1: /* $Id: imach.c,v 1.187 2015/04/29 09:11:15 brouard Exp $
2: $State: Exp $
3: $Log: imach.c,v $
4: Revision 1.187 2015/04/29 09:11:15 brouard
5: *** empty log message ***
6:
7: Revision 1.186 2015/04/23 12:01:52 brouard
8: Summary: V1*age is working now, version 0.98q1
9:
10: Some codes had been disabled in order to simplify and Vn*age was
11: working in the optimization phase, ie, giving correct MLE parameters,
12: but, as usual, outputs were not correct and program core dumped.
13:
14: Revision 1.185 2015/03/11 13:26:42 brouard
15: Summary: Inclusion of compile and links command line for Intel Compiler
16:
17: Revision 1.184 2015/03/11 11:52:39 brouard
18: Summary: Back from Windows 8. Intel Compiler
19:
20: Revision 1.183 2015/03/10 20:34:32 brouard
21: Summary: 0.98q0, trying with directest, mnbrak fixed
22:
23: We use directest instead of original Powell test; probably no
24: incidence on the results, but better justifications;
25: We fixed Numerical Recipes mnbrak routine which was wrong and gave
26: wrong results.
27:
28: Revision 1.182 2015/02/12 08:19:57 brouard
29: Summary: Trying to keep directest which seems simpler and more general
30: Author: Nicolas Brouard
31:
32: Revision 1.181 2015/02/11 23:22:24 brouard
33: Summary: Comments on Powell added
34:
35: Author:
36:
37: Revision 1.180 2015/02/11 17:33:45 brouard
38: Summary: Finishing move from main to function (hpijx and prevalence_limit)
39:
40: Revision 1.179 2015/01/04 09:57:06 brouard
41: Summary: back to OS/X
42:
43: Revision 1.178 2015/01/04 09:35:48 brouard
44: *** empty log message ***
45:
46: Revision 1.177 2015/01/03 18:40:56 brouard
47: Summary: Still testing ilc32 on OSX
48:
49: Revision 1.176 2015/01/03 16:45:04 brouard
50: *** empty log message ***
51:
52: Revision 1.175 2015/01/03 16:33:42 brouard
53: *** empty log message ***
54:
55: Revision 1.174 2015/01/03 16:15:49 brouard
56: Summary: Still in cross-compilation
57:
58: Revision 1.173 2015/01/03 12:06:26 brouard
59: Summary: trying to detect cross-compilation
60:
61: Revision 1.172 2014/12/27 12:07:47 brouard
62: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
63:
64: Revision 1.171 2014/12/23 13:26:59 brouard
65: Summary: Back from Visual C
66:
67: Still problem with utsname.h on Windows
68:
69: Revision 1.170 2014/12/23 11:17:12 brouard
70: Summary: Cleaning some \%% back to %%
71:
72: The escape was mandatory for a specific compiler (which one?), but too many warnings.
73:
74: Revision 1.169 2014/12/22 23:08:31 brouard
75: Summary: 0.98p
76:
77: Outputs some informations on compiler used, OS etc. Testing on different platforms.
78:
79: Revision 1.168 2014/12/22 15:17:42 brouard
80: Summary: update
81:
82: Revision 1.167 2014/12/22 13:50:56 brouard
83: Summary: Testing uname and compiler version and if compiled 32 or 64
84:
85: Testing on Linux 64
86:
87: Revision 1.166 2014/12/22 11:40:47 brouard
88: *** empty log message ***
89:
90: Revision 1.165 2014/12/16 11:20:36 brouard
91: Summary: After compiling on Visual C
92:
93: * imach.c (Module): Merging 1.61 to 1.162
94:
95: Revision 1.164 2014/12/16 10:52:11 brouard
96: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
97:
98: * imach.c (Module): Merging 1.61 to 1.162
99:
100: Revision 1.163 2014/12/16 10:30:11 brouard
101: * imach.c (Module): Merging 1.61 to 1.162
102:
103: Revision 1.162 2014/09/25 11:43:39 brouard
104: Summary: temporary backup 0.99!
105:
106: Revision 1.1 2014/09/16 11:06:58 brouard
107: Summary: With some code (wrong) for nlopt
108:
109: Author:
110:
111: Revision 1.161 2014/09/15 20:41:41 brouard
112: Summary: Problem with macro SQR on Intel compiler
113:
114: Revision 1.160 2014/09/02 09:24:05 brouard
115: *** empty log message ***
116:
117: Revision 1.159 2014/09/01 10:34:10 brouard
118: Summary: WIN32
119: Author: Brouard
120:
121: Revision 1.158 2014/08/27 17:11:51 brouard
122: *** empty log message ***
123:
124: Revision 1.157 2014/08/27 16:26:55 brouard
125: Summary: Preparing windows Visual studio version
126: Author: Brouard
127:
128: In order to compile on Visual studio, time.h is now correct and time_t
129: and tm struct should be used. difftime should be used but sometimes I
130: just make the differences in raw time format (time(&now).
131: Trying to suppress #ifdef LINUX
132: Add xdg-open for __linux in order to open default browser.
133:
134: Revision 1.156 2014/08/25 20:10:10 brouard
135: *** empty log message ***
136:
137: Revision 1.155 2014/08/25 18:32:34 brouard
138: Summary: New compile, minor changes
139: Author: Brouard
140:
141: Revision 1.154 2014/06/20 17:32:08 brouard
142: Summary: Outputs now all graphs of convergence to period prevalence
143:
144: Revision 1.153 2014/06/20 16:45:46 brouard
145: Summary: If 3 live state, convergence to period prevalence on same graph
146: Author: Brouard
147:
148: Revision 1.152 2014/06/18 17:54:09 brouard
149: Summary: open browser, use gnuplot on same dir than imach if not found in the path
150:
151: Revision 1.151 2014/06/18 16:43:30 brouard
152: *** empty log message ***
153:
154: Revision 1.150 2014/06/18 16:42:35 brouard
155: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
156: Author: brouard
157:
158: Revision 1.149 2014/06/18 15:51:14 brouard
159: Summary: Some fixes in parameter files errors
160: Author: Nicolas Brouard
161:
162: Revision 1.148 2014/06/17 17:38:48 brouard
163: Summary: Nothing new
164: Author: Brouard
165:
166: Just a new packaging for OS/X version 0.98nS
167:
168: Revision 1.147 2014/06/16 10:33:11 brouard
169: *** empty log message ***
170:
171: Revision 1.146 2014/06/16 10:20:28 brouard
172: Summary: Merge
173: Author: Brouard
174:
175: Merge, before building revised version.
176:
177: Revision 1.145 2014/06/10 21:23:15 brouard
178: Summary: Debugging with valgrind
179: Author: Nicolas Brouard
180:
181: Lot of changes in order to output the results with some covariates
182: After the Edimburgh REVES conference 2014, it seems mandatory to
183: improve the code.
184: No more memory valgrind error but a lot has to be done in order to
185: continue the work of splitting the code into subroutines.
186: Also, decodemodel has been improved. Tricode is still not
187: optimal. nbcode should be improved. Documentation has been added in
188: the source code.
189:
190: Revision 1.143 2014/01/26 09:45:38 brouard
191: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
192:
193: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
194: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
195:
196: Revision 1.142 2014/01/26 03:57:36 brouard
197: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
198:
199: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
200:
201: Revision 1.141 2014/01/26 02:42:01 brouard
202: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
203:
204: Revision 1.140 2011/09/02 10:37:54 brouard
205: Summary: times.h is ok with mingw32 now.
206:
207: Revision 1.139 2010/06/14 07:50:17 brouard
208: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
209: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
210:
211: Revision 1.138 2010/04/30 18:19:40 brouard
212: *** empty log message ***
213:
214: Revision 1.137 2010/04/29 18:11:38 brouard
215: (Module): Checking covariates for more complex models
216: than V1+V2. A lot of change to be done. Unstable.
217:
218: Revision 1.136 2010/04/26 20:30:53 brouard
219: (Module): merging some libgsl code. Fixing computation
220: of likelione (using inter/intrapolation if mle = 0) in order to
221: get same likelihood as if mle=1.
222: Some cleaning of code and comments added.
223:
224: Revision 1.135 2009/10/29 15:33:14 brouard
225: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
226:
227: Revision 1.134 2009/10/29 13:18:53 brouard
228: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
229:
230: Revision 1.133 2009/07/06 10:21:25 brouard
231: just nforces
232:
233: Revision 1.132 2009/07/06 08:22:05 brouard
234: Many tings
235:
236: Revision 1.131 2009/06/20 16:22:47 brouard
237: Some dimensions resccaled
238:
239: Revision 1.130 2009/05/26 06:44:34 brouard
240: (Module): Max Covariate is now set to 20 instead of 8. A
241: lot of cleaning with variables initialized to 0. Trying to make
242: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
243:
244: Revision 1.129 2007/08/31 13:49:27 lievre
245: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
246:
247: Revision 1.128 2006/06/30 13:02:05 brouard
248: (Module): Clarifications on computing e.j
249:
250: Revision 1.127 2006/04/28 18:11:50 brouard
251: (Module): Yes the sum of survivors was wrong since
252: imach-114 because nhstepm was no more computed in the age
253: loop. Now we define nhstepma in the age loop.
254: (Module): In order to speed up (in case of numerous covariates) we
255: compute health expectancies (without variances) in a first step
256: and then all the health expectancies with variances or standard
257: deviation (needs data from the Hessian matrices) which slows the
258: computation.
259: In the future we should be able to stop the program is only health
260: expectancies and graph are needed without standard deviations.
261:
262: Revision 1.126 2006/04/28 17:23:28 brouard
263: (Module): Yes the sum of survivors was wrong since
264: imach-114 because nhstepm was no more computed in the age
265: loop. Now we define nhstepma in the age loop.
266: Version 0.98h
267:
268: Revision 1.125 2006/04/04 15:20:31 lievre
269: Errors in calculation of health expectancies. Age was not initialized.
270: Forecasting file added.
271:
272: Revision 1.124 2006/03/22 17:13:53 lievre
273: Parameters are printed with %lf instead of %f (more numbers after the comma).
274: The log-likelihood is printed in the log file
275:
276: Revision 1.123 2006/03/20 10:52:43 brouard
277: * imach.c (Module): <title> changed, corresponds to .htm file
278: name. <head> headers where missing.
279:
280: * imach.c (Module): Weights can have a decimal point as for
281: English (a comma might work with a correct LC_NUMERIC environment,
282: otherwise the weight is truncated).
283: Modification of warning when the covariates values are not 0 or
284: 1.
285: Version 0.98g
286:
287: Revision 1.122 2006/03/20 09:45:41 brouard
288: (Module): Weights can have a decimal point as for
289: English (a comma might work with a correct LC_NUMERIC environment,
290: otherwise the weight is truncated).
291: Modification of warning when the covariates values are not 0 or
292: 1.
293: Version 0.98g
294:
295: Revision 1.121 2006/03/16 17:45:01 lievre
296: * imach.c (Module): Comments concerning covariates added
297:
298: * imach.c (Module): refinements in the computation of lli if
299: status=-2 in order to have more reliable computation if stepm is
300: not 1 month. Version 0.98f
301:
302: Revision 1.120 2006/03/16 15:10:38 lievre
303: (Module): refinements in the computation of lli if
304: status=-2 in order to have more reliable computation if stepm is
305: not 1 month. Version 0.98f
306:
307: Revision 1.119 2006/03/15 17:42:26 brouard
308: (Module): Bug if status = -2, the loglikelihood was
309: computed as likelihood omitting the logarithm. Version O.98e
310:
311: Revision 1.118 2006/03/14 18:20:07 brouard
312: (Module): varevsij Comments added explaining the second
313: table of variances if popbased=1 .
314: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
315: (Module): Function pstamp added
316: (Module): Version 0.98d
317:
318: Revision 1.117 2006/03/14 17:16:22 brouard
319: (Module): varevsij Comments added explaining the second
320: table of variances if popbased=1 .
321: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
322: (Module): Function pstamp added
323: (Module): Version 0.98d
324:
325: Revision 1.116 2006/03/06 10:29:27 brouard
326: (Module): Variance-covariance wrong links and
327: varian-covariance of ej. is needed (Saito).
328:
329: Revision 1.115 2006/02/27 12:17:45 brouard
330: (Module): One freematrix added in mlikeli! 0.98c
331:
332: Revision 1.114 2006/02/26 12:57:58 brouard
333: (Module): Some improvements in processing parameter
334: filename with strsep.
335:
336: Revision 1.113 2006/02/24 14:20:24 brouard
337: (Module): Memory leaks checks with valgrind and:
338: datafile was not closed, some imatrix were not freed and on matrix
339: allocation too.
340:
341: Revision 1.112 2006/01/30 09:55:26 brouard
342: (Module): Back to gnuplot.exe instead of wgnuplot.exe
343:
344: Revision 1.111 2006/01/25 20:38:18 brouard
345: (Module): Lots of cleaning and bugs added (Gompertz)
346: (Module): Comments can be added in data file. Missing date values
347: can be a simple dot '.'.
348:
349: Revision 1.110 2006/01/25 00:51:50 brouard
350: (Module): Lots of cleaning and bugs added (Gompertz)
351:
352: Revision 1.109 2006/01/24 19:37:15 brouard
353: (Module): Comments (lines starting with a #) are allowed in data.
354:
355: Revision 1.108 2006/01/19 18:05:42 lievre
356: Gnuplot problem appeared...
357: To be fixed
358:
359: Revision 1.107 2006/01/19 16:20:37 brouard
360: Test existence of gnuplot in imach path
361:
362: Revision 1.106 2006/01/19 13:24:36 brouard
363: Some cleaning and links added in html output
364:
365: Revision 1.105 2006/01/05 20:23:19 lievre
366: *** empty log message ***
367:
368: Revision 1.104 2005/09/30 16:11:43 lievre
369: (Module): sump fixed, loop imx fixed, and simplifications.
370: (Module): If the status is missing at the last wave but we know
371: that the person is alive, then we can code his/her status as -2
372: (instead of missing=-1 in earlier versions) and his/her
373: contributions to the likelihood is 1 - Prob of dying from last
374: health status (= 1-p13= p11+p12 in the easiest case of somebody in
375: the healthy state at last known wave). Version is 0.98
376:
377: Revision 1.103 2005/09/30 15:54:49 lievre
378: (Module): sump fixed, loop imx fixed, and simplifications.
379:
380: Revision 1.102 2004/09/15 17:31:30 brouard
381: Add the possibility to read data file including tab characters.
382:
383: Revision 1.101 2004/09/15 10:38:38 brouard
384: Fix on curr_time
385:
386: Revision 1.100 2004/07/12 18:29:06 brouard
387: Add version for Mac OS X. Just define UNIX in Makefile
388:
389: Revision 1.99 2004/06/05 08:57:40 brouard
390: *** empty log message ***
391:
392: Revision 1.98 2004/05/16 15:05:56 brouard
393: New version 0.97 . First attempt to estimate force of mortality
394: directly from the data i.e. without the need of knowing the health
395: state at each age, but using a Gompertz model: log u =a + b*age .
396: This is the basic analysis of mortality and should be done before any
397: other analysis, in order to test if the mortality estimated from the
398: cross-longitudinal survey is different from the mortality estimated
399: from other sources like vital statistic data.
400:
401: The same imach parameter file can be used but the option for mle should be -3.
402:
403: Agnès, who wrote this part of the code, tried to keep most of the
404: former routines in order to include the new code within the former code.
405:
406: The output is very simple: only an estimate of the intercept and of
407: the slope with 95% confident intervals.
408:
409: Current limitations:
410: A) Even if you enter covariates, i.e. with the
411: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
412: B) There is no computation of Life Expectancy nor Life Table.
413:
414: Revision 1.97 2004/02/20 13:25:42 lievre
415: Version 0.96d. Population forecasting command line is (temporarily)
416: suppressed.
417:
418: Revision 1.96 2003/07/15 15:38:55 brouard
419: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
420: rewritten within the same printf. Workaround: many printfs.
421:
422: Revision 1.95 2003/07/08 07:54:34 brouard
423: * imach.c (Repository):
424: (Repository): Using imachwizard code to output a more meaningful covariance
425: matrix (cov(a12,c31) instead of numbers.
426:
427: Revision 1.94 2003/06/27 13:00:02 brouard
428: Just cleaning
429:
430: Revision 1.93 2003/06/25 16:33:55 brouard
431: (Module): On windows (cygwin) function asctime_r doesn't
432: exist so I changed back to asctime which exists.
433: (Module): Version 0.96b
434:
435: Revision 1.92 2003/06/25 16:30:45 brouard
436: (Module): On windows (cygwin) function asctime_r doesn't
437: exist so I changed back to asctime which exists.
438:
439: Revision 1.91 2003/06/25 15:30:29 brouard
440: * imach.c (Repository): Duplicated warning errors corrected.
441: (Repository): Elapsed time after each iteration is now output. It
442: helps to forecast when convergence will be reached. Elapsed time
443: is stamped in powell. We created a new html file for the graphs
444: concerning matrix of covariance. It has extension -cov.htm.
445:
446: Revision 1.90 2003/06/24 12:34:15 brouard
447: (Module): Some bugs corrected for windows. Also, when
448: mle=-1 a template is output in file "or"mypar.txt with the design
449: of the covariance matrix to be input.
450:
451: Revision 1.89 2003/06/24 12:30:52 brouard
452: (Module): Some bugs corrected for windows. Also, when
453: mle=-1 a template is output in file "or"mypar.txt with the design
454: of the covariance matrix to be input.
455:
456: Revision 1.88 2003/06/23 17:54:56 brouard
457: * 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.
458:
459: Revision 1.87 2003/06/18 12:26:01 brouard
460: Version 0.96
461:
462: Revision 1.86 2003/06/17 20:04:08 brouard
463: (Module): Change position of html and gnuplot routines and added
464: routine fileappend.
465:
466: Revision 1.85 2003/06/17 13:12:43 brouard
467: * imach.c (Repository): Check when date of death was earlier that
468: current date of interview. It may happen when the death was just
469: prior to the death. In this case, dh was negative and likelihood
470: was wrong (infinity). We still send an "Error" but patch by
471: assuming that the date of death was just one stepm after the
472: interview.
473: (Repository): Because some people have very long ID (first column)
474: we changed int to long in num[] and we added a new lvector for
475: memory allocation. But we also truncated to 8 characters (left
476: truncation)
477: (Repository): No more line truncation errors.
478:
479: Revision 1.84 2003/06/13 21:44:43 brouard
480: * imach.c (Repository): Replace "freqsummary" at a correct
481: place. It differs from routine "prevalence" which may be called
482: many times. Probs is memory consuming and must be used with
483: parcimony.
484: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
485:
486: Revision 1.83 2003/06/10 13:39:11 lievre
487: *** empty log message ***
488:
489: Revision 1.82 2003/06/05 15:57:20 brouard
490: Add log in imach.c and fullversion number is now printed.
491:
492: */
493: /*
494: Interpolated Markov Chain
495:
496: Short summary of the programme:
497:
498: This program computes Healthy Life Expectancies from
499: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
500: first survey ("cross") where individuals from different ages are
501: interviewed on their health status or degree of disability (in the
502: case of a health survey which is our main interest) -2- at least a
503: second wave of interviews ("longitudinal") which measure each change
504: (if any) in individual health status. Health expectancies are
505: computed from the time spent in each health state according to a
506: model. More health states you consider, more time is necessary to reach the
507: Maximum Likelihood of the parameters involved in the model. The
508: simplest model is the multinomial logistic model where pij is the
509: probability to be observed in state j at the second wave
510: conditional to be observed in state i at the first wave. Therefore
511: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
512: 'age' is age and 'sex' is a covariate. If you want to have a more
513: complex model than "constant and age", you should modify the program
514: where the markup *Covariates have to be included here again* invites
515: you to do it. More covariates you add, slower the
516: convergence.
517:
518: The advantage of this computer programme, compared to a simple
519: multinomial logistic model, is clear when the delay between waves is not
520: identical for each individual. Also, if a individual missed an
521: intermediate interview, the information is lost, but taken into
522: account using an interpolation or extrapolation.
523:
524: hPijx is the probability to be observed in state i at age x+h
525: conditional to the observed state i at age x. The delay 'h' can be
526: split into an exact number (nh*stepm) of unobserved intermediate
527: states. This elementary transition (by month, quarter,
528: semester or year) is modelled as a multinomial logistic. The hPx
529: matrix is simply the matrix product of nh*stepm elementary matrices
530: and the contribution of each individual to the likelihood is simply
531: hPijx.
532:
533: Also this programme outputs the covariance matrix of the parameters but also
534: of the life expectancies. It also computes the period (stable) prevalence.
535:
536: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
537: Institut national d'études démographiques, Paris.
538: This software have been partly granted by Euro-REVES, a concerted action
539: from the European Union.
540: It is copyrighted identically to a GNU software product, ie programme and
541: software can be distributed freely for non commercial use. Latest version
542: can be accessed at http://euroreves.ined.fr/imach .
543:
544: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
545: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
546:
547: **********************************************************************/
548: /*
549: main
550: read parameterfile
551: read datafile
552: concatwav
553: freqsummary
554: if (mle >= 1)
555: mlikeli
556: print results files
557: if mle==1
558: computes hessian
559: read end of parameter file: agemin, agemax, bage, fage, estepm
560: begin-prev-date,...
561: open gnuplot file
562: open html file
563: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
564: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
565: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
566: freexexit2 possible for memory heap.
567:
568: h Pij x | pij_nom ficrestpij
569: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
570: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
571: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
572:
573: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
574: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
575: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
576: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
577: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
578:
579: forecasting if prevfcast==1 prevforecast call prevalence()
580: health expectancies
581: Variance-covariance of DFLE
582: prevalence()
583: movingaverage()
584: varevsij()
585: if popbased==1 varevsij(,popbased)
586: total life expectancies
587: Variance of period (stable) prevalence
588: end
589: */
590:
591: /* #define DEBUG */
592: /* #define DEBUGBRENT */
593: #define POWELL /* Instead of NLOPT */
594: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
595: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
596:
597: #include <math.h>
598: #include <stdio.h>
599: #include <stdlib.h>
600: #include <string.h>
601:
602: #ifdef _WIN32
603: #include <io.h>
604: #include <windows.h>
605: #include <tchar.h>
606: #else
607: #include <unistd.h>
608: #endif
609:
610: #include <limits.h>
611: #include <sys/types.h>
612:
613: #if defined(__GNUC__)
614: #include <sys/utsname.h> /* Doesn't work on Windows */
615: #endif
616:
617: #include <sys/stat.h>
618: #include <errno.h>
619: /* extern int errno; */
620:
621: /* #ifdef LINUX */
622: /* #include <time.h> */
623: /* #include "timeval.h" */
624: /* #else */
625: /* #include <sys/time.h> */
626: /* #endif */
627:
628: #include <time.h>
629:
630: #ifdef GSL
631: #include <gsl/gsl_errno.h>
632: #include <gsl/gsl_multimin.h>
633: #endif
634:
635:
636: #ifdef NLOPT
637: #include <nlopt.h>
638: typedef struct {
639: double (* function)(double [] );
640: } myfunc_data ;
641: #endif
642:
643: /* #include <libintl.h> */
644: /* #define _(String) gettext (String) */
645:
646: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
647:
648: #define GNUPLOTPROGRAM "gnuplot"
649: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
650: #define FILENAMELENGTH 132
651:
652: #define GLOCK_ERROR_NOPATH -1 /* empty path */
653: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
654:
655: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
656: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
657:
658: #define NINTERVMAX 8
659: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
660: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
661: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
662: #define codtabm(h,k) 1 & (h-1) >> (k-1) ;
663: #define MAXN 20000
664: #define YEARM 12. /**< Number of months per year */
665: #define AGESUP 130
666: #define AGEBASE 40
667: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
668: #ifdef _WIN32
669: #define DIRSEPARATOR '\\'
670: #define CHARSEPARATOR "\\"
671: #define ODIRSEPARATOR '/'
672: #else
673: #define DIRSEPARATOR '/'
674: #define CHARSEPARATOR "/"
675: #define ODIRSEPARATOR '\\'
676: #endif
677:
678: /* $Id: imach.c,v 1.187 2015/04/29 09:11:15 brouard Exp $ */
679: /* $State: Exp $ */
680:
681: char version[]="Imach version 0.98q1, April 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
682: char fullversion[]="$Revision: 1.187 $ $Date: 2015/04/29 09:11:15 $";
683: char strstart[80];
684: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
685: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
686: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
687: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
688: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
689: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
690: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
691: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
692: int cptcovprodnoage=0; /**< Number of covariate products without age */
693: int cptcoveff=0; /* Total number of covariates to vary for printing results */
694: int cptcov=0; /* Working variable */
695: int npar=NPARMAX;
696: int nlstate=2; /* Number of live states */
697: int ndeath=1; /* Number of dead states */
698: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
699: int popbased=0;
700:
701: int *wav; /* Number of waves for this individuual 0 is possible */
702: int maxwav=0; /* Maxim number of waves */
703: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
704: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
705: int gipmx=0, gsw=0; /* Global variables on the number of contributions
706: to the likelihood and the sum of weights (done by funcone)*/
707: int mle=1, weightopt=0;
708: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
709: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
710: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
711: * wave mi and wave mi+1 is not an exact multiple of stepm. */
712: int countcallfunc=0; /* Count the number of calls to func */
713: double jmean=1; /* Mean space between 2 waves */
714: double **matprod2(); /* test */
715: double **oldm, **newm, **savm; /* Working pointers to matrices */
716: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
717: /*FILE *fic ; */ /* Used in readdata only */
718: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
719: FILE *ficlog, *ficrespow;
720: int globpr=0; /* Global variable for printing or not */
721: double fretone; /* Only one call to likelihood */
722: long ipmx=0; /* Number of contributions */
723: double sw; /* Sum of weights */
724: char filerespow[FILENAMELENGTH];
725: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
726: FILE *ficresilk;
727: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
728: FILE *ficresprobmorprev;
729: FILE *fichtm, *fichtmcov; /* Html File */
730: FILE *ficreseij;
731: char filerese[FILENAMELENGTH];
732: FILE *ficresstdeij;
733: char fileresstde[FILENAMELENGTH];
734: FILE *ficrescveij;
735: char filerescve[FILENAMELENGTH];
736: FILE *ficresvij;
737: char fileresv[FILENAMELENGTH];
738: FILE *ficresvpl;
739: char fileresvpl[FILENAMELENGTH];
740: char title[MAXLINE];
741: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
742: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
743: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
744: char command[FILENAMELENGTH];
745: int outcmd=0;
746:
747: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
748:
749: char filelog[FILENAMELENGTH]; /* Log file */
750: char filerest[FILENAMELENGTH];
751: char fileregp[FILENAMELENGTH];
752: char popfile[FILENAMELENGTH];
753:
754: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
755:
756: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
757: /* struct timezone tzp; */
758: /* extern int gettimeofday(); */
759: struct tm tml, *gmtime(), *localtime();
760:
761: extern time_t time();
762:
763: struct tm start_time, end_time, curr_time, last_time, forecast_time;
764: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
765: struct tm tm;
766:
767: char strcurr[80], strfor[80];
768:
769: char *endptr;
770: long lval;
771: double dval;
772:
773: #define NR_END 1
774: #define FREE_ARG char*
775: #define FTOL 1.0e-10
776:
777: #define NRANSI
778: #define ITMAX 200
779:
780: #define TOL 2.0e-4
781:
782: #define CGOLD 0.3819660
783: #define ZEPS 1.0e-10
784: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
785:
786: #define GOLD 1.618034
787: #define GLIMIT 100.0
788: #define TINY 1.0e-20
789:
790: static double maxarg1,maxarg2;
791: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
792: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
793:
794: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
795: #define rint(a) floor(a+0.5)
796: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
797: #define mytinydouble 1.0e-16
798: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
799: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
800: /* static double dsqrarg; */
801: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
802: static double sqrarg;
803: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
804: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
805: int agegomp= AGEGOMP;
806:
807: int imx;
808: int stepm=1;
809: /* Stepm, step in month: minimum step interpolation*/
810:
811: int estepm;
812: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
813:
814: int m,nb;
815: long *num;
816: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
817: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
818: double **pmmij, ***probs;
819: double *ageexmed,*agecens;
820: double dateintmean=0;
821:
822: double *weight;
823: int **s; /* Status */
824: double *agedc;
825: double **covar; /**< covar[j,i], value of jth covariate for individual i,
826: * covar=matrix(0,NCOVMAX,1,n);
827: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
828: double idx;
829: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
830: int *Ndum; /** Freq of modality (tricode */
831: int **codtab; /**< codtab=imatrix(1,100,1,10); */
832: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
833: double *lsurv, *lpop, *tpop;
834:
835: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
836: double ftolhess; /**< Tolerance for computing hessian */
837:
838: /**************** split *************************/
839: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
840: {
841: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
842: the name of the file (name), its extension only (ext) and its first part of the name (finame)
843: */
844: char *ss; /* pointer */
845: int l1=0, l2=0; /* length counters */
846:
847: l1 = strlen(path ); /* length of path */
848: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
849: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
850: if ( ss == NULL ) { /* no directory, so determine current directory */
851: strcpy( name, path ); /* we got the fullname name because no directory */
852: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
853: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
854: /* get current working directory */
855: /* extern char* getcwd ( char *buf , int len);*/
856: #ifdef WIN32
857: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
858: #else
859: if (getcwd(dirc, FILENAME_MAX) == NULL) {
860: #endif
861: return( GLOCK_ERROR_GETCWD );
862: }
863: /* got dirc from getcwd*/
864: printf(" DIRC = %s \n",dirc);
865: } else { /* strip direcotry from path */
866: ss++; /* after this, the filename */
867: l2 = strlen( ss ); /* length of filename */
868: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
869: strcpy( name, ss ); /* save file name */
870: strncpy( dirc, path, l1 - l2 ); /* now the directory */
871: dirc[l1-l2] = '\0'; /* add zero */
872: printf(" DIRC2 = %s \n",dirc);
873: }
874: /* We add a separator at the end of dirc if not exists */
875: l1 = strlen( dirc ); /* length of directory */
876: if( dirc[l1-1] != DIRSEPARATOR ){
877: dirc[l1] = DIRSEPARATOR;
878: dirc[l1+1] = 0;
879: printf(" DIRC3 = %s \n",dirc);
880: }
881: ss = strrchr( name, '.' ); /* find last / */
882: if (ss >0){
883: ss++;
884: strcpy(ext,ss); /* save extension */
885: l1= strlen( name);
886: l2= strlen(ss)+1;
887: strncpy( finame, name, l1-l2);
888: finame[l1-l2]= 0;
889: }
890:
891: return( 0 ); /* we're done */
892: }
893:
894:
895: /******************************************/
896:
897: void replace_back_to_slash(char *s, char*t)
898: {
899: int i;
900: int lg=0;
901: i=0;
902: lg=strlen(t);
903: for(i=0; i<= lg; i++) {
904: (s[i] = t[i]);
905: if (t[i]== '\\') s[i]='/';
906: }
907: }
908:
909: char *trimbb(char *out, char *in)
910: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
911: char *s;
912: s=out;
913: while (*in != '\0'){
914: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
915: in++;
916: }
917: *out++ = *in++;
918: }
919: *out='\0';
920: return s;
921: }
922:
923: /* char *substrchaine(char *out, char *in, char *chain) */
924: /* { */
925: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
926: /* char *s, *t; */
927: /* t=in;s=out; */
928: /* while ((*in != *chain) && (*in != '\0')){ */
929: /* *out++ = *in++; */
930: /* } */
931:
932: /* /\* *in matches *chain *\/ */
933: /* while ((*in++ == *chain++) && (*in != '\0')){ */
934: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
935: /* } */
936: /* in--; chain--; */
937: /* while ( (*in != '\0')){ */
938: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
939: /* *out++ = *in++; */
940: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
941: /* } */
942: /* *out='\0'; */
943: /* out=s; */
944: /* return out; */
945: /* } */
946: char *substrchaine(char *out, char *in, char *chain)
947: {
948: /* Substract chain 'chain' from 'in', return and output 'out' */
949: /* in="V1+V1*age+age*age+V2", chain="age*age" */
950:
951: char *strloc;
952:
953: strcpy (out, in);
954: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
955: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
956: if(strloc != NULL){
957: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
958: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
959: /* strcpy (strloc, strloc +strlen(chain));*/
960: }
961: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
962: return out;
963: }
964:
965:
966: char *cutl(char *blocc, char *alocc, char *in, char occ)
967: {
968: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
969: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
970: gives blocc="abcdef" and alocc="ghi2j".
