurr_time;
1398: itmp = strlen(strcurr);
1399: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1400: strcurr[itmp-1]='\0';
1401: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1402: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1403: for(niterf=10;niterf<=30;niterf+=10){
1404: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1405: forecast_time = *localtime(&rforecast_time);
1406: strcpy(strfor,asctime(&forecast_time));
1407: itmp = strlen(strfor);
1408: if(strfor[itmp-1]=='\n')
1409: strfor[itmp-1]='\0';
1410: 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);
1411: 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);
1412: }
1413: }
1414: for (i=1;i<=n;i++) {
1415: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1416: fptt=(*fret);
1417: #ifdef DEBUG
1418: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1419: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1420: #endif
1421: printf("%d",i);fflush(stdout);
1422: fprintf(ficlog,"%d",i);fflush(ficlog);
1423: linmin(p,xit,n,fret,func);
1424: if (fabs(fptt-(*fret)) > del) {
1425: del=fabs(fptt-(*fret));
1426: ibig=i;
1427: }
1428: #ifdef DEBUG
1429: printf("%d %.12e",i,(*fret));
1430: fprintf(ficlog,"%d %.12e",i,(*fret));
1431: for (j=1;j<=n;j++) {
1432: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1433: printf(" x(%d)=%.12e",j,xit[j]);
1434: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1435: }
1436: for(j=1;j<=n;j++) {
1437: printf(" p(%d)=%.12e",j,p[j]);
1438: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1439: }
1440: printf("\n");
1441: fprintf(ficlog,"\n");
1442: #endif
1443: } /* end i */
1444: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1445: #ifdef DEBUG
1446: int k[2],l;
1447: k[0]=1;
1448: k[1]=-1;
1449: printf("Max: %.12e",(*func)(p));
1450: fprintf(ficlog,"Max: %.12e",(*func)(p));
1451: for (j=1;j<=n;j++) {
1452: printf(" %.12e",p[j]);
1453: fprintf(ficlog," %.12e",p[j]);
1454: }
1455: printf("\n");
1456: fprintf(ficlog,"\n");
1457: for(l=0;l<=1;l++) {
1458: for (j=1;j<=n;j++) {
1459: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1460: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1461: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1462: }
1463: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1464: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1465: }
1466: #endif
1467:
1468:
1469: free_vector(xit,1,n);
1470: free_vector(xits,1,n);
1471: free_vector(ptt,1,n);
1472: free_vector(pt,1,n);
1473: return;
1474: }
1475: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1476: for (j=1;j<=n;j++) { /* Computes an extrapolated point */
1477: ptt[j]=2.0*p[j]-pt[j];
1478: xit[j]=p[j]-pt[j];
1479: pt[j]=p[j];
1480: }
1481: fptt=(*func)(ptt);
1482: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1483: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1484: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1485: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1486: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1487: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1488: /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
1489: /* Thus we compare delta(2h) with observed f1-f3 */
1490: /* or best gain on one ancient line 'del' with total */
1491: /* gain f1-f2 = f1 - f2 - 'del' with del */
1492: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1493:
1494: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
1495: t= t- del*SQR(fp-fptt);
1496: printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
1497: 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);
1498: #ifdef DEBUG
1499: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1500: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1501: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1502: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1503: 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);
1504: 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);
1505: #endif
1506: if (t < 0.0) { /* Then we use it for last direction */
1507: linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
1508: for (j=1;j<=n;j++) {
1509: xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
1510: xi[j][n]=xit[j]; /* and nth direction by the extrapolated */
1511: }
1512: printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1513: fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1514:
1515: #ifdef DEBUG
1516: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1517: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1518: for(j=1;j<=n;j++){
1519: printf(" %.12e",xit[j]);
1520: fprintf(ficlog," %.12e",xit[j]);
1521: }
1522: printf("\n");
1523: fprintf(ficlog,"\n");
1524: #endif
1525: } /* end of t negative */
1526: } /* end if (fptt < fp) */
1527: }
1528: }
1529:
1530: /**** Prevalence limit (stable or period prevalence) ****************/
1531:
1532: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1533: {
1534: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1535: matrix by transitions matrix until convergence is reached */
1536:
1537: int i, ii,j,k;
1538: double min, max, maxmin, maxmax,sumnew=0.;
1539: /* double **matprod2(); */ /* test */
1540: double **out, cov[NCOVMAX+1], **pmij();
1541: double **newm;
1542: double agefin, delaymax=50 ; /* Max number of years to converge */
1543:
1544: for (ii=1;ii<=nlstate+ndeath;ii++)
1545: for (j=1;j<=nlstate+ndeath;j++){
1546: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1547: }
1548:
1549: cov[1]=1.;
1550:
1551: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1552: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1553: newm=savm;
1554: /* Covariates have to be included here again */
1555: cov[2]=agefin;
1556:
1557: for (k=1; k<=cptcovn;k++) {
1558: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1559: /*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]]);*/
1560: }
1561: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1562: /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
1563: /* cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
1564:
1565: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1566: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1567: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1568: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1569: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1570: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1571:
1572: savm=oldm;
1573: oldm=newm;
1574: maxmax=0.;
1575: for(j=1;j<=nlstate;j++){
1576: min=1.;
1577: max=0.;
1578: for(i=1; i<=nlstate; i++) {
1579: sumnew=0;
1580: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1581: prlim[i][j]= newm[i][j]/(1-sumnew);
1582: /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
1583: max=FMAX(max,prlim[i][j]);
1584: min=FMIN(min,prlim[i][j]);
1585: }
1586: maxmin=max-min;
1587: maxmax=FMAX(maxmax,maxmin);
1588: } /* j loop */
1589: if(maxmax < ftolpl){
1590: return prlim;
1591: }
1592: } /* age loop */
1593: return prlim; /* should not reach here */
1594: }
1595:
1596: /*************** transition probabilities ***************/
1597:
1598: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1599: {
1600: /* According to parameters values stored in x and the covariate's values stored in cov,
1601: computes the probability to be observed in state j being in state i by appying the
1602: model to the ncovmodel covariates (including constant and age).
1603: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1604: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1605: ncth covariate in the global vector x is given by the formula:
1606: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1607: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1608: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1609: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1610: Outputs ps[i][j] the probability to be observed in j being in j according to
1611: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1612: */
1613: double s1, lnpijopii;
1614: /*double t34;*/
1615: int i,j, nc, ii, jj;
1616:
1617: for(i=1; i<= nlstate; i++){
1618: for(j=1; j<i;j++){
1619: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1620: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1621: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1622: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1623: }
1624: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1625: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1626: }
1627: for(j=i+1; j<=nlstate+ndeath;j++){
1628: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1629: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
1630: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
1631: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1632: }
1633: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1634: }
1635: }
1636:
1637: for(i=1; i<= nlstate; i++){
1638: s1=0;
1639: for(j=1; j<i; j++){
1640: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1641: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1642: }
1643: for(j=i+1; j<=nlstate+ndeath; j++){
1644: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1645: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1646: }
1647: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1648: ps[i][i]=1./(s1+1.);
1649: /* Computing other pijs */
1650: for(j=1; j<i; j++)
1651: ps[i][j]= exp(ps[i][j])*ps[i][i];
1652: for(j=i+1; j<=nlstate+ndeath; j++)
1653: ps[i][j]= exp(ps[i][j])*ps[i][i];
1654: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1655: } /* end i */
1656:
1657: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1658: for(jj=1; jj<= nlstate+ndeath; jj++){
1659: ps[ii][jj]=0;
1660: ps[ii][ii]=1;
1661: }
1662: }
1663:
1664:
1665: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1666: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1667: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
1668: /* } */
1669: /* printf("\n "); */
1670: /* } */
1671: /* printf("\n ");printf("%lf ",cov[2]);*/
1672: /*
1673: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1674: goto end;*/
1675: return ps;
1676: }
1677:
1678: /**************** Product of 2 matrices ******************/
1679:
1680: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1681: {
1682: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1683: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1684: /* in, b, out are matrice of pointers which should have been initialized
1685: before: only the contents of out is modified. The function returns
1686: a pointer to pointers identical to out */
1687: int i, j, k;
1688: for(i=nrl; i<= nrh; i++)
1689: for(k=ncolol; k<=ncoloh; k++){
1690: out[i][k]=0.;
1691: for(j=ncl; j<=nch; j++)
1692: out[i][k] +=in[i][j]*b[j][k];
1693: }
1694: return out;
1695: }
1696:
1697:
1698: /************* Higher Matrix Product ***************/
1699:
1700: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1701: {
1702: /* Computes the transition matrix starting at age 'age' over
1703: 'nhstepm*hstepm*stepm' months (i.e. until
1704: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1705: nhstepm*hstepm matrices.
1706: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1707: (typically every 2 years instead of every month which is too big
1708: for the memory).
1709: Model is determined by parameters x and covariates have to be
1710: included manually here.
1711:
1712: */
1713:
1714: int i, j, d, h, k;
1715: double **out, cov[NCOVMAX+1];
1716: double **newm;
1717:
1718: /* Hstepm could be zero and should return the unit matrix */
1719: for (i=1;i<=nlstate+ndeath;i++)
1720: for (j=1;j<=nlstate+ndeath;j++){
1721: oldm[i][j]=(i==j ? 1.0 : 0.0);
1722: po[i][j][0]=(i==j ? 1.0 : 0.0);
1723: }
1724: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1725: for(h=1; h <=nhstepm; h++){
1726: for(d=1; d <=hstepm; d++){
1727: newm=savm;
1728: /* Covariates have to be included here again */
1729: cov[1]=1.;
1730: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1731: for (k=1; k<=cptcovn;k++)
1732: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1733: for (k=1; k<=cptcovage;k++)
1734: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1735: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1736: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1737:
1738:
1739: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1740: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1741: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1742: pmij(pmmij,cov,ncovmodel,x,nlstate));
1743: savm=oldm;
1744: oldm=newm;
1745: }
1746: for(i=1; i<=nlstate+ndeath; i++)
1747: for(j=1;j<=nlstate+ndeath;j++) {
1748: po[i][j][h]=newm[i][j];
1749: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1750: }
1751: /*printf("h=%d ",h);*/
1752: } /* end h */
1753: /* printf("\n H=%d \n",h); */
1754: return po;
1755: }
1756:
1757: #ifdef NLOPT
1758: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
1759: double fret;
1760: double *xt;
1761: int j;
1762: myfunc_data *d2 = (myfunc_data *) pd;
1763: /* xt = (p1-1); */
1764: xt=vector(1,n);
1765: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
1766:
1767: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
1768: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
1769: printf("Function = %.12lf ",fret);
1770: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
1771: printf("\n");
1772: free_vector(xt,1,n);
1773: return fret;
1774: }
1775: #endif
1776:
1777: /*************** log-likelihood *************/
1778: double func( double *x)
1779: {
1780: int i, ii, j, k, mi, d, kk;
1781: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1782: double **out;
1783: double sw; /* Sum of weights */
1784: double lli; /* Individual log likelihood */
1785: int s1, s2;
1786: double bbh, survp;
1787: long ipmx;
1788: /*extern weight */
1789: /* We are differentiating ll according to initial status */
1790: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1791: /*for(i=1;i<imx;i++)
1792: printf(" %d\n",s[4][i]);
1793: */
1794:
1795: ++countcallfunc;
1796:
1797: cov[1]=1.;
1798:
1799: for(k=1; k<=nlstate; k++) ll[k]=0.;
1800:
1801: if(mle==1){
1802: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1803: /* Computes the values of the ncovmodel covariates of the model
1804: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
1805: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
1806: to be observed in j being in i according to the model.
1807: */
1808: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1809: cov[2+k]=covar[Tvar[k]][i];
1810: }
1811: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1812: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1813: has been calculated etc */
1814: for(mi=1; mi<= wav[i]-1; mi++){
1815: for (ii=1;ii<=nlstate+ndeath;ii++)
1816: for (j=1;j<=nlstate+ndeath;j++){
1817: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1818: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1819: }
1820: for(d=0; d<dh[mi][i]; d++){
1821: newm=savm;
1822: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1823: for (kk=1; kk<=cptcovage;kk++) {
1824: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
1825: }
1826: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1827: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1828: savm=oldm;
1829: oldm=newm;
1830: } /* end mult */
1831:
1832: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1833: /* But now since version 0.9 we anticipate for bias at large stepm.
1834: * If stepm is larger than one month (smallest stepm) and if the exact delay
1835: * (in months) between two waves is not a multiple of stepm, we rounded to
1836: * the nearest (and in case of equal distance, to the lowest) interval but now
1837: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1838: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1839: * probability in order to take into account the bias as a fraction of the way
1840: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1841: * -stepm/2 to stepm/2 .
1842: * For stepm=1 the results are the same as for previous versions of Imach.
1843: * For stepm > 1 the results are less biased than in previous versions.
1844: */
1845: s1=s[mw[mi][i]][i];
1846: s2=s[mw[mi+1][i]][i];
1847: bbh=(double)bh[mi][i]/(double)stepm;
1848: /* bias bh is positive if real duration
1849: * is higher than the multiple of stepm and negative otherwise.
1850: */
1851: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1852: if( s2 > nlstate){
1853: /* i.e. if s2 is a death state and if the date of death is known
1854: then the contribution to the likelihood is the probability to
1855: die between last step unit time and current step unit time,
1856: which is also equal to probability to die before dh
1857: minus probability to die before dh-stepm .
1858: In version up to 0.92 likelihood was computed
1859: as if date of death was unknown. Death was treated as any other
1860: health state: the date of the interview describes the actual state
1861: and not the date of a change in health state. The former idea was
1862: to consider that at each interview the state was recorded
1863: (healthy, disable or death) and IMaCh was corrected; but when we
1864: introduced the exact date of death then we should have modified
1865: the contribution of an exact death to the likelihood. This new
1866: contribution is smaller and very dependent of the step unit
1867: stepm. It is no more the probability to die between last interview
1868: and month of death but the probability to survive from last
1869: interview up to one month before death multiplied by the
1870: probability to die within a month. Thanks to Chris
1871: Jackson for correcting this bug. Former versions increased
1872: mortality artificially. The bad side is that we add another loop
1873: which slows down the processing. The difference can be up to 10%
1874: lower mortality.
1875: */
1876: lli=log(out[s1][s2] - savm[s1][s2]);
1877:
1878:
1879: } else if (s2==-2) {
1880: for (j=1,survp=0. ; j<=nlstate; j++)
1881: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1882: /*survp += out[s1][j]; */
1883: lli= log(survp);
1884: }
1885:
1886: else if (s2==-4) {
1887: for (j=3,survp=0. ; j<=nlstate; j++)
1888: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1889: lli= log(survp);
1890: }
1891:
1892: else if (s2==-5) {
1893: for (j=1,survp=0. ; j<=2; j++)
1894: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1895: lli= log(survp);
1896: }
1897:
1898: else{
1899: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1900: /* 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 */
1901: }
1902: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1903: /*if(lli ==000.0)*/
1904: /*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); */
1905: ipmx +=1;
1906: sw += weight[i];
1907: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1908: } /* end of wave */
1909: } /* end of individual */
1910: } else if(mle==2){
1911: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1912: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1913: for(mi=1; mi<= wav[i]-1; mi++){
1914: for (ii=1;ii<=nlstate+ndeath;ii++)
1915: for (j=1;j<=nlstate+ndeath;j++){
1916: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1917: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1918: }
1919: for(d=0; d<=dh[mi][i]; d++){
1920: newm=savm;
1921: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1922: for (kk=1; kk<=cptcovage;kk++) {
1923: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1924: }
1925: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1926: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1927: savm=oldm;
1928: oldm=newm;
1929: } /* end mult */
1930:
1931: s1=s[mw[mi][i]][i];
1932: s2=s[mw[mi+1][i]][i];
1933: bbh=(double)bh[mi][i]/(double)stepm;
1934: 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 */
1935: ipmx +=1;
1936: sw += weight[i];
1937: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1938: } /* end of wave */
1939: } /* end of individual */
1940: } else if(mle==3){ /* exponential inter-extrapolation */
1941: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1942: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1943: for(mi=1; mi<= wav[i]-1; mi++){
1944: for (ii=1;ii<=nlstate+ndeath;ii++)
1945: for (j=1;j<=nlstate+ndeath;j++){
1946: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1947: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1948: }
1949: for(d=0; d<dh[mi][i]; d++){
1950: newm=savm;
1951: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1952: for (kk=1; kk<=cptcovage;kk++) {
1953: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1954: }
1955: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1956: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1957: savm=oldm;
1958: oldm=newm;
1959: } /* end mult */
1960:
1961: s1=s[mw[mi][i]][i];
1962: s2=s[mw[mi+1][i]][i];
1963: bbh=(double)bh[mi][i]/(double)stepm;
1964: 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 */
1965: ipmx +=1;
1966: sw += weight[i];
1967: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1968: } /* end of wave */
1969: } /* end of individual */
1970: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1971: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1972: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1973: for(mi=1; mi<= wav[i]-1; mi++){
1974: for (ii=1;ii<=nlstate+ndeath;ii++)
1975: for (j=1;j<=nlstate+ndeath;j++){
1976: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1977: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1978: }
1979: for(d=0; d<dh[mi][i]; d++){
1980: newm=savm;
1981: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1982: for (kk=1; kk<=cptcovage;kk++) {
1983: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1984: }
1985:
1986: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1987: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1988: savm=oldm;
1989: oldm=newm;
1990: } /* end mult */
1991:
1992: s1=s[mw[mi][i]][i];
1993: s2=s[mw[mi+1][i]][i];
1994: if( s2 > nlstate){
1995: lli=log(out[s1][s2] - savm[s1][s2]);
1996: }else{
1997: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1998: }
1999: ipmx +=1;
2000: sw += weight[i];
2001: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2002: /* 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]); */
2003: } /* end of wave */
2004: } /* end of individual */
2005: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
2006: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2007: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2008: for(mi=1; mi<= wav[i]-1; mi++){
2009: for (ii=1;ii<=nlstate+ndeath;ii++)
2010: for (j=1;j<=nlstate+ndeath;j++){
2011: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2012: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2013: }
2014: for(d=0; d<dh[mi][i]; d++){
2015: newm=savm;
2016: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2017: for (kk=1; kk<=cptcovage;kk++) {
2018: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2019: }
2020:
2021: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2022: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2023: savm=oldm;
2024: oldm=newm;
2025: } /* end mult */
2026:
2027: s1=s[mw[mi][i]][i];
2028: s2=s[mw[mi+1][i]][i];
2029: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2030: ipmx +=1;
2031: sw += weight[i];
2032: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2033: /*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]);*/
2034: } /* end of wave */
2035: } /* end of individual */
2036: } /* End of if */
2037: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2038: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2039: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2040: return -l;
2041: }
2042:
2043: /*************** log-likelihood *************/
2044: double funcone( double *x)
2045: {
2046: /* Same as likeli but slower because of a lot of printf and if */
2047: int i, ii, j, k, mi, d, kk;
2048: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
2049: double **out;
2050: double lli; /* Individual log likelihood */
2051: double llt;
2052: int s1, s2;
2053: double bbh, survp;
2054: /*extern weight */
2055: /* We are differentiating ll according to initial status */
2056: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2057: /*for(i=1;i<imx;i++)
2058: printf(" %d\n",s[4][i]);
2059: */
2060: cov[1]=1.;
2061:
2062: for(k=1; k<=nlstate; k++) ll[k]=0.;
2063:
2064: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2065: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2066: for(mi=1; mi<= wav[i]-1; mi++){
2067: for (ii=1;ii<=nlstate+ndeath;ii++)
2068: for (j=1;j<=nlstate+ndeath;j++){
2069: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2070: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2071: }
2072: for(d=0; d<dh[mi][i]; d++){
2073: newm=savm;
2074: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2075: for (kk=1; kk<=cptcovage;kk++) {
2076: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2077: }
2078: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2079: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2080: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2081: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2082: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
2083: savm=oldm;
2084: oldm=newm;
2085: } /* end mult */
2086:
2087: s1=s[mw[mi][i]][i];
2088: s2=s[mw[mi+1][i]][i];
2089: bbh=(double)bh[mi][i]/(double)stepm;
2090: /* bias is positive if real duration
2091: * is higher than the multiple of stepm and negative otherwise.
