Annotation of imach/src/imach.c, revision 1.184
1.184 ! brouard 1: /* $Id: imach.c,v 1.183 2015/03/10 20:34:32 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.184 ! brouard 4: Revision 1.183 2015/03/10 20:34:32 brouard
! 5: Summary: 0.98q0, trying with directest, mnbrak fixed
! 6:
! 7: We use directest instead of original Powell test; probably no
! 8: incidence on the results, but better justifications;
! 9: We fixed Numerical Recipes mnbrak routine which was wrong and gave
! 10: wrong results.
! 11:
1.183 brouard 12: Revision 1.182 2015/02/12 08:19:57 brouard
13: Summary: Trying to keep directest which seems simpler and more general
14: Author: Nicolas Brouard
15:
1.182 brouard 16: Revision 1.181 2015/02/11 23:22:24 brouard
17: Summary: Comments on Powell added
18:
19: Author:
20:
1.181 brouard 21: Revision 1.180 2015/02/11 17:33:45 brouard
22: Summary: Finishing move from main to function (hpijx and prevalence_limit)
23:
1.180 brouard 24: Revision 1.179 2015/01/04 09:57:06 brouard
25: Summary: back to OS/X
26:
1.179 brouard 27: Revision 1.178 2015/01/04 09:35:48 brouard
28: *** empty log message ***
29:
1.178 brouard 30: Revision 1.177 2015/01/03 18:40:56 brouard
31: Summary: Still testing ilc32 on OSX
32:
1.177 brouard 33: Revision 1.176 2015/01/03 16:45:04 brouard
34: *** empty log message ***
35:
1.176 brouard 36: Revision 1.175 2015/01/03 16:33:42 brouard
37: *** empty log message ***
38:
1.175 brouard 39: Revision 1.174 2015/01/03 16:15:49 brouard
40: Summary: Still in cross-compilation
41:
1.174 brouard 42: Revision 1.173 2015/01/03 12:06:26 brouard
43: Summary: trying to detect cross-compilation
44:
1.173 brouard 45: Revision 1.172 2014/12/27 12:07:47 brouard
46: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
47:
1.172 brouard 48: Revision 1.171 2014/12/23 13:26:59 brouard
49: Summary: Back from Visual C
50:
51: Still problem with utsname.h on Windows
52:
1.171 brouard 53: Revision 1.170 2014/12/23 11:17:12 brouard
54: Summary: Cleaning some \%% back to %%
55:
56: The escape was mandatory for a specific compiler (which one?), but too many warnings.
57:
1.170 brouard 58: Revision 1.169 2014/12/22 23:08:31 brouard
59: Summary: 0.98p
60:
61: Outputs some informations on compiler used, OS etc. Testing on different platforms.
62:
1.169 brouard 63: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 64: Summary: update
1.169 brouard 65:
1.168 brouard 66: Revision 1.167 2014/12/22 13:50:56 brouard
67: Summary: Testing uname and compiler version and if compiled 32 or 64
68:
69: Testing on Linux 64
70:
1.167 brouard 71: Revision 1.166 2014/12/22 11:40:47 brouard
72: *** empty log message ***
73:
1.166 brouard 74: Revision 1.165 2014/12/16 11:20:36 brouard
75: Summary: After compiling on Visual C
76:
77: * imach.c (Module): Merging 1.61 to 1.162
78:
1.165 brouard 79: Revision 1.164 2014/12/16 10:52:11 brouard
80: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
81:
82: * imach.c (Module): Merging 1.61 to 1.162
83:
1.164 brouard 84: Revision 1.163 2014/12/16 10:30:11 brouard
85: * imach.c (Module): Merging 1.61 to 1.162
86:
1.163 brouard 87: Revision 1.162 2014/09/25 11:43:39 brouard
88: Summary: temporary backup 0.99!
89:
1.162 brouard 90: Revision 1.1 2014/09/16 11:06:58 brouard
91: Summary: With some code (wrong) for nlopt
92:
93: Author:
94:
95: Revision 1.161 2014/09/15 20:41:41 brouard
96: Summary: Problem with macro SQR on Intel compiler
97:
1.161 brouard 98: Revision 1.160 2014/09/02 09:24:05 brouard
99: *** empty log message ***
100:
1.160 brouard 101: Revision 1.159 2014/09/01 10:34:10 brouard
102: Summary: WIN32
103: Author: Brouard
104:
1.159 brouard 105: Revision 1.158 2014/08/27 17:11:51 brouard
106: *** empty log message ***
107:
1.158 brouard 108: Revision 1.157 2014/08/27 16:26:55 brouard
109: Summary: Preparing windows Visual studio version
110: Author: Brouard
111:
112: In order to compile on Visual studio, time.h is now correct and time_t
113: and tm struct should be used. difftime should be used but sometimes I
114: just make the differences in raw time format (time(&now).
115: Trying to suppress #ifdef LINUX
116: Add xdg-open for __linux in order to open default browser.
117:
1.157 brouard 118: Revision 1.156 2014/08/25 20:10:10 brouard
119: *** empty log message ***
120:
1.156 brouard 121: Revision 1.155 2014/08/25 18:32:34 brouard
122: Summary: New compile, minor changes
123: Author: Brouard
124:
1.155 brouard 125: Revision 1.154 2014/06/20 17:32:08 brouard
126: Summary: Outputs now all graphs of convergence to period prevalence
127:
1.154 brouard 128: Revision 1.153 2014/06/20 16:45:46 brouard
129: Summary: If 3 live state, convergence to period prevalence on same graph
130: Author: Brouard
131:
1.153 brouard 132: Revision 1.152 2014/06/18 17:54:09 brouard
133: Summary: open browser, use gnuplot on same dir than imach if not found in the path
134:
1.152 brouard 135: Revision 1.151 2014/06/18 16:43:30 brouard
136: *** empty log message ***
137:
1.151 brouard 138: Revision 1.150 2014/06/18 16:42:35 brouard
139: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
140: Author: brouard
141:
1.150 brouard 142: Revision 1.149 2014/06/18 15:51:14 brouard
143: Summary: Some fixes in parameter files errors
144: Author: Nicolas Brouard
145:
1.149 brouard 146: Revision 1.148 2014/06/17 17:38:48 brouard
147: Summary: Nothing new
148: Author: Brouard
149:
150: Just a new packaging for OS/X version 0.98nS
151:
1.148 brouard 152: Revision 1.147 2014/06/16 10:33:11 brouard
153: *** empty log message ***
154:
1.147 brouard 155: Revision 1.146 2014/06/16 10:20:28 brouard
156: Summary: Merge
157: Author: Brouard
158:
159: Merge, before building revised version.
160:
1.146 brouard 161: Revision 1.145 2014/06/10 21:23:15 brouard
162: Summary: Debugging with valgrind
163: Author: Nicolas Brouard
164:
165: Lot of changes in order to output the results with some covariates
166: After the Edimburgh REVES conference 2014, it seems mandatory to
167: improve the code.
168: No more memory valgrind error but a lot has to be done in order to
169: continue the work of splitting the code into subroutines.
170: Also, decodemodel has been improved. Tricode is still not
171: optimal. nbcode should be improved. Documentation has been added in
172: the source code.
173:
1.144 brouard 174: Revision 1.143 2014/01/26 09:45:38 brouard
175: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
176:
177: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
178: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
179:
1.143 brouard 180: Revision 1.142 2014/01/26 03:57:36 brouard
181: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
182:
183: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
184:
1.142 brouard 185: Revision 1.141 2014/01/26 02:42:01 brouard
186: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
187:
1.141 brouard 188: Revision 1.140 2011/09/02 10:37:54 brouard
189: Summary: times.h is ok with mingw32 now.
190:
1.140 brouard 191: Revision 1.139 2010/06/14 07:50:17 brouard
192: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
193: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
194:
1.139 brouard 195: Revision 1.138 2010/04/30 18:19:40 brouard
196: *** empty log message ***
197:
1.138 brouard 198: Revision 1.137 2010/04/29 18:11:38 brouard
199: (Module): Checking covariates for more complex models
200: than V1+V2. A lot of change to be done. Unstable.
201:
1.137 brouard 202: Revision 1.136 2010/04/26 20:30:53 brouard
203: (Module): merging some libgsl code. Fixing computation
204: of likelione (using inter/intrapolation if mle = 0) in order to
205: get same likelihood as if mle=1.
206: Some cleaning of code and comments added.
207:
1.136 brouard 208: Revision 1.135 2009/10/29 15:33:14 brouard
209: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
210:
1.135 brouard 211: Revision 1.134 2009/10/29 13:18:53 brouard
212: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
213:
1.134 brouard 214: Revision 1.133 2009/07/06 10:21:25 brouard
215: just nforces
216:
1.133 brouard 217: Revision 1.132 2009/07/06 08:22:05 brouard
218: Many tings
219:
1.132 brouard 220: Revision 1.131 2009/06/20 16:22:47 brouard
221: Some dimensions resccaled
222:
1.131 brouard 223: Revision 1.130 2009/05/26 06:44:34 brouard
224: (Module): Max Covariate is now set to 20 instead of 8. A
225: lot of cleaning with variables initialized to 0. Trying to make
226: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
227:
1.130 brouard 228: Revision 1.129 2007/08/31 13:49:27 lievre
229: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
230:
1.129 lievre 231: Revision 1.128 2006/06/30 13:02:05 brouard
232: (Module): Clarifications on computing e.j
233:
1.128 brouard 234: Revision 1.127 2006/04/28 18:11:50 brouard
235: (Module): Yes the sum of survivors was wrong since
236: imach-114 because nhstepm was no more computed in the age
237: loop. Now we define nhstepma in the age loop.
238: (Module): In order to speed up (in case of numerous covariates) we
239: compute health expectancies (without variances) in a first step
240: and then all the health expectancies with variances or standard
241: deviation (needs data from the Hessian matrices) which slows the
242: computation.
243: In the future we should be able to stop the program is only health
244: expectancies and graph are needed without standard deviations.
245:
1.127 brouard 246: Revision 1.126 2006/04/28 17:23:28 brouard
247: (Module): Yes the sum of survivors was wrong since
248: imach-114 because nhstepm was no more computed in the age
249: loop. Now we define nhstepma in the age loop.
250: Version 0.98h
251:
1.126 brouard 252: Revision 1.125 2006/04/04 15:20:31 lievre
253: Errors in calculation of health expectancies. Age was not initialized.
254: Forecasting file added.
255:
256: Revision 1.124 2006/03/22 17:13:53 lievre
257: Parameters are printed with %lf instead of %f (more numbers after the comma).
258: The log-likelihood is printed in the log file
259:
260: Revision 1.123 2006/03/20 10:52:43 brouard
261: * imach.c (Module): <title> changed, corresponds to .htm file
262: name. <head> headers where missing.
263:
264: * imach.c (Module): Weights can have a decimal point as for
265: English (a comma might work with a correct LC_NUMERIC environment,
266: otherwise the weight is truncated).
267: Modification of warning when the covariates values are not 0 or
268: 1.
269: Version 0.98g
270:
271: Revision 1.122 2006/03/20 09:45:41 brouard
272: (Module): Weights can have a decimal point as for
273: English (a comma might work with a correct LC_NUMERIC environment,
274: otherwise the weight is truncated).
275: Modification of warning when the covariates values are not 0 or
276: 1.
277: Version 0.98g
278:
279: Revision 1.121 2006/03/16 17:45:01 lievre
280: * imach.c (Module): Comments concerning covariates added
281:
282: * imach.c (Module): refinements in the computation of lli if
283: status=-2 in order to have more reliable computation if stepm is
284: not 1 month. Version 0.98f
285:
286: Revision 1.120 2006/03/16 15:10:38 lievre
287: (Module): refinements in the computation of lli if
288: status=-2 in order to have more reliable computation if stepm is
289: not 1 month. Version 0.98f
290:
291: Revision 1.119 2006/03/15 17:42:26 brouard
292: (Module): Bug if status = -2, the loglikelihood was
293: computed as likelihood omitting the logarithm. Version O.98e
294:
295: Revision 1.118 2006/03/14 18:20:07 brouard
296: (Module): varevsij Comments added explaining the second
297: table of variances if popbased=1 .
298: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
299: (Module): Function pstamp added
300: (Module): Version 0.98d
301:
302: Revision 1.117 2006/03/14 17:16:22 brouard
303: (Module): varevsij Comments added explaining the second
304: table of variances if popbased=1 .
305: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
306: (Module): Function pstamp added
307: (Module): Version 0.98d
308:
309: Revision 1.116 2006/03/06 10:29:27 brouard
310: (Module): Variance-covariance wrong links and
311: varian-covariance of ej. is needed (Saito).
312:
313: Revision 1.115 2006/02/27 12:17:45 brouard
314: (Module): One freematrix added in mlikeli! 0.98c
315:
316: Revision 1.114 2006/02/26 12:57:58 brouard
317: (Module): Some improvements in processing parameter
318: filename with strsep.
319:
320: Revision 1.113 2006/02/24 14:20:24 brouard
321: (Module): Memory leaks checks with valgrind and:
322: datafile was not closed, some imatrix were not freed and on matrix
323: allocation too.
324:
325: Revision 1.112 2006/01/30 09:55:26 brouard
326: (Module): Back to gnuplot.exe instead of wgnuplot.exe
327:
328: Revision 1.111 2006/01/25 20:38:18 brouard
329: (Module): Lots of cleaning and bugs added (Gompertz)
330: (Module): Comments can be added in data file. Missing date values
331: can be a simple dot '.'.
332:
333: Revision 1.110 2006/01/25 00:51:50 brouard
334: (Module): Lots of cleaning and bugs added (Gompertz)
335:
336: Revision 1.109 2006/01/24 19:37:15 brouard
337: (Module): Comments (lines starting with a #) are allowed in data.
338:
339: Revision 1.108 2006/01/19 18:05:42 lievre
340: Gnuplot problem appeared...
341: To be fixed
342:
343: Revision 1.107 2006/01/19 16:20:37 brouard
344: Test existence of gnuplot in imach path
345:
346: Revision 1.106 2006/01/19 13:24:36 brouard
347: Some cleaning and links added in html output
348:
349: Revision 1.105 2006/01/05 20:23:19 lievre
350: *** empty log message ***
351:
352: Revision 1.104 2005/09/30 16:11:43 lievre
353: (Module): sump fixed, loop imx fixed, and simplifications.
354: (Module): If the status is missing at the last wave but we know
355: that the person is alive, then we can code his/her status as -2
356: (instead of missing=-1 in earlier versions) and his/her
357: contributions to the likelihood is 1 - Prob of dying from last
358: health status (= 1-p13= p11+p12 in the easiest case of somebody in
359: the healthy state at last known wave). Version is 0.98
360:
361: Revision 1.103 2005/09/30 15:54:49 lievre
362: (Module): sump fixed, loop imx fixed, and simplifications.
363:
364: Revision 1.102 2004/09/15 17:31:30 brouard
365: Add the possibility to read data file including tab characters.
366:
367: Revision 1.101 2004/09/15 10:38:38 brouard
368: Fix on curr_time
369:
370: Revision 1.100 2004/07/12 18:29:06 brouard
371: Add version for Mac OS X. Just define UNIX in Makefile
372:
373: Revision 1.99 2004/06/05 08:57:40 brouard
374: *** empty log message ***
375:
376: Revision 1.98 2004/05/16 15:05:56 brouard
377: New version 0.97 . First attempt to estimate force of mortality
378: directly from the data i.e. without the need of knowing the health
379: state at each age, but using a Gompertz model: log u =a + b*age .
380: This is the basic analysis of mortality and should be done before any
381: other analysis, in order to test if the mortality estimated from the
382: cross-longitudinal survey is different from the mortality estimated
383: from other sources like vital statistic data.
384:
385: The same imach parameter file can be used but the option for mle should be -3.
386:
1.133 brouard 387: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 388: former routines in order to include the new code within the former code.
389:
390: The output is very simple: only an estimate of the intercept and of
391: the slope with 95% confident intervals.
392:
393: Current limitations:
394: A) Even if you enter covariates, i.e. with the
395: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
396: B) There is no computation of Life Expectancy nor Life Table.
397:
398: Revision 1.97 2004/02/20 13:25:42 lievre
399: Version 0.96d. Population forecasting command line is (temporarily)
400: suppressed.
401:
402: Revision 1.96 2003/07/15 15:38:55 brouard
403: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
404: rewritten within the same printf. Workaround: many printfs.
405:
406: Revision 1.95 2003/07/08 07:54:34 brouard
407: * imach.c (Repository):
408: (Repository): Using imachwizard code to output a more meaningful covariance
409: matrix (cov(a12,c31) instead of numbers.
410:
411: Revision 1.94 2003/06/27 13:00:02 brouard
412: Just cleaning
413:
414: Revision 1.93 2003/06/25 16:33:55 brouard
415: (Module): On windows (cygwin) function asctime_r doesn't
416: exist so I changed back to asctime which exists.
417: (Module): Version 0.96b
418:
419: Revision 1.92 2003/06/25 16:30:45 brouard
420: (Module): On windows (cygwin) function asctime_r doesn't
421: exist so I changed back to asctime which exists.
422:
423: Revision 1.91 2003/06/25 15:30:29 brouard
424: * imach.c (Repository): Duplicated warning errors corrected.
425: (Repository): Elapsed time after each iteration is now output. It
426: helps to forecast when convergence will be reached. Elapsed time
427: is stamped in powell. We created a new html file for the graphs
428: concerning matrix of covariance. It has extension -cov.htm.
429:
430: Revision 1.90 2003/06/24 12:34:15 brouard
431: (Module): Some bugs corrected for windows. Also, when
432: mle=-1 a template is output in file "or"mypar.txt with the design
433: of the covariance matrix to be input.
434:
435: Revision 1.89 2003/06/24 12:30:52 brouard
436: (Module): Some bugs corrected for windows. Also, when
437: mle=-1 a template is output in file "or"mypar.txt with the design
438: of the covariance matrix to be input.
439:
440: Revision 1.88 2003/06/23 17:54:56 brouard
441: * 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.
442:
443: Revision 1.87 2003/06/18 12:26:01 brouard
444: Version 0.96
445:
446: Revision 1.86 2003/06/17 20:04:08 brouard
447: (Module): Change position of html and gnuplot routines and added
448: routine fileappend.
449:
450: Revision 1.85 2003/06/17 13:12:43 brouard
451: * imach.c (Repository): Check when date of death was earlier that
452: current date of interview. It may happen when the death was just
453: prior to the death. In this case, dh was negative and likelihood
454: was wrong (infinity). We still send an "Error" but patch by
455: assuming that the date of death was just one stepm after the
456: interview.
457: (Repository): Because some people have very long ID (first column)
458: we changed int to long in num[] and we added a new lvector for
459: memory allocation. But we also truncated to 8 characters (left
460: truncation)
461: (Repository): No more line truncation errors.
462:
463: Revision 1.84 2003/06/13 21:44:43 brouard
464: * imach.c (Repository): Replace "freqsummary" at a correct
465: place. It differs from routine "prevalence" which may be called
466: many times. Probs is memory consuming and must be used with
467: parcimony.
468: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
469:
470: Revision 1.83 2003/06/10 13:39:11 lievre
471: *** empty log message ***
472:
473: Revision 1.82 2003/06/05 15:57:20 brouard
474: Add log in imach.c and fullversion number is now printed.
475:
476: */
477: /*
478: Interpolated Markov Chain
479:
480: Short summary of the programme:
481:
482: This program computes Healthy Life Expectancies from
483: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
484: first survey ("cross") where individuals from different ages are
485: interviewed on their health status or degree of disability (in the
486: case of a health survey which is our main interest) -2- at least a
487: second wave of interviews ("longitudinal") which measure each change
488: (if any) in individual health status. Health expectancies are
489: computed from the time spent in each health state according to a
490: model. More health states you consider, more time is necessary to reach the
491: Maximum Likelihood of the parameters involved in the model. The
492: simplest model is the multinomial logistic model where pij is the
493: probability to be observed in state j at the second wave
494: conditional to be observed in state i at the first wave. Therefore
495: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
496: 'age' is age and 'sex' is a covariate. If you want to have a more
497: complex model than "constant and age", you should modify the program
498: where the markup *Covariates have to be included here again* invites
499: you to do it. More covariates you add, slower the
500: convergence.
501:
502: The advantage of this computer programme, compared to a simple
503: multinomial logistic model, is clear when the delay between waves is not
504: identical for each individual. Also, if a individual missed an
505: intermediate interview, the information is lost, but taken into
506: account using an interpolation or extrapolation.
507:
508: hPijx is the probability to be observed in state i at age x+h
509: conditional to the observed state i at age x. The delay 'h' can be
510: split into an exact number (nh*stepm) of unobserved intermediate
511: states. This elementary transition (by month, quarter,
512: semester or year) is modelled as a multinomial logistic. The hPx
513: matrix is simply the matrix product of nh*stepm elementary matrices
514: and the contribution of each individual to the likelihood is simply
515: hPijx.
516:
517: Also this programme outputs the covariance matrix of the parameters but also
518: of the life expectancies. It also computes the period (stable) prevalence.
519:
1.133 brouard 520: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
521: Institut national d'études démographiques, Paris.
1.126 brouard 522: This software have been partly granted by Euro-REVES, a concerted action
523: from the European Union.
524: It is copyrighted identically to a GNU software product, ie programme and
525: software can be distributed freely for non commercial use. Latest version
526: can be accessed at http://euroreves.ined.fr/imach .
527:
528: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
529: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
530:
531: **********************************************************************/
532: /*
533: main
534: read parameterfile
535: read datafile
536: concatwav
537: freqsummary
538: if (mle >= 1)
539: mlikeli
540: print results files
541: if mle==1
542: computes hessian
543: read end of parameter file: agemin, agemax, bage, fage, estepm
544: begin-prev-date,...
545: open gnuplot file
546: open html file
1.145 brouard 547: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
548: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
549: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
550: freexexit2 possible for memory heap.
551:
552: h Pij x | pij_nom ficrestpij
553: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
554: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
555: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
556:
557: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
558: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
559: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
560: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
561: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
562:
1.126 brouard 563: forecasting if prevfcast==1 prevforecast call prevalence()
564: health expectancies
565: Variance-covariance of DFLE
566: prevalence()
567: movingaverage()
568: varevsij()
569: if popbased==1 varevsij(,popbased)
570: total life expectancies
571: Variance of period (stable) prevalence
572: end
573: */
574:
1.165 brouard 575: #define POWELL /* Instead of NLOPT */
1.183 brouard 576: /* #define POWELLORIGINAL */ /* Don't use Directest to decide new direction but original Powell test */
1.184 ! brouard 577: /* #define MNBRAKORIGINAL */ /* Don't use mnbrak fix */
1.126 brouard 578:
579: #include <math.h>
580: #include <stdio.h>
581: #include <stdlib.h>
582: #include <string.h>
1.159 brouard 583:
584: #ifdef _WIN32
585: #include <io.h>
1.172 brouard 586: #include <windows.h>
587: #include <tchar.h>
1.159 brouard 588: #else
1.126 brouard 589: #include <unistd.h>
1.159 brouard 590: #endif
1.126 brouard 591:
592: #include <limits.h>
593: #include <sys/types.h>
1.171 brouard 594:
595: #if defined(__GNUC__)
596: #include <sys/utsname.h> /* Doesn't work on Windows */
597: #endif
598:
1.126 brouard 599: #include <sys/stat.h>
600: #include <errno.h>
1.159 brouard 601: /* extern int errno; */
1.126 brouard 602:
1.157 brouard 603: /* #ifdef LINUX */
604: /* #include <time.h> */
605: /* #include "timeval.h" */
606: /* #else */
607: /* #include <sys/time.h> */
608: /* #endif */
609:
1.126 brouard 610: #include <time.h>
611:
1.136 brouard 612: #ifdef GSL
613: #include <gsl/gsl_errno.h>
614: #include <gsl/gsl_multimin.h>
615: #endif
616:
1.167 brouard 617:
1.162 brouard 618: #ifdef NLOPT
619: #include <nlopt.h>
620: typedef struct {
621: double (* function)(double [] );
622: } myfunc_data ;
623: #endif
624:
1.126 brouard 625: /* #include <libintl.h> */
626: /* #define _(String) gettext (String) */
627:
1.141 brouard 628: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 629:
630: #define GNUPLOTPROGRAM "gnuplot"
631: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
632: #define FILENAMELENGTH 132
633:
634: #define GLOCK_ERROR_NOPATH -1 /* empty path */
635: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
636:
1.144 brouard 637: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
638: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 639:
640: #define NINTERVMAX 8
1.144 brouard 641: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
642: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
643: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.145 brouard 644: #define codtabm(h,k) 1 & (h-1) >> (k-1) ;
1.126 brouard 645: #define MAXN 20000
1.144 brouard 646: #define YEARM 12. /**< Number of months per year */
1.126 brouard 647: #define AGESUP 130
648: #define AGEBASE 40
1.164 brouard 649: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 650: #ifdef _WIN32
651: #define DIRSEPARATOR '\\'
652: #define CHARSEPARATOR "\\"
653: #define ODIRSEPARATOR '/'
654: #else
1.126 brouard 655: #define DIRSEPARATOR '/'
656: #define CHARSEPARATOR "/"
657: #define ODIRSEPARATOR '\\'
658: #endif
659:
1.184 ! brouard 660: /* $Id: imach.c,v 1.183 2015/03/10 20:34:32 brouard Exp $ */
1.126 brouard 661: /* $State: Exp $ */
662:
1.183 brouard 663: char version[]="Imach version 0.98q0, March 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
1.184 ! brouard 664: char fullversion[]="$Revision: 1.183 $ $Date: 2015/03/10 20:34:32 $";
1.126 brouard 665: char strstart[80];
666: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 667: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.133 brouard 668: int nvar=0, nforce=0; /* Number of variables, number of forces */
1.145 brouard 669: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
670: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
671: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
672: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
673: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
674: int cptcovprodnoage=0; /**< Number of covariate products without age */
675: int cptcoveff=0; /* Total number of covariates to vary for printing results */
676: int cptcov=0; /* Working variable */
1.126 brouard 677: int npar=NPARMAX;
678: int nlstate=2; /* Number of live states */
679: int ndeath=1; /* Number of dead states */
1.130 brouard 680: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.126 brouard 681: int popbased=0;
682:
683: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 684: int maxwav=0; /* Maxim number of waves */
685: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
686: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
687: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 688: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 689: int mle=1, weightopt=0;
1.126 brouard 690: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
691: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
692: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
693: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 694: int countcallfunc=0; /* Count the number of calls to func */
1.130 brouard 695: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 696: double **matprod2(); /* test */
1.126 brouard 697: double **oldm, **newm, **savm; /* Working pointers to matrices */
698: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.136 brouard 699: /*FILE *fic ; */ /* Used in readdata only */
700: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.126 brouard 701: FILE *ficlog, *ficrespow;
1.130 brouard 702: int globpr=0; /* Global variable for printing or not */
1.126 brouard 703: double fretone; /* Only one call to likelihood */
1.130 brouard 704: long ipmx=0; /* Number of contributions */
1.126 brouard 705: double sw; /* Sum of weights */
706: char filerespow[FILENAMELENGTH];
707: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
708: FILE *ficresilk;
709: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
710: FILE *ficresprobmorprev;
711: FILE *fichtm, *fichtmcov; /* Html File */
712: FILE *ficreseij;
713: char filerese[FILENAMELENGTH];
714: FILE *ficresstdeij;
715: char fileresstde[FILENAMELENGTH];
716: FILE *ficrescveij;
717: char filerescve[FILENAMELENGTH];
718: FILE *ficresvij;
719: char fileresv[FILENAMELENGTH];
720: FILE *ficresvpl;
721: char fileresvpl[FILENAMELENGTH];
722: char title[MAXLINE];
723: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
724: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
725: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
726: char command[FILENAMELENGTH];
727: int outcmd=0;
728:
729: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
730:
731: char filelog[FILENAMELENGTH]; /* Log file */
732: char filerest[FILENAMELENGTH];
733: char fileregp[FILENAMELENGTH];
734: char popfile[FILENAMELENGTH];
735:
736: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
737:
1.157 brouard 738: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
739: /* struct timezone tzp; */
740: /* extern int gettimeofday(); */
741: struct tm tml, *gmtime(), *localtime();
742:
743: extern time_t time();
744:
745: struct tm start_time, end_time, curr_time, last_time, forecast_time;
746: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
747: struct tm tm;
748:
1.126 brouard 749: char strcurr[80], strfor[80];
750:
751: char *endptr;
752: long lval;
753: double dval;
754:
755: #define NR_END 1
756: #define FREE_ARG char*
757: #define FTOL 1.0e-10
758:
759: #define NRANSI
760: #define ITMAX 200
761:
762: #define TOL 2.0e-4
763:
764: #define CGOLD 0.3819660
765: #define ZEPS 1.0e-10
766: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
767:
768: #define GOLD 1.618034
769: #define GLIMIT 100.0
770: #define TINY 1.0e-20
771:
772: static double maxarg1,maxarg2;
773: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
774: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
775:
776: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
777: #define rint(a) floor(a+0.5)
1.166 brouard 778: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 779: #define mytinydouble 1.0e-16
1.166 brouard 780: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
781: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
782: /* static double dsqrarg; */
783: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 784: static double sqrarg;
785: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
786: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
787: int agegomp= AGEGOMP;
788:
789: int imx;
790: int stepm=1;
791: /* Stepm, step in month: minimum step interpolation*/
792:
793: int estepm;
794: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
795:
796: int m,nb;
797: long *num;
798: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
799: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
800: double **pmmij, ***probs;
801: double *ageexmed,*agecens;
802: double dateintmean=0;
803:
804: double *weight;
805: int **s; /* Status */
1.141 brouard 806: double *agedc;
1.145 brouard 807: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 808: * covar=matrix(0,NCOVMAX,1,n);
809: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
810: double idx;
811: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.145 brouard 812: int *Ndum; /** Freq of modality (tricode */
1.141 brouard 813: int **codtab; /**< codtab=imatrix(1,100,1,10); */
814: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.126 brouard 815: double *lsurv, *lpop, *tpop;
816:
1.143 brouard 817: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
818: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 819:
820: /**************** split *************************/
821: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
822: {
823: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
824: the name of the file (name), its extension only (ext) and its first part of the name (finame)
825: */
826: char *ss; /* pointer */
827: int l1, l2; /* length counters */
828:
829: l1 = strlen(path ); /* length of path */
830: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
831: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
832: if ( ss == NULL ) { /* no directory, so determine current directory */
833: strcpy( name, path ); /* we got the fullname name because no directory */
834: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
835: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
836: /* get current working directory */
837: /* extern char* getcwd ( char *buf , int len);*/
1.184 ! brouard 838: #ifdef WIN32
! 839: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
! 840: #else
! 841: if (getcwd(dirc, FILENAME_MAX) == NULL) {
! 842: #endif
1.126 brouard 843: return( GLOCK_ERROR_GETCWD );
844: }
845: /* got dirc from getcwd*/
846: printf(" DIRC = %s \n",dirc);
847: } else { /* strip direcotry from path */
848: ss++; /* after this, the filename */
849: l2 = strlen( ss ); /* length of filename */
850: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
851: strcpy( name, ss ); /* save file name */
852: strncpy( dirc, path, l1 - l2 ); /* now the directory */
853: dirc[l1-l2] = 0; /* add zero */
854: printf(" DIRC2 = %s \n",dirc);
855: }
856: /* We add a separator at the end of dirc if not exists */
857: l1 = strlen( dirc ); /* length of directory */
858: if( dirc[l1-1] != DIRSEPARATOR ){
859: dirc[l1] = DIRSEPARATOR;
860: dirc[l1+1] = 0;
861: printf(" DIRC3 = %s \n",dirc);
862: }
863: ss = strrchr( name, '.' ); /* find last / */
864: if (ss >0){
865: ss++;
866: strcpy(ext,ss); /* save extension */
867: l1= strlen( name);
868: l2= strlen(ss)+1;
869: strncpy( finame, name, l1-l2);
870: finame[l1-l2]= 0;
871: }
872:
873: return( 0 ); /* we're done */
874: }
875:
876:
877: /******************************************/
878:
879: void replace_back_to_slash(char *s, char*t)
880: {
881: int i;
882: int lg=0;
883: i=0;
884: lg=strlen(t);
885: for(i=0; i<= lg; i++) {
886: (s[i] = t[i]);
887: if (t[i]== '\\') s[i]='/';
888: }
889: }
890:
1.132 brouard 891: char *trimbb(char *out, char *in)
1.137 brouard 892: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 893: char *s;
894: s=out;
895: while (*in != '\0'){
1.137 brouard 896: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 897: in++;
898: }
899: *out++ = *in++;
900: }
901: *out='\0';
902: return s;
903: }
904:
1.145 brouard 905: char *cutl(char *blocc, char *alocc, char *in, char occ)
906: {
907: /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ'
908: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
909: gives blocc="abcdef2ghi" and alocc="j".