971: If occ is not found blocc is null and alocc is equal to in. Returns blocc
972: */
973: char *s, *t;
974: t=in;s=in;
975: while ((*in != occ) && (*in != '\0')){
976: *alocc++ = *in++;
977: }
978: if( *in == occ){
979: *(alocc)='\0';
980: s=++in;
981: }
982:
983: if (s == t) {/* occ not found */
984: *(alocc-(in-s))='\0';
985: in=s;
986: }
987: while ( *in != '\0'){
988: *blocc++ = *in++;
989: }
990:
991: *blocc='\0';
992: return t;
993: }
994: char *cutv(char *blocc, char *alocc, char *in, char occ)
995: {
996: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
997: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
998: gives blocc="abcdef2ghi" and alocc="j".
999: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1000: */
1001: char *s, *t;
1002: t=in;s=in;
1003: while (*in != '\0'){
1004: while( *in == occ){
1005: *blocc++ = *in++;
1006: s=in;
1007: }
1008: *blocc++ = *in++;
1009: }
1010: if (s == t) /* occ not found */
1011: *(blocc-(in-s))='\0';
1012: else
1013: *(blocc-(in-s)-1)='\0';
1014: in=s;
1015: while ( *in != '\0'){
1016: *alocc++ = *in++;
1017: }
1018:
1019: *alocc='\0';
1020: return s;
1021: }
1022:
1023: int nbocc(char *s, char occ)
1024: {
1025: int i,j=0;
1026: int lg=20;
1027: i=0;
1028: lg=strlen(s);
1029: for(i=0; i<= lg; i++) {
1030: if (s[i] == occ ) j++;
1031: }
1032: return j;
1033: }
1034:
1035: /* void cutv(char *u,char *v, char*t, char occ) */
1036: /* { */
1037: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1038: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1039: /* gives u="abcdef2ghi" and v="j" *\/ */
1040: /* int i,lg,j,p=0; */
1041: /* i=0; */
1042: /* lg=strlen(t); */
1043: /* for(j=0; j<=lg-1; j++) { */
1044: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1045: /* } */
1046:
1047: /* for(j=0; j<p; j++) { */
1048: /* (u[j] = t[j]); */
1049: /* } */
1050: /* u[p]='\0'; */
1051:
1052: /* for(j=0; j<= lg; j++) { */
1053: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1054: /* } */
1055: /* } */
1056:
1057: #ifdef _WIN32
1058: char * strsep(char **pp, const char *delim)
1059: {
1060: char *p, *q;
1061:
1062: if ((p = *pp) == NULL)
1063: return 0;
1064: if ((q = strpbrk (p, delim)) != NULL)
1065: {
1066: *pp = q + 1;
1067: *q = '\0';
1068: }
1069: else
1070: *pp = 0;
1071: return p;
1072: }
1073: #endif
1074:
1075: /********************** nrerror ********************/
1076:
1077: void nrerror(char error_text[])
1078: {
1079: fprintf(stderr,"ERREUR ...\n");
1080: fprintf(stderr,"%s\n",error_text);
1081: exit(EXIT_FAILURE);
1082: }
1083: /*********************** vector *******************/
1084: double *vector(int nl, int nh)
1085: {
1086: double *v;
1087: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1088: if (!v) nrerror("allocation failure in vector");
1089: return v-nl+NR_END;
1090: }
1091:
1092: /************************ free vector ******************/
1093: void free_vector(double*v, int nl, int nh)
1094: {
1095: free((FREE_ARG)(v+nl-NR_END));
1096: }
1097:
1098: /************************ivector *******************************/
1099: int *ivector(long nl,long nh)
1100: {
1101: int *v;
1102: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1103: if (!v) nrerror("allocation failure in ivector");
1104: return v-nl+NR_END;
1105: }
1106:
1107: /******************free ivector **************************/
1108: void free_ivector(int *v, long nl, long nh)
1109: {
1110: free((FREE_ARG)(v+nl-NR_END));
1111: }
1112:
1113: /************************lvector *******************************/
1114: long *lvector(long nl,long nh)
1115: {
1116: long *v;
1117: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1118: if (!v) nrerror("allocation failure in ivector");
1119: return v-nl+NR_END;
1120: }
1121:
1122: /******************free lvector **************************/
1123: void free_lvector(long *v, long nl, long nh)
1124: {
1125: free((FREE_ARG)(v+nl-NR_END));
1126: }
1127:
1128: /******************* imatrix *******************************/
1129: int **imatrix(long nrl, long nrh, long ncl, long nch)
1130: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1131: {
1132: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1133: int **m;
1134:
1135: /* allocate pointers to rows */
1136: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1137: if (!m) nrerror("allocation failure 1 in matrix()");
1138: m += NR_END;
1139: m -= nrl;
1140:
1141:
1142: /* allocate rows and set pointers to them */
1143: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1144: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1145: m[nrl] += NR_END;
1146: m[nrl] -= ncl;
1147:
1148: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1149:
1150: /* return pointer to array of pointers to rows */
1151: return m;
1152: }
1153:
1154: /****************** free_imatrix *************************/
1155: void free_imatrix(m,nrl,nrh,ncl,nch)
1156: int **m;
1157: long nch,ncl,nrh,nrl;
1158: /* free an int matrix allocated by imatrix() */
1159: {
1160: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1161: free((FREE_ARG) (m+nrl-NR_END));
1162: }
1163:
1164: /******************* matrix *******************************/
1165: double **matrix(long nrl, long nrh, long ncl, long nch)
1166: {
1167: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1168: double **m;
1169:
1170: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1171: if (!m) nrerror("allocation failure 1 in matrix()");
1172: m += NR_END;
1173: m -= nrl;
1174:
1175: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1176: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1177: m[nrl] += NR_END;
1178: m[nrl] -= ncl;
1179:
1180: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1181: return m;
1182: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1183: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1184: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1185: */
1186: }
1187:
1188: /*************************free matrix ************************/
1189: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1190: {
1191: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1192: free((FREE_ARG)(m+nrl-NR_END));
1193: }
1194:
1195: /******************* ma3x *******************************/
1196: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1197: {
1198: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1199: double ***m;
1200:
1201: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1202: if (!m) nrerror("allocation failure 1 in matrix()");
1203: m += NR_END;
1204: m -= nrl;
1205:
1206: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1207: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1208: m[nrl] += NR_END;
1209: m[nrl] -= ncl;
1210:
1211: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1212:
1213: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1214: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1215: m[nrl][ncl] += NR_END;
1216: m[nrl][ncl] -= nll;
1217: for (j=ncl+1; j<=nch; j++)
1218: m[nrl][j]=m[nrl][j-1]+nlay;
1219:
1220: for (i=nrl+1; i<=nrh; i++) {
1221: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1222: for (j=ncl+1; j<=nch; j++)
1223: m[i][j]=m[i][j-1]+nlay;
1224: }
1225: return m;
1226: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1227: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1228: */
1229: }
1230:
1231: /*************************free ma3x ************************/
1232: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1233: {
1234: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1235: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1236: free((FREE_ARG)(m+nrl-NR_END));
1237: }
1238:
1239: /*************** function subdirf ***********/
1240: char *subdirf(char fileres[])
1241: {
1242: /* Caution optionfilefiname is hidden */
1243: strcpy(tmpout,optionfilefiname);
1244: strcat(tmpout,"/"); /* Add to the right */
1245: strcat(tmpout,fileres);
1246: return tmpout;
1247: }
1248:
1249: /*************** function subdirf2 ***********/
1250: char *subdirf2(char fileres[], char *preop)
1251: {
1252:
1253: /* Caution optionfilefiname is hidden */
1254: strcpy(tmpout,optionfilefiname);
1255: strcat(tmpout,"/");
1256: strcat(tmpout,preop);
1257: strcat(tmpout,fileres);
1258: return tmpout;
1259: }
1260:
1261: /*************** function subdirf3 ***********/
1262: char *subdirf3(char fileres[], char *preop, char *preop2)
1263: {
1264:
1265: /* Caution optionfilefiname is hidden */
1266: strcpy(tmpout,optionfilefiname);
1267: strcat(tmpout,"/");
1268: strcat(tmpout,preop);
1269: strcat(tmpout,preop2);
1270: strcat(tmpout,fileres);
1271: return tmpout;
1272: }
1273:
1274: char *asc_diff_time(long time_sec, char ascdiff[])
1275: {
1276: long sec_left, days, hours, minutes;
1277: days = (time_sec) / (60*60*24);
1278: sec_left = (time_sec) % (60*60*24);
1279: hours = (sec_left) / (60*60) ;
1280: sec_left = (sec_left) %(60*60);
1281: minutes = (sec_left) /60;
1282: sec_left = (sec_left) % (60);
1283: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1284: return ascdiff;
1285: }
1286:
1287: /***************** f1dim *************************/
1288: extern int ncom;
1289: extern double *pcom,*xicom;
1290: extern double (*nrfunc)(double []);
1291:
1292: double f1dim(double x)
1293: {
1294: int j;
1295: double f;
1296: double *xt;
1297:
1298: xt=vector(1,ncom);
1299: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1300: f=(*nrfunc)(xt);
1301: free_vector(xt,1,ncom);
1302: return f;
1303: }
1304:
1305: /*****************brent *************************/
1306: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1307: {
1308: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1309: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1310: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1311: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1312: * returned function value.
1313: */
1314: int iter;
1315: double a,b,d,etemp;
1316: double fu=0,fv,fw,fx;
1317: double ftemp=0.;
1318: double p,q,r,tol1,tol2,u,v,w,x,xm;
1319: double e=0.0;
1320:
1321: a=(ax < cx ? ax : cx);
1322: b=(ax > cx ? ax : cx);
1323: x=w=v=bx;
1324: fw=fv=fx=(*f)(x);
1325: for (iter=1;iter<=ITMAX;iter++) {
1326: xm=0.5*(a+b);
1327: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1328: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1329: printf(".");fflush(stdout);
1330: fprintf(ficlog,".");fflush(ficlog);
1331: #ifdef DEBUGBRENT
1332: 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);
1333: 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);
1334: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1335: #endif
1336: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1337: *xmin=x;
1338: return fx;
1339: }
1340: ftemp=fu;
1341: if (fabs(e) > tol1) {
1342: r=(x-w)*(fx-fv);
1343: q=(x-v)*(fx-fw);
1344: p=(x-v)*q-(x-w)*r;
1345: q=2.0*(q-r);
1346: if (q > 0.0) p = -p;
1347: q=fabs(q);
1348: etemp=e;
1349: e=d;
1350: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1351: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1352: else {
1353: d=p/q;
1354: u=x+d;
1355: if (u-a < tol2 || b-u < tol2)
1356: d=SIGN(tol1,xm-x);
1357: }
1358: } else {
1359: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1360: }
1361: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1362: fu=(*f)(u);
1363: if (fu <= fx) {
1364: if (u >= x) a=x; else b=x;
1365: SHFT(v,w,x,u)
1366: SHFT(fv,fw,fx,fu)
1367: } else {
1368: if (u < x) a=u; else b=u;
1369: if (fu <= fw || w == x) {
1370: v=w;
1371: w=u;
1372: fv=fw;
1373: fw=fu;
1374: } else if (fu <= fv || v == x || v == w) {
1375: v=u;
1376: fv=fu;
1377: }
1378: }
1379: }
1380: nrerror("Too many iterations in brent");
1381: *xmin=x;
1382: return fx;
1383: }
1384:
1385: /****************** mnbrak ***********************/
1386:
1387: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1388: double (*func)(double))
1389: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1390: the downhill direction (defined by the function as evaluated at the initial points) and returns
1391: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1392: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1393: */
1394: double ulim,u,r,q, dum;
1395: double fu;
1396:
1397: double scale=10.;
1398: int iterscale=0;
1399:
1400: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1401: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1402:
1403:
1404: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1405: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1406: /* *bx = *ax - (*ax - *bx)/scale; */
1407: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1408: /* } */
1409:
1410: if (*fb > *fa) {
1411: SHFT(dum,*ax,*bx,dum)
1412: SHFT(dum,*fb,*fa,dum)
1413: }
1414: *cx=(*bx)+GOLD*(*bx-*ax);
1415: *fc=(*func)(*cx);
1416: #ifdef DEBUG
1417: printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1418: fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1419: #endif
1420: while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
1421: r=(*bx-*ax)*(*fb-*fc);
1422: q=(*bx-*cx)*(*fb-*fa);
1423: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1424: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1425: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1426: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1427: fu=(*func)(u);
1428: #ifdef DEBUG
1429: /* f(x)=A(x-u)**2+f(u) */
1430: double A, fparabu;
1431: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1432: fparabu= *fa - A*(*ax-u)*(*ax-u);
1433: 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);
1434: 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);
1435: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1436: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1437: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1438: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1439: #endif
1440: #ifdef MNBRAKORIGINAL
1441: #else
1442: if (fu > *fc) {
1443: #ifdef DEBUG
1444: printf("mnbrak4 fu > fc \n");
1445: fprintf(ficlog, "mnbrak4 fu > fc\n");
1446: #endif
1447: /* SHFT(u,*cx,*cx,u) /\* ie a=c, c=u and u=c; in that case, next SHFT(a,b,c,u) will give a=b=b, b=c=u, c=u=c and *\/ */
1448: /* SHFT(*fa,*fc,fu,*fc) /\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\/ */
1449: dum=u; /* Shifting c and u */
1450: u = *cx;
1451: *cx = dum;
1452: dum = fu;
1453: fu = *fc;
1454: *fc =dum;
1455: } else { /* end */
1456: #ifdef DEBUG
1457: printf("mnbrak3 fu < fc \n");
1458: fprintf(ficlog, "mnbrak3 fu < fc\n");
1459: #endif
1460: dum=u; /* Shifting c and u */
1461: u = *cx;
1462: *cx = dum;
1463: dum = fu;
1464: fu = *fc;
1465: *fc =dum;
1466: }
1467: #endif
1468: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1469: #ifdef DEBUG
1470: printf("mnbrak2 u after c but before ulim\n");
1471: fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
1472: #endif
1473: fu=(*func)(u);
1474: if (fu < *fc) {
1475: #ifdef DEBUG
1476: printf("mnbrak2 u after c but before ulim AND fu < fc\n");
1477: fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
1478: #endif
1479: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1480: SHFT(*fb,*fc,fu,(*func)(u))
1481: }
1482: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1483: #ifdef DEBUG
1484: printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1485: fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1486: #endif
1487: u=ulim;
1488: fu=(*func)(u);
1489: } else { /* u could be left to b (if r > q parabola has a maximum) */
1490: #ifdef DEBUG
1491: printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1492: fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1493: #endif
1494: u=(*cx)+GOLD*(*cx-*bx);
1495: fu=(*func)(u);
1496: } /* end tests */
1497: SHFT(*ax,*bx,*cx,u)
1498: SHFT(*fa,*fb,*fc,fu)
1499: #ifdef DEBUG
1500: printf("mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
1501: fprintf(ficlog, "mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
1502: #endif
1503: } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
1504: }
1505:
1506: /*************** linmin ************************/
1507: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1508: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1509: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1510: the value of func at the returned location p . This is actually all accomplished by calling the
1511: routines mnbrak and brent .*/
1512: int ncom;
1513: double *pcom,*xicom;
1514: double (*nrfunc)(double []);
1515:
1516: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1517: {
1518: double brent(double ax, double bx, double cx,
1519: double (*f)(double), double tol, double *xmin);
1520: double f1dim(double x);
1521: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1522: double *fc, double (*func)(double));
1523: int j;
1524: double xx,xmin,bx,ax;
1525: double fx,fb,fa;
1526:
1527: double scale=10., axs, xxs, xxss; /* Scale added for infinity */
1528:
1529: ncom=n;
1530: pcom=vector(1,n);
1531: xicom=vector(1,n);
1532: nrfunc=func;
1533: for (j=1;j<=n;j++) {
1534: pcom[j]=p[j];
1535: xicom[j]=xi[j];
1536: }
1537:
1538: axs=0.0;
1539: xxss=1; /* 1 and using scale */
1540: xxs=1;
1541: do{
1542: ax=0.;
1543: xx= xxs;
1544: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
1545: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
1546: /* xt[x,j]=pcom[j]+x*xicom[j] f(ax) = f(xt(a,j=1,n)) = f(p(j) + 0 * xi(j)) and f(xx) = f(xt(x, j=1,n)) = f(p(j) + 1 * xi(j)) */
1547: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
1548: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
1549: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
1550: /* Find a bracket a,x,b in direction n=xi ie xicom, order may change. Scale is [0:xxs*xi[j]] et non plus [0:xi[j]]*/
1551: if (fx != fx){
1552: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
1553: printf("\nLinmin NAN : input [axs=%lf:xxs=%lf], mnbrak outputs fx=%lf <(fb=%lf and fa=%lf) with xx=%lf in [ax=%lf:bx=%lf] \n", axs, xxs, fx,fb, fa, xx, ax, bx);
1554: }
1555: }while(fx != fx);
1556:
1557: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
1558: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
1559: /* fmin = f(p[j] + xmin * xi[j]) */
1560: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
1561: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1562: #ifdef DEBUG
1563: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1564: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1565: #endif
1566: printf("linmin end ");
1567: for (j=1;j<=n;j++) {
1568: printf(" before xi[%d]=%12.8f", j,xi[j]);
1569: xi[j] *= xmin; /* xi rescaled by xmin: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
1570: if(xxs <1.0)
1571: printf(" after xi[%d]=%12.8f, xmin=%12.8f, ax=%12.8f, xx=%12.8f, bx=%12.8f, xxs=%12.8f", j,xi[j], xmin, ax, xx, bx,xxs );
1572: p[j] += xi[j]; /* Parameters values are updated accordingly */
1573: }
1574: printf("\n");
1575: free_vector(xicom,1,n);
1576: free_vector(pcom,1,n);
1577: }
1578:
1579:
1580: /*************** powell ************************/
1581: /*
1582: Minimization of a function func of n variables. Input consists of an initial starting point
1583: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1584: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1585: such that failure to decrease by more than this amount on one iteration signals doneness. On
1586: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1587: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1588: */
1589: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1590: double (*func)(double []))
1591: {
1592: void linmin(double p[], double xi[], int n, double *fret,
1593: double (*func)(double []));
1594: int i,ibig,j;
1595: double del,t,*pt,*ptt,*xit;
1596: double directest;
1597: double fp,fptt;
1598: double *xits;
1599: int niterf, itmp;
1600:
1601: pt=vector(1,n);
1602: ptt=vector(1,n);
1603: xit=vector(1,n);
1604: xits=vector(1,n);
1605: *fret=(*func)(p);
1606: for (j=1;j<=n;j++) pt[j]=p[j];
1607: rcurr_time = time(NULL);
1608: for (*iter=1;;++(*iter)) {
1609: fp=(*fret); /* From former iteration or initial value */
1610: ibig=0;
1611: del=0.0;
1612: rlast_time=rcurr_time;
1613: /* (void) gettimeofday(&curr_time,&tzp); */
1614: rcurr_time = time(NULL);
1615: curr_time = *localtime(&rcurr_time);
1616: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1617: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1618: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1619: for (i=1;i<=n;i++) {
1620: printf(" %d %.12f",i, p[i]);
1621: fprintf(ficlog," %d %.12lf",i, p[i]);
1622: fprintf(ficrespow," %.12lf", p[i]);
1623: }
1624: printf("\n");
1625: fprintf(ficlog,"\n");
1626: fprintf(ficrespow,"\n");fflush(ficrespow);
1627: if(*iter <=3){
1628: tml = *localtime(&rcurr_time);
1629: strcpy(strcurr,asctime(&tml));
1630: rforecast_time=rcurr_time;
1631: itmp = strlen(strcurr);
1632: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1633: strcurr[itmp-1]='\0';
1634: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1635: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1636: for(niterf=10;niterf<=30;niterf+=10){
1637: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1638: forecast_time = *localtime(&rforecast_time);
1639: strcpy(strfor,asctime(&forecast_time));
1640: itmp = strlen(strfor);
1641: if(strfor[itmp-1]=='\n')
1642: strfor[itmp-1]='\0';
1643: 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);
1644: 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);
1645: }
1646: }
1647: for (i=1;i<=n;i++) { /* For each direction i */
1648: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1649: fptt=(*fret);
1650: #ifdef DEBUG
1651: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1652: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1653: #endif
1654: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1655: fprintf(ficlog,"%d",i);fflush(ficlog);
1656: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input. Outputs are fret(new point p) p is updated and xit rescaled */
1657: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions
1658: because that direction will be replaced unless the gain del is small
1659: in comparison with the 'probable' gain, mu^2, with the last average direction.
1660: Unless the n directions are conjugate some gain in the determinant may be obtained
1661: with the new direction.
1662: */
1663: del=fabs(fptt-(*fret));
1664: ibig=i;
1665: }
1666: #ifdef DEBUG
1667: printf("%d %.12e",i,(*fret));
1668: fprintf(ficlog,"%d %.12e",i,(*fret));
1669: for (j=1;j<=n;j++) {
1670: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1671: printf(" x(%d)=%.12e",j,xit[j]);
1672: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1673: }
1674: for(j=1;j<=n;j++) {
1675: printf(" p(%d)=%.12e",j,p[j]);
1676: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1677: }
1678: printf("\n");
1679: fprintf(ficlog,"\n");
1680: #endif
1681: } /* end loop on each direction i */
1682: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1683: /* But p and xit have been updated at the end of linmin and do not produce *fret any more! */
1684: /* New value of last point Pn is not computed, P(n-1) */
1685: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1686: #ifdef DEBUG
1687: int k[2],l;
1688: k[0]=1;
1689: k[1]=-1;
1690: printf("Max: %.12e",(*func)(p));
1691: fprintf(ficlog,"Max: %.12e",(*func)(p));
1692: for (j=1;j<=n;j++) {
1693: printf(" %.12e",p[j]);
1694: fprintf(ficlog," %.12e",p[j]);
1695: }
1696: printf("\n");
1697: fprintf(ficlog,"\n");
1698: for(l=0;l<=1;l++) {
1699: for (j=1;j<=n;j++) {
1700: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1701: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1702: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1703: }
1704: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1705: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1706: }
1707: #endif
1708:
1709:
1710: free_vector(xit,1,n);
1711: free_vector(xits,1,n);
1712: free_vector(ptt,1,n);
1713: free_vector(pt,1,n);
1714: return;
1715: }
1716: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1717: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1718: ptt[j]=2.0*p[j]-pt[j];
1719: xit[j]=p[j]-pt[j];
1720: pt[j]=p[j];
1721: }
1722: fptt=(*func)(ptt); /* f_3 */
1723: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1724: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1725: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1726: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1727: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1728: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1729: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
1730: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1731: #ifdef NRCORIGINAL
1732: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
1733: #else
1734: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
1735: t= t- del*SQR(fp-fptt);
1736: #endif
1737: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
1738: #ifdef DEBUG
1739: printf("t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
1740: fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
1741: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1742: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1743: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1744: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1745: 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);
1746: 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);
1747: #endif
1748: #ifdef POWELLORIGINAL
1749: if (t < 0.0) { /* Then we use it for new direction */
1750: #else
1751: if (directest*t < 0.0) { /* Contradiction between both tests */
1752: printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
1753: printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1754: fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
1755: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1756: }
1757: if (directest < 0.0) { /* Then we use it for new direction */
1758: #endif
1759: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1760: for (j=1;j<=n;j++) {
1761: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
1762: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
1763: }
1764: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1765: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1766:
1767: #ifdef DEBUG
1768: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1769: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1770: for(j=1;j<=n;j++){
1771: printf(" %.12e",xit[j]);
1772: fprintf(ficlog," %.12e",xit[j]);
1773: }
1774: printf("\n");
1775: fprintf(ficlog,"\n");
1776: #endif
1777: } /* end of t negative */
1778: } /* end if (fptt < fp) */
1779: }
1780: }
1781:
1782: /**** Prevalence limit (stable or period prevalence) ****************/
1783:
1784: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1785: {
1786: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1787: matrix by transitions matrix until convergence is reached */
1788:
1789: int i, ii,j,k;
1790: double min, max, maxmin, maxmax,sumnew=0.;
1791: /* double **matprod2(); */ /* test */
1792: double **out, cov[NCOVMAX+1], **pmij();
1793: double **newm;
1794: double agefin, delaymax=50 ; /* Max number of years to converge */
1795:
1796: for (ii=1;ii<=nlstate+ndeath;ii++)
1797: for (j=1;j<=nlstate+ndeath;j++){
1798: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1799: }
1800:
1801: cov[1]=1.;
1802:
1803: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1804: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1805: newm=savm;
1806: /* Covariates have to be included here again */
1807: cov[2]=agefin;
1808: if(nagesqr==1)
1809: cov[3]= agefin*agefin;;
1810: for (k=1; k<=cptcovn;k++) {
1811: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1812: /*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]]);*/
1813: }
1814: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1815: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]*cov[2];
1816: for (k=1; k<=cptcovprod;k++) /* Useless */
1817: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1818:
1819: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1820: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1821: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1822: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1823: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1824: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1825:
1826: savm=oldm;
1827: oldm=newm;
1828: maxmax=0.;
1829: for(j=1;j<=nlstate;j++){
1830: min=1.;
1831: max=0.;
1832: for(i=1; i<=nlstate; i++) {
1833: sumnew=0;
1834: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1835: prlim[i][j]= newm[i][j]/(1-sumnew);
1836: /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
1837: max=FMAX(max,prlim[i][j]);
1838: min=FMIN(min,prlim[i][j]);
1839: }
1840: maxmin=max-min;
1841: maxmax=FMAX(maxmax,maxmin);
1842: } /* j loop */
1843: if(maxmax < ftolpl){
1844: return prlim;
1845: }
1846: } /* age loop */
1847: return prlim; /* should not reach here */
1848: }
1849:
1850: /*************** transition probabilities ***************/
1851:
1852: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1853: {
1854: /* According to parameters values stored in x and the covariate's values stored in cov,
1855: computes the probability to be observed in state j being in state i by appying the
1856: model to the ncovmodel covariates (including constant and age).