2092: */
2093: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2094: lli=log(out[s1][s2] - savm[s1][s2]);
2095: } else if (s2==-2) {
2096: for (j=1,survp=0. ; j<=nlstate; j++)
2097: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2098: lli= log(survp);
2099: }else if (mle==1){
2100: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2101: } else if(mle==2){
2102: 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 */
2103: } else if(mle==3){ /* exponential inter-extrapolation */
2104: 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 */
2105: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2106: lli=log(out[s1][s2]); /* Original formula */
2107: } else{ /* mle=0 back to 1 */
2108: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2109: /*lli=log(out[s1][s2]); */ /* Original formula */
2110: } /* End of if */
2111: ipmx +=1;
2112: sw += weight[i];
2113: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2114: /*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]); */
2115: if(globpr){
2116: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
2117: %11.6f %11.6f %11.6f ", \
2118: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
2119: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2120: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2121: llt +=ll[k]*gipmx/gsw;
2122: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2123: }
2124: fprintf(ficresilk," %10.6f\n", -llt);
2125: }
2126: } /* end of wave */
2127: } /* end of individual */
2128: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2129: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2130: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2131: if(globpr==0){ /* First time we count the contributions and weights */
2132: gipmx=ipmx;
2133: gsw=sw;
2134: }
2135: return -l;
2136: }
2137:
2138:
2139: /*************** function likelione ***********/
2140: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2141: {
2142: /* This routine should help understanding what is done with
2143: the selection of individuals/waves and
2144: to check the exact contribution to the likelihood.
2145: Plotting could be done.
2146: */
2147: int k;
2148:
2149: if(*globpri !=0){ /* Just counts and sums, no printings */
2150: strcpy(fileresilk,"ilk");
2151: strcat(fileresilk,fileres);
2152: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2153: printf("Problem with resultfile: %s\n", fileresilk);
2154: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2155: }
2156: 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");
2157: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
2158: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2159: for(k=1; k<=nlstate; k++)
2160: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2161: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2162: }
2163:
2164: *fretone=(*funcone)(p);
2165: if(*globpri !=0){
2166: fclose(ficresilk);
2167: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
2168: fflush(fichtm);
2169: }
2170: return;
2171: }
2172:
2173:
2174: /*********** Maximum Likelihood Estimation ***************/
2175:
2176: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2177: {
2178: int i,j, iter=0;
2179: double **xi;
2180: double fret;
2181: double fretone; /* Only one call to likelihood */
2182: /* char filerespow[FILENAMELENGTH];*/
2183:
2184: #ifdef NLOPT
2185: int creturn;
2186: nlopt_opt opt;
2187: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2188: double *lb;
2189: double minf; /* the minimum objective value, upon return */
2190: double * p1; /* Shifted parameters from 0 instead of 1 */
2191: myfunc_data dinst, *d = &dinst;
2192: #endif
2193:
2194:
2195: xi=matrix(1,npar,1,npar);
2196: for (i=1;i<=npar;i++)
2197: for (j=1;j<=npar;j++)
2198: xi[i][j]=(i==j ? 1.0 : 0.0);
2199: printf("Powell\n"); fprintf(ficlog,"Powell\n");
2200: strcpy(filerespow,"pow");
2201: strcat(filerespow,fileres);
2202: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2203: printf("Problem with resultfile: %s\n", filerespow);
2204: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2205: }
2206: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2207: for (i=1;i<=nlstate;i++)
2208: for(j=1;j<=nlstate+ndeath;j++)
2209: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2210: fprintf(ficrespow,"\n");
2211: #ifdef POWELL
2212: powell(p,xi,npar,ftol,&iter,&fret,func);
2213: #endif
2214:
2215: #ifdef NLOPT
2216: #ifdef NEWUOA
2217: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2218: #else
2219: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2220: #endif
2221: lb=vector(0,npar-1);
2222: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2223: nlopt_set_lower_bounds(opt, lb);
2224: nlopt_set_initial_step1(opt, 0.1);
2225:
2226: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2227: d->function = func;
2228: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2229: nlopt_set_min_objective(opt, myfunc, d);
2230: nlopt_set_xtol_rel(opt, ftol);
2231: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2232: printf("nlopt failed! %d\n",creturn);
2233: }
2234: else {
2235: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2236: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2237: iter=1; /* not equal */
2238: }
2239: nlopt_destroy(opt);
2240: #endif
2241: free_matrix(xi,1,npar,1,npar);
2242: fclose(ficrespow);
2243: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2244: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2245: fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2246:
2247: }
2248:
2249: /**** Computes Hessian and covariance matrix ***/
2250: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
2251: {
2252: double **a,**y,*x,pd;
2253: double **hess;
2254: int i, j;
2255: int *indx;
2256:
2257: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
2258: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
2259: void lubksb(double **a, int npar, int *indx, double b[]) ;
2260: void ludcmp(double **a, int npar, int *indx, double *d) ;
2261: double gompertz(double p[]);
2262: hess=matrix(1,npar,1,npar);
2263:
2264: printf("\nCalculation of the hessian matrix. Wait...\n");
2265: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2266: for (i=1;i<=npar;i++){
2267: printf("%d",i);fflush(stdout);
2268: fprintf(ficlog,"%d",i);fflush(ficlog);
2269:
2270: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2271:
2272: /* printf(" %f ",p[i]);
2273: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2274: }
2275:
2276: for (i=1;i<=npar;i++) {
2277: for (j=1;j<=npar;j++) {
2278: if (j>i) {
2279: printf(".%d%d",i,j);fflush(stdout);
2280: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
2281: hess[i][j]=hessij(p,delti,i,j,func,npar);
2282:
2283: hess[j][i]=hess[i][j];
2284: /*printf(" %lf ",hess[i][j]);*/
2285: }
2286: }
2287: }
2288: printf("\n");
2289: fprintf(ficlog,"\n");
2290:
2291: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2292: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2293:
2294: a=matrix(1,npar,1,npar);
2295: y=matrix(1,npar,1,npar);
2296: x=vector(1,npar);
2297: indx=ivector(1,npar);
2298: for (i=1;i<=npar;i++)
2299: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2300: ludcmp(a,npar,indx,&pd);
2301:
2302: for (j=1;j<=npar;j++) {
2303: for (i=1;i<=npar;i++) x[i]=0;
2304: x[j]=1;
2305: lubksb(a,npar,indx,x);
2306: for (i=1;i<=npar;i++){
2307: matcov[i][j]=x[i];
2308: }
2309: }
2310:
2311: printf("\n#Hessian matrix#\n");
2312: fprintf(ficlog,"\n#Hessian matrix#\n");
2313: for (i=1;i<=npar;i++) {
2314: for (j=1;j<=npar;j++) {
2315: printf("%.3e ",hess[i][j]);
2316: fprintf(ficlog,"%.3e ",hess[i][j]);
2317: }
2318: printf("\n");
2319: fprintf(ficlog,"\n");
2320: }
2321:
2322: /* Recompute Inverse */
2323: for (i=1;i<=npar;i++)
2324: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
2325: ludcmp(a,npar,indx,&pd);
2326:
2327: /* printf("\n#Hessian matrix recomputed#\n");
2328:
2329: for (j=1;j<=npar;j++) {
2330: for (i=1;i<=npar;i++) x[i]=0;
2331: x[j]=1;
2332: lubksb(a,npar,indx,x);
2333: for (i=1;i<=npar;i++){
2334: y[i][j]=x[i];
2335: printf("%.3e ",y[i][j]);
2336: fprintf(ficlog,"%.3e ",y[i][j]);
2337: }
2338: printf("\n");
2339: fprintf(ficlog,"\n");
2340: }
2341: */
2342:
2343: free_matrix(a,1,npar,1,npar);
2344: free_matrix(y,1,npar,1,npar);
2345: free_vector(x,1,npar);
2346: free_ivector(indx,1,npar);
2347: free_matrix(hess,1,npar,1,npar);
2348:
2349:
2350: }
2351:
2352: /*************** hessian matrix ****************/
2353: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2354: {
2355: int i;
2356: int l=1, lmax=20;
2357: double k1,k2;
2358: double p2[MAXPARM+1]; /* identical to x */
2359: double res;
2360: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2361: double fx;
2362: int k=0,kmax=10;
2363: double l1;
2364:
2365: fx=func(x);
2366: for (i=1;i<=npar;i++) p2[i]=x[i];
2367: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
2368: l1=pow(10,l);
2369: delts=delt;
2370: for(k=1 ; k <kmax; k=k+1){
2371: delt = delta*(l1*k);
2372: p2[theta]=x[theta] +delt;
2373: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
2374: p2[theta]=x[theta]-delt;
2375: k2=func(p2)-fx;
2376: /*res= (k1-2.0*fx+k2)/delt/delt; */
2377: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2378:
2379: #ifdef DEBUGHESS
2380: 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);
2381: 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);
2382: #endif
2383: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2384: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2385: k=kmax;
2386: }
2387: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
2388: k=kmax; l=lmax*10;
2389: }
2390: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2391: delts=delt;
2392: }
2393: }
2394: }
2395: delti[theta]=delts;
2396: return res;
2397:
2398: }
2399:
2400: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2401: {
2402: int i;
2403: int l=1, lmax=20;
2404: double k1,k2,k3,k4,res,fx;
2405: double p2[MAXPARM+1];
2406: int k;
2407:
2408: fx=func(x);
2409: for (k=1; k<=2; k++) {
2410: for (i=1;i<=npar;i++) p2[i]=x[i];
2411: p2[thetai]=x[thetai]+delti[thetai]/k;
2412: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2413: k1=func(p2)-fx;
2414:
2415: p2[thetai]=x[thetai]+delti[thetai]/k;
2416: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2417: k2=func(p2)-fx;
2418:
2419: p2[thetai]=x[thetai]-delti[thetai]/k;
2420: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2421: k3=func(p2)-fx;
2422:
2423: p2[thetai]=x[thetai]-delti[thetai]/k;
2424: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2425: k4=func(p2)-fx;
2426: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2427: #ifdef DEBUG
2428: 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);
2429: 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);
2430: #endif
2431: }
2432: return res;
2433: }
2434:
2435: /************** Inverse of matrix **************/
2436: void ludcmp(double **a, int n, int *indx, double *d)
2437: {
2438: int i,imax,j,k;
2439: double big,dum,sum,temp;
2440: double *vv;
2441:
2442: vv=vector(1,n);
2443: *d=1.0;
2444: for (i=1;i<=n;i++) {
2445: big=0.0;
2446: for (j=1;j<=n;j++)
2447: if ((temp=fabs(a[i][j])) > big) big=temp;
2448: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2449: vv[i]=1.0/big;
2450: }
2451: for (j=1;j<=n;j++) {
2452: for (i=1;i<j;i++) {
2453: sum=a[i][j];
2454: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2455: a[i][j]=sum;
2456: }
2457: big=0.0;
2458: for (i=j;i<=n;i++) {
2459: sum=a[i][j];
2460: for (k=1;k<j;k++)
2461: sum -= a[i][k]*a[k][j];
2462: a[i][j]=sum;
2463: if ( (dum=vv[i]*fabs(sum)) >= big) {
2464: big=dum;
2465: imax=i;
2466: }
2467: }
2468: if (j != imax) {
2469: for (k=1;k<=n;k++) {
2470: dum=a[imax][k];
2471: a[imax][k]=a[j][k];
2472: a[j][k]=dum;
2473: }
2474: *d = -(*d);
2475: vv[imax]=vv[j];
2476: }
2477: indx[j]=imax;
2478: if (a[j][j] == 0.0) a[j][j]=TINY;
2479: if (j != n) {
2480: dum=1.0/(a[j][j]);
2481: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2482: }
2483: }
2484: free_vector(vv,1,n); /* Doesn't work */
2485: ;
2486: }
2487:
2488: void lubksb(double **a, int n, int *indx, double b[])
2489: {
2490: int i,ii=0,ip,j;
2491: double sum;
2492:
2493: for (i=1;i<=n;i++) {
2494: ip=indx[i];
2495: sum=b[ip];
2496: b[ip]=b[i];
2497: if (ii)
2498: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2499: else if (sum) ii=i;
2500: b[i]=sum;
2501: }
2502: for (i=n;i>=1;i--) {
2503: sum=b[i];
2504: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2505: b[i]=sum/a[i][i];
2506: }
2507: }
2508:
2509: void pstamp(FILE *fichier)
2510: {
2511: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2512: }
2513:
2514: /************ Frequencies ********************/
2515: 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[])
2516: { /* Some frequencies */
2517:
2518: int i, m, jk, j1, bool, z1,j;
2519: int first;
2520: double ***freq; /* Frequencies */
2521: double *pp, **prop;
2522: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2523: char fileresp[FILENAMELENGTH];
2524:
2525: pp=vector(1,nlstate);
2526: prop=matrix(1,nlstate,iagemin,iagemax+3);
2527: strcpy(fileresp,"p");
2528: strcat(fileresp,fileres);
2529: if((ficresp=fopen(fileresp,"w"))==NULL) {
2530: printf("Problem with prevalence resultfile: %s\n", fileresp);
2531: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2532: exit(0);
2533: }
2534: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2535: j1=0;
2536:
2537: j=cptcoveff;
2538: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2539:
2540: first=1;
2541:
2542: /* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */
2543: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
2544: /* j1++; */
2545: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
2546: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2547: scanf("%d", i);*/
2548: for (i=-5; i<=nlstate+ndeath; i++)
2549: for (jk=-5; jk<=nlstate+ndeath; jk++)
2550: for(m=iagemin; m <= iagemax+3; m++)
2551: freq[i][jk][m]=0;
2552:
2553: for (i=1; i<=nlstate; i++)
2554: for(m=iagemin; m <= iagemax+3; m++)
2555: prop[i][m]=0;
2556:
2557: dateintsum=0;
2558: k2cpt=0;
2559: for (i=1; i<=imx; i++) {
2560: bool=1;
2561: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
2562: for (z1=1; z1<=cptcoveff; z1++)
2563: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
2564: /* Tests if the value of each of the covariates of i is equal to filter j1 */
2565: bool=0;
2566: /* 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",
2567: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
2568: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
2569: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
2570: }
2571: }
2572:
2573: if (bool==1){
2574: for(m=firstpass; m<=lastpass; m++){
2575: k2=anint[m][i]+(mint[m][i]/12.);
2576: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2577: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2578: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2579: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2580: if (m<lastpass) {
2581: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2582: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2583: }
2584:
2585: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2586: dateintsum=dateintsum+k2;
2587: k2cpt++;
2588: }
2589: /*}*/
2590: }
2591: }
2592: } /* end i */
2593:
2594: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2595: pstamp(ficresp);
2596: if (cptcovn>0) {
2597: fprintf(ficresp, "\n#********** Variable ");
2598: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2599: fprintf(ficresp, "**********\n#");
2600: fprintf(ficlog, "\n#********** Variable ");
2601: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2602: fprintf(ficlog, "**********\n#");
2603: }
2604: for(i=1; i<=nlstate;i++)
2605: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2606: fprintf(ficresp, "\n");
2607:
2608: for(i=iagemin; i <= iagemax+3; i++){
2609: if(i==iagemax+3){
2610: fprintf(ficlog,"Total");
2611: }else{
2612: if(first==1){
2613: first=0;
2614: printf("See log file for details...\n");
2615: }
2616: fprintf(ficlog,"Age %d", i);
2617: }
2618: for(jk=1; jk <=nlstate ; jk++){
2619: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2620: pp[jk] += freq[jk][m][i];
2621: }
2622: for(jk=1; jk <=nlstate ; jk++){
2623: for(m=-1, pos=0; m <=0 ; m++)
2624: pos += freq[jk][m][i];
2625: if(pp[jk]>=1.e-10){
2626: if(first==1){
2627: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2628: }
2629: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2630: }else{
2631: if(first==1)
2632: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2633: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2634: }
2635: }
2636:
2637: for(jk=1; jk <=nlstate ; jk++){
2638: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2639: pp[jk] += freq[jk][m][i];
2640: }
2641: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2642: pos += pp[jk];
2643: posprop += prop[jk][i];
2644: }
2645: for(jk=1; jk <=nlstate ; jk++){
2646: if(pos>=1.e-5){
2647: if(first==1)
2648: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2649: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2650: }else{
2651: if(first==1)
2652: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2653: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2654: }
2655: if( i <= iagemax){
2656: if(pos>=1.e-5){
2657: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2658: /*probs[i][jk][j1]= pp[jk]/pos;*/
2659: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2660: }
2661: else
2662: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2663: }
2664: }
2665:
2666: for(jk=-1; jk <=nlstate+ndeath; jk++)
2667: for(m=-1; m <=nlstate+ndeath; m++)
2668: if(freq[jk][m][i] !=0 ) {
2669: if(first==1)
2670: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2671: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2672: }
2673: if(i <= iagemax)
2674: fprintf(ficresp,"\n");
2675: if(first==1)
2676: printf("Others in log...\n");
2677: fprintf(ficlog,"\n");
2678: }
2679: /*}*/
2680: }
2681: dateintmean=dateintsum/k2cpt;
2682:
2683: fclose(ficresp);
2684: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2685: free_vector(pp,1,nlstate);
2686: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2687: /* End of Freq */
2688: }
2689:
2690: /************ Prevalence ********************/
2691: 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)
2692: {
2693: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2694: in each health status at the date of interview (if between dateprev1 and dateprev2).
2695: We still use firstpass and lastpass as another selection.
2696: */
2697:
2698: int i, m, jk, j1, bool, z1,j;
2699:
2700: double **prop;
2701: double posprop;
2702: double y2; /* in fractional years */
2703: int iagemin, iagemax;
2704: int first; /** to stop verbosity which is redirected to log file */
2705:
2706: iagemin= (int) agemin;
2707: iagemax= (int) agemax;
2708: /*pp=vector(1,nlstate);*/
2709: prop=matrix(1,nlstate,iagemin,iagemax+3);
2710: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2711: j1=0;
2712:
2713: /*j=cptcoveff;*/
2714: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2715:
2716: first=1;
2717: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
2718: /*for(i1=1; i1<=ncodemax[k1];i1++){
2719: j1++;*/
2720:
2721: for (i=1; i<=nlstate; i++)
2722: for(m=iagemin; m <= iagemax+3; m++)
2723: prop[i][m]=0.0;
2724:
2725: for (i=1; i<=imx; i++) { /* Each individual */
2726: bool=1;
2727: if (cptcovn>0) {
2728: for (z1=1; z1<=cptcoveff; z1++)
2729: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2730: bool=0;
2731: }
2732: if (bool==1) {
2733: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2734: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2735: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2736: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2737: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2738: 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);
2739: if (s[m][i]>0 && s[m][i]<=nlstate) {
2740: /*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]]);*/
2741: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2742: prop[s[m][i]][iagemax+3] += weight[i];
2743: }
2744: }
2745: } /* end selection of waves */
2746: }
2747: }
2748: for(i=iagemin; i <= iagemax+3; i++){
2749: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2750: posprop += prop[jk][i];
2751: }
2752:
2753: for(jk=1; jk <=nlstate ; jk++){
2754: if( i <= iagemax){
2755: if(posprop>=1.e-5){
2756: probs[i][jk][j1]= prop[jk][i]/posprop;
2757: } else{
2758: if(first==1){
2759: first=0;
2760: 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]);
2761: }
2762: }
2763: }
2764: }/* end jk */
2765: }/* end i */
2766: /*} *//* end i1 */
2767: } /* end j1 */
2768:
2769: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2770: /*free_vector(pp,1,nlstate);*/
2771: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2772: } /* End of prevalence */
2773:
2774: /************* Waves Concatenation ***************/
2775:
2776: 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)
2777: {
2778: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2779: Death is a valid wave (if date is known).
2780: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2781: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2782: and mw[mi+1][i]. dh depends on stepm.