910: If occ is not found blocc is null and alocc is equal to in. Returns blocc
911: */
1.160 brouard 912: char *s, *t;
1.145 brouard 913: t=in;s=in;
914: while ((*in != occ) && (*in != '\0')){
915: *alocc++ = *in++;
916: }
917: if( *in == occ){
918: *(alocc)='\0';
919: s=++in;
920: }
921:
922: if (s == t) {/* occ not found */
923: *(alocc-(in-s))='\0';
924: in=s;
925: }
926: while ( *in != '\0'){
927: *blocc++ = *in++;
928: }
929:
930: *blocc='\0';
931: return t;
932: }
1.137 brouard 933: char *cutv(char *blocc, char *alocc, char *in, char occ)
934: {
935: /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
936: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
937: gives blocc="abcdef2ghi" and alocc="j".
938: If occ is not found blocc is null and alocc is equal to in. Returns alocc
939: */
940: char *s, *t;
941: t=in;s=in;
942: while (*in != '\0'){
943: while( *in == occ){
944: *blocc++ = *in++;
945: s=in;
946: }
947: *blocc++ = *in++;
948: }
949: if (s == t) /* occ not found */
950: *(blocc-(in-s))='\0';
951: else
952: *(blocc-(in-s)-1)='\0';
953: in=s;
954: while ( *in != '\0'){
955: *alocc++ = *in++;
956: }
957:
958: *alocc='\0';
959: return s;
960: }
961:
1.126 brouard 962: int nbocc(char *s, char occ)
963: {
964: int i,j=0;
965: int lg=20;
966: i=0;
967: lg=strlen(s);
968: for(i=0; i<= lg; i++) {
969: if (s[i] == occ ) j++;
970: }
971: return j;
972: }
973:
1.137 brouard 974: /* void cutv(char *u,char *v, char*t, char occ) */
975: /* { */
976: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
977: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
978: /* gives u="abcdef2ghi" and v="j" *\/ */
979: /* int i,lg,j,p=0; */
980: /* i=0; */
981: /* lg=strlen(t); */
982: /* for(j=0; j<=lg-1; j++) { */
983: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
984: /* } */
1.126 brouard 985:
1.137 brouard 986: /* for(j=0; j<p; j++) { */
987: /* (u[j] = t[j]); */
988: /* } */
989: /* u[p]='\0'; */
1.126 brouard 990:
1.137 brouard 991: /* for(j=0; j<= lg; j++) { */
992: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
993: /* } */
994: /* } */
1.126 brouard 995:
1.160 brouard 996: #ifdef _WIN32
997: char * strsep(char **pp, const char *delim)
998: {
999: char *p, *q;
1000:
1001: if ((p = *pp) == NULL)
1002: return 0;
1003: if ((q = strpbrk (p, delim)) != NULL)
1004: {
1005: *pp = q + 1;
1006: *q = '\0';
1007: }
1008: else
1009: *pp = 0;
1010: return p;
1011: }
1012: #endif
1013:
1.126 brouard 1014: /********************** nrerror ********************/
1015:
1016: void nrerror(char error_text[])
1017: {
1018: fprintf(stderr,"ERREUR ...\n");
1019: fprintf(stderr,"%s\n",error_text);
1020: exit(EXIT_FAILURE);
1021: }
1022: /*********************** vector *******************/
1023: double *vector(int nl, int nh)
1024: {
1025: double *v;
1026: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1027: if (!v) nrerror("allocation failure in vector");
1028: return v-nl+NR_END;
1029: }
1030:
1031: /************************ free vector ******************/
1032: void free_vector(double*v, int nl, int nh)
1033: {
1034: free((FREE_ARG)(v+nl-NR_END));
1035: }
1036:
1037: /************************ivector *******************************/
1038: int *ivector(long nl,long nh)
1039: {
1040: int *v;
1041: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1042: if (!v) nrerror("allocation failure in ivector");
1043: return v-nl+NR_END;
1044: }
1045:
1046: /******************free ivector **************************/
1047: void free_ivector(int *v, long nl, long nh)
1048: {
1049: free((FREE_ARG)(v+nl-NR_END));
1050: }
1051:
1052: /************************lvector *******************************/
1053: long *lvector(long nl,long nh)
1054: {
1055: long *v;
1056: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1057: if (!v) nrerror("allocation failure in ivector");
1058: return v-nl+NR_END;
1059: }
1060:
1061: /******************free lvector **************************/
1062: void free_lvector(long *v, long nl, long nh)
1063: {
1064: free((FREE_ARG)(v+nl-NR_END));
1065: }
1066:
1067: /******************* imatrix *******************************/
1068: int **imatrix(long nrl, long nrh, long ncl, long nch)
1069: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1070: {
1071: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1072: int **m;
1073:
1074: /* allocate pointers to rows */
1075: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1076: if (!m) nrerror("allocation failure 1 in matrix()");
1077: m += NR_END;
1078: m -= nrl;
1079:
1080:
1081: /* allocate rows and set pointers to them */
1082: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1083: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1084: m[nrl] += NR_END;
1085: m[nrl] -= ncl;
1086:
1087: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1088:
1089: /* return pointer to array of pointers to rows */
1090: return m;
1091: }
1092:
1093: /****************** free_imatrix *************************/
1094: void free_imatrix(m,nrl,nrh,ncl,nch)
1095: int **m;
1096: long nch,ncl,nrh,nrl;
1097: /* free an int matrix allocated by imatrix() */
1098: {
1099: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1100: free((FREE_ARG) (m+nrl-NR_END));
1101: }
1102:
1103: /******************* matrix *******************************/
1104: double **matrix(long nrl, long nrh, long ncl, long nch)
1105: {
1106: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1107: double **m;
1108:
1109: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1110: if (!m) nrerror("allocation failure 1 in matrix()");
1111: m += NR_END;
1112: m -= nrl;
1113:
1114: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1115: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1116: m[nrl] += NR_END;
1117: m[nrl] -= ncl;
1118:
1119: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1120: return m;
1.145 brouard 1121: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1122: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1123: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1124: */
1125: }
1126:
1127: /*************************free matrix ************************/
1128: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1129: {
1130: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1131: free((FREE_ARG)(m+nrl-NR_END));
1132: }
1133:
1134: /******************* ma3x *******************************/
1135: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1136: {
1137: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1138: double ***m;
1139:
1140: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1141: if (!m) nrerror("allocation failure 1 in matrix()");
1142: m += NR_END;
1143: m -= nrl;
1144:
1145: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1146: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1147: m[nrl] += NR_END;
1148: m[nrl] -= ncl;
1149:
1150: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1151:
1152: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1153: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1154: m[nrl][ncl] += NR_END;
1155: m[nrl][ncl] -= nll;
1156: for (j=ncl+1; j<=nch; j++)
1157: m[nrl][j]=m[nrl][j-1]+nlay;
1158:
1159: for (i=nrl+1; i<=nrh; i++) {
1160: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1161: for (j=ncl+1; j<=nch; j++)
1162: m[i][j]=m[i][j-1]+nlay;
1163: }
1164: return m;
1165: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1166: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1167: */
1168: }
1169:
1170: /*************************free ma3x ************************/
1171: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1172: {
1173: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1174: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1175: free((FREE_ARG)(m+nrl-NR_END));
1176: }
1177:
1178: /*************** function subdirf ***********/
1179: char *subdirf(char fileres[])
1180: {
1181: /* Caution optionfilefiname is hidden */
1182: strcpy(tmpout,optionfilefiname);
1183: strcat(tmpout,"/"); /* Add to the right */
1184: strcat(tmpout,fileres);
1185: return tmpout;
1186: }
1187:
1188: /*************** function subdirf2 ***********/
1189: char *subdirf2(char fileres[], char *preop)
1190: {
1191:
1192: /* Caution optionfilefiname is hidden */
1193: strcpy(tmpout,optionfilefiname);
1194: strcat(tmpout,"/");
1195: strcat(tmpout,preop);
1196: strcat(tmpout,fileres);
1197: return tmpout;
1198: }
1199:
1200: /*************** function subdirf3 ***********/
1201: char *subdirf3(char fileres[], char *preop, char *preop2)
1202: {
1203:
1204: /* Caution optionfilefiname is hidden */
1205: strcpy(tmpout,optionfilefiname);
1206: strcat(tmpout,"/");
1207: strcat(tmpout,preop);
1208: strcat(tmpout,preop2);
1209: strcat(tmpout,fileres);
1210: return tmpout;
1211: }
1212:
1.162 brouard 1213: char *asc_diff_time(long time_sec, char ascdiff[])
1214: {
1215: long sec_left, days, hours, minutes;
1216: days = (time_sec) / (60*60*24);
1217: sec_left = (time_sec) % (60*60*24);
1218: hours = (sec_left) / (60*60) ;
1219: sec_left = (sec_left) %(60*60);
1220: minutes = (sec_left) /60;
1221: sec_left = (sec_left) % (60);
1222: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1223: return ascdiff;
1224: }
1225:
1.126 brouard 1226: /***************** f1dim *************************/
1227: extern int ncom;
1228: extern double *pcom,*xicom;
1229: extern double (*nrfunc)(double []);
1230:
1231: double f1dim(double x)
1232: {
1233: int j;
1234: double f;
1235: double *xt;
1236:
1237: xt=vector(1,ncom);
1238: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1239: f=(*nrfunc)(xt);
1240: free_vector(xt,1,ncom);
1241: return f;
1242: }
1243:
1244: /*****************brent *************************/
1245: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1246: {
1247: int iter;
1248: double a,b,d,etemp;
1.159 brouard 1249: double fu=0,fv,fw,fx;
1.164 brouard 1250: double ftemp=0.;
1.126 brouard 1251: double p,q,r,tol1,tol2,u,v,w,x,xm;
1252: double e=0.0;
1253:
1254: a=(ax < cx ? ax : cx);
1255: b=(ax > cx ? ax : cx);
1256: x=w=v=bx;
1257: fw=fv=fx=(*f)(x);
1258: for (iter=1;iter<=ITMAX;iter++) {
1259: xm=0.5*(a+b);
1260: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1261: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1262: printf(".");fflush(stdout);
1263: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1264: #ifdef DEBUGBRENT
1.126 brouard 1265: 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);
1266: 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);
1267: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1268: #endif
1269: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1270: *xmin=x;
1271: return fx;
1272: }
1273: ftemp=fu;
1274: if (fabs(e) > tol1) {
1275: r=(x-w)*(fx-fv);
1276: q=(x-v)*(fx-fw);
1277: p=(x-v)*q-(x-w)*r;
1278: q=2.0*(q-r);
1279: if (q > 0.0) p = -p;
1280: q=fabs(q);
1281: etemp=e;
1282: e=d;
1283: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1284: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1285: else {
1286: d=p/q;
1287: u=x+d;
1288: if (u-a < tol2 || b-u < tol2)
1289: d=SIGN(tol1,xm-x);
1290: }
1291: } else {
1292: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1293: }
1294: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1295: fu=(*f)(u);
1296: if (fu <= fx) {
1297: if (u >= x) a=x; else b=x;
1298: SHFT(v,w,x,u)
1.183 brouard 1299: SHFT(fv,fw,fx,fu)
1300: } else {
1301: if (u < x) a=u; else b=u;
1302: if (fu <= fw || w == x) {
1303: v=w;
1304: w=u;
1305: fv=fw;
1306: fw=fu;
1307: } else if (fu <= fv || v == x || v == w) {
1308: v=u;
1309: fv=fu;
1310: }
1311: }
1.126 brouard 1312: }
1313: nrerror("Too many iterations in brent");
1314: *xmin=x;
1315: return fx;
1316: }
1317:
1318: /****************** mnbrak ***********************/
1319:
1320: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1321: double (*func)(double))
1.183 brouard 1322: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1323: the downhill direction (defined by the function as evaluated at the initial points) and returns
1324: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1325: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1326: */
1.126 brouard 1327: double ulim,u,r,q, dum;
1328: double fu;
1329:
1330: *fa=(*func)(*ax);
1331: *fb=(*func)(*bx);
1332: if (*fb > *fa) {
1333: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1334: SHFT(dum,*fb,*fa,dum)
1335: }
1.126 brouard 1336: *cx=(*bx)+GOLD*(*bx-*ax);
1337: *fc=(*func)(*cx);
1.183 brouard 1338: #ifdef DEBUG
1339: printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1340: fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1341: #endif
1342: while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
1.126 brouard 1343: r=(*bx-*ax)*(*fb-*fc);
1344: q=(*bx-*cx)*(*fb-*fa);
1345: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 1346: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1347: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1348: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 1349: fu=(*func)(u);
1.163 brouard 1350: #ifdef DEBUG
1351: /* f(x)=A(x-u)**2+f(u) */
1352: double A, fparabu;
1353: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1354: fparabu= *fa - A*(*ax-u)*(*ax-u);
1355: 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);
1356: 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);
1.183 brouard 1357: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1358: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1359: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1360: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 1361: #endif
1.184 ! brouard 1362: #ifdef MNBRAKORIGINAL
1.183 brouard 1363: #else
1364: if (fu > *fc) {
1365: #ifdef DEBUG
1366: printf("mnbrak4 fu > fc \n");
1367: fprintf(ficlog, "mnbrak4 fu > fc\n");
1368: #endif
1369: /* 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 *\/ */
1370: /* SHFT(*fa,*fc,fu,*fc) /\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\/ */
1371: dum=u; /* Shifting c and u */
1372: u = *cx;
1373: *cx = dum;
1374: dum = fu;
1375: fu = *fc;
1376: *fc =dum;
1377: } else { /* end */
1378: #ifdef DEBUG
1379: printf("mnbrak3 fu < fc \n");
1380: fprintf(ficlog, "mnbrak3 fu < fc\n");
1381: #endif
1382: dum=u; /* Shifting c and u */
1383: u = *cx;
1384: *cx = dum;
1385: dum = fu;
1386: fu = *fc;
1387: *fc =dum;
1388: }
1389: #endif
1.162 brouard 1390: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 1391: #ifdef DEBUG
1392: printf("mnbrak2 u after c but before ulim\n");
1393: fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
1394: #endif
1.126 brouard 1395: fu=(*func)(u);
1396: if (fu < *fc) {
1.183 brouard 1397: #ifdef DEBUG
1398: printf("mnbrak2 u after c but before ulim AND fu < fc\n");
1399: fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
1400: #endif
1.126 brouard 1401: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1.183 brouard 1402: SHFT(*fb,*fc,fu,(*func)(u))
1403: }
1.162 brouard 1404: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 1405: #ifdef DEBUG
1406: printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1407: fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1408: #endif
1.126 brouard 1409: u=ulim;
1410: fu=(*func)(u);
1.183 brouard 1411: } else { /* u could be left to b (if r > q parabola has a maximum) */
1412: #ifdef DEBUG
1413: printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1414: fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1415: #endif
1.126 brouard 1416: u=(*cx)+GOLD*(*cx-*bx);
1417: fu=(*func)(u);
1.183 brouard 1418: } /* end tests */
1.126 brouard 1419: SHFT(*ax,*bx,*cx,u)
1.183 brouard 1420: SHFT(*fa,*fb,*fc,fu)
1421: #ifdef DEBUG
1422: 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);
1423: 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);
1424: #endif
1425: } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
1.126 brouard 1426: }
1427:
1428: /*************** linmin ************************/
1.162 brouard 1429: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1430: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1431: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1432: the value of func at the returned location p . This is actually all accomplished by calling the
1433: routines mnbrak and brent .*/
1.126 brouard 1434: int ncom;
1435: double *pcom,*xicom;
1436: double (*nrfunc)(double []);
1437:
1438: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1439: {
1440: double brent(double ax, double bx, double cx,
1441: double (*f)(double), double tol, double *xmin);
1442: double f1dim(double x);
1443: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1444: double *fc, double (*func)(double));
1445: int j;
1446: double xx,xmin,bx,ax;
1447: double fx,fb,fa;
1448:
1449: ncom=n;
1450: pcom=vector(1,n);
1451: xicom=vector(1,n);
1452: nrfunc=func;
1453: for (j=1;j<=n;j++) {
1454: pcom[j]=p[j];
1455: xicom[j]=xi[j];
1456: }
1457: ax=0.0;
1458: xx=1.0;
1.162 brouard 1459: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
1460: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
1.126 brouard 1461: #ifdef DEBUG
1462: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1463: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1464: #endif
1465: for (j=1;j<=n;j++) {
1466: xi[j] *= xmin;
1467: p[j] += xi[j];
1468: }
1469: free_vector(xicom,1,n);
1470: free_vector(pcom,1,n);
1471: }
1472:
1473:
1474: /*************** powell ************************/
1.162 brouard 1475: /*
1476: Minimization of a function func of n variables. Input consists of an initial starting point
1477: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1478: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1479: such that failure to decrease by more than this amount on one iteration signals doneness. On
1480: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1481: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1482: */
1.126 brouard 1483: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1484: double (*func)(double []))
1485: {
1486: void linmin(double p[], double xi[], int n, double *fret,
1487: double (*func)(double []));
1488: int i,ibig,j;
1489: double del,t,*pt,*ptt,*xit;
1.181 brouard 1490: double directest;
1.126 brouard 1491: double fp,fptt;
1492: double *xits;
1493: int niterf, itmp;
1494:
1495: pt=vector(1,n);
1496: ptt=vector(1,n);
1497: xit=vector(1,n);
1498: xits=vector(1,n);
1499: *fret=(*func)(p);
1500: for (j=1;j<=n;j++) pt[j]=p[j];
1.157 brouard 1501: rcurr_time = time(NULL);
1.126 brouard 1502: for (*iter=1;;++(*iter)) {
1503: fp=(*fret);
1504: ibig=0;
1505: del=0.0;
1.157 brouard 1506: rlast_time=rcurr_time;
1507: /* (void) gettimeofday(&curr_time,&tzp); */
1508: rcurr_time = time(NULL);
1509: curr_time = *localtime(&rcurr_time);
1510: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1511: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1512: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.126 brouard 1513: for (i=1;i<=n;i++) {
1514: printf(" %d %.12f",i, p[i]);
1515: fprintf(ficlog," %d %.12lf",i, p[i]);
1516: fprintf(ficrespow," %.12lf", p[i]);
1517: }
1518: printf("\n");
1519: fprintf(ficlog,"\n");
1520: fprintf(ficrespow,"\n");fflush(ficrespow);
1521: if(*iter <=3){
1.157 brouard 1522: tml = *localtime(&rcurr_time);
1523: strcpy(strcurr,asctime(&tml));
1524: rforecast_time=rcurr_time;
1.126 brouard 1525: itmp = strlen(strcurr);
1526: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1527: strcurr[itmp-1]='\0';
1.162 brouard 1528: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 1529: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 1530: for(niterf=10;niterf<=30;niterf+=10){
1.157 brouard 1531: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1532: forecast_time = *localtime(&rforecast_time);
1533: strcpy(strfor,asctime(&forecast_time));
1.126 brouard 1534: itmp = strlen(strfor);
1535: if(strfor[itmp-1]=='\n')
1536: strfor[itmp-1]='\0';
1.157 brouard 1537: 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);
1538: 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);
1.126 brouard 1539: }
1540: }
1541: for (i=1;i<=n;i++) {
1542: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1543: fptt=(*fret);
1544: #ifdef DEBUG
1.164 brouard 1545: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1546: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 1547: #endif
1548: printf("%d",i);fflush(stdout);
1549: fprintf(ficlog,"%d",i);fflush(ficlog);
1.183 brouard 1550: linmin(p,xit,n,fret,func); /* xit[n] has been loaded for direction i */
1.181 brouard 1551: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions
1552: because that direction will be replaced unless the gain del is small
1553: in comparison with the 'probable' gain, mu^2, with the last average direction.
1554: Unless the n directions are conjugate some gain in the determinant may be obtained
1555: with the new direction.
1556: */
1.126 brouard 1557: del=fabs(fptt-(*fret));
1558: ibig=i;
1559: }
1560: #ifdef DEBUG
1561: printf("%d %.12e",i,(*fret));
1562: fprintf(ficlog,"%d %.12e",i,(*fret));
1563: for (j=1;j<=n;j++) {
1564: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1565: printf(" x(%d)=%.12e",j,xit[j]);
1566: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1567: }
1568: for(j=1;j<=n;j++) {
1.162 brouard 1569: printf(" p(%d)=%.12e",j,p[j]);
1570: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 1571: }
1572: printf("\n");
1573: fprintf(ficlog,"\n");
1574: #endif
1.162 brouard 1575: } /* end i */
1.182 brouard 1576: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1.126 brouard 1577: #ifdef DEBUG
1578: int k[2],l;
1579: k[0]=1;
1580: k[1]=-1;
1581: printf("Max: %.12e",(*func)(p));
1582: fprintf(ficlog,"Max: %.12e",(*func)(p));
1583: for (j=1;j<=n;j++) {
1584: printf(" %.12e",p[j]);
1585: fprintf(ficlog," %.12e",p[j]);
1586: }
1587: printf("\n");
1588: fprintf(ficlog,"\n");
1589: for(l=0;l<=1;l++) {
1590: for (j=1;j<=n;j++) {
1591: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1592: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1593: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1594: }
1595: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1596: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1597: }
1598: #endif
1599:
1600:
1601: free_vector(xit,1,n);
1602: free_vector(xits,1,n);
1603: free_vector(ptt,1,n);
1604: free_vector(pt,1,n);
1605: return;
1606: }
1607: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1.181 brouard 1608: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 1609: ptt[j]=2.0*p[j]-pt[j];
1610: xit[j]=p[j]-pt[j];
1611: pt[j]=p[j];
1612: }
1.181 brouard 1613: fptt=(*func)(ptt); /* f_3 */
1.161 brouard 1614: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.162 brouard 1615: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 1616: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 1617: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1618: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1619: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.181 brouard 1620: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
1.161 brouard 1621: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.183 brouard 1622: #ifdef NRCORIGINAL
1623: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
1624: #else
1625: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
1.161 brouard 1626: t= t- del*SQR(fp-fptt);
1.183 brouard 1627: #endif
1.182 brouard 1628: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
1.161 brouard 1629: #ifdef DEBUG
1.181 brouard 1630: 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);
1631: 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);
1.161 brouard 1632: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1633: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1634: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1635: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1636: 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);
1637: 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);
1638: #endif
1.183 brouard 1639: #ifdef POWELLORIGINAL
1640: if (t < 0.0) { /* Then we use it for new direction */
1641: #else
1.182 brouard 1642: if (directest*t < 0.0) { /* Contradiction between both tests */
1.184 ! brouard 1643: printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
1.182 brouard 1644: printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1.184 ! brouard 1645: fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
1.182 brouard 1646: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1647: }
1.181 brouard 1648: if (directest < 0.0) { /* Then we use it for new direction */
1649: #endif
1650: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction.*/
1.126 brouard 1651: for (j=1;j<=n;j++) {
1.181 brouard 1652: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
1653: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
1.126 brouard 1654: }
1.181 brouard 1655: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1656: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1.161 brouard 1657:
1.126 brouard 1658: #ifdef DEBUG
1.164 brouard 1659: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1660: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1.126 brouard 1661: for(j=1;j<=n;j++){
1662: printf(" %.12e",xit[j]);
1663: fprintf(ficlog," %.12e",xit[j]);
1664: }
1665: printf("\n");
1666: fprintf(ficlog,"\n");
1667: #endif
1.162 brouard 1668: } /* end of t negative */
1669: } /* end if (fptt < fp) */
1.126 brouard 1670: }
1671: }
1672:
1673: /**** Prevalence limit (stable or period prevalence) ****************/
1674:
1675: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1676: {
1677: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1678: matrix by transitions matrix until convergence is reached */
1.169 brouard 1679:
1.126 brouard 1680: int i, ii,j,k;
1681: double min, max, maxmin, maxmax,sumnew=0.;
1.145 brouard 1682: /* double **matprod2(); */ /* test */
1.131 brouard 1683: double **out, cov[NCOVMAX+1], **pmij();
1.126 brouard 1684: double **newm;
1685: double agefin, delaymax=50 ; /* Max number of years to converge */
1.169 brouard 1686:
1.126 brouard 1687: for (ii=1;ii<=nlstate+ndeath;ii++)
1688: for (j=1;j<=nlstate+ndeath;j++){
1689: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1690: }
1.169 brouard 1691:
1692: cov[1]=1.;
1693:
1694: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.126 brouard 1695: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1696: newm=savm;
1697: /* Covariates have to be included here again */
1.138 brouard 1698: cov[2]=agefin;
1699:
1700: for (k=1; k<=cptcovn;k++) {
1701: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.145 brouard 1702: /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
1.138 brouard 1703: }
1.145 brouard 1704: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1705: /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
1706: /* cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
1.138 brouard 1707:
1708: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1709: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1710: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 1711: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1712: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.142 brouard 1713: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 1714:
1.126 brouard 1715: savm=oldm;
1716: oldm=newm;
1717: maxmax=0.;
1718: for(j=1;j<=nlstate;j++){
1719: min=1.;
1720: max=0.;
1721: for(i=1; i<=nlstate; i++) {
1722: sumnew=0;
1723: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1724: prlim[i][j]= newm[i][j]/(1-sumnew);
1.145 brouard 1725: /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
1.126 brouard 1726: max=FMAX(max,prlim[i][j]);
1727: min=FMIN(min,prlim[i][j]);
1728: }
1729: maxmin=max-min;
1730: maxmax=FMAX(maxmax,maxmin);
1.169 brouard 1731: } /* j loop */
1.126 brouard 1732: if(maxmax < ftolpl){
1733: return prlim;
1734: }
1.169 brouard 1735: } /* age loop */
1736: return prlim; /* should not reach here */
1.126 brouard 1737: }
1738:
1739: /*************** transition probabilities ***************/
1740:
1741: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1742: {
1.138 brouard 1743: /* According to parameters values stored in x and the covariate's values stored in cov,
1744: computes the probability to be observed in state j being in state i by appying the
1745: model to the ncovmodel covariates (including constant and age).