1857: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1858: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1859: ncth covariate in the global vector x is given by the formula:
1860: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1861: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1862: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1863: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1864: Outputs ps[i][j] the probability to be observed in j being in j according to
1865: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1866: */
1867: double s1, lnpijopii;
1868: /*double t34;*/
1869: int i,j, nc, ii, jj;
1870:
1871: for(i=1; i<= nlstate; i++){
1872: for(j=1; j<i;j++){
1873: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1874: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1875: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1876: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1877: }
1878: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1879: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1880: }
1881: for(j=i+1; j<=nlstate+ndeath;j++){
1882: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1883: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
1884: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
1885: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1886: }
1887: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1888: }
1889: }
1890:
1891: for(i=1; i<= nlstate; i++){
1892: s1=0;
1893: for(j=1; j<i; j++){
1894: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1895: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1896: }
1897: for(j=i+1; j<=nlstate+ndeath; j++){
1898: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1899: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1900: }
1901: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1902: ps[i][i]=1./(s1+1.);
1903: /* Computing other pijs */
1904: for(j=1; j<i; j++)
1905: ps[i][j]= exp(ps[i][j])*ps[i][i];
1906: for(j=i+1; j<=nlstate+ndeath; j++)
1907: ps[i][j]= exp(ps[i][j])*ps[i][i];
1908: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1909: } /* end i */
1910:
1911: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1912: for(jj=1; jj<= nlstate+ndeath; jj++){
1913: ps[ii][jj]=0;
1914: ps[ii][ii]=1;
1915: }
1916: }
1917:
1918:
1919: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1920: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1921: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
1922: /* } */
1923: /* printf("\n "); */
1924: /* } */
1925: /* printf("\n ");printf("%lf ",cov[2]);*/
1926: /*
1927: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1928: goto end;*/
1929: return ps;
1930: }
1931:
1932: /**************** Product of 2 matrices ******************/
1933:
1934: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1935: {
1936: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1937: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1938: /* in, b, out are matrice of pointers which should have been initialized
1939: before: only the contents of out is modified. The function returns
1940: a pointer to pointers identical to out */
1941: int i, j, k;
1942: for(i=nrl; i<= nrh; i++)
1943: for(k=ncolol; k<=ncoloh; k++){
1944: out[i][k]=0.;
1945: for(j=ncl; j<=nch; j++)
1946: out[i][k] +=in[i][j]*b[j][k];
1947: }
1948: return out;
1949: }
1950:
1951:
1952: /************* Higher Matrix Product ***************/
1953:
1954: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1955: {
1956: /* Computes the transition matrix starting at age 'age' over
1957: 'nhstepm*hstepm*stepm' months (i.e. until
1958: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1959: nhstepm*hstepm matrices.
1960: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1961: (typically every 2 years instead of every month which is too big
1962: for the memory).
1963: Model is determined by parameters x and covariates have to be
1964: included manually here.
1965:
1966: */
1967:
1968: int i, j, d, h, k;
1969: double **out, cov[NCOVMAX+1];
1970: double **newm;
1971: double agexact;
1972:
1973: /* Hstepm could be zero and should return the unit matrix */
1974: for (i=1;i<=nlstate+ndeath;i++)
1975: for (j=1;j<=nlstate+ndeath;j++){
1976: oldm[i][j]=(i==j ? 1.0 : 0.0);
1977: po[i][j][0]=(i==j ? 1.0 : 0.0);
1978: }
1979: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1980: for(h=1; h <=nhstepm; h++){
1981: for(d=1; d <=hstepm; d++){
1982: newm=savm;
1983: /* Covariates have to be included here again */
1984: cov[1]=1.;
1985: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1986: cov[2]=agexact;
1987: if(nagesqr==1)
1988: cov[3]= agexact*agexact;
1989: for (k=1; k<=cptcovn;k++)
1990: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1991: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
1992: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1993: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
1994: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1995: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1996:
1997:
1998: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1999: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
2000: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
2001: pmij(pmmij,cov,ncovmodel,x,nlstate));
2002: savm=oldm;
2003: oldm=newm;
2004: }
2005: for(i=1; i<=nlstate+ndeath; i++)
2006: for(j=1;j<=nlstate+ndeath;j++) {
2007: po[i][j][h]=newm[i][j];
2008: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
2009: }
2010: /*printf("h=%d ",h);*/
2011: } /* end h */
2012: /* printf("\n H=%d \n",h); */
2013: return po;
2014: }
2015:
2016: #ifdef NLOPT
2017: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
2018: double fret;
2019: double *xt;
2020: int j;
2021: myfunc_data *d2 = (myfunc_data *) pd;
2022: /* xt = (p1-1); */
2023: xt=vector(1,n);
2024: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
2025:
2026: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
2027: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
2028: printf("Function = %.12lf ",fret);
2029: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
2030: printf("\n");
2031: free_vector(xt,1,n);
2032: return fret;
2033: }
2034: #endif
2035:
2036: /*************** log-likelihood *************/
2037: double func( double *x)
2038: {
2039: int i, ii, j, k, mi, d, kk;
2040: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
2041: double **out;
2042: double sw; /* Sum of weights */
2043: double lli; /* Individual log likelihood */
2044: int s1, s2;
2045: double bbh, survp;
2046: long ipmx;
2047: double agexact;
2048: /*extern weight */
2049: /* We are differentiating ll according to initial status */
2050: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2051: /*for(i=1;i<imx;i++)
2052: printf(" %d\n",s[4][i]);
2053: */
2054:
2055: ++countcallfunc;
2056:
2057: cov[1]=1.;
2058:
2059: for(k=1; k<=nlstate; k++) ll[k]=0.;
2060:
2061: if(mle==1){
2062: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2063: /* Computes the values of the ncovmodel covariates of the model
2064: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
2065: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
2066: to be observed in j being in i according to the model.
2067: */
2068: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
2069: cov[2+nagesqr+k]=covar[Tvar[k]][i];
2070: }
2071: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
2072: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
2073: has been calculated etc */
2074: for(mi=1; mi<= wav[i]-1; mi++){
2075: for (ii=1;ii<=nlstate+ndeath;ii++)
2076: for (j=1;j<=nlstate+ndeath;j++){
2077: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2078: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2079: }
2080: for(d=0; d<dh[mi][i]; d++){
2081: newm=savm;
2082: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2083: cov[2]=agexact;
2084: if(nagesqr==1)
2085: cov[3]= agexact*agexact;
2086: for (kk=1; kk<=cptcovage;kk++) {
2087: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
2088: }
2089: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2090: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2091: savm=oldm;
2092: oldm=newm;
2093: } /* end mult */
2094:
2095: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
2096: /* But now since version 0.9 we anticipate for bias at large stepm.
2097: * If stepm is larger than one month (smallest stepm) and if the exact delay
2098: * (in months) between two waves is not a multiple of stepm, we rounded to
2099: * the nearest (and in case of equal distance, to the lowest) interval but now
2100: * we keep into memory the bias bh[mi][i] and also the previous matrix product
2101: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
2102: * probability in order to take into account the bias as a fraction of the way
2103: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
2104: * -stepm/2 to stepm/2 .
2105: * For stepm=1 the results are the same as for previous versions of Imach.
2106: * For stepm > 1 the results are less biased than in previous versions.
2107: */
2108: s1=s[mw[mi][i]][i];
2109: s2=s[mw[mi+1][i]][i];
2110: bbh=(double)bh[mi][i]/(double)stepm;
2111: /* bias bh is positive if real duration
2112: * is higher than the multiple of stepm and negative otherwise.
2113: */
2114: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
2115: if( s2 > nlstate){
2116: /* i.e. if s2 is a death state and if the date of death is known
2117: then the contribution to the likelihood is the probability to
2118: die between last step unit time and current step unit time,
2119: which is also equal to probability to die before dh
2120: minus probability to die before dh-stepm .
2121: In version up to 0.92 likelihood was computed
2122: as if date of death was unknown. Death was treated as any other
2123: health state: the date of the interview describes the actual state
2124: and not the date of a change in health state. The former idea was
2125: to consider that at each interview the state was recorded
2126: (healthy, disable or death) and IMaCh was corrected; but when we
2127: introduced the exact date of death then we should have modified
2128: the contribution of an exact death to the likelihood. This new
2129: contribution is smaller and very dependent of the step unit
2130: stepm. It is no more the probability to die between last interview
2131: and month of death but the probability to survive from last
2132: interview up to one month before death multiplied by the
2133: probability to die within a month. Thanks to Chris
2134: Jackson for correcting this bug. Former versions increased
2135: mortality artificially. The bad side is that we add another loop
2136: which slows down the processing. The difference can be up to 10%
2137: lower mortality.
2138: */
2139: /* If, at the beginning of the maximization mostly, the
2140: cumulative probability or probability to be dead is
2141: constant (ie = 1) over time d, the difference is equal to
2142: 0. out[s1][3] = savm[s1][3]: probability, being at state
2143: s1 at precedent wave, to be dead a month before current
2144: wave is equal to probability, being at state s1 at
2145: precedent wave, to be dead at mont of the current
2146: wave. Then the observed probability (that this person died)
2147: is null according to current estimated parameter. In fact,
2148: it should be very low but not zero otherwise the log go to
2149: infinity.
2150: */
2151: /* #ifdef INFINITYORIGINAL */
2152: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2153: /* #else */
2154: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
2155: /* lli=log(mytinydouble); */
2156: /* else */
2157: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2158: /* #endif */
2159: lli=log(out[s1][s2] - savm[s1][s2]);
2160:
2161: } else if (s2==-2) {
2162: for (j=1,survp=0. ; j<=nlstate; j++)
2163: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2164: /*survp += out[s1][j]; */
2165: lli= log(survp);
2166: }
2167:
2168: else if (s2==-4) {
2169: for (j=3,survp=0. ; j<=nlstate; j++)
2170: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2171: lli= log(survp);
2172: }
2173:
2174: else if (s2==-5) {
2175: for (j=1,survp=0. ; j<=2; j++)
2176: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2177: lli= log(survp);
2178: }
2179:
2180: else{
2181: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2182: /* 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 */
2183: }
2184: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
2185: /*if(lli ==000.0)*/
2186: /*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); */
2187: ipmx +=1;
2188: sw += weight[i];
2189: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2190: /* if (lli < log(mytinydouble)){ */
2191: /* printf("Close to inf lli = %.10lf < %.10lf i= %d mi= %d, s[%d][i]=%d s1=%d s2=%d\n", lli,log(mytinydouble), i, mi,mw[mi][i], s[mw[mi][i]][i], s1,s2); */
2192: /* fprintf(ficlog,"Close to inf lli = %.10lf i= %d mi= %d, s[mw[mi][i]][i]=%d\n", lli, i, mi,s[mw[mi][i]][i]); */
2193: /* } */
2194: } /* end of wave */
2195: } /* end of individual */
2196: } else if(mle==2){
2197: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2198: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
2199: for(mi=1; mi<= wav[i]-1; mi++){
2200: for (ii=1;ii<=nlstate+ndeath;ii++)
2201: for (j=1;j<=nlstate+ndeath;j++){
2202: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2203: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2204: }
2205: for(d=0; d<=dh[mi][i]; d++){
2206: newm=savm;
2207: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2208: cov[2]=agexact;
2209: if(nagesqr==1)
2210: cov[3]= agexact*agexact;
2211: for (kk=1; kk<=cptcovage;kk++) {
2212: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
2213: }
2214: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2215: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2216: savm=oldm;
2217: oldm=newm;
2218: } /* end mult */
2219:
2220: s1=s[mw[mi][i]][i];
2221: s2=s[mw[mi+1][i]][i];
2222: bbh=(double)bh[mi][i]/(double)stepm;
2223: 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 */
2224: ipmx +=1;
2225: sw += weight[i];
2226: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2227: } /* end of wave */
2228: } /* end of individual */
2229: } else if(mle==3){ /* exponential inter-extrapolation */
2230: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2231: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
2232: for(mi=1; mi<= wav[i]-1; mi++){
2233: for (ii=1;ii<=nlstate+ndeath;ii++)
2234: for (j=1;j<=nlstate+ndeath;j++){
2235: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2236: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2237: }
2238: for(d=0; d<dh[mi][i]; d++){
2239: newm=savm;
2240: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2241: cov[2]=agexact;
2242: if(nagesqr==1)
2243: cov[3]= agexact*agexact;
2244: for (kk=1; kk<=cptcovage;kk++) {
2245: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
2246: }
2247: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2248: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2249: savm=oldm;
2250: oldm=newm;
2251: } /* end mult */
2252:
2253: s1=s[mw[mi][i]][i];
2254: s2=s[mw[mi+1][i]][i];
2255: bbh=(double)bh[mi][i]/(double)stepm;
2256: 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 */
2257: ipmx +=1;
2258: sw += weight[i];
2259: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2260: } /* end of wave */
2261: } /* end of individual */
2262: }else if (mle==4){ /* ml=4 no inter-extrapolation */
2263: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2264: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
2265: for(mi=1; mi<= wav[i]-1; mi++){
2266: for (ii=1;ii<=nlstate+ndeath;ii++)
2267: for (j=1;j<=nlstate+ndeath;j++){
2268: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2269: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2270: }
2271: for(d=0; d<dh[mi][i]; d++){
2272: newm=savm;
2273: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2274: cov[2]=agexact;
2275: if(nagesqr==1)
2276: cov[3]= agexact*agexact;
2277: for (kk=1; kk<=cptcovage;kk++) {
2278: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
2279: }
2280:
2281: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2282: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2283: savm=oldm;
2284: oldm=newm;
2285: } /* end mult */
2286:
2287: s1=s[mw[mi][i]][i];
2288: s2=s[mw[mi+1][i]][i];
2289: if( s2 > nlstate){
2290: lli=log(out[s1][s2] - savm[s1][s2]);
2291: }else{
2292: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2293: }
2294: ipmx +=1;
2295: sw += weight[i];
2296: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2297: /* 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]); */
2298: } /* end of wave */
2299: } /* end of individual */
2300: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
2301: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2302: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
2303: for(mi=1; mi<= wav[i]-1; mi++){
2304: for (ii=1;ii<=nlstate+ndeath;ii++)
2305: for (j=1;j<=nlstate+ndeath;j++){
2306: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2307: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2308: }
2309: for(d=0; d<dh[mi][i]; d++){
2310: newm=savm;
2311: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2312: cov[2]=agexact;
2313: if(nagesqr==1)
2314: cov[3]= agexact*agexact;
2315: for (kk=1; kk<=cptcovage;kk++) {
2316: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
2317: }
2318:
2319: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2320: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2321: savm=oldm;
2322: oldm=newm;
2323: } /* end mult */
2324:
2325: s1=s[mw[mi][i]][i];
2326: s2=s[mw[mi+1][i]][i];
2327: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2328: ipmx +=1;
2329: sw += weight[i];
2330: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2331: /*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]);*/
2332: } /* end of wave */
2333: } /* end of individual */
2334: } /* End of if */
2335: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2336: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2337: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2338: return -l;
2339: }
2340:
2341: /*************** log-likelihood *************/
2342: double funcone( double *x)
2343: {
2344: /* Same as likeli but slower because of a lot of printf and if */
2345: int i, ii, j, k, mi, d, kk;
2346: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
2347: double **out;
2348: double lli; /* Individual log likelihood */
2349: double llt;
2350: int s1, s2;
2351: double bbh, survp;
2352: double agexact;
2353: /*extern weight */
2354: /* We are differentiating ll according to initial status */
2355: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2356: /*for(i=1;i<imx;i++)
2357: printf(" %d\n",s[4][i]);
2358: */
2359: cov[1]=1.;
2360:
2361: for(k=1; k<=nlstate; k++) ll[k]=0.;
2362:
2363: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2364: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
2365: for(mi=1; mi<= wav[i]-1; mi++){
2366: for (ii=1;ii<=nlstate+ndeath;ii++)
2367: for (j=1;j<=nlstate+ndeath;j++){
2368: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2369: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2370: }
2371: for(d=0; d<dh[mi][i]; d++){
2372: newm=savm;
2373: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2374: cov[2]=agexact;
2375: if(nagesqr==1)
2376: cov[3]= agexact*agexact;
2377: for (kk=1; kk<=cptcovage;kk++) {
2378: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
2379: }
2380:
2381: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2382: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2383: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2384: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2385: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
2386: savm=oldm;
2387: oldm=newm;
2388: } /* end mult */
2389:
2390: s1=s[mw[mi][i]][i];
2391: s2=s[mw[mi+1][i]][i];
2392: bbh=(double)bh[mi][i]/(double)stepm;
2393: /* bias is positive if real duration
2394: * is higher than the multiple of stepm and negative otherwise.
2395: */
2396: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2397: lli=log(out[s1][s2] - savm[s1][s2]);
2398: } else if (s2==-2) {
2399: for (j=1,survp=0. ; j<=nlstate; j++)
2400: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2401: lli= log(survp);
2402: }else if (mle==1){
2403: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2404: } else if(mle==2){
2405: 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 */
2406: } else if(mle==3){ /* exponential inter-extrapolation */
2407: 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 */
2408: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2409: lli=log(out[s1][s2]); /* Original formula */
2410: } else{ /* mle=0 back to 1 */
2411: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2412: /*lli=log(out[s1][s2]); */ /* Original formula */
2413: } /* End of if */
2414: ipmx +=1;
2415: sw += weight[i];
2416: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2417: /*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]); */
2418: if(globpr){
2419: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
2420: %11.6f %11.6f %11.6f ", \
2421: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
2422: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2423: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2424: llt +=ll[k]*gipmx/gsw;
2425: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2426: }
2427: fprintf(ficresilk," %10.6f\n", -llt);
2428: }
2429: } /* end of wave */
2430: } /* end of individual */
2431: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2432: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2433: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2434: if(globpr==0){ /* First time we count the contributions and weights */
2435: gipmx=ipmx;
2436: gsw=sw;
2437: }
2438: return -l;
2439: }
2440:
2441:
2442: /*************** function likelione ***********/
2443: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2444: {
2445: /* This routine should help understanding what is done with
2446: the selection of individuals/waves and
2447: to check the exact contribution to the likelihood.
2448: Plotting could be done.
2449: */
2450: int k;
2451:
2452: if(*globpri !=0){ /* Just counts and sums, no printings */
2453: strcpy(fileresilk,"ilk");
2454: strcat(fileresilk,fileres);
2455: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2456: printf("Problem with resultfile: %s\n", fileresilk);
2457: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2458: }
2459: 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");
2460: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
2461: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2462: for(k=1; k<=nlstate; k++)
2463: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2464: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2465: }
2466:
2467: *fretone=(*funcone)(p);
2468: if(*globpri !=0){
2469: fclose(ficresilk);
2470: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
2471: fflush(fichtm);
2472: }
2473: return;
2474: }
2475:
2476:
2477: /*********** Maximum Likelihood Estimation ***************/
2478:
2479: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2480: {
2481: int i,j, iter=0;
2482: double **xi;
2483: double fret;
2484: double fretone; /* Only one call to likelihood */
2485: /* char filerespow[FILENAMELENGTH];*/
2486:
2487: #ifdef NLOPT
2488: int creturn;
2489: nlopt_opt opt;
2490: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2491: double *lb;
2492: double minf; /* the minimum objective value, upon return */
2493: double * p1; /* Shifted parameters from 0 instead of 1 */
2494: myfunc_data dinst, *d = &dinst;
2495: #endif
2496:
2497:
2498: xi=matrix(1,npar,1,npar);
2499: for (i=1;i<=npar;i++)
2500: for (j=1;j<=npar;j++)
2501: xi[i][j]=(i==j ? 1.0 : 0.0);
2502: printf("Powell\n"); fprintf(ficlog,"Powell\n");
2503: strcpy(filerespow,"pow");
2504: strcat(filerespow,fileres);
2505: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2506: printf("Problem with resultfile: %s\n", filerespow);
2507: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2508: }
2509: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2510: for (i=1;i<=nlstate;i++)
2511: for(j=1;j<=nlstate+ndeath;j++)
2512: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2513: fprintf(ficrespow,"\n");
2514: #ifdef POWELL
2515: powell(p,xi,npar,ftol,&iter,&fret,func);
2516: #endif
2517:
2518: #ifdef NLOPT
2519: #ifdef NEWUOA
2520: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2521: #else
2522: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2523: #endif
2524: lb=vector(0,npar-1);
2525: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2526: nlopt_set_lower_bounds(opt, lb);
2527: nlopt_set_initial_step1(opt, 0.1);
2528:
2529: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2530: d->function = func;
2531: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2532: nlopt_set_min_objective(opt, myfunc, d);
2533: nlopt_set_xtol_rel(opt, ftol);
2534: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2535: printf("nlopt failed! %d\n",creturn);
2536: }
2537: else {
2538: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2539: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2540: iter=1; /* not equal */
2541: }
2542: nlopt_destroy(opt);
2543: #endif
2544: free_matrix(xi,1,npar,1,npar);
2545: fclose(ficrespow);
2546: printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2547: fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2548: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2549:
2550: }
2551:
2552: /**** Computes Hessian and covariance matrix ***/
2553: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
2554: {
2555: double **a,**y,*x,pd;
2556: double **hess;
2557: int i, j;
2558: int *indx;
2559:
2560: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
2561: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
2562: void lubksb(double **a, int npar, int *indx, double b[]) ;
2563: void ludcmp(double **a, int npar, int *indx, double *d) ;
2564: double gompertz(double p[]);
2565: hess=matrix(1,npar,1,npar);
2566:
2567: printf("\nCalculation of the hessian matrix. Wait...\n");
2568: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2569: for (i=1;i<=npar;i++){
2570: printf("%d",i);fflush(stdout);
2571: fprintf(ficlog,"%d",i);fflush(ficlog);
2572:
2573: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2574:
2575: /* printf(" %f ",p[i]);
2576: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2577: }
2578:
2579: for (i=1;i<=npar;i++) {
2580: for (j=1;j<=npar;j++) {
2581: if (j>i) {
2582: printf(".%d%d",i,j);fflush(stdout);
2583: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
2584: hess[i][j]=hessij(p,delti,i,j,func,npar);
2585:
2586: hess[j][i]=hess[i][j];
2587: /*printf(" %lf ",hess[i][j]);*/
2588: }
2589: }
2590: }
2591: printf("\n");
2592: fprintf(ficlog,"\n");
2593:
2594: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2595: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2596:
2597: a=matrix(1,npar,1,npar);
2598: y=matrix(1,npar,1,npar);
2599: x=vector(1,npar);
2600: indx=ivector(1,npar);
2601: for (i=1;i<=npar;i++)
2602: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2603: ludcmp(a,npar,indx,&pd);
2604:
2605: for (j=1;j<=npar;j++) {
2606: for (i=1;i<=npar;i++) x[i]=0;
2607: x[j]=1;
2608: lubksb(a,npar,indx,x);
2609: for (i=1;i<=npar;i++){
2610: matcov[i][j]=x[i];
2611: }
2612: }
2613:
2614: printf("\n#Hessian matrix#\n");
2615: fprintf(ficlog,"\n#Hessian matrix#\n");
2616: for (i=1;i<=npar;i++) {
2617: for (j=1;j<=npar;j++) {
2618: printf("%.3e ",hess[i][j]);
2619: fprintf(ficlog,"%.3e ",hess[i][j]);
2620: }
2621: printf("\n");
2622: fprintf(ficlog,"\n");
2623: }
2624:
2625: /* Recompute Inverse */
2626: for (i=1;i<=npar;i++)
2627: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
2628: ludcmp(a,npar,indx,&pd);
2629:
2630: /* printf("\n#Hessian matrix recomputed#\n");
2631:
2632: for (j=1;j<=npar;j++) {
2633: for (i=1;i<=npar;i++) x[i]=0;
2634: x[j]=1;
2635: lubksb(a,npar,indx,x);
2636: for (i=1;i<=npar;i++){
2637: y[i][j]=x[i];
2638: printf("%.3e ",y[i][j]);
2639: fprintf(ficlog,"%.3e ",y[i][j]);
2640: }
2641: printf("\n");
2642: fprintf(ficlog,"\n");
2643: }
2644: */
2645:
2646: free_matrix(a,1,npar,1,npar);
2647: free_matrix(y,1,npar,1,npar);
2648: free_vector(x,1,npar);
2649: free_ivector(indx,1,npar);
2650: free_matrix(hess,1,npar,1,npar);
2651:
2652:
2653: }
2654:
2655: /*************** hessian matrix ****************/
2656: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2657: {
2658: int i;
2659: int l=1, lmax=20;
2660: double k1,k2;
2661: double p2[MAXPARM+1]; /* identical to x */
2662: double res;
2663: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2664: double fx;
2665: int k=0,kmax=10;
2666: double l1;
2667:
2668: fx=func(x);
2669: for (i=1;i<=npar;i++) p2[i]=x[i];
2670: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
2671: l1=pow(10,l);
2672: delts=delt;
2673: for(k=1 ; k <kmax; k=k+1){
2674: delt = delta*(l1*k);
2675: p2[theta]=x[theta] +delt;
2676: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
2677: p2[theta]=x[theta]-delt;
2678: k2=func(p2)-fx;
2679: /*res= (k1-2.0*fx+k2)/delt/delt; */
2680: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2681:
2682: #ifdef DEBUGHESS
2683: 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);
2684: 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);
2685: #endif
2686: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2687: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2688: k=kmax;
2689: }
2690: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
2691: k=kmax; l=lmax*10;
2692: }
2693: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2694: delts=delt;
2695: }
2696: }
2697: }
2698: delti[theta]=delts;
2699: return res;
2700:
2701: }
2702:
2703: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2704: {
2705: int i;
2706: int l=1, lmax=20;
2707: double k1,k2,k3,k4,res,fx;
2708: double p2[MAXPARM+1];
2709: int k;
2710:
2711: fx=func(x);
2712: for (k=1; k<=2; k++) {
2713: for (i=1;i<=npar;i++) p2[i]=x[i];
2714: p2[thetai]=x[thetai]+delti[thetai]/k;
2715: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2716: k1=func(p2)-fx;
2717:
2718: p2[thetai]=x[thetai]+delti[thetai]/k;
2719: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2720: k2=func(p2)-fx;
2721:
2722: p2[thetai]=x[thetai]-delti[thetai]/k;
2723: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2724: k3=func(p2)-fx;
2725:
2726: p2[thetai]=x[thetai]-delti[thetai]/k;
2727: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2728: k4=func(p2)-fx;
2729: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2730: #ifdef DEBUG
2731: 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);
2732: 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);
2733: #endif
2734: }
2735: return res;
2736: }
2737:
2738: /************** Inverse of matrix **************/
2739: void ludcmp(double **a, int n, int *indx, double *d)
2740: {
2741: int i,imax,j,k;
2742: double big,dum,sum,temp;
2743: double *vv;
2744:
2745: vv=vector(1,n);
2746: *d=1.0;
2747: for (i=1;i<=n;i++) {
2748: big=0.0;
2749: for (j=1;j<=n;j++)
2750: if ((temp=fabs(a[i][j])) > big) big=temp;
2751: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2752: vv[i]=1.0/big;
2753: }
2754: for (j=1;j<=n;j++) {
2755: for (i=1;i<j;i++) {
2756: sum=a[i][j];
2757: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2758: a[i][j]=sum;
2759: }
2760: big=0.0;
2761: for (i=j;i<=n;i++) {
2762: sum=a[i][j];
2763: for (k=1;k<j;k++)
2764: sum -= a[i][k]*a[k][j];
2765: a[i][j]=sum;
2766: if ( (dum=vv[i]*fabs(sum)) >= big) {
2767: big=dum;
2768: imax=i;
2769: }
2770: }
2771: if (j != imax) {
2772: for (k=1;k<=n;k++) {
2773: dum=a[imax][k];
2774: a[imax][k]=a[j][k];
2775: a[j][k]=dum;
2776: }
2777: *d = -(*d);
2778: vv[imax]=vv[j];
2779: }
2780: indx[j]=imax;
2781: if (a[j][j] == 0.0) a[j][j]=TINY;
2782: if (j != n) {
2783: dum=1.0/(a[j][j]);
2784: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2785: }
2786: }
2787: free_vector(vv,1,n); /* Doesn't work */
2788: ;
2789: }
2790:
2791: void lubksb(double **a, int n, int *indx, double b[])
2792: {
2793: int i,ii=0,ip,j;
2794: double sum;
2795:
2796: for (i=1;i<=n;i++) {
2797: ip=indx[i];
2798: sum=b[ip];
2799: b[ip]=b[i];
2800: if (ii)
2801: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2802: else if (sum) ii=i;
2803: b[i]=sum;
2804: }
2805: for (i=n;i>=1;i--) {
2806: sum=b[i];
2807: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2808: b[i]=sum/a[i][i];
2809: }
2810: }
2811:
2812: void pstamp(FILE *fichier)
2813: {
2814: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2815: }
2816:
2817: /************ Frequencies ********************/
2818: 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[])
2819: { /* Some frequencies */
2820:
2821: int i, m, jk, j1, bool, z1,j;
2822: int first;
2823: double ***freq; /* Frequencies */
2824: double *pp, **prop;
2825: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2826: char fileresp[FILENAMELENGTH];
2827:
2828: pp=vector(1,nlstate);
2829: prop=matrix(1,nlstate,iagemin,iagemax+3);
2830: strcpy(fileresp,"p");
2831: strcat(fileresp,fileres);
2832: if((ficresp=fopen(fileresp,"w"))==NULL) {
2833: printf("Problem with prevalence resultfile: %s\n", fileresp);
2834: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2835: exit(0);
2836: }
2837: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2838: j1=0;
2839:
2840: j=cptcoveff;
2841: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2842:
2843: first=1;
2844:
2845: /* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */
2846: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
2847: /* j1++; */
2848: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
2849: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2850: scanf("%d", i);*/
2851: for (i=-5; i<=nlstate+ndeath; i++)
2852: for (jk=-5; jk<=nlstate+ndeath; jk++)
2853: for(m=iagemin; m <= iagemax+3; m++)
2854: freq[i][jk][m]=0;
2855:
2856: for (i=1; i<=nlstate; i++)
2857: for(m=iagemin; m <= iagemax+3; m++)
2858: prop[i][m]=0;
2859:
2860: dateintsum=0;
2861: k2cpt=0;
2862: for (i=1; i<=imx; i++) {
2863: bool=1;
2864: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
2865: for (z1=1; z1<=cptcoveff; z1++)
2866: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
2867: /* Tests if the value of each of the covariates of i is equal to filter j1 */
2868: bool=0;
2869: /* 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",
2870: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
2871: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
2872: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
2873: }
2874: }
2875:
2876: if (bool==1){
2877: for(m=firstpass; m<=lastpass; m++){
2878: k2=anint[m][i]+(mint[m][i]/12.);
2879: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2880: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2881: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2882: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2883: if (m<lastpass) {
2884: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2885: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2886: }
2887:
2888: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2889: dateintsum=dateintsum+k2;
2890: k2cpt++;
2891: }
2892: /*}*/
2893: }
2894: }
2895: } /* end i */
2896:
2897: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2898: pstamp(ficresp);
2899: if (cptcovn>0) {
2900: fprintf(ficresp, "\n#********** Variable ");
2901: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2902: fprintf(ficresp, "**********\n#");
2903: fprintf(ficlog, "\n#********** Variable ");
2904: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2905: fprintf(ficlog, "**********\n#");
2906: }
2907: for(i=1; i<=nlstate;i++)
2908: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2909: fprintf(ficresp, "\n");
2910:
2911: for(i=iagemin; i <= iagemax+3; i++){
2912: if(i==iagemax+3){
2913: fprintf(ficlog,"Total");
2914: }else{
2915: if(first==1){
2916: first=0;
2917: printf("See log file for details...\n");
2918: }
2919: fprintf(ficlog,"Age %d", i);
2920: }
2921: for(jk=1; jk <=nlstate ; jk++){
2922: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2923: pp[jk] += freq[jk][m][i];
2924: }
2925: for(jk=1; jk <=nlstate ; jk++){
2926: for(m=-1, pos=0; m <=0 ; m++)
2927: pos += freq[jk][m][i];
2928: if(pp[jk]>=1.e-10){
2929: if(first==1){
2930: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2931: }
2932: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2933: }else{
2934: if(first==1)
2935: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2936: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2937: }
2938: }
2939:
2940: for(jk=1; jk <=nlstate ; jk++){
2941: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2942: pp[jk] += freq[jk][m][i];
2943: }
2944: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2945: pos += pp[jk];
2946: posprop += prop[jk][i];
2947: }
2948: for(jk=1; jk <=nlstate ; jk++){
2949: if(pos>=1.e-5){
2950: if(first==1)
2951: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2952: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2953: }else{
2954: if(first==1)
2955: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2956: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2957: }
2958: if( i <= iagemax){
2959: if(pos>=1.e-5){
2960: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2961: /*probs[i][jk][j1]= pp[jk]/pos;*/
2962: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2963: }
2964: else
2965: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2966: }
2967: }
2968:
2969: for(jk=-1; jk <=nlstate+ndeath; jk++)
2970: for(m=-1; m <=nlstate+ndeath; m++)
2971: if(freq[jk][m][i] !=0 ) {
2972: if(first==1)
2973: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2974: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2975: }
2976: if(i <= iagemax)
2977: fprintf(ficresp,"\n");
2978: if(first==1)
2979: printf("Others in log...\n");
2980: fprintf(ficlog,"\n");
2981: }
2982: /*}*/
2983: }
2984: dateintmean=dateintsum/k2cpt;
2985:
2986: fclose(ficresp);
2987: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2988: free_vector(pp,1,nlstate);
2989: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2990: /* End of Freq */
2991: }
2992:
2993: /************ Prevalence ********************/
2994: 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)
2995: {
2996: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2997: in each health status at the date of interview (if between dateprev1 and dateprev2).