2783: */
2784:
2785: int i, mi, m;
2786: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2787: double sum=0., jmean=0.;*/
2788: int first;
2789: int j, k=0,jk, ju, jl;
2790: double sum=0.;
2791: first=0;
2792: jmin=100000;
2793: jmax=-1;
2794: jmean=0.;
2795: for(i=1; i<=imx; i++){
2796: mi=0;
2797: m=firstpass;
2798: while(s[m][i] <= nlstate){
2799: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2800: mw[++mi][i]=m;
2801: if(m >=lastpass)
2802: break;
2803: else
2804: m++;
2805: }/* end while */
2806: if (s[m][i] > nlstate){
2807: mi++; /* Death is another wave */
2808: /* if(mi==0) never been interviewed correctly before death */
2809: /* Only death is a correct wave */
2810: mw[mi][i]=m;
2811: }
2812:
2813: wav[i]=mi;
2814: if(mi==0){
2815: nbwarn++;
2816: if(first==0){
2817: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2818: first=1;
2819: }
2820: if(first==1){
2821: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2822: }
2823: } /* end mi==0 */
2824: } /* End individuals */
2825:
2826: for(i=1; i<=imx; i++){
2827: for(mi=1; mi<wav[i];mi++){
2828: if (stepm <=0)
2829: dh[mi][i]=1;
2830: else{
2831: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2832: if (agedc[i] < 2*AGESUP) {
2833: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2834: if(j==0) j=1; /* Survives at least one month after exam */
2835: else if(j<0){
2836: nberr++;
2837: 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]);
2838: j=1; /* Temporary Dangerous patch */
2839: 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);
2840: 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]);
2841: 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);
2842: }
2843: k=k+1;
2844: if (j >= jmax){
2845: jmax=j;
2846: ijmax=i;
2847: }
2848: if (j <= jmin){
2849: jmin=j;
2850: ijmin=i;
2851: }
2852: sum=sum+j;
2853: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2854: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2855: }
2856: }
2857: else{
2858: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2859: /* 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]); */
2860:
2861: k=k+1;
2862: if (j >= jmax) {
2863: jmax=j;
2864: ijmax=i;
2865: }
2866: else if (j <= jmin){
2867: jmin=j;
2868: ijmin=i;
2869: }
2870: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2871: /*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]);*/
2872: if(j<0){
2873: nberr++;
2874: 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]);
2875: 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]);
2876: }
2877: sum=sum+j;
2878: }
2879: jk= j/stepm;
2880: jl= j -jk*stepm;
2881: ju= j -(jk+1)*stepm;
2882: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2883: if(jl==0){
2884: dh[mi][i]=jk;
2885: bh[mi][i]=0;
2886: }else{ /* We want a negative bias in order to only have interpolation ie
2887: * to avoid the price of an extra matrix product in likelihood */
2888: dh[mi][i]=jk+1;
2889: bh[mi][i]=ju;
2890: }
2891: }else{
2892: if(jl <= -ju){
2893: dh[mi][i]=jk;
2894: bh[mi][i]=jl; /* bias is positive if real duration
2895: * is higher than the multiple of stepm and negative otherwise.
2896: */
2897: }
2898: else{
2899: dh[mi][i]=jk+1;
2900: bh[mi][i]=ju;
2901: }
2902: if(dh[mi][i]==0){
2903: dh[mi][i]=1; /* At least one step */
2904: bh[mi][i]=ju; /* At least one step */
2905: /* 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);*/
2906: }
2907: } /* end if mle */
2908: }
2909: } /* end wave */
2910: }
2911: jmean=sum/k;
2912: 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);
2913: 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);
2914: }
2915:
2916: /*********** Tricode ****************************/
2917: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
2918: {
2919: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
2920: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
2921: * Boring subroutine which should only output nbcode[Tvar[j]][k]
2922: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
2923: * nbcode[Tvar[j]][1]=
2924: */
2925:
2926: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
2927: int modmaxcovj=0; /* Modality max of covariates j */
2928: int cptcode=0; /* Modality max of covariates j */
2929: int modmincovj=0; /* Modality min of covariates j */
2930:
2931:
2932: cptcoveff=0;
2933:
2934: for (k=-1; k < maxncov; k++) Ndum[k]=0;
2935: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
2936:
2937: /* Loop on covariates without age and products */
2938: for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
2939: for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the
2940: modality of this covariate Vj*/
2941: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
2942: * If product of Vn*Vm, still boolean *:
2943: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
2944: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
2945: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
2946: modality of the nth covariate of individual i. */
2947: if (ij > modmaxcovj)
2948: modmaxcovj=ij;
2949: else if (ij < modmincovj)
2950: modmincovj=ij;
2951: if ((ij < -1) && (ij > NCOVMAX)){
2952: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
2953: exit(1);
2954: }else
2955: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
2956: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
2957: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
2958: /* getting the maximum value of the modality of the covariate
2959: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
2960: female is 1, then modmaxcovj=1.*/
2961: }
2962: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
2963: cptcode=modmaxcovj;
2964: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
2965: /*for (i=0; i<=cptcode; i++) {*/
2966: for (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
2967: printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
2968: if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
2969: ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
2970: }
2971: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
2972: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
2973: } /* Ndum[-1] number of undefined modalities */
2974:
2975: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
2976: /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
2977: /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
2978: modmincovj=3; modmaxcovj = 7;
2979: There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
2980: which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy
2981: variables V1_1 and V1_2.
2982: nbcode[Tvar[j]][ij]=k;
2983: nbcode[Tvar[j]][1]=0;
2984: nbcode[Tvar[j]][2]=1;
2985: nbcode[Tvar[j]][3]=2;
2986: */
2987: ij=1; /* ij is similar to i but can jumps over null modalities */
2988: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
2989: for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
2990: /*recode from 0 */
2991: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
2992: nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode.
2993: k is a modality. If we have model=V1+V1*sex
2994: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
2995: ij++;
2996: }
2997: if (ij > ncodemax[j]) break;
2998: } /* end of loop on */
2999: } /* end of loop on modality */
3000: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
3001:
3002: for (k=-1; k< maxncov; k++) Ndum[k]=0;
3003:
3004: for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
3005: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
3006: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
3007: Ndum[ij]++;
3008: }
3009:
3010: ij=1;
3011: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
3012: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
3013: if((Ndum[i]!=0) && (i<=ncovcol)){
3014: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
3015: Tvaraff[ij]=i; /*For printing (unclear) */
3016: ij++;
3017: }else
3018: Tvaraff[ij]=0;
3019: }
3020: ij--;
3021: cptcoveff=ij; /*Number of total covariates*/
3022:
3023: }
3024:
3025:
3026: /*********** Health Expectancies ****************/
3027:
3028: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
3029:
3030: {
3031: /* Health expectancies, no variances */
3032: int i, j, nhstepm, hstepm, h, nstepm;
3033: int nhstepma, nstepma; /* Decreasing with age */
3034: double age, agelim, hf;
3035: double ***p3mat;
3036: double eip;
3037:
3038: pstamp(ficreseij);
3039: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3040: fprintf(ficreseij,"# Age");
3041: for(i=1; i<=nlstate;i++){
3042: for(j=1; j<=nlstate;j++){
3043: fprintf(ficreseij," e%1d%1d ",i,j);
3044: }
3045: fprintf(ficreseij," e%1d. ",i);
3046: }
3047: fprintf(ficreseij,"\n");
3048:
3049:
3050: if(estepm < stepm){
3051: printf ("Problem %d lower than %d\n",estepm, stepm);
3052: }
3053: else hstepm=estepm;
3054: /* We compute the life expectancy from trapezoids spaced every estepm months
3055: * This is mainly to measure the difference between two models: for example
3056: * if stepm=24 months pijx are given only every 2 years and by summing them
3057: * we are calculating an estimate of the Life Expectancy assuming a linear
3058: * progression in between and thus overestimating or underestimating according
3059: * to the curvature of the survival function. If, for the same date, we
3060: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3061: * to compare the new estimate of Life expectancy with the same linear
3062: * hypothesis. A more precise result, taking into account a more precise
3063: * curvature will be obtained if estepm is as small as stepm. */
3064:
3065: /* For example we decided to compute the life expectancy with the smallest unit */
3066: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3067: nhstepm is the number of hstepm from age to agelim
3068: nstepm is the number of stepm from age to agelin.
3069: Look at hpijx to understand the reason of that which relies in memory size
3070: and note for a fixed period like estepm months */
3071: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3072: survival function given by stepm (the optimization length). Unfortunately it
3073: means that if the survival funtion is printed only each two years of age and if
3074: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3075: results. So we changed our mind and took the option of the best precision.
3076: */
3077: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3078:
3079: agelim=AGESUP;
3080: /* If stepm=6 months */
3081: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3082: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3083:
3084: /* nhstepm age range expressed in number of stepm */
3085: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3086: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3087: /* if (stepm >= YEARM) hstepm=1;*/
3088: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3089: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3090:
3091: for (age=bage; age<=fage; age ++){
3092: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3093: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3094: /* if (stepm >= YEARM) hstepm=1;*/
3095: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3096:
3097: /* If stepm=6 months */
3098: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3099: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3100:
3101: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3102:
3103: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3104:
3105: printf("%d|",(int)age);fflush(stdout);
3106: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3107:
3108: /* Computing expectancies */
3109: for(i=1; i<=nlstate;i++)
3110: for(j=1; j<=nlstate;j++)
3111: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3112: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3113:
3114: /* 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]);*/
3115:
3116: }
3117:
3118: fprintf(ficreseij,"%3.0f",age );
3119: for(i=1; i<=nlstate;i++){
3120: eip=0;
3121: for(j=1; j<=nlstate;j++){
3122: eip +=eij[i][j][(int)age];
3123: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3124: }
3125: fprintf(ficreseij,"%9.4f", eip );
3126: }
3127: fprintf(ficreseij,"\n");
3128:
3129: }
3130: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3131: printf("\n");
3132: fprintf(ficlog,"\n");
3133:
3134: }
3135:
3136: 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[] )
3137:
3138: {
3139: /* Covariances of health expectancies eij and of total life expectancies according
3140: to initial status i, ei. .
3141: */
3142: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3143: int nhstepma, nstepma; /* Decreasing with age */
3144: double age, agelim, hf;
3145: double ***p3matp, ***p3matm, ***varhe;
3146: double **dnewm,**doldm;
3147: double *xp, *xm;
3148: double **gp, **gm;
3149: double ***gradg, ***trgradg;
3150: int theta;
3151:
3152: double eip, vip;
3153:
3154: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
3155: xp=vector(1,npar);
3156: xm=vector(1,npar);
3157: dnewm=matrix(1,nlstate*nlstate,1,npar);
3158: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3159:
3160: pstamp(ficresstdeij);
3161: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3162: fprintf(ficresstdeij,"# Age");
3163: for(i=1; i<=nlstate;i++){
3164: for(j=1; j<=nlstate;j++)
3165: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3166: fprintf(ficresstdeij," e%1d. ",i);
3167: }
3168: fprintf(ficresstdeij,"\n");
3169:
3170: pstamp(ficrescveij);
3171: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3172: fprintf(ficrescveij,"# Age");
3173: for(i=1; i<=nlstate;i++)
3174: for(j=1; j<=nlstate;j++){
3175: cptj= (j-1)*nlstate+i;
3176: for(i2=1; i2<=nlstate;i2++)
3177: for(j2=1; j2<=nlstate;j2++){
3178: cptj2= (j2-1)*nlstate+i2;
3179: if(cptj2 <= cptj)
3180: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3181: }
3182: }
3183: fprintf(ficrescveij,"\n");
3184:
3185: if(estepm < stepm){
3186: printf ("Problem %d lower than %d\n",estepm, stepm);
3187: }
3188: else hstepm=estepm;
3189: /* We compute the life expectancy from trapezoids spaced every estepm months
3190: * This is mainly to measure the difference between two models: for example
3191: * if stepm=24 months pijx are given only every 2 years and by summing them
3192: * we are calculating an estimate of the Life Expectancy assuming a linear
3193: * progression in between and thus overestimating or underestimating according
3194: * to the curvature of the survival function. If, for the same date, we
3195: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3196: * to compare the new estimate of Life expectancy with the same linear
3197: * hypothesis. A more precise result, taking into account a more precise
3198: * curvature will be obtained if estepm is as small as stepm. */
3199:
3200: /* For example we decided to compute the life expectancy with the smallest unit */
3201: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3202: nhstepm is the number of hstepm from age to agelim
3203: nstepm is the number of stepm from age to agelin.
3204: Look at hpijx to understand the reason of that which relies in memory size
3205: and note for a fixed period like estepm months */
3206: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3207: survival function given by stepm (the optimization length). Unfortunately it
3208: means that if the survival funtion is printed only each two years of age and if
3209: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3210: results. So we changed our mind and took the option of the best precision.
3211: */
3212: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3213:
3214: /* If stepm=6 months */
3215: /* nhstepm age range expressed in number of stepm */
3216: agelim=AGESUP;
3217: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3218: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3219: /* if (stepm >= YEARM) hstepm=1;*/
3220: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3221:
3222: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3223: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3224: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3225: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3226: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3227: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3228:
3229: for (age=bage; age<=fage; age ++){
3230: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3231: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3232: /* if (stepm >= YEARM) hstepm=1;*/
3233: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3234:
3235: /* If stepm=6 months */
3236: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3237: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3238:
3239: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3240:
3241: /* Computing Variances of health expectancies */
3242: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3243: decrease memory allocation */
3244: for(theta=1; theta <=npar; theta++){
3245: for(i=1; i<=npar; i++){
3246: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3247: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3248: }
3249: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3250: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3251:
3252: for(j=1; j<= nlstate; j++){
3253: for(i=1; i<=nlstate; i++){
3254: for(h=0; h<=nhstepm-1; h++){
3255: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3256: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3257: }
3258: }
3259: }
3260:
3261: for(ij=1; ij<= nlstate*nlstate; ij++)
3262: for(h=0; h<=nhstepm-1; h++){
3263: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3264: }
3265: }/* End theta */
3266:
3267:
3268: for(h=0; h<=nhstepm-1; h++)
3269: for(j=1; j<=nlstate*nlstate;j++)
3270: for(theta=1; theta <=npar; theta++)
3271: trgradg[h][j][theta]=gradg[h][theta][j];
3272:
3273:
3274: for(ij=1;ij<=nlstate*nlstate;ij++)
3275: for(ji=1;ji<=nlstate*nlstate;ji++)
3276: varhe[ij][ji][(int)age] =0.;
3277:
3278: printf("%d|",(int)age);fflush(stdout);
3279: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3280: for(h=0;h<=nhstepm-1;h++){
3281: for(k=0;k<=nhstepm-1;k++){
3282: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3283: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3284: for(ij=1;ij<=nlstate*nlstate;ij++)
3285: for(ji=1;ji<=nlstate*nlstate;ji++)
3286: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3287: }
3288: }
3289:
3290: /* Computing expectancies */
3291: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3292: for(i=1; i<=nlstate;i++)
3293: for(j=1; j<=nlstate;j++)
3294: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3295: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3296:
3297: /* 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]);*/
3298:
3299: }
3300:
3301: fprintf(ficresstdeij,"%3.0f",age );
3302: for(i=1; i<=nlstate;i++){
3303: eip=0.;
3304: vip=0.;
3305: for(j=1; j<=nlstate;j++){
3306: eip += eij[i][j][(int)age];
3307: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3308: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3309: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3310: }
3311: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3312: }
3313: fprintf(ficresstdeij,"\n");
3314:
3315: fprintf(ficrescveij,"%3.0f",age );
3316: for(i=1; i<=nlstate;i++)
3317: for(j=1; j<=nlstate;j++){
3318: cptj= (j-1)*nlstate+i;
3319: for(i2=1; i2<=nlstate;i2++)
3320: for(j2=1; j2<=nlstate;j2++){
3321: cptj2= (j2-1)*nlstate+i2;
3322: if(cptj2 <= cptj)
3323: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3324: }
3325: }
3326: fprintf(ficrescveij,"\n");
3327:
3328: }
3329: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3330: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3331: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3332: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3333: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3334: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3335: printf("\n");
3336: fprintf(ficlog,"\n");
3337:
3338: free_vector(xm,1,npar);
3339: free_vector(xp,1,npar);
3340: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3341: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3342: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3343: }
3344:
3345: /************ Variance ******************/
3346: 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[])
3347: {
3348: /* Variance of health expectancies */
3349: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3350: /* double **newm;*/
3351: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
3352:
3353: int movingaverage();
3354: double **dnewm,**doldm;
3355: double **dnewmp,**doldmp;
3356: int i, j, nhstepm, hstepm, h, nstepm ;
3357: int k;
3358: double *xp;
3359: double **gp, **gm; /* for var eij */
3360: double ***gradg, ***trgradg; /*for var eij */
3361: double **gradgp, **trgradgp; /* for var p point j */
3362: double *gpp, *gmp; /* for var p point j */
3363: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3364: double ***p3mat;
3365: double age,agelim, hf;
3366: double ***mobaverage;
3367: int theta;
3368: char digit[4];
3369: char digitp[25];
3370:
3371: char fileresprobmorprev[FILENAMELENGTH];
3372:
3373: if(popbased==1){
3374: if(mobilav!=0)
3375: strcpy(digitp,"-populbased-mobilav-");
3376: else strcpy(digitp,"-populbased-nomobil-");
3377: }
3378: else
3379: strcpy(digitp,"-stablbased-");
3380:
3381: if (mobilav!=0) {
3382: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3383: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3384: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3385: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3386: }
3387: }
3388:
3389: strcpy(fileresprobmorprev,"prmorprev");
3390: sprintf(digit,"%-d",ij);
3391: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3392: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3393: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
3394: strcat(fileresprobmorprev,fileres);
3395: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3396: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3397: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3398: }
3399: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3400:
3401: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3402: pstamp(ficresprobmorprev);
3403: 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);
3404: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3405: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3406: fprintf(ficresprobmorprev," p.%-d SE",j);
3407: for(i=1; i<=nlstate;i++)
3408: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3409: }
3410: fprintf(ficresprobmorprev,"\n");
3411: fprintf(ficgp,"\n# Routine varevsij");
3412: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
3413: 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");
3414: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3415: /* } */
3416: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3417: pstamp(ficresvij);
3418: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3419: if(popbased==1)
3420: 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);
3421: else
3422: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3423: fprintf(ficresvij,"# Age");
3424: for(i=1; i<=nlstate;i++)
3425: for(j=1; j<=nlstate;j++)
3426: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3427: fprintf(ficresvij,"\n");
3428:
3429: xp=vector(1,npar);
3430: dnewm=matrix(1,nlstate,1,npar);
3431: doldm=matrix(1,nlstate,1,nlstate);
3432: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3433: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3434:
3435: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3436: gpp=vector(nlstate+1,nlstate+ndeath);
3437: gmp=vector(nlstate+1,nlstate+ndeath);
3438: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3439:
3440: if(estepm < stepm){
3441: printf ("Problem %d lower than %d\n",estepm, stepm);
3442: }
3443: else hstepm=estepm;
3444: /* For example we decided to compute the life expectancy with the smallest unit */
3445: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3446: nhstepm is the number of hstepm from age to agelim
3447: nstepm is the number of stepm from age to agelin.
3448: Look at function hpijx to understand why (it is linked to memory size questions) */
3449: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3450: survival function given by stepm (the optimization length). Unfortunately it
3451: means that if the survival funtion is printed every two years of age and if
3452: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3453: results. So we changed our mind and took the option of the best precision.
3454: */
3455: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3456: agelim = AGESUP;
3457: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3458: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3459: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3460: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3461: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3462: gp=matrix(0,nhstepm,1,nlstate);
3463: gm=matrix(0,nhstepm,1,nlstate);
3464:
3465:
3466: for(theta=1; theta <=npar; theta++){
3467: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3468: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3469: }
3470: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3471: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3472:
3473: if (popbased==1) {
3474: if(mobilav ==0){
3475: for(i=1; i<=nlstate;i++)
3476: prlim[i][i]=probs[(int)age][i][ij];
3477: }else{ /* mobilav */
3478: for(i=1; i<=nlstate;i++)
3479: prlim[i][i]=mobaverage[(int)age][i][ij];
3480: }
3481: }
3482:
3483: for(j=1; j<= nlstate; j++){
3484: for(h=0; h<=nhstepm; h++){
3485: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3486: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3487: }
3488: }
3489: /* This for computing probability of death (h=1 means
3490: computed over hstepm matrices product = hstepm*stepm months)
3491: as a weighted average of prlim.
3492: */
3493: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3494: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3495: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3496: }
3497: /* end probability of death */
3498:
3499: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3500: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3501: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3502: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3503:
3504: if (popbased==1) {
3505: if(mobilav ==0){
3506: for(i=1; i<=nlstate;i++)
3507: prlim[i][i]=probs[(int)age][i][ij];
3508: }else{ /* mobilav */
3509: for(i=1; i<=nlstate;i++)
3510: prlim[i][i]=mobaverage[(int)age][i][ij];
3511: }
3512: }
3513:
3514: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
3515: for(h=0; h<=nhstepm; h++){
3516: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3517: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3518: }
3519: }
3520: /* This for computing probability of death (h=1 means
3521: computed over hstepm matrices product = hstepm*stepm months)
3522: as a weighted average of prlim.