1746: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1747: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1748: ncth covariate in the global vector x is given by the formula:
1749: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1750: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1751: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1752: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1753: Outputs ps[i][j] the probability to be observed in j being in j according to
1754: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1755: */
1756: double s1, lnpijopii;
1.126 brouard 1757: /*double t34;*/
1.164 brouard 1758: int i,j, nc, ii, jj;
1.126 brouard 1759:
1760: for(i=1; i<= nlstate; i++){
1761: for(j=1; j<i;j++){
1.138 brouard 1762: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1763: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1764: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1765: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 1766: }
1.138 brouard 1767: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1768: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 1769: }
1770: for(j=i+1; j<=nlstate+ndeath;j++){
1.138 brouard 1771: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1772: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
1773: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
1774: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1.126 brouard 1775: }
1.138 brouard 1776: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1.126 brouard 1777: }
1778: }
1779:
1780: for(i=1; i<= nlstate; i++){
1781: s1=0;
1.131 brouard 1782: for(j=1; j<i; j++){
1.138 brouard 1783: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 1784: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1785: }
1786: for(j=i+1; j<=nlstate+ndeath; j++){
1.138 brouard 1787: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 1788: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1789: }
1.138 brouard 1790: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1.126 brouard 1791: ps[i][i]=1./(s1+1.);
1.138 brouard 1792: /* Computing other pijs */
1.126 brouard 1793: for(j=1; j<i; j++)
1794: ps[i][j]= exp(ps[i][j])*ps[i][i];
1795: for(j=i+1; j<=nlstate+ndeath; j++)
1796: ps[i][j]= exp(ps[i][j])*ps[i][i];
1797: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1798: } /* end i */
1799:
1800: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1801: for(jj=1; jj<= nlstate+ndeath; jj++){
1802: ps[ii][jj]=0;
1803: ps[ii][ii]=1;
1804: }
1805: }
1806:
1.145 brouard 1807:
1808: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1809: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1810: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
1811: /* } */
1812: /* printf("\n "); */
1813: /* } */
1814: /* printf("\n ");printf("%lf ",cov[2]);*/
1815: /*
1.126 brouard 1816: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1817: goto end;*/
1818: return ps;
1819: }
1820:
1821: /**************** Product of 2 matrices ******************/
1822:
1.145 brouard 1823: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 1824: {
1825: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1826: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1827: /* in, b, out are matrice of pointers which should have been initialized
1828: before: only the contents of out is modified. The function returns
1829: a pointer to pointers identical to out */
1.145 brouard 1830: int i, j, k;
1.126 brouard 1831: for(i=nrl; i<= nrh; i++)
1.145 brouard 1832: for(k=ncolol; k<=ncoloh; k++){
1833: out[i][k]=0.;
1834: for(j=ncl; j<=nch; j++)
1835: out[i][k] +=in[i][j]*b[j][k];
1836: }
1.126 brouard 1837: return out;
1838: }
1839:
1840:
1841: /************* Higher Matrix Product ***************/
1842:
1843: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1844: {
1845: /* Computes the transition matrix starting at age 'age' over
1846: 'nhstepm*hstepm*stepm' months (i.e. until
1847: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1848: nhstepm*hstepm matrices.
1849: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1850: (typically every 2 years instead of every month which is too big
1851: for the memory).
1852: Model is determined by parameters x and covariates have to be
1853: included manually here.
1854:
1855: */
1856:
1857: int i, j, d, h, k;
1.131 brouard 1858: double **out, cov[NCOVMAX+1];
1.126 brouard 1859: double **newm;
1860:
1861: /* Hstepm could be zero and should return the unit matrix */
1862: for (i=1;i<=nlstate+ndeath;i++)
1863: for (j=1;j<=nlstate+ndeath;j++){
1864: oldm[i][j]=(i==j ? 1.0 : 0.0);
1865: po[i][j][0]=(i==j ? 1.0 : 0.0);
1866: }
1867: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1868: for(h=1; h <=nhstepm; h++){
1869: for(d=1; d <=hstepm; d++){
1870: newm=savm;
1871: /* Covariates have to be included here again */
1872: cov[1]=1.;
1873: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1.131 brouard 1874: for (k=1; k<=cptcovn;k++)
1875: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.126 brouard 1876: for (k=1; k<=cptcovage;k++)
1877: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1.145 brouard 1878: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.126 brouard 1879: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1880:
1881:
1882: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1883: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1884: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1885: pmij(pmmij,cov,ncovmodel,x,nlstate));
1886: savm=oldm;
1887: oldm=newm;
1888: }
1889: for(i=1; i<=nlstate+ndeath; i++)
1890: for(j=1;j<=nlstate+ndeath;j++) {
1891: po[i][j][h]=newm[i][j];
1.128 brouard 1892: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 1893: }
1.128 brouard 1894: /*printf("h=%d ",h);*/
1.126 brouard 1895: } /* end h */
1.128 brouard 1896: /* printf("\n H=%d \n",h); */
1.126 brouard 1897: return po;
1898: }
1899:
1.162 brouard 1900: #ifdef NLOPT
1901: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
1902: double fret;
1903: double *xt;
1904: int j;
1905: myfunc_data *d2 = (myfunc_data *) pd;
1906: /* xt = (p1-1); */
1907: xt=vector(1,n);
1908: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
1909:
1910: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
1911: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
1912: printf("Function = %.12lf ",fret);
1913: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
1914: printf("\n");
1915: free_vector(xt,1,n);
1916: return fret;
1917: }
1918: #endif
1.126 brouard 1919:
1920: /*************** log-likelihood *************/
1921: double func( double *x)
1922: {
1923: int i, ii, j, k, mi, d, kk;
1.131 brouard 1924: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 1925: double **out;
1926: double sw; /* Sum of weights */
1927: double lli; /* Individual log likelihood */
1928: int s1, s2;
1929: double bbh, survp;
1930: long ipmx;
1931: /*extern weight */
1932: /* We are differentiating ll according to initial status */
1933: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1934: /*for(i=1;i<imx;i++)
1935: printf(" %d\n",s[4][i]);
1936: */
1.162 brouard 1937:
1938: ++countcallfunc;
1939:
1.126 brouard 1940: cov[1]=1.;
1941:
1942: for(k=1; k<=nlstate; k++) ll[k]=0.;
1943:
1944: if(mle==1){
1945: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.138 brouard 1946: /* Computes the values of the ncovmodel covariates of the model
1947: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
1948: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
1949: to be observed in j being in i according to the model.
1950: */
1.145 brouard 1951: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1952: cov[2+k]=covar[Tvar[k]][i];
1953: }
1.137 brouard 1954: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1.138 brouard 1955: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1.137 brouard 1956: has been calculated etc */
1.126 brouard 1957: for(mi=1; mi<= wav[i]-1; mi++){
1958: for (ii=1;ii<=nlstate+ndeath;ii++)
1959: for (j=1;j<=nlstate+ndeath;j++){
1960: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1961: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1962: }
1963: for(d=0; d<dh[mi][i]; d++){
1964: newm=savm;
1965: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1966: for (kk=1; kk<=cptcovage;kk++) {
1.137 brouard 1967: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
1.126 brouard 1968: }
1969: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1970: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1971: savm=oldm;
1972: oldm=newm;
1973: } /* end mult */
1974:
1975: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1976: /* But now since version 0.9 we anticipate for bias at large stepm.
1977: * If stepm is larger than one month (smallest stepm) and if the exact delay
1978: * (in months) between two waves is not a multiple of stepm, we rounded to
1979: * the nearest (and in case of equal distance, to the lowest) interval but now
1980: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1981: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1982: * probability in order to take into account the bias as a fraction of the way
1983: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1984: * -stepm/2 to stepm/2 .
1985: * For stepm=1 the results are the same as for previous versions of Imach.
1986: * For stepm > 1 the results are less biased than in previous versions.
1987: */
1988: s1=s[mw[mi][i]][i];
1989: s2=s[mw[mi+1][i]][i];
1990: bbh=(double)bh[mi][i]/(double)stepm;
1991: /* bias bh is positive if real duration
1992: * is higher than the multiple of stepm and negative otherwise.
1993: */
1994: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1995: if( s2 > nlstate){
1996: /* i.e. if s2 is a death state and if the date of death is known
1997: then the contribution to the likelihood is the probability to
1998: die between last step unit time and current step unit time,
1999: which is also equal to probability to die before dh
2000: minus probability to die before dh-stepm .
2001: In version up to 0.92 likelihood was computed
2002: as if date of death was unknown. Death was treated as any other
2003: health state: the date of the interview describes the actual state
2004: and not the date of a change in health state. The former idea was
2005: to consider that at each interview the state was recorded
2006: (healthy, disable or death) and IMaCh was corrected; but when we
2007: introduced the exact date of death then we should have modified
2008: the contribution of an exact death to the likelihood. This new
2009: contribution is smaller and very dependent of the step unit
2010: stepm. It is no more the probability to die between last interview
2011: and month of death but the probability to survive from last
2012: interview up to one month before death multiplied by the
2013: probability to die within a month. Thanks to Chris
2014: Jackson for correcting this bug. Former versions increased
2015: mortality artificially. The bad side is that we add another loop
2016: which slows down the processing. The difference can be up to 10%
2017: lower mortality.
2018: */
1.183 brouard 2019: /* If, at the beginning of the maximization mostly, the
2020: cumulative probability or probability to be dead is
2021: constant (ie = 1) over time d, the difference is equal to
2022: 0. out[s1][3] = savm[s1][3]: probability, being at state
2023: s1 at precedent wave, to be dead a month before current
2024: wave is equal to probability, being at state s1 at
2025: precedent wave, to be dead at mont of the current
2026: wave. Then the observed probability (that this person died)
2027: is null according to current estimated parameter. In fact,
2028: it should be very low but not zero otherwise the log go to
2029: infinity.
2030: */
2031: /* #ifdef INFINITYORIGINAL */
2032: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2033: /* #else */
2034: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
2035: /* lli=log(mytinydouble); */
2036: /* else */
2037: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2038: /* #endif */
2039: lli=log(out[s1][s2] - savm[s1][s2]);
1.126 brouard 2040:
2041: } else if (s2==-2) {
2042: for (j=1,survp=0. ; j<=nlstate; j++)
2043: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2044: /*survp += out[s1][j]; */
2045: lli= log(survp);
2046: }
2047:
2048: else if (s2==-4) {
2049: for (j=3,survp=0. ; j<=nlstate; j++)
2050: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2051: lli= log(survp);
2052: }
2053:
2054: else if (s2==-5) {
2055: for (j=1,survp=0. ; j<=2; j++)
2056: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2057: lli= log(survp);
2058: }
2059:
2060: else{
2061: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2062: /* 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 */
2063: }
2064: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
2065: /*if(lli ==000.0)*/
2066: /*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); */
2067: ipmx +=1;
2068: sw += weight[i];
2069: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.183 brouard 2070: /* if (lli < log(mytinydouble)){ */
2071: /* 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); */
2072: /* 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]); */
2073: /* } */
1.126 brouard 2074: } /* end of wave */
2075: } /* end of individual */
2076: } else if(mle==2){
2077: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2078: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2079: for(mi=1; mi<= wav[i]-1; mi++){
2080: for (ii=1;ii<=nlstate+ndeath;ii++)
2081: for (j=1;j<=nlstate+ndeath;j++){
2082: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2083: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2084: }
2085: for(d=0; d<=dh[mi][i]; d++){
2086: newm=savm;
2087: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2088: for (kk=1; kk<=cptcovage;kk++) {
2089: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2090: }
2091: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2092: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2093: savm=oldm;
2094: oldm=newm;
2095: } /* end mult */
2096:
2097: s1=s[mw[mi][i]][i];
2098: s2=s[mw[mi+1][i]][i];
2099: bbh=(double)bh[mi][i]/(double)stepm;
2100: 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 */
2101: ipmx +=1;
2102: sw += weight[i];
2103: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2104: } /* end of wave */
2105: } /* end of individual */
2106: } else if(mle==3){ /* exponential inter-extrapolation */
2107: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2108: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2109: for(mi=1; mi<= wav[i]-1; mi++){
2110: for (ii=1;ii<=nlstate+ndeath;ii++)
2111: for (j=1;j<=nlstate+ndeath;j++){
2112: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2113: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2114: }
2115: for(d=0; d<dh[mi][i]; d++){
2116: newm=savm;
2117: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2118: for (kk=1; kk<=cptcovage;kk++) {
2119: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2120: }
2121: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2122: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2123: savm=oldm;
2124: oldm=newm;
2125: } /* end mult */
2126:
2127: s1=s[mw[mi][i]][i];
2128: s2=s[mw[mi+1][i]][i];
2129: bbh=(double)bh[mi][i]/(double)stepm;
2130: 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 */
2131: ipmx +=1;
2132: sw += weight[i];
2133: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2134: } /* end of wave */
2135: } /* end of individual */
2136: }else if (mle==4){ /* ml=4 no inter-extrapolation */
2137: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2138: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2139: for(mi=1; mi<= wav[i]-1; mi++){
2140: for (ii=1;ii<=nlstate+ndeath;ii++)
2141: for (j=1;j<=nlstate+ndeath;j++){
2142: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2143: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2144: }
2145: for(d=0; d<dh[mi][i]; d++){
2146: newm=savm;
2147: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2148: for (kk=1; kk<=cptcovage;kk++) {
2149: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2150: }
2151:
2152: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2153: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2154: savm=oldm;
2155: oldm=newm;
2156: } /* end mult */
2157:
2158: s1=s[mw[mi][i]][i];
2159: s2=s[mw[mi+1][i]][i];
2160: if( s2 > nlstate){
2161: lli=log(out[s1][s2] - savm[s1][s2]);
2162: }else{
2163: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2164: }
2165: ipmx +=1;
2166: sw += weight[i];
2167: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2168: /* 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]); */
2169: } /* end of wave */
2170: } /* end of individual */
2171: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
2172: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2173: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2174: for(mi=1; mi<= wav[i]-1; mi++){
2175: for (ii=1;ii<=nlstate+ndeath;ii++)
2176: for (j=1;j<=nlstate+ndeath;j++){
2177: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2178: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2179: }
2180: for(d=0; d<dh[mi][i]; d++){
2181: newm=savm;
2182: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2183: for (kk=1; kk<=cptcovage;kk++) {
2184: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2185: }
2186:
2187: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2188: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2189: savm=oldm;
2190: oldm=newm;
2191: } /* end mult */
2192:
2193: s1=s[mw[mi][i]][i];
2194: s2=s[mw[mi+1][i]][i];
2195: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2196: ipmx +=1;
2197: sw += weight[i];
2198: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2199: /*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]);*/
2200: } /* end of wave */
2201: } /* end of individual */
2202: } /* End of if */
2203: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2204: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2205: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2206: return -l;
2207: }
2208:
2209: /*************** log-likelihood *************/
2210: double funcone( double *x)
2211: {
2212: /* Same as likeli but slower because of a lot of printf and if */
2213: int i, ii, j, k, mi, d, kk;
1.131 brouard 2214: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2215: double **out;
2216: double lli; /* Individual log likelihood */
2217: double llt;
2218: int s1, s2;
2219: double bbh, survp;
2220: /*extern weight */
2221: /* We are differentiating ll according to initial status */
2222: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2223: /*for(i=1;i<imx;i++)
2224: printf(" %d\n",s[4][i]);
2225: */
2226: cov[1]=1.;
2227:
2228: for(k=1; k<=nlstate; k++) ll[k]=0.;
2229:
2230: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2231: for (k=1; k<=cptcovn;k++) cov[2+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: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2241: for (kk=1; kk<=cptcovage;kk++) {
2242: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2243: }
1.145 brouard 2244: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.126 brouard 2245: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2246: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1.145 brouard 2247: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2248: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
1.126 brouard 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: /* bias is positive if real duration
2257: * is higher than the multiple of stepm and negative otherwise.
2258: */
2259: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2260: lli=log(out[s1][s2] - savm[s1][s2]);
2261: } else if (s2==-2) {
2262: for (j=1,survp=0. ; j<=nlstate; j++)
2263: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2264: lli= log(survp);
2265: }else if (mle==1){
2266: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2267: } else if(mle==2){
2268: 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 */
2269: } else if(mle==3){ /* exponential inter-extrapolation */
2270: 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 */
2271: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2272: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 2273: } else{ /* mle=0 back to 1 */
2274: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2275: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 2276: } /* End of if */
2277: ipmx +=1;
2278: sw += weight[i];
2279: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 2280: /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
1.126 brouard 2281: if(globpr){
1.141 brouard 2282: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
1.126 brouard 2283: %11.6f %11.6f %11.6f ", \
2284: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
2285: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2286: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2287: llt +=ll[k]*gipmx/gsw;
2288: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2289: }
2290: fprintf(ficresilk," %10.6f\n", -llt);
2291: }
2292: } /* end of wave */
2293: } /* end of individual */
2294: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2295: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2296: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2297: if(globpr==0){ /* First time we count the contributions and weights */
2298: gipmx=ipmx;
2299: gsw=sw;
2300: }
2301: return -l;
2302: }
2303:
2304:
2305: /*************** function likelione ***********/
2306: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2307: {
2308: /* This routine should help understanding what is done with
2309: the selection of individuals/waves and
2310: to check the exact contribution to the likelihood.
2311: Plotting could be done.
2312: */
2313: int k;
2314:
2315: if(*globpri !=0){ /* Just counts and sums, no printings */
2316: strcpy(fileresilk,"ilk");
2317: strcat(fileresilk,fileres);
2318: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2319: printf("Problem with resultfile: %s\n", fileresilk);
2320: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2321: }
2322: 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");
2323: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
2324: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2325: for(k=1; k<=nlstate; k++)
2326: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2327: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2328: }
2329:
2330: *fretone=(*funcone)(p);
2331: if(*globpri !=0){
2332: fclose(ficresilk);
2333: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
2334: fflush(fichtm);
2335: }
2336: return;
2337: }
2338:
2339:
2340: /*********** Maximum Likelihood Estimation ***************/
2341:
2342: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2343: {
1.165 brouard 2344: int i,j, iter=0;
1.126 brouard 2345: double **xi;
2346: double fret;
2347: double fretone; /* Only one call to likelihood */
2348: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 2349:
2350: #ifdef NLOPT
2351: int creturn;
2352: nlopt_opt opt;
2353: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2354: double *lb;
2355: double minf; /* the minimum objective value, upon return */
2356: double * p1; /* Shifted parameters from 0 instead of 1 */
2357: myfunc_data dinst, *d = &dinst;
2358: #endif
2359:
2360:
1.126 brouard 2361: xi=matrix(1,npar,1,npar);
2362: for (i=1;i<=npar;i++)
2363: for (j=1;j<=npar;j++)
2364: xi[i][j]=(i==j ? 1.0 : 0.0);
2365: printf("Powell\n"); fprintf(ficlog,"Powell\n");
2366: strcpy(filerespow,"pow");
2367: strcat(filerespow,fileres);
2368: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2369: printf("Problem with resultfile: %s\n", filerespow);
2370: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2371: }
2372: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2373: for (i=1;i<=nlstate;i++)
2374: for(j=1;j<=nlstate+ndeath;j++)
2375: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2376: fprintf(ficrespow,"\n");
1.162 brouard 2377: #ifdef POWELL
1.126 brouard 2378: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 2379: #endif
1.126 brouard 2380:
1.162 brouard 2381: #ifdef NLOPT
2382: #ifdef NEWUOA
2383: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2384: #else
2385: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2386: #endif
2387: lb=vector(0,npar-1);
2388: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2389: nlopt_set_lower_bounds(opt, lb);
2390: nlopt_set_initial_step1(opt, 0.1);
2391:
2392: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2393: d->function = func;
2394: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2395: nlopt_set_min_objective(opt, myfunc, d);
2396: nlopt_set_xtol_rel(opt, ftol);
2397: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2398: printf("nlopt failed! %d\n",creturn);
2399: }
2400: else {
2401: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2402: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2403: iter=1; /* not equal */
2404: }
2405: nlopt_destroy(opt);
2406: #endif
1.126 brouard 2407: free_matrix(xi,1,npar,1,npar);
2408: fclose(ficrespow);
1.180 brouard 2409: printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2410: fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2411: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 2412:
2413: }
2414:
2415: /**** Computes Hessian and covariance matrix ***/
2416: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
2417: {
2418: double **a,**y,*x,pd;
2419: double **hess;
1.164 brouard 2420: int i, j;
1.126 brouard 2421: int *indx;
2422:
2423: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
2424: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
2425: void lubksb(double **a, int npar, int *indx, double b[]) ;
2426: void ludcmp(double **a, int npar, int *indx, double *d) ;
2427: double gompertz(double p[]);
2428: hess=matrix(1,npar,1,npar);
2429:
2430: printf("\nCalculation of the hessian matrix. Wait...\n");
2431: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2432: for (i=1;i<=npar;i++){
2433: printf("%d",i);fflush(stdout);
2434: fprintf(ficlog,"%d",i);fflush(ficlog);
2435:
2436: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2437:
2438: /* printf(" %f ",p[i]);
2439: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2440: }
2441:
2442: for (i=1;i<=npar;i++) {
2443: for (j=1;j<=npar;j++) {
2444: if (j>i) {
2445: printf(".%d%d",i,j);fflush(stdout);
2446: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
2447: hess[i][j]=hessij(p,delti,i,j,func,npar);
2448:
2449: hess[j][i]=hess[i][j];
2450: /*printf(" %lf ",hess[i][j]);*/
2451: }
2452: }
2453: }
2454: printf("\n");
2455: fprintf(ficlog,"\n");
2456:
2457: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2458: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2459:
2460: a=matrix(1,npar,1,npar);
2461: y=matrix(1,npar,1,npar);
2462: x=vector(1,npar);
2463: indx=ivector(1,npar);
2464: for (i=1;i<=npar;i++)
2465: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2466: ludcmp(a,npar,indx,&pd);
2467:
2468: for (j=1;j<=npar;j++) {
2469: for (i=1;i<=npar;i++) x[i]=0;
2470: x[j]=1;
2471: lubksb(a,npar,indx,x);
2472: for (i=1;i<=npar;i++){
2473: matcov[i][j]=x[i];
2474: }
2475: }
2476:
2477: printf("\n#Hessian matrix#\n");
2478: fprintf(ficlog,"\n#Hessian matrix#\n");
2479: for (i=1;i<=npar;i++) {
2480: for (j=1;j<=npar;j++) {
2481: printf("%.3e ",hess[i][j]);
2482: fprintf(ficlog,"%.3e ",hess[i][j]);
2483: }
2484: printf("\n");
2485: fprintf(ficlog,"\n");
2486: }
2487:
2488: /* Recompute Inverse */
2489: for (i=1;i<=npar;i++)
2490: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
2491: ludcmp(a,npar,indx,&pd);
2492:
2493: /* printf("\n#Hessian matrix recomputed#\n");
2494:
2495: for (j=1;j<=npar;j++) {
2496: for (i=1;i<=npar;i++) x[i]=0;
2497: x[j]=1;
2498: lubksb(a,npar,indx,x);
2499: for (i=1;i<=npar;i++){
2500: y[i][j]=x[i];
2501: printf("%.3e ",y[i][j]);
2502: fprintf(ficlog,"%.3e ",y[i][j]);
2503: }
2504: printf("\n");
2505: fprintf(ficlog,"\n");
2506: }
2507: */
2508:
2509: free_matrix(a,1,npar,1,npar);
2510: free_matrix(y,1,npar,1,npar);
2511: free_vector(x,1,npar);
2512: free_ivector(indx,1,npar);
2513: free_matrix(hess,1,npar,1,npar);
2514:
2515:
2516: }
2517:
2518: /*************** hessian matrix ****************/
2519: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2520: {
2521: int i;
2522: int l=1, lmax=20;
2523: double k1,k2;
1.132 brouard 2524: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 2525: double res;
2526: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2527: double fx;
2528: int k=0,kmax=10;
2529: double l1;
2530:
2531: fx=func(x);
2532: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 2533: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 2534: l1=pow(10,l);
2535: delts=delt;
2536: for(k=1 ; k <kmax; k=k+1){
2537: delt = delta*(l1*k);
2538: p2[theta]=x[theta] +delt;
1.145 brouard 2539: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 2540: p2[theta]=x[theta]-delt;
2541: k2=func(p2)-fx;
2542: /*res= (k1-2.0*fx+k2)/delt/delt; */
2543: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2544:
1.132 brouard 2545: #ifdef DEBUGHESS
1.126 brouard 2546: 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);
2547: 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);
2548: #endif
2549: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2550: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2551: k=kmax;
2552: }
2553: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 2554: k=kmax; l=lmax*10;
1.126 brouard 2555: }
2556: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2557: delts=delt;
2558: }
2559: }
2560: }
2561: delti[theta]=delts;
2562: return res;
2563:
2564: }
2565:
2566: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2567: {
2568: int i;
1.164 brouard 2569: int l=1, lmax=20;
1.126 brouard 2570: double k1,k2,k3,k4,res,fx;
1.132 brouard 2571: double p2[MAXPARM+1];
1.126 brouard 2572: int k;
2573:
2574: fx=func(x);
2575: for (k=1; k<=2; k++) {
2576: for (i=1;i<=npar;i++) p2[i]=x[i];
2577: p2[thetai]=x[thetai]+delti[thetai]/k;
2578: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2579: k1=func(p2)-fx;
2580:
2581: p2[thetai]=x[thetai]+delti[thetai]/k;
2582: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2583: k2=func(p2)-fx;
2584:
2585: p2[thetai]=x[thetai]-delti[thetai]/k;
2586: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2587: k3=func(p2)-fx;
2588:
2589: p2[thetai]=x[thetai]-delti[thetai]/k;
2590: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2591: k4=func(p2)-fx;
2592: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2593: #ifdef DEBUG
2594: 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);
2595: 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);
2596: #endif
2597: }
2598: return res;
2599: }
2600:
2601: /************** Inverse of matrix **************/
2602: void ludcmp(double **a, int n, int *indx, double *d)
2603: {
2604: int i,imax,j,k;
2605: double big,dum,sum,temp;
2606: double *vv;
2607:
2608: vv=vector(1,n);
2609: *d=1.0;
2610: for (i=1;i<=n;i++) {
2611: big=0.0;
2612: for (j=1;j<=n;j++)
2613: if ((temp=fabs(a[i][j])) > big) big=temp;
2614: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2615: vv[i]=1.0/big;
2616: }
2617: for (j=1;j<=n;j++) {
2618: for (i=1;i<j;i++) {
2619: sum=a[i][j];
2620: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2621: a[i][j]=sum;
2622: }
2623: big=0.0;
2624: for (i=j;i<=n;i++) {
2625: sum=a[i][j];
2626: for (k=1;k<j;k++)
2627: sum -= a[i][k]*a[k][j];
2628: a[i][j]=sum;
2629: if ( (dum=vv[i]*fabs(sum)) >= big) {
2630: big=dum;
2631: imax=i;
2632: }
2633: }
2634: if (j != imax) {
2635: for (k=1;k<=n;k++) {
2636: dum=a[imax][k];
2637: a[imax][k]=a[j][k];
2638: a[j][k]=dum;
2639: }
2640: *d = -(*d);
2641: vv[imax]=vv[j];
2642: }
2643: indx[j]=imax;
2644: if (a[j][j] == 0.0) a[j][j]=TINY;
2645: if (j != n) {
2646: dum=1.0/(a[j][j]);
2647: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2648: }
2649: }
2650: free_vector(vv,1,n); /* Doesn't work */
2651: ;
2652: }
2653:
2654: void lubksb(double **a, int n, int *indx, double b[])
2655: {
2656: int i,ii=0,ip,j;
2657: double sum;
2658:
2659: for (i=1;i<=n;i++) {
2660: ip=indx[i];
2661: sum=b[ip];
2662: b[ip]=b[i];
2663: if (ii)
2664: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2665: else if (sum) ii=i;
2666: b[i]=sum;
2667: }
2668: for (i=n;i>=1;i--) {
2669: sum=b[i];
2670: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2671: b[i]=sum/a[i][i];
2672: }
2673: }
2674:
2675: void pstamp(FILE *fichier)
2676: {
2677: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2678: }
2679:
2680: /************ Frequencies ********************/
2681: 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[])
2682: { /* Some frequencies */
2683:
1.164 brouard 2684: int i, m, jk, j1, bool, z1,j;
1.126 brouard 2685: int first;
2686: double ***freq; /* Frequencies */
2687: double *pp, **prop;
2688: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2689: char fileresp[FILENAMELENGTH];
2690:
2691: pp=vector(1,nlstate);
2692: prop=matrix(1,nlstate,iagemin,iagemax+3);
2693: strcpy(fileresp,"p");
2694: strcat(fileresp,fileres);
2695: if((ficresp=fopen(fileresp,"w"))==NULL) {
2696: printf("Problem with prevalence resultfile: %s\n", fileresp);
2697: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2698: exit(0);
2699: }
2700: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2701: j1=0;
2702:
2703: j=cptcoveff;
2704: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2705:
2706: first=1;
2707:
1.169 brouard 2708: /* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */
2709: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
2710: /* j1++; */
1.145 brouard 2711: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
1.126 brouard 2712: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2713: scanf("%d", i);*/
2714: for (i=-5; i<=nlstate+ndeath; i++)
2715: for (jk=-5; jk<=nlstate+ndeath; jk++)
2716: for(m=iagemin; m <= iagemax+3; m++)
2717: freq[i][jk][m]=0;
1.143 brouard 2718:
2719: for (i=1; i<=nlstate; i++)
2720: for(m=iagemin; m <= iagemax+3; m++)
2721: prop[i][m]=0;
1.126 brouard 2722:
2723: dateintsum=0;
2724: k2cpt=0;
2725: for (i=1; i<=imx; i++) {
2726: bool=1;
1.144 brouard 2727: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
2728: for (z1=1; z1<=cptcoveff; z1++)
2729: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
1.145 brouard 2730: /* Tests if the value of each of the covariates of i is equal to filter j1 */
1.144 brouard 2731: bool=0;
1.145 brouard 2732: /* 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",
2733: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
2734: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
1.144 brouard 2735: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
2736: }
1.126 brouard 2737: }
1.144 brouard 2738:
1.126 brouard 2739: if (bool==1){
2740: for(m=firstpass; m<=lastpass; m++){
2741: k2=anint[m][i]+(mint[m][i]/12.);
2742: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2743: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2744: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2745: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2746: if (m<lastpass) {
2747: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2748: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2749: }
2750:
2751: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2752: dateintsum=dateintsum+k2;
2753: k2cpt++;
2754: }
2755: /*}*/
2756: }
2757: }
1.145 brouard 2758: } /* end i */
1.126 brouard 2759:
2760: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2761: pstamp(ficresp);
2762: if (cptcovn>0) {
2763: fprintf(ficresp, "\n#********** Variable ");
2764: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2765: fprintf(ficresp, "**********\n#");
1.143 brouard 2766: fprintf(ficlog, "\n#********** Variable ");
2767: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2768: fprintf(ficlog, "**********\n#");
1.126 brouard 2769: }
2770: for(i=1; i<=nlstate;i++)
2771: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2772: fprintf(ficresp, "\n");
2773:
2774: for(i=iagemin; i <= iagemax+3; i++){
2775: if(i==iagemax+3){
2776: fprintf(ficlog,"Total");
2777: }else{
2778: if(first==1){
2779: first=0;
2780: printf("See log file for details...\n");
2781: }
2782: fprintf(ficlog,"Age %d", i);
2783: }
2784: for(jk=1; jk <=nlstate ; jk++){
2785: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2786: pp[jk] += freq[jk][m][i];
2787: }
2788: for(jk=1; jk <=nlstate ; jk++){
2789: for(m=-1, pos=0; m <=0 ; m++)
2790: pos += freq[jk][m][i];
2791: if(pp[jk]>=1.e-10){
2792: if(first==1){
1.132 brouard 2793: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1.126 brouard 2794: }
2795: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2796: }else{
2797: if(first==1)
2798: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2799: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2800: }
2801: }
2802:
2803: for(jk=1; jk <=nlstate ; jk++){
2804: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2805: pp[jk] += freq[jk][m][i];
2806: }
2807: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2808: pos += pp[jk];
2809: posprop += prop[jk][i];
2810: }
2811: for(jk=1; jk <=nlstate ; jk++){
2812: if(pos>=1.e-5){
2813: if(first==1)
2814: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2815: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2816: }else{
2817: if(first==1)
2818: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2819: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2820: }
2821: if( i <= iagemax){
2822: if(pos>=1.e-5){
2823: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2824: /*probs[i][jk][j1]= pp[jk]/pos;*/
2825: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2826: }
2827: else
2828: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2829: }
2830: }
2831:
2832: for(jk=-1; jk <=nlstate+ndeath; jk++)
2833: for(m=-1; m <=nlstate+ndeath; m++)
2834: if(freq[jk][m][i] !=0 ) {
2835: if(first==1)
2836: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2837: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2838: }
2839: if(i <= iagemax)
2840: fprintf(ficresp,"\n");
2841: if(first==1)
2842: printf("Others in log...\n");
2843: fprintf(ficlog,"\n");
2844: }
1.145 brouard 2845: /*}*/
1.126 brouard 2846: }
2847: dateintmean=dateintsum/k2cpt;
2848:
2849: fclose(ficresp);
2850: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2851: free_vector(pp,1,nlstate);
2852: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2853: /* End of Freq */
2854: }
2855:
2856: /************ Prevalence ********************/
2857: 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)
2858: {
2859: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2860: in each health status at the date of interview (if between dateprev1 and dateprev2).