2998: We still use firstpass and lastpass as another selection.
2999: */
3000:
3001: int i, m, jk, j1, bool, z1,j;
3002:
3003: double **prop;
3004: double posprop;
3005: double y2; /* in fractional years */
3006: int iagemin, iagemax;
3007: int first; /** to stop verbosity which is redirected to log file */
3008:
3009: iagemin= (int) agemin;
3010: iagemax= (int) agemax;
3011: /*pp=vector(1,nlstate);*/
3012: prop=matrix(1,nlstate,iagemin,iagemax+3);
3013: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
3014: j1=0;
3015:
3016: /*j=cptcoveff;*/
3017: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3018:
3019: first=1;
3020: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
3021: /*for(i1=1; i1<=ncodemax[k1];i1++){
3022: j1++;*/
3023:
3024: for (i=1; i<=nlstate; i++)
3025: for(m=iagemin; m <= iagemax+3; m++)
3026: prop[i][m]=0.0;
3027:
3028: for (i=1; i<=imx; i++) { /* Each individual */
3029: bool=1;
3030: if (cptcovn>0) {
3031: for (z1=1; z1<=cptcoveff; z1++)
3032: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
3033: bool=0;
3034: }
3035: if (bool==1) {
3036: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
3037: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
3038: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
3039: if(agev[m][i]==0) agev[m][i]=iagemax+1;
3040: if(agev[m][i]==1) agev[m][i]=iagemax+2;
3041: 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);
3042: if (s[m][i]>0 && s[m][i]<=nlstate) {
3043: /*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]]);*/
3044: prop[s[m][i]][(int)agev[m][i]] += weight[i];
3045: prop[s[m][i]][iagemax+3] += weight[i];
3046: }
3047: }
3048: } /* end selection of waves */
3049: }
3050: }
3051: for(i=iagemin; i <= iagemax+3; i++){
3052: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
3053: posprop += prop[jk][i];
3054: }
3055:
3056: for(jk=1; jk <=nlstate ; jk++){
3057: if( i <= iagemax){
3058: if(posprop>=1.e-5){
3059: probs[i][jk][j1]= prop[jk][i]/posprop;
3060: } else{
3061: if(first==1){
3062: first=0;
3063: 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]);
3064: }
3065: }
3066: }
3067: }/* end jk */
3068: }/* end i */
3069: /*} *//* end i1 */
3070: } /* end j1 */
3071:
3072: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
3073: /*free_vector(pp,1,nlstate);*/
3074: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
3075: } /* End of prevalence */
3076:
3077: /************* Waves Concatenation ***************/
3078:
3079: 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)
3080: {
3081: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
3082: Death is a valid wave (if date is known).
3083: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
3084: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3085: and mw[mi+1][i]. dh depends on stepm.
3086: */
3087:
3088: int i, mi, m;
3089: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
3090: double sum=0., jmean=0.;*/
3091: int first;
3092: int j, k=0,jk, ju, jl;
3093: double sum=0.;
3094: first=0;
3095: jmin=100000;
3096: jmax=-1;
3097: jmean=0.;
3098: for(i=1; i<=imx; i++){
3099: mi=0;
3100: m=firstpass;
3101: while(s[m][i] <= nlstate){
3102: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
3103: mw[++mi][i]=m;
3104: if(m >=lastpass)
3105: break;
3106: else
3107: m++;
3108: }/* end while */
3109: if (s[m][i] > nlstate){
3110: mi++; /* Death is another wave */
3111: /* if(mi==0) never been interviewed correctly before death */
3112: /* Only death is a correct wave */
3113: mw[mi][i]=m;
3114: }
3115:
3116: wav[i]=mi;
3117: if(mi==0){
3118: nbwarn++;
3119: if(first==0){
3120: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
3121: first=1;
3122: }
3123: if(first==1){
3124: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
3125: }
3126: } /* end mi==0 */
3127: } /* End individuals */
3128:
3129: for(i=1; i<=imx; i++){
3130: for(mi=1; mi<wav[i];mi++){
3131: if (stepm <=0)
3132: dh[mi][i]=1;
3133: else{
3134: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
3135: if (agedc[i] < 2*AGESUP) {
3136: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
3137: if(j==0) j=1; /* Survives at least one month after exam */
3138: else if(j<0){
3139: nberr++;
3140: 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]);
3141: j=1; /* Temporary Dangerous patch */
3142: 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);
3143: 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]);
3144: 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);
3145: }
3146: k=k+1;
3147: if (j >= jmax){
3148: jmax=j;
3149: ijmax=i;
3150: }
3151: if (j <= jmin){
3152: jmin=j;
3153: ijmin=i;
3154: }
3155: sum=sum+j;
3156: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
3157: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
3158: }
3159: }
3160: else{
3161: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
3162: /* 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]); */
3163:
3164: k=k+1;
3165: if (j >= jmax) {
3166: jmax=j;
3167: ijmax=i;
3168: }
3169: else if (j <= jmin){
3170: jmin=j;
3171: ijmin=i;
3172: }
3173: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
3174: /*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]);*/
3175: if(j<0){
3176: nberr++;
3177: 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]);
3178: 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]);
3179: }
3180: sum=sum+j;
3181: }
3182: jk= j/stepm;
3183: jl= j -jk*stepm;
3184: ju= j -(jk+1)*stepm;
3185: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
3186: if(jl==0){
3187: dh[mi][i]=jk;
3188: bh[mi][i]=0;
3189: }else{ /* We want a negative bias in order to only have interpolation ie
3190: * to avoid the price of an extra matrix product in likelihood */
3191: dh[mi][i]=jk+1;
3192: bh[mi][i]=ju;
3193: }
3194: }else{
3195: if(jl <= -ju){
3196: dh[mi][i]=jk;
3197: bh[mi][i]=jl; /* bias is positive if real duration
3198: * is higher than the multiple of stepm and negative otherwise.
3199: */
3200: }
3201: else{
3202: dh[mi][i]=jk+1;
3203: bh[mi][i]=ju;
3204: }
3205: if(dh[mi][i]==0){
3206: dh[mi][i]=1; /* At least one step */
3207: bh[mi][i]=ju; /* At least one step */
3208: /* 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);*/
3209: }
3210: } /* end if mle */
3211: }
3212: } /* end wave */
3213: }
3214: jmean=sum/k;
3215: 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);
3216: 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);
3217: }
3218:
3219: /*********** Tricode ****************************/
3220: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
3221: {
3222: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
3223: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
3224: * Boring subroutine which should only output nbcode[Tvar[j]][k]
3225: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
3226: * nbcode[Tvar[j]][1]=
3227: */
3228:
3229: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
3230: int modmaxcovj=0; /* Modality max of covariates j */
3231: int cptcode=0; /* Modality max of covariates j */
3232: int modmincovj=0; /* Modality min of covariates j */
3233:
3234:
3235: cptcoveff=0;
3236:
3237: for (k=-1; k < maxncov; k++) Ndum[k]=0;
3238: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
3239:
3240: /* Loop on covariates without age and products */
3241: for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
3242: for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
3243: modality of this covariate Vj*/
3244: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
3245: * If product of Vn*Vm, still boolean *:
3246: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
3247: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
3248: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
3249: modality of the nth covariate of individual i. */
3250: if (ij > modmaxcovj)
3251: modmaxcovj=ij;
3252: else if (ij < modmincovj)
3253: modmincovj=ij;
3254: if ((ij < -1) && (ij > NCOVMAX)){
3255: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
3256: exit(1);
3257: }else
3258: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
3259: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
3260: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
3261: /* getting the maximum value of the modality of the covariate
3262: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
3263: female is 1, then modmaxcovj=1.*/
3264: } /* end for loop on individuals */
3265: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
3266: cptcode=modmaxcovj;
3267: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
3268: /*for (i=0; i<=cptcode; i++) {*/
3269: for (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
3270: printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], i, Ndum[i]);
3271: if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
3272: ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
3273: }
3274: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
3275: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
3276: } /* Ndum[-1] number of undefined modalities */
3277:
3278: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
3279: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
3280: If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125;
3281: modmincovj=3; modmaxcovj = 7;
3282: There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
3283: which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
3284: defining two dummy variables: variables V1_1 and V1_2.
3285: nbcode[Tvar[j]][ij]=k;
3286: nbcode[Tvar[j]][1]=0;
3287: nbcode[Tvar[j]][2]=1;
3288: nbcode[Tvar[j]][3]=2;
3289: */
3290: ij=1; /* ij is similar to i but can jumps over null modalities */
3291: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
3292: for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
3293: /*recode from 0 */
3294: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
3295: nbcode[Tvar[j]][ij]=k; /* stores the modality k in an array nbcode.
3296: k is a modality. If we have model=V1+V1*sex
3297: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
3298: ij++;
3299: }
3300: if (ij > ncodemax[j]) break;
3301: } /* end of loop on */
3302: } /* end of loop on modality */
3303: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
3304:
3305: for (k=-1; k< maxncov; k++) Ndum[k]=0;
3306:
3307: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
3308: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
3309: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
3310: Ndum[ij]++; /* Might be supersed V1 + V1*age */
3311: }
3312:
3313: ij=1;
3314: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
3315: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
3316: if((Ndum[i]!=0) && (i<=ncovcol)){
3317: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
3318: Tvaraff[ij]=i; /*For printing (unclear) */
3319: ij++;
3320: }else
3321: Tvaraff[ij]=0;
3322: }
3323: ij--;
3324: cptcoveff=ij; /*Number of total covariates*/
3325:
3326: }
3327:
3328:
3329: /*********** Health Expectancies ****************/
3330:
3331: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
3332:
3333: {
3334: /* Health expectancies, no variances */
3335: int i, j, nhstepm, hstepm, h, nstepm;
3336: int nhstepma, nstepma; /* Decreasing with age */
3337: double age, agelim, hf;
3338: double ***p3mat;
3339: double eip;
3340:
3341: pstamp(ficreseij);
3342: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3343: fprintf(ficreseij,"# Age");
3344: for(i=1; i<=nlstate;i++){
3345: for(j=1; j<=nlstate;j++){
3346: fprintf(ficreseij," e%1d%1d ",i,j);
3347: }
3348: fprintf(ficreseij," e%1d. ",i);
3349: }
3350: fprintf(ficreseij,"\n");
3351:
3352:
3353: if(estepm < stepm){
3354: printf ("Problem %d lower than %d\n",estepm, stepm);
3355: }
3356: else hstepm=estepm;
3357: /* We compute the life expectancy from trapezoids spaced every estepm months
3358: * This is mainly to measure the difference between two models: for example
3359: * if stepm=24 months pijx are given only every 2 years and by summing them
3360: * we are calculating an estimate of the Life Expectancy assuming a linear
3361: * progression in between and thus overestimating or underestimating according
3362: * to the curvature of the survival function. If, for the same date, we
3363: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3364: * to compare the new estimate of Life expectancy with the same linear
3365: * hypothesis. A more precise result, taking into account a more precise
3366: * curvature will be obtained if estepm is as small as stepm. */
3367:
3368: /* For example we decided to compute the life expectancy with the smallest unit */
3369: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3370: nhstepm is the number of hstepm from age to agelim
3371: nstepm is the number of stepm from age to agelin.
3372: Look at hpijx to understand the reason of that which relies in memory size
3373: and note for a fixed period like estepm months */
3374: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3375: survival function given by stepm (the optimization length). Unfortunately it
3376: means that if the survival funtion is printed only each two years of age and if
3377: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3378: results. So we changed our mind and took the option of the best precision.
3379: */
3380: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3381:
3382: agelim=AGESUP;
3383: /* If stepm=6 months */
3384: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3385: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3386:
3387: /* nhstepm age range expressed in number of stepm */
3388: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3389: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3390: /* if (stepm >= YEARM) hstepm=1;*/
3391: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3392: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3393:
3394: for (age=bage; age<=fage; age ++){
3395: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3396: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3397: /* if (stepm >= YEARM) hstepm=1;*/
3398: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3399:
3400: /* If stepm=6 months */
3401: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3402: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3403:
3404: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3405:
3406: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3407:
3408: printf("%d|",(int)age);fflush(stdout);
3409: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3410:
3411: /* Computing expectancies */
3412: for(i=1; i<=nlstate;i++)
3413: for(j=1; j<=nlstate;j++)
3414: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3415: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3416:
3417: /* 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]);*/
3418:
3419: }
3420:
3421: fprintf(ficreseij,"%3.0f",age );
3422: for(i=1; i<=nlstate;i++){
3423: eip=0;
3424: for(j=1; j<=nlstate;j++){
3425: eip +=eij[i][j][(int)age];
3426: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3427: }
3428: fprintf(ficreseij,"%9.4f", eip );
3429: }
3430: fprintf(ficreseij,"\n");
3431:
3432: }
3433: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3434: printf("\n");
3435: fprintf(ficlog,"\n");
3436:
3437: }
3438:
3439: 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[] )
3440:
3441: {
3442: /* Covariances of health expectancies eij and of total life expectancies according
3443: to initial status i, ei. .
3444: */
3445: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3446: int nhstepma, nstepma; /* Decreasing with age */
3447: double age, agelim, hf;
3448: double ***p3matp, ***p3matm, ***varhe;
3449: double **dnewm,**doldm;
3450: double *xp, *xm;
3451: double **gp, **gm;
3452: double ***gradg, ***trgradg;
3453: int theta;
3454:
3455: double eip, vip;
3456:
3457: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
3458: xp=vector(1,npar);
3459: xm=vector(1,npar);
3460: dnewm=matrix(1,nlstate*nlstate,1,npar);
3461: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3462:
3463: pstamp(ficresstdeij);
3464: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3465: fprintf(ficresstdeij,"# Age");
3466: for(i=1; i<=nlstate;i++){
3467: for(j=1; j<=nlstate;j++)
3468: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3469: fprintf(ficresstdeij," e%1d. ",i);
3470: }
3471: fprintf(ficresstdeij,"\n");
3472:
3473: pstamp(ficrescveij);
3474: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3475: fprintf(ficrescveij,"# Age");
3476: for(i=1; i<=nlstate;i++)
3477: for(j=1; j<=nlstate;j++){
3478: cptj= (j-1)*nlstate+i;
3479: for(i2=1; i2<=nlstate;i2++)
3480: for(j2=1; j2<=nlstate;j2++){
3481: cptj2= (j2-1)*nlstate+i2;
3482: if(cptj2 <= cptj)
3483: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3484: }
3485: }
3486: fprintf(ficrescveij,"\n");
3487:
3488: if(estepm < stepm){
3489: printf ("Problem %d lower than %d\n",estepm, stepm);
3490: }
3491: else hstepm=estepm;
3492: /* We compute the life expectancy from trapezoids spaced every estepm months
3493: * This is mainly to measure the difference between two models: for example
3494: * if stepm=24 months pijx are given only every 2 years and by summing them
3495: * we are calculating an estimate of the Life Expectancy assuming a linear
3496: * progression in between and thus overestimating or underestimating according
3497: * to the curvature of the survival function. If, for the same date, we
3498: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3499: * to compare the new estimate of Life expectancy with the same linear
3500: * hypothesis. A more precise result, taking into account a more precise
3501: * curvature will be obtained if estepm is as small as stepm. */
3502:
3503: /* For example we decided to compute the life expectancy with the smallest unit */
3504: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3505: nhstepm is the number of hstepm from age to agelim
3506: nstepm is the number of stepm from age to agelin.
3507: Look at hpijx to understand the reason of that which relies in memory size
3508: and note for a fixed period like estepm months */
3509: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3510: survival function given by stepm (the optimization length). Unfortunately it
3511: means that if the survival funtion is printed only each two years of age and if
3512: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3513: results. So we changed our mind and took the option of the best precision.
3514: */
3515: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3516:
3517: /* If stepm=6 months */
3518: /* nhstepm age range expressed in number of stepm */
3519: agelim=AGESUP;
3520: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3521: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3522: /* if (stepm >= YEARM) hstepm=1;*/
3523: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3524:
3525: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3526: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3527: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3528: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3529: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3530: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3531:
3532: for (age=bage; age<=fage; age ++){
3533: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3534: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3535: /* if (stepm >= YEARM) hstepm=1;*/
3536: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3537:
3538: /* If stepm=6 months */
3539: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3540: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3541:
3542: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3543:
3544: /* Computing Variances of health expectancies */
3545: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3546: decrease memory allocation */
3547: for(theta=1; theta <=npar; theta++){
3548: for(i=1; i<=npar; i++){
3549: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3550: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3551: }
3552: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3553: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3554:
3555: for(j=1; j<= nlstate; j++){
3556: for(i=1; i<=nlstate; i++){
3557: for(h=0; h<=nhstepm-1; h++){
3558: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3559: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3560: }
3561: }
3562: }
3563:
3564: for(ij=1; ij<= nlstate*nlstate; ij++)
3565: for(h=0; h<=nhstepm-1; h++){
3566: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3567: }
3568: }/* End theta */
3569:
3570:
3571: for(h=0; h<=nhstepm-1; h++)
3572: for(j=1; j<=nlstate*nlstate;j++)
3573: for(theta=1; theta <=npar; theta++)
3574: trgradg[h][j][theta]=gradg[h][theta][j];
3575:
3576:
3577: for(ij=1;ij<=nlstate*nlstate;ij++)
3578: for(ji=1;ji<=nlstate*nlstate;ji++)
3579: varhe[ij][ji][(int)age] =0.;
3580:
3581: printf("%d|",(int)age);fflush(stdout);
3582: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3583: for(h=0;h<=nhstepm-1;h++){
3584: for(k=0;k<=nhstepm-1;k++){
3585: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3586: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3587: for(ij=1;ij<=nlstate*nlstate;ij++)
3588: for(ji=1;ji<=nlstate*nlstate;ji++)
3589: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3590: }
3591: }
3592:
3593: /* Computing expectancies */
3594: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3595: for(i=1; i<=nlstate;i++)
3596: for(j=1; j<=nlstate;j++)
3597: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3598: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3599:
3600: /* 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]);*/
3601:
3602: }
3603:
3604: fprintf(ficresstdeij,"%3.0f",age );
3605: for(i=1; i<=nlstate;i++){
3606: eip=0.;
3607: vip=0.;
3608: for(j=1; j<=nlstate;j++){
3609: eip += eij[i][j][(int)age];
3610: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3611: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3612: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3613: }
3614: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3615: }
3616: fprintf(ficresstdeij,"\n");
3617:
3618: fprintf(ficrescveij,"%3.0f",age );
3619: for(i=1; i<=nlstate;i++)
3620: for(j=1; j<=nlstate;j++){
3621: cptj= (j-1)*nlstate+i;
3622: for(i2=1; i2<=nlstate;i2++)
3623: for(j2=1; j2<=nlstate;j2++){
3624: cptj2= (j2-1)*nlstate+i2;
3625: if(cptj2 <= cptj)
3626: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3627: }
3628: }
3629: fprintf(ficrescveij,"\n");
3630:
3631: }
3632: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3633: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3634: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3635: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3636: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3637: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3638: printf("\n");
3639: fprintf(ficlog,"\n");
3640:
3641: free_vector(xm,1,npar);
3642: free_vector(xp,1,npar);
3643: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3644: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3645: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3646: }
3647:
3648: /************ Variance ******************/
3649: 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[])
3650: {
3651: /* Variance of health expectancies */
3652: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3653: /* double **newm;*/
3654: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
3655:
3656: int movingaverage();
3657: double **dnewm,**doldm;
3658: double **dnewmp,**doldmp;
3659: int i, j, nhstepm, hstepm, h, nstepm ;
3660: int k;
3661: double *xp;
3662: double **gp, **gm; /* for var eij */
3663: double ***gradg, ***trgradg; /*for var eij */
3664: double **gradgp, **trgradgp; /* for var p point j */
3665: double *gpp, *gmp; /* for var p point j */
3666: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3667: double ***p3mat;
3668: double age,agelim, hf;
3669: double ***mobaverage;
3670: int theta;
3671: char digit[4];
3672: char digitp[25];
3673:
3674: char fileresprobmorprev[FILENAMELENGTH];
3675:
3676: if(popbased==1){
3677: if(mobilav!=0)
3678: strcpy(digitp,"-populbased-mobilav-");
3679: else strcpy(digitp,"-populbased-nomobil-");
3680: }
3681: else
3682: strcpy(digitp,"-stablbased-");
3683:
3684: if (mobilav!=0) {
3685: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3686: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3687: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3688: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3689: }
3690: }
3691:
3692: strcpy(fileresprobmorprev,"prmorprev");
3693: sprintf(digit,"%-d",ij);
3694: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3695: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3696: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
3697: strcat(fileresprobmorprev,fileres);
3698: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3699: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3700: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3701: }
3702: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3703:
3704: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3705: pstamp(ficresprobmorprev);
3706: 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);
3707: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3708: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3709: fprintf(ficresprobmorprev," p.%-d SE",j);
3710: for(i=1; i<=nlstate;i++)
3711: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3712: }
3713: fprintf(ficresprobmorprev,"\n");
3714: fprintf(ficgp,"\n# Routine varevsij");
3715: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
3716: 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");
3717: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3718: /* } */
3719: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3720: pstamp(ficresvij);
3721: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3722: if(popbased==1)
3723: 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);
3724: else
3725: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3726: fprintf(ficresvij,"# Age");
3727: for(i=1; i<=nlstate;i++)
3728: for(j=1; j<=nlstate;j++)
3729: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3730: fprintf(ficresvij,"\n");
3731:
3732: xp=vector(1,npar);
3733: dnewm=matrix(1,nlstate,1,npar);
3734: doldm=matrix(1,nlstate,1,nlstate);
3735: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3736: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3737:
3738: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3739: gpp=vector(nlstate+1,nlstate+ndeath);
3740: gmp=vector(nlstate+1,nlstate+ndeath);
3741: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3742:
3743: if(estepm < stepm){
3744: printf ("Problem %d lower than %d\n",estepm, stepm);
3745: }
3746: else hstepm=estepm;
3747: /* For example we decided to compute the life expectancy with the smallest unit */
3748: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3749: nhstepm is the number of hstepm from age to agelim
3750: nstepm is the number of stepm from age to agelin.
3751: Look at function hpijx to understand why (it is linked to memory size questions) */
3752: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3753: survival function given by stepm (the optimization length). Unfortunately it
3754: means that if the survival funtion is printed every two years of age and if
3755: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3756: results. So we changed our mind and took the option of the best precision.