3523: */
3524: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3525: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3526: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3527: }
3528: /* end probability of death */
3529:
3530: for(j=1; j<= nlstate; j++) /* vareij */
3531: for(h=0; h<=nhstepm; h++){
3532: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3533: }
3534:
3535: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3536: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3537: }
3538:
3539: } /* End theta */
3540:
3541: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3542:
3543: for(h=0; h<=nhstepm; h++) /* veij */
3544: for(j=1; j<=nlstate;j++)
3545: for(theta=1; theta <=npar; theta++)
3546: trgradg[h][j][theta]=gradg[h][theta][j];
3547:
3548: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3549: for(theta=1; theta <=npar; theta++)
3550: trgradgp[j][theta]=gradgp[theta][j];
3551:
3552:
3553: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3554: for(i=1;i<=nlstate;i++)
3555: for(j=1;j<=nlstate;j++)
3556: vareij[i][j][(int)age] =0.;
3557:
3558: for(h=0;h<=nhstepm;h++){
3559: for(k=0;k<=nhstepm;k++){
3560: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3561: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3562: for(i=1;i<=nlstate;i++)
3563: for(j=1;j<=nlstate;j++)
3564: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3565: }
3566: }
3567:
3568: /* pptj */
3569: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3570: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3571: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3572: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3573: varppt[j][i]=doldmp[j][i];
3574: /* end ppptj */
3575: /* x centered again */
3576: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3577: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3578:
3579: if (popbased==1) {
3580: if(mobilav ==0){
3581: for(i=1; i<=nlstate;i++)
3582: prlim[i][i]=probs[(int)age][i][ij];
3583: }else{ /* mobilav */
3584: for(i=1; i<=nlstate;i++)
3585: prlim[i][i]=mobaverage[(int)age][i][ij];
3586: }
3587: }
3588:
3589: /* This for computing probability of death (h=1 means
3590: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3591: as a weighted average of prlim.
3592: */
3593: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3594: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3595: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3596: }
3597: /* end probability of death */
3598:
3599: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3600: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3601: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3602: for(i=1; i<=nlstate;i++){
3603: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3604: }
3605: }
3606: fprintf(ficresprobmorprev,"\n");
3607:
3608: fprintf(ficresvij,"%.0f ",age );
3609: for(i=1; i<=nlstate;i++)
3610: for(j=1; j<=nlstate;j++){
3611: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3612: }
3613: fprintf(ficresvij,"\n");
3614: free_matrix(gp,0,nhstepm,1,nlstate);
3615: free_matrix(gm,0,nhstepm,1,nlstate);
3616: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3617: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3618: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3619: } /* End age */
3620: free_vector(gpp,nlstate+1,nlstate+ndeath);
3621: free_vector(gmp,nlstate+1,nlstate+ndeath);
3622: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3623: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3624: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
3625: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
3626: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
3627: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3628: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3629: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
3630: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
3631: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
3632: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
3633: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3634: 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);
3635: /* 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);
3636: */
3637: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3638: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3639:
3640: free_vector(xp,1,npar);
3641: free_matrix(doldm,1,nlstate,1,nlstate);
3642: free_matrix(dnewm,1,nlstate,1,npar);
3643: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3644: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3645: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3646: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3647: fclose(ficresprobmorprev);
3648: fflush(ficgp);
3649: fflush(fichtm);
3650: } /* end varevsij */
3651:
3652: /************ Variance of prevlim ******************/
3653: 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[])
3654: {
3655: /* Variance of prevalence limit */
3656: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
3657:
3658: double **dnewm,**doldm;
3659: int i, j, nhstepm, hstepm;
3660: double *xp;
3661: double *gp, *gm;
3662: double **gradg, **trgradg;
3663: double age,agelim;
3664: int theta;
3665:
3666: pstamp(ficresvpl);
3667: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3668: fprintf(ficresvpl,"# Age");
3669: for(i=1; i<=nlstate;i++)
3670: fprintf(ficresvpl," %1d-%1d",i,i);
3671: fprintf(ficresvpl,"\n");
3672:
3673: xp=vector(1,npar);
3674: dnewm=matrix(1,nlstate,1,npar);
3675: doldm=matrix(1,nlstate,1,nlstate);
3676:
3677: hstepm=1*YEARM; /* Every year of age */
3678: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3679: agelim = AGESUP;
3680: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3681: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3682: if (stepm >= YEARM) hstepm=1;
3683: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3684: gradg=matrix(1,npar,1,nlstate);
3685: gp=vector(1,nlstate);
3686: gm=vector(1,nlstate);
3687:
3688: for(theta=1; theta <=npar; theta++){
3689: for(i=1; i<=npar; i++){ /* Computes gradient */
3690: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3691: }
3692: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3693: for(i=1;i<=nlstate;i++)
3694: gp[i] = prlim[i][i];
3695:
3696: for(i=1; i<=npar; i++) /* Computes gradient */
3697: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3698: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3699: for(i=1;i<=nlstate;i++)
3700: gm[i] = prlim[i][i];
3701:
3702: for(i=1;i<=nlstate;i++)
3703: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3704: } /* End theta */
3705:
3706: trgradg =matrix(1,nlstate,1,npar);
3707:
3708: for(j=1; j<=nlstate;j++)
3709: for(theta=1; theta <=npar; theta++)
3710: trgradg[j][theta]=gradg[theta][j];
3711:
3712: for(i=1;i<=nlstate;i++)
3713: varpl[i][(int)age] =0.;
3714: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3715: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3716: for(i=1;i<=nlstate;i++)
3717: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3718:
3719: fprintf(ficresvpl,"%.0f ",age );
3720: for(i=1; i<=nlstate;i++)
3721: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3722: fprintf(ficresvpl,"\n");
3723: free_vector(gp,1,nlstate);
3724: free_vector(gm,1,nlstate);
3725: free_matrix(gradg,1,npar,1,nlstate);
3726: free_matrix(trgradg,1,nlstate,1,npar);
3727: } /* End age */
3728:
3729: free_vector(xp,1,npar);
3730: free_matrix(doldm,1,nlstate,1,npar);
3731: free_matrix(dnewm,1,nlstate,1,nlstate);
3732:
3733: }
3734:
3735: /************ Variance of one-step probabilities ******************/
3736: 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[])
3737: {
3738: int i, j=0, k1, l1, tj;
3739: int k2, l2, j1, z1;
3740: int k=0, l;
3741: int first=1, first1, first2;
3742: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3743: double **dnewm,**doldm;
3744: double *xp;
3745: double *gp, *gm;
3746: double **gradg, **trgradg;
3747: double **mu;
3748: double age, cov[NCOVMAX+1];
3749: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3750: int theta;
3751: char fileresprob[FILENAMELENGTH];
3752: char fileresprobcov[FILENAMELENGTH];
3753: char fileresprobcor[FILENAMELENGTH];
3754: double ***varpij;
3755:
3756: strcpy(fileresprob,"prob");
3757: strcat(fileresprob,fileres);
3758: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3759: printf("Problem with resultfile: %s\n", fileresprob);
3760: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3761: }
3762: strcpy(fileresprobcov,"probcov");
3763: strcat(fileresprobcov,fileres);
3764: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3765: printf("Problem with resultfile: %s\n", fileresprobcov);
3766: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3767: }
3768: strcpy(fileresprobcor,"probcor");
3769: strcat(fileresprobcor,fileres);
3770: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3771: printf("Problem with resultfile: %s\n", fileresprobcor);
3772: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3773: }
3774: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3775: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3776: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3777: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3778: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3779: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3780: pstamp(ficresprob);
3781: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3782: fprintf(ficresprob,"# Age");
3783: pstamp(ficresprobcov);
3784: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3785: fprintf(ficresprobcov,"# Age");
3786: pstamp(ficresprobcor);
3787: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3788: fprintf(ficresprobcor,"# Age");
3789:
3790:
3791: for(i=1; i<=nlstate;i++)
3792: for(j=1; j<=(nlstate+ndeath);j++){
3793: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3794: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3795: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3796: }
3797: /* fprintf(ficresprob,"\n");
3798: fprintf(ficresprobcov,"\n");
3799: fprintf(ficresprobcor,"\n");
3800: */
3801: xp=vector(1,npar);
3802: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3803: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3804: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3805: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3806: first=1;
3807: fprintf(ficgp,"\n# Routine varprob");
3808: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3809: fprintf(fichtm,"\n");
3810:
3811: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3812: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3813: file %s<br>\n",optionfilehtmcov);
3814: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3815: and drawn. It helps understanding how is the covariance between two incidences.\
3816: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3817: 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. \
3818: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3819: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3820: standard deviations wide on each axis. <br>\
3821: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3822: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3823: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3824:
3825: cov[1]=1;
3826: /* tj=cptcoveff; */
3827: tj = (int) pow(2,cptcoveff);
3828: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3829: j1=0;
3830: for(j1=1; j1<=tj;j1++){
3831: /*for(i1=1; i1<=ncodemax[t];i1++){ */
3832: /*j1++;*/
3833: if (cptcovn>0) {
3834: fprintf(ficresprob, "\n#********** Variable ");
3835: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3836: fprintf(ficresprob, "**********\n#\n");
3837: fprintf(ficresprobcov, "\n#********** Variable ");
3838: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3839: fprintf(ficresprobcov, "**********\n#\n");
3840:
3841: fprintf(ficgp, "\n#********** Variable ");
3842: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3843: fprintf(ficgp, "**********\n#\n");
3844:
3845:
3846: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
3847: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3848: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
3849:
3850: fprintf(ficresprobcor, "\n#********** Variable ");
3851: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3852: fprintf(ficresprobcor, "**********\n#");
3853: }
3854:
3855: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3856: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3857: gp=vector(1,(nlstate)*(nlstate+ndeath));
3858: gm=vector(1,(nlstate)*(nlstate+ndeath));
3859: for (age=bage; age<=fage; age ++){
3860: cov[2]=age;
3861: for (k=1; k<=cptcovn;k++) {
3862: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
3863: * 1 1 1 1 1
3864: * 2 2 1 1 1
3865: * 3 1 2 1 1
3866: */
3867: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
3868: }
3869: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3870: for (k=1; k<=cptcovprod;k++)
3871: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3872:
3873:
3874: for(theta=1; theta <=npar; theta++){
3875: for(i=1; i<=npar; i++)
3876: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3877:
3878: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3879:
3880: k=0;
3881: for(i=1; i<= (nlstate); i++){
3882: for(j=1; j<=(nlstate+ndeath);j++){
3883: k=k+1;
3884: gp[k]=pmmij[i][j];
3885: }
3886: }
3887:
3888: for(i=1; i<=npar; i++)
3889: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
3890:
3891: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3892: k=0;
3893: for(i=1; i<=(nlstate); i++){
3894: for(j=1; j<=(nlstate+ndeath);j++){
3895: k=k+1;
3896: gm[k]=pmmij[i][j];
3897: }
3898: }
3899:
3900: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3901: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3902: }
3903:
3904: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3905: for(theta=1; theta <=npar; theta++)
3906: trgradg[j][theta]=gradg[theta][j];
3907:
3908: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3909: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3910:
3911: pmij(pmmij,cov,ncovmodel,x,nlstate);
3912:
3913: k=0;
3914: for(i=1; i<=(nlstate); i++){
3915: for(j=1; j<=(nlstate+ndeath);j++){
3916: k=k+1;
3917: mu[k][(int) age]=pmmij[i][j];
3918: }
3919: }
3920: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3921: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3922: varpij[i][j][(int)age] = doldm[i][j];
3923:
3924: /*printf("\n%d ",(int)age);
3925: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3926: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3927: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3928: }*/
3929:
3930: fprintf(ficresprob,"\n%d ",(int)age);
3931: fprintf(ficresprobcov,"\n%d ",(int)age);
3932: fprintf(ficresprobcor,"\n%d ",(int)age);
3933:
3934: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3935: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3936: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3937: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3938: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3939: }
3940: i=0;
3941: for (k=1; k<=(nlstate);k++){
3942: for (l=1; l<=(nlstate+ndeath);l++){
3943: i++;
3944: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3945: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3946: for (j=1; j<=i;j++){
3947: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
3948: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3949: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3950: }
3951: }
3952: }/* end of loop for state */
3953: } /* end of loop for age */
3954: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3955: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3956: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3957: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3958:
3959: /* Confidence intervalle of pij */
3960: /*
3961: fprintf(ficgp,"\nunset parametric;unset label");
3962: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3963: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3964: 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);
3965: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3966: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3967: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3968: */
3969:
3970: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3971: first1=1;first2=2;
3972: for (k2=1; k2<=(nlstate);k2++){
3973: for (l2=1; l2<=(nlstate+ndeath);l2++){
3974: if(l2==k2) continue;
3975: j=(k2-1)*(nlstate+ndeath)+l2;
3976: for (k1=1; k1<=(nlstate);k1++){
3977: for (l1=1; l1<=(nlstate+ndeath);l1++){
3978: if(l1==k1) continue;
3979: i=(k1-1)*(nlstate+ndeath)+l1;
3980: if(i<=j) continue;
3981: for (age=bage; age<=fage; age ++){
3982: if ((int)age %5==0){
3983: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3984: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3985: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3986: mu1=mu[i][(int) age]/stepm*YEARM ;
3987: mu2=mu[j][(int) age]/stepm*YEARM;
3988: c12=cv12/sqrt(v1*v2);
3989: /* Computing eigen value of matrix of covariance */
3990: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3991: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3992: if ((lc2 <0) || (lc1 <0) ){
3993: if(first2==1){
3994: first1=0;
3995: 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);
3996: }
3997: 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);
3998: /* lc1=fabs(lc1); */ /* If we want to have them positive */
3999: /* lc2=fabs(lc2); */
4000: }
4001:
4002: /* Eigen vectors */
4003: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
4004: /*v21=sqrt(1.-v11*v11); *//* error */
4005: v21=(lc1-v1)/cv12*v11;
4006: v12=-v21;
4007: v22=v11;
4008: tnalp=v21/v11;
4009: if(first1==1){
4010: first1=0;
4011: 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);
4012: }
4013: 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);
4014: /*printf(fignu*/
4015: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
4016: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
4017: if(first==1){
4018: first=0;
4019: fprintf(ficgp,"\nset parametric;unset label");
4020: 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);
4021: fprintf(ficgp,"\nset ter png small size 320, 240");
4022: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
4023: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
4024: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
4025: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
4026: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4027: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4028: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
4029: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4030: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4031: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4032: 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",\
4033: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4034: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4035: }else{
4036: first=0;
4037: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4038: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4039: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4040: 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",\
4041: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4042: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4043: }/* if first */
4044: } /* age mod 5 */
4045: } /* end loop age */
4046: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4047: first=1;
4048: } /*l12 */
4049: } /* k12 */
4050: } /*l1 */
4051: }/* k1 */
4052: /* } */ /* loop covariates */
4053: }
4054: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4055: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4056: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4057: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4058: free_vector(xp,1,npar);
4059: fclose(ficresprob);
4060: fclose(ficresprobcov);
4061: fclose(ficresprobcor);
4062: fflush(ficgp);
4063: fflush(fichtmcov);
4064: }
4065:
4066:
4067: /******************* Printing html file ***********/
4068: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
4069: int lastpass, int stepm, int weightopt, char model[],\
4070: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
4071: int popforecast, int estepm ,\
4072: double jprev1, double mprev1,double anprev1, \
4073: double jprev2, double mprev2,double anprev2){
4074: int jj1, k1, i1, cpt;
4075:
4076: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4077: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4078: </ul>");
4079: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
4080: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
4081: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
4082: fprintf(fichtm,"\
4083: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
4084: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
4085: fprintf(fichtm,"\
4086: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
4087: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
4088: fprintf(fichtm,"\
4089: - (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): \
4090: <a href=\"%s\">%s</a> <br>\n",
4091: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
4092: fprintf(fichtm,"\
4093: - Population projections by age and states: \
4094: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
4095:
4096: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4097:
4098: m=pow(2,cptcoveff);
4099: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4100:
4101: jj1=0;
4102: for(k1=1; k1<=m;k1++){
4103: for(i1=1; i1<=ncodemax[k1];i1++){
4104: jj1++;
4105: if (cptcovn > 0) {
4106: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4107: for (cpt=1; cpt<=cptcoveff;cpt++)
4108: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4109: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4110: }
4111: /* Pij */
4112: 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> \
4113: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
4114: /* Quasi-incidences */
4115: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
4116: 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> \
4117: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
4118: /* Period (stable) prevalence in each health state */
4119: for(cpt=1; cpt<=nlstate;cpt++){
4120: 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> \
4121: <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
4122: }
4123: for(cpt=1; cpt<=nlstate;cpt++) {
4124: 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> \
4125: <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
4126: }
4127: } /* end i1 */
4128: }/* End k1 */
4129: fprintf(fichtm,"</ul>");
4130:
4131:
4132: fprintf(fichtm,"\
4133: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
4134: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
4135:
4136: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4137: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
4138: fprintf(fichtm,"\
4139: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4140: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
4141:
4142: fprintf(fichtm,"\
4143: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4144: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
4145: fprintf(fichtm,"\
4146: - 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): \
4147: <a href=\"%s\">%s</a> <br>\n</li>",
4148: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
4149: fprintf(fichtm,"\
4150: - (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): \
4151: <a href=\"%s\">%s</a> <br>\n</li>",
4152: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
4153: fprintf(fichtm,"\
4154: - 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",
4155: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
4156: fprintf(fichtm,"\
4157: - 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",
4158: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
4159: fprintf(fichtm,"\
4160: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
4161: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
4162:
4163: /* if(popforecast==1) fprintf(fichtm,"\n */
4164: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4165: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4166: /* <br>",fileres,fileres,fileres,fileres); */
4167: /* else */
4168: /* 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); */
4169: fflush(fichtm);
4170: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4171:
4172: m=pow(2,cptcoveff);
4173: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4174:
4175: jj1=0;
4176: for(k1=1; k1<=m;k1++){
4177: for(i1=1; i1<=ncodemax[k1];i1++){
4178: jj1++;
4179: if (cptcovn > 0) {
4180: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4181: for (cpt=1; cpt<=cptcoveff;cpt++)
4182: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4183: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4184: }
4185: for(cpt=1; cpt<=nlstate;cpt++) {
4186: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
4187: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
4188: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
4189: }
4190: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
4191: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4192: true period expectancies (those weighted with period prevalences are also\
4193: drawn in addition to the population based expectancies computed using\
4194: observed and cahotic prevalences: %s%d.png<br>\
4195: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
4196: } /* end i1 */
4197: }/* End k1 */
4198: fprintf(fichtm,"</ul>");
4199: fflush(fichtm);
4200: }
4201:
4202: /******************* Gnuplot file **************/
4203: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4204:
4205: char dirfileres[132],optfileres[132];
4206: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
4207: int ng=0;
4208: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4209: /* printf("Problem with file %s",optionfilegnuplot); */
4210: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4211: /* } */
4212:
4213: /*#ifdef windows */
4214: fprintf(ficgp,"cd \"%s\" \n",pathc);
4215: /*#endif */
4216: m=pow(2,cptcoveff);
4217:
4218: strcpy(dirfileres,optionfilefiname);
4219: strcpy(optfileres,"vpl");
4220: /* 1eme*/
4221: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
4222: for (cpt=1; cpt<= nlstate ; cpt ++) {
4223: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
4224: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
4225: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
4226: fprintf(ficgp,"set xlabel \"Age\" \n\
4227: set ylabel \"Probability\" \n\
4228: set ter png small size 320, 240\n\
4229: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
4230:
4231: for (i=1; i<= nlstate ; i ++) {
4232: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
4233: else fprintf(ficgp," \%%*lf (\%%*lf)");
4234: }
4235: 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);
4236: for (i=1; i<= nlstate ; i ++) {
4237: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
4238: else fprintf(ficgp," \%%*lf (\%%*lf)");
4239: }
4240: fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
4241: for (i=1; i<= nlstate ; i ++) {
4242: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
4243: else fprintf(ficgp," \%%*lf (\%%*lf)");
4244: }
4245: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
4246: }
4247: }
4248: /*2 eme*/
4249: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
4250: for (k1=1; k1<= m ; k1 ++) {
4251: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
4252: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
4253:
4254: for (i=1; i<= nlstate+1 ; i ++) {
4255: k=2*i;
4256: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4257: for (j=1; j<= nlstate+1 ; j ++) {
4258: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
4259: else fprintf(ficgp," \%%*lf (\%%*lf)");
4260: }
4261: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
4262: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
4263: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4264: for (j=1; j<= nlstate+1 ; j ++) {
4265: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
4266: else fprintf(ficgp," \%%*lf (\%%*lf)");
4267: }
4268: fprintf(ficgp,"\" t\"\" w l lt 0,");
4269: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4270: for (j=1; j<= nlstate+1 ; j ++) {
4271: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
4272: else fprintf(ficgp," \%%*lf (\%%*lf)");
4273: }
4274: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4275: else fprintf(ficgp,"\" t\"\" w l lt 0,");
4276: }
4277: }
4278:
4279: /*3eme*/
4280:
4281: for (k1=1; k1<= m ; k1 ++) {
4282: for (cpt=1; cpt<= nlstate ; cpt ++) {
4283: /* k=2+nlstate*(2*cpt-2); */
4284: k=2+(nlstate+1)*(cpt-1);
4285: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
4286: fprintf(ficgp,"set ter png small size 320, 240\n\
4287: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
4288: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4289: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4290: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4291: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4292: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4293: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4294:
4295: */
4296: for (i=1; i< nlstate ; i ++) {
4297: 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);
4298: /* 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);*/
4299:
4300: }
4301: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
4302: }
4303: }
4304:
4305: /* CV preval stable (period) */
4306: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
4307: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
4308: k=3;
4309: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
4310: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
4311: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
4312: set ter png small size 320, 240\n\
4313: unset log y\n\
4314: plot [%.f:%.f] ", ageminpar, agemaxpar);
4315: for (i=1; i<= nlstate ; i ++){
4316: if(i==1)
4317: fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
4318: else
4319: fprintf(ficgp,", '' ");
4320: l=(nlstate+ndeath)*(i-1)+1;
4321: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
4322: for (j=1; j<= (nlstate-1) ; j ++)
4323: fprintf(ficgp,"+$%d",k+l+j);
4324: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
4325: } /* nlstate */
4326: fprintf(ficgp,"\n");
4327: } /* end cpt state*/
4328: } /* end covariate */
4329:
4330: /* proba elementaires */
4331: for(i=1,jk=1; i <=nlstate; i++){
4332: for(k=1; k <=(nlstate+ndeath); k++){
4333: if (k != i) {
4334: for(j=1; j <=ncovmodel; j++){
4335: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
4336: jk++;
4337: fprintf(ficgp,"\n");
4338: }
4339: }
4340: }
4341: }
4342: /*goto avoid;*/
4343: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
4344: for(jk=1; jk <=m; jk++) {
4345: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
4346: if (ng==2)
4347: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
4348: else
4349: fprintf(ficgp,"\nset title \"Probability\"\n");
4350: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
4351: i=1;
4352: for(k2=1; k2<=nlstate; k2++) {
4353: k3=i;
4354: for(k=1; k<=(nlstate+ndeath); k++) {
4355: if (k != k2){
4356: if(ng==2)
4357: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
4358: else
4359: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
4360: ij=1;/* To be checked else nbcode[0][0] wrong */
4361: for(j=3; j <=ncovmodel; j++) {
4362: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
4363: /* /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
4364: /* ij++; */
4365: /* } */
4366: /* else */
4367: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4368: }
4369: fprintf(ficgp,")/(1");
4370:
4371: for(k1=1; k1 <=nlstate; k1++){
4372: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
4373: ij=1;
4374: for(j=3; j <=ncovmodel; j++){
4375: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
4376: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
4377: /* ij++; */
4378: /* } */
4379: /* else */
4380: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4381: }
4382: fprintf(ficgp,")");
4383: }
4384: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
4385: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
4386: i=i+ncovmodel;
4387: }
4388: } /* end k */
4389: } /* end k2 */
4390: } /* end jk */
4391: } /* end ng */
4392: /* avoid: */
4393: fflush(ficgp);
4394: } /* end gnuplot */
4395:
4396:
4397: /*************** Moving average **************/
4398: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
4399:
4400: int i, cpt, cptcod;
4401: int modcovmax =1;
4402: int mobilavrange, mob;
4403: double age;
4404:
4405: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
4406: a covariate has 2 modalities */
4407: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
4408:
4409: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
4410: if(mobilav==1) mobilavrange=5; /* default */
4411: else mobilavrange=mobilav;
4412: for (age=bage; age<=fage; age++)
4413: for (i=1; i<=nlstate;i++)
4414: for (cptcod=1;cptcod<=modcovmax;cptcod++)
4415: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
4416: /* We keep the original values on the extreme ages bage, fage and for
4417: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
4418: we use a 5 terms etc. until the borders are no more concerned.