2861: We still use firstpass and lastpass as another selection.
2862: */
2863:
1.164 brouard 2864: int i, m, jk, j1, bool, z1,j;
2865:
2866: double **prop;
2867: double posprop;
1.126 brouard 2868: double y2; /* in fractional years */
2869: int iagemin, iagemax;
1.145 brouard 2870: int first; /** to stop verbosity which is redirected to log file */
1.126 brouard 2871:
2872: iagemin= (int) agemin;
2873: iagemax= (int) agemax;
2874: /*pp=vector(1,nlstate);*/
2875: prop=matrix(1,nlstate,iagemin,iagemax+3);
2876: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2877: j1=0;
2878:
1.145 brouard 2879: /*j=cptcoveff;*/
1.126 brouard 2880: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2881:
1.145 brouard 2882: first=1;
2883: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
2884: /*for(i1=1; i1<=ncodemax[k1];i1++){
2885: j1++;*/
1.126 brouard 2886:
2887: for (i=1; i<=nlstate; i++)
2888: for(m=iagemin; m <= iagemax+3; m++)
2889: prop[i][m]=0.0;
2890:
2891: for (i=1; i<=imx; i++) { /* Each individual */
2892: bool=1;
2893: if (cptcovn>0) {
2894: for (z1=1; z1<=cptcoveff; z1++)
2895: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2896: bool=0;
2897: }
2898: if (bool==1) {
2899: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2900: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2901: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2902: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2903: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2904: 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);
2905: if (s[m][i]>0 && s[m][i]<=nlstate) {
2906: /*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]]);*/
2907: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2908: prop[s[m][i]][iagemax+3] += weight[i];
2909: }
2910: }
2911: } /* end selection of waves */
2912: }
2913: }
2914: for(i=iagemin; i <= iagemax+3; i++){
2915: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2916: posprop += prop[jk][i];
2917: }
1.145 brouard 2918:
1.126 brouard 2919: for(jk=1; jk <=nlstate ; jk++){
2920: if( i <= iagemax){
2921: if(posprop>=1.e-5){
2922: probs[i][jk][j1]= prop[jk][i]/posprop;
1.145 brouard 2923: } else{
2924: if(first==1){
2925: first=0;
2926: 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]);
2927: }
2928: }
1.126 brouard 2929: }
2930: }/* end jk */
2931: }/* end i */
1.145 brouard 2932: /*} *//* end i1 */
2933: } /* end j1 */
1.126 brouard 2934:
2935: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2936: /*free_vector(pp,1,nlstate);*/
2937: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2938: } /* End of prevalence */
2939:
2940: /************* Waves Concatenation ***************/
2941:
2942: 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)
2943: {
2944: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2945: Death is a valid wave (if date is known).
2946: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2947: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2948: and mw[mi+1][i]. dh depends on stepm.
2949: */
2950:
2951: int i, mi, m;
2952: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2953: double sum=0., jmean=0.;*/
2954: int first;
2955: int j, k=0,jk, ju, jl;
2956: double sum=0.;
2957: first=0;
1.164 brouard 2958: jmin=100000;
1.126 brouard 2959: jmax=-1;
2960: jmean=0.;
2961: for(i=1; i<=imx; i++){
2962: mi=0;
2963: m=firstpass;
2964: while(s[m][i] <= nlstate){
2965: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2966: mw[++mi][i]=m;
2967: if(m >=lastpass)
2968: break;
2969: else
2970: m++;
2971: }/* end while */
2972: if (s[m][i] > nlstate){
2973: mi++; /* Death is another wave */
2974: /* if(mi==0) never been interviewed correctly before death */
2975: /* Only death is a correct wave */
2976: mw[mi][i]=m;
2977: }
2978:
2979: wav[i]=mi;
2980: if(mi==0){
2981: nbwarn++;
2982: if(first==0){
2983: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2984: first=1;
2985: }
2986: if(first==1){
2987: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2988: }
2989: } /* end mi==0 */
2990: } /* End individuals */
2991:
2992: for(i=1; i<=imx; i++){
2993: for(mi=1; mi<wav[i];mi++){
2994: if (stepm <=0)
2995: dh[mi][i]=1;
2996: else{
2997: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2998: if (agedc[i] < 2*AGESUP) {
2999: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
3000: if(j==0) j=1; /* Survives at least one month after exam */
3001: else if(j<0){
3002: nberr++;
3003: 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]);
3004: j=1; /* Temporary Dangerous patch */
3005: 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);
3006: 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]);
3007: 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);
3008: }
3009: k=k+1;
3010: if (j >= jmax){
3011: jmax=j;
3012: ijmax=i;
3013: }
3014: if (j <= jmin){
3015: jmin=j;
3016: ijmin=i;
3017: }
3018: sum=sum+j;
3019: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
3020: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
3021: }
3022: }
3023: else{
3024: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
3025: /* 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]); */
3026:
3027: k=k+1;
3028: if (j >= jmax) {
3029: jmax=j;
3030: ijmax=i;
3031: }
3032: else if (j <= jmin){
3033: jmin=j;
3034: ijmin=i;
3035: }
3036: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
3037: /*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]);*/
3038: if(j<0){
3039: nberr++;
3040: 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]);
3041: 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]);
3042: }
3043: sum=sum+j;
3044: }
3045: jk= j/stepm;
3046: jl= j -jk*stepm;
3047: ju= j -(jk+1)*stepm;
3048: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
3049: if(jl==0){
3050: dh[mi][i]=jk;
3051: bh[mi][i]=0;
3052: }else{ /* We want a negative bias in order to only have interpolation ie
1.136 brouard 3053: * to avoid the price of an extra matrix product in likelihood */
1.126 brouard 3054: dh[mi][i]=jk+1;
3055: bh[mi][i]=ju;
3056: }
3057: }else{
3058: if(jl <= -ju){
3059: dh[mi][i]=jk;
3060: bh[mi][i]=jl; /* bias is positive if real duration
3061: * is higher than the multiple of stepm and negative otherwise.
3062: */
3063: }
3064: else{
3065: dh[mi][i]=jk+1;
3066: bh[mi][i]=ju;
3067: }
3068: if(dh[mi][i]==0){
3069: dh[mi][i]=1; /* At least one step */
3070: bh[mi][i]=ju; /* At least one step */
3071: /* 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);*/
3072: }
3073: } /* end if mle */
3074: }
3075: } /* end wave */
3076: }
3077: jmean=sum/k;
3078: printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
1.141 brouard 3079: fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
1.126 brouard 3080: }
3081:
3082: /*********** Tricode ****************************/
1.145 brouard 3083: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 3084: {
1.144 brouard 3085: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
3086: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
1.169 brouard 3087: * Boring subroutine which should only output nbcode[Tvar[j]][k]
1.145 brouard 3088: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
1.169 brouard 3089: * nbcode[Tvar[j]][1]=
1.144 brouard 3090: */
1.130 brouard 3091:
1.145 brouard 3092: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 3093: int modmaxcovj=0; /* Modality max of covariates j */
1.145 brouard 3094: int cptcode=0; /* Modality max of covariates j */
3095: int modmincovj=0; /* Modality min of covariates j */
3096:
3097:
1.126 brouard 3098: cptcoveff=0;
3099:
1.145 brouard 3100: for (k=-1; k < maxncov; k++) Ndum[k]=0;
1.144 brouard 3101: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 3102:
1.145 brouard 3103: /* Loop on covariates without age and products */
3104: for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
3105: for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the
1.136 brouard 3106: modality of this covariate Vj*/
1.145 brouard 3107: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
3108: * If product of Vn*Vm, still boolean *:
3109: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
3110: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
3111: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
1.136 brouard 3112: modality of the nth covariate of individual i. */
1.145 brouard 3113: if (ij > modmaxcovj)
3114: modmaxcovj=ij;
3115: else if (ij < modmincovj)
3116: modmincovj=ij;
3117: if ((ij < -1) && (ij > NCOVMAX)){
3118: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
3119: exit(1);
3120: }else
1.136 brouard 3121: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
1.145 brouard 3122: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
1.126 brouard 3123: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.136 brouard 3124: /* getting the maximum value of the modality of the covariate
3125: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
3126: female is 1, then modmaxcovj=1.*/
1.126 brouard 3127: }
1.145 brouard 3128: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
3129: cptcode=modmaxcovj;
1.137 brouard 3130: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
1.145 brouard 3131: /*for (i=0; i<=cptcode; i++) {*/
3132: for (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
3133: printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
3134: if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
3135: ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
3136: }
3137: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
3138: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
1.131 brouard 3139: } /* Ndum[-1] number of undefined modalities */
1.126 brouard 3140:
1.136 brouard 3141: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
1.145 brouard 3142: /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
3143: /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
3144: modmincovj=3; modmaxcovj = 7;
3145: There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
3146: which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy
3147: variables V1_1 and V1_2.
3148: nbcode[Tvar[j]][ij]=k;
3149: nbcode[Tvar[j]][1]=0;
3150: nbcode[Tvar[j]][2]=1;
3151: nbcode[Tvar[j]][3]=2;
3152: */
3153: ij=1; /* ij is similar to i but can jumps over null modalities */
3154: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
3155: for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
3156: /*recode from 0 */
1.131 brouard 3157: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
3158: nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode.
3159: k is a modality. If we have model=V1+V1*sex
3160: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
1.126 brouard 3161: ij++;
3162: }
3163: if (ij > ncodemax[j]) break;
1.137 brouard 3164: } /* end of loop on */
3165: } /* end of loop on modality */
3166: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
3167:
1.145 brouard 3168: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.137 brouard 3169:
1.145 brouard 3170: for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
3171: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
3172: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
3173: Ndum[ij]++;
3174: }
1.126 brouard 3175:
3176: ij=1;
1.145 brouard 3177: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
3178: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
1.126 brouard 3179: if((Ndum[i]!=0) && (i<=ncovcol)){
1.145 brouard 3180: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
3181: Tvaraff[ij]=i; /*For printing (unclear) */
1.126 brouard 3182: ij++;
1.145 brouard 3183: }else
3184: Tvaraff[ij]=0;
1.126 brouard 3185: }
1.131 brouard 3186: ij--;
1.144 brouard 3187: cptcoveff=ij; /*Number of total covariates*/
1.145 brouard 3188:
1.126 brouard 3189: }
3190:
1.145 brouard 3191:
1.126 brouard 3192: /*********** Health Expectancies ****************/
3193:
1.127 brouard 3194: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
1.126 brouard 3195:
3196: {
3197: /* Health expectancies, no variances */
1.164 brouard 3198: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 3199: int nhstepma, nstepma; /* Decreasing with age */
3200: double age, agelim, hf;
3201: double ***p3mat;
3202: double eip;
3203:
3204: pstamp(ficreseij);
3205: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3206: fprintf(ficreseij,"# Age");
3207: for(i=1; i<=nlstate;i++){
3208: for(j=1; j<=nlstate;j++){
3209: fprintf(ficreseij," e%1d%1d ",i,j);
3210: }
3211: fprintf(ficreseij," e%1d. ",i);
3212: }
3213: fprintf(ficreseij,"\n");
3214:
3215:
3216: if(estepm < stepm){
3217: printf ("Problem %d lower than %d\n",estepm, stepm);
3218: }
3219: else hstepm=estepm;
3220: /* We compute the life expectancy from trapezoids spaced every estepm months
3221: * This is mainly to measure the difference between two models: for example
3222: * if stepm=24 months pijx are given only every 2 years and by summing them
3223: * we are calculating an estimate of the Life Expectancy assuming a linear
3224: * progression in between and thus overestimating or underestimating according
3225: * to the curvature of the survival function. If, for the same date, we
3226: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3227: * to compare the new estimate of Life expectancy with the same linear
3228: * hypothesis. A more precise result, taking into account a more precise
3229: * curvature will be obtained if estepm is as small as stepm. */
3230:
3231: /* For example we decided to compute the life expectancy with the smallest unit */
3232: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3233: nhstepm is the number of hstepm from age to agelim
3234: nstepm is the number of stepm from age to agelin.
3235: Look at hpijx to understand the reason of that which relies in memory size
3236: and note for a fixed period like estepm months */
3237: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3238: survival function given by stepm (the optimization length). Unfortunately it
3239: means that if the survival funtion is printed only each two years of age and if
3240: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3241: results. So we changed our mind and took the option of the best precision.
3242: */
3243: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3244:
3245: agelim=AGESUP;
3246: /* If stepm=6 months */
3247: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3248: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3249:
3250: /* nhstepm age range expressed in number of stepm */
3251: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3252: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3253: /* if (stepm >= YEARM) hstepm=1;*/
3254: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3255: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3256:
3257: for (age=bage; age<=fage; age ++){
3258: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3259: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3260: /* if (stepm >= YEARM) hstepm=1;*/
3261: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3262:
3263: /* If stepm=6 months */
3264: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3265: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3266:
3267: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3268:
3269: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3270:
3271: printf("%d|",(int)age);fflush(stdout);
3272: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3273:
3274: /* Computing expectancies */
3275: for(i=1; i<=nlstate;i++)
3276: for(j=1; j<=nlstate;j++)
3277: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3278: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3279:
3280: /* 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]);*/
3281:
3282: }
3283:
3284: fprintf(ficreseij,"%3.0f",age );
3285: for(i=1; i<=nlstate;i++){
3286: eip=0;
3287: for(j=1; j<=nlstate;j++){
3288: eip +=eij[i][j][(int)age];
3289: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3290: }
3291: fprintf(ficreseij,"%9.4f", eip );
3292: }
3293: fprintf(ficreseij,"\n");
3294:
3295: }
3296: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3297: printf("\n");
3298: fprintf(ficlog,"\n");
3299:
3300: }
3301:
1.127 brouard 3302: void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
1.126 brouard 3303:
3304: {
3305: /* Covariances of health expectancies eij and of total life expectancies according
3306: to initial status i, ei. .
3307: */
3308: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3309: int nhstepma, nstepma; /* Decreasing with age */
3310: double age, agelim, hf;
3311: double ***p3matp, ***p3matm, ***varhe;
3312: double **dnewm,**doldm;
3313: double *xp, *xm;
3314: double **gp, **gm;
3315: double ***gradg, ***trgradg;
3316: int theta;
3317:
3318: double eip, vip;
3319:
3320: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
3321: xp=vector(1,npar);
3322: xm=vector(1,npar);
3323: dnewm=matrix(1,nlstate*nlstate,1,npar);
3324: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3325:
3326: pstamp(ficresstdeij);
3327: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3328: fprintf(ficresstdeij,"# Age");
3329: for(i=1; i<=nlstate;i++){
3330: for(j=1; j<=nlstate;j++)
3331: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3332: fprintf(ficresstdeij," e%1d. ",i);
3333: }
3334: fprintf(ficresstdeij,"\n");
3335:
3336: pstamp(ficrescveij);
3337: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3338: fprintf(ficrescveij,"# Age");
3339: for(i=1; i<=nlstate;i++)
3340: for(j=1; j<=nlstate;j++){
3341: cptj= (j-1)*nlstate+i;
3342: for(i2=1; i2<=nlstate;i2++)
3343: for(j2=1; j2<=nlstate;j2++){
3344: cptj2= (j2-1)*nlstate+i2;
3345: if(cptj2 <= cptj)
3346: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3347: }
3348: }
3349: fprintf(ficrescveij,"\n");
3350:
3351: if(estepm < stepm){
3352: printf ("Problem %d lower than %d\n",estepm, stepm);
3353: }
3354: else hstepm=estepm;
3355: /* We compute the life expectancy from trapezoids spaced every estepm months
3356: * This is mainly to measure the difference between two models: for example
3357: * if stepm=24 months pijx are given only every 2 years and by summing them
3358: * we are calculating an estimate of the Life Expectancy assuming a linear
3359: * progression in between and thus overestimating or underestimating according
3360: * to the curvature of the survival function. If, for the same date, we
3361: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3362: * to compare the new estimate of Life expectancy with the same linear
3363: * hypothesis. A more precise result, taking into account a more precise
3364: * curvature will be obtained if estepm is as small as stepm. */
3365:
3366: /* For example we decided to compute the life expectancy with the smallest unit */
3367: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3368: nhstepm is the number of hstepm from age to agelim
3369: nstepm is the number of stepm from age to agelin.
3370: Look at hpijx to understand the reason of that which relies in memory size
3371: and note for a fixed period like estepm months */
3372: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3373: survival function given by stepm (the optimization length). Unfortunately it
3374: means that if the survival funtion is printed only each two years of age and if
3375: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3376: results. So we changed our mind and took the option of the best precision.
3377: */
3378: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3379:
3380: /* If stepm=6 months */
3381: /* nhstepm age range expressed in number of stepm */
3382: agelim=AGESUP;
3383: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3384: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3385: /* if (stepm >= YEARM) hstepm=1;*/
3386: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3387:
3388: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3389: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3390: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3391: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3392: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3393: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3394:
3395: for (age=bage; age<=fage; age ++){
3396: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3397: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3398: /* if (stepm >= YEARM) hstepm=1;*/
3399: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3400:
3401: /* If stepm=6 months */
3402: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3403: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3404:
3405: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3406:
3407: /* Computing Variances of health expectancies */
3408: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3409: decrease memory allocation */
3410: for(theta=1; theta <=npar; theta++){
3411: for(i=1; i<=npar; i++){
3412: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3413: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3414: }
3415: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3416: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3417:
3418: for(j=1; j<= nlstate; j++){
3419: for(i=1; i<=nlstate; i++){
3420: for(h=0; h<=nhstepm-1; h++){
3421: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3422: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3423: }
3424: }
3425: }
3426:
3427: for(ij=1; ij<= nlstate*nlstate; ij++)
3428: for(h=0; h<=nhstepm-1; h++){
3429: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3430: }
3431: }/* End theta */
3432:
3433:
3434: for(h=0; h<=nhstepm-1; h++)
3435: for(j=1; j<=nlstate*nlstate;j++)
3436: for(theta=1; theta <=npar; theta++)
3437: trgradg[h][j][theta]=gradg[h][theta][j];
3438:
3439:
3440: for(ij=1;ij<=nlstate*nlstate;ij++)
3441: for(ji=1;ji<=nlstate*nlstate;ji++)
3442: varhe[ij][ji][(int)age] =0.;
3443:
3444: printf("%d|",(int)age);fflush(stdout);
3445: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3446: for(h=0;h<=nhstepm-1;h++){
3447: for(k=0;k<=nhstepm-1;k++){
3448: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3449: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3450: for(ij=1;ij<=nlstate*nlstate;ij++)
3451: for(ji=1;ji<=nlstate*nlstate;ji++)
3452: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3453: }
3454: }
3455:
3456: /* Computing expectancies */
3457: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3458: for(i=1; i<=nlstate;i++)
3459: for(j=1; j<=nlstate;j++)
3460: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3461: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3462:
3463: /* 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]);*/
3464:
3465: }
3466:
3467: fprintf(ficresstdeij,"%3.0f",age );
3468: for(i=1; i<=nlstate;i++){
3469: eip=0.;
3470: vip=0.;
3471: for(j=1; j<=nlstate;j++){
3472: eip += eij[i][j][(int)age];
3473: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3474: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3475: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3476: }
3477: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3478: }
3479: fprintf(ficresstdeij,"\n");
3480:
3481: fprintf(ficrescveij,"%3.0f",age );
3482: for(i=1; i<=nlstate;i++)
3483: for(j=1; j<=nlstate;j++){
3484: cptj= (j-1)*nlstate+i;
3485: for(i2=1; i2<=nlstate;i2++)
3486: for(j2=1; j2<=nlstate;j2++){
3487: cptj2= (j2-1)*nlstate+i2;
3488: if(cptj2 <= cptj)
3489: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3490: }
3491: }
3492: fprintf(ficrescveij,"\n");
3493:
3494: }
3495: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3496: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3497: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3498: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3499: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3500: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3501: printf("\n");
3502: fprintf(ficlog,"\n");
3503:
3504: free_vector(xm,1,npar);
3505: free_vector(xp,1,npar);
3506: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3507: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3508: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3509: }
3510:
3511: /************ Variance ******************/
3512: 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[])
3513: {
3514: /* Variance of health expectancies */
3515: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3516: /* double **newm;*/
1.169 brouard 3517: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
3518:
3519: int movingaverage();
1.126 brouard 3520: double **dnewm,**doldm;
3521: double **dnewmp,**doldmp;
3522: int i, j, nhstepm, hstepm, h, nstepm ;
1.164 brouard 3523: int k;
1.126 brouard 3524: double *xp;
3525: double **gp, **gm; /* for var eij */
3526: double ***gradg, ***trgradg; /*for var eij */
3527: double **gradgp, **trgradgp; /* for var p point j */
3528: double *gpp, *gmp; /* for var p point j */
3529: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3530: double ***p3mat;
3531: double age,agelim, hf;
3532: double ***mobaverage;
3533: int theta;
3534: char digit[4];
3535: char digitp[25];
3536:
3537: char fileresprobmorprev[FILENAMELENGTH];
3538:
3539: if(popbased==1){
3540: if(mobilav!=0)
3541: strcpy(digitp,"-populbased-mobilav-");
3542: else strcpy(digitp,"-populbased-nomobil-");
3543: }
3544: else
3545: strcpy(digitp,"-stablbased-");
3546:
3547: if (mobilav!=0) {
3548: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3549: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3550: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3551: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3552: }
3553: }
3554:
3555: strcpy(fileresprobmorprev,"prmorprev");
3556: sprintf(digit,"%-d",ij);
3557: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3558: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3559: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
3560: strcat(fileresprobmorprev,fileres);
3561: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3562: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3563: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3564: }
3565: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3566:
3567: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3568: pstamp(ficresprobmorprev);
3569: 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);
3570: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3571: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3572: fprintf(ficresprobmorprev," p.%-d SE",j);
3573: for(i=1; i<=nlstate;i++)
3574: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3575: }
3576: fprintf(ficresprobmorprev,"\n");
3577: fprintf(ficgp,"\n# Routine varevsij");
3578: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
3579: 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");
3580: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3581: /* } */
3582: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3583: pstamp(ficresvij);
3584: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3585: if(popbased==1)
1.128 brouard 3586: fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
1.126 brouard 3587: else
3588: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3589: fprintf(ficresvij,"# Age");
3590: for(i=1; i<=nlstate;i++)
3591: for(j=1; j<=nlstate;j++)
3592: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3593: fprintf(ficresvij,"\n");
3594:
3595: xp=vector(1,npar);
3596: dnewm=matrix(1,nlstate,1,npar);
3597: doldm=matrix(1,nlstate,1,nlstate);
3598: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3599: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3600:
3601: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3602: gpp=vector(nlstate+1,nlstate+ndeath);
3603: gmp=vector(nlstate+1,nlstate+ndeath);
3604: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3605:
3606: if(estepm < stepm){
3607: printf ("Problem %d lower than %d\n",estepm, stepm);
3608: }
3609: else hstepm=estepm;
3610: /* For example we decided to compute the life expectancy with the smallest unit */
3611: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3612: nhstepm is the number of hstepm from age to agelim
3613: nstepm is the number of stepm from age to agelin.
1.128 brouard 3614: Look at function hpijx to understand why (it is linked to memory size questions) */
1.126 brouard 3615: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3616: survival function given by stepm (the optimization length). Unfortunately it
3617: means that if the survival funtion is printed every two years of age and if
3618: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3619: results. So we changed our mind and took the option of the best precision.
3620: */
3621: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3622: agelim = AGESUP;
3623: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3624: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3625: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3626: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3627: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3628: gp=matrix(0,nhstepm,1,nlstate);
3629: gm=matrix(0,nhstepm,1,nlstate);
3630:
3631:
3632: for(theta=1; theta <=npar; theta++){
3633: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3634: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3635: }
3636: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3637: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3638:
3639: if (popbased==1) {
3640: if(mobilav ==0){
3641: for(i=1; i<=nlstate;i++)
3642: prlim[i][i]=probs[(int)age][i][ij];
3643: }else{ /* mobilav */
3644: for(i=1; i<=nlstate;i++)
3645: prlim[i][i]=mobaverage[(int)age][i][ij];
3646: }
3647: }
3648:
3649: for(j=1; j<= nlstate; j++){
3650: for(h=0; h<=nhstepm; h++){
3651: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3652: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3653: }
3654: }
3655: /* This for computing probability of death (h=1 means
3656: computed over hstepm matrices product = hstepm*stepm months)
3657: as a weighted average of prlim.