3757: */
3758: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3759: agelim = AGESUP;
3760: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3761: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3762: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3763: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3764: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3765: gp=matrix(0,nhstepm,1,nlstate);
3766: gm=matrix(0,nhstepm,1,nlstate);
3767:
3768:
3769: for(theta=1; theta <=npar; theta++){
3770: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3771: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3772: }
3773: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3774: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3775:
3776: if (popbased==1) {
3777: if(mobilav ==0){
3778: for(i=1; i<=nlstate;i++)
3779: prlim[i][i]=probs[(int)age][i][ij];
3780: }else{ /* mobilav */
3781: for(i=1; i<=nlstate;i++)
3782: prlim[i][i]=mobaverage[(int)age][i][ij];
3783: }
3784: }
3785:
3786: for(j=1; j<= nlstate; j++){
3787: for(h=0; h<=nhstepm; h++){
3788: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3789: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3790: }
3791: }
3792: /* This for computing probability of death (h=1 means
3793: computed over hstepm matrices product = hstepm*stepm months)
3794: as a weighted average of prlim.
3795: */
3796: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3797: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3798: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3799: }
3800: /* end probability of death */
3801:
3802: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3803: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3804: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3805: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3806:
3807: if (popbased==1) {
3808: if(mobilav ==0){
3809: for(i=1; i<=nlstate;i++)
3810: prlim[i][i]=probs[(int)age][i][ij];
3811: }else{ /* mobilav */
3812: for(i=1; i<=nlstate;i++)
3813: prlim[i][i]=mobaverage[(int)age][i][ij];
3814: }
3815: }
3816:
3817: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
3818: for(h=0; h<=nhstepm; h++){
3819: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3820: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3821: }
3822: }
3823: /* This for computing probability of death (h=1 means
3824: computed over hstepm matrices product = hstepm*stepm months)
3825: as a weighted average of prlim.
3826: */
3827: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3828: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3829: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3830: }
3831: /* end probability of death */
3832:
3833: for(j=1; j<= nlstate; j++) /* vareij */
3834: for(h=0; h<=nhstepm; h++){
3835: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3836: }
3837:
3838: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3839: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3840: }
3841:
3842: } /* End theta */
3843:
3844: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3845:
3846: for(h=0; h<=nhstepm; h++) /* veij */
3847: for(j=1; j<=nlstate;j++)
3848: for(theta=1; theta <=npar; theta++)
3849: trgradg[h][j][theta]=gradg[h][theta][j];
3850:
3851: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3852: for(theta=1; theta <=npar; theta++)
3853: trgradgp[j][theta]=gradgp[theta][j];
3854:
3855:
3856: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3857: for(i=1;i<=nlstate;i++)
3858: for(j=1;j<=nlstate;j++)
3859: vareij[i][j][(int)age] =0.;
3860:
3861: for(h=0;h<=nhstepm;h++){
3862: for(k=0;k<=nhstepm;k++){
3863: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3864: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3865: for(i=1;i<=nlstate;i++)
3866: for(j=1;j<=nlstate;j++)
3867: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3868: }
3869: }
3870:
3871: /* pptj */
3872: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3873: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3874: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3875: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3876: varppt[j][i]=doldmp[j][i];
3877: /* end ppptj */
3878: /* x centered again */
3879: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3880: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3881:
3882: if (popbased==1) {
3883: if(mobilav ==0){
3884: for(i=1; i<=nlstate;i++)
3885: prlim[i][i]=probs[(int)age][i][ij];
3886: }else{ /* mobilav */
3887: for(i=1; i<=nlstate;i++)
3888: prlim[i][i]=mobaverage[(int)age][i][ij];
3889: }
3890: }
3891:
3892: /* This for computing probability of death (h=1 means
3893: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3894: as a weighted average of prlim.
3895: */
3896: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3897: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3898: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3899: }
3900: /* end probability of death */
3901:
3902: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3903: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3904: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3905: for(i=1; i<=nlstate;i++){
3906: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3907: }
3908: }
3909: fprintf(ficresprobmorprev,"\n");
3910:
3911: fprintf(ficresvij,"%.0f ",age );
3912: for(i=1; i<=nlstate;i++)
3913: for(j=1; j<=nlstate;j++){
3914: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3915: }
3916: fprintf(ficresvij,"\n");
3917: free_matrix(gp,0,nhstepm,1,nlstate);
3918: free_matrix(gm,0,nhstepm,1,nlstate);
3919: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3920: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3921: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3922: } /* End age */
3923: free_vector(gpp,nlstate+1,nlstate+ndeath);
3924: free_vector(gmp,nlstate+1,nlstate+ndeath);
3925: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3926: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3927: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
3928: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
3929: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
3930: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3931: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3932: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
3933: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
3934: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
3935: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
3936: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3937: 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);
3938: /* 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);
3939: */
3940: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3941: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3942:
3943: free_vector(xp,1,npar);
3944: free_matrix(doldm,1,nlstate,1,nlstate);
3945: free_matrix(dnewm,1,nlstate,1,npar);
3946: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3947: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3948: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3949: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3950: fclose(ficresprobmorprev);
3951: fflush(ficgp);
3952: fflush(fichtm);
3953: } /* end varevsij */
3954:
3955: /************ Variance of prevlim ******************/
3956: 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[])
3957: {
3958: /* Variance of prevalence limit */
3959: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
3960:
3961: double **dnewm,**doldm;
3962: int i, j, nhstepm, hstepm;
3963: double *xp;
3964: double *gp, *gm;
3965: double **gradg, **trgradg;
3966: double age,agelim;
3967: int theta;
3968:
3969: pstamp(ficresvpl);
3970: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3971: fprintf(ficresvpl,"# Age");
3972: for(i=1; i<=nlstate;i++)
3973: fprintf(ficresvpl," %1d-%1d",i,i);
3974: fprintf(ficresvpl,"\n");
3975:
3976: xp=vector(1,npar);
3977: dnewm=matrix(1,nlstate,1,npar);
3978: doldm=matrix(1,nlstate,1,nlstate);
3979:
3980: hstepm=1*YEARM; /* Every year of age */
3981: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3982: agelim = AGESUP;
3983: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3984: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3985: if (stepm >= YEARM) hstepm=1;
3986: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3987: gradg=matrix(1,npar,1,nlstate);
3988: gp=vector(1,nlstate);
3989: gm=vector(1,nlstate);
3990:
3991: for(theta=1; theta <=npar; theta++){
3992: for(i=1; i<=npar; i++){ /* Computes gradient */
3993: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3994: }
3995: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3996: for(i=1;i<=nlstate;i++)
3997: gp[i] = prlim[i][i];
3998:
3999: for(i=1; i<=npar; i++) /* Computes gradient */
4000: xp[i] = x[i] - (i==theta ?delti[theta]:0);
4001: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
4002: for(i=1;i<=nlstate;i++)
4003: gm[i] = prlim[i][i];
4004:
4005: for(i=1;i<=nlstate;i++)
4006: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
4007: } /* End theta */
4008:
4009: trgradg =matrix(1,nlstate,1,npar);
4010:
4011: for(j=1; j<=nlstate;j++)
4012: for(theta=1; theta <=npar; theta++)
4013: trgradg[j][theta]=gradg[theta][j];
4014:
4015: for(i=1;i<=nlstate;i++)
4016: varpl[i][(int)age] =0.;
4017: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
4018: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
4019: for(i=1;i<=nlstate;i++)
4020: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
4021:
4022: fprintf(ficresvpl,"%.0f ",age );
4023: for(i=1; i<=nlstate;i++)
4024: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
4025: fprintf(ficresvpl,"\n");
4026: free_vector(gp,1,nlstate);
4027: free_vector(gm,1,nlstate);
4028: free_matrix(gradg,1,npar,1,nlstate);
4029: free_matrix(trgradg,1,nlstate,1,npar);
4030: } /* End age */
4031:
4032: free_vector(xp,1,npar);
4033: free_matrix(doldm,1,nlstate,1,npar);
4034: free_matrix(dnewm,1,nlstate,1,nlstate);
4035:
4036: }
4037:
4038: /************ Variance of one-step probabilities ******************/
4039: 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[])
4040: {
4041: int i, j=0, k1, l1, tj;
4042: int k2, l2, j1, z1;
4043: int k=0, l;
4044: int first=1, first1, first2;
4045: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
4046: double **dnewm,**doldm;
4047: double *xp;
4048: double *gp, *gm;
4049: double **gradg, **trgradg;
4050: double **mu;
4051: double age, cov[NCOVMAX+1];
4052: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
4053: int theta;
4054: char fileresprob[FILENAMELENGTH];
4055: char fileresprobcov[FILENAMELENGTH];
4056: char fileresprobcor[FILENAMELENGTH];
4057: double ***varpij;
4058:
4059: strcpy(fileresprob,"prob");
4060: strcat(fileresprob,fileres);
4061: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
4062: printf("Problem with resultfile: %s\n", fileresprob);
4063: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
4064: }
4065: strcpy(fileresprobcov,"probcov");
4066: strcat(fileresprobcov,fileres);
4067: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
4068: printf("Problem with resultfile: %s\n", fileresprobcov);
4069: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
4070: }
4071: strcpy(fileresprobcor,"probcor");
4072: strcat(fileresprobcor,fileres);
4073: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
4074: printf("Problem with resultfile: %s\n", fileresprobcor);
4075: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
4076: }
4077: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4078: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4079: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4080: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4081: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4082: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4083: pstamp(ficresprob);
4084: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
4085: fprintf(ficresprob,"# Age");
4086: pstamp(ficresprobcov);
4087: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
4088: fprintf(ficresprobcov,"# Age");
4089: pstamp(ficresprobcor);
4090: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
4091: fprintf(ficresprobcor,"# Age");
4092:
4093:
4094: for(i=1; i<=nlstate;i++)
4095: for(j=1; j<=(nlstate+ndeath);j++){
4096: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
4097: fprintf(ficresprobcov," p%1d-%1d ",i,j);
4098: fprintf(ficresprobcor," p%1d-%1d ",i,j);
4099: }
4100: /* fprintf(ficresprob,"\n");
4101: fprintf(ficresprobcov,"\n");
4102: fprintf(ficresprobcor,"\n");
4103: */
4104: xp=vector(1,npar);
4105: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4106: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4107: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
4108: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
4109: first=1;
4110: fprintf(ficgp,"\n# Routine varprob");
4111: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
4112: fprintf(fichtm,"\n");
4113:
4114: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
4115: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
4116: file %s<br>\n",optionfilehtmcov);
4117: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
4118: and drawn. It helps understanding how is the covariance between two incidences.\
4119: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
4120: 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. \
4121: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
4122: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
4123: standard deviations wide on each axis. <br>\
4124: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
4125: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
4126: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
4127:
4128: cov[1]=1;
4129: /* tj=cptcoveff; */
4130: tj = (int) pow(2,cptcoveff);
4131: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
4132: j1=0;
4133: for(j1=1; j1<=tj;j1++){
4134: /*for(i1=1; i1<=ncodemax[t];i1++){ */
4135: /*j1++;*/
4136: if (cptcovn>0) {
4137: fprintf(ficresprob, "\n#********** Variable ");
4138: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4139: fprintf(ficresprob, "**********\n#\n");
4140: fprintf(ficresprobcov, "\n#********** Variable ");
4141: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4142: fprintf(ficresprobcov, "**********\n#\n");
4143:
4144: fprintf(ficgp, "\n#********** Variable ");
4145: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4146: fprintf(ficgp, "**********\n#\n");
4147:
4148:
4149: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
4150: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4151: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
4152:
4153: fprintf(ficresprobcor, "\n#********** Variable ");
4154: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4155: fprintf(ficresprobcor, "**********\n#");
4156: }
4157:
4158: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
4159: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4160: gp=vector(1,(nlstate)*(nlstate+ndeath));
4161: gm=vector(1,(nlstate)*(nlstate+ndeath));
4162: for (age=bage; age<=fage; age ++){
4163: cov[2]=age;
4164: if(nagesqr==1)
4165: cov[3]= age*age;
4166: for (k=1; k<=cptcovn;k++) {
4167: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
4168: * 1 1 1 1 1
4169: * 2 2 1 1 1
4170: * 3 1 2 1 1
4171: */
4172: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
4173: }
4174: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
4175: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
4176: for (k=1; k<=cptcovprod;k++)
4177: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
4178:
4179:
4180: for(theta=1; theta <=npar; theta++){
4181: for(i=1; i<=npar; i++)
4182: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
4183:
4184: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4185:
4186: k=0;
4187: for(i=1; i<= (nlstate); i++){
4188: for(j=1; j<=(nlstate+ndeath);j++){
4189: k=k+1;
4190: gp[k]=pmmij[i][j];
4191: }
4192: }
4193:
4194: for(i=1; i<=npar; i++)
4195: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
4196:
4197: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4198: k=0;
4199: for(i=1; i<=(nlstate); i++){
4200: for(j=1; j<=(nlstate+ndeath);j++){
4201: k=k+1;
4202: gm[k]=pmmij[i][j];
4203: }
4204: }
4205:
4206: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
4207: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
4208: }
4209:
4210: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
4211: for(theta=1; theta <=npar; theta++)
4212: trgradg[j][theta]=gradg[theta][j];
4213:
4214: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
4215: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
4216:
4217: pmij(pmmij,cov,ncovmodel,x,nlstate);
4218:
4219: k=0;
4220: for(i=1; i<=(nlstate); i++){
4221: for(j=1; j<=(nlstate+ndeath);j++){
4222: k=k+1;
4223: mu[k][(int) age]=pmmij[i][j];
4224: }
4225: }
4226: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
4227: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
4228: varpij[i][j][(int)age] = doldm[i][j];
4229:
4230: /*printf("\n%d ",(int)age);
4231: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4232: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4233: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4234: }*/
4235:
4236: fprintf(ficresprob,"\n%d ",(int)age);
4237: fprintf(ficresprobcov,"\n%d ",(int)age);
4238: fprintf(ficresprobcor,"\n%d ",(int)age);
4239:
4240: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
4241: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
4242: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4243: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
4244: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
4245: }
4246: i=0;
4247: for (k=1; k<=(nlstate);k++){
4248: for (l=1; l<=(nlstate+ndeath);l++){
4249: i++;
4250: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
4251: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
4252: for (j=1; j<=i;j++){
4253: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
4254: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
4255: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
4256: }
4257: }
4258: }/* end of loop for state */
4259: } /* end of loop for age */
4260: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
4261: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
4262: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4263: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4264:
4265: /* Confidence intervalle of pij */
4266: /*
4267: fprintf(ficgp,"\nunset parametric;unset label");
4268: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
4269: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
4270: 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);
4271: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
4272: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
4273: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
4274: */
4275:
4276: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
4277: first1=1;first2=2;
4278: for (k2=1; k2<=(nlstate);k2++){
4279: for (l2=1; l2<=(nlstate+ndeath);l2++){
4280: if(l2==k2) continue;
4281: j=(k2-1)*(nlstate+ndeath)+l2;
4282: for (k1=1; k1<=(nlstate);k1++){
4283: for (l1=1; l1<=(nlstate+ndeath);l1++){
4284: if(l1==k1) continue;
4285: i=(k1-1)*(nlstate+ndeath)+l1;
4286: if(i<=j) continue;
4287: for (age=bage; age<=fage; age ++){
4288: if ((int)age %5==0){
4289: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
4290: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
4291: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
4292: mu1=mu[i][(int) age]/stepm*YEARM ;
4293: mu2=mu[j][(int) age]/stepm*YEARM;
4294: c12=cv12/sqrt(v1*v2);
4295: /* Computing eigen value of matrix of covariance */
4296: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4297: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4298: if ((lc2 <0) || (lc1 <0) ){
4299: if(first2==1){
4300: first1=0;
4301: 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);
4302: }
4303: 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);
4304: /* lc1=fabs(lc1); */ /* If we want to have them positive */
4305: /* lc2=fabs(lc2); */
4306: }
4307:
4308: /* Eigen vectors */
4309: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
4310: /*v21=sqrt(1.-v11*v11); *//* error */
4311: v21=(lc1-v1)/cv12*v11;
4312: v12=-v21;
4313: v22=v11;
4314: tnalp=v21/v11;
4315: if(first1==1){
4316: first1=0;
4317: 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);
4318: }
4319: 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);
4320: /*printf(fignu*/
4321: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
4322: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
4323: if(first==1){
4324: first=0;
4325: fprintf(ficgp,"\nset parametric;unset label");
4326: 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);
4327: fprintf(ficgp,"\nset ter png small size 320, 240");
4328: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
4329: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
4330: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
4331: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
4332: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4333: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4334: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
4335: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4336: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4337: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4338: 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",\
4339: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4340: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4341: }else{
4342: first=0;
4343: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4344: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4345: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4346: 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",\
4347: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4348: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4349: }/* if first */
4350: } /* age mod 5 */
4351: } /* end loop age */
4352: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4353: first=1;
4354: } /*l12 */
4355: } /* k12 */
4356: } /*l1 */
4357: }/* k1 */
4358: /* } */ /* loop covariates */
4359: }
4360: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4361: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4362: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4363: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4364: free_vector(xp,1,npar);
4365: fclose(ficresprob);
4366: fclose(ficresprobcov);
4367: fclose(ficresprobcor);
4368: fflush(ficgp);
4369: fflush(fichtmcov);
4370: }
4371:
4372:
4373: /******************* Printing html file ***********/
4374: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
4375: int lastpass, int stepm, int weightopt, char model[],\
4376: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
4377: int popforecast, int estepm ,\
4378: double jprev1, double mprev1,double anprev1, \
4379: double jprev2, double mprev2,double anprev2){
4380: int jj1, k1, i1, cpt;
4381:
4382: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4383: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4384: </ul>");
4385: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
4386: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
4387: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
4388: fprintf(fichtm,"\
4389: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
4390: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
4391: fprintf(fichtm,"\
4392: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
4393: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
4394: fprintf(fichtm,"\
4395: - (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): \
4396: <a href=\"%s\">%s</a> <br>\n",
4397: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
4398: fprintf(fichtm,"\
4399: - Population projections by age and states: \
4400: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
4401:
4402: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4403:
4404: m=pow(2,cptcoveff);
4405: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4406:
4407: jj1=0;
4408: for(k1=1; k1<=m;k1++){
4409: for(i1=1; i1<=ncodemax[k1];i1++){
4410: jj1++;
4411: if (cptcovn > 0) {
4412: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4413: for (cpt=1; cpt<=cptcoveff;cpt++)
4414: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4415: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4416: }
4417: /* Pij */
4418: 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> \
4419: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
4420: /* Quasi-incidences */
4421: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
4422: 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> \
4423: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
4424: /* Period (stable) prevalence in each health state */
4425: for(cpt=1; cpt<=nlstate;cpt++){
4426: 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> \
4427: <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
4428: }
4429: for(cpt=1; cpt<=nlstate;cpt++) {
4430: 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> \
4431: <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
4432: }
4433: } /* end i1 */
4434: }/* End k1 */
4435: fprintf(fichtm,"</ul>");
4436:
4437:
4438: fprintf(fichtm,"\
4439: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
4440: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
4441:
4442: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4443: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
4444: fprintf(fichtm,"\
4445: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4446: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
4447:
4448: fprintf(fichtm,"\
4449: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4450: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
4451: fprintf(fichtm,"\
4452: - 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): \
4453: <a href=\"%s\">%s</a> <br>\n</li>",
4454: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
4455: fprintf(fichtm,"\
4456: - (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): \
4457: <a href=\"%s\">%s</a> <br>\n</li>",
4458: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
4459: fprintf(fichtm,"\
4460: - 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",
4461: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
4462: fprintf(fichtm,"\
4463: - 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",
4464: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
4465: fprintf(fichtm,"\
4466: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
4467: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
4468:
4469: /* if(popforecast==1) fprintf(fichtm,"\n */
4470: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4471: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4472: /* <br>",fileres,fileres,fileres,fileres); */
4473: /* else */
4474: /* 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); */
4475: fflush(fichtm);
4476: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4477:
4478: m=pow(2,cptcoveff);
4479: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4480:
4481: jj1=0;
4482: for(k1=1; k1<=m;k1++){
4483: for(i1=1; i1<=ncodemax[k1];i1++){
4484: jj1++;
4485: if (cptcovn > 0) {
4486: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4487: for (cpt=1; cpt<=cptcoveff;cpt++)
4488: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4489: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4490: }
4491: for(cpt=1; cpt<=nlstate;cpt++) {
4492: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
4493: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
4494: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
4495: }
4496: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
4497: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4498: true period expectancies (those weighted with period prevalences are also\
4499: drawn in addition to the population based expectancies computed using\
4500: observed and cahotic prevalences: %s%d.png<br>\
4501: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
4502: } /* end i1 */
4503: }/* End k1 */
4504: fprintf(fichtm,"</ul>");
4505: fflush(fichtm);
4506: }
4507:
4508: /******************* Gnuplot file **************/
4509: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4510:
4511: char dirfileres[132],optfileres[132];
4512: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
4513: int ng=0;
4514: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4515: /* printf("Problem with file %s",optionfilegnuplot); */
4516: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4517: /* } */
4518:
4519: /*#ifdef windows */
4520: fprintf(ficgp,"cd \"%s\" \n",pathc);
4521: /*#endif */
4522: m=pow(2,cptcoveff);
4523:
4524: strcpy(dirfileres,optionfilefiname);
4525: strcpy(optfileres,"vpl");
4526: /* 1eme*/
4527: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
4528: for (cpt=1; cpt<= nlstate ; cpt ++) {
4529: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
4530: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
4531: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
4532: fprintf(ficgp,"set xlabel \"Age\" \n\
4533: set ylabel \"Probability\" \n\
4534: set ter png small size 320, 240\n\
4535: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
4536:
4537: for (i=1; i<= nlstate ; i ++) {
4538: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4539: else fprintf(ficgp," %%*lf (%%*lf)");
4540: }
4541: 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);
4542: for (i=1; i<= nlstate ; i ++) {
4543: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4544: else fprintf(ficgp," %%*lf (%%*lf)");
4545: }
4546: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
4547: for (i=1; i<= nlstate ; i ++) {
4548: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4549: else fprintf(ficgp," %%*lf (%%*lf)");
4550: }
4551: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
4552: }
4553: }
4554: /*2 eme*/
4555: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
4556: for (k1=1; k1<= m ; k1 ++) {
4557: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
4558: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
4559:
4560: for (i=1; i<= nlstate+1 ; i ++) {
4561: k=2*i;
4562: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4563: for (j=1; j<= nlstate+1 ; j ++) {
4564: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4565: else fprintf(ficgp," %%*lf (%%*lf)");
4566: }
4567: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
4568: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
4569: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4570: for (j=1; j<= nlstate+1 ; j ++) {
4571: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4572: else fprintf(ficgp," %%*lf (%%*lf)");
4573: }
4574: fprintf(ficgp,"\" t\"\" w l lt 0,");
4575: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4576: for (j=1; j<= nlstate+1 ; j ++) {
4577: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4578: else fprintf(ficgp," %%*lf (%%*lf)");
4579: }
4580: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4581: else fprintf(ficgp,"\" t\"\" w l lt 0,");
4582: }
4583: }
4584:
4585: /*3eme*/
4586:
4587: for (k1=1; k1<= m ; k1 ++) {
4588: for (cpt=1; cpt<= nlstate ; cpt ++) {
4589: /* k=2+nlstate*(2*cpt-2); */
4590: k=2+(nlstate+1)*(cpt-1);
4591: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
4592: fprintf(ficgp,"set ter png small size 320, 240\n\
4593: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
4594: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4595: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4596: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4597: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4598: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4599: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4600:
4601: */
4602: for (i=1; i< nlstate ; i ++) {
4603: 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);
4604: /* 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);*/
4605:
4606: }
4607: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
4608: }
4609: }
4610:
4611: /* CV preval stable (period) */
4612: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
4613: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
4614: k=3;
4615: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
4616: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
4617: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
4618: set ter png small size 320, 240\n\
4619: unset log y\n\
4620: plot [%.f:%.f] ", ageminpar, agemaxpar);
4621: for (i=1; i<= nlstate ; i ++){
4622: if(i==1)
4623: fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
4624: else
4625: fprintf(ficgp,", '' ");
4626: l=(nlstate+ndeath)*(i-1)+1;
4627: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
4628: for (j=1; j<= (nlstate-1) ; j ++)
4629: fprintf(ficgp,"+$%d",k+l+j);
4630: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
4631: } /* nlstate */
4632: fprintf(ficgp,"\n");
4633: } /* end cpt state*/
4634: } /* end covariate */
4635:
4636: /* proba elementaires */
4637: fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
4638: for(i=1,jk=1; i <=nlstate; i++){
4639: fprintf(ficgp,"# initial state %d\n",i);
4640: for(k=1; k <=(nlstate+ndeath); k++){
4641: if (k != i) {
4642: fprintf(ficgp,"# current state %d\n",k);
4643: for(j=1; j <=ncovmodel; j++){
4644: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
4645: jk++;
4646: }
4647: fprintf(ficgp,"\n");
4648: }
4649: }
4650: }
4651: fprintf(ficgp,"##############\n#\n");
4652:
4653: /*goto avoid;*/
4654: fprintf(ficgp,"\n##############\n#Graphics of of probabilities or incidences\n#############\n");
4655: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
4656: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
4657: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
4658: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
4659: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
4660: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
4661: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
4662: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
4663: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
4664: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
4665: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
4666: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
4667: fprintf(ficgp,"#\n");
4668: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
4669: fprintf(ficgp,"# ng=%d\n",ng);
4670: fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);
4671: for(jk=1; jk <=m; jk++) {
4672: fprintf(ficgp,"# jk=%d\n",jk);
4673: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
4674: if (ng==2)
4675: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
4676: else
4677: fprintf(ficgp,"\nset title \"Probability\"\n");
4678: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
4679: i=1;
4680: for(k2=1; k2<=nlstate; k2++) {
4681: k3=i;
4682: for(k=1; k<=(nlstate+ndeath); k++) {
4683: if (k != k2){
4684: if(ng==2)
4685: if(nagesqr==0)
4686: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
4687: else /* nagesqr =1 */
4688: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
4689: else
4690: if(nagesqr==0)
4691: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
4692: else /* nagesqr =1 */
4693: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
4694: ij=1;/* To be checked else nbcode[0][0] wrong */
4695: for(j=3; j <=ncovmodel-nagesqr; j++) {
4696: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /* Bug valgrind */
4697: fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
4698: ij++;
4699: }
4700: else
4701: fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4702: }
4703: fprintf(ficgp,")/(1");
4704:
4705: for(k1=1; k1 <=nlstate; k1++){
4706: if(nagesqr==0)
4707: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
4708: else /* nagesqr =1 */
4709: fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr);
4710:
4711: ij=1;
4712: for(j=3; j <=ncovmodel-nagesqr; j++){
4713: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
4714: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
4715: ij++;
4716: }
4717: else
4718: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4719: }
4720: fprintf(ficgp,")");
4721: }
4722: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
4723: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
4724: i=i+ncovmodel;
4725: }
4726: } /* end k */
4727: } /* end k2 */
4728: } /* end jk */
4729: } /* end ng */
4730: /* avoid: */
4731: fflush(ficgp);
4732: } /* end gnuplot */
4733:
4734:
4735: /*************** Moving average **************/
4736: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
4737:
4738: int i, cpt, cptcod;
4739: int modcovmax =1;
4740: int mobilavrange, mob;
4741: double age;
4742:
4743: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
4744: a covariate has 2 modalities */
4745: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
4746:
4747: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
4748: if(mobilav==1) mobilavrange=5; /* default */
4749: else mobilavrange=mobilav;
4750: for (age=bage; age<=fage; age++)
4751: for (i=1; i<=nlstate;i++)
4752: for (cptcod=1;cptcod<=modcovmax;cptcod++)
4753: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
4754: /* We keep the original values on the extreme ages bage, fage and for
4755: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
4756: we use a 5 terms etc. until the borders are no more concerned.
4757: */
4758: for (mob=3;mob <=mobilavrange;mob=mob+2){
4759: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
4760: for (i=1; i<=nlstate;i++){
4761: for (cptcod=1;cptcod<=modcovmax;cptcod++){
4762: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
4763: for (cpt=1;cpt<=(mob-1)/2;cpt++){
4764: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
4765: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
4766: }
4767: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
4768: }
4769: }
4770: }/* end age */
4771: }/* end mob */
4772: }else return -1;
4773: return 0;
4774: }/* End movingaverage */
4775:
4776:
4777: /************** Forecasting ******************/
4778: 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){
4779: /* proj1, year, month, day of starting projection
4780: agemin, agemax range of age
4781: dateprev1 dateprev2 range of dates during which prevalence is computed
4782: anproj2 year of en of projection (same day and month as proj1).