4419: */
4420: for (mob=3;mob <=mobilavrange;mob=mob+2){
4421: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
4422: for (i=1; i<=nlstate;i++){
4423: for (cptcod=1;cptcod<=modcovmax;cptcod++){
4424: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
4425: for (cpt=1;cpt<=(mob-1)/2;cpt++){
4426: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
4427: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
4428: }
4429: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
4430: }
4431: }
4432: }/* end age */
4433: }/* end mob */
4434: }else return -1;
4435: return 0;
4436: }/* End movingaverage */
4437:
4438:
4439: /************** Forecasting ******************/
4440: void 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){
4441: /* proj1, year, month, day of starting projection
4442: agemin, agemax range of age
4443: dateprev1 dateprev2 range of dates during which prevalence is computed
4444: anproj2 year of en of projection (same day and month as proj1).
4445: */
4446: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
4447: double agec; /* generic age */
4448: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
4449: double *popeffectif,*popcount;
4450: double ***p3mat;
4451: double ***mobaverage;
4452: char fileresf[FILENAMELENGTH];
4453:
4454: agelim=AGESUP;
4455: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4456:
4457: strcpy(fileresf,"f");
4458: strcat(fileresf,fileres);
4459: if((ficresf=fopen(fileresf,"w"))==NULL) {
4460: printf("Problem with forecast resultfile: %s\n", fileresf);
4461: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
4462: }
4463: printf("Computing forecasting: result on file '%s' \n", fileresf);
4464: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
4465:
4466: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4467:
4468: if (mobilav!=0) {
4469: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4470: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4471: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4472: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4473: }
4474: }
4475:
4476: stepsize=(int) (stepm+YEARM-1)/YEARM;
4477: if (stepm<=12) stepsize=1;
4478: if(estepm < stepm){
4479: printf ("Problem %d lower than %d\n",estepm, stepm);
4480: }
4481: else hstepm=estepm;
4482:
4483: hstepm=hstepm/stepm;
4484: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
4485: fractional in yp1 */
4486: anprojmean=yp;
4487: yp2=modf((yp1*12),&yp);
4488: mprojmean=yp;
4489: yp1=modf((yp2*30.5),&yp);
4490: jprojmean=yp;
4491: if(jprojmean==0) jprojmean=1;
4492: if(mprojmean==0) jprojmean=1;
4493:
4494: i1=cptcoveff;
4495: if (cptcovn < 1){i1=1;}
4496:
4497: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4498:
4499: fprintf(ficresf,"#****** Routine prevforecast **\n");
4500:
4501: /* if (h==(int)(YEARM*yearp)){ */
4502: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4503: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4504: k=k+1;
4505: fprintf(ficresf,"\n#******");
4506: for(j=1;j<=cptcoveff;j++) {
4507: 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]]);
4508: }
4509: fprintf(ficresf,"******\n");
4510: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4511: for(j=1; j<=nlstate+ndeath;j++){
4512: for(i=1; i<=nlstate;i++)
4513: fprintf(ficresf," p%d%d",i,j);
4514: fprintf(ficresf," p.%d",j);
4515: }
4516: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4517: fprintf(ficresf,"\n");
4518: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4519:
4520: for (agec=fage; agec>=(ageminpar-1); agec--){
4521: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4522: nhstepm = nhstepm/hstepm;
4523: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4524: oldm=oldms;savm=savms;
4525: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4526:
4527: for (h=0; h<=nhstepm; h++){
4528: if (h*hstepm/YEARM*stepm ==yearp) {
4529: fprintf(ficresf,"\n");
4530: for(j=1;j<=cptcoveff;j++)
4531: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4532: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4533: }
4534: for(j=1; j<=nlstate+ndeath;j++) {
4535: ppij=0.;
4536: for(i=1; i<=nlstate;i++) {
4537: if (mobilav==1)
4538: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4539: else {
4540: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4541: }
4542: if (h*hstepm/YEARM*stepm== yearp) {
4543: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4544: }
4545: } /* end i */
4546: if (h*hstepm/YEARM*stepm==yearp) {
4547: fprintf(ficresf," %.3f", ppij);
4548: }
4549: }/* end j */
4550: } /* end h */
4551: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4552: } /* end agec */
4553: } /* end yearp */
4554: } /* end cptcod */
4555: } /* end cptcov */
4556:
4557: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4558:
4559: fclose(ficresf);
4560: }
4561:
4562: /************** Forecasting *****not tested NB*************/
4563: void 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){
4564:
4565: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4566: int *popage;
4567: double calagedatem, agelim, kk1, kk2;
4568: double *popeffectif,*popcount;
4569: double ***p3mat,***tabpop,***tabpopprev;
4570: double ***mobaverage;
4571: char filerespop[FILENAMELENGTH];
4572:
4573: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4574: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4575: agelim=AGESUP;
4576: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4577:
4578: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4579:
4580:
4581: strcpy(filerespop,"pop");
4582: strcat(filerespop,fileres);
4583: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4584: printf("Problem with forecast resultfile: %s\n", filerespop);
4585: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4586: }
4587: printf("Computing forecasting: result on file '%s' \n", filerespop);
4588: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4589:
4590: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4591:
4592: if (mobilav!=0) {
4593: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4594: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4595: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4596: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4597: }
4598: }
4599:
4600: stepsize=(int) (stepm+YEARM-1)/YEARM;
4601: if (stepm<=12) stepsize=1;
4602:
4603: agelim=AGESUP;
4604:
4605: hstepm=1;
4606: hstepm=hstepm/stepm;
4607:
4608: if (popforecast==1) {
4609: if((ficpop=fopen(popfile,"r"))==NULL) {
4610: printf("Problem with population file : %s\n",popfile);exit(0);
4611: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4612: }
4613: popage=ivector(0,AGESUP);
4614: popeffectif=vector(0,AGESUP);
4615: popcount=vector(0,AGESUP);
4616:
4617: i=1;
4618: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4619:
4620: imx=i;
4621: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4622: }
4623:
4624: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4625: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4626: k=k+1;
4627: fprintf(ficrespop,"\n#******");
4628: for(j=1;j<=cptcoveff;j++) {
4629: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4630: }
4631: fprintf(ficrespop,"******\n");
4632: fprintf(ficrespop,"# Age");
4633: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4634: if (popforecast==1) fprintf(ficrespop," [Population]");
4635:
4636: for (cpt=0; cpt<=0;cpt++) {
4637: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4638:
4639: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4640: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4641: nhstepm = nhstepm/hstepm;
4642:
4643: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4644: oldm=oldms;savm=savms;
4645: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4646:
4647: for (h=0; h<=nhstepm; h++){
4648: if (h==(int) (calagedatem+YEARM*cpt)) {
4649: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4650: }
4651: for(j=1; j<=nlstate+ndeath;j++) {
4652: kk1=0.;kk2=0;
4653: for(i=1; i<=nlstate;i++) {
4654: if (mobilav==1)
4655: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4656: else {
4657: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4658: }
4659: }
4660: if (h==(int)(calagedatem+12*cpt)){
4661: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4662: /*fprintf(ficrespop," %.3f", kk1);
4663: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4664: }
4665: }
4666: for(i=1; i<=nlstate;i++){
4667: kk1=0.;
4668: for(j=1; j<=nlstate;j++){
4669: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4670: }
4671: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
4672: }
4673:
4674: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
4675: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4676: }
4677: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4678: }
4679: }
4680:
4681: /******/
4682:
4683: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4684: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4685: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4686: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4687: nhstepm = nhstepm/hstepm;
4688:
4689: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4690: oldm=oldms;savm=savms;
4691: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4692: for (h=0; h<=nhstepm; h++){
4693: if (h==(int) (calagedatem+YEARM*cpt)) {
4694: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4695: }
4696: for(j=1; j<=nlstate+ndeath;j++) {
4697: kk1=0.;kk2=0;
4698: for(i=1; i<=nlstate;i++) {
4699: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4700: }
4701: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
4702: }
4703: }
4704: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4705: }
4706: }
4707: }
4708: }
4709:
4710: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4711:
4712: if (popforecast==1) {
4713: free_ivector(popage,0,AGESUP);
4714: free_vector(popeffectif,0,AGESUP);
4715: free_vector(popcount,0,AGESUP);
4716: }
4717: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4718: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4719: fclose(ficrespop);
4720: } /* End of popforecast */
4721:
4722: int fileappend(FILE *fichier, char *optionfich)
4723: {
4724: if((fichier=fopen(optionfich,"a"))==NULL) {
4725: printf("Problem with file: %s\n", optionfich);
4726: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4727: return (0);
4728: }
4729: fflush(fichier);
4730: return (1);
4731: }
4732:
4733:
4734: /**************** function prwizard **********************/
4735: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4736: {
4737:
4738: /* Wizard to print covariance matrix template */
4739:
4740: char ca[32], cb[32];
4741: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
4742: int numlinepar;
4743:
4744: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4745: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4746: for(i=1; i <=nlstate; i++){
4747: jj=0;
4748: for(j=1; j <=nlstate+ndeath; j++){
4749: if(j==i) continue;
4750: jj++;
4751: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4752: printf("%1d%1d",i,j);
4753: fprintf(ficparo,"%1d%1d",i,j);
4754: for(k=1; k<=ncovmodel;k++){
4755: /* printf(" %lf",param[i][j][k]); */
4756: /* fprintf(ficparo," %lf",param[i][j][k]); */
4757: printf(" 0.");
4758: fprintf(ficparo," 0.");
4759: }
4760: printf("\n");
4761: fprintf(ficparo,"\n");
4762: }
4763: }
4764: printf("# Scales (for hessian or gradient estimation)\n");
4765: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4766: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4767: for(i=1; i <=nlstate; i++){
4768: jj=0;
4769: for(j=1; j <=nlstate+ndeath; j++){
4770: if(j==i) continue;
4771: jj++;
4772: fprintf(ficparo,"%1d%1d",i,j);
4773: printf("%1d%1d",i,j);
4774: fflush(stdout);
4775: for(k=1; k<=ncovmodel;k++){
4776: /* printf(" %le",delti3[i][j][k]); */
4777: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4778: printf(" 0.");
4779: fprintf(ficparo," 0.");
4780: }
4781: numlinepar++;
4782: printf("\n");
4783: fprintf(ficparo,"\n");
4784: }
4785: }
4786: printf("# Covariance matrix\n");
4787: /* # 121 Var(a12)\n\ */
4788: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4789: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4790: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4791: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4792: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4793: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4794: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4795: fflush(stdout);
4796: fprintf(ficparo,"# Covariance matrix\n");
4797: /* # 121 Var(a12)\n\ */
4798: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4799: /* # ...\n\ */
4800: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4801:
4802: for(itimes=1;itimes<=2;itimes++){
4803: jj=0;
4804: for(i=1; i <=nlstate; i++){
4805: for(j=1; j <=nlstate+ndeath; j++){
4806: if(j==i) continue;
4807: for(k=1; k<=ncovmodel;k++){
4808: jj++;
4809: ca[0]= k+'a'-1;ca[1]='\0';
4810: if(itimes==1){
4811: printf("#%1d%1d%d",i,j,k);
4812: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4813: }else{
4814: printf("%1d%1d%d",i,j,k);
4815: fprintf(ficparo,"%1d%1d%d",i,j,k);
4816: /* printf(" %.5le",matcov[i][j]); */
4817: }
4818: ll=0;
4819: for(li=1;li <=nlstate; li++){
4820: for(lj=1;lj <=nlstate+ndeath; lj++){
4821: if(lj==li) continue;
4822: for(lk=1;lk<=ncovmodel;lk++){
4823: ll++;
4824: if(ll<=jj){
4825: cb[0]= lk +'a'-1;cb[1]='\0';
4826: if(ll<jj){
4827: if(itimes==1){
4828: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4829: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4830: }else{
4831: printf(" 0.");
4832: fprintf(ficparo," 0.");
4833: }
4834: }else{
4835: if(itimes==1){
4836: printf(" Var(%s%1d%1d)",ca,i,j);
4837: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4838: }else{
4839: printf(" 0.");
4840: fprintf(ficparo," 0.");
4841: }
4842: }
4843: }
4844: } /* end lk */
4845: } /* end lj */
4846: } /* end li */
4847: printf("\n");
4848: fprintf(ficparo,"\n");
4849: numlinepar++;
4850: } /* end k*/
4851: } /*end j */
4852: } /* end i */
4853: } /* end itimes */
4854:
4855: } /* end of prwizard */
4856: /******************* Gompertz Likelihood ******************************/
4857: double gompertz(double x[])
4858: {
4859: double A,B,L=0.0,sump=0.,num=0.;
4860: int i,n=0; /* n is the size of the sample */
4861:
4862: for (i=0;i<=imx-1 ; i++) {
4863: sump=sump+weight[i];
4864: /* sump=sump+1;*/
4865: num=num+1;
4866: }
4867:
4868:
4869: /* for (i=0; i<=imx; i++)
4870: 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]);*/
4871:
4872: for (i=1;i<=imx ; i++)
4873: {
4874: if (cens[i] == 1 && wav[i]>1)
4875: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
4876:
4877: if (cens[i] == 0 && wav[i]>1)
4878: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4879: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
4880:
4881: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4882: if (wav[i] > 1 ) { /* ??? */
4883: L=L+A*weight[i];
4884: /* 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]);*/
4885: }
4886: }
4887:
4888: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4889:
4890: return -2*L*num/sump;
4891: }
4892:
4893: #ifdef GSL
4894: /******************* Gompertz_f Likelihood ******************************/
4895: double gompertz_f(const gsl_vector *v, void *params)
4896: {
4897: double A,B,LL=0.0,sump=0.,num=0.;
4898: double *x= (double *) v->data;
4899: int i,n=0; /* n is the size of the sample */
4900:
4901: for (i=0;i<=imx-1 ; i++) {
4902: sump=sump+weight[i];
4903: /* sump=sump+1;*/
4904: num=num+1;
4905: }
4906:
4907:
4908: /* for (i=0; i<=imx; i++)
4909: 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]);*/
4910: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
4911: for (i=1;i<=imx ; i++)
4912: {
4913: if (cens[i] == 1 && wav[i]>1)
4914: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
4915:
4916: if (cens[i] == 0 && wav[i]>1)
4917: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
4918: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
4919:
4920: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4921: if (wav[i] > 1 ) { /* ??? */
4922: LL=LL+A*weight[i];
4923: /* 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]);*/
4924: }
4925: }
4926:
4927: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4928: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
4929:
4930: return -2*LL*num/sump;
4931: }
4932: #endif
4933:
4934: /******************* Printing html file ***********/
4935: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4936: int lastpass, int stepm, int weightopt, char model[],\
4937: int imx, double p[],double **matcov,double agemortsup){
4938: int i,k;
4939:
4940: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4941: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4942: for (i=1;i<=2;i++)
4943: 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]));
4944: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4945: fprintf(fichtm,"</ul>");
4946:
4947: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4948:
4949: 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>");
4950:
4951: for (k=agegomp;k<(agemortsup-2);k++)
4952: 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]);
4953:
4954:
4955: fflush(fichtm);
4956: }
4957:
4958: /******************* Gnuplot file **************/
4959: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4960:
4961: char dirfileres[132],optfileres[132];
4962:
4963: int ng;
4964:
4965:
4966: /*#ifdef windows */
4967: fprintf(ficgp,"cd \"%s\" \n",pathc);
4968: /*#endif */
4969:
4970:
4971: strcpy(dirfileres,optionfilefiname);
4972: strcpy(optfileres,"vpl");
4973: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4974: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
4975: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
4976: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
4977: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4978:
4979: }
4980:
4981: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
4982: {
4983:
4984: /*-------- data file ----------*/
4985: FILE *fic;
4986: char dummy[]=" ";
4987: int i=0, j=0, n=0;
4988: int linei, month, year,iout;
4989: char line[MAXLINE], linetmp[MAXLINE];
4990: char stra[MAXLINE], strb[MAXLINE];
4991: char *stratrunc;
4992: int lstra;
4993:
4994:
4995: if((fic=fopen(datafile,"r"))==NULL) {
4996: printf("Problem while opening datafile: %s\n", datafile);return 1;
4997: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
4998: }
4999:
5000: i=1;
5001: linei=0;
5002: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
5003: linei=linei+1;
5004: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
5005: if(line[j] == '\t')
5006: line[j] = ' ';
5007: }
5008: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
5009: ;
5010: };
5011: line[j+1]=0; /* Trims blanks at end of line */
5012: if(line[0]=='#'){
5013: fprintf(ficlog,"Comment line\n%s\n",line);
5014: printf("Comment line\n%s\n",line);
5015: continue;
5016: }
5017: trimbb(linetmp,line); /* Trims multiple blanks in line */
5018: strcpy(line, linetmp);
5019:
5020:
5021: for (j=maxwav;j>=1;j--){
5022: cutv(stra, strb, line, ' ');
5023: if(strb[0]=='.') { /* Missing status */
5024: lval=-1;
5025: }else{
5026: errno=0;
5027: lval=strtol(strb,&endptr,10);
5028: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
5029: if( strb[0]=='\0' || (*endptr != '\0')){
5030: 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);
5031: 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);
5032: return 1;
5033: }
5034: }
5035: s[j][i]=lval;
5036:
5037: strcpy(line,stra);
5038: cutv(stra, strb,line,' ');
5039: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
5040: }
5041: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
5042: month=99;
5043: year=9999;
5044: }else{
5045: 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);
5046: 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);
5047: return 1;
5048: }
5049: anint[j][i]= (double) year;
5050: mint[j][i]= (double)month;
5051: strcpy(line,stra);
5052: } /* ENd Waves */
5053:
5054: cutv(stra, strb,line,' ');
5055: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
5056: }
5057: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
5058: month=99;
5059: year=9999;
5060: }else{
5061: 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);
5062: 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);
5063: return 1;
5064: }
5065: andc[i]=(double) year;
5066: moisdc[i]=(double) month;
5067: strcpy(line,stra);
5068:
5069: cutv(stra, strb,line,' ');
5070: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
5071: }
5072: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
5073: month=99;
5074: year=9999;
5075: }else{
5076: 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);
5077: 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);
5078: return 1;
5079: }
5080: if (year==9999) {
5081: 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);
5082: 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);
5083: return 1;
5084:
5085: }
5086: annais[i]=(double)(year);
5087: moisnais[i]=(double)(month);
5088: strcpy(line,stra);
5089:
5090: cutv(stra, strb,line,' ');
5091: errno=0;
5092: dval=strtod(strb,&endptr);
5093: if( strb[0]=='\0' || (*endptr != '\0')){
5094: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
5095: 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);
5096: fflush(ficlog);
5097: return 1;
5098: }
5099: weight[i]=dval;
5100: strcpy(line,stra);
5101:
5102: for (j=ncovcol;j>=1;j--){
5103: cutv(stra, strb,line,' ');
5104: if(strb[0]=='.') { /* Missing status */
5105: lval=-1;
5106: }else{
5107: errno=0;
5108: lval=strtol(strb,&endptr,10);
5109: if( strb[0]=='\0' || (*endptr != '\0')){
5110: 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);
5111: 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);
5112: return 1;
5113: }
5114: }
5115: if(lval <-1 || lval >1){
5116: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
5117: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5118: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5119: For example, for multinomial values like 1, 2 and 3,\n \
5120: build V1=0 V2=0 for the reference value (1),\n \
5121: V1=1 V2=0 for (2) \n \
5122: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5123: output of IMaCh is often meaningless.\n \
5124: Exiting.\n",lval,linei, i,line,j);
5125: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
5126: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5127: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5128: For example, for multinomial values like 1, 2 and 3,\n \
5129: build V1=0 V2=0 for the reference value (1),\n \
5130: V1=1 V2=0 for (2) \n \
5131: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5132: output of IMaCh is often meaningless.\n \
5133: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
5134: return 1;
5135: }
5136: covar[j][i]=(double)(lval);
5137: strcpy(line,stra);
5138: }
5139: lstra=strlen(stra);
5140:
5141: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
5142: stratrunc = &(stra[lstra-9]);
5143: num[i]=atol(stratrunc);
5144: }
5145: else
5146: num[i]=atol(stra);
5147: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
5148: 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;}*/
5149:
5150: i=i+1;
5151: } /* End loop reading data */
5152:
5153: *imax=i-1; /* Number of individuals */
5154: fclose(fic);
5155:
5156: return (0);
5157: /* endread: */
5158: printf("Exiting readdata: ");
5159: fclose(fic);
5160: return (1);
5161:
5162:
5163:
5164: }
5165: void removespace(char *str) {
5166: char *p1 = str, *p2 = str;
5167: do
5168: while (*p2 == ' ')
5169: p2++;
5170: while (*p1++ == *p2++);
5171: }
5172:
5173: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
5174: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
5175: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
5176: * - cptcovn or number of covariates k of the models excluding age*products =6
5177: * - cptcovage number of covariates with age*products =2
5178: * - cptcovs number of simple covariates
5179: * - 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
5180: * which is a new column after the 9 (ncovcol) variables.