3658: */
3659: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3660: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3661: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3662: }
3663: /* end probability of death */
3664:
3665: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3666: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3667: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3668: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3669:
3670: if (popbased==1) {
3671: if(mobilav ==0){
3672: for(i=1; i<=nlstate;i++)
3673: prlim[i][i]=probs[(int)age][i][ij];
3674: }else{ /* mobilav */
3675: for(i=1; i<=nlstate;i++)
3676: prlim[i][i]=mobaverage[(int)age][i][ij];
3677: }
3678: }
3679:
1.128 brouard 3680: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
1.126 brouard 3681: for(h=0; h<=nhstepm; h++){
3682: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3683: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3684: }
3685: }
3686: /* This for computing probability of death (h=1 means
3687: computed over hstepm matrices product = hstepm*stepm months)
3688: as a weighted average of prlim.
3689: */
3690: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3691: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3692: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3693: }
3694: /* end probability of death */
3695:
3696: for(j=1; j<= nlstate; j++) /* vareij */
3697: for(h=0; h<=nhstepm; h++){
3698: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3699: }
3700:
3701: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3702: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3703: }
3704:
3705: } /* End theta */
3706:
3707: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3708:
3709: for(h=0; h<=nhstepm; h++) /* veij */
3710: for(j=1; j<=nlstate;j++)
3711: for(theta=1; theta <=npar; theta++)
3712: trgradg[h][j][theta]=gradg[h][theta][j];
3713:
3714: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3715: for(theta=1; theta <=npar; theta++)
3716: trgradgp[j][theta]=gradgp[theta][j];
3717:
3718:
3719: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3720: for(i=1;i<=nlstate;i++)
3721: for(j=1;j<=nlstate;j++)
3722: vareij[i][j][(int)age] =0.;
3723:
3724: for(h=0;h<=nhstepm;h++){
3725: for(k=0;k<=nhstepm;k++){
3726: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3727: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3728: for(i=1;i<=nlstate;i++)
3729: for(j=1;j<=nlstate;j++)
3730: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3731: }
3732: }
3733:
3734: /* pptj */
3735: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3736: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3737: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3738: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3739: varppt[j][i]=doldmp[j][i];
3740: /* end ppptj */
3741: /* x centered again */
3742: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3743: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3744:
3745: if (popbased==1) {
3746: if(mobilav ==0){
3747: for(i=1; i<=nlstate;i++)
3748: prlim[i][i]=probs[(int)age][i][ij];
3749: }else{ /* mobilav */
3750: for(i=1; i<=nlstate;i++)
3751: prlim[i][i]=mobaverage[(int)age][i][ij];
3752: }
3753: }
3754:
3755: /* This for computing probability of death (h=1 means
3756: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3757: as a weighted average of prlim.
3758: */
3759: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3760: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3761: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3762: }
3763: /* end probability of death */
3764:
3765: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3766: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3767: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3768: for(i=1; i<=nlstate;i++){
3769: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3770: }
3771: }
3772: fprintf(ficresprobmorprev,"\n");
3773:
3774: fprintf(ficresvij,"%.0f ",age );
3775: for(i=1; i<=nlstate;i++)
3776: for(j=1; j<=nlstate;j++){
3777: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3778: }
3779: fprintf(ficresvij,"\n");
3780: free_matrix(gp,0,nhstepm,1,nlstate);
3781: free_matrix(gm,0,nhstepm,1,nlstate);
3782: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3783: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3784: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3785: } /* End age */
3786: free_vector(gpp,nlstate+1,nlstate+ndeath);
3787: free_vector(gmp,nlstate+1,nlstate+ndeath);
3788: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3789: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.145 brouard 3790: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
1.126 brouard 3791: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
1.131 brouard 3792: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.126 brouard 3793: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3794: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3795: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.145 brouard 3796: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
1.170 brouard 3797: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
1.145 brouard 3798: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
1.126 brouard 3799: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3800: 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);
3801: /* 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);
3802: */
3803: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3804: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3805:
3806: free_vector(xp,1,npar);
3807: free_matrix(doldm,1,nlstate,1,nlstate);
3808: free_matrix(dnewm,1,nlstate,1,npar);
3809: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3810: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3811: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3812: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3813: fclose(ficresprobmorprev);
3814: fflush(ficgp);
3815: fflush(fichtm);
3816: } /* end varevsij */
3817:
3818: /************ Variance of prevlim ******************/
3819: 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[])
3820: {
3821: /* Variance of prevalence limit */
3822: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 3823:
1.126 brouard 3824: double **dnewm,**doldm;
3825: int i, j, nhstepm, hstepm;
3826: double *xp;
3827: double *gp, *gm;
3828: double **gradg, **trgradg;
3829: double age,agelim;
3830: int theta;
3831:
3832: pstamp(ficresvpl);
3833: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3834: fprintf(ficresvpl,"# Age");
3835: for(i=1; i<=nlstate;i++)
3836: fprintf(ficresvpl," %1d-%1d",i,i);
3837: fprintf(ficresvpl,"\n");
3838:
3839: xp=vector(1,npar);
3840: dnewm=matrix(1,nlstate,1,npar);
3841: doldm=matrix(1,nlstate,1,nlstate);
3842:
3843: hstepm=1*YEARM; /* Every year of age */
3844: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3845: agelim = AGESUP;
3846: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3847: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3848: if (stepm >= YEARM) hstepm=1;
3849: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3850: gradg=matrix(1,npar,1,nlstate);
3851: gp=vector(1,nlstate);
3852: gm=vector(1,nlstate);
3853:
3854: for(theta=1; theta <=npar; theta++){
3855: for(i=1; i<=npar; i++){ /* Computes gradient */
3856: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3857: }
3858: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3859: for(i=1;i<=nlstate;i++)
3860: gp[i] = prlim[i][i];
3861:
3862: for(i=1; i<=npar; i++) /* Computes gradient */
3863: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3864: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3865: for(i=1;i<=nlstate;i++)
3866: gm[i] = prlim[i][i];
3867:
3868: for(i=1;i<=nlstate;i++)
3869: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3870: } /* End theta */
3871:
3872: trgradg =matrix(1,nlstate,1,npar);
3873:
3874: for(j=1; j<=nlstate;j++)
3875: for(theta=1; theta <=npar; theta++)
3876: trgradg[j][theta]=gradg[theta][j];
3877:
3878: for(i=1;i<=nlstate;i++)
3879: varpl[i][(int)age] =0.;
3880: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3881: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3882: for(i=1;i<=nlstate;i++)
3883: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3884:
3885: fprintf(ficresvpl,"%.0f ",age );
3886: for(i=1; i<=nlstate;i++)
3887: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3888: fprintf(ficresvpl,"\n");
3889: free_vector(gp,1,nlstate);
3890: free_vector(gm,1,nlstate);
3891: free_matrix(gradg,1,npar,1,nlstate);
3892: free_matrix(trgradg,1,nlstate,1,npar);
3893: } /* End age */
3894:
3895: free_vector(xp,1,npar);
3896: free_matrix(doldm,1,nlstate,1,npar);
3897: free_matrix(dnewm,1,nlstate,1,nlstate);
3898:
3899: }
3900:
3901: /************ Variance of one-step probabilities ******************/
3902: 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[])
3903: {
1.164 brouard 3904: int i, j=0, k1, l1, tj;
1.126 brouard 3905: int k2, l2, j1, z1;
1.164 brouard 3906: int k=0, l;
1.145 brouard 3907: int first=1, first1, first2;
1.126 brouard 3908: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3909: double **dnewm,**doldm;
3910: double *xp;
3911: double *gp, *gm;
3912: double **gradg, **trgradg;
3913: double **mu;
1.164 brouard 3914: double age, cov[NCOVMAX+1];
1.126 brouard 3915: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3916: int theta;
3917: char fileresprob[FILENAMELENGTH];
3918: char fileresprobcov[FILENAMELENGTH];
3919: char fileresprobcor[FILENAMELENGTH];
3920: double ***varpij;
3921:
3922: strcpy(fileresprob,"prob");
3923: strcat(fileresprob,fileres);
3924: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3925: printf("Problem with resultfile: %s\n", fileresprob);
3926: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3927: }
3928: strcpy(fileresprobcov,"probcov");
3929: strcat(fileresprobcov,fileres);
3930: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3931: printf("Problem with resultfile: %s\n", fileresprobcov);
3932: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3933: }
3934: strcpy(fileresprobcor,"probcor");
3935: strcat(fileresprobcor,fileres);
3936: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3937: printf("Problem with resultfile: %s\n", fileresprobcor);
3938: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3939: }
3940: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3941: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3942: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3943: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3944: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3945: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3946: pstamp(ficresprob);
3947: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3948: fprintf(ficresprob,"# Age");
3949: pstamp(ficresprobcov);
3950: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3951: fprintf(ficresprobcov,"# Age");
3952: pstamp(ficresprobcor);
3953: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3954: fprintf(ficresprobcor,"# Age");
3955:
3956:
3957: for(i=1; i<=nlstate;i++)
3958: for(j=1; j<=(nlstate+ndeath);j++){
3959: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3960: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3961: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3962: }
3963: /* fprintf(ficresprob,"\n");
3964: fprintf(ficresprobcov,"\n");
3965: fprintf(ficresprobcor,"\n");
3966: */
1.131 brouard 3967: xp=vector(1,npar);
1.126 brouard 3968: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3969: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3970: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3971: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3972: first=1;
3973: fprintf(ficgp,"\n# Routine varprob");
3974: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3975: fprintf(fichtm,"\n");
3976:
3977: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3978: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3979: file %s<br>\n",optionfilehtmcov);
3980: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3981: and drawn. It helps understanding how is the covariance between two incidences.\
3982: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3983: 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. \
3984: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3985: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3986: standard deviations wide on each axis. <br>\
3987: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3988: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3989: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3990:
3991: cov[1]=1;
1.145 brouard 3992: /* tj=cptcoveff; */
3993: tj = (int) pow(2,cptcoveff);
1.126 brouard 3994: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3995: j1=0;
1.145 brouard 3996: for(j1=1; j1<=tj;j1++){
3997: /*for(i1=1; i1<=ncodemax[t];i1++){ */
3998: /*j1++;*/
1.126 brouard 3999: if (cptcovn>0) {
4000: fprintf(ficresprob, "\n#********** Variable ");
4001: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4002: fprintf(ficresprob, "**********\n#\n");
4003: fprintf(ficresprobcov, "\n#********** Variable ");
4004: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4005: fprintf(ficresprobcov, "**********\n#\n");
4006:
4007: fprintf(ficgp, "\n#********** Variable ");
4008: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4009: fprintf(ficgp, "**********\n#\n");
4010:
4011:
4012: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
4013: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4014: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
4015:
4016: fprintf(ficresprobcor, "\n#********** Variable ");
4017: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4018: fprintf(ficresprobcor, "**********\n#");
4019: }
4020:
1.145 brouard 4021: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
4022: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4023: gp=vector(1,(nlstate)*(nlstate+ndeath));
4024: gm=vector(1,(nlstate)*(nlstate+ndeath));
1.126 brouard 4025: for (age=bage; age<=fage; age ++){
4026: cov[2]=age;
4027: for (k=1; k<=cptcovn;k++) {
1.145 brouard 4028: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
4029: * 1 1 1 1 1
4030: * 2 2 1 1 1
4031: * 3 1 2 1 1
4032: */
4033: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
1.126 brouard 4034: }
4035: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
4036: for (k=1; k<=cptcovprod;k++)
4037: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
4038:
4039:
4040: for(theta=1; theta <=npar; theta++){
4041: for(i=1; i<=npar; i++)
4042: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
4043:
4044: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4045:
4046: k=0;
4047: for(i=1; i<= (nlstate); i++){
4048: for(j=1; j<=(nlstate+ndeath);j++){
4049: k=k+1;
4050: gp[k]=pmmij[i][j];
4051: }
4052: }
4053:
4054: for(i=1; i<=npar; i++)
4055: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
4056:
4057: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4058: k=0;
4059: for(i=1; i<=(nlstate); i++){
4060: for(j=1; j<=(nlstate+ndeath);j++){
4061: k=k+1;
4062: gm[k]=pmmij[i][j];
4063: }
4064: }
4065:
4066: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
4067: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
4068: }
4069:
4070: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
4071: for(theta=1; theta <=npar; theta++)
4072: trgradg[j][theta]=gradg[theta][j];
4073:
4074: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
4075: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
4076:
4077: pmij(pmmij,cov,ncovmodel,x,nlstate);
4078:
4079: k=0;
4080: for(i=1; i<=(nlstate); i++){
4081: for(j=1; j<=(nlstate+ndeath);j++){
4082: k=k+1;
4083: mu[k][(int) age]=pmmij[i][j];
4084: }
4085: }
4086: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
4087: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
4088: varpij[i][j][(int)age] = doldm[i][j];
4089:
4090: /*printf("\n%d ",(int)age);
4091: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4092: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4093: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4094: }*/
4095:
4096: fprintf(ficresprob,"\n%d ",(int)age);
4097: fprintf(ficresprobcov,"\n%d ",(int)age);
4098: fprintf(ficresprobcor,"\n%d ",(int)age);
4099:
4100: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
4101: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
4102: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4103: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
4104: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
4105: }
4106: i=0;
4107: for (k=1; k<=(nlstate);k++){
4108: for (l=1; l<=(nlstate+ndeath);l++){
1.145 brouard 4109: i++;
1.126 brouard 4110: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
4111: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
4112: for (j=1; j<=i;j++){
1.145 brouard 4113: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
1.126 brouard 4114: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
4115: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
4116: }
4117: }
4118: }/* end of loop for state */
4119: } /* end of loop for age */
1.145 brouard 4120: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
4121: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
4122: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4123: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4124:
1.126 brouard 4125: /* Confidence intervalle of pij */
4126: /*
1.131 brouard 4127: fprintf(ficgp,"\nunset parametric;unset label");
1.126 brouard 4128: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
4129: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
4130: 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);
4131: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
4132: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
4133: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
4134: */
4135:
4136: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
1.145 brouard 4137: first1=1;first2=2;
1.126 brouard 4138: for (k2=1; k2<=(nlstate);k2++){
4139: for (l2=1; l2<=(nlstate+ndeath);l2++){
4140: if(l2==k2) continue;
4141: j=(k2-1)*(nlstate+ndeath)+l2;
4142: for (k1=1; k1<=(nlstate);k1++){
4143: for (l1=1; l1<=(nlstate+ndeath);l1++){
4144: if(l1==k1) continue;
4145: i=(k1-1)*(nlstate+ndeath)+l1;
4146: if(i<=j) continue;
4147: for (age=bage; age<=fage; age ++){
4148: if ((int)age %5==0){
4149: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
4150: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
4151: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
4152: mu1=mu[i][(int) age]/stepm*YEARM ;
4153: mu2=mu[j][(int) age]/stepm*YEARM;
4154: c12=cv12/sqrt(v1*v2);
4155: /* Computing eigen value of matrix of covariance */
4156: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4157: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
1.135 brouard 4158: if ((lc2 <0) || (lc1 <0) ){
1.145 brouard 4159: if(first2==1){
4160: first1=0;
4161: 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);
4162: }
4163: 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);
4164: /* lc1=fabs(lc1); */ /* If we want to have them positive */
4165: /* lc2=fabs(lc2); */
1.135 brouard 4166: }
4167:
1.126 brouard 4168: /* Eigen vectors */
4169: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
4170: /*v21=sqrt(1.-v11*v11); *//* error */
4171: v21=(lc1-v1)/cv12*v11;
4172: v12=-v21;
4173: v22=v11;
4174: tnalp=v21/v11;
4175: if(first1==1){
4176: first1=0;
4177: 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);
4178: }
4179: 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);
4180: /*printf(fignu*/
4181: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
4182: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
4183: if(first==1){
4184: first=0;
4185: fprintf(ficgp,"\nset parametric;unset label");
4186: fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
1.145 brouard 4187: fprintf(ficgp,"\nset ter png small size 320, 240");
1.126 brouard 4188: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
4189: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
4190: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
4191: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
4192: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4193: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4194: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
4195: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4196: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4197: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4198: 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",\
4199: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4200: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4201: }else{
4202: first=0;
4203: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4204: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4205: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4206: 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",\
4207: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4208: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4209: }/* if first */
4210: } /* age mod 5 */
4211: } /* end loop age */
4212: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4213: first=1;
4214: } /*l12 */
4215: } /* k12 */
4216: } /*l1 */
4217: }/* k1 */
1.169 brouard 4218: /* } */ /* loop covariates */
1.126 brouard 4219: }
4220: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4221: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4222: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4223: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4224: free_vector(xp,1,npar);
4225: fclose(ficresprob);
4226: fclose(ficresprobcov);
4227: fclose(ficresprobcor);
4228: fflush(ficgp);
4229: fflush(fichtmcov);
4230: }
4231:
4232:
4233: /******************* Printing html file ***********/
4234: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
4235: int lastpass, int stepm, int weightopt, char model[],\
4236: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
4237: int popforecast, int estepm ,\
4238: double jprev1, double mprev1,double anprev1, \
4239: double jprev2, double mprev2,double anprev2){
4240: int jj1, k1, i1, cpt;
4241:
4242: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4243: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4244: </ul>");
4245: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
4246: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
4247: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
4248: fprintf(fichtm,"\
4249: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
4250: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
4251: fprintf(fichtm,"\
4252: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
4253: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
4254: fprintf(fichtm,"\
1.128 brouard 4255: - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
1.126 brouard 4256: <a href=\"%s\">%s</a> <br>\n",
4257: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
4258: fprintf(fichtm,"\
4259: - Population projections by age and states: \
4260: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
4261:
4262: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4263:
1.145 brouard 4264: m=pow(2,cptcoveff);
1.126 brouard 4265: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4266:
4267: jj1=0;
4268: for(k1=1; k1<=m;k1++){
4269: for(i1=1; i1<=ncodemax[k1];i1++){
4270: jj1++;
4271: if (cptcovn > 0) {
4272: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4273: for (cpt=1; cpt<=cptcoveff;cpt++)
4274: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4275: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4276: }
4277: /* Pij */
1.145 brouard 4278: 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> \
4279: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.126 brouard 4280: /* Quasi-incidences */
4281: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.145 brouard 4282: 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> \
4283: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.126 brouard 4284: /* Period (stable) prevalence in each health state */
1.154 brouard 4285: for(cpt=1; cpt<=nlstate;cpt++){
1.166 brouard 4286: 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> \
4287: <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
1.126 brouard 4288: }
4289: for(cpt=1; cpt<=nlstate;cpt++) {
1.154 brouard 4290: 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> \
4291: <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
1.126 brouard 4292: }
4293: } /* end i1 */
4294: }/* End k1 */
4295: fprintf(fichtm,"</ul>");
4296:
4297:
4298: fprintf(fichtm,"\
4299: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
4300: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
4301:
4302: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4303: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
4304: fprintf(fichtm,"\
4305: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4306: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
4307:
4308: fprintf(fichtm,"\
4309: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4310: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
4311: fprintf(fichtm,"\
4312: - 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): \
4313: <a href=\"%s\">%s</a> <br>\n</li>",
4314: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
4315: fprintf(fichtm,"\
4316: - (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): \
4317: <a href=\"%s\">%s</a> <br>\n</li>",
4318: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
4319: fprintf(fichtm,"\
1.128 brouard 4320: - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
1.126 brouard 4321: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
4322: fprintf(fichtm,"\
1.128 brouard 4323: - 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",
4324: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
1.126 brouard 4325: fprintf(fichtm,"\
4326: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
4327: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
4328:
4329: /* if(popforecast==1) fprintf(fichtm,"\n */
4330: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4331: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4332: /* <br>",fileres,fileres,fileres,fileres); */
4333: /* else */
4334: /* 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); */
4335: fflush(fichtm);
4336: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4337:
1.145 brouard 4338: m=pow(2,cptcoveff);
1.126 brouard 4339: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4340:
4341: jj1=0;
4342: for(k1=1; k1<=m;k1++){
4343: for(i1=1; i1<=ncodemax[k1];i1++){
4344: jj1++;
4345: if (cptcovn > 0) {
4346: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4347: for (cpt=1; cpt<=cptcoveff;cpt++)
4348: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4349: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4350: }
4351: for(cpt=1; cpt<=nlstate;cpt++) {
4352: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
1.145 brouard 4353: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
4354: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
1.126 brouard 4355: }
4356: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 4357: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4358: true period expectancies (those weighted with period prevalences are also\
4359: drawn in addition to the population based expectancies computed using\
4360: observed and cahotic prevalences: %s%d.png<br>\
1.126 brouard 4361: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
4362: } /* end i1 */
4363: }/* End k1 */
4364: fprintf(fichtm,"</ul>");
4365: fflush(fichtm);
4366: }
4367:
4368: /******************* Gnuplot file **************/
4369: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4370:
4371: char dirfileres[132],optfileres[132];
1.164 brouard 4372: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
1.130 brouard 4373: int ng=0;
1.126 brouard 4374: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4375: /* printf("Problem with file %s",optionfilegnuplot); */
4376: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4377: /* } */
4378:
4379: /*#ifdef windows */
4380: fprintf(ficgp,"cd \"%s\" \n",pathc);
4381: /*#endif */
4382: m=pow(2,cptcoveff);
4383:
4384: strcpy(dirfileres,optionfilefiname);
4385: strcpy(optfileres,"vpl");
4386: /* 1eme*/
1.153 brouard 4387: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
1.126 brouard 4388: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.145 brouard 4389: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
4390: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
4391: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
1.126 brouard 4392: fprintf(ficgp,"set xlabel \"Age\" \n\
4393: set ylabel \"Probability\" \n\
1.145 brouard 4394: set ter png small size 320, 240\n\
1.170 brouard 4395: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126 brouard 4396:
4397: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4398: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4399: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4400: }
1.170 brouard 4401: fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126 brouard 4402: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4403: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4404: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4405: }
1.170 brouard 4406: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126 brouard 4407: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4408: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4409: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4410: }
1.145 brouard 4411: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
1.126 brouard 4412: }
4413: }
4414: /*2 eme*/
1.153 brouard 4415: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
1.126 brouard 4416: for (k1=1; k1<= m ; k1 ++) {
4417: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
1.145 brouard 4418: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
1.126 brouard 4419:
4420: for (i=1; i<= nlstate+1 ; i ++) {
4421: k=2*i;
1.170 brouard 4422: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126 brouard 4423: for (j=1; j<= nlstate+1 ; j ++) {
1.170 brouard 4424: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4425: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4426: }
4427: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
4428: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
1.170 brouard 4429: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126 brouard 4430: for (j=1; j<= nlstate+1 ; j ++) {
1.170 brouard 4431: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4432: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4433: }
1.145 brouard 4434: fprintf(ficgp,"\" t\"\" w l lt 0,");
1.170 brouard 4435: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126 brouard 4436: for (j=1; j<= nlstate+1 ; j ++) {
1.170 brouard 4437: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4438: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4439: }
1.145 brouard 4440: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4441: else fprintf(ficgp,"\" t\"\" w l lt 0,");
1.126 brouard 4442: }
4443: }
4444:
4445: /*3eme*/
4446:
4447: for (k1=1; k1<= m ; k1 ++) {
4448: for (cpt=1; cpt<= nlstate ; cpt ++) {
4449: /* k=2+nlstate*(2*cpt-2); */
4450: k=2+(nlstate+1)*(cpt-1);
4451: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
1.145 brouard 4452: fprintf(ficgp,"set ter png small size 320, 240\n\
1.126 brouard 4453: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
4454: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4455: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4456: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4457: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4458: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4459: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4460:
4461: */
4462: for (i=1; i< nlstate ; i ++) {
4463: 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);
4464: /* 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);*/
4465:
4466: }
4467: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
4468: }
4469: }
4470:
4471: /* CV preval stable (period) */
1.153 brouard 4472: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
4473: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.126 brouard 4474: k=3;
1.153 brouard 4475: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
1.145 brouard 4476: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
1.126 brouard 4477: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.145 brouard 4478: set ter png small size 320, 240\n\
1.126 brouard 4479: unset log y\n\
1.153 brouard 4480: plot [%.f:%.f] ", ageminpar, agemaxpar);
4481: for (i=1; i<= nlstate ; i ++){
4482: if(i==1)
4483: fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
4484: else
4485: fprintf(ficgp,", '' ");
1.154 brouard 4486: l=(nlstate+ndeath)*(i-1)+1;
4487: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
1.153 brouard 4488: for (j=1; j<= (nlstate-1) ; j ++)
4489: fprintf(ficgp,"+$%d",k+l+j);
4490: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
4491: } /* nlstate */
4492: fprintf(ficgp,"\n");
4493: } /* end cpt state*/
4494: } /* end covariate */
1.126 brouard 4495:
4496: /* proba elementaires */
4497: for(i=1,jk=1; i <=nlstate; i++){
4498: for(k=1; k <=(nlstate+ndeath); k++){
4499: if (k != i) {
4500: for(j=1; j <=ncovmodel; j++){
4501: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
4502: jk++;
4503: fprintf(ficgp,"\n");
4504: }
4505: }
4506: }
4507: }
1.145 brouard 4508: /*goto avoid;*/
1.126 brouard 4509: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
4510: for(jk=1; jk <=m; jk++) {
1.145 brouard 4511: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
1.126 brouard 4512: if (ng==2)
4513: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
4514: else
4515: fprintf(ficgp,"\nset title \"Probability\"\n");
1.145 brouard 4516: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
1.126 brouard 4517: i=1;
4518: for(k2=1; k2<=nlstate; k2++) {
4519: k3=i;
4520: for(k=1; k<=(nlstate+ndeath); k++) {
4521: if (k != k2){
4522: if(ng==2)
4523: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
4524: else
4525: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
1.141 brouard 4526: ij=1;/* To be checked else nbcode[0][0] wrong */
1.126 brouard 4527: for(j=3; j <=ncovmodel; j++) {
1.145 brouard 4528: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
4529: /* /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
4530: /* ij++; */
4531: /* } */
4532: /* else */
1.126 brouard 4533: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4534: }
4535: fprintf(ficgp,")/(1");
4536:
4537: for(k1=1; k1 <=nlstate; k1++){
4538: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
4539: ij=1;
4540: for(j=3; j <=ncovmodel; j++){
1.145 brouard 4541: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
4542: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
4543: /* ij++; */
4544: /* } */
4545: /* else */
1.126 brouard 4546: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4547: }
4548: fprintf(ficgp,")");
4549: }
4550: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
4551: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
4552: i=i+ncovmodel;
4553: }
4554: } /* end k */
4555: } /* end k2 */
4556: } /* end jk */
4557: } /* end ng */
1.164 brouard 4558: /* avoid: */
1.126 brouard 4559: fflush(ficgp);
4560: } /* end gnuplot */
4561:
4562:
4563: /*************** Moving average **************/
4564: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
4565:
4566: int i, cpt, cptcod;
4567: int modcovmax =1;
4568: int mobilavrange, mob;
4569: double age;
4570:
4571: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
4572: a covariate has 2 modalities */
4573: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
4574:
4575: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
4576: if(mobilav==1) mobilavrange=5; /* default */
4577: else mobilavrange=mobilav;
4578: for (age=bage; age<=fage; age++)
4579: for (i=1; i<=nlstate;i++)
4580: for (cptcod=1;cptcod<=modcovmax;cptcod++)
4581: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
4582: /* We keep the original values on the extreme ages bage, fage and for
4583: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
4584: we use a 5 terms etc. until the borders are no more concerned.
4585: */
4586: for (mob=3;mob <=mobilavrange;mob=mob+2){
4587: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
4588: for (i=1; i<=nlstate;i++){
4589: for (cptcod=1;cptcod<=modcovmax;cptcod++){
4590: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
4591: for (cpt=1;cpt<=(mob-1)/2;cpt++){
4592: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
4593: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
4594: }
4595: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
4596: }
4597: }
4598: }/* end age */
4599: }/* end mob */
4600: }else return -1;
4601: return 0;
4602: }/* End movingaverage */
4603:
4604:
4605: /************** Forecasting ******************/
1.169 brouard 4606: 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){
1.126 brouard 4607: /* proj1, year, month, day of starting projection
4608: agemin, agemax range of age
4609: dateprev1 dateprev2 range of dates during which prevalence is computed
4610: anproj2 year of en of projection (same day and month as proj1).
