Annotation of imach/src/imach.c, revision 1.188
1.188 ! brouard 1: /* $Id: imach.c,v 1.187 2015/04/29 09:11:15 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.188 ! brouard 4: Revision 1.187 2015/04/29 09:11:15 brouard
! 5: *** empty log message ***
! 6:
1.187 brouard 7: Revision 1.186 2015/04/23 12:01:52 brouard
8: Summary: V1*age is working now, version 0.98q1
9:
10: Some codes had been disabled in order to simplify and Vn*age was
11: working in the optimization phase, ie, giving correct MLE parameters,
12: but, as usual, outputs were not correct and program core dumped.
13:
1.186 brouard 14: Revision 1.185 2015/03/11 13:26:42 brouard
15: Summary: Inclusion of compile and links command line for Intel Compiler
16:
1.185 brouard 17: Revision 1.184 2015/03/11 11:52:39 brouard
18: Summary: Back from Windows 8. Intel Compiler
19:
1.184 brouard 20: Revision 1.183 2015/03/10 20:34:32 brouard
21: Summary: 0.98q0, trying with directest, mnbrak fixed
22:
23: We use directest instead of original Powell test; probably no
24: incidence on the results, but better justifications;
25: We fixed Numerical Recipes mnbrak routine which was wrong and gave
26: wrong results.
27:
1.183 brouard 28: Revision 1.182 2015/02/12 08:19:57 brouard
29: Summary: Trying to keep directest which seems simpler and more general
30: Author: Nicolas Brouard
31:
1.182 brouard 32: Revision 1.181 2015/02/11 23:22:24 brouard
33: Summary: Comments on Powell added
34:
35: Author:
36:
1.181 brouard 37: Revision 1.180 2015/02/11 17:33:45 brouard
38: Summary: Finishing move from main to function (hpijx and prevalence_limit)
39:
1.180 brouard 40: Revision 1.179 2015/01/04 09:57:06 brouard
41: Summary: back to OS/X
42:
1.179 brouard 43: Revision 1.178 2015/01/04 09:35:48 brouard
44: *** empty log message ***
45:
1.178 brouard 46: Revision 1.177 2015/01/03 18:40:56 brouard
47: Summary: Still testing ilc32 on OSX
48:
1.177 brouard 49: Revision 1.176 2015/01/03 16:45:04 brouard
50: *** empty log message ***
51:
1.176 brouard 52: Revision 1.175 2015/01/03 16:33:42 brouard
53: *** empty log message ***
54:
1.175 brouard 55: Revision 1.174 2015/01/03 16:15:49 brouard
56: Summary: Still in cross-compilation
57:
1.174 brouard 58: Revision 1.173 2015/01/03 12:06:26 brouard
59: Summary: trying to detect cross-compilation
60:
1.173 brouard 61: Revision 1.172 2014/12/27 12:07:47 brouard
62: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
63:
1.172 brouard 64: Revision 1.171 2014/12/23 13:26:59 brouard
65: Summary: Back from Visual C
66:
67: Still problem with utsname.h on Windows
68:
1.171 brouard 69: Revision 1.170 2014/12/23 11:17:12 brouard
70: Summary: Cleaning some \%% back to %%
71:
72: The escape was mandatory for a specific compiler (which one?), but too many warnings.
73:
1.170 brouard 74: Revision 1.169 2014/12/22 23:08:31 brouard
75: Summary: 0.98p
76:
77: Outputs some informations on compiler used, OS etc. Testing on different platforms.
78:
1.169 brouard 79: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 80: Summary: update
1.169 brouard 81:
1.168 brouard 82: Revision 1.167 2014/12/22 13:50:56 brouard
83: Summary: Testing uname and compiler version and if compiled 32 or 64
84:
85: Testing on Linux 64
86:
1.167 brouard 87: Revision 1.166 2014/12/22 11:40:47 brouard
88: *** empty log message ***
89:
1.166 brouard 90: Revision 1.165 2014/12/16 11:20:36 brouard
91: Summary: After compiling on Visual C
92:
93: * imach.c (Module): Merging 1.61 to 1.162
94:
1.165 brouard 95: Revision 1.164 2014/12/16 10:52:11 brouard
96: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
97:
98: * imach.c (Module): Merging 1.61 to 1.162
99:
1.164 brouard 100: Revision 1.163 2014/12/16 10:30:11 brouard
101: * imach.c (Module): Merging 1.61 to 1.162
102:
1.163 brouard 103: Revision 1.162 2014/09/25 11:43:39 brouard
104: Summary: temporary backup 0.99!
105:
1.162 brouard 106: Revision 1.1 2014/09/16 11:06:58 brouard
107: Summary: With some code (wrong) for nlopt
108:
109: Author:
110:
111: Revision 1.161 2014/09/15 20:41:41 brouard
112: Summary: Problem with macro SQR on Intel compiler
113:
1.161 brouard 114: Revision 1.160 2014/09/02 09:24:05 brouard
115: *** empty log message ***
116:
1.160 brouard 117: Revision 1.159 2014/09/01 10:34:10 brouard
118: Summary: WIN32
119: Author: Brouard
120:
1.159 brouard 121: Revision 1.158 2014/08/27 17:11:51 brouard
122: *** empty log message ***
123:
1.158 brouard 124: Revision 1.157 2014/08/27 16:26:55 brouard
125: Summary: Preparing windows Visual studio version
126: Author: Brouard
127:
128: In order to compile on Visual studio, time.h is now correct and time_t
129: and tm struct should be used. difftime should be used but sometimes I
130: just make the differences in raw time format (time(&now).