5181: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
5182: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
5183: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
5184: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
5185: */
5186: {
5187: int i, j, k, ks;
5188: int j1, k1, k2;
5189: char modelsav[80];
5190: char stra[80], strb[80], strc[80], strd[80],stre[80];
5191:
5192: /*removespace(model);*/
5193: if (strlen(model) >1){ /* If there is at least 1 covariate */
5194: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
5195: j=nbocc(model,'+'); /**< j=Number of '+' */
5196: j1=nbocc(model,'*'); /**< j1=Number of '*' */
5197: cptcovs=j+1-j1; /**< Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2 */
5198: cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
5199: /* including age products which are counted in cptcovage.
5200: * but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
5201: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
5202: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
5203: strcpy(modelsav,model);
5204: if (strstr(model,"AGE") !=0){
5205: printf("Error. AGE must be in lower case 'age' model=%s ",model);
5206: fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
5207: return 1;
5208: }
5209: if (strstr(model,"v") !=0){
5210: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
5211: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
5212: return 1;
5213: }
5214:
5215: /* Design
5216: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
5217: * < ncovcol=8 >
5218: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
5219: * k= 1 2 3 4 5 6 7 8
5220: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
5221: * covar[k,i], value of kth covariate if not including age for individual i:
5222: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
5223: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
5224: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
5225: * Tage[++cptcovage]=k
5226: * if products, new covar are created after ncovcol with k1
5227: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
5228: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
5229: * 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
5230: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
5231: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
5232: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
5233: * < ncovcol=8 >
5234: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
5235: * k= 1 2 3 4 5 6 7 8 9 10 11 12
5236: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
5237: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5238: * p Tprod[1]@2={ 6, 5}
5239: *p Tvard[1][1]@4= {7, 8, 5, 6}
5240: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
5241: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
5242: *How to reorganize?
5243: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
5244: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5245: * {2, 1, 4, 8, 5, 6, 3, 7}
5246: * Struct []
5247: */
5248:
5249: /* This loop fills the array Tvar from the string 'model'.*/
5250: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
5251: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
5252: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
5253: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
5254: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
5255: /* k=1 Tvar[1]=2 (from V2) */
5256: /* k=5 Tvar[5] */
5257: /* for (k=1; k<=cptcovn;k++) { */
5258: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
5259: /* } */
5260: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
5261: /*
5262: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
5263: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
5264: Tvar[k]=0;
5265: cptcovage=0;
5266: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
5267: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5268: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
5269: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
5270: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5271: /*scanf("%d",i);*/
5272: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
5273: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
5274: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
5275: /* covar is not filled and then is empty */
5276: cptcovprod--;
5277: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
5278: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
5279: cptcovage++; /* Sums the number of covariates which include age as a product */
5280: Tage[cptcovage]=k; /* Tage[1] = 4 */
5281: /*printf("stre=%s ", stre);*/
5282: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
5283: cptcovprod--;
5284: cutl(stre,strb,strc,'V');
5285: Tvar[k]=atoi(stre);
5286: cptcovage++;
5287: Tage[cptcovage]=k;
5288: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
5289: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
5290: cptcovn++;
5291: cptcovprodnoage++;k1++;
5292: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5293: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
5294: because this model-covariate is a construction we invent a new column
5295: ncovcol + k1
5296: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
5297: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
5298: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
5299: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
5300: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
5301: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
5302: k2=k2+2;
5303: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
5304: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
5305: for (i=1; i<=lastobs;i++){
5306: /* Computes the new covariate which is a product of
5307: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
5308: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
5309: }
5310: } /* End age is not in the model */
5311: } /* End if model includes a product */
5312: else { /* no more sum */
5313: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5314: /* scanf("%d",i);*/
5315: cutl(strd,strc,strb,'V');
5316: ks++; /**< Number of simple covariates */
5317: cptcovn++;
5318: Tvar[k]=atoi(strd);
5319: }
5320: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
5321: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5322: scanf("%d",i);*/
5323: } /* end of loop + */
5324: } /* end model */
5325:
5326: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5327: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5328:
5329: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5330: printf("cptcovprod=%d ", cptcovprod);
5331: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5332:
5333: scanf("%d ",i);*/
5334:
5335:
5336: return (0); /* with covar[new additional covariate if product] and Tage if age */
5337: /*endread:*/
5338: printf("Exiting decodemodel: ");
5339: return (1);
5340: }
5341:
5342: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
5343: {
5344: int i, m;
5345:
5346: for (i=1; i<=imx; i++) {
5347: for(m=2; (m<= maxwav); m++) {
5348: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5349: anint[m][i]=9999;
5350: s[m][i]=-1;
5351: }
5352: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
5353: *nberr = *nberr + 1;
5354: 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 (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
5355: 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 (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
5356: s[m][i]=-1;
5357: }
5358: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
5359: (*nberr)++;
5360: 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]);
5361: 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]);
5362: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5363: }
5364: }
5365: }
5366:
5367: for (i=1; i<=imx; i++) {
5368: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5369: for(m=firstpass; (m<= lastpass); m++){
5370: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5371: if (s[m][i] >= nlstate+1) {
5372: if(agedc[i]>0){
5373: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
5374: agev[m][i]=agedc[i];
5375: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
5376: }else {
5377: if ((int)andc[i]!=9999){
5378: nbwarn++;
5379: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5380: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5381: agev[m][i]=-1;
5382: }
5383: }
5384: } /* agedc > 0 */
5385: }
5386: else if(s[m][i] !=9){ /* Standard case, age in fractional
5387: years but with the precision of a month */
5388: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5389: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5390: agev[m][i]=1;
5391: else if(agev[m][i] < *agemin){
5392: *agemin=agev[m][i];
5393: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
5394: }
5395: else if(agev[m][i] >*agemax){
5396: *agemax=agev[m][i];
5397: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
5398: }
5399: /*agev[m][i]=anint[m][i]-annais[i];*/
5400: /* agev[m][i] = age[i]+2*m;*/
5401: }
5402: else { /* =9 */
5403: agev[m][i]=1;
5404: s[m][i]=-1;
5405: }
5406: }
5407: else /*= 0 Unknown */
5408: agev[m][i]=1;
5409: }
5410:
5411: }
5412: for (i=1; i<=imx; i++) {
5413: for(m=firstpass; (m<=lastpass); m++){
5414: if (s[m][i] > (nlstate+ndeath)) {
5415: (*nberr)++;
5416: 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);
5417: 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);
5418: return 1;
5419: }
5420: }
5421: }
5422:
5423: /*for (i=1; i<=imx; i++){
5424: for (m=firstpass; (m<lastpass); m++){
5425: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5426: }
5427:
5428: }*/
5429:
5430:
5431: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5432: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5433:
5434: return (0);
5435: /* endread:*/
5436: printf("Exiting calandcheckages: ");
5437: return (1);
5438: }
5439:
5440: void syscompilerinfo()
5441: {
5442: /* #include "syscompilerinfo.h"*/
5443: /* #include <gnu/libc-version.h> */ /* Only on gnu */
5444:
5445: printf("Compiled with:");fprintf(ficlog,"Compiled with:");
5446: #if defined(__clang__)
5447: printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
5448: #endif
5449: #if defined(__ICC) || defined(__INTEL_COMPILER)
5450: printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
5451: #endif
5452: #if defined(__GNUC__) || defined(__GNUG__)
5453: printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
5454: #endif
5455: #if defined(__HP_cc) || defined(__HP_aCC)
5456: printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
5457: #endif
5458: #if defined(__IBMC__) || defined(__IBMCPP__)
5459: printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
5460: #endif
5461: #if defined(_MSC_VER)
5462: printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
5463: #endif
5464: #if defined(__PGI)
5465: printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
5466: #endif
5467: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
5468: printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
5469: #endif
5470: printf(". ");fprintf(ficlog,". ");
5471:
5472: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
5473: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
5474: // Windows (x64 and x86)
5475: #elif __unix__ // all unices, not all compilers
5476: // Unix
5477: #elif __linux__
5478: // linux
5479: #elif __APPLE__
5480: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though...
5481: #endif
5482:
5483: /* __MINGW32__ */
5484: /* __CYGWIN__ */
5485: /* __MINGW64__ */
5486: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
5487: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
5488: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
5489: /* _WIN64 // Defined for applications for Win64. */
5490: /* _M_X64 // Defined for compilations that target x64 processors. */
5491: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
5492: #include <stdint.h>
5493: #if UINTPTR_MAX == 0xffffffff
5494: printf(" 32-bit."); /* 32-bit */
5495: #elif UINTPTR_MAX == 0xffffffffffffffff
5496: printf(" 64-bit.");/* 64-bit */
5497: #else
5498: printf(" wtf-bit."); /* wtf */
5499: #endif
5500:
5501: struct utsname sysInfo;
5502:
5503: if (uname(&sysInfo) != -1) {
5504: printf(" %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
5505: fprintf(ficlog," %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
5506: }
5507: else
5508: perror("uname() error");
5509: #if defined(__GNUC__)
5510: # if defined(__GNUC_PATCHLEVEL__)
5511: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
5512: + __GNUC_MINOR__ * 100 \
5513: + __GNUC_PATCHLEVEL__)
5514: # else
5515: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
5516: + __GNUC_MINOR__ * 100)
5517: # endif
5518: printf("GNU C version %d.\n", __GNUC_VERSION__);
5519: fprintf(ficlog, "GNU C version %d.\n", __GNUC_VERSION__);
5520: #endif
5521: #if defined(_MSC_VER)
5522: printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);
5523: fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);
5524: #endif
5525:
5526: /* printf("GNU libc version: %s\n", gnu_get_libc_version()); */
5527:
5528: }
5529:
5530: /***********************************************/
5531: /**************** Main Program *****************/
5532: /***********************************************/
5533:
5534: int main(int argc, char *argv[])
5535: {
5536: #ifdef GSL
5537: const gsl_multimin_fminimizer_type *T;
5538: size_t iteri = 0, it;
5539: int rval = GSL_CONTINUE;
5540: int status = GSL_SUCCESS;
5541: double ssval;
5542: #endif
5543: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
5544: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
5545:
5546: int jj, ll, li, lj, lk;
5547: int numlinepar=0; /* Current linenumber of parameter file */
5548: int itimes;
5549: int NDIM=2;
5550: int vpopbased=0;
5551:
5552: char ca[32], cb[32];
5553: /* FILE *fichtm; *//* Html File */
5554: /* FILE *ficgp;*/ /*Gnuplot File */
5555: struct stat info;
5556: double agedeb;
5557: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
5558:
5559: double fret;
5560: double dum; /* Dummy variable */
5561: double ***p3mat;
5562: double ***mobaverage;
5563:
5564: char line[MAXLINE];
5565: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
5566: char pathr[MAXLINE], pathimach[MAXLINE];
5567: char *tok, *val; /* pathtot */
5568: int firstobs=1, lastobs=10;
5569: int c, h , cpt;
5570: int jl;
5571: int i1, j1, jk, stepsize;
5572: int *tab;
5573: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
5574: int mobilav=0,popforecast=0;
5575: int hstepm, nhstepm;
5576: int agemortsup;
5577: float sumlpop=0.;
5578: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
5579: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
5580:
5581: double bage=0, fage=110, age, agelim, agebase;
5582: double ftolpl=FTOL;
5583: double **prlim;
5584: double ***param; /* Matrix of parameters */
5585: double *p;
5586: double **matcov; /* Matrix of covariance */
5587: double ***delti3; /* Scale */
5588: double *delti; /* Scale */
5589: double ***eij, ***vareij;
5590: double **varpl; /* Variances of prevalence limits by age */
5591: double *epj, vepp;
5592:
5593: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
5594: double **ximort;
5595: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
5596: int *dcwave;
5597:
5598: char z[1]="c";
5599:
5600: /*char *strt;*/
5601: char strtend[80];
5602:
5603:
5604: /* setlocale (LC_ALL, ""); */
5605: /* bindtextdomain (PACKAGE, LOCALEDIR); */
5606: /* textdomain (PACKAGE); */
5607: /* setlocale (LC_CTYPE, ""); */
5608: /* setlocale (LC_MESSAGES, ""); */
5609:
5610: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
5611: rstart_time = time(NULL);
5612: /* (void) gettimeofday(&start_time,&tzp);*/
5613: start_time = *localtime(&rstart_time);
5614: curr_time=start_time;
5615: /*tml = *localtime(&start_time.tm_sec);*/
5616: /* strcpy(strstart,asctime(&tml)); */
5617: strcpy(strstart,asctime(&start_time));
5618:
5619: /* printf("Localtime (at start)=%s",strstart); */
5620: /* tp.tm_sec = tp.tm_sec +86400; */
5621: /* tm = *localtime(&start_time.tm_sec); */
5622: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
5623: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
5624: /* tmg.tm_hour=tmg.tm_hour + 1; */
5625: /* tp.tm_sec = mktime(&tmg); */
5626: /* strt=asctime(&tmg); */
5627: /* printf("Time(after) =%s",strstart); */
5628: /* (void) time (&time_value);
5629: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
5630: * tm = *localtime(&time_value);
5631: * strstart=asctime(&tm);
5632: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
5633: */
5634:
5635: nberr=0; /* Number of errors and warnings */
5636: nbwarn=0;
5637: getcwd(pathcd, size);
5638:
5639: printf("\n%s\n%s",version,fullversion);
5640: if(argc <=1){
5641: printf("\nEnter the parameter file name: ");
5642: fgets(pathr,FILENAMELENGTH,stdin);
5643: i=strlen(pathr);
5644: if(pathr[i-1]=='\n')
5645: pathr[i-1]='\0';
5646: i=strlen(pathr);
5647: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
5648: pathr[i-1]='\0';
5649: for (tok = pathr; tok != NULL; ){
5650: printf("Pathr |%s|\n",pathr);
5651: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
5652: printf("val= |%s| pathr=%s\n",val,pathr);
5653: strcpy (pathtot, val);
5654: if(pathr[0] == '\0') break; /* Dirty */
5655: }
5656: }
5657: else{
5658: strcpy(pathtot,argv[1]);
5659: }
5660: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
5661: /*cygwin_split_path(pathtot,path,optionfile);
5662: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
5663: /* cutv(path,optionfile,pathtot,'\\');*/
5664:
5665: /* Split argv[0], imach program to get pathimach */
5666: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
5667: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5668: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5669: /* strcpy(pathimach,argv[0]); */
5670: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
5671: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
5672: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
5673: chdir(path); /* Can be a relative path */
5674: if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
5675: printf("Current directory %s!\n",pathcd);
5676: strcpy(command,"mkdir ");
5677: strcat(command,optionfilefiname);
5678: if((outcmd=system(command)) != 0){
5679: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
5680: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
5681: /* fclose(ficlog); */
5682: /* exit(1); */
5683: }
5684: /* if((imk=mkdir(optionfilefiname))<0){ */
5685: /* perror("mkdir"); */
5686: /* } */
5687:
5688: /*-------- arguments in the command line --------*/
5689:
5690: /* Log file */
5691: strcat(filelog, optionfilefiname);
5692: strcat(filelog,".log"); /* */
5693: if((ficlog=fopen(filelog,"w"))==NULL) {
5694: printf("Problem with logfile %s\n",filelog);
5695: goto end;
5696: }
5697: fprintf(ficlog,"Log filename:%s\n",filelog);
5698: fprintf(ficlog,"\n%s\n%s",version,fullversion);
5699: fprintf(ficlog,"\nEnter the parameter file name: \n");
5700: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
5701: path=%s \n\
5702: optionfile=%s\n\
5703: optionfilext=%s\n\
5704: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
5705:
5706: syscompilerinfo();
5707:
5708: printf("Local time (at start):%s",strstart);
5709: fprintf(ficlog,"Local time (at start): %s",strstart);
5710: fflush(ficlog);
5711: /* (void) gettimeofday(&curr_time,&tzp); */
5712: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
5713:
5714: /* */
5715: strcpy(fileres,"r");
5716: strcat(fileres, optionfilefiname);
5717: strcat(fileres,".txt"); /* Other files have txt extension */
5718:
5719: /*---------arguments file --------*/
5720:
5721: if((ficpar=fopen(optionfile,"r"))==NULL) {
5722: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
5723: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
5724: fflush(ficlog);
5725: /* goto end; */
5726: exit(70);
5727: }
5728:
5729:
5730:
5731: strcpy(filereso,"o");
5732: strcat(filereso,fileres);
5733: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
5734: printf("Problem with Output resultfile: %s\n", filereso);
5735: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
5736: fflush(ficlog);
5737: goto end;
5738: }
5739:
5740: /* Reads comments: lines beginning with '#' */
5741: numlinepar=0;
5742: while((c=getc(ficpar))=='#' && c!= EOF){
5743: ungetc(c,ficpar);
5744: fgets(line, MAXLINE, ficpar);
5745: numlinepar++;
5746: fputs(line,stdout);
5747: fputs(line,ficparo);
5748: fputs(line,ficlog);
5749: }
5750: ungetc(c,ficpar);
5751:
5752: 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);
5753: numlinepar++;