4611: */
1.164 brouard 4612: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
1.126 brouard 4613: double agec; /* generic age */
4614: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
4615: double *popeffectif,*popcount;
4616: double ***p3mat;
4617: double ***mobaverage;
4618: char fileresf[FILENAMELENGTH];
4619:
4620: agelim=AGESUP;
4621: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4622:
4623: strcpy(fileresf,"f");
4624: strcat(fileresf,fileres);
4625: if((ficresf=fopen(fileresf,"w"))==NULL) {
4626: printf("Problem with forecast resultfile: %s\n", fileresf);
4627: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
4628: }
4629: printf("Computing forecasting: result on file '%s' \n", fileresf);
4630: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
4631:
4632: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4633:
4634: if (mobilav!=0) {
4635: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4636: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4637: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4638: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4639: }
4640: }
4641:
4642: stepsize=(int) (stepm+YEARM-1)/YEARM;
4643: if (stepm<=12) stepsize=1;
4644: if(estepm < stepm){
4645: printf ("Problem %d lower than %d\n",estepm, stepm);
4646: }
4647: else hstepm=estepm;
4648:
4649: hstepm=hstepm/stepm;
4650: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
4651: fractional in yp1 */
4652: anprojmean=yp;
4653: yp2=modf((yp1*12),&yp);
4654: mprojmean=yp;
4655: yp1=modf((yp2*30.5),&yp);
4656: jprojmean=yp;
4657: if(jprojmean==0) jprojmean=1;
4658: if(mprojmean==0) jprojmean=1;
4659:
4660: i1=cptcoveff;
4661: if (cptcovn < 1){i1=1;}
4662:
4663: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4664:
4665: fprintf(ficresf,"#****** Routine prevforecast **\n");
4666:
4667: /* if (h==(int)(YEARM*yearp)){ */
4668: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4669: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4670: k=k+1;
4671: fprintf(ficresf,"\n#******");
4672: for(j=1;j<=cptcoveff;j++) {
4673: 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]]);
4674: }
4675: fprintf(ficresf,"******\n");
4676: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4677: for(j=1; j<=nlstate+ndeath;j++){
4678: for(i=1; i<=nlstate;i++)
4679: fprintf(ficresf," p%d%d",i,j);
4680: fprintf(ficresf," p.%d",j);
4681: }
4682: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4683: fprintf(ficresf,"\n");
4684: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4685:
4686: for (agec=fage; agec>=(ageminpar-1); agec--){
4687: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4688: nhstepm = nhstepm/hstepm;
4689: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4690: oldm=oldms;savm=savms;
4691: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4692:
4693: for (h=0; h<=nhstepm; h++){
4694: if (h*hstepm/YEARM*stepm ==yearp) {
4695: fprintf(ficresf,"\n");
4696: for(j=1;j<=cptcoveff;j++)
4697: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4698: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4699: }
4700: for(j=1; j<=nlstate+ndeath;j++) {
4701: ppij=0.;
4702: for(i=1; i<=nlstate;i++) {
4703: if (mobilav==1)
4704: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4705: else {
4706: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4707: }
4708: if (h*hstepm/YEARM*stepm== yearp) {
4709: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4710: }
4711: } /* end i */
4712: if (h*hstepm/YEARM*stepm==yearp) {
4713: fprintf(ficresf," %.3f", ppij);
4714: }
4715: }/* end j */
4716: } /* end h */
4717: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4718: } /* end agec */
4719: } /* end yearp */
4720: } /* end cptcod */
4721: } /* end cptcov */
4722:
4723: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4724:
4725: fclose(ficresf);
4726: }
4727:
4728: /************** Forecasting *****not tested NB*************/
1.169 brouard 4729: 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){
1.126 brouard 4730:
4731: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4732: int *popage;
4733: double calagedatem, agelim, kk1, kk2;
4734: double *popeffectif,*popcount;
4735: double ***p3mat,***tabpop,***tabpopprev;
4736: double ***mobaverage;
4737: char filerespop[FILENAMELENGTH];
4738:
4739: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4740: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4741: agelim=AGESUP;
4742: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4743:
4744: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4745:
4746:
4747: strcpy(filerespop,"pop");
4748: strcat(filerespop,fileres);
4749: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4750: printf("Problem with forecast resultfile: %s\n", filerespop);
4751: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4752: }
4753: printf("Computing forecasting: result on file '%s' \n", filerespop);
4754: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4755:
4756: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4757:
4758: if (mobilav!=0) {
4759: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4760: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4761: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4762: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4763: }
4764: }
4765:
4766: stepsize=(int) (stepm+YEARM-1)/YEARM;
4767: if (stepm<=12) stepsize=1;
4768:
4769: agelim=AGESUP;
4770:
4771: hstepm=1;
4772: hstepm=hstepm/stepm;
4773:
4774: if (popforecast==1) {
4775: if((ficpop=fopen(popfile,"r"))==NULL) {
4776: printf("Problem with population file : %s\n",popfile);exit(0);
4777: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4778: }
4779: popage=ivector(0,AGESUP);
4780: popeffectif=vector(0,AGESUP);
4781: popcount=vector(0,AGESUP);
4782:
4783: i=1;
4784: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4785:
4786: imx=i;
4787: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4788: }
4789:
4790: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4791: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4792: k=k+1;
4793: fprintf(ficrespop,"\n#******");
4794: for(j=1;j<=cptcoveff;j++) {
4795: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4796: }
4797: fprintf(ficrespop,"******\n");
4798: fprintf(ficrespop,"# Age");
4799: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4800: if (popforecast==1) fprintf(ficrespop," [Population]");
4801:
4802: for (cpt=0; cpt<=0;cpt++) {
4803: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4804:
4805: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4806: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4807: nhstepm = nhstepm/hstepm;
4808:
4809: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4810: oldm=oldms;savm=savms;
4811: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4812:
4813: for (h=0; h<=nhstepm; h++){
4814: if (h==(int) (calagedatem+YEARM*cpt)) {
4815: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4816: }
4817: for(j=1; j<=nlstate+ndeath;j++) {
4818: kk1=0.;kk2=0;
4819: for(i=1; i<=nlstate;i++) {
4820: if (mobilav==1)
4821: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4822: else {
4823: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4824: }
4825: }
4826: if (h==(int)(calagedatem+12*cpt)){
4827: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4828: /*fprintf(ficrespop," %.3f", kk1);
4829: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4830: }
4831: }
4832: for(i=1; i<=nlstate;i++){
4833: kk1=0.;
4834: for(j=1; j<=nlstate;j++){
4835: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4836: }
4837: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
4838: }
4839:
4840: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
4841: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4842: }
4843: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4844: }
4845: }
4846:
4847: /******/
4848:
4849: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4850: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4851: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4852: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4853: nhstepm = nhstepm/hstepm;
4854:
4855: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4856: oldm=oldms;savm=savms;
4857: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4858: for (h=0; h<=nhstepm; h++){
4859: if (h==(int) (calagedatem+YEARM*cpt)) {
4860: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4861: }
4862: for(j=1; j<=nlstate+ndeath;j++) {
4863: kk1=0.;kk2=0;
4864: for(i=1; i<=nlstate;i++) {
4865: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4866: }
4867: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
4868: }
4869: }
4870: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4871: }
4872: }
4873: }
4874: }
4875:
4876: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4877:
4878: if (popforecast==1) {
4879: free_ivector(popage,0,AGESUP);
4880: free_vector(popeffectif,0,AGESUP);
4881: free_vector(popcount,0,AGESUP);
4882: }
4883: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4884: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4885: fclose(ficrespop);
4886: } /* End of popforecast */
4887:
4888: int fileappend(FILE *fichier, char *optionfich)
4889: {
4890: if((fichier=fopen(optionfich,"a"))==NULL) {
4891: printf("Problem with file: %s\n", optionfich);
4892: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4893: return (0);
4894: }
4895: fflush(fichier);
4896: return (1);
4897: }
4898:
4899:
4900: /**************** function prwizard **********************/
4901: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4902: {
4903:
4904: /* Wizard to print covariance matrix template */
4905:
1.164 brouard 4906: char ca[32], cb[32];
4907: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 4908: int numlinepar;
4909:
4910: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4911: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4912: for(i=1; i <=nlstate; i++){
4913: jj=0;
4914: for(j=1; j <=nlstate+ndeath; j++){
4915: if(j==i) continue;
4916: jj++;
4917: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4918: printf("%1d%1d",i,j);
4919: fprintf(ficparo,"%1d%1d",i,j);
4920: for(k=1; k<=ncovmodel;k++){
4921: /* printf(" %lf",param[i][j][k]); */
4922: /* fprintf(ficparo," %lf",param[i][j][k]); */
4923: printf(" 0.");
4924: fprintf(ficparo," 0.");
4925: }
4926: printf("\n");
4927: fprintf(ficparo,"\n");
4928: }
4929: }
4930: printf("# Scales (for hessian or gradient estimation)\n");
4931: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4932: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4933: for(i=1; i <=nlstate; i++){
4934: jj=0;
4935: for(j=1; j <=nlstate+ndeath; j++){
4936: if(j==i) continue;
4937: jj++;
4938: fprintf(ficparo,"%1d%1d",i,j);
4939: printf("%1d%1d",i,j);
4940: fflush(stdout);
4941: for(k=1; k<=ncovmodel;k++){
4942: /* printf(" %le",delti3[i][j][k]); */
4943: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4944: printf(" 0.");
4945: fprintf(ficparo," 0.");
4946: }
4947: numlinepar++;
4948: printf("\n");
4949: fprintf(ficparo,"\n");
4950: }
4951: }
4952: printf("# Covariance matrix\n");
4953: /* # 121 Var(a12)\n\ */
4954: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4955: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4956: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4957: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4958: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4959: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4960: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4961: fflush(stdout);
4962: fprintf(ficparo,"# Covariance matrix\n");
4963: /* # 121 Var(a12)\n\ */
4964: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4965: /* # ...\n\ */
4966: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4967:
4968: for(itimes=1;itimes<=2;itimes++){
4969: jj=0;
4970: for(i=1; i <=nlstate; i++){
4971: for(j=1; j <=nlstate+ndeath; j++){
4972: if(j==i) continue;
4973: for(k=1; k<=ncovmodel;k++){
4974: jj++;
4975: ca[0]= k+'a'-1;ca[1]='\0';
4976: if(itimes==1){
4977: printf("#%1d%1d%d",i,j,k);
4978: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4979: }else{
4980: printf("%1d%1d%d",i,j,k);
4981: fprintf(ficparo,"%1d%1d%d",i,j,k);
4982: /* printf(" %.5le",matcov[i][j]); */
4983: }
4984: ll=0;
4985: for(li=1;li <=nlstate; li++){
4986: for(lj=1;lj <=nlstate+ndeath; lj++){
4987: if(lj==li) continue;
4988: for(lk=1;lk<=ncovmodel;lk++){
4989: ll++;
4990: if(ll<=jj){
4991: cb[0]= lk +'a'-1;cb[1]='\0';
4992: if(ll<jj){
4993: if(itimes==1){
4994: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4995: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4996: }else{
4997: printf(" 0.");
4998: fprintf(ficparo," 0.");
4999: }
5000: }else{
5001: if(itimes==1){
5002: printf(" Var(%s%1d%1d)",ca,i,j);
5003: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
5004: }else{
5005: printf(" 0.");
5006: fprintf(ficparo," 0.");
5007: }
5008: }
5009: }
5010: } /* end lk */
5011: } /* end lj */
5012: } /* end li */
5013: printf("\n");
5014: fprintf(ficparo,"\n");
5015: numlinepar++;
5016: } /* end k*/
5017: } /*end j */
5018: } /* end i */
5019: } /* end itimes */
5020:
5021: } /* end of prwizard */
5022: /******************* Gompertz Likelihood ******************************/
5023: double gompertz(double x[])
5024: {
5025: double A,B,L=0.0,sump=0.,num=0.;
5026: int i,n=0; /* n is the size of the sample */
5027:
5028: for (i=0;i<=imx-1 ; i++) {
5029: sump=sump+weight[i];
5030: /* sump=sump+1;*/
5031: num=num+1;
5032: }
5033:
5034:
5035: /* for (i=0; i<=imx; i++)
5036: 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]);*/
5037:
5038: for (i=1;i<=imx ; i++)
5039: {
5040: if (cens[i] == 1 && wav[i]>1)
5041: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
5042:
5043: if (cens[i] == 0 && wav[i]>1)
5044: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
5045: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
5046:
5047: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5048: if (wav[i] > 1 ) { /* ??? */
5049: L=L+A*weight[i];
5050: /* 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]);*/
5051: }
5052: }
5053:
5054: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5055:
5056: return -2*L*num/sump;
5057: }
5058:
1.136 brouard 5059: #ifdef GSL
5060: /******************* Gompertz_f Likelihood ******************************/
5061: double gompertz_f(const gsl_vector *v, void *params)
5062: {
5063: double A,B,LL=0.0,sump=0.,num=0.;
5064: double *x= (double *) v->data;
5065: int i,n=0; /* n is the size of the sample */
5066:
5067: for (i=0;i<=imx-1 ; i++) {
5068: sump=sump+weight[i];
5069: /* sump=sump+1;*/
5070: num=num+1;
5071: }
5072:
5073:
5074: /* for (i=0; i<=imx; i++)
5075: 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]);*/
5076: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
5077: for (i=1;i<=imx ; i++)
5078: {
5079: if (cens[i] == 1 && wav[i]>1)
5080: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
5081:
5082: if (cens[i] == 0 && wav[i]>1)
5083: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
5084: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
5085:
5086: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5087: if (wav[i] > 1 ) { /* ??? */
5088: LL=LL+A*weight[i];
5089: /* 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]);*/
5090: }
5091: }
5092:
5093: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5094: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
5095:
5096: return -2*LL*num/sump;
5097: }
5098: #endif
5099:
1.126 brouard 5100: /******************* Printing html file ***********/
5101: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
5102: int lastpass, int stepm, int weightopt, char model[],\
5103: int imx, double p[],double **matcov,double agemortsup){
5104: int i,k;
5105:
5106: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
5107: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
5108: for (i=1;i<=2;i++)
5109: 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]));
5110: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
5111: fprintf(fichtm,"</ul>");
5112:
5113: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
5114:
5115: 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>");
5116:
5117: for (k=agegomp;k<(agemortsup-2);k++)
5118: 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]);
5119:
5120:
5121: fflush(fichtm);
5122: }
5123:
5124: /******************* Gnuplot file **************/
5125: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
5126:
5127: char dirfileres[132],optfileres[132];
1.164 brouard 5128:
1.126 brouard 5129: int ng;
5130:
5131:
5132: /*#ifdef windows */
5133: fprintf(ficgp,"cd \"%s\" \n",pathc);
5134: /*#endif */
5135:
5136:
5137: strcpy(dirfileres,optionfilefiname);
5138: strcpy(optfileres,"vpl");
5139: fprintf(ficgp,"set out \"graphmort.png\"\n ");
5140: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.145 brouard 5141: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
5142: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 5143: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
5144:
5145: }
5146:
1.136 brouard 5147: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
5148: {
1.126 brouard 5149:
1.136 brouard 5150: /*-------- data file ----------*/
5151: FILE *fic;
5152: char dummy[]=" ";
1.164 brouard 5153: int i=0, j=0, n=0;
1.136 brouard 5154: int linei, month, year,iout;
5155: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 5156: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 5157: char *stratrunc;
5158: int lstra;
1.126 brouard 5159:
5160:
1.136 brouard 5161: if((fic=fopen(datafile,"r"))==NULL) {
5162: printf("Problem while opening datafile: %s\n", datafile);return 1;
5163: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
5164: }
1.126 brouard 5165:
1.136 brouard 5166: i=1;
5167: linei=0;
5168: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
5169: linei=linei+1;
5170: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
5171: if(line[j] == '\t')
5172: line[j] = ' ';
5173: }
5174: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
5175: ;
5176: };
5177: line[j+1]=0; /* Trims blanks at end of line */
5178: if(line[0]=='#'){
5179: fprintf(ficlog,"Comment line\n%s\n",line);
5180: printf("Comment line\n%s\n",line);
5181: continue;
5182: }
5183: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 5184: strcpy(line, linetmp);
1.136 brouard 5185:
1.126 brouard 5186:
1.136 brouard 5187: for (j=maxwav;j>=1;j--){
1.137 brouard 5188: cutv(stra, strb, line, ' ');
1.136 brouard 5189: if(strb[0]=='.') { /* Missing status */
5190: lval=-1;
5191: }else{
5192: errno=0;
5193: lval=strtol(strb,&endptr,10);
5194: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
5195: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5196: 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);
5197: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
1.136 brouard 5198: return 1;
5199: }
5200: }
5201: s[j][i]=lval;
5202:
5203: strcpy(line,stra);
5204: cutv(stra, strb,line,' ');
1.169 brouard 5205: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5206: }
1.169 brouard 5207: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5208: month=99;
5209: year=9999;
5210: }else{
1.141 brouard 5211: 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);
5212: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
1.136 brouard 5213: return 1;
5214: }
5215: anint[j][i]= (double) year;
5216: mint[j][i]= (double)month;
5217: strcpy(line,stra);
5218: } /* ENd Waves */
5219:
5220: cutv(stra, strb,line,' ');
1.169 brouard 5221: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5222: }
1.169 brouard 5223: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5224: month=99;
5225: year=9999;
5226: }else{
1.141 brouard 5227: 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);
5228: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);
1.136 brouard 5229: return 1;
5230: }
5231: andc[i]=(double) year;
5232: moisdc[i]=(double) month;
5233: strcpy(line,stra);
5234:
5235: cutv(stra, strb,line,' ');
1.169 brouard 5236: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5237: }
1.169 brouard 5238: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 5239: month=99;
5240: year=9999;
5241: }else{
1.141 brouard 5242: 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);
5243: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);
1.136 brouard 5244: return 1;
5245: }
5246: if (year==9999) {
1.141 brouard 5247: 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);
5248: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
1.136 brouard 5249: return 1;
1.126 brouard 5250:
1.136 brouard 5251: }
5252: annais[i]=(double)(year);
5253: moisnais[i]=(double)(month);
5254: strcpy(line,stra);
5255:
5256: cutv(stra, strb,line,' ');
5257: errno=0;
5258: dval=strtod(strb,&endptr);
5259: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5260: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
5261: fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
1.136 brouard 5262: fflush(ficlog);
5263: return 1;
5264: }
5265: weight[i]=dval;
5266: strcpy(line,stra);
5267:
5268: for (j=ncovcol;j>=1;j--){
5269: cutv(stra, strb,line,' ');
5270: if(strb[0]=='.') { /* Missing status */
5271: lval=-1;
5272: }else{
5273: errno=0;
5274: lval=strtol(strb,&endptr,10);
5275: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5276: 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);
5277: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line);fflush(ficlog);
1.136 brouard 5278: return 1;
5279: }
5280: }
5281: if(lval <-1 || lval >1){
1.141 brouard 5282: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5283: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5284: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5285: For example, for multinomial values like 1, 2 and 3,\n \
5286: build V1=0 V2=0 for the reference value (1),\n \
5287: V1=1 V2=0 for (2) \n \
5288: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5289: output of IMaCh is often meaningless.\n \
5290: Exiting.\n",lval,linei, i,line,j);
1.141 brouard 5291: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5292: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5293: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5294: For example, for multinomial values like 1, 2 and 3,\n \
5295: build V1=0 V2=0 for the reference value (1),\n \
5296: V1=1 V2=0 for (2) \n \
5297: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5298: output of IMaCh is often meaningless.\n \
5299: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
5300: return 1;
5301: }
5302: covar[j][i]=(double)(lval);
5303: strcpy(line,stra);
5304: }
5305: lstra=strlen(stra);
5306:
5307: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
5308: stratrunc = &(stra[lstra-9]);
5309: num[i]=atol(stratrunc);
5310: }
5311: else
5312: num[i]=atol(stra);
5313: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
5314: 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;}*/
5315:
5316: i=i+1;
5317: } /* End loop reading data */
1.126 brouard 5318:
1.136 brouard 5319: *imax=i-1; /* Number of individuals */
5320: fclose(fic);
5321:
5322: return (0);
1.164 brouard 5323: /* endread: */
1.136 brouard 5324: printf("Exiting readdata: ");
5325: fclose(fic);
5326: return (1);
1.126 brouard 5327:
5328:
5329:
1.136 brouard 5330: }
1.145 brouard 5331: void removespace(char *str) {
5332: char *p1 = str, *p2 = str;
5333: do
5334: while (*p2 == ' ')
5335: p2++;
1.169 brouard 5336: while (*p1++ == *p2++);
1.145 brouard 5337: }
5338:
5339: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
5340: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
5341: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
5342: * - cptcovn or number of covariates k of the models excluding age*products =6
5343: * - cptcovage number of covariates with age*products =2
5344: * - cptcovs number of simple covariates
5345: * - 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
5346: * which is a new column after the 9 (ncovcol) variables.
5347: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
5348: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
5349: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
5350: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
5351: */
1.136 brouard 5352: {
1.145 brouard 5353: int i, j, k, ks;
1.164 brouard 5354: int j1, k1, k2;
1.136 brouard 5355: char modelsav[80];
1.145 brouard 5356: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.136 brouard 5357:
1.145 brouard 5358: /*removespace(model);*/
1.136 brouard 5359: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 5360: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
5361: j=nbocc(model,'+'); /**< j=Number of '+' */
5362: j1=nbocc(model,'*'); /**< j1=Number of '*' */
5363: cptcovs=j+1-j1; /**< Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2 */
5364: cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
5365: /* including age products which are counted in cptcovage.
1.169 brouard 5366: * but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
1.145 brouard 5367: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
5368: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
1.136 brouard 5369: strcpy(modelsav,model);
1.137 brouard 5370: if (strstr(model,"AGE") !=0){
5371: printf("Error. AGE must be in lower case 'age' model=%s ",model);
5372: fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
1.136 brouard 5373: return 1;
5374: }
1.141 brouard 5375: if (strstr(model,"v") !=0){
5376: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
5377: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
5378: return 1;
5379: }
1.136 brouard 5380:
1.145 brouard 5381: /* Design
5382: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
5383: * < ncovcol=8 >
5384: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
5385: * k= 1 2 3 4 5 6 7 8
5386: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
5387: * covar[k,i], value of kth covariate if not including age for individual i:
5388: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
5389: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
5390: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
5391: * Tage[++cptcovage]=k
5392: * if products, new covar are created after ncovcol with k1
5393: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
5394: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
5395: * 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
5396: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
5397: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
5398: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
5399: * < ncovcol=8 >
5400: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
5401: * k= 1 2 3 4 5 6 7 8 9 10 11 12
5402: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
5403: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5404: * p Tprod[1]@2={ 6, 5}
5405: *p Tvard[1][1]@4= {7, 8, 5, 6}
5406: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
5407: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
5408: *How to reorganize?