4783: */
4784: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
4785: double agec; /* generic age */
4786: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
4787: double *popeffectif,*popcount;
4788: double ***p3mat;
4789: double ***mobaverage;
4790: char fileresf[FILENAMELENGTH];
4791:
4792: agelim=AGESUP;
4793: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4794:
4795: strcpy(fileresf,"f");
4796: strcat(fileresf,fileres);
4797: if((ficresf=fopen(fileresf,"w"))==NULL) {
4798: printf("Problem with forecast resultfile: %s\n", fileresf);
4799: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
4800: }
4801: printf("Computing forecasting: result on file '%s' \n", fileresf);
4802: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
4803:
4804: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4805:
4806: if (mobilav!=0) {
4807: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4808: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4809: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4810: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4811: }
4812: }
4813:
4814: stepsize=(int) (stepm+YEARM-1)/YEARM;
4815: if (stepm<=12) stepsize=1;
4816: if(estepm < stepm){
4817: printf ("Problem %d lower than %d\n",estepm, stepm);
4818: }
4819: else hstepm=estepm;
4820:
4821: hstepm=hstepm/stepm;
4822: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
4823: fractional in yp1 */
4824: anprojmean=yp;
4825: yp2=modf((yp1*12),&yp);
4826: mprojmean=yp;
4827: yp1=modf((yp2*30.5),&yp);
4828: jprojmean=yp;
4829: if(jprojmean==0) jprojmean=1;
4830: if(mprojmean==0) jprojmean=1;
4831:
4832: i1=cptcoveff;
4833: if (cptcovn < 1){i1=1;}
4834:
4835: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4836:
4837: fprintf(ficresf,"#****** Routine prevforecast **\n");
4838:
4839: /* if (h==(int)(YEARM*yearp)){ */
4840: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4841: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4842: k=k+1;
4843: fprintf(ficresf,"\n#******");
4844: for(j=1;j<=cptcoveff;j++) {
4845: 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]]);
4846: }
4847: fprintf(ficresf,"******\n");
4848: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4849: for(j=1; j<=nlstate+ndeath;j++){
4850: for(i=1; i<=nlstate;i++)
4851: fprintf(ficresf," p%d%d",i,j);
4852: fprintf(ficresf," p.%d",j);
4853: }
4854: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4855: fprintf(ficresf,"\n");
4856: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4857:
4858: for (agec=fage; agec>=(ageminpar-1); agec--){
4859: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4860: nhstepm = nhstepm/hstepm;
4861: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4862: oldm=oldms;savm=savms;
4863: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4864:
4865: for (h=0; h<=nhstepm; h++){
4866: if (h*hstepm/YEARM*stepm ==yearp) {
4867: fprintf(ficresf,"\n");
4868: for(j=1;j<=cptcoveff;j++)
4869: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4870: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4871: }
4872: for(j=1; j<=nlstate+ndeath;j++) {
4873: ppij=0.;
4874: for(i=1; i<=nlstate;i++) {
4875: if (mobilav==1)
4876: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4877: else {
4878: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4879: }
4880: if (h*hstepm/YEARM*stepm== yearp) {
4881: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4882: }
4883: } /* end i */
4884: if (h*hstepm/YEARM*stepm==yearp) {
4885: fprintf(ficresf," %.3f", ppij);
4886: }
4887: }/* end j */
4888: } /* end h */
4889: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4890: } /* end agec */
4891: } /* end yearp */
4892: } /* end cptcod */
4893: } /* end cptcov */
4894:
4895: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4896:
4897: fclose(ficresf);
4898: }
4899:
4900: /************** Forecasting *****not tested NB*************/
4901: 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){
4902:
4903: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4904: int *popage;
4905: double calagedatem, agelim, kk1, kk2;
4906: double *popeffectif,*popcount;
4907: double ***p3mat,***tabpop,***tabpopprev;
4908: double ***mobaverage;
4909: char filerespop[FILENAMELENGTH];
4910:
4911: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4912: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4913: agelim=AGESUP;
4914: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4915:
4916: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4917:
4918:
4919: strcpy(filerespop,"pop");
4920: strcat(filerespop,fileres);
4921: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4922: printf("Problem with forecast resultfile: %s\n", filerespop);
4923: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4924: }
4925: printf("Computing forecasting: result on file '%s' \n", filerespop);
4926: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4927:
4928: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4929:
4930: if (mobilav!=0) {
4931: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4932: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4933: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4934: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4935: }
4936: }
4937:
4938: stepsize=(int) (stepm+YEARM-1)/YEARM;
4939: if (stepm<=12) stepsize=1;
4940:
4941: agelim=AGESUP;
4942:
4943: hstepm=1;
4944: hstepm=hstepm/stepm;
4945:
4946: if (popforecast==1) {
4947: if((ficpop=fopen(popfile,"r"))==NULL) {
4948: printf("Problem with population file : %s\n",popfile);exit(0);
4949: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4950: }
4951: popage=ivector(0,AGESUP);
4952: popeffectif=vector(0,AGESUP);
4953: popcount=vector(0,AGESUP);
4954:
4955: i=1;
4956: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4957:
4958: imx=i;
4959: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4960: }
4961:
4962: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4963: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4964: k=k+1;
4965: fprintf(ficrespop,"\n#******");
4966: for(j=1;j<=cptcoveff;j++) {
4967: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4968: }
4969: fprintf(ficrespop,"******\n");
4970: fprintf(ficrespop,"# Age");
4971: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4972: if (popforecast==1) fprintf(ficrespop," [Population]");
4973:
4974: for (cpt=0; cpt<=0;cpt++) {
4975: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4976:
4977: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4978: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4979: nhstepm = nhstepm/hstepm;
4980:
4981: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4982: oldm=oldms;savm=savms;
4983: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4984:
4985: for (h=0; h<=nhstepm; h++){
4986: if (h==(int) (calagedatem+YEARM*cpt)) {
4987: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4988: }
4989: for(j=1; j<=nlstate+ndeath;j++) {
4990: kk1=0.;kk2=0;
4991: for(i=1; i<=nlstate;i++) {
4992: if (mobilav==1)
4993: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4994: else {
4995: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4996: }
4997: }
4998: if (h==(int)(calagedatem+12*cpt)){
4999: tabpop[(int)(agedeb)][j][cptcod]=kk1;
5000: /*fprintf(ficrespop," %.3f", kk1);
5001: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
5002: }
5003: }
5004: for(i=1; i<=nlstate;i++){
5005: kk1=0.;
5006: for(j=1; j<=nlstate;j++){
5007: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
5008: }
5009: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
5010: }
5011:
5012: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
5013: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
5014: }
5015: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5016: }
5017: }
5018:
5019: /******/
5020:
5021: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
5022: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5023: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5024: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5025: nhstepm = nhstepm/hstepm;
5026:
5027: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5028: oldm=oldms;savm=savms;
5029: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5030: for (h=0; h<=nhstepm; h++){
5031: if (h==(int) (calagedatem+YEARM*cpt)) {
5032: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5033: }
5034: for(j=1; j<=nlstate+ndeath;j++) {
5035: kk1=0.;kk2=0;
5036: for(i=1; i<=nlstate;i++) {
5037: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
5038: }
5039: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
5040: }
5041: }
5042: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5043: }
5044: }
5045: }
5046: }
5047:
5048: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5049:
5050: if (popforecast==1) {
5051: free_ivector(popage,0,AGESUP);
5052: free_vector(popeffectif,0,AGESUP);
5053: free_vector(popcount,0,AGESUP);
5054: }
5055: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5056: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5057: fclose(ficrespop);
5058: } /* End of popforecast */
5059:
5060: int fileappend(FILE *fichier, char *optionfich)
5061: {
5062: if((fichier=fopen(optionfich,"a"))==NULL) {
5063: printf("Problem with file: %s\n", optionfich);
5064: fprintf(ficlog,"Problem with file: %s\n", optionfich);
5065: return (0);
5066: }
5067: fflush(fichier);
5068: return (1);
5069: }
5070:
5071:
5072: /**************** function prwizard **********************/
5073: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
5074: {
5075:
5076: /* Wizard to print covariance matrix template */
5077:
5078: char ca[32], cb[32];
5079: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
5080: int numlinepar;
5081:
5082: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5083: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5084: for(i=1; i <=nlstate; i++){
5085: jj=0;
5086: for(j=1; j <=nlstate+ndeath; j++){
5087: if(j==i) continue;
5088: jj++;
5089: /*ca[0]= k+'a'-1;ca[1]='\0';*/
5090: printf("%1d%1d",i,j);
5091: fprintf(ficparo,"%1d%1d",i,j);
5092: for(k=1; k<=ncovmodel;k++){
5093: /* printf(" %lf",param[i][j][k]); */
5094: /* fprintf(ficparo," %lf",param[i][j][k]); */
5095: printf(" 0.");
5096: fprintf(ficparo," 0.");
5097: }
5098: printf("\n");
5099: fprintf(ficparo,"\n");
5100: }
5101: }
5102: printf("# Scales (for hessian or gradient estimation)\n");
5103: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
5104: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
5105: for(i=1; i <=nlstate; i++){
5106: jj=0;
5107: for(j=1; j <=nlstate+ndeath; j++){
5108: if(j==i) continue;
5109: jj++;
5110: fprintf(ficparo,"%1d%1d",i,j);
5111: printf("%1d%1d",i,j);
5112: fflush(stdout);
5113: for(k=1; k<=ncovmodel;k++){
5114: /* printf(" %le",delti3[i][j][k]); */
5115: /* fprintf(ficparo," %le",delti3[i][j][k]); */
5116: printf(" 0.");
5117: fprintf(ficparo," 0.");
5118: }
5119: numlinepar++;
5120: printf("\n");
5121: fprintf(ficparo,"\n");
5122: }
5123: }
5124: printf("# Covariance matrix\n");
5125: /* # 121 Var(a12)\n\ */
5126: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5127: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5128: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5129: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5130: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5131: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5132: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5133: fflush(stdout);
5134: fprintf(ficparo,"# Covariance matrix\n");
5135: /* # 121 Var(a12)\n\ */
5136: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5137: /* # ...\n\ */
5138: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5139:
5140: for(itimes=1;itimes<=2;itimes++){
5141: jj=0;
5142: for(i=1; i <=nlstate; i++){
5143: for(j=1; j <=nlstate+ndeath; j++){
5144: if(j==i) continue;
5145: for(k=1; k<=ncovmodel;k++){
5146: jj++;
5147: ca[0]= k+'a'-1;ca[1]='\0';
5148: if(itimes==1){
5149: printf("#%1d%1d%d",i,j,k);
5150: fprintf(ficparo,"#%1d%1d%d",i,j,k);
5151: }else{
5152: printf("%1d%1d%d",i,j,k);
5153: fprintf(ficparo,"%1d%1d%d",i,j,k);
5154: /* printf(" %.5le",matcov[i][j]); */
5155: }
5156: ll=0;
5157: for(li=1;li <=nlstate; li++){
5158: for(lj=1;lj <=nlstate+ndeath; lj++){
5159: if(lj==li) continue;
5160: for(lk=1;lk<=ncovmodel;lk++){
5161: ll++;
5162: if(ll<=jj){
5163: cb[0]= lk +'a'-1;cb[1]='\0';
5164: if(ll<jj){
5165: if(itimes==1){
5166: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5167: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5168: }else{
5169: printf(" 0.");
5170: fprintf(ficparo," 0.");
5171: }
5172: }else{
5173: if(itimes==1){
5174: printf(" Var(%s%1d%1d)",ca,i,j);
5175: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
5176: }else{
5177: printf(" 0.");
5178: fprintf(ficparo," 0.");
5179: }
5180: }
5181: }
5182: } /* end lk */
5183: } /* end lj */
5184: } /* end li */
5185: printf("\n");
5186: fprintf(ficparo,"\n");
5187: numlinepar++;
5188: } /* end k*/
5189: } /*end j */
5190: } /* end i */
5191: } /* end itimes */
5192:
5193: } /* end of prwizard */
5194: /******************* Gompertz Likelihood ******************************/
5195: double gompertz(double x[])
5196: {
5197: double A,B,L=0.0,sump=0.,num=0.;
5198: int i,n=0; /* n is the size of the sample */
5199:
5200: for (i=0;i<=imx-1 ; i++) {
5201: sump=sump+weight[i];
5202: /* sump=sump+1;*/
5203: num=num+1;
5204: }
5205:
5206:
5207: /* for (i=0; i<=imx; i++)
5208: 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]);*/
5209:
5210: for (i=1;i<=imx ; i++)
5211: {
5212: if (cens[i] == 1 && wav[i]>1)
5213: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
5214:
5215: if (cens[i] == 0 && wav[i]>1)
5216: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
5217: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
5218:
5219: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5220: if (wav[i] > 1 ) { /* ??? */
5221: L=L+A*weight[i];
5222: /* 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]);*/
5223: }
5224: }
5225:
5226: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5227:
5228: return -2*L*num/sump;
5229: }
5230:
5231: #ifdef GSL
5232: /******************* Gompertz_f Likelihood ******************************/
5233: double gompertz_f(const gsl_vector *v, void *params)
5234: {
5235: double A,B,LL=0.0,sump=0.,num=0.;
5236: double *x= (double *) v->data;
5237: int i,n=0; /* n is the size of the sample */
5238:
5239: for (i=0;i<=imx-1 ; i++) {
5240: sump=sump+weight[i];
5241: /* sump=sump+1;*/
5242: num=num+1;
5243: }
5244:
5245:
5246: /* for (i=0; i<=imx; i++)
5247: 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]);*/
5248: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
5249: for (i=1;i<=imx ; i++)
5250: {
5251: if (cens[i] == 1 && wav[i]>1)
5252: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
5253:
5254: if (cens[i] == 0 && wav[i]>1)
5255: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
5256: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
5257:
5258: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5259: if (wav[i] > 1 ) { /* ??? */
5260: LL=LL+A*weight[i];
5261: /* 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]);*/
5262: }
5263: }
5264:
5265: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5266: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
5267:
5268: return -2*LL*num/sump;
5269: }
5270: #endif
5271:
5272: /******************* Printing html file ***********/
5273: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
5274: int lastpass, int stepm, int weightopt, char model[],\
5275: int imx, double p[],double **matcov,double agemortsup){
5276: int i,k;
5277:
5278: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
5279: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
5280: for (i=1;i<=2;i++)
5281: 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]));
5282: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
5283: fprintf(fichtm,"</ul>");
5284:
5285: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
5286:
5287: 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>");
5288:
5289: for (k=agegomp;k<(agemortsup-2);k++)
5290: 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]);
5291:
5292:
5293: fflush(fichtm);
5294: }
5295:
5296: /******************* Gnuplot file **************/
5297: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
5298:
5299: char dirfileres[132],optfileres[132];
5300:
5301: int ng;
5302:
5303:
5304: /*#ifdef windows */
5305: fprintf(ficgp,"cd \"%s\" \n",pathc);
5306: /*#endif */
5307:
5308:
5309: strcpy(dirfileres,optionfilefiname);
5310: strcpy(optfileres,"vpl");
5311: fprintf(ficgp,"set out \"graphmort.png\"\n ");
5312: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
5313: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
5314: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
5315: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
5316:
5317: }
5318:
5319: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
5320: {
5321:
5322: /*-------- data file ----------*/
5323: FILE *fic;
5324: char dummy[]=" ";
5325: int i=0, j=0, n=0;
5326: int linei, month, year,iout;
5327: char line[MAXLINE], linetmp[MAXLINE];
5328: char stra[MAXLINE], strb[MAXLINE];
5329: char *stratrunc;
5330: int lstra;
5331:
5332:
5333: if((fic=fopen(datafile,"r"))==NULL) {
5334: printf("Problem while opening datafile: %s\n", datafile);return 1;
5335: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
5336: }
5337:
5338: i=1;
5339: linei=0;
5340: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
5341: linei=linei+1;
5342: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
5343: if(line[j] == '\t')
5344: line[j] = ' ';
5345: }
5346: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
5347: ;
5348: };
5349: line[j+1]=0; /* Trims blanks at end of line */
5350: if(line[0]=='#'){
5351: fprintf(ficlog,"Comment line\n%s\n",line);
5352: printf("Comment line\n%s\n",line);
5353: continue;
5354: }
5355: trimbb(linetmp,line); /* Trims multiple blanks in line */
5356: strcpy(line, linetmp);
5357:
5358:
5359: for (j=maxwav;j>=1;j--){
5360: cutv(stra, strb, line, ' ');
5361: if(strb[0]=='.') { /* Missing status */
5362: lval=-1;
5363: }else{
5364: errno=0;
5365: lval=strtol(strb,&endptr,10);
5366: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
5367: if( strb[0]=='\0' || (*endptr != '\0')){
5368: 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);
5369: 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);
5370: return 1;
5371: }
5372: }
5373: s[j][i]=lval;
5374:
5375: strcpy(line,stra);
5376: cutv(stra, strb,line,' ');
5377: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
5378: }
5379: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
5380: month=99;
5381: year=9999;
5382: }else{
5383: 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);
5384: 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);
5385: return 1;
5386: }
5387: anint[j][i]= (double) year;
5388: mint[j][i]= (double)month;
5389: strcpy(line,stra);
5390: } /* ENd Waves */
5391:
5392: cutv(stra, strb,line,' ');
5393: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
5394: }
5395: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
5396: month=99;
5397: year=9999;
5398: }else{
5399: 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);
5400: 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);
5401: return 1;
5402: }
5403: andc[i]=(double) year;
5404: moisdc[i]=(double) month;
5405: strcpy(line,stra);
5406:
5407: cutv(stra, strb,line,' ');
5408: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
5409: }
5410: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
5411: month=99;
5412: year=9999;
5413: }else{
5414: 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);
5415: 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);
5416: return 1;
5417: }
5418: if (year==9999) {
5419: 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);
5420: 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);
5421: return 1;
5422:
5423: }
5424: annais[i]=(double)(year);
5425: moisnais[i]=(double)(month);
5426: strcpy(line,stra);
5427:
5428: cutv(stra, strb,line,' ');
5429: errno=0;
5430: dval=strtod(strb,&endptr);
5431: if( strb[0]=='\0' || (*endptr != '\0')){
5432: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
5433: 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);
5434: fflush(ficlog);
5435: return 1;
5436: }
5437: weight[i]=dval;
5438: strcpy(line,stra);
5439:
5440: for (j=ncovcol;j>=1;j--){
5441: cutv(stra, strb,line,' ');
5442: if(strb[0]=='.') { /* Missing status */
5443: lval=-1;
5444: }else{
5445: errno=0;
5446: lval=strtol(strb,&endptr,10);
5447: if( strb[0]=='\0' || (*endptr != '\0')){
5448: 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);
5449: 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);
5450: return 1;
5451: }
5452: }
5453: if(lval <-1 || lval >1){
5454: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
5455: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5456: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5457: For example, for multinomial values like 1, 2 and 3,\n \
5458: build V1=0 V2=0 for the reference value (1),\n \
5459: V1=1 V2=0 for (2) \n \
5460: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5461: output of IMaCh is often meaningless.\n \
5462: Exiting.\n",lval,linei, i,line,j);
5463: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
5464: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5465: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5466: For example, for multinomial values like 1, 2 and 3,\n \
5467: build V1=0 V2=0 for the reference value (1),\n \
5468: V1=1 V2=0 for (2) \n \
5469: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5470: output of IMaCh is often meaningless.\n \
5471: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
5472: return 1;
5473: }
5474: covar[j][i]=(double)(lval);
5475: strcpy(line,stra);
5476: }
5477: lstra=strlen(stra);
5478:
5479: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
5480: stratrunc = &(stra[lstra-9]);
5481: num[i]=atol(stratrunc);
5482: }
5483: else
5484: num[i]=atol(stra);
5485: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
5486: 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;}*/
5487:
5488: i=i+1;
5489: } /* End loop reading data */
5490:
5491: *imax=i-1; /* Number of individuals */
5492: fclose(fic);
5493:
5494: return (0);
5495: /* endread: */
5496: printf("Exiting readdata: ");
5497: fclose(fic);
5498: return (1);
5499:
5500:
5501:
5502: }
5503: void removespace(char *str) {
5504: char *p1 = str, *p2 = str;
5505: do
5506: while (*p2 == ' ')
5507: p2++;
5508: while (*p1++ == *p2++);
5509: }
5510:
5511: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
5512: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
5513: * - nagesqr = 1 if age*age in the model, otherwise 0.
5514: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
5515: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
5516: * - cptcovage number of covariates with age*products =2
5517: * - cptcovs number of simple covariates
5518: * - 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
5519: * which is a new column after the 9 (ncovcol) variables.
5520: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
5521: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
5522: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
5523: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
5524: */
5525: {
5526: int i, j, k, ks;
5527: int j1, k1, k2;
5528: char modelsav[80];
5529: char stra[80], strb[80], strc[80], strd[80],stre[80];
5530: char *strpt;
5531:
5532: /*removespace(model);*/
5533: if (strlen(model) >1){ /* If there is at least 1 covariate */
5534: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
5535: if (strstr(model,"AGE") !=0){
5536: printf("Error. AGE must be in lower case 'age' model=1+age+%s ",model);
5537: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s ",model);fflush(ficlog);
5538: return 1;
5539: }
5540: if (strstr(model,"v") !=0){
5541: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
5542: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
5543: return 1;
5544: }
5545: strcpy(modelsav,model);
5546: if ((strpt=strstr(model,"age*age")) !=0){
5547: printf(" strpt=%s, model=%s\n",strpt, model);
5548: if(strpt != model){
5549: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
5550: 'model=1+age+age*age+V1' or 'model=1+age+age*age+V1+V1*age', please swap as well as \n \
5551: corresponding column of parameters.\n",model);
5552: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
5553: 'model=1+age+age*age+V1' or 'model=1+age+age*age+V1+V1*age', please swap as well as \n \
5554: corresponding column of parameters.\n",model); fflush(ficlog);
5555: return 1;
5556: }
5557:
5558: nagesqr=1;
5559: if (strstr(model,"+age*age") !=0)
5560: substrchaine(modelsav, model, "+age*age");
5561: else if (strstr(model,"age*age+") !=0)
5562: substrchaine(modelsav, model, "age*age+");
5563: else
5564: substrchaine(modelsav, model, "age*age");
5565: }else
5566: nagesqr=0;
5567: if (strlen(modelsav) >1){
5568: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
5569: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
5570: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2 */
5571: cptcovt= j+1; /* Number of total covariates in the model, not including
5572: * cst, age and age*age
5573: * V1+V1*age+ V3 + V3*V4+age*age=> 4*/
5574: /* including age products which are counted in cptcovage.
5575: * but the covariates which are products must be treated
5576: * separately: ncovn=4- 2=2 (V1+V3). */
5577: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
5578: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
5579:
5580:
5581: /* Design
5582: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
5583: * < ncovcol=8 >
5584: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
5585: * k= 1 2 3 4 5 6 7 8
5586: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
5587: * covar[k,i], value of kth covariate if not including age for individual i:
5588: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
5589: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
5590: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
5591: * Tage[++cptcovage]=k
5592: * if products, new covar are created after ncovcol with k1
5593: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
5594: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
5595: * 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
5596: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
5597: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
5598: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
5599: * < ncovcol=8 >
5600: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
5601: * k= 1 2 3 4 5 6 7 8 9 10 11 12
5602: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
5603: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5604: * p Tprod[1]@2={ 6, 5}
5605: *p Tvard[1][1]@4= {7, 8, 5, 6}
5606: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
5607: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
5608: *How to reorganize?