5754: 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);
5755: 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);
5756: 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);
5757: fflush(ficlog);
5758: while((c=getc(ficpar))=='#' && c!= EOF){
5759: ungetc(c,ficpar);
5760: fgets(line, MAXLINE, ficpar);
5761: numlinepar++;
5762: fputs(line, stdout);
5763: //puts(line);
5764: fputs(line,ficparo);
5765: fputs(line,ficlog);
5766: }
5767: ungetc(c,ficpar);
5768:
5769:
5770: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
5771: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
5772: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
5773: v1+v2*age+v2*v3 makes cptcovn = 3
5774: */
5775: if (strlen(model)>1)
5776: 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*/
5777: else
5778: ncovmodel=2;
5779: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
5780: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
5781: npar= nforce*ncovmodel; /* Number of parameters like aij*/
5782: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
5783: 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);
5784: 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);
5785: fflush(stdout);
5786: fclose (ficlog);
5787: goto end;
5788: }
5789: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5790: delti=delti3[1][1];
5791: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
5792: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
5793: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5794: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5795: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5796: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5797: fclose (ficparo);
5798: fclose (ficlog);
5799: goto end;
5800: exit(0);
5801: }
5802: else if(mle==-3) {
5803: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5804: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5805: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5806: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5807: matcov=matrix(1,npar,1,npar);
5808: }
5809: else{
5810: /* Read guessed parameters */
5811: /* Reads comments: lines beginning with '#' */
5812: while((c=getc(ficpar))=='#' && c!= EOF){
5813: ungetc(c,ficpar);
5814: fgets(line, MAXLINE, ficpar);
5815: numlinepar++;
5816: fputs(line,stdout);
5817: fputs(line,ficparo);
5818: fputs(line,ficlog);
5819: }
5820: ungetc(c,ficpar);
5821:
5822: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5823: for(i=1; i <=nlstate; i++){
5824: j=0;
5825: for(jj=1; jj <=nlstate+ndeath; jj++){
5826: if(jj==i) continue;
5827: j++;
5828: fscanf(ficpar,"%1d%1d",&i1,&j1);
5829: if ((i1 != i) && (j1 != j)){
5830: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
5831: It might be a problem of design; if ncovcol and the model are correct\n \
5832: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
5833: exit(1);
5834: }
5835: fprintf(ficparo,"%1d%1d",i1,j1);
5836: if(mle==1)
5837: printf("%1d%1d",i,j);
5838: fprintf(ficlog,"%1d%1d",i,j);
5839: for(k=1; k<=ncovmodel;k++){
5840: fscanf(ficpar," %lf",¶m[i][j][k]);
5841: if(mle==1){
5842: printf(" %lf",param[i][j][k]);
5843: fprintf(ficlog," %lf",param[i][j][k]);
5844: }
5845: else
5846: fprintf(ficlog," %lf",param[i][j][k]);
5847: fprintf(ficparo," %lf",param[i][j][k]);
5848: }
5849: fscanf(ficpar,"\n");
5850: numlinepar++;
5851: if(mle==1)
5852: printf("\n");
5853: fprintf(ficlog,"\n");
5854: fprintf(ficparo,"\n");
5855: }
5856: }
5857: fflush(ficlog);
5858:
5859: /* Reads scales values */
5860: p=param[1][1];
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: for(i=1; i <=nlstate; i++){
5874: for(j=1; j <=nlstate+ndeath-1; j++){
5875: fscanf(ficpar,"%1d%1d",&i1,&j1);
5876: if ( (i1-i) * (j1-j) != 0){
5877: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
5878: exit(1);
5879: }
5880: printf("%1d%1d",i,j);
5881: fprintf(ficparo,"%1d%1d",i1,j1);
5882: fprintf(ficlog,"%1d%1d",i1,j1);
5883: for(k=1; k<=ncovmodel;k++){
5884: fscanf(ficpar,"%le",&delti3[i][j][k]);
5885: printf(" %le",delti3[i][j][k]);
5886: fprintf(ficparo," %le",delti3[i][j][k]);
5887: fprintf(ficlog," %le",delti3[i][j][k]);
5888: }
5889: fscanf(ficpar,"\n");
5890: numlinepar++;
5891: printf("\n");
5892: fprintf(ficparo,"\n");
5893: fprintf(ficlog,"\n");
5894: }
5895: }
5896: fflush(ficlog);
5897:
5898: /* Reads covariance matrix */
5899: delti=delti3[1][1];
5900:
5901:
5902: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
5903:
5904: /* Reads comments: lines beginning with '#' */
5905: while((c=getc(ficpar))=='#' && c!= EOF){
5906: ungetc(c,ficpar);
5907: fgets(line, MAXLINE, ficpar);
5908: numlinepar++;
5909: fputs(line,stdout);
5910: fputs(line,ficparo);
5911: fputs(line,ficlog);
5912: }
5913: ungetc(c,ficpar);
5914:
5915: matcov=matrix(1,npar,1,npar);
5916: for(i=1; i <=npar; i++)
5917: for(j=1; j <=npar; j++) matcov[i][j]=0.;
5918:
5919: for(i=1; i <=npar; i++){
5920: fscanf(ficpar,"%s",str);
5921: if(mle==1)
5922: printf("%s",str);
5923: fprintf(ficlog,"%s",str);
5924: fprintf(ficparo,"%s",str);
5925: for(j=1; j <=i; j++){
5926: fscanf(ficpar," %le",&matcov[i][j]);
5927: if(mle==1){
5928: printf(" %.5le",matcov[i][j]);
5929: }
5930: fprintf(ficlog," %.5le",matcov[i][j]);
5931: fprintf(ficparo," %.5le",matcov[i][j]);
5932: }
5933: fscanf(ficpar,"\n");
5934: numlinepar++;
5935: if(mle==1)
5936: printf("\n");
5937: fprintf(ficlog,"\n");
5938: fprintf(ficparo,"\n");
5939: }
5940: for(i=1; i <=npar; i++)
5941: for(j=i+1;j<=npar;j++)
5942: matcov[i][j]=matcov[j][i];
5943:
5944: if(mle==1)
5945: printf("\n");
5946: fprintf(ficlog,"\n");
5947:
5948: fflush(ficlog);
5949:
5950: /*-------- Rewriting parameter file ----------*/
5951: strcpy(rfileres,"r"); /* "Rparameterfile */
5952: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
5953: strcat(rfileres,"."); /* */
5954: strcat(rfileres,optionfilext); /* Other files have txt extension */
5955: if((ficres =fopen(rfileres,"w"))==NULL) {
5956: printf("Problem writing new parameter file: %s\n", fileres);goto end;
5957: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
5958: }
5959: fprintf(ficres,"#%s\n",version);
5960: } /* End of mle != -3 */
5961:
5962:
5963: n= lastobs;
5964: num=lvector(1,n);
5965: moisnais=vector(1,n);
5966: annais=vector(1,n);
5967: moisdc=vector(1,n);
5968: andc=vector(1,n);
5969: agedc=vector(1,n);
5970: cod=ivector(1,n);
5971: weight=vector(1,n);
5972: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
5973: mint=matrix(1,maxwav,1,n);
5974: anint=matrix(1,maxwav,1,n);
5975: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
5976: tab=ivector(1,NCOVMAX);
5977: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
5978:
5979: /* Reads data from file datafile */
5980: if (readdata(datafile, firstobs, lastobs, &imx)==1)
5981: goto end;
5982:
5983: /* Calculation of the number of parameters from char model */
5984: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
5985: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
5986: k=3 V4 Tvar[k=3]= 4 (from V4)
5987: k=2 V1 Tvar[k=2]= 1 (from V1)
5988: k=1 Tvar[1]=2 (from V2)
5989: */
5990: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
5991: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
5992: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
5993: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
5994: */
5995: /* For model-covariate k tells which data-covariate to use but
5996: because this model-covariate is a construction we invent a new column
5997: ncovcol + k1
5998: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
5999: Tvar[3=V1*V4]=4+1 etc */
6000: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
6001: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
6002: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
6003: */
6004: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
6005: 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
6006: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
6007: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
6008: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
6009: 4 covariates (3 plus signs)
6010: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
6011: */
6012:
6013: if(decodemodel(model, lastobs) == 1)
6014: goto end;
6015:
6016: if((double)(lastobs-imx)/(double)imx > 1.10){
6017: nbwarn++;
6018: 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);
6019: 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);
6020: }
6021: /* if(mle==1){*/
6022: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
6023: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
6024: }
6025:
6026: /*-calculation of age at interview from date of interview and age at death -*/
6027: agev=matrix(1,maxwav,1,imx);
6028:
6029: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
6030: goto end;
6031:
6032:
6033: agegomp=(int)agemin;
6034: free_vector(moisnais,1,n);
6035: free_vector(annais,1,n);
6036: /* free_matrix(mint,1,maxwav,1,n);
6037: free_matrix(anint,1,maxwav,1,n);*/
6038: free_vector(moisdc,1,n);
6039: free_vector(andc,1,n);
6040: /* */
6041:
6042: wav=ivector(1,imx);
6043: dh=imatrix(1,lastpass-firstpass+1,1,imx);
6044: bh=imatrix(1,lastpass-firstpass+1,1,imx);
6045: mw=imatrix(1,lastpass-firstpass+1,1,imx);
6046:
6047: /* Concatenates waves */
6048: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
6049: /* */
6050:
6051: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
6052:
6053: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
6054: ncodemax[1]=1;
6055: Ndum =ivector(-1,NCOVMAX);
6056: if (ncovmodel > 2)
6057: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
6058:
6059: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
6060: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
6061: h=0;
6062:
6063:
6064: /*if (cptcovn > 0) */
6065:
6066:
6067: m=pow(2,cptcoveff);
6068:
6069: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
6070: 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 */
6071: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
6072: for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
6073: h++;
6074: if (h>m)
6075: h=1;
6076: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
6077: * h 1 2 3 4
6078: *______________________________
6079: * 1 i=1 1 i=1 1 i=1 1 i=1 1
6080: * 2 2 1 1 1
6081: * 3 i=2 1 2 1 1
6082: * 4 2 2 1 1
6083: * 5 i=3 1 i=2 1 2 1
6084: * 6 2 1 2 1
6085: * 7 i=4 1 2 2 1
6086: * 8 2 2 2 1
6087: * 9 i=5 1 i=3 1 i=2 1 1
6088: * 10 2 1 1 1
6089: * 11 i=6 1 2 1 1
6090: * 12 2 2 1 1
6091: * 13 i=7 1 i=4 1 2 1
6092: * 14 2 1 2 1
6093: * 15 i=8 1 2 2 1
6094: * 16 2 2 2 1
6095: */
6096: codtab[h][k]=j;
6097: /*codtab[h][Tvar[k]]=j;*/
6098: 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]]);
6099: }
6100: }
6101: }
6102: }
6103: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
6104: codtab[1][2]=1;codtab[2][2]=2; */
6105: /* for(i=1; i <=m ;i++){
6106: for(k=1; k <=cptcovn; k++){
6107: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
6108: }
6109: printf("\n");
6110: }
6111: scanf("%d",i);*/
6112:
6113: free_ivector(Ndum,-1,NCOVMAX);
6114:
6115:
6116:
6117: /*------------ gnuplot -------------*/
6118: strcpy(optionfilegnuplot,optionfilefiname);
6119: if(mle==-3)
6120: strcat(optionfilegnuplot,"-mort");
6121: strcat(optionfilegnuplot,".gp");
6122:
6123: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
6124: printf("Problem with file %s",optionfilegnuplot);
6125: }
6126: else{
6127: fprintf(ficgp,"\n# %s\n", version);
6128: fprintf(ficgp,"# %s\n", optionfilegnuplot);
6129: //fprintf(ficgp,"set missing 'NaNq'\n");
6130: fprintf(ficgp,"set datafile missing 'NaNq'\n");
6131: }
6132: /* fclose(ficgp);*/
6133: /*--------- index.htm --------*/
6134:
6135: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
6136: if(mle==-3)
6137: strcat(optionfilehtm,"-mort");
6138: strcat(optionfilehtm,".htm");
6139: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
6140: printf("Problem with %s \n",optionfilehtm);
6141: exit(0);
6142: }
6143:
6144: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
6145: strcat(optionfilehtmcov,"-cov.htm");
6146: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
6147: printf("Problem with %s \n",optionfilehtmcov), exit(0);
6148: }
6149: else{
6150: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6151: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6152: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
6153: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
6154: }
6155:
6156: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6157: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6158: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
6159: \n\
6160: <hr size=\"2\" color=\"#EC5E5E\">\
6161: <ul><li><h4>Parameter files</h4>\n\
6162: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
6163: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
6164: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
6165: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
6166: - Date and time at start: %s</ul>\n",\
6167: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
6168: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
6169: fileres,fileres,\
6170: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
6171: fflush(fichtm);
6172:
6173: strcpy(pathr,path);
6174: strcat(pathr,optionfilefiname);
6175: chdir(optionfilefiname); /* Move to directory named optionfile */
6176:
6177: /* Calculates basic frequencies. Computes observed prevalence at single age
6178: and prints on file fileres'p'. */
6179: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
6180:
6181: fprintf(fichtm,"\n");
6182: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
6183: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
6184: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
6185: imx,agemin,agemax,jmin,jmax,jmean);
6186: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6187: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6188: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6189: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6190: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
6191:
6192:
6193: /* For Powell, parameters are in a vector p[] starting at p[1]
6194: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
6195: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
6196:
6197: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
6198:
6199: if (mle==-3){
6200: ximort=matrix(1,NDIM,1,NDIM);
6201: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
6202: cens=ivector(1,n);
6203: ageexmed=vector(1,n);
6204: agecens=vector(1,n);
6205: dcwave=ivector(1,n);
6206:
6207: for (i=1; i<=imx; i++){
6208: dcwave[i]=-1;
6209: for (m=firstpass; m<=lastpass; m++)
6210: if (s[m][i]>nlstate) {
6211: dcwave[i]=m;
6212: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
6213: break;
6214: }
6215: }
6216:
6217: for (i=1; i<=imx; i++) {
6218: if (wav[i]>0){
6219: ageexmed[i]=agev[mw[1][i]][i];
6220: j=wav[i];
6221: agecens[i]=1.;
6222:
6223: if (ageexmed[i]> 1 && wav[i] > 0){
6224: agecens[i]=agev[mw[j][i]][i];
6225: cens[i]= 1;
6226: }else if (ageexmed[i]< 1)
6227: cens[i]= -1;
6228: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
6229: cens[i]=0 ;
6230: }
6231: else cens[i]=-1;
6232: }
6233:
6234: for (i=1;i<=NDIM;i++) {
6235: for (j=1;j<=NDIM;j++)
6236: ximort[i][j]=(i == j ? 1.0 : 0.0);
6237: }
6238:
6239: /*p[1]=0.0268; p[NDIM]=0.083;*/
6240: /*printf("%lf %lf", p[1], p[2]);*/
6241:
6242:
6243: #ifdef GSL
6244: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
6245: #else
6246: printf("Powell\n"); fprintf(ficlog,"Powell\n");
6247: #endif
6248: strcpy(filerespow,"pow-mort");
6249: strcat(filerespow,fileres);
6250: if((ficrespow=fopen(filerespow,"w"))==NULL) {
6251: printf("Problem with resultfile: %s\n", filerespow);
6252: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
6253: }
6254: #ifdef GSL
6255: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
6256: #else
6257: fprintf(ficrespow,"# Powell\n# iter -2*LL");
6258: #endif
6259: /* for (i=1;i<=nlstate;i++)
6260: for(j=1;j<=nlstate+ndeath;j++)
6261: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
6262: */
6263: fprintf(ficrespow,"\n");
6264: #ifdef GSL
6265: /* gsl starts here */
6266: T = gsl_multimin_fminimizer_nmsimplex;
6267: gsl_multimin_fminimizer *sfm = NULL;
6268: gsl_vector *ss, *x;
6269: gsl_multimin_function minex_func;
6270:
6271: /* Initial vertex size vector */
6272: ss = gsl_vector_alloc (NDIM);
6273:
6274: if (ss == NULL){
6275: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
6276: }
6277: /* Set all step sizes to 1 */
6278: gsl_vector_set_all (ss, 0.001);
6279:
6280: /* Starting point */
6281:
6282: x = gsl_vector_alloc (NDIM);
6283:
6284: if (x == NULL){
6285: gsl_vector_free(ss);
6286: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
6287: }
6288:
6289: /* Initialize method and iterate */
6290: /* p[1]=0.0268; p[NDIM]=0.083; */
6291: /* gsl_vector_set(x, 0, 0.0268); */
6292: /* gsl_vector_set(x, 1, 0.083); */
6293: gsl_vector_set(x, 0, p[1]);
6294: gsl_vector_set(x, 1, p[2]);
6295:
6296: minex_func.f = &gompertz_f;
6297: minex_func.n = NDIM;
6298: minex_func.params = (void *)&p; /* ??? */
6299:
6300: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
6301: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
6302:
6303: printf("Iterations beginning .....\n\n");
6304: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
6305:
6306: iteri=0;
6307: while (rval == GSL_CONTINUE){
6308: iteri++;
6309: status = gsl_multimin_fminimizer_iterate(sfm);
6310:
6311: if (status) printf("error: %s\n", gsl_strerror (status));
6312: fflush(0);
6313:
6314: if (status)
6315: break;
6316:
6317: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
6318: ssval = gsl_multimin_fminimizer_size (sfm);
6319:
6320: if (rval == GSL_SUCCESS)
6321: printf ("converged to a local maximum at\n");
6322:
6323: printf("%5d ", iteri);
6324: for (it = 0; it < NDIM; it++){
6325: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
6326: }
6327: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
6328: }
6329:
6330: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
6331:
6332: gsl_vector_free(x); /* initial values */
6333: gsl_vector_free(ss); /* inital step size */
6334: for (it=0; it<NDIM; it++){
6335: p[it+1]=gsl_vector_get(sfm->x,it);
6336: fprintf(ficrespow," %.12lf", p[it]);
6337: }
6338: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
6339: #endif
6340: #ifdef POWELL
6341: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
6342: #endif
6343: fclose(ficrespow);
6344:
6345: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
6346:
6347: for(i=1; i <=NDIM; i++)
6348: for(j=i+1;j<=NDIM;j++)
6349: matcov[i][j]=matcov[j][i];
6350:
6351: printf("\nCovariance matrix\n ");
6352: for(i=1; i <=NDIM; i++) {
6353: for(j=1;j<=NDIM;j++){
6354: printf("%f ",matcov[i][j]);
6355: }
6356: printf("\n ");
6357: }
6358:
6359: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
6360: for (i=1;i<=NDIM;i++)
6361: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
6362:
6363: lsurv=vector(1,AGESUP);
6364: lpop=vector(1,AGESUP);
6365: tpop=vector(1,AGESUP);
6366: lsurv[agegomp]=100000;
6367:
6368: for (k=agegomp;k<=AGESUP;k++) {
6369: agemortsup=k;
6370: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
6371: }
6372:
6373: for (k=agegomp;k<agemortsup;k++)
6374: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
6375:
6376: for (k=agegomp;k<agemortsup;k++){
6377: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
6378: sumlpop=sumlpop+lpop[k];
6379: }
6380:
6381: tpop[agegomp]=sumlpop;
6382: for (k=agegomp;k<(agemortsup-3);k++){
6383: /* tpop[k+1]=2;*/
6384: tpop[k+1]=tpop[k]-lpop[k];
6385: }
6386:
6387:
6388: printf("\nAge lx qx dx Lx Tx e(x)\n");
6389: for (k=agegomp;k<(agemortsup-2);k++)
6390: 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]);
6391:
6392:
6393: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6394: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6395:
6396: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
6397: stepm, weightopt,\
6398: model,imx,p,matcov,agemortsup);
6399:
6400: free_vector(lsurv,1,AGESUP);
6401: free_vector(lpop,1,AGESUP);
6402: free_vector(tpop,1,AGESUP);
6403: #ifdef GSL
6404: free_ivector(cens,1,n);
6405: free_vector(agecens,1,n);
6406: free_ivector(dcwave,1,n);
6407: free_matrix(ximort,1,NDIM,1,NDIM);
6408: #endif
6409: } /* Endof if mle==-3 */
6410:
6411: else{ /* For mle >=1 */
6412: globpr=0;/* debug */
6413: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6414: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6415: for (k=1; k<=npar;k++)
6416: printf(" %d %8.5f",k,p[k]);
6417: printf("\n");
6418: globpr=1; /* to print the contributions */