5409: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
5410: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5411: * {2, 1, 4, 8, 5, 6, 3, 7}
5412: * Struct []
5413: */
5414:
1.136 brouard 5415: /* This loop fills the array Tvar from the string 'model'.*/
5416: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
1.137 brouard 5417: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
5418: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
5419: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
5420: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
5421: /* k=1 Tvar[1]=2 (from V2) */
5422: /* k=5 Tvar[5] */
5423: /* for (k=1; k<=cptcovn;k++) { */
5424: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
5425: /* } */
5426: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.145 brouard 5427: /*
5428: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
5429: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
5430: Tvar[k]=0;
5431: cptcovage=0;
5432: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
5433: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5434: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
1.137 brouard 5435: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
1.136 brouard 5436: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5437: /*scanf("%d",i);*/
1.145 brouard 5438: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
5439: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
5440: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
5441: /* covar is not filled and then is empty */
1.136 brouard 5442: cptcovprod--;
1.145 brouard 5443: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
5444: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
1.136 brouard 5445: cptcovage++; /* Sums the number of covariates which include age as a product */
1.137 brouard 5446: Tage[cptcovage]=k; /* Tage[1] = 4 */
1.136 brouard 5447: /*printf("stre=%s ", stre);*/
1.137 brouard 5448: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
1.136 brouard 5449: cptcovprod--;
1.145 brouard 5450: cutl(stre,strb,strc,'V');
1.136 brouard 5451: Tvar[k]=atoi(stre);
5452: cptcovage++;
5453: Tage[cptcovage]=k;
1.137 brouard 5454: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
5455: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
1.145 brouard 5456: cptcovn++;
5457: cptcovprodnoage++;k1++;
5458: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5459: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
1.137 brouard 5460: because this model-covariate is a construction we invent a new column
5461: ncovcol + k1
5462: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
5463: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
1.145 brouard 5464: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
1.137 brouard 5465: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
1.145 brouard 5466: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
5467: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
5468: k2=k2+2;
5469: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
5470: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
1.137 brouard 5471: for (i=1; i<=lastobs;i++){
5472: /* Computes the new covariate which is a product of
1.145 brouard 5473: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
1.136 brouard 5474: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
1.137 brouard 5475: }
5476: } /* End age is not in the model */
5477: } /* End if model includes a product */
1.136 brouard 5478: else { /* no more sum */
5479: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5480: /* scanf("%d",i);*/
1.145 brouard 5481: cutl(strd,strc,strb,'V');
5482: ks++; /**< Number of simple covariates */
5483: cptcovn++;
5484: Tvar[k]=atoi(strd);
1.136 brouard 5485: }
1.137 brouard 5486: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
1.136 brouard 5487: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5488: scanf("%d",i);*/
5489: } /* end of loop + */
5490: } /* end model */
5491:
5492: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5493: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5494:
5495: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5496: printf("cptcovprod=%d ", cptcovprod);
5497: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5498:
5499: scanf("%d ",i);*/
5500:
5501:
1.137 brouard 5502: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 5503: /*endread:*/
1.136 brouard 5504: printf("Exiting decodemodel: ");
5505: return (1);
5506: }
5507:
1.169 brouard 5508: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.136 brouard 5509: {
5510: int i, m;
5511:
5512: for (i=1; i<=imx; i++) {
5513: for(m=2; (m<= maxwav); m++) {
5514: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5515: anint[m][i]=9999;
5516: s[m][i]=-1;
5517: }
5518: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169 brouard 5519: *nberr = *nberr + 1;
5520: 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);
5521: 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);
1.136 brouard 5522: s[m][i]=-1;
5523: }
5524: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 5525: (*nberr)++;
1.136 brouard 5526: 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]);
5527: 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]);
5528: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5529: }
5530: }
5531: }
5532:
5533: for (i=1; i<=imx; i++) {
5534: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5535: for(m=firstpass; (m<= lastpass); m++){
5536: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5537: if (s[m][i] >= nlstate+1) {
1.169 brouard 5538: if(agedc[i]>0){
5539: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 5540: agev[m][i]=agedc[i];
5541: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 5542: }else {
1.136 brouard 5543: if ((int)andc[i]!=9999){
5544: nbwarn++;
5545: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5546: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5547: agev[m][i]=-1;
5548: }
5549: }
1.169 brouard 5550: } /* agedc > 0 */
1.136 brouard 5551: }
5552: else if(s[m][i] !=9){ /* Standard case, age in fractional
5553: years but with the precision of a month */
5554: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5555: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5556: agev[m][i]=1;
5557: else if(agev[m][i] < *agemin){
5558: *agemin=agev[m][i];
5559: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
5560: }
5561: else if(agev[m][i] >*agemax){
5562: *agemax=agev[m][i];
1.156 brouard 5563: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 5564: }
5565: /*agev[m][i]=anint[m][i]-annais[i];*/
5566: /* agev[m][i] = age[i]+2*m;*/
5567: }
5568: else { /* =9 */
5569: agev[m][i]=1;
5570: s[m][i]=-1;
5571: }
5572: }
5573: else /*= 0 Unknown */
5574: agev[m][i]=1;
5575: }
5576:
5577: }
5578: for (i=1; i<=imx; i++) {
5579: for(m=firstpass; (m<=lastpass); m++){
5580: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 5581: (*nberr)++;
1.136 brouard 5582: 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);
5583: 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);
5584: return 1;
5585: }
5586: }
5587: }
5588:
5589: /*for (i=1; i<=imx; i++){
5590: for (m=firstpass; (m<lastpass); m++){
5591: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5592: }
5593:
5594: }*/
5595:
5596:
1.139 brouard 5597: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5598: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 5599:
5600: return (0);
1.164 brouard 5601: /* endread:*/
1.136 brouard 5602: printf("Exiting calandcheckages: ");
5603: return (1);
5604: }
5605:
1.172 brouard 5606: #if defined(_MSC_VER)
5607: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5608: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5609: //#include "stdafx.h"
5610: //#include <stdio.h>
5611: //#include <tchar.h>
5612: //#include <windows.h>
5613: //#include <iostream>
5614: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
5615:
5616: LPFN_ISWOW64PROCESS fnIsWow64Process;
5617:
5618: BOOL IsWow64()
5619: {
5620: BOOL bIsWow64 = FALSE;
5621:
5622: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
5623: // (HANDLE, PBOOL);
5624:
5625: //LPFN_ISWOW64PROCESS fnIsWow64Process;
5626:
5627: HMODULE module = GetModuleHandle(_T("kernel32"));
5628: const char funcName[] = "IsWow64Process";
5629: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
5630: GetProcAddress(module, funcName);
5631:
5632: if (NULL != fnIsWow64Process)
5633: {
5634: if (!fnIsWow64Process(GetCurrentProcess(),
5635: &bIsWow64))
5636: //throw std::exception("Unknown error");
5637: printf("Unknown error\n");
5638: }
5639: return bIsWow64 != FALSE;
5640: }
5641: #endif
1.177 brouard 5642:
1.169 brouard 5643: void syscompilerinfo()
1.167 brouard 5644: {
5645: /* #include "syscompilerinfo.h"*/
1.184 ! brouard 5646: /* command line Intel compiler 64bit windows:
! 5647: /GS /W3 /Gy /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32"
! 5648: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
! 5649: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo
! 5650: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
! 5651: /*
! 5652: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
! 5653: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
! 5654: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
! 5655: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
1.177 brouard 5656: #if defined __INTEL_COMPILER
1.178 brouard 5657: #if defined(__GNUC__)
5658: struct utsname sysInfo; /* For Intel on Linux and OS/X */
5659: #endif
1.177 brouard 5660: #elif defined(__GNUC__)
1.179 brouard 5661: #ifndef __APPLE__
1.174 brouard 5662: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 5663: #endif
1.177 brouard 5664: struct utsname sysInfo;
1.178 brouard 5665: int cross = CROSS;
5666: if (cross){
5667: printf("Cross-");
5668: fprintf(ficlog, "Cross-");
5669: }
1.174 brouard 5670: #endif
5671:
1.171 brouard 5672: #include <stdint.h>
1.178 brouard 5673:
1.169 brouard 5674: printf("Compiled with:");fprintf(ficlog,"Compiled with:");
5675: #if defined(__clang__)
5676: printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
5677: #endif
5678: #if defined(__ICC) || defined(__INTEL_COMPILER)
5679: printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
5680: #endif
5681: #if defined(__GNUC__) || defined(__GNUG__)
5682: printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
5683: #endif
5684: #if defined(__HP_cc) || defined(__HP_aCC)
5685: printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
5686: #endif
5687: #if defined(__IBMC__) || defined(__IBMCPP__)
5688: printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
5689: #endif
5690: #if defined(_MSC_VER)
5691: printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
5692: #endif
5693: #if defined(__PGI)
5694: printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
5695: #endif
5696: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
5697: printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 5698: #endif
1.174 brouard 5699: printf(" for ");fprintf(ficlog," for ");
1.169 brouard 5700:
1.167 brouard 5701: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
5702: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
5703: // Windows (x64 and x86)
1.174 brouard 5704: printf("Windows (x64 and x86) ");fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 5705: #elif __unix__ // all unices, not all compilers
5706: // Unix
1.174 brouard 5707: printf("Unix ");fprintf(ficlog,"Unix ");
1.167 brouard 5708: #elif __linux__
5709: // linux
1.174 brouard 5710: printf("linux ");fprintf(ficlog,"linux ");
1.167 brouard 5711: #elif __APPLE__
1.174 brouard 5712: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
5713: printf("Mac OS ");fprintf(ficlog,"Mac OS ");
1.167 brouard 5714: #endif
5715:
5716: /* __MINGW32__ */
5717: /* __CYGWIN__ */
5718: /* __MINGW64__ */
5719: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
5720: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
5721: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
5722: /* _WIN64 // Defined for applications for Win64. */
5723: /* _M_X64 // Defined for compilations that target x64 processors. */
5724: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 5725:
1.167 brouard 5726: #if UINTPTR_MAX == 0xffffffff
1.174 brouard 5727: printf(" 32-bit"); fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 5728: #elif UINTPTR_MAX == 0xffffffffffffffff
1.174 brouard 5729: printf(" 64-bit"); fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 5730: #else
1.174 brouard 5731: printf(" wtf-bit"); fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 5732: #endif
5733:
1.169 brouard 5734: #if defined(__GNUC__)
5735: # if defined(__GNUC_PATCHLEVEL__)
5736: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
5737: + __GNUC_MINOR__ * 100 \
5738: + __GNUC_PATCHLEVEL__)
5739: # else
5740: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
5741: + __GNUC_MINOR__ * 100)
5742: # endif
1.174 brouard 5743: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
5744: fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 5745:
5746: if (uname(&sysInfo) != -1) {
5747: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
5748: fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
5749: }
5750: else
5751: perror("uname() error");
1.179 brouard 5752: //#ifndef __INTEL_COMPILER
5753: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 5754: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.179 brouard 5755: fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 5756: #endif
1.169 brouard 5757: #endif
1.172 brouard 5758:
5759: // void main()
5760: // {
1.169 brouard 5761: #if defined(_MSC_VER)
1.174 brouard 5762: if (IsWow64()){
1.176 brouard 5763: printf("The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
5764: fprintf(ficlog, "The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 5765: }
5766: else{
1.176 brouard 5767: printf("The process is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.178 brouard 5768: fprintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 5769: }
1.172 brouard 5770: // printf("\nPress Enter to continue...");
5771: // getchar();
5772: // }
5773:
1.169 brouard 5774: #endif
5775:
1.167 brouard 5776:
5777: }
1.136 brouard 5778:
1.180 brouard 5779: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){
5780: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
5781: int i, j, k, i1 ;
5782: double ftolpl = 1.e-10;
5783: double age, agebase, agelim;
5784:
5785: strcpy(filerespl,"pl");
5786: strcat(filerespl,fileres);
5787: if((ficrespl=fopen(filerespl,"w"))==NULL) {
5788: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
5789: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
5790: }
5791: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
5792: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
5793: pstamp(ficrespl);
5794: fprintf(ficrespl,"# Period (stable) prevalence \n");
5795: fprintf(ficrespl,"#Age ");
5796: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
5797: fprintf(ficrespl,"\n");
5798:
5799: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
5800:
5801: agebase=ageminpar;
5802: agelim=agemaxpar;
5803:
5804: i1=pow(2,cptcoveff);
5805: if (cptcovn < 1){i1=1;}
5806:
5807: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5808: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
5809: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5810: k=k+1;
5811: /* to clean */
5812: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);
5813: fprintf(ficrespl,"\n#******");
5814: printf("\n#******");
5815: fprintf(ficlog,"\n#******");
5816: for(j=1;j<=cptcoveff;j++) {
5817: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5818: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5819: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5820: }
5821: fprintf(ficrespl,"******\n");
5822: printf("******\n");
5823: fprintf(ficlog,"******\n");
5824:
5825: fprintf(ficrespl,"#Age ");
5826: for(j=1;j<=cptcoveff;j++) {
5827: fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5828: }
5829: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
5830: fprintf(ficrespl,"\n");
5831:
5832: for (age=agebase; age<=agelim; age++){
5833: /* for (age=agebase; age<=agebase; age++){ */
5834: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5835: fprintf(ficrespl,"%.0f ",age );
5836: for(j=1;j<=cptcoveff;j++)
5837: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5838: for(i=1; i<=nlstate;i++)
5839: fprintf(ficrespl," %.5f", prlim[i][i]);
5840: fprintf(ficrespl,"\n");
5841: } /* Age */
5842: /* was end of cptcod */
5843: } /* cptcov */
1.184 ! brouard 5844: return 0;
1.180 brouard 5845: }
5846:
5847: int hPijx(double *p, int bage, int fage){
5848: /*------------- h Pij x at various ages ------------*/
5849:
5850: int stepsize;
5851: int agelim;
5852: int hstepm;
5853: int nhstepm;
5854: int h, i, i1, j, k;
5855:
5856: double agedeb;
5857: double ***p3mat;
5858:
5859: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
5860: if((ficrespij=fopen(filerespij,"w"))==NULL) {
5861: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
5862: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
5863: }
5864: printf("Computing pij: result on file '%s' \n", filerespij);
5865: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
5866:
5867: stepsize=(int) (stepm+YEARM-1)/YEARM;
5868: /*if (stepm<=24) stepsize=2;*/
5869:
5870: agelim=AGESUP;
5871: hstepm=stepsize*YEARM; /* Every year of age */
5872: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
5873:
5874: /* hstepm=1; aff par mois*/
5875: pstamp(ficrespij);
5876: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
5877: i1= pow(2,cptcoveff);
1.183 brouard 5878: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
5879: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
5880: /* k=k+1; */
5881: for (k=1; k <= (int) pow(2,cptcoveff); k++){
5882: fprintf(ficrespij,"\n#****** ");
5883: for(j=1;j<=cptcoveff;j++)
5884: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5885: fprintf(ficrespij,"******\n");
5886:
5887: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
5888: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5889: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
5890:
5891: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 5892:
1.183 brouard 5893: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5894: oldm=oldms;savm=savms;
5895: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5896: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
5897: for(i=1; i<=nlstate;i++)
5898: for(j=1; j<=nlstate+ndeath;j++)
5899: fprintf(ficrespij," %1d-%1d",i,j);
5900: fprintf(ficrespij,"\n");
5901: for (h=0; h<=nhstepm; h++){
5902: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
5903: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 5904: for(i=1; i<=nlstate;i++)
5905: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 5906: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 5907: fprintf(ficrespij,"\n");
5908: }
1.183 brouard 5909: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5910: fprintf(ficrespij,"\n");
5911: }
1.180 brouard 5912: /*}*/
5913: }
1.184 ! brouard 5914: return 0;
1.180 brouard 5915: }
5916:
5917:
1.136 brouard 5918: /***********************************************/
5919: /**************** Main Program *****************/
5920: /***********************************************/
5921:
5922: int main(int argc, char *argv[])
5923: {
5924: #ifdef GSL
5925: const gsl_multimin_fminimizer_type *T;
5926: size_t iteri = 0, it;
5927: int rval = GSL_CONTINUE;
5928: int status = GSL_SUCCESS;
5929: double ssval;
5930: #endif
5931: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 5932: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
5933:
5934: int jj, ll, li, lj, lk;
1.136 brouard 5935: int numlinepar=0; /* Current linenumber of parameter file */
5936: int itimes;
5937: int NDIM=2;
5938: int vpopbased=0;
5939:
1.164 brouard 5940: char ca[32], cb[32];
1.136 brouard 5941: /* FILE *fichtm; *//* Html File */
5942: /* FILE *ficgp;*/ /*Gnuplot File */
5943: struct stat info;
1.164 brouard 5944: double agedeb;
1.136 brouard 5945: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
5946:
1.165 brouard 5947: double fret;
1.136 brouard 5948: double dum; /* Dummy variable */
5949: double ***p3mat;
5950: double ***mobaverage;
1.164 brouard 5951:
5952: char line[MAXLINE];
1.136 brouard 5953: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
5954: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 5955: char *tok, *val; /* pathtot */
1.136 brouard 5956: int firstobs=1, lastobs=10;
1.164 brouard 5957: int c, h , cpt;
5958: int jl;
5959: int i1, j1, jk, stepsize;
5960: int *tab;
1.136 brouard 5961: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
5962: int mobilav=0,popforecast=0;
5963: int hstepm, nhstepm;
5964: int agemortsup;
5965: float sumlpop=0.;
5966: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
5967: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
5968:
1.164 brouard 5969: double bage=0, fage=110, age, agelim, agebase;
1.136 brouard 5970: double ftolpl=FTOL;
5971: double **prlim;
5972: double ***param; /* Matrix of parameters */
5973: double *p;
5974: double **matcov; /* Matrix of covariance */
5975: double ***delti3; /* Scale */
5976: double *delti; /* Scale */
5977: double ***eij, ***vareij;
5978: double **varpl; /* Variances of prevalence limits by age */
5979: double *epj, vepp;
1.164 brouard 5980:
1.136 brouard 5981: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
5982: double **ximort;
1.145 brouard 5983: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 5984: int *dcwave;
5985:
1.164 brouard 5986: char z[1]="c";
1.136 brouard 5987:
5988: /*char *strt;*/
5989: char strtend[80];
1.126 brouard 5990:
1.164 brouard 5991:
1.126 brouard 5992: /* setlocale (LC_ALL, ""); */
5993: /* bindtextdomain (PACKAGE, LOCALEDIR); */
5994: /* textdomain (PACKAGE); */
5995: /* setlocale (LC_CTYPE, ""); */
5996: /* setlocale (LC_MESSAGES, ""); */
5997:
5998: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 5999: rstart_time = time(NULL);
6000: /* (void) gettimeofday(&start_time,&tzp);*/
6001: start_time = *localtime(&rstart_time);
1.126 brouard 6002: curr_time=start_time;
1.157 brouard 6003: /*tml = *localtime(&start_time.tm_sec);*/
6004: /* strcpy(strstart,asctime(&tml)); */
6005: strcpy(strstart,asctime(&start_time));
1.126 brouard 6006:
6007: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 6008: /* tp.tm_sec = tp.tm_sec +86400; */
6009: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 6010: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
6011: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
6012: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 6013: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 6014: /* strt=asctime(&tmg); */
6015: /* printf("Time(after) =%s",strstart); */
6016: /* (void) time (&time_value);
6017: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
6018: * tm = *localtime(&time_value);
6019: * strstart=asctime(&tm);
6020: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
6021: */
6022:
6023: nberr=0; /* Number of errors and warnings */
6024: nbwarn=0;
1.184 ! brouard 6025: #ifdef WIN32
! 6026: _getcwd(pathcd, size);
! 6027: #else
1.126 brouard 6028: getcwd(pathcd, size);
1.184 ! brouard 6029: #endif
1.126 brouard 6030:
6031: printf("\n%s\n%s",version,fullversion);
6032: if(argc <=1){
6033: printf("\nEnter the parameter file name: ");
6034: fgets(pathr,FILENAMELENGTH,stdin);
6035: i=strlen(pathr);
6036: if(pathr[i-1]=='\n')
6037: pathr[i-1]='\0';
1.156 brouard 6038: i=strlen(pathr);
6039: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
6040: pathr[i-1]='\0';
1.126 brouard 6041: for (tok = pathr; tok != NULL; ){
6042: printf("Pathr |%s|\n",pathr);
6043: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
6044: printf("val= |%s| pathr=%s\n",val,pathr);
6045: strcpy (pathtot, val);
6046: if(pathr[0] == '\0') break; /* Dirty */
6047: }
6048: }
6049: else{
6050: strcpy(pathtot,argv[1]);
6051: }
6052: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
6053: /*cygwin_split_path(pathtot,path,optionfile);
6054: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
6055: /* cutv(path,optionfile,pathtot,'\\');*/
6056:
6057: /* Split argv[0], imach program to get pathimach */
6058: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
6059: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6060: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6061: /* strcpy(pathimach,argv[0]); */
6062: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
6063: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
6064: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 ! brouard 6065: #ifdef WIN32
! 6066: _chdir(path); /* Can be a relative path */
! 6067: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
! 6068: #else
1.126 brouard 6069: chdir(path); /* Can be a relative path */
1.184 ! brouard 6070: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
! 6071: #endif
! 6072: printf("Current directory %s!\n",pathcd);
1.126 brouard 6073: strcpy(command,"mkdir ");
6074: strcat(command,optionfilefiname);
6075: if((outcmd=system(command)) != 0){
1.169 brouard 6076: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 6077: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
6078: /* fclose(ficlog); */
6079: /* exit(1); */
6080: }
6081: /* if((imk=mkdir(optionfilefiname))<0){ */
6082: /* perror("mkdir"); */
6083: /* } */
6084:
6085: /*-------- arguments in the command line --------*/
6086:
6087: /* Log file */
6088: strcat(filelog, optionfilefiname);
6089: strcat(filelog,".log"); /* */
6090: if((ficlog=fopen(filelog,"w"))==NULL) {
6091: printf("Problem with logfile %s\n",filelog);
6092: goto end;
6093: }
6094: fprintf(ficlog,"Log filename:%s\n",filelog);
6095: fprintf(ficlog,"\n%s\n%s",version,fullversion);
6096: fprintf(ficlog,"\nEnter the parameter file name: \n");
6097: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
6098: path=%s \n\
6099: optionfile=%s\n\
6100: optionfilext=%s\n\
1.156 brouard 6101: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 6102:
1.167 brouard 6103: syscompilerinfo();
6104:
1.126 brouard 6105: printf("Local time (at start):%s",strstart);
6106: fprintf(ficlog,"Local time (at start): %s",strstart);
6107: fflush(ficlog);
6108: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 6109: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 6110:
6111: /* */
6112: strcpy(fileres,"r");
6113: strcat(fileres, optionfilefiname);
6114: strcat(fileres,".txt"); /* Other files have txt extension */
6115:
6116: /*---------arguments file --------*/
6117:
6118: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 6119: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
6120: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 6121: fflush(ficlog);
1.149 brouard 6122: /* goto end; */
6123: exit(70);
1.126 brouard 6124: }
6125:
6126:
6127:
6128: strcpy(filereso,"o");
6129: strcat(filereso,fileres);
6130: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
6131: printf("Problem with Output resultfile: %s\n", filereso);
6132: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
6133: fflush(ficlog);
6134: goto end;
6135: }
6136:
6137: /* Reads comments: lines beginning with '#' */
6138: numlinepar=0;
6139: while((c=getc(ficpar))=='#' && c!= EOF){
6140: ungetc(c,ficpar);
6141: fgets(line, MAXLINE, ficpar);
6142: numlinepar++;
1.141 brouard 6143: fputs(line,stdout);
1.126 brouard 6144: fputs(line,ficparo);
6145: fputs(line,ficlog);
6146: }
6147: ungetc(c,ficpar);
6148:
6149: fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
6150: numlinepar++;
6151: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
6152: fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
6153: fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
6154: fflush(ficlog);
6155: while((c=getc(ficpar))=='#' && c!= EOF){
6156: ungetc(c,ficpar);
6157: fgets(line, MAXLINE, ficpar);
6158: numlinepar++;
1.141 brouard 6159: fputs(line, stdout);
6160: //puts(line);
1.126 brouard 6161: fputs(line,ficparo);
6162: fputs(line,ficlog);
6163: }
6164: ungetc(c,ficpar);
6165:
6166:
1.145 brouard 6167: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.136 brouard 6168: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
6169: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
6170: v1+v2*age+v2*v3 makes cptcovn = 3
6171: */
6172: if (strlen(model)>1)
1.145 brouard 6173: 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*/
6174: else
6175: ncovmodel=2;
1.126 brouard 6176: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
1.133 brouard 6177: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
6178: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 6179: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
6180: 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);
6181: 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);
6182: fflush(stdout);
6183: fclose (ficlog);
6184: goto end;
6185: }
1.126 brouard 6186: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6187: delti=delti3[1][1];
6188: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
6189: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
6190: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
6191: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
6192: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
6193: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6194: fclose (ficparo);
6195: fclose (ficlog);
6196: goto end;
6197: exit(0);
6198: }
6199: else if(mle==-3) {
6200: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
6201: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
6202: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
6203: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6204: matcov=matrix(1,npar,1,npar);
6205: }
6206: else{
1.145 brouard 6207: /* Read guessed parameters */
1.126 brouard 6208: /* Reads comments: lines beginning with '#' */
6209: while((c=getc(ficpar))=='#' && c!= EOF){
6210: ungetc(c,ficpar);
6211: fgets(line, MAXLINE, ficpar);
6212: numlinepar++;
1.141 brouard 6213: fputs(line,stdout);
1.126 brouard 6214: fputs(line,ficparo);
6215: fputs(line,ficlog);
6216: }
6217: ungetc(c,ficpar);
6218:
6219: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6220: for(i=1; i <=nlstate; i++){
6221: j=0;
6222: for(jj=1; jj <=nlstate+ndeath; jj++){
6223: if(jj==i) continue;
6224: j++;
6225: fscanf(ficpar,"%1d%1d",&i1,&j1);
6226: if ((i1 != i) && (j1 != j)){
6227: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
6228: It might be a problem of design; if ncovcol and the model are correct\n \
6229: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
6230: exit(1);
6231: }
6232: fprintf(ficparo,"%1d%1d",i1,j1);
6233: if(mle==1)
6234: printf("%1d%1d",i,j);
6235: fprintf(ficlog,"%1d%1d",i,j);
6236: for(k=1; k<=ncovmodel;k++){
6237: fscanf(ficpar," %lf",¶m[i][j][k]);
6238: if(mle==1){
6239: printf(" %lf",param[i][j][k]);
6240: fprintf(ficlog," %lf",param[i][j][k]);
6241: }
6242: else
6243: fprintf(ficlog," %lf",param[i][j][k]);
6244: fprintf(ficparo," %lf",param[i][j][k]);
6245: }
6246: fscanf(ficpar,"\n");
6247: numlinepar++;
6248: if(mle==1)
6249: printf("\n");
6250: fprintf(ficlog,"\n");
6251: fprintf(ficparo,"\n");
6252: }
6253: }
6254: fflush(ficlog);
6255:
1.145 brouard 6256: /* Reads scales values */
1.126 brouard 6257: p=param[1][1];
6258:
6259: /* Reads comments: lines beginning with '#' */
6260: while((c=getc(ficpar))=='#' && c!= EOF){
6261: ungetc(c,ficpar);
6262: fgets(line, MAXLINE, ficpar);
6263: numlinepar++;
1.141 brouard 6264: fputs(line,stdout);
1.126 brouard 6265: fputs(line,ficparo);
6266: fputs(line,ficlog);
6267: }
6268: ungetc(c,ficpar);
6269:
6270: for(i=1; i <=nlstate; i++){
6271: for(j=1; j <=nlstate+ndeath-1; j++){
6272: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.164 brouard 6273: if ( (i1-i) * (j1-j) != 0){
1.126 brouard 6274: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
6275: exit(1);
6276: }
6277: printf("%1d%1d",i,j);
6278: fprintf(ficparo,"%1d%1d",i1,j1);
6279: fprintf(ficlog,"%1d%1d",i1,j1);
6280: for(k=1; k<=ncovmodel;k++){
6281: fscanf(ficpar,"%le",&delti3[i][j][k]);
6282: printf(" %le",delti3[i][j][k]);
6283: fprintf(ficparo," %le",delti3[i][j][k]);
6284: fprintf(ficlog," %le",delti3[i][j][k]);
6285: }
6286: fscanf(ficpar,"\n");
6287: numlinepar++;
6288: printf("\n");
6289: fprintf(ficparo,"\n");
6290: fprintf(ficlog,"\n");
6291: }
6292: }
6293: fflush(ficlog);
6294:
1.145 brouard 6295: /* Reads covariance matrix */
1.126 brouard 6296: delti=delti3[1][1];
6297:
6298:
6299: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
6300:
6301: /* Reads comments: lines beginning with '#' */
6302: while((c=getc(ficpar))=='#' && c!= EOF){
6303: ungetc(c,ficpar);
6304: fgets(line, MAXLINE, ficpar);
6305: numlinepar++;
1.141 brouard 6306: fputs(line,stdout);
1.126 brouard 6307: fputs(line,ficparo);
6308: fputs(line,ficlog);
6309: }
6310: ungetc(c,ficpar);
6311:
6312: matcov=matrix(1,npar,1,npar);
1.131 brouard 6313: for(i=1; i <=npar; i++)
6314: for(j=1; j <=npar; j++) matcov[i][j]=0.;
6315:
1.126 brouard 6316: for(i=1; i <=npar; i++){
1.145 brouard 6317: fscanf(ficpar,"%s",str);
1.126 brouard 6318: if(mle==1)
6319: printf("%s",str);
6320: fprintf(ficlog,"%s",str);
6321: fprintf(ficparo,"%s",str);
6322: for(j=1; j <=i; j++){
6323: fscanf(ficpar," %le",&matcov[i][j]);
6324: if(mle==1){
6325: printf(" %.5le",matcov[i][j]);
6326: }
6327: fprintf(ficlog," %.5le",matcov[i][j]);
6328: fprintf(ficparo," %.5le",matcov[i][j]);
6329: }
6330: fscanf(ficpar,"\n");
6331: numlinepar++;
6332: if(mle==1)
6333: printf("\n");
6334: fprintf(ficlog,"\n");
6335: fprintf(ficparo,"\n");
6336: }
6337: for(i=1; i <=npar; i++)
6338: for(j=i+1;j<=npar;j++)
6339: matcov[i][j]=matcov[j][i];
6340:
6341: if(mle==1)
6342: printf("\n");
6343: fprintf(ficlog,"\n");
6344:
6345: fflush(ficlog);
6346:
6347: /*-------- Rewriting parameter file ----------*/
6348: strcpy(rfileres,"r"); /* "Rparameterfile */
6349: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
6350: strcat(rfileres,"."); /* */
6351: strcat(rfileres,optionfilext); /* Other files have txt extension */
6352: if((ficres =fopen(rfileres,"w"))==NULL) {
6353: printf("Problem writing new parameter file: %s\n", fileres);goto end;
6354: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
6355: }
6356: fprintf(ficres,"#%s\n",version);
6357: } /* End of mle != -3 */
6358:
6359:
6360: n= lastobs;
6361: num=lvector(1,n);
6362: moisnais=vector(1,n);
6363: annais=vector(1,n);
6364: moisdc=vector(1,n);
6365: andc=vector(1,n);
6366: agedc=vector(1,n);
6367: cod=ivector(1,n);
6368: weight=vector(1,n);
6369: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
6370: mint=matrix(1,maxwav,1,n);
6371: anint=matrix(1,maxwav,1,n);
1.131 brouard 6372: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 6373: tab=ivector(1,NCOVMAX);
1.144 brouard 6374: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.126 brouard 6375:
1.136 brouard 6376: /* Reads data from file datafile */
6377: if (readdata(datafile, firstobs, lastobs, &imx)==1)
6378: goto end;
6379:
6380: /* Calculation of the number of parameters from char model */
1.137 brouard 6381: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
6382: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
6383: k=3 V4 Tvar[k=3]= 4 (from V4)
6384: k=2 V1 Tvar[k=2]= 1 (from V1)
6385: k=1 Tvar[1]=2 (from V2)
6386: */
6387: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
6388: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
6389: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
6390: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
6391: */
6392: /* For model-covariate k tells which data-covariate to use but
6393: because this model-covariate is a construction we invent a new column
6394: ncovcol + k1
6395: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
6396: Tvar[3=V1*V4]=4+1 etc */
1.145 brouard 6397: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
1.137 brouard 6398: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
6399: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