5609: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
5610: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5611: * {2, 1, 4, 8, 5, 6, 3, 7}
5612: * Struct []
5613: */
5614:
5615: /* This loop fills the array Tvar from the string 'model'.*/
5616: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
5617: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
5618: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
5619: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
5620: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
5621: /* k=1 Tvar[1]=2 (from V2) */
5622: /* k=5 Tvar[5] */
5623: /* for (k=1; k<=cptcovn;k++) { */
5624: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
5625: /* } */
5626: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2]; */
5627: /*
5628: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
5629: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
5630: Tvar[k]=0;
5631: cptcovage=0;
5632: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
5633: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5634: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
5635: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
5636: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5637: /*scanf("%d",i);*/
5638: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
5639: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
5640: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
5641: /* covar is not filled and then is empty */
5642: cptcovprod--;
5643: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
5644: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
5645: cptcovage++; /* Sums the number of covariates which include age as a product */
5646: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
5647: /*printf("stre=%s ", stre);*/
5648: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
5649: cptcovprod--;
5650: cutl(stre,strb,strc,'V');
5651: Tvar[k]=atoi(stre);
5652: cptcovage++;
5653: Tage[cptcovage]=k;
5654: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
5655: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
5656: cptcovn++;
5657: cptcovprodnoage++;k1++;
5658: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5659: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
5660: because this model-covariate is a construction we invent a new column
5661: ncovcol + k1
5662: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
5663: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
5664: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
5665: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
5666: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
5667: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
5668: k2=k2+2;
5669: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
5670: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
5671: for (i=1; i<=lastobs;i++){
5672: /* Computes the new covariate which is a product of
5673: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
5674: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
5675: }
5676: } /* End age is not in the model */
5677: } /* End if model includes a product */
5678: else { /* no more sum */
5679: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5680: /* scanf("%d",i);*/
5681: cutl(strd,strc,strb,'V');
5682: ks++; /**< Number of simple covariates */
5683: cptcovn++;
5684: Tvar[k]=atoi(strd);
5685: }
5686: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
5687: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5688: scanf("%d",i);*/
5689: } /* end of loop + on total covariates */
5690: } /* end if strlen(modelsave == 0) age*age might exist */
5691: } /* end if strlen(model == 0) */
5692:
5693: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5694: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5695:
5696: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5697: printf("cptcovprod=%d ", cptcovprod);
5698: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5699:
5700: scanf("%d ",i);*/
5701:
5702:
5703: return (0); /* with covar[new additional covariate if product] and Tage if age */
5704: /*endread:*/
5705: printf("Exiting decodemodel: ");
5706: return (1);
5707: }
5708:
5709: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
5710: {
5711: int i, m;
5712:
5713: for (i=1; i<=imx; i++) {
5714: for(m=2; (m<= maxwav); m++) {
5715: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5716: anint[m][i]=9999;
5717: s[m][i]=-1;
5718: }
5719: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
5720: *nberr = *nberr + 1;
5721: 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);
5722: 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);
5723: s[m][i]=-1;
5724: }
5725: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
5726: (*nberr)++;
5727: 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]);
5728: 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]);
5729: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5730: }
5731: }
5732: }
5733:
5734: for (i=1; i<=imx; i++) {
5735: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5736: for(m=firstpass; (m<= lastpass); m++){
5737: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5738: if (s[m][i] >= nlstate+1) {
5739: if(agedc[i]>0){
5740: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
5741: agev[m][i]=agedc[i];
5742: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
5743: }else {
5744: if ((int)andc[i]!=9999){
5745: nbwarn++;
5746: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5747: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5748: agev[m][i]=-1;
5749: }
5750: }
5751: } /* agedc > 0 */
5752: }
5753: else if(s[m][i] !=9){ /* Standard case, age in fractional
5754: years but with the precision of a month */
5755: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5756: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5757: agev[m][i]=1;
5758: else if(agev[m][i] < *agemin){
5759: *agemin=agev[m][i];
5760: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
5761: }
5762: else if(agev[m][i] >*agemax){
5763: *agemax=agev[m][i];
5764: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
5765: }
5766: /*agev[m][i]=anint[m][i]-annais[i];*/
5767: /* agev[m][i] = age[i]+2*m;*/
5768: }
5769: else { /* =9 */
5770: agev[m][i]=1;
5771: s[m][i]=-1;
5772: }
5773: }
5774: else /*= 0 Unknown */
5775: agev[m][i]=1;
5776: }
5777:
5778: }
5779: for (i=1; i<=imx; i++) {
5780: for(m=firstpass; (m<=lastpass); m++){
5781: if (s[m][i] > (nlstate+ndeath)) {
5782: (*nberr)++;
5783: 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);
5784: 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);
5785: return 1;
5786: }
5787: }
5788: }
5789:
5790: /*for (i=1; i<=imx; i++){
5791: for (m=firstpass; (m<lastpass); m++){
5792: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5793: }
5794:
5795: }*/
5796:
5797:
5798: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5799: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5800:
5801: return (0);
5802: /* endread:*/
5803: printf("Exiting calandcheckages: ");
5804: return (1);
5805: }
5806:
5807: #if defined(_MSC_VER)
5808: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5809: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5810: //#include "stdafx.h"
5811: //#include <stdio.h>
5812: //#include <tchar.h>
5813: //#include <windows.h>
5814: //#include <iostream>
5815: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
5816:
5817: LPFN_ISWOW64PROCESS fnIsWow64Process;
5818:
5819: BOOL IsWow64()
5820: {
5821: BOOL bIsWow64 = FALSE;
5822:
5823: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
5824: // (HANDLE, PBOOL);
5825:
5826: //LPFN_ISWOW64PROCESS fnIsWow64Process;
5827:
5828: HMODULE module = GetModuleHandle(_T("kernel32"));
5829: const char funcName[] = "IsWow64Process";
5830: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
5831: GetProcAddress(module, funcName);
5832:
5833: if (NULL != fnIsWow64Process)
5834: {
5835: if (!fnIsWow64Process(GetCurrentProcess(),
5836: &bIsWow64))
5837: //throw std::exception("Unknown error");
5838: printf("Unknown error\n");
5839: }
5840: return bIsWow64 != FALSE;
5841: }
5842: #endif
5843:
5844: void syscompilerinfo()
5845: {
5846: /* #include "syscompilerinfo.h"*/
5847: /* command line Intel compiler 32bit windows, XP compatible:*/
5848: /* /GS /W3 /Gy
5849: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
5850: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
5851: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
5852: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
5853: */
5854: /* 64 bits */
5855: /*
5856: /GS /W3 /Gy
5857: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
5858: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
5859: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
5860: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
5861: /* Optimization are useless and O3 is slower than O2 */
5862: /*
5863: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
5864: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
5865: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
5866: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
5867: */
5868: /* Link is */ /* /OUT:"visual studio
5869: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
5870: /PDB:"visual studio
5871: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
5872: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
5873: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
5874: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
5875: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
5876: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
5877: uiAccess='false'"
5878: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
5879: /NOLOGO /TLBID:1
5880: */
5881: #if defined __INTEL_COMPILER
5882: #if defined(__GNUC__)
5883: struct utsname sysInfo; /* For Intel on Linux and OS/X */
5884: #endif
5885: #elif defined(__GNUC__)
5886: #ifndef __APPLE__
5887: #include <gnu/libc-version.h> /* Only on gnu */
5888: #endif
5889: struct utsname sysInfo;
5890: int cross = CROSS;
5891: if (cross){
5892: printf("Cross-");
5893: fprintf(ficlog, "Cross-");
5894: }
5895: #endif
5896:
5897: #include <stdint.h>
5898:
5899: printf("Compiled with:");fprintf(ficlog,"Compiled with:");
5900: #if defined(__clang__)
5901: printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
5902: #endif
5903: #if defined(__ICC) || defined(__INTEL_COMPILER)
5904: printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
5905: #endif
5906: #if defined(__GNUC__) || defined(__GNUG__)
5907: printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
5908: #endif
5909: #if defined(__HP_cc) || defined(__HP_aCC)
5910: printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
5911: #endif
5912: #if defined(__IBMC__) || defined(__IBMCPP__)
5913: printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
5914: #endif
5915: #if defined(_MSC_VER)
5916: printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
5917: #endif
5918: #if defined(__PGI)
5919: printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
5920: #endif
5921: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
5922: printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
5923: #endif
5924: printf(" for ");fprintf(ficlog," for ");
5925:
5926: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
5927: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
5928: // Windows (x64 and x86)
5929: printf("Windows (x64 and x86) ");fprintf(ficlog,"Windows (x64 and x86) ");
5930: #elif __unix__ // all unices, not all compilers
5931: // Unix
5932: printf("Unix ");fprintf(ficlog,"Unix ");
5933: #elif __linux__
5934: // linux
5935: printf("linux ");fprintf(ficlog,"linux ");
5936: #elif __APPLE__
5937: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
5938: printf("Mac OS ");fprintf(ficlog,"Mac OS ");
5939: #endif
5940:
5941: /* __MINGW32__ */
5942: /* __CYGWIN__ */
5943: /* __MINGW64__ */
5944: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
5945: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
5946: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
5947: /* _WIN64 // Defined for applications for Win64. */
5948: /* _M_X64 // Defined for compilations that target x64 processors. */
5949: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
5950:
5951: #if UINTPTR_MAX == 0xffffffff
5952: printf(" 32-bit"); fprintf(ficlog," 32-bit");/* 32-bit */
5953: #elif UINTPTR_MAX == 0xffffffffffffffff
5954: printf(" 64-bit"); fprintf(ficlog," 64-bit");/* 64-bit */
5955: #else
5956: printf(" wtf-bit"); fprintf(ficlog," wtf-bit");/* wtf */
5957: #endif
5958:
5959: #if defined(__GNUC__)
5960: # if defined(__GNUC_PATCHLEVEL__)
5961: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
5962: + __GNUC_MINOR__ * 100 \
5963: + __GNUC_PATCHLEVEL__)
5964: # else
5965: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
5966: + __GNUC_MINOR__ * 100)
5967: # endif
5968: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
5969: fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
5970:
5971: if (uname(&sysInfo) != -1) {
5972: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
5973: fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
5974: }
5975: else
5976: perror("uname() error");
5977: //#ifndef __INTEL_COMPILER
5978: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
5979: printf("GNU libc version: %s\n", gnu_get_libc_version());
5980: fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
5981: #endif
5982: #endif
5983:
5984: // void main()
5985: // {
5986: #if defined(_MSC_VER)
5987: if (IsWow64()){
5988: printf("The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
5989: fprintf(ficlog, "The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
5990: }
5991: else{
5992: printf("The process is not running under WOW64 (i.e probably on a 64bit Windows).\n");
5993: fprintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
5994: }
5995: // printf("\nPress Enter to continue...");
5996: // getchar();
5997: // }
5998:
5999: #endif
6000:
6001:
6002: }
6003:
6004: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){
6005: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6006: int i, j, k, i1 ;
6007: double ftolpl = 1.e-10;
6008: double age, agebase, agelim;
6009:
6010: strcpy(filerespl,"pl");
6011: strcat(filerespl,fileres);
6012: if((ficrespl=fopen(filerespl,"w"))==NULL) {
6013: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6014: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6015: }
6016: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6017: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6018: pstamp(ficrespl);
6019: fprintf(ficrespl,"# Period (stable) prevalence \n");
6020: fprintf(ficrespl,"#Age ");
6021: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
6022: fprintf(ficrespl,"\n");
6023:
6024: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
6025:
6026: agebase=ageminpar;
6027: agelim=agemaxpar;
6028:
6029: i1=pow(2,cptcoveff);
6030: if (cptcovn < 1){i1=1;}
6031:
6032: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6033: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
6034: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6035: k=k+1;
6036: /* to clean */
6037: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);
6038: fprintf(ficrespl,"\n#******");
6039: printf("\n#******");
6040: fprintf(ficlog,"\n#******");
6041: for(j=1;j<=cptcoveff;j++) {
6042: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6043: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6044: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6045: }
6046: fprintf(ficrespl,"******\n");
6047: printf("******\n");
6048: fprintf(ficlog,"******\n");
6049:
6050: fprintf(ficrespl,"#Age ");
6051: for(j=1;j<=cptcoveff;j++) {
6052: fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6053: }
6054: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
6055: fprintf(ficrespl,"\n");
6056:
6057: for (age=agebase; age<=agelim; age++){
6058: /* for (age=agebase; age<=agebase; age++){ */
6059: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6060: fprintf(ficrespl,"%.0f ",age );
6061: for(j=1;j<=cptcoveff;j++)
6062: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6063: for(i=1; i<=nlstate;i++)
6064: fprintf(ficrespl," %.5f", prlim[i][i]);
6065: fprintf(ficrespl,"\n");
6066: } /* Age */
6067: /* was end of cptcod */
6068: } /* cptcov */
6069: return 0;
6070: }
6071:
6072: int hPijx(double *p, int bage, int fage){
6073: /*------------- h Pij x at various ages ------------*/
6074:
6075: int stepsize;
6076: int agelim;
6077: int hstepm;
6078: int nhstepm;
6079: int h, i, i1, j, k;
6080:
6081: double agedeb;
6082: double ***p3mat;
6083:
6084: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
6085: if((ficrespij=fopen(filerespij,"w"))==NULL) {
6086: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
6087: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
6088: }
6089: printf("Computing pij: result on file '%s' \n", filerespij);
6090: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
6091:
6092: stepsize=(int) (stepm+YEARM-1)/YEARM;
6093: /*if (stepm<=24) stepsize=2;*/
6094:
6095: agelim=AGESUP;
6096: hstepm=stepsize*YEARM; /* Every year of age */
6097: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
6098:
6099: /* hstepm=1; aff par mois*/
6100: pstamp(ficrespij);
6101: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
6102: i1= pow(2,cptcoveff);
6103: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
6104: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
6105: /* k=k+1; */
6106: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6107: fprintf(ficrespij,"\n#****** ");
6108: for(j=1;j<=cptcoveff;j++)
6109: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6110: fprintf(ficrespij,"******\n");
6111:
6112: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
6113: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6114: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6115:
6116: /* nhstepm=nhstepm*YEARM; aff par mois*/
6117:
6118: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6119: oldm=oldms;savm=savms;
6120: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
6121: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
6122: for(i=1; i<=nlstate;i++)
6123: for(j=1; j<=nlstate+ndeath;j++)
6124: fprintf(ficrespij," %1d-%1d",i,j);
6125: fprintf(ficrespij,"\n");
6126: for (h=0; h<=nhstepm; h++){
6127: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
6128: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
6129: for(i=1; i<=nlstate;i++)
6130: for(j=1; j<=nlstate+ndeath;j++)
6131: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
6132: fprintf(ficrespij,"\n");
6133: }
6134: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6135: fprintf(ficrespij,"\n");
6136: }
6137: /*}*/
6138: }
6139: return 0;
6140: }
6141:
6142:
6143: /***********************************************/
6144: /**************** Main Program *****************/
6145: /***********************************************/
6146:
6147: int main(int argc, char *argv[])
6148: {
6149: #ifdef GSL
6150: const gsl_multimin_fminimizer_type *T;
6151: size_t iteri = 0, it;
6152: int rval = GSL_CONTINUE;
6153: int status = GSL_SUCCESS;
6154: double ssval;
6155: #endif
6156: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
6157: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
6158:
6159: int jj, ll, li, lj, lk;
6160: int numlinepar=0; /* Current linenumber of parameter file */
6161: int itimes;
6162: int NDIM=2;
6163: int vpopbased=0;
6164:
6165: char ca[32], cb[32];
6166: /* FILE *fichtm; *//* Html File */
6167: /* FILE *ficgp;*/ /*Gnuplot File */
6168: struct stat info;
6169: double agedeb;
6170: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
6171:
6172: double fret;
6173: double dum; /* Dummy variable */
6174: double ***p3mat;
6175: double ***mobaverage;
6176:
6177: char line[MAXLINE];
6178: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
6179: char pathr[MAXLINE], pathimach[MAXLINE];
6180: char *tok, *val; /* pathtot */
6181: int firstobs=1, lastobs=10;
6182: int c, h , cpt;
6183: int jl;
6184: int i1, j1, jk, stepsize;
6185: int *tab;
6186: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
6187: int mobilav=0,popforecast=0;
6188: int hstepm, nhstepm;
6189: int agemortsup;
6190: float sumlpop=0.;
6191: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
6192: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
6193:
6194: double bage=0, fage=110, age, agelim, agebase;
6195: double ftolpl=FTOL;
6196: double **prlim;
6197: double ***param; /* Matrix of parameters */
6198: double *p;
6199: double **matcov; /* Matrix of covariance */
6200: double ***delti3; /* Scale */
6201: double *delti; /* Scale */
6202: double ***eij, ***vareij;
6203: double **varpl; /* Variances of prevalence limits by age */
6204: double *epj, vepp;
6205:
6206: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
6207: double **ximort;
6208: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
6209: int *dcwave;
6210:
6211: char z[1]="c";
6212:
6213: /*char *strt;*/
6214: char strtend[80];
6215:
6216:
6217: /* setlocale (LC_ALL, ""); */
6218: /* bindtextdomain (PACKAGE, LOCALEDIR); */
6219: /* textdomain (PACKAGE); */
6220: /* setlocale (LC_CTYPE, ""); */
6221: /* setlocale (LC_MESSAGES, ""); */
6222:
6223: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
6224: rstart_time = time(NULL);
6225: /* (void) gettimeofday(&start_time,&tzp);*/
6226: start_time = *localtime(&rstart_time);
6227: curr_time=start_time;
6228: /*tml = *localtime(&start_time.tm_sec);*/
6229: /* strcpy(strstart,asctime(&tml)); */
6230: strcpy(strstart,asctime(&start_time));
6231:
6232: /* printf("Localtime (at start)=%s",strstart); */
6233: /* tp.tm_sec = tp.tm_sec +86400; */
6234: /* tm = *localtime(&start_time.tm_sec); */
6235: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
6236: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
6237: /* tmg.tm_hour=tmg.tm_hour + 1; */
6238: /* tp.tm_sec = mktime(&tmg); */
6239: /* strt=asctime(&tmg); */
6240: /* printf("Time(after) =%s",strstart); */
6241: /* (void) time (&time_value);
6242: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
6243: * tm = *localtime(&time_value);
6244: * strstart=asctime(&tm);
6245: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
6246: */
6247:
6248: nberr=0; /* Number of errors and warnings */
6249: nbwarn=0;
6250: #ifdef WIN32
6251: _getcwd(pathcd, size);
6252: #else
6253: getcwd(pathcd, size);
6254: #endif
6255:
6256: printf("\n%s\n%s",version,fullversion);
6257: if(argc <=1){
6258: printf("\nEnter the parameter file name: ");
6259: fgets(pathr,FILENAMELENGTH,stdin);
6260: i=strlen(pathr);
6261: if(pathr[i-1]=='\n')
6262: pathr[i-1]='\0';
6263: i=strlen(pathr);
6264: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
6265: pathr[i-1]='\0';
6266: for (tok = pathr; tok != NULL; ){
6267: printf("Pathr |%s|\n",pathr);
6268: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
6269: printf("val= |%s| pathr=%s\n",val,pathr);
6270: strcpy (pathtot, val);
6271: if(pathr[0] == '\0') break; /* Dirty */
6272: }
6273: }
6274: else{
6275: strcpy(pathtot,argv[1]);
6276: }
6277: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
6278: /*cygwin_split_path(pathtot,path,optionfile);
6279: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
6280: /* cutv(path,optionfile,pathtot,'\\');*/
6281:
6282: /* Split argv[0], imach program to get pathimach */
6283: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
6284: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6285: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6286: /* strcpy(pathimach,argv[0]); */
6287: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
6288: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
6289: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
6290: #ifdef WIN32
6291: _chdir(path); /* Can be a relative path */
6292: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
6293: #else
6294: chdir(path); /* Can be a relative path */
6295: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
6296: #endif
6297: printf("Current directory %s!\n",pathcd);
6298: strcpy(command,"mkdir ");
6299: strcat(command,optionfilefiname);
6300: if((outcmd=system(command)) != 0){
6301: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
6302: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
6303: /* fclose(ficlog); */
6304: /* exit(1); */
6305: }
6306: /* if((imk=mkdir(optionfilefiname))<0){ */
6307: /* perror("mkdir"); */
6308: /* } */
6309:
6310: /*-------- arguments in the command line --------*/
6311:
6312: /* Main Log file */
6313: strcat(filelog, optionfilefiname);
6314: strcat(filelog,".log"); /* */
6315: if((ficlog=fopen(filelog,"w"))==NULL) {
6316: printf("Problem with logfile %s\n",filelog);
6317: goto end;
6318: }
6319: fprintf(ficlog,"Log filename:%s\n",filelog);
6320: fprintf(ficlog,"\n%s\n%s",version,fullversion);
6321: fprintf(ficlog,"\nEnter the parameter file name: \n");
6322: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
6323: path=%s \n\
6324: optionfile=%s\n\
6325: optionfilext=%s\n\
6326: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
6327:
6328: syscompilerinfo();
6329:
6330: printf("Local time (at start):%s",strstart);
6331: fprintf(ficlog,"Local time (at start): %s",strstart);
6332: fflush(ficlog);
6333: /* (void) gettimeofday(&curr_time,&tzp); */
6334: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
6335:
6336: /* */
6337: strcpy(fileres,"r");
6338: strcat(fileres, optionfilefiname);
6339: strcat(fileres,".txt"); /* Other files have txt extension */
6340:
6341: /* Main ---------arguments file --------*/
6342:
6343: if((ficpar=fopen(optionfile,"r"))==NULL) {
6344: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
6345: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
6346: fflush(ficlog);
6347: /* goto end; */
6348: exit(70);
6349: }
6350:
6351:
6352:
6353: strcpy(filereso,"o");
6354: strcat(filereso,fileres);
6355: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
6356: printf("Problem with Output resultfile: %s\n", filereso);
6357: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
6358: fflush(ficlog);
6359: goto end;
6360: }
6361:
6362: /* Reads comments: lines beginning with '#' */
6363: numlinepar=0;
6364: while((c=getc(ficpar))=='#' && c!= EOF){
6365: ungetc(c,ficpar);
6366: fgets(line, MAXLINE, ficpar);
6367: numlinepar++;
6368: fputs(line,stdout);
6369: fputs(line,ficparo);
6370: fputs(line,ficlog);
6371: }
6372: ungetc(c,ficpar);
6373:
6374: 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=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
6375: numlinepar++;
6376: 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=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
6377: if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the model */
6378: model[strlen(model)-1]='\0';
6379: 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=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
6380: 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=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
6381: fflush(ficlog);
6382: if(model[0]=='#'|| model[0]== '\0'){
6383: printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
6384: 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
6385: 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \
6386: if(mle != -1){
6387: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
6388: exit(1);
6389: }
6390: }
6391: while((c=getc(ficpar))=='#' && c!= EOF){
6392: ungetc(c,ficpar);
6393: fgets(line, MAXLINE, ficpar);
6394: numlinepar++;
6395: fputs(line, stdout);
6396: //puts(line);
6397: fputs(line,ficparo);
6398: fputs(line,ficlog);
6399: }
6400: ungetc(c,ficpar);
6401:
6402:
6403: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
6404: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
6405: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
6406: v1+v2*age+v2*v3 makes cptcovn = 3
6407: */
6408: if (strlen(model)>1)
6409: 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,age*age makes 3*/
6410: else
6411: ncovmodel=2; /* Constant and age */
6412: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
6413: npar= nforce*ncovmodel; /* Number of parameters like aij*/
6414: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
6415: 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);
6416: 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);
6417: fflush(stdout);
6418: fclose (ficlog);
6419: goto end;
6420: }
6421: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6422: delti=delti3[1][1];
6423: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
6424: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
6425: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
6426: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
6427: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
6428: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6429: fclose (ficparo);
6430: fclose (ficlog);
6431: goto end;
6432: exit(0);
6433: }
6434: else if(mle==-3) { /* Main Wizard */
6435: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
6436: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
6437: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
6438: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6439: matcov=matrix(1,npar,1,npar);
6440: }
6441: else{
6442: /* Read guessed parameters */
6443: /* Reads comments: lines beginning with '#' */
6444: while((c=getc(ficpar))=='#' && c!= EOF){
6445: ungetc(c,ficpar);
6446: fgets(line, MAXLINE, ficpar);
6447: numlinepar++;
6448: fputs(line,stdout);
6449: fputs(line,ficparo);
6450: fputs(line,ficlog);
6451: }
6452: ungetc(c,ficpar);
6453:
6454: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6455: for(i=1; i <=nlstate; i++){
6456: j=0;
6457: for(jj=1; jj <=nlstate+ndeath; jj++){
6458: if(jj==i) continue;
6459: j++;
6460: fscanf(ficpar,"%1d%1d",&i1,&j1);
6461: if ((i1 != i) && (j1 != j)){
6462: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
6463: It might be a problem of design; if ncovcol and the model are correct\n \
6464: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
6465: exit(1);
6466: }
6467: fprintf(ficparo,"%1d%1d",i1,j1);
6468: if(mle==1)
6469: printf("%1d%1d",i,j);
6470: fprintf(ficlog,"%1d%1d",i,j);
6471: for(k=1; k<=ncovmodel;k++){
6472: fscanf(ficpar," %lf",¶m[i][j][k]);
6473: if(mle==1){
6474: printf(" %lf",param[i][j][k]);
6475: fprintf(ficlog," %lf",param[i][j][k]);
6476: }
6477: else
6478: fprintf(ficlog," %lf",param[i][j][k]);
6479: fprintf(ficparo," %lf",param[i][j][k]);
6480: }
6481: fscanf(ficpar,"\n");
6482: numlinepar++;
6483: if(mle==1)
6484: printf("\n");
6485: fprintf(ficlog,"\n");
6486: fprintf(ficparo,"\n");
6487: }
6488: }
6489: fflush(ficlog);
6490:
6491: /* Reads scales values */
6492: p=param[1][1];
6493:
6494: /* Reads comments: lines beginning with '#' */
6495: while((c=getc(ficpar))=='#' && c!= EOF){
6496: ungetc(c,ficpar);
6497: fgets(line, MAXLINE, ficpar);
6498: numlinepar++;
6499: fputs(line,stdout);
6500: fputs(line,ficparo);
6501: fputs(line,ficlog);
6502: }
6503: ungetc(c,ficpar);
6504:
6505: for(i=1; i <=nlstate; i++){
6506: for(j=1; j <=nlstate+ndeath-1; j++){
6507: fscanf(ficpar,"%1d%1d",&i1,&j1);
6508: if ( (i1-i) * (j1-j) != 0){
6509: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
6510: exit(1);
6511: }
6512: printf("%1d%1d",i,j);
6513: fprintf(ficparo,"%1d%1d",i1,j1);
6514: fprintf(ficlog,"%1d%1d",i1,j1);
6515: for(k=1; k<=ncovmodel;k++){
6516: fscanf(ficpar,"%le",&delti3[i][j][k]);
6517: printf(" %le",delti3[i][j][k]);
6518: fprintf(ficparo," %le",delti3[i][j][k]);
6519: fprintf(ficlog," %le",delti3[i][j][k]);
6520: }
6521: fscanf(ficpar,"\n");
6522: numlinepar++;
6523: printf("\n");
6524: fprintf(ficparo,"\n");
6525: fprintf(ficlog,"\n");
6526: }
6527: }
6528: fflush(ficlog);
6529:
6530: /* Reads covariance matrix */
6531: delti=delti3[1][1];
6532:
6533:
6534: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
6535:
6536: /* Reads comments: lines beginning with '#' */
6537: while((c=getc(ficpar))=='#' && c!= EOF){
6538: ungetc(c,ficpar);
6539: fgets(line, MAXLINE, ficpar);
6540: numlinepar++;
6541: fputs(line,stdout);
6542: fputs(line,ficparo);
6543: fputs(line,ficlog);
6544: }
6545: ungetc(c,ficpar);
6546:
6547: matcov=matrix(1,npar,1,npar);
6548: for(i=1; i <=npar; i++)
6549: for(j=1; j <=npar; j++) matcov[i][j]=0.;
6550:
6551: for(i=1; i <=npar; i++){
6552: fscanf(ficpar,"%s",str);
6553: if(mle==1)
6554: printf("%s",str);
6555: fprintf(ficlog,"%s",str);
6556: fprintf(ficparo,"%s",str);
6557: for(j=1; j <=i; j++){
6558: fscanf(ficpar," %le",&matcov[i][j]);
6559: if(mle==1){
6560: printf(" %.5le",matcov[i][j]);
6561: }
6562: fprintf(ficlog," %.5le",matcov[i][j]);
6563: fprintf(ficparo," %.5le",matcov[i][j]);
6564: }
6565: fscanf(ficpar,"\n");
6566: numlinepar++;
6567: if(mle==1)
6568: printf("\n");
6569: fprintf(ficlog,"\n");
6570: fprintf(ficparo,"\n");
6571: }
6572: for(i=1; i <=npar; i++)
6573: for(j=i+1;j<=npar;j++)
6574: matcov[i][j]=matcov[j][i];
6575:
6576: if(mle==1)
6577: printf("\n");
6578: fprintf(ficlog,"\n");
6579:
6580: fflush(ficlog);
6581:
6582: /*-------- Rewriting parameter file ----------*/
6583: strcpy(rfileres,"r"); /* "Rparameterfile */
6584: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
6585: strcat(rfileres,"."); /* */
6586: strcat(rfileres,optionfilext); /* Other files have txt extension */
6587: if((ficres =fopen(rfileres,"w"))==NULL) {
6588: printf("Problem writing new parameter file: %s\n", fileres);goto end;
6589: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
6590: }
6591: fprintf(ficres,"#%s\n",version);
6592: } /* End of mle != -3 */
6593:
6594: /* Main data
6595: */
6596: n= lastobs;
6597: num=lvector(1,n);
6598: moisnais=vector(1,n);
6599: annais=vector(1,n);
6600: moisdc=vector(1,n);
6601: andc=vector(1,n);
6602: agedc=vector(1,n);
6603: cod=ivector(1,n);
6604: weight=vector(1,n);
6605: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
6606: mint=matrix(1,maxwav,1,n);
6607: anint=matrix(1,maxwav,1,n);
6608: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
6609: tab=ivector(1,NCOVMAX);
6610: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
6611:
6612: /* Reads data from file datafile */
6613: if (readdata(datafile, firstobs, lastobs, &imx)==1)
6614: goto end;
6615:
6616: /* Calculation of the number of parameters from char model */
6617: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
6618: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
6619: k=3 V4 Tvar[k=3]= 4 (from V4)
6620: k=2 V1 Tvar[k=2]= 1 (from V1)
6621: k=1 Tvar[1]=2 (from V2)
6622: */
6623: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
6624: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
6625: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
6626: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
6627: */
6628: /* For model-covariate k tells which data-covariate to use but
6629: because this model-covariate is a construction we invent a new column
6630: ncovcol + k1
6631: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
6632: Tvar[3=V1*V4]=4+1 etc */