6419: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6420: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6421: for (k=1; k<=npar;k++)
6422: printf(" %d %8.5f",k,p[k]);
6423: printf("\n");
6424: if(mle>=1){ /* Could be 1 or 2 */
6425: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
6426: }
6427:
6428: /*--------- results files --------------*/
6429: 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);
6430:
6431:
6432: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6433: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6434: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6435: for(i=1,jk=1; i <=nlstate; i++){
6436: for(k=1; k <=(nlstate+ndeath); k++){
6437: if (k != i) {
6438: printf("%d%d ",i,k);
6439: fprintf(ficlog,"%d%d ",i,k);
6440: fprintf(ficres,"%1d%1d ",i,k);
6441: for(j=1; j <=ncovmodel; j++){
6442: printf("%lf ",p[jk]);
6443: fprintf(ficlog,"%lf ",p[jk]);
6444: fprintf(ficres,"%lf ",p[jk]);
6445: jk++;
6446: }
6447: printf("\n");
6448: fprintf(ficlog,"\n");
6449: fprintf(ficres,"\n");
6450: }
6451: }
6452: }
6453: if(mle!=0){
6454: /* Computing hessian and covariance matrix */
6455: ftolhess=ftol; /* Usually correct */
6456: hesscov(matcov, p, npar, delti, ftolhess, func);
6457: }
6458: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
6459: printf("# Scales (for hessian or gradient estimation)\n");
6460: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
6461: for(i=1,jk=1; i <=nlstate; i++){
6462: for(j=1; j <=nlstate+ndeath; j++){
6463: if (j!=i) {
6464: fprintf(ficres,"%1d%1d",i,j);
6465: printf("%1d%1d",i,j);
6466: fprintf(ficlog,"%1d%1d",i,j);
6467: for(k=1; k<=ncovmodel;k++){
6468: printf(" %.5e",delti[jk]);
6469: fprintf(ficlog," %.5e",delti[jk]);
6470: fprintf(ficres," %.5e",delti[jk]);
6471: jk++;
6472: }
6473: printf("\n");
6474: fprintf(ficlog,"\n");
6475: fprintf(ficres,"\n");
6476: }
6477: }
6478: }
6479:
6480: 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");
6481: if(mle>=1)
6482: 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");
6483: 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");
6484: /* # 121 Var(a12)\n\ */
6485: /* # 122 Cov(b12,a12) Var(b12)\n\ */
6486: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
6487: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
6488: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
6489: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
6490: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
6491: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
6492:
6493:
6494: /* Just to have a covariance matrix which will be more understandable
6495: even is we still don't want to manage dictionary of variables
6496: */
6497: for(itimes=1;itimes<=2;itimes++){
6498: jj=0;
6499: for(i=1; i <=nlstate; i++){
6500: for(j=1; j <=nlstate+ndeath; j++){
6501: if(j==i) continue;
6502: for(k=1; k<=ncovmodel;k++){
6503: jj++;
6504: ca[0]= k+'a'-1;ca[1]='\0';
6505: if(itimes==1){
6506: if(mle>=1)
6507: printf("#%1d%1d%d",i,j,k);
6508: fprintf(ficlog,"#%1d%1d%d",i,j,k);
6509: fprintf(ficres,"#%1d%1d%d",i,j,k);
6510: }else{
6511: if(mle>=1)
6512: printf("%1d%1d%d",i,j,k);
6513: fprintf(ficlog,"%1d%1d%d",i,j,k);
6514: fprintf(ficres,"%1d%1d%d",i,j,k);
6515: }
6516: ll=0;
6517: for(li=1;li <=nlstate; li++){
6518: for(lj=1;lj <=nlstate+ndeath; lj++){
6519: if(lj==li) continue;
6520: for(lk=1;lk<=ncovmodel;lk++){
6521: ll++;
6522: if(ll<=jj){
6523: cb[0]= lk +'a'-1;cb[1]='\0';
6524: if(ll<jj){
6525: if(itimes==1){
6526: if(mle>=1)
6527: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6528: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6529: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6530: }else{
6531: if(mle>=1)
6532: printf(" %.5e",matcov[jj][ll]);
6533: fprintf(ficlog," %.5e",matcov[jj][ll]);
6534: fprintf(ficres," %.5e",matcov[jj][ll]);
6535: }
6536: }else{
6537: if(itimes==1){
6538: if(mle>=1)
6539: printf(" Var(%s%1d%1d)",ca,i,j);
6540: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
6541: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
6542: }else{
6543: if(mle>=1)
6544: printf(" %.5e",matcov[jj][ll]);
6545: fprintf(ficlog," %.5e",matcov[jj][ll]);
6546: fprintf(ficres," %.5e",matcov[jj][ll]);
6547: }
6548: }
6549: }
6550: } /* end lk */
6551: } /* end lj */
6552: } /* end li */
6553: if(mle>=1)
6554: printf("\n");
6555: fprintf(ficlog,"\n");
6556: fprintf(ficres,"\n");
6557: numlinepar++;
6558: } /* end k*/
6559: } /*end j */
6560: } /* end i */
6561: } /* end itimes */
6562:
6563: fflush(ficlog);
6564: fflush(ficres);
6565:
6566: while((c=getc(ficpar))=='#' && c!= EOF){
6567: ungetc(c,ficpar);
6568: fgets(line, MAXLINE, ficpar);
6569: fputs(line,stdout);
6570: fputs(line,ficparo);
6571: }
6572: ungetc(c,ficpar);
6573:
6574: estepm=0;
6575: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
6576: if (estepm==0 || estepm < stepm) estepm=stepm;
6577: if (fage <= 2) {
6578: bage = ageminpar;
6579: fage = agemaxpar;
6580: }
6581:
6582: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
6583: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6584: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6585:
6586: while((c=getc(ficpar))=='#' && c!= EOF){
6587: ungetc(c,ficpar);
6588: fgets(line, MAXLINE, ficpar);
6589: fputs(line,stdout);
6590: fputs(line,ficparo);
6591: }
6592: ungetc(c,ficpar);
6593:
6594: 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);
6595: 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);
6596: 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);
6597: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
6598: 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);
6599:
6600: while((c=getc(ficpar))=='#' && c!= EOF){
6601: ungetc(c,ficpar);
6602: fgets(line, MAXLINE, ficpar);
6603: fputs(line,stdout);
6604: fputs(line,ficparo);
6605: }
6606: ungetc(c,ficpar);
6607:
6608:
6609: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
6610: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
6611:
6612: fscanf(ficpar,"pop_based=%d\n",&popbased);
6613: fprintf(ficparo,"pop_based=%d\n",popbased);
6614: fprintf(ficres,"pop_based=%d\n",popbased);
6615:
6616: while((c=getc(ficpar))=='#' && c!= EOF){
6617: ungetc(c,ficpar);
6618: fgets(line, MAXLINE, ficpar);
6619: fputs(line,stdout);
6620: fputs(line,ficparo);
6621: }
6622: ungetc(c,ficpar);
6623:
6624: 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);
6625: 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);
6626: 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);
6627: 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);
6628: 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);
6629: /* day and month of proj2 are not used but only year anproj2.*/
6630:
6631:
6632:
6633: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
6634: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
6635:
6636: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6637: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6638:
6639: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
6640: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
6641: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
6642:
6643: /*------------ free_vector -------------*/
6644: /* chdir(path); */
6645:
6646: free_ivector(wav,1,imx);
6647: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
6648: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
6649: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
6650: free_lvector(num,1,n);
6651: free_vector(agedc,1,n);
6652: /*free_matrix(covar,0,NCOVMAX,1,n);*/
6653: /*free_matrix(covar,1,NCOVMAX,1,n);*/
6654: fclose(ficparo);
6655: fclose(ficres);
6656:
6657:
6658: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6659: #include "prevlim.h" /* Use ficrespl, ficlog */
6660: fclose(ficrespl);
6661:
6662: #ifdef FREEEXIT2
6663: #include "freeexit2.h"
6664: #endif
6665:
6666: /*------------- h Pij x at various ages ------------*/
6667: #include "hpijx.h"
6668: fclose(ficrespij);
6669:
6670: /*-------------- Variance of one-step probabilities---*/
6671: k=1;
6672: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
6673:
6674:
6675: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6676: for(i=1;i<=AGESUP;i++)
6677: for(j=1;j<=NCOVMAX;j++)
6678: for(k=1;k<=NCOVMAX;k++)
6679: probs[i][j][k]=0.;
6680:
6681: /*---------- Forecasting ------------------*/
6682: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
6683: if(prevfcast==1){
6684: /* if(stepm ==1){*/
6685: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
6686: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
6687: /* } */
6688: /* else{ */
6689: /* erreur=108; */
6690: /* 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); */
6691: /* 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); */
6692: /* } */
6693: }
6694:
6695:
6696: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
6697:
6698: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
6699: /* 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",\
6700: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
6701: */
6702:
6703: if (mobilav!=0) {
6704: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6705: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
6706: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
6707: printf(" Error in movingaverage mobilav=%d\n",mobilav);
6708: }
6709: }
6710:
6711:
6712: /*---------- Health expectancies, no variances ------------*/
6713:
6714: strcpy(filerese,"e");
6715: strcat(filerese,fileres);
6716: if((ficreseij=fopen(filerese,"w"))==NULL) {
6717: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6718: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6719: }
6720: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
6721: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
6722: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6723: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6724:
6725: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6726: fprintf(ficreseij,"\n#****** ");
6727: for(j=1;j<=cptcoveff;j++) {
6728: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6729: }
6730: fprintf(ficreseij,"******\n");
6731:
6732: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6733: oldm=oldms;savm=savms;
6734: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
6735:
6736: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6737: /*}*/
6738: }
6739: fclose(ficreseij);
6740:
6741:
6742: /*---------- Health expectancies and variances ------------*/
6743:
6744:
6745: strcpy(filerest,"t");
6746: strcat(filerest,fileres);
6747: if((ficrest=fopen(filerest,"w"))==NULL) {
6748: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
6749: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
6750: }
6751: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6752: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6753:
6754:
6755: strcpy(fileresstde,"stde");
6756: strcat(fileresstde,fileres);
6757: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
6758: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6759: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6760: }
6761: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6762: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6763:
6764: strcpy(filerescve,"cve");
6765: strcat(filerescve,fileres);
6766: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
6767: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6768: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6769: }
6770: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6771: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6772:
6773: strcpy(fileresv,"v");
6774: strcat(fileresv,fileres);
6775: if((ficresvij=fopen(fileresv,"w"))==NULL) {
6776: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
6777: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
6778: }
6779: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6780: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6781:
6782: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6783: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6784:
6785: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6786: fprintf(ficrest,"\n#****** ");
6787: for(j=1;j<=cptcoveff;j++)
6788: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6789: fprintf(ficrest,"******\n");
6790:
6791: fprintf(ficresstdeij,"\n#****** ");
6792: fprintf(ficrescveij,"\n#****** ");
6793: for(j=1;j<=cptcoveff;j++) {
6794: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6795: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6796: }
6797: fprintf(ficresstdeij,"******\n");
6798: fprintf(ficrescveij,"******\n");
6799:
6800: fprintf(ficresvij,"\n#****** ");
6801: for(j=1;j<=cptcoveff;j++)
6802: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6803: fprintf(ficresvij,"******\n");
6804:
6805: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6806: oldm=oldms;savm=savms;
6807: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
6808: /*
6809: */
6810: /* goto endfree; */
6811:
6812: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6813: pstamp(ficrest);
6814:
6815:
6816: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
6817: oldm=oldms;savm=savms; /* Segmentation fault */
6818: cptcod= 0; /* To be deleted */
6819: 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 */
6820: 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 ");
6821: if(vpopbased==1)
6822: 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);
6823: else
6824: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
6825: fprintf(ficrest,"# Age e.. (std) ");
6826: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
6827: fprintf(ficrest,"\n");
6828:
6829: epj=vector(1,nlstate+1);
6830: for(age=bage; age <=fage ;age++){
6831: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6832: if (vpopbased==1) {
6833: if(mobilav ==0){
6834: for(i=1; i<=nlstate;i++)
6835: prlim[i][i]=probs[(int)age][i][k];
6836: }else{ /* mobilav */
6837: for(i=1; i<=nlstate;i++)
6838: prlim[i][i]=mobaverage[(int)age][i][k];
6839: }
6840: }
6841:
6842: fprintf(ficrest," %4.0f",age);
6843: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
6844: for(i=1, epj[j]=0.;i <=nlstate;i++) {
6845: epj[j] += prlim[i][i]*eij[i][j][(int)age];
6846: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
6847: }
6848: epj[nlstate+1] +=epj[j];
6849: }
6850:
6851: for(i=1, vepp=0.;i <=nlstate;i++)
6852: for(j=1;j <=nlstate;j++)
6853: vepp += vareij[i][j][(int)age];
6854: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
6855: for(j=1;j <=nlstate;j++){
6856: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
6857: }
6858: fprintf(ficrest,"\n");
6859: }
6860: }
6861: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6862: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6863: free_vector(epj,1,nlstate+1);
6864: /*}*/
6865: }
6866: free_vector(weight,1,n);
6867: free_imatrix(Tvard,1,NCOVMAX,1,2);
6868: free_imatrix(s,1,maxwav+1,1,n);
6869: free_matrix(anint,1,maxwav,1,n);
6870: free_matrix(mint,1,maxwav,1,n);
6871: free_ivector(cod,1,n);
6872: free_ivector(tab,1,NCOVMAX);
6873: fclose(ficresstdeij);
6874: fclose(ficrescveij);
6875: fclose(ficresvij);
6876: fclose(ficrest);
6877: fclose(ficpar);
6878:
6879: /*------- Variance of period (stable) prevalence------*/
6880:
6881: strcpy(fileresvpl,"vpl");
6882: strcat(fileresvpl,fileres);
6883: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
6884: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
6885: exit(0);
6886: }
6887: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
6888:
6889: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6890: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6891:
6892: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6893: fprintf(ficresvpl,"\n#****** ");
6894: for(j=1;j<=cptcoveff;j++)
6895: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6896: fprintf(ficresvpl,"******\n");
6897:
6898: varpl=matrix(1,nlstate,(int) bage, (int) fage);
6899: oldm=oldms;savm=savms;
6900: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
6901: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
6902: /*}*/
6903: }
6904:
6905: fclose(ficresvpl);
6906:
6907: /*---------- End : free ----------------*/
6908: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6909: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6910: } /* mle==-3 arrives here for freeing */
6911: /* endfree:*/
6912: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
6913: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
6914: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
6915: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
6916: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
6917: free_matrix(covar,0,NCOVMAX,1,n);
6918: free_matrix(matcov,1,npar,1,npar);
6919: /*free_vector(delti,1,npar);*/
6920: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6921: free_matrix(agev,1,maxwav,1,imx);
6922: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6923:
6924: free_ivector(ncodemax,1,NCOVMAX);
6925: free_ivector(Tvar,1,NCOVMAX);
6926: free_ivector(Tprod,1,NCOVMAX);
6927: free_ivector(Tvaraff,1,NCOVMAX);
6928: free_ivector(Tage,1,NCOVMAX);
6929:
6930: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
6931: free_imatrix(codtab,1,100,1,10);
6932: fflush(fichtm);
6933: fflush(ficgp);
6934:
6935:
6936: if((nberr >0) || (nbwarn>0)){
6937: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
6938: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
6939: }else{
6940: printf("End of Imach\n");
6941: fprintf(ficlog,"End of Imach\n");
6942: }
6943: printf("See log file on %s\n",filelog);
6944: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
6945: /*(void) gettimeofday(&end_time,&tzp);*/
6946: rend_time = time(NULL);
6947: end_time = *localtime(&rend_time);
6948: /* tml = *localtime(&end_time.tm_sec); */
6949: strcpy(strtend,asctime(&end_time));
6950: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
6951: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
6952: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
6953:
6954: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
6955: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
6956: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
6957: /* printf("Total time was %d uSec.\n", total_usecs);*/
6958: /* if(fileappend(fichtm,optionfilehtm)){ */
6959: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6960: fclose(fichtm);
6961: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6962: fclose(fichtmcov);
6963: fclose(ficgp);
6964: fclose(ficlog);
6965: /*------ End -----------*/
6966:
6967:
6968: printf("Before Current directory %s!\n",pathcd);
6969: if(chdir(pathcd) != 0)
6970: printf("Can't move to directory %s!\n",path);
6971: if(getcwd(pathcd,MAXLINE) > 0)
6972: printf("Current directory %s!\n",pathcd);
6973: /*strcat(plotcmd,CHARSEPARATOR);*/
6974: sprintf(plotcmd,"gnuplot");
6975: #ifdef _WIN32
6976: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
6977: #endif
6978: if(!stat(plotcmd,&info)){
6979: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
6980: if(!stat(getenv("GNUPLOTBIN"),&info)){
6981: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
6982: }else
6983: strcpy(pplotcmd,plotcmd);
6984: #ifdef __unix
6985: strcpy(plotcmd,GNUPLOTPROGRAM);
6986: if(!stat(plotcmd,&info)){
6987: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
6988: }else
6989: strcpy(pplotcmd,plotcmd);
6990: #endif
6991: }else
6992: strcpy(pplotcmd,plotcmd);
6993:
6994: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
6995: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
6996:
6997: if((outcmd=system(plotcmd)) != 0){
6998: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
6999: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
7000: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
7001: if((outcmd=system(plotcmd)) != 0)
7002: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
7003: }
7004: printf(" Successful, please wait...");
7005: while (z[0] != 'q') {
7006: /* chdir(path); */
7007: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
7008: scanf("%s",z);
7009: /* if (z[0] == 'c') system("./imach"); */
7010: if (z[0] == 'e') {
7011: #ifdef __APPLE__
7012: sprintf(pplotcmd, "open %s", optionfilehtm);
7013: #elif __linux
7014: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
7015: #else
7016: sprintf(pplotcmd, "%s", optionfilehtm);
7017: #endif
7018: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
7019: system(pplotcmd);
7020: }
7021: else if (z[0] == 'g') system(plotcmd);
7022: else if (z[0] == 'q') exit(0);
7023: }
7024: end:
7025: while (z[0] != 'q') {
7026: printf("\nType q for exiting: ");
7027: scanf("%s",z);
7028: }
7029: }
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