6400: */
1.145 brouard 6401: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
6402: Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1] and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
1.141 brouard 6403: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
6404: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 6405: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 6406: 4 covariates (3 plus signs)
6407: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
6408: */
1.136 brouard 6409:
6410: if(decodemodel(model, lastobs) == 1)
6411: goto end;
6412:
1.137 brouard 6413: if((double)(lastobs-imx)/(double)imx > 1.10){
6414: nbwarn++;
6415: 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);
6416: 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);
6417: }
1.136 brouard 6418: /* if(mle==1){*/
1.137 brouard 6419: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
6420: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 6421: }
6422:
6423: /*-calculation of age at interview from date of interview and age at death -*/
6424: agev=matrix(1,maxwav,1,imx);
6425:
6426: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
6427: goto end;
6428:
1.126 brouard 6429:
1.136 brouard 6430: agegomp=(int)agemin;
6431: free_vector(moisnais,1,n);
6432: free_vector(annais,1,n);
1.126 brouard 6433: /* free_matrix(mint,1,maxwav,1,n);
6434: free_matrix(anint,1,maxwav,1,n);*/
6435: free_vector(moisdc,1,n);
6436: free_vector(andc,1,n);
1.145 brouard 6437: /* */
6438:
1.126 brouard 6439: wav=ivector(1,imx);
6440: dh=imatrix(1,lastpass-firstpass+1,1,imx);
6441: bh=imatrix(1,lastpass-firstpass+1,1,imx);
6442: mw=imatrix(1,lastpass-firstpass+1,1,imx);
6443:
6444: /* Concatenates waves */
6445: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 brouard 6446: /* */
6447:
1.126 brouard 6448: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
6449:
6450: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
6451: ncodemax[1]=1;
1.145 brouard 6452: Ndum =ivector(-1,NCOVMAX);
6453: if (ncovmodel > 2)
6454: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
6455:
6456: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
6457: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
6458: h=0;
6459:
6460:
6461: /*if (cptcovn > 0) */
1.126 brouard 6462:
1.145 brouard 6463:
1.126 brouard 6464: m=pow(2,cptcoveff);
6465:
1.131 brouard 6466: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
1.143 brouard 6467: 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 */
6468: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
6469: for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
1.126 brouard 6470: h++;
1.141 brouard 6471: if (h>m)
1.136 brouard 6472: h=1;
1.144 brouard 6473: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.143 brouard 6474: * h 1 2 3 4
6475: *______________________________
6476: * 1 i=1 1 i=1 1 i=1 1 i=1 1
6477: * 2 2 1 1 1
6478: * 3 i=2 1 2 1 1
6479: * 4 2 2 1 1
6480: * 5 i=3 1 i=2 1 2 1
6481: * 6 2 1 2 1
6482: * 7 i=4 1 2 2 1
6483: * 8 2 2 2 1
6484: * 9 i=5 1 i=3 1 i=2 1 1
6485: * 10 2 1 1 1
6486: * 11 i=6 1 2 1 1
6487: * 12 2 2 1 1
6488: * 13 i=7 1 i=4 1 2 1
6489: * 14 2 1 2 1
6490: * 15 i=8 1 2 2 1
6491: * 16 2 2 2 1
6492: */
1.141 brouard 6493: codtab[h][k]=j;
1.145 brouard 6494: /*codtab[h][Tvar[k]]=j;*/
1.130 brouard 6495: printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
1.126 brouard 6496: }
6497: }
6498: }
6499: }
6500: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
6501: codtab[1][2]=1;codtab[2][2]=2; */
6502: /* for(i=1; i <=m ;i++){
6503: for(k=1; k <=cptcovn; k++){
1.131 brouard 6504: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
1.126 brouard 6505: }
6506: printf("\n");
6507: }
6508: scanf("%d",i);*/
1.145 brouard 6509:
6510: free_ivector(Ndum,-1,NCOVMAX);
6511:
6512:
1.126 brouard 6513:
6514: /*------------ gnuplot -------------*/
6515: strcpy(optionfilegnuplot,optionfilefiname);
6516: if(mle==-3)
6517: strcat(optionfilegnuplot,"-mort");
6518: strcat(optionfilegnuplot,".gp");
6519:
6520: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
6521: printf("Problem with file %s",optionfilegnuplot);
6522: }
6523: else{
6524: fprintf(ficgp,"\n# %s\n", version);
6525: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 6526: //fprintf(ficgp,"set missing 'NaNq'\n");
6527: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 6528: }
6529: /* fclose(ficgp);*/
6530: /*--------- index.htm --------*/
6531:
6532: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
6533: if(mle==-3)
6534: strcat(optionfilehtm,"-mort");
6535: strcat(optionfilehtm,".htm");
6536: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 6537: printf("Problem with %s \n",optionfilehtm);
6538: exit(0);
1.126 brouard 6539: }
6540:
6541: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
6542: strcat(optionfilehtmcov,"-cov.htm");
6543: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
6544: printf("Problem with %s \n",optionfilehtmcov), exit(0);
6545: }
6546: else{
6547: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6548: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6549: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
6550: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
6551: }
6552:
6553: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6554: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6555: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
6556: \n\
6557: <hr size=\"2\" color=\"#EC5E5E\">\
6558: <ul><li><h4>Parameter files</h4>\n\
6559: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
6560: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
6561: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
6562: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
6563: - Date and time at start: %s</ul>\n",\
6564: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
6565: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
6566: fileres,fileres,\
6567: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
6568: fflush(fichtm);
6569:
6570: strcpy(pathr,path);
6571: strcat(pathr,optionfilefiname);
1.184 ! brouard 6572: #ifdef WIN32
! 6573: _chdir(optionfilefiname); /* Move to directory named optionfile */
! 6574: #else
1.126 brouard 6575: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 ! brouard 6576: #endif
! 6577:
1.126 brouard 6578:
6579: /* Calculates basic frequencies. Computes observed prevalence at single age
6580: and prints on file fileres'p'. */
6581: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
6582:
6583: fprintf(fichtm,"\n");
6584: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
6585: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
6586: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
6587: imx,agemin,agemax,jmin,jmax,jmean);
6588: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6589: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6590: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6591: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6592: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
6593:
6594:
6595: /* For Powell, parameters are in a vector p[] starting at p[1]
6596: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
6597: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
6598:
6599: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
6600:
6601: if (mle==-3){
1.136 brouard 6602: ximort=matrix(1,NDIM,1,NDIM);
6603: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 6604: cens=ivector(1,n);
6605: ageexmed=vector(1,n);
6606: agecens=vector(1,n);
6607: dcwave=ivector(1,n);
6608:
6609: for (i=1; i<=imx; i++){
6610: dcwave[i]=-1;
6611: for (m=firstpass; m<=lastpass; m++)
6612: if (s[m][i]>nlstate) {
6613: dcwave[i]=m;
6614: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
6615: break;
6616: }
6617: }
6618:
6619: for (i=1; i<=imx; i++) {
6620: if (wav[i]>0){
6621: ageexmed[i]=agev[mw[1][i]][i];
6622: j=wav[i];
6623: agecens[i]=1.;
6624:
6625: if (ageexmed[i]> 1 && wav[i] > 0){
6626: agecens[i]=agev[mw[j][i]][i];
6627: cens[i]= 1;
6628: }else if (ageexmed[i]< 1)
6629: cens[i]= -1;
6630: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
6631: cens[i]=0 ;
6632: }
6633: else cens[i]=-1;
6634: }
6635:
6636: for (i=1;i<=NDIM;i++) {
6637: for (j=1;j<=NDIM;j++)
6638: ximort[i][j]=(i == j ? 1.0 : 0.0);
6639: }
6640:
1.145 brouard 6641: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 6642: /*printf("%lf %lf", p[1], p[2]);*/
6643:
6644:
1.136 brouard 6645: #ifdef GSL
6646: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 6647: #else
1.126 brouard 6648: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 6649: #endif
1.126 brouard 6650: strcpy(filerespow,"pow-mort");
6651: strcat(filerespow,fileres);
6652: if((ficrespow=fopen(filerespow,"w"))==NULL) {
6653: printf("Problem with resultfile: %s\n", filerespow);
6654: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
6655: }
1.136 brouard 6656: #ifdef GSL
6657: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 6658: #else
1.126 brouard 6659: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 6660: #endif
1.126 brouard 6661: /* for (i=1;i<=nlstate;i++)
6662: for(j=1;j<=nlstate+ndeath;j++)
6663: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
6664: */
6665: fprintf(ficrespow,"\n");
1.136 brouard 6666: #ifdef GSL
6667: /* gsl starts here */
6668: T = gsl_multimin_fminimizer_nmsimplex;
6669: gsl_multimin_fminimizer *sfm = NULL;
6670: gsl_vector *ss, *x;
6671: gsl_multimin_function minex_func;
6672:
6673: /* Initial vertex size vector */
6674: ss = gsl_vector_alloc (NDIM);
6675:
6676: if (ss == NULL){
6677: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
6678: }
6679: /* Set all step sizes to 1 */
6680: gsl_vector_set_all (ss, 0.001);
6681:
6682: /* Starting point */
1.126 brouard 6683:
1.136 brouard 6684: x = gsl_vector_alloc (NDIM);
6685:
6686: if (x == NULL){
6687: gsl_vector_free(ss);
6688: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
6689: }
6690:
6691: /* Initialize method and iterate */
6692: /* p[1]=0.0268; p[NDIM]=0.083; */
6693: /* gsl_vector_set(x, 0, 0.0268); */
6694: /* gsl_vector_set(x, 1, 0.083); */
6695: gsl_vector_set(x, 0, p[1]);
6696: gsl_vector_set(x, 1, p[2]);
6697:
6698: minex_func.f = &gompertz_f;
6699: minex_func.n = NDIM;
6700: minex_func.params = (void *)&p; /* ??? */
6701:
6702: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
6703: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
6704:
6705: printf("Iterations beginning .....\n\n");
6706: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
6707:
6708: iteri=0;
6709: while (rval == GSL_CONTINUE){
6710: iteri++;
6711: status = gsl_multimin_fminimizer_iterate(sfm);
6712:
6713: if (status) printf("error: %s\n", gsl_strerror (status));
6714: fflush(0);
6715:
6716: if (status)
6717: break;
6718:
6719: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
6720: ssval = gsl_multimin_fminimizer_size (sfm);
6721:
6722: if (rval == GSL_SUCCESS)
6723: printf ("converged to a local maximum at\n");
6724:
6725: printf("%5d ", iteri);
6726: for (it = 0; it < NDIM; it++){
6727: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
6728: }
6729: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
6730: }
6731:
6732: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
6733:
6734: gsl_vector_free(x); /* initial values */
6735: gsl_vector_free(ss); /* inital step size */
6736: for (it=0; it<NDIM; it++){
6737: p[it+1]=gsl_vector_get(sfm->x,it);
6738: fprintf(ficrespow," %.12lf", p[it]);
6739: }
6740: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
6741: #endif
6742: #ifdef POWELL
6743: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
6744: #endif
1.126 brouard 6745: fclose(ficrespow);
6746:
6747: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
6748:
6749: for(i=1; i <=NDIM; i++)
6750: for(j=i+1;j<=NDIM;j++)
6751: matcov[i][j]=matcov[j][i];
6752:
6753: printf("\nCovariance matrix\n ");
6754: for(i=1; i <=NDIM; i++) {
6755: for(j=1;j<=NDIM;j++){
6756: printf("%f ",matcov[i][j]);
6757: }
6758: printf("\n ");
6759: }
6760:
6761: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
6762: for (i=1;i<=NDIM;i++)
6763: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
6764:
6765: lsurv=vector(1,AGESUP);
6766: lpop=vector(1,AGESUP);
6767: tpop=vector(1,AGESUP);
6768: lsurv[agegomp]=100000;
6769:
6770: for (k=agegomp;k<=AGESUP;k++) {
6771: agemortsup=k;
6772: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
6773: }
6774:
6775: for (k=agegomp;k<agemortsup;k++)
6776: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
6777:
6778: for (k=agegomp;k<agemortsup;k++){
6779: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
6780: sumlpop=sumlpop+lpop[k];
6781: }
6782:
6783: tpop[agegomp]=sumlpop;
6784: for (k=agegomp;k<(agemortsup-3);k++){
6785: /* tpop[k+1]=2;*/
6786: tpop[k+1]=tpop[k]-lpop[k];
6787: }
6788:
6789:
6790: printf("\nAge lx qx dx Lx Tx e(x)\n");
6791: for (k=agegomp;k<(agemortsup-2);k++)
6792: 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]);
6793:
6794:
6795: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6796: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6797:
6798: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
6799: stepm, weightopt,\
6800: model,imx,p,matcov,agemortsup);
6801:
6802: free_vector(lsurv,1,AGESUP);
6803: free_vector(lpop,1,AGESUP);
6804: free_vector(tpop,1,AGESUP);
1.136 brouard 6805: #ifdef GSL
6806: free_ivector(cens,1,n);
6807: free_vector(agecens,1,n);
6808: free_ivector(dcwave,1,n);
6809: free_matrix(ximort,1,NDIM,1,NDIM);
6810: #endif
1.126 brouard 6811: } /* Endof if mle==-3 */
6812:
6813: else{ /* For mle >=1 */
1.132 brouard 6814: globpr=0;/* debug */
6815: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 6816: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6817: for (k=1; k<=npar;k++)
6818: printf(" %d %8.5f",k,p[k]);
6819: printf("\n");
6820: globpr=1; /* to print the contributions */
6821: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6822: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6823: for (k=1; k<=npar;k++)
6824: printf(" %d %8.5f",k,p[k]);
6825: printf("\n");
6826: if(mle>=1){ /* Could be 1 or 2 */
6827: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
6828: }
6829:
6830: /*--------- results files --------------*/
6831: fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
6832:
6833:
6834: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6835: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6836: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6837: for(i=1,jk=1; i <=nlstate; i++){
6838: for(k=1; k <=(nlstate+ndeath); k++){
6839: if (k != i) {
6840: printf("%d%d ",i,k);
6841: fprintf(ficlog,"%d%d ",i,k);
6842: fprintf(ficres,"%1d%1d ",i,k);
6843: for(j=1; j <=ncovmodel; j++){
6844: printf("%lf ",p[jk]);
6845: fprintf(ficlog,"%lf ",p[jk]);
6846: fprintf(ficres,"%lf ",p[jk]);
6847: jk++;
6848: }
6849: printf("\n");
6850: fprintf(ficlog,"\n");
6851: fprintf(ficres,"\n");
6852: }
6853: }
6854: }
6855: if(mle!=0){
6856: /* Computing hessian and covariance matrix */
6857: ftolhess=ftol; /* Usually correct */
6858: hesscov(matcov, p, npar, delti, ftolhess, func);
6859: }
6860: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
6861: printf("# Scales (for hessian or gradient estimation)\n");
6862: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
6863: for(i=1,jk=1; i <=nlstate; i++){
6864: for(j=1; j <=nlstate+ndeath; j++){
6865: if (j!=i) {
6866: fprintf(ficres,"%1d%1d",i,j);
6867: printf("%1d%1d",i,j);
6868: fprintf(ficlog,"%1d%1d",i,j);
6869: for(k=1; k<=ncovmodel;k++){
6870: printf(" %.5e",delti[jk]);
6871: fprintf(ficlog," %.5e",delti[jk]);
6872: fprintf(ficres," %.5e",delti[jk]);
6873: jk++;
6874: }
6875: printf("\n");
6876: fprintf(ficlog,"\n");
6877: fprintf(ficres,"\n");
6878: }
6879: }
6880: }
6881:
6882: 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");
6883: if(mle>=1)
6884: 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");
6885: 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");
6886: /* # 121 Var(a12)\n\ */
6887: /* # 122 Cov(b12,a12) Var(b12)\n\ */
6888: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
6889: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
6890: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
6891: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
6892: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
6893: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
6894:
6895:
6896: /* Just to have a covariance matrix which will be more understandable
6897: even is we still don't want to manage dictionary of variables
6898: */
6899: for(itimes=1;itimes<=2;itimes++){
6900: jj=0;
6901: for(i=1; i <=nlstate; i++){
6902: for(j=1; j <=nlstate+ndeath; j++){
6903: if(j==i) continue;
6904: for(k=1; k<=ncovmodel;k++){
6905: jj++;
6906: ca[0]= k+'a'-1;ca[1]='\0';
6907: if(itimes==1){
6908: if(mle>=1)
6909: printf("#%1d%1d%d",i,j,k);
6910: fprintf(ficlog,"#%1d%1d%d",i,j,k);
6911: fprintf(ficres,"#%1d%1d%d",i,j,k);
6912: }else{
6913: if(mle>=1)
6914: printf("%1d%1d%d",i,j,k);
6915: fprintf(ficlog,"%1d%1d%d",i,j,k);
6916: fprintf(ficres,"%1d%1d%d",i,j,k);
6917: }
6918: ll=0;
6919: for(li=1;li <=nlstate; li++){
6920: for(lj=1;lj <=nlstate+ndeath; lj++){
6921: if(lj==li) continue;
6922: for(lk=1;lk<=ncovmodel;lk++){
6923: ll++;
6924: if(ll<=jj){
6925: cb[0]= lk +'a'-1;cb[1]='\0';
6926: if(ll<jj){
6927: if(itimes==1){
6928: if(mle>=1)
6929: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6930: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6931: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6932: }else{
6933: if(mle>=1)
6934: printf(" %.5e",matcov[jj][ll]);
6935: fprintf(ficlog," %.5e",matcov[jj][ll]);
6936: fprintf(ficres," %.5e",matcov[jj][ll]);
6937: }
6938: }else{
6939: if(itimes==1){
6940: if(mle>=1)
6941: printf(" Var(%s%1d%1d)",ca,i,j);
6942: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
6943: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
6944: }else{
6945: if(mle>=1)
6946: printf(" %.5e",matcov[jj][ll]);
6947: fprintf(ficlog," %.5e",matcov[jj][ll]);
6948: fprintf(ficres," %.5e",matcov[jj][ll]);
6949: }
6950: }
6951: }
6952: } /* end lk */
6953: } /* end lj */
6954: } /* end li */
6955: if(mle>=1)
6956: printf("\n");
6957: fprintf(ficlog,"\n");
6958: fprintf(ficres,"\n");
6959: numlinepar++;
6960: } /* end k*/
6961: } /*end j */
6962: } /* end i */
6963: } /* end itimes */
6964:
6965: fflush(ficlog);
6966: fflush(ficres);
6967:
6968: while((c=getc(ficpar))=='#' && c!= EOF){
6969: ungetc(c,ficpar);
6970: fgets(line, MAXLINE, ficpar);
1.141 brouard 6971: fputs(line,stdout);
1.126 brouard 6972: fputs(line,ficparo);
6973: }
6974: ungetc(c,ficpar);
6975:
6976: estepm=0;
6977: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
6978: if (estepm==0 || estepm < stepm) estepm=stepm;
6979: if (fage <= 2) {
6980: bage = ageminpar;
6981: fage = agemaxpar;
6982: }
6983:
6984: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
6985: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6986: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6987:
6988: while((c=getc(ficpar))=='#' && c!= EOF){
6989: ungetc(c,ficpar);
6990: fgets(line, MAXLINE, ficpar);
1.141 brouard 6991: fputs(line,stdout);
1.126 brouard 6992: fputs(line,ficparo);
6993: }
6994: ungetc(c,ficpar);
6995:
6996: 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);
6997: 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);
6998: 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);
6999: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
7000: 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);
7001:
7002: while((c=getc(ficpar))=='#' && c!= EOF){
7003: ungetc(c,ficpar);
7004: fgets(line, MAXLINE, ficpar);
1.141 brouard 7005: fputs(line,stdout);
1.126 brouard 7006: fputs(line,ficparo);
7007: }
7008: ungetc(c,ficpar);
7009:
7010:
7011: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
7012: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
7013:
7014: fscanf(ficpar,"pop_based=%d\n",&popbased);
7015: fprintf(ficparo,"pop_based=%d\n",popbased);
7016: fprintf(ficres,"pop_based=%d\n",popbased);
7017:
7018: while((c=getc(ficpar))=='#' && c!= EOF){
7019: ungetc(c,ficpar);
7020: fgets(line, MAXLINE, ficpar);
1.141 brouard 7021: fputs(line,stdout);
1.126 brouard 7022: fputs(line,ficparo);
7023: }
7024: ungetc(c,ficpar);
7025:
7026: 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);
7027: 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);
7028: 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);
7029: 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);
7030: 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);
7031: /* day and month of proj2 are not used but only year anproj2.*/
7032:
7033:
7034:
1.145 brouard 7035: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
7036: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 7037:
7038: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
7039: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
7040:
7041: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
7042: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
7043: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
7044:
7045: /*------------ free_vector -------------*/
7046: /* chdir(path); */
7047:
7048: free_ivector(wav,1,imx);
7049: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
7050: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
7051: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
7052: free_lvector(num,1,n);
7053: free_vector(agedc,1,n);
7054: /*free_matrix(covar,0,NCOVMAX,1,n);*/
7055: /*free_matrix(covar,1,NCOVMAX,1,n);*/
7056: fclose(ficparo);
7057: fclose(ficres);
7058:
7059:
7060: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 7061: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
7062: prlim=matrix(1,nlstate,1,nlstate);
7063: prevalence_limit(p, prlim, ageminpar, agemaxpar);
1.126 brouard 7064: fclose(ficrespl);
7065:
1.145 brouard 7066: #ifdef FREEEXIT2
7067: #include "freeexit2.h"
7068: #endif
7069:
1.126 brouard 7070: /*------------- h Pij x at various ages ------------*/
1.180 brouard 7071: /*#include "hpijx.h"*/
7072: hPijx(p, bage, fage);
1.145 brouard 7073: fclose(ficrespij);
1.126 brouard 7074:
1.145 brouard 7075: /*-------------- Variance of one-step probabilities---*/
7076: k=1;
1.126 brouard 7077: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
7078:
7079:
7080: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7081: for(i=1;i<=AGESUP;i++)
7082: for(j=1;j<=NCOVMAX;j++)
7083: for(k=1;k<=NCOVMAX;k++)
7084: probs[i][j][k]=0.;
7085:
7086: /*---------- Forecasting ------------------*/
7087: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
7088: if(prevfcast==1){
7089: /* if(stepm ==1){*/
7090: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
7091: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
7092: /* } */
7093: /* else{ */
7094: /* erreur=108; */
7095: /* 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); */
7096: /* 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); */
7097: /* } */
7098: }
7099:
7100:
1.127 brouard 7101: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
7102:
7103: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
7104: /* 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",\
7105: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
7106: */
1.126 brouard 7107:
1.127 brouard 7108: if (mobilav!=0) {
7109: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7110: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
7111: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
7112: printf(" Error in movingaverage mobilav=%d\n",mobilav);
7113: }
1.126 brouard 7114: }
7115:
7116:
1.127 brouard 7117: /*---------- Health expectancies, no variances ------------*/
7118:
1.126 brouard 7119: strcpy(filerese,"e");
7120: strcat(filerese,fileres);
7121: if((ficreseij=fopen(filerese,"w"))==NULL) {
7122: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
7123: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
7124: }
7125: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
7126: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.145 brouard 7127: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7128: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7129:
7130: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.127 brouard 7131: fprintf(ficreseij,"\n#****** ");
7132: for(j=1;j<=cptcoveff;j++) {
7133: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7134: }
7135: fprintf(ficreseij,"******\n");
7136:
7137: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7138: oldm=oldms;savm=savms;
7139: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
7140:
7141: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.145 brouard 7142: /*}*/
1.127 brouard 7143: }
7144: fclose(ficreseij);
7145:
7146:
7147: /*---------- Health expectancies and variances ------------*/
7148:
7149:
7150: strcpy(filerest,"t");
7151: strcat(filerest,fileres);
7152: if((ficrest=fopen(filerest,"w"))==NULL) {
7153: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
7154: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
7155: }
7156: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
7157: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
7158:
1.126 brouard 7159:
7160: strcpy(fileresstde,"stde");
7161: strcat(fileresstde,fileres);
7162: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
7163: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
7164: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
7165: }
7166: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
7167: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
7168:
7169: strcpy(filerescve,"cve");
7170: strcat(filerescve,fileres);
7171: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
7172: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
7173: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
7174: }
7175: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
7176: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
7177:
7178: strcpy(fileresv,"v");
7179: strcat(fileresv,fileres);
7180: if((ficresvij=fopen(fileresv,"w"))==NULL) {
7181: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
7182: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
7183: }
7184: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
7185: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
7186:
1.145 brouard 7187: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7188: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7189:
7190: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7191: fprintf(ficrest,"\n#****** ");
1.126 brouard 7192: for(j=1;j<=cptcoveff;j++)
7193: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7194: fprintf(ficrest,"******\n");
7195:
7196: fprintf(ficresstdeij,"\n#****** ");
7197: fprintf(ficrescveij,"\n#****** ");
7198: for(j=1;j<=cptcoveff;j++) {
7199: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7200: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7201: }
7202: fprintf(ficresstdeij,"******\n");
7203: fprintf(ficrescveij,"******\n");
7204:
7205: fprintf(ficresvij,"\n#****** ");
7206: for(j=1;j<=cptcoveff;j++)
7207: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7208: fprintf(ficresvij,"******\n");
7209:
7210: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7211: oldm=oldms;savm=savms;
1.127 brouard 7212: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
1.145 brouard 7213: /*
7214: */
7215: /* goto endfree; */
1.126 brouard 7216:
7217: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7218: pstamp(ficrest);
1.145 brouard 7219:
7220:
1.128 brouard 7221: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.145 brouard 7222: oldm=oldms;savm=savms; /* Segmentation fault */
1.161 brouard 7223: cptcod= 0; /* To be deleted */
7224: 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 */
1.145 brouard 7225: fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# (weighted average of eij where weights are ");
1.128 brouard 7226: if(vpopbased==1)
7227: 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);
7228: else
7229: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
7230: fprintf(ficrest,"# Age e.. (std) ");
7231: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
7232: fprintf(ficrest,"\n");
1.126 brouard 7233:
1.128 brouard 7234: epj=vector(1,nlstate+1);
7235: for(age=bage; age <=fage ;age++){
7236: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
7237: if (vpopbased==1) {
7238: if(mobilav ==0){
7239: for(i=1; i<=nlstate;i++)
7240: prlim[i][i]=probs[(int)age][i][k];
7241: }else{ /* mobilav */
7242: for(i=1; i<=nlstate;i++)
7243: prlim[i][i]=mobaverage[(int)age][i][k];
7244: }
1.126 brouard 7245: }
7246:
1.128 brouard 7247: fprintf(ficrest," %4.0f",age);
7248: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
7249: for(i=1, epj[j]=0.;i <=nlstate;i++) {
7250: epj[j] += prlim[i][i]*eij[i][j][(int)age];
7251: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
7252: }
7253: epj[nlstate+1] +=epj[j];
1.126 brouard 7254: }
7255:
1.128 brouard 7256: for(i=1, vepp=0.;i <=nlstate;i++)
7257: for(j=1;j <=nlstate;j++)
7258: vepp += vareij[i][j][(int)age];
7259: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
7260: for(j=1;j <=nlstate;j++){
7261: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
7262: }
7263: fprintf(ficrest,"\n");
1.126 brouard 7264: }
7265: }
7266: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
7267: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
7268: free_vector(epj,1,nlstate+1);
1.145 brouard 7269: /*}*/
1.126 brouard 7270: }
7271: free_vector(weight,1,n);
1.145 brouard 7272: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.126 brouard 7273: free_imatrix(s,1,maxwav+1,1,n);
7274: free_matrix(anint,1,maxwav,1,n);
7275: free_matrix(mint,1,maxwav,1,n);
7276: free_ivector(cod,1,n);
7277: free_ivector(tab,1,NCOVMAX);
7278: fclose(ficresstdeij);
7279: fclose(ficrescveij);
7280: fclose(ficresvij);
7281: fclose(ficrest);
7282: fclose(ficpar);
7283:
7284: /*------- Variance of period (stable) prevalence------*/
7285:
7286: strcpy(fileresvpl,"vpl");
7287: strcat(fileresvpl,fileres);
7288: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
7289: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
7290: exit(0);
7291: }
7292: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
7293:
1.145 brouard 7294: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7295: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7296:
7297: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7298: fprintf(ficresvpl,"\n#****** ");
1.126 brouard 7299: for(j=1;j<=cptcoveff;j++)
7300: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7301: fprintf(ficresvpl,"******\n");
7302:
7303: varpl=matrix(1,nlstate,(int) bage, (int) fage);
7304: oldm=oldms;savm=savms;
7305: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
7306: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 7307: /*}*/
1.126 brouard 7308: }
7309:
7310: fclose(ficresvpl);
7311:
7312: /*---------- End : free ----------------*/
7313: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7314: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7315: } /* mle==-3 arrives here for freeing */
1.164 brouard 7316: /* endfree:*/
1.141 brouard 7317: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.126 brouard 7318: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
7319: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
7320: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
7321: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
7322: free_matrix(covar,0,NCOVMAX,1,n);
7323: free_matrix(matcov,1,npar,1,npar);
7324: /*free_vector(delti,1,npar);*/
7325: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7326: free_matrix(agev,1,maxwav,1,imx);
7327: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7328:
1.145 brouard 7329: free_ivector(ncodemax,1,NCOVMAX);
7330: free_ivector(Tvar,1,NCOVMAX);
7331: free_ivector(Tprod,1,NCOVMAX);
7332: free_ivector(Tvaraff,1,NCOVMAX);
7333: free_ivector(Tage,1,NCOVMAX);
1.126 brouard 7334:
7335: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
7336: free_imatrix(codtab,1,100,1,10);
7337: fflush(fichtm);
7338: fflush(ficgp);
7339:
7340:
7341: if((nberr >0) || (nbwarn>0)){
7342: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
7343: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
7344: }else{
7345: printf("End of Imach\n");
7346: fprintf(ficlog,"End of Imach\n");
7347: }
7348: printf("See log file on %s\n",filelog);
7349: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 7350: /*(void) gettimeofday(&end_time,&tzp);*/
7351: rend_time = time(NULL);
7352: end_time = *localtime(&rend_time);
7353: /* tml = *localtime(&end_time.tm_sec); */
7354: strcpy(strtend,asctime(&end_time));
1.126 brouard 7355: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
7356: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 7357: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.126 brouard 7358:
1.157 brouard 7359: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
7360: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
7361: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 7362: /* printf("Total time was %d uSec.\n", total_usecs);*/
7363: /* if(fileappend(fichtm,optionfilehtm)){ */
7364: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7365: fclose(fichtm);
7366: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7367: fclose(fichtmcov);
7368: fclose(ficgp);
7369: fclose(ficlog);
7370: /*------ End -----------*/
7371:
7372:
7373: printf("Before Current directory %s!\n",pathcd);
1.184 ! brouard 7374: #ifdef WIN32
! 7375: if (_chdir(pathcd) != 0)
! 7376: printf("Can't move to directory %s!\n",path);
! 7377: if(_getcwd(pathcd,MAXLINE) > 0)
! 7378: #else
1.126 brouard 7379: if(chdir(pathcd) != 0)
1.184 ! brouard 7380: printf("Can't move to directory %s!\n", path);
! 7381: if (getcwd(pathcd, MAXLINE) > 0)
! 7382: #endif
1.126 brouard 7383: printf("Current directory %s!\n",pathcd);
7384: /*strcat(plotcmd,CHARSEPARATOR);*/
7385: sprintf(plotcmd,"gnuplot");
1.157 brouard 7386: #ifdef _WIN32
1.126 brouard 7387: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
7388: #endif
7389: if(!stat(plotcmd,&info)){
1.158 brouard 7390: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 7391: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 7392: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 7393: }else
7394: strcpy(pplotcmd,plotcmd);
1.157 brouard 7395: #ifdef __unix
1.126 brouard 7396: strcpy(plotcmd,GNUPLOTPROGRAM);
7397: if(!stat(plotcmd,&info)){
1.158 brouard 7398: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 7399: }else
7400: strcpy(pplotcmd,plotcmd);
7401: #endif
7402: }else
7403: strcpy(pplotcmd,plotcmd);
7404:
7405: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 7406: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 7407:
7408: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 7409: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 7410: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 7411: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 7412: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 7413: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 7414: }
1.158 brouard 7415: printf(" Successful, please wait...");
1.126 brouard 7416: while (z[0] != 'q') {
7417: /* chdir(path); */
1.154 brouard 7418: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 7419: scanf("%s",z);
7420: /* if (z[0] == 'c') system("./imach"); */
7421: if (z[0] == 'e') {
1.158 brouard 7422: #ifdef __APPLE__
1.152 brouard 7423: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 7424: #elif __linux
7425: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 7426: #else
1.152 brouard 7427: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 7428: #endif
7429: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
7430: system(pplotcmd);
1.126 brouard 7431: }
7432: else if (z[0] == 'g') system(plotcmd);
7433: else if (z[0] == 'q') exit(0);
7434: }
7435: end:
7436: while (z[0] != 'q') {
7437: printf("\nType q for exiting: ");
7438: scanf("%s",z);
7439: }
7440: }
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