6633: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
6634: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
6635: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
6636: */
6637: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
6638: 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
6639: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
6640: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
6641: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
6642: 4 covariates (3 plus signs)
6643: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
6644: */
6645:
6646: /* Main decodemodel */
6647:
6648:
6649: if(decodemodel(model, lastobs) == 1)
6650: goto end;
6651:
6652: if((double)(lastobs-imx)/(double)imx > 1.10){
6653: nbwarn++;
6654: 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);
6655: 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);
6656: }
6657: /* if(mle==1){*/
6658: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
6659: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
6660: }
6661:
6662: /*-calculation of age at interview from date of interview and age at death -*/
6663: agev=matrix(1,maxwav,1,imx);
6664:
6665: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
6666: goto end;
6667:
6668:
6669: agegomp=(int)agemin;
6670: free_vector(moisnais,1,n);
6671: free_vector(annais,1,n);
6672: /* free_matrix(mint,1,maxwav,1,n);
6673: free_matrix(anint,1,maxwav,1,n);*/
6674: free_vector(moisdc,1,n);
6675: free_vector(andc,1,n);
6676: /* */
6677:
6678: wav=ivector(1,imx);
6679: dh=imatrix(1,lastpass-firstpass+1,1,imx);
6680: bh=imatrix(1,lastpass-firstpass+1,1,imx);
6681: mw=imatrix(1,lastpass-firstpass+1,1,imx);
6682:
6683: /* Concatenates waves */
6684: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
6685: /* */
6686:
6687: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
6688:
6689: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
6690: ncodemax[1]=1;
6691: Ndum =ivector(-1,NCOVMAX);
6692: if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */
6693: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
6694: /* Nbcode gives the value of the lth modality of jth covariate, in
6695: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
6696: /* 1 to ncodemax[j] is the maximum value of this jth covariate */
6697:
6698: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
6699: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
6700: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
6701: h=0;
6702:
6703:
6704: /*if (cptcovn > 0) */
6705:
6706:
6707: m=pow(2,cptcoveff);
6708:
6709: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
6710: 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 */
6711: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
6712: for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
6713: h++;
6714: if (h>m)
6715: h=1;
6716: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
6717: * For k=4 covariates, h goes from 1 to 2**k
6718: * codtabm(h,k)= 1 & (h-1) >> (k-1) ;
6719: * h\k 1 2 3 4
6720: *______________________________
6721: * 1 i=1 1 i=1 1 i=1 1 i=1 1
6722: * 2 2 1 1 1
6723: * 3 i=2 1 2 1 1
6724: * 4 2 2 1 1
6725: * 5 i=3 1 i=2 1 2 1
6726: * 6 2 1 2 1
6727: * 7 i=4 1 2 2 1
6728: * 8 2 2 2 1
6729: * 9 i=5 1 i=3 1 i=2 1 1
6730: * 10 2 1 1 1
6731: * 11 i=6 1 2 1 1
6732: * 12 2 2 1 1
6733: * 13 i=7 1 i=4 1 2 1
6734: * 14 2 1 2 1
6735: * 15 i=8 1 2 2 1
6736: * 16 2 2 2 1
6737: */
6738: codtab[h][k]=j;
6739: /* codtab[12][3]=1; */
6740: /*codtab[h][Tvar[k]]=j;*/
6741: 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]]);
6742: }
6743: }
6744: }
6745: }
6746: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
6747: codtab[1][2]=1;codtab[2][2]=2; */
6748: /* for(i=1; i <=m ;i++){
6749: for(k=1; k <=cptcovn; k++){
6750: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
6751: }
6752: printf("\n");
6753: }
6754: scanf("%d",i);*/
6755:
6756: free_ivector(Ndum,-1,NCOVMAX);
6757:
6758:
6759:
6760: /* Initialisation of ----------- gnuplot -------------*/
6761: strcpy(optionfilegnuplot,optionfilefiname);
6762: if(mle==-3)
6763: strcat(optionfilegnuplot,"-mort");
6764: strcat(optionfilegnuplot,".gp");
6765:
6766: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
6767: printf("Problem with file %s",optionfilegnuplot);
6768: }
6769: else{
6770: fprintf(ficgp,"\n# %s\n", version);
6771: fprintf(ficgp,"# %s\n", optionfilegnuplot);
6772: //fprintf(ficgp,"set missing 'NaNq'\n");
6773: fprintf(ficgp,"set datafile missing 'NaNq'\n");
6774: }
6775: /* fclose(ficgp);*/
6776:
6777:
6778: /* Initialisation of --------- index.htm --------*/
6779:
6780: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
6781: if(mle==-3)
6782: strcat(optionfilehtm,"-mort");
6783: strcat(optionfilehtm,".htm");
6784: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
6785: printf("Problem with %s \n",optionfilehtm);
6786: exit(0);
6787: }
6788:
6789: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
6790: strcat(optionfilehtmcov,"-cov.htm");
6791: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
6792: printf("Problem with %s \n",optionfilehtmcov), exit(0);
6793: }
6794: else{
6795: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6796: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6797: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
6798: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
6799: }
6800:
6801: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6802: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6803: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
6804: \n\
6805: <hr size=\"2\" color=\"#EC5E5E\">\
6806: <ul><li><h4>Parameter files</h4>\n\
6807: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
6808: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
6809: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
6810: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
6811: - Date and time at start: %s</ul>\n",\
6812: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
6813: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
6814: fileres,fileres,\
6815: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
6816: fflush(fichtm);
6817:
6818: strcpy(pathr,path);
6819: strcat(pathr,optionfilefiname);
6820: #ifdef WIN32
6821: _chdir(optionfilefiname); /* Move to directory named optionfile */
6822: #else
6823: chdir(optionfilefiname); /* Move to directory named optionfile */
6824: #endif
6825:
6826:
6827: /* Calculates basic frequencies. Computes observed prevalence at single age
6828: and prints on file fileres'p'. */
6829: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
6830:
6831: fprintf(fichtm,"\n");
6832: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
6833: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
6834: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
6835: imx,agemin,agemax,jmin,jmax,jmean);
6836: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6837: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6838: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6839: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6840: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
6841:
6842:
6843: /* For Powell, parameters are in a vector p[] starting at p[1]
6844: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
6845: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
6846:
6847: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
6848: /* For mortality only */
6849: if (mle==-3){
6850: ximort=matrix(1,NDIM,1,NDIM);
6851: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
6852: cens=ivector(1,n);
6853: ageexmed=vector(1,n);
6854: agecens=vector(1,n);
6855: dcwave=ivector(1,n);
6856:
6857: for (i=1; i<=imx; i++){
6858: dcwave[i]=-1;
6859: for (m=firstpass; m<=lastpass; m++)
6860: if (s[m][i]>nlstate) {
6861: dcwave[i]=m;
6862: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
6863: break;
6864: }
6865: }
6866:
6867: for (i=1; i<=imx; i++) {
6868: if (wav[i]>0){
6869: ageexmed[i]=agev[mw[1][i]][i];
6870: j=wav[i];
6871: agecens[i]=1.;
6872:
6873: if (ageexmed[i]> 1 && wav[i] > 0){
6874: agecens[i]=agev[mw[j][i]][i];
6875: cens[i]= 1;
6876: }else if (ageexmed[i]< 1)
6877: cens[i]= -1;
6878: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
6879: cens[i]=0 ;
6880: }
6881: else cens[i]=-1;
6882: }
6883:
6884: for (i=1;i<=NDIM;i++) {
6885: for (j=1;j<=NDIM;j++)
6886: ximort[i][j]=(i == j ? 1.0 : 0.0);
6887: }
6888:
6889: /*p[1]=0.0268; p[NDIM]=0.083;*/
6890: /*printf("%lf %lf", p[1], p[2]);*/
6891:
6892:
6893: #ifdef GSL
6894: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
6895: #else
6896: printf("Powell\n"); fprintf(ficlog,"Powell\n");
6897: #endif
6898: strcpy(filerespow,"pow-mort");
6899: strcat(filerespow,fileres);
6900: if((ficrespow=fopen(filerespow,"w"))==NULL) {
6901: printf("Problem with resultfile: %s\n", filerespow);
6902: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
6903: }
6904: #ifdef GSL
6905: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
6906: #else
6907: fprintf(ficrespow,"# Powell\n# iter -2*LL");
6908: #endif
6909: /* for (i=1;i<=nlstate;i++)
6910: for(j=1;j<=nlstate+ndeath;j++)
6911: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
6912: */
6913: fprintf(ficrespow,"\n");
6914: #ifdef GSL
6915: /* gsl starts here */
6916: T = gsl_multimin_fminimizer_nmsimplex;
6917: gsl_multimin_fminimizer *sfm = NULL;
6918: gsl_vector *ss, *x;
6919: gsl_multimin_function minex_func;
6920:
6921: /* Initial vertex size vector */
6922: ss = gsl_vector_alloc (NDIM);
6923:
6924: if (ss == NULL){
6925: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
6926: }
6927: /* Set all step sizes to 1 */
6928: gsl_vector_set_all (ss, 0.001);
6929:
6930: /* Starting point */
6931:
6932: x = gsl_vector_alloc (NDIM);
6933:
6934: if (x == NULL){
6935: gsl_vector_free(ss);
6936: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
6937: }
6938:
6939: /* Initialize method and iterate */
6940: /* p[1]=0.0268; p[NDIM]=0.083; */
6941: /* gsl_vector_set(x, 0, 0.0268); */
6942: /* gsl_vector_set(x, 1, 0.083); */
6943: gsl_vector_set(x, 0, p[1]);
6944: gsl_vector_set(x, 1, p[2]);
6945:
6946: minex_func.f = &gompertz_f;
6947: minex_func.n = NDIM;
6948: minex_func.params = (void *)&p; /* ??? */
6949:
6950: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
6951: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
6952:
6953: printf("Iterations beginning .....\n\n");
6954: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
6955:
6956: iteri=0;
6957: while (rval == GSL_CONTINUE){
6958: iteri++;
6959: status = gsl_multimin_fminimizer_iterate(sfm);
6960:
6961: if (status) printf("error: %s\n", gsl_strerror (status));
6962: fflush(0);
6963:
6964: if (status)
6965: break;
6966:
6967: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
6968: ssval = gsl_multimin_fminimizer_size (sfm);
6969:
6970: if (rval == GSL_SUCCESS)
6971: printf ("converged to a local maximum at\n");
6972:
6973: printf("%5d ", iteri);
6974: for (it = 0; it < NDIM; it++){
6975: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
6976: }
6977: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
6978: }
6979:
6980: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
6981:
6982: gsl_vector_free(x); /* initial values */
6983: gsl_vector_free(ss); /* inital step size */
6984: for (it=0; it<NDIM; it++){
6985: p[it+1]=gsl_vector_get(sfm->x,it);
6986: fprintf(ficrespow," %.12lf", p[it]);
6987: }
6988: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
6989: #endif
6990: #ifdef POWELL
6991: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
6992: #endif
6993: fclose(ficrespow);
6994:
6995: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
6996:
6997: for(i=1; i <=NDIM; i++)
6998: for(j=i+1;j<=NDIM;j++)
6999: matcov[i][j]=matcov[j][i];
7000:
7001: printf("\nCovariance matrix\n ");
7002: for(i=1; i <=NDIM; i++) {
7003: for(j=1;j<=NDIM;j++){
7004: printf("%f ",matcov[i][j]);
7005: }
7006: printf("\n ");
7007: }
7008:
7009: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
7010: for (i=1;i<=NDIM;i++)
7011: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
7012:
7013: lsurv=vector(1,AGESUP);
7014: lpop=vector(1,AGESUP);
7015: tpop=vector(1,AGESUP);
7016: lsurv[agegomp]=100000;
7017:
7018: for (k=agegomp;k<=AGESUP;k++) {
7019: agemortsup=k;
7020: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
7021: }
7022:
7023: for (k=agegomp;k<agemortsup;k++)
7024: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
7025:
7026: for (k=agegomp;k<agemortsup;k++){
7027: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
7028: sumlpop=sumlpop+lpop[k];
7029: }
7030:
7031: tpop[agegomp]=sumlpop;
7032: for (k=agegomp;k<(agemortsup-3);k++){
7033: /* tpop[k+1]=2;*/
7034: tpop[k+1]=tpop[k]-lpop[k];
7035: }
7036:
7037:
7038: printf("\nAge lx qx dx Lx Tx e(x)\n");
7039: for (k=agegomp;k<(agemortsup-2);k++)
7040: 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]);
7041:
7042:
7043: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
7044: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
7045:
7046: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
7047: stepm, weightopt,\
7048: model,imx,p,matcov,agemortsup);
7049:
7050: free_vector(lsurv,1,AGESUP);
7051: free_vector(lpop,1,AGESUP);
7052: free_vector(tpop,1,AGESUP);
7053: #ifdef GSL
7054: free_ivector(cens,1,n);
7055: free_vector(agecens,1,n);
7056: free_ivector(dcwave,1,n);
7057: free_matrix(ximort,1,NDIM,1,NDIM);
7058: #endif
7059: } /* Endof if mle==-3 mortality only */
7060: /* Standard maximisation */
7061: else{ /* For mle >=1 */
7062: globpr=0;/* debug */
7063: /* Computes likelihood for initial parameters */
7064: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
7065: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7066: for (k=1; k<=npar;k++)
7067: printf(" %d %8.5f",k,p[k]);
7068: printf("\n");
7069: globpr=1; /* again, to print the contributions */
7070: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
7071: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7072: for (k=1; k<=npar;k++)
7073: printf(" %d %8.5f",k,p[k]);
7074: printf("\n");
7075: if(mle>=1){ /* Could be 1 or 2, Real Maximisation */
7076: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
7077: }
7078:
7079: /*--------- results files --------------*/
7080: 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=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
7081:
7082:
7083: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7084: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7085: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7086: for(i=1,jk=1; i <=nlstate; i++){
7087: for(k=1; k <=(nlstate+ndeath); k++){
7088: if (k != i) {
7089: printf("%d%d ",i,k);
7090: fprintf(ficlog,"%d%d ",i,k);
7091: fprintf(ficres,"%1d%1d ",i,k);
7092: for(j=1; j <=ncovmodel; j++){
7093: printf("%lf ",p[jk]);
7094: fprintf(ficlog,"%lf ",p[jk]);
7095: fprintf(ficres,"%lf ",p[jk]);
7096: jk++;
7097: }
7098: printf("\n");
7099: fprintf(ficlog,"\n");
7100: fprintf(ficres,"\n");
7101: }
7102: }
7103: }
7104: if(mle!=0){
7105: /* Computing hessian and covariance matrix */
7106: ftolhess=ftol; /* Usually correct */
7107: hesscov(matcov, p, npar, delti, ftolhess, func);
7108: }
7109: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
7110: printf("# Scales (for hessian or gradient estimation)\n");
7111: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
7112: for(i=1,jk=1; i <=nlstate; i++){
7113: for(j=1; j <=nlstate+ndeath; j++){
7114: if (j!=i) {
7115: fprintf(ficres,"%1d%1d",i,j);
7116: printf("%1d%1d",i,j);
7117: fprintf(ficlog,"%1d%1d",i,j);
7118: for(k=1; k<=ncovmodel;k++){
7119: printf(" %.5e",delti[jk]);
7120: fprintf(ficlog," %.5e",delti[jk]);
7121: fprintf(ficres," %.5e",delti[jk]);
7122: jk++;
7123: }
7124: printf("\n");
7125: fprintf(ficlog,"\n");
7126: fprintf(ficres,"\n");
7127: }
7128: }
7129: }
7130:
7131: 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");
7132: if(mle>=1)
7133: 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");
7134: 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");
7135: /* # 121 Var(a12)\n\ */
7136: /* # 122 Cov(b12,a12) Var(b12)\n\ */
7137: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
7138: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
7139: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
7140: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
7141: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
7142: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
7143:
7144:
7145: /* Just to have a covariance matrix which will be more understandable
7146: even is we still don't want to manage dictionary of variables
7147: */
7148: for(itimes=1;itimes<=2;itimes++){
7149: jj=0;
7150: for(i=1; i <=nlstate; i++){
7151: for(j=1; j <=nlstate+ndeath; j++){
7152: if(j==i) continue;
7153: for(k=1; k<=ncovmodel;k++){
7154: jj++;
7155: ca[0]= k+'a'-1;ca[1]='\0';
7156: if(itimes==1){
7157: if(mle>=1)
7158: printf("#%1d%1d%d",i,j,k);
7159: fprintf(ficlog,"#%1d%1d%d",i,j,k);
7160: fprintf(ficres,"#%1d%1d%d",i,j,k);
7161: }else{
7162: if(mle>=1)
7163: printf("%1d%1d%d",i,j,k);
7164: fprintf(ficlog,"%1d%1d%d",i,j,k);
7165: fprintf(ficres,"%1d%1d%d",i,j,k);
7166: }
7167: ll=0;
7168: for(li=1;li <=nlstate; li++){
7169: for(lj=1;lj <=nlstate+ndeath; lj++){
7170: if(lj==li) continue;
7171: for(lk=1;lk<=ncovmodel;lk++){
7172: ll++;
7173: if(ll<=jj){
7174: cb[0]= lk +'a'-1;cb[1]='\0';
7175: if(ll<jj){
7176: if(itimes==1){
7177: if(mle>=1)
7178: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7179: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7180: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7181: }else{
7182: if(mle>=1)
7183: printf(" %.5e",matcov[jj][ll]);
7184: fprintf(ficlog," %.5e",matcov[jj][ll]);
7185: fprintf(ficres," %.5e",matcov[jj][ll]);
7186: }
7187: }else{
7188: if(itimes==1){
7189: if(mle>=1)
7190: printf(" Var(%s%1d%1d)",ca,i,j);
7191: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
7192: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
7193: }else{
7194: if(mle>=1)
7195: printf(" %.5e",matcov[jj][ll]);
7196: fprintf(ficlog," %.5e",matcov[jj][ll]);
7197: fprintf(ficres," %.5e",matcov[jj][ll]);
7198: }
7199: }
7200: }
7201: } /* end lk */
7202: } /* end lj */
7203: } /* end li */
7204: if(mle>=1)
7205: printf("\n");
7206: fprintf(ficlog,"\n");
7207: fprintf(ficres,"\n");
7208: numlinepar++;
7209: } /* end k*/
7210: } /*end j */
7211: } /* end i */
7212: } /* end itimes */
7213:
7214: fflush(ficlog);
7215: fflush(ficres);
7216:
7217: while((c=getc(ficpar))=='#' && c!= EOF){
7218: ungetc(c,ficpar);
7219: fgets(line, MAXLINE, ficpar);
7220: fputs(line,stdout);
7221: fputs(line,ficparo);
7222: }
7223: ungetc(c,ficpar);
7224:
7225: estepm=0;
7226: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
7227: if (estepm==0 || estepm < stepm) estepm=stepm;
7228: if (fage <= 2) {
7229: bage = ageminpar;
7230: fage = agemaxpar;
7231: }
7232:
7233: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
7234: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
7235: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
7236:
7237: /* Other stuffs, more or less useful */
7238: while((c=getc(ficpar))=='#' && c!= EOF){
7239: ungetc(c,ficpar);
7240: fgets(line, MAXLINE, ficpar);
7241: fputs(line,stdout);
7242: fputs(line,ficparo);
7243: }
7244: ungetc(c,ficpar);
7245:
7246: 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);
7247: 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);
7248: 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);
7249: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
7250: 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);
7251:
7252: while((c=getc(ficpar))=='#' && c!= EOF){
7253: ungetc(c,ficpar);
7254: fgets(line, MAXLINE, ficpar);
7255: fputs(line,stdout);
7256: fputs(line,ficparo);
7257: }
7258: ungetc(c,ficpar);
7259:
7260:
7261: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
7262: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
7263:
7264: fscanf(ficpar,"pop_based=%d\n",&popbased);
7265: fprintf(ficparo,"pop_based=%d\n",popbased);
7266: fprintf(ficres,"pop_based=%d\n",popbased);
7267:
7268: while((c=getc(ficpar))=='#' && c!= EOF){
7269: ungetc(c,ficpar);
7270: fgets(line, MAXLINE, ficpar);
7271: fputs(line,stdout);
7272: fputs(line,ficparo);
7273: }
7274: ungetc(c,ficpar);
7275:
7276: 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);
7277: 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);
7278: 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);
7279: 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);
7280: 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);
7281: /* day and month of proj2 are not used but only year anproj2.*/
7282:
7283:
7284:
7285: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
7286: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
7287:
7288: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
7289: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
7290:
7291: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
7292: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
7293: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
7294:
7295: /*------------ free_vector -------------*/
7296: /* chdir(path); */
7297:
7298: free_ivector(wav,1,imx);
7299: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
7300: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
7301: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
7302: free_lvector(num,1,n);
7303: free_vector(agedc,1,n);
7304: /*free_matrix(covar,0,NCOVMAX,1,n);*/
7305: /*free_matrix(covar,1,NCOVMAX,1,n);*/
7306: fclose(ficparo);
7307: fclose(ficres);
7308:
7309:
7310: /* Other results (useful)*/
7311:
7312:
7313: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
7314: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
7315: prlim=matrix(1,nlstate,1,nlstate);
7316: prevalence_limit(p, prlim, ageminpar, agemaxpar);
7317: fclose(ficrespl);
7318:
7319: #ifdef FREEEXIT2
7320: #include "freeexit2.h"
7321: #endif
7322:
7323: /*------------- h Pij x at various ages ------------*/
7324: /*#include "hpijx.h"*/
7325: hPijx(p, bage, fage);
7326: fclose(ficrespij);
7327:
7328: /*-------------- Variance of one-step probabilities---*/
7329: k=1;
7330: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
7331:
7332:
7333: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7334: for(i=1;i<=AGESUP;i++)
7335: for(j=1;j<=NCOVMAX;j++)
7336: for(k=1;k<=NCOVMAX;k++)
7337: probs[i][j][k]=0.;
7338:
7339: /*---------- Forecasting ------------------*/
7340: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
7341: if(prevfcast==1){
7342: /* if(stepm ==1){*/
7343: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
7344: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
7345: /* } */
7346: /* else{ */
7347: /* erreur=108; */
7348: /* 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); */
7349: /* 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); */
7350: /* } */
7351: }
7352:
7353: /* ------ Other prevalence ratios------------ */
7354:
7355: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
7356:
7357: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
7358: /* 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",\
7359: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
7360: */
7361:
7362: if (mobilav!=0) {
7363: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7364: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
7365: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
7366: printf(" Error in movingaverage mobilav=%d\n",mobilav);
7367: }
7368: }
7369:
7370:
7371: /*---------- Health expectancies, no variances ------------*/
7372:
7373: strcpy(filerese,"e");
7374: strcat(filerese,fileres);
7375: if((ficreseij=fopen(filerese,"w"))==NULL) {
7376: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
7377: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
7378: }
7379: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
7380: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
7381: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7382: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7383:
7384: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7385: fprintf(ficreseij,"\n#****** ");
7386: for(j=1;j<=cptcoveff;j++) {
7387: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7388: }
7389: fprintf(ficreseij,"******\n");
7390:
7391: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7392: oldm=oldms;savm=savms;
7393: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
7394:
7395: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
7396: /*}*/
7397: }
7398: fclose(ficreseij);
7399:
7400:
7401: /*---------- Health expectancies and variances ------------*/
7402:
7403:
7404: strcpy(filerest,"t");
7405: strcat(filerest,fileres);
7406: if((ficrest=fopen(filerest,"w"))==NULL) {
7407: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
7408: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
7409: }
7410: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
7411: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
7412:
7413:
7414: strcpy(fileresstde,"stde");
7415: strcat(fileresstde,fileres);
7416: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
7417: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
7418: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
7419: }
7420: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
7421: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
7422:
7423: strcpy(filerescve,"cve");
7424: strcat(filerescve,fileres);
7425: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
7426: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
7427: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
7428: }
7429: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
7430: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
7431:
7432: strcpy(fileresv,"v");
7433: strcat(fileresv,fileres);
7434: if((ficresvij=fopen(fileresv,"w"))==NULL) {
7435: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
7436: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
7437: }
7438: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
7439: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
7440:
7441: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7442: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7443:
7444: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7445: fprintf(ficrest,"\n#****** ");
7446: for(j=1;j<=cptcoveff;j++)
7447: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7448: fprintf(ficrest,"******\n");
7449:
7450: fprintf(ficresstdeij,"\n#****** ");
7451: fprintf(ficrescveij,"\n#****** ");
7452: for(j=1;j<=cptcoveff;j++) {
7453: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7454: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7455: }
7456: fprintf(ficresstdeij,"******\n");
7457: fprintf(ficrescveij,"******\n");
7458:
7459: fprintf(ficresvij,"\n#****** ");
7460: for(j=1;j<=cptcoveff;j++)
7461: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7462: fprintf(ficresvij,"******\n");
7463:
7464: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7465: oldm=oldms;savm=savms;
7466: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
7467: /*
7468: */
7469: /* goto endfree; */
7470:
7471: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7472: pstamp(ficrest);
7473:
7474:
7475: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
7476: oldm=oldms;savm=savms; /* Segmentation fault */
7477: cptcod= 0; /* To be deleted */
7478: 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 */
7479: 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 ");
7480: if(vpopbased==1)
7481: 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);
7482: else
7483: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
7484: fprintf(ficrest,"# Age e.. (std) ");
7485: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
7486: fprintf(ficrest,"\n");
7487:
7488: epj=vector(1,nlstate+1);
7489: for(age=bage; age <=fage ;age++){
7490: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
7491: if (vpopbased==1) {
7492: if(mobilav ==0){
7493: for(i=1; i<=nlstate;i++)
7494: prlim[i][i]=probs[(int)age][i][k];
7495: }else{ /* mobilav */
7496: for(i=1; i<=nlstate;i++)
7497: prlim[i][i]=mobaverage[(int)age][i][k];
7498: }
7499: }
7500:
7501: fprintf(ficrest," %4.0f",age);
7502: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
7503: for(i=1, epj[j]=0.;i <=nlstate;i++) {
7504: epj[j] += prlim[i][i]*eij[i][j][(int)age];
7505: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
7506: }
7507: epj[nlstate+1] +=epj[j];
7508: }
7509:
7510: for(i=1, vepp=0.;i <=nlstate;i++)
7511: for(j=1;j <=nlstate;j++)
7512: vepp += vareij[i][j][(int)age];
7513: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
7514: for(j=1;j <=nlstate;j++){
7515: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
7516: }
7517: fprintf(ficrest,"\n");
7518: }
7519: }
7520: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
7521: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
7522: free_vector(epj,1,nlstate+1);
7523: /*}*/
7524: }
7525: free_vector(weight,1,n);
7526: free_imatrix(Tvard,1,NCOVMAX,1,2);
7527: free_imatrix(s,1,maxwav+1,1,n);
7528: free_matrix(anint,1,maxwav,1,n);
7529: free_matrix(mint,1,maxwav,1,n);
7530: free_ivector(cod,1,n);
7531: free_ivector(tab,1,NCOVMAX);
7532: fclose(ficresstdeij);
7533: fclose(ficrescveij);
7534: fclose(ficresvij);
7535: fclose(ficrest);
7536: fclose(ficpar);
7537:
7538: /*------- Variance of period (stable) prevalence------*/
7539:
7540: strcpy(fileresvpl,"vpl");
7541: strcat(fileresvpl,fileres);
7542: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
7543: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
7544: exit(0);
7545: }
7546: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
7547:
7548: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7549: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7550:
7551: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7552: fprintf(ficresvpl,"\n#****** ");
7553: for(j=1;j<=cptcoveff;j++)
7554: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7555: fprintf(ficresvpl,"******\n");
7556:
7557: varpl=matrix(1,nlstate,(int) bage, (int) fage);
7558: oldm=oldms;savm=savms;
7559: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
7560: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
7561: /*}*/
7562: }
7563:
7564: fclose(ficresvpl);
7565:
7566: /*---------- End : free ----------------*/
7567: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7568: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7569: } /* mle==-3 arrives here for freeing */
7570: /* endfree:*/
7571: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
7572: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
7573: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
7574: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
7575: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
7576: free_matrix(covar,0,NCOVMAX,1,n);
7577: free_matrix(matcov,1,npar,1,npar);
7578: /*free_vector(delti,1,npar);*/
7579: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7580: free_matrix(agev,1,maxwav,1,imx);
7581: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7582:
7583: free_ivector(ncodemax,1,NCOVMAX);
7584: free_ivector(Tvar,1,NCOVMAX);
7585: free_ivector(Tprod,1,NCOVMAX);
7586: free_ivector(Tvaraff,1,NCOVMAX);
7587: free_ivector(Tage,1,NCOVMAX);
7588:
7589: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
7590: free_imatrix(codtab,1,100,1,10);
7591: fflush(fichtm);
7592: fflush(ficgp);
7593:
7594:
7595: if((nberr >0) || (nbwarn>0)){
7596: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
7597: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
7598: }else{
7599: printf("End of Imach\n");
7600: fprintf(ficlog,"End of Imach\n");
7601: }
7602: printf("See log file on %s\n",filelog);
7603: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
7604: /*(void) gettimeofday(&end_time,&tzp);*/
7605: rend_time = time(NULL);
7606: end_time = *localtime(&rend_time);
7607: /* tml = *localtime(&end_time.tm_sec); */
7608: strcpy(strtend,asctime(&end_time));
7609: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
7610: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
7611: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
7612:
7613: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
7614: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
7615: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
7616: /* printf("Total time was %d uSec.\n", total_usecs);*/
7617: /* if(fileappend(fichtm,optionfilehtm)){ */
7618: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7619: fclose(fichtm);
7620: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7621: fclose(fichtmcov);
7622: fclose(ficgp);
7623: fclose(ficlog);
7624: /*------ End -----------*/
7625:
7626:
7627: printf("Before Current directory %s!\n",pathcd);
7628: #ifdef WIN32
7629: if (_chdir(pathcd) != 0)
7630: printf("Can't move to directory %s!\n",path);
7631: if(_getcwd(pathcd,MAXLINE) > 0)
7632: #else
7633: if(chdir(pathcd) != 0)
7634: printf("Can't move to directory %s!\n", path);
7635: if (getcwd(pathcd, MAXLINE) > 0)
7636: #endif
7637: printf("Current directory %s!\n",pathcd);
7638: /*strcat(plotcmd,CHARSEPARATOR);*/
7639: sprintf(plotcmd,"gnuplot");
7640: #ifdef _WIN32
7641: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
7642: #endif
7643: if(!stat(plotcmd,&info)){
7644: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
7645: if(!stat(getenv("GNUPLOTBIN"),&info)){
7646: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
7647: }else
7648: strcpy(pplotcmd,plotcmd);
7649: #ifdef __unix
7650: strcpy(plotcmd,GNUPLOTPROGRAM);
7651: if(!stat(plotcmd,&info)){
7652: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
7653: }else
7654: strcpy(pplotcmd,plotcmd);
7655: #endif
7656: }else
7657: strcpy(pplotcmd,plotcmd);
7658:
7659: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
7660: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
7661:
7662: if((outcmd=system(plotcmd)) != 0){
7663: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
7664: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
7665: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
7666: if((outcmd=system(plotcmd)) != 0)
7667: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
7668: }
7669: printf(" Successful, please wait...");
7670: while (z[0] != 'q') {
7671: /* chdir(path); */
7672: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
7673: scanf("%s",z);
7674: /* if (z[0] == 'c') system("./imach"); */
7675: if (z[0] == 'e') {
7676: #ifdef __APPLE__
7677: sprintf(pplotcmd, "open %s", optionfilehtm);
7678: #elif __linux
7679: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
7680: #else
7681: sprintf(pplotcmd, "%s", optionfilehtm);
7682: #endif
7683: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
7684: system(pplotcmd);
7685: }
7686: else if (z[0] == 'g') system(plotcmd);
7687: else if (z[0] == 'q') exit(0);
7688: }
7689: end:
7690: while (z[0] != 'q') {
7691: printf("\nType q for exiting: ");
7692: scanf("%s",z);
7693: }
7694: }
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