131: Trying to suppress #ifdef LINUX
132: Add xdg-open for __linux in order to open default browser.
133:
1.157 brouard 134: Revision 1.156 2014/08/25 20:10:10 brouard
135: *** empty log message ***
136:
1.156 brouard 137: Revision 1.155 2014/08/25 18:32:34 brouard
138: Summary: New compile, minor changes
139: Author: Brouard
140:
1.155 brouard 141: Revision 1.154 2014/06/20 17:32:08 brouard
142: Summary: Outputs now all graphs of convergence to period prevalence
143:
1.154 brouard 144: Revision 1.153 2014/06/20 16:45:46 brouard
145: Summary: If 3 live state, convergence to period prevalence on same graph
146: Author: Brouard
147:
1.153 brouard 148: Revision 1.152 2014/06/18 17:54:09 brouard
149: Summary: open browser, use gnuplot on same dir than imach if not found in the path
150:
1.152 brouard 151: Revision 1.151 2014/06/18 16:43:30 brouard
152: *** empty log message ***
153:
1.151 brouard 154: Revision 1.150 2014/06/18 16:42:35 brouard
155: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
156: Author: brouard
157:
1.150 brouard 158: Revision 1.149 2014/06/18 15:51:14 brouard
159: Summary: Some fixes in parameter files errors
160: Author: Nicolas Brouard
161:
1.149 brouard 162: Revision 1.148 2014/06/17 17:38:48 brouard
163: Summary: Nothing new
164: Author: Brouard
165:
166: Just a new packaging for OS/X version 0.98nS
167:
1.148 brouard 168: Revision 1.147 2014/06/16 10:33:11 brouard
169: *** empty log message ***
170:
1.147 brouard 171: Revision 1.146 2014/06/16 10:20:28 brouard
172: Summary: Merge
173: Author: Brouard
174:
175: Merge, before building revised version.
176:
1.146 brouard 177: Revision 1.145 2014/06/10 21:23:15 brouard
178: Summary: Debugging with valgrind
179: Author: Nicolas Brouard
180:
181: Lot of changes in order to output the results with some covariates
182: After the Edimburgh REVES conference 2014, it seems mandatory to
183: improve the code.
184: No more memory valgrind error but a lot has to be done in order to
185: continue the work of splitting the code into subroutines.
186: Also, decodemodel has been improved. Tricode is still not
187: optimal. nbcode should be improved. Documentation has been added in
188: the source code.
189:
1.144 brouard 190: Revision 1.143 2014/01/26 09:45:38 brouard
191: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
192:
193: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
194: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
195:
1.143 brouard 196: Revision 1.142 2014/01/26 03:57:36 brouard
197: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
198:
199: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
200:
1.142 brouard 201: Revision 1.141 2014/01/26 02:42:01 brouard
202: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
203:
1.141 brouard 204: Revision 1.140 2011/09/02 10:37:54 brouard
205: Summary: times.h is ok with mingw32 now.
206:
1.140 brouard 207: Revision 1.139 2010/06/14 07:50:17 brouard
208: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
209: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
210:
1.139 brouard 211: Revision 1.138 2010/04/30 18:19:40 brouard
212: *** empty log message ***
213:
1.138 brouard 214: Revision 1.137 2010/04/29 18:11:38 brouard
215: (Module): Checking covariates for more complex models
216: than V1+V2. A lot of change to be done. Unstable.
217:
1.137 brouard 218: Revision 1.136 2010/04/26 20:30:53 brouard
219: (Module): merging some libgsl code. Fixing computation
220: of likelione (using inter/intrapolation if mle = 0) in order to
221: get same likelihood as if mle=1.
222: Some cleaning of code and comments added.
223:
1.136 brouard 224: Revision 1.135 2009/10/29 15:33:14 brouard
225: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
226:
1.135 brouard 227: Revision 1.134 2009/10/29 13:18:53 brouard
228: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
229:
1.134 brouard 230: Revision 1.133 2009/07/06 10:21:25 brouard
231: just nforces
232:
1.133 brouard 233: Revision 1.132 2009/07/06 08:22:05 brouard
234: Many tings
235:
1.132 brouard 236: Revision 1.131 2009/06/20 16:22:47 brouard
237: Some dimensions resccaled
238:
1.131 brouard 239: Revision 1.130 2009/05/26 06:44:34 brouard
240: (Module): Max Covariate is now set to 20 instead of 8. A
241: lot of cleaning with variables initialized to 0. Trying to make
242: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
243:
1.130 brouard 244: Revision 1.129 2007/08/31 13:49:27 lievre
245: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
246:
1.129 lievre 247: Revision 1.128 2006/06/30 13:02:05 brouard
248: (Module): Clarifications on computing e.j
249:
1.128 brouard 250: Revision 1.127 2006/04/28 18:11:50 brouard
251: (Module): Yes the sum of survivors was wrong since
252: imach-114 because nhstepm was no more computed in the age
253: loop. Now we define nhstepma in the age loop.
254: (Module): In order to speed up (in case of numerous covariates) we
255: compute health expectancies (without variances) in a first step
256: and then all the health expectancies with variances or standard
257: deviation (needs data from the Hessian matrices) which slows the
258: computation.
259: In the future we should be able to stop the program is only health
260: expectancies and graph are needed without standard deviations.
261:
1.127 brouard 262: Revision 1.126 2006/04/28 17:23:28 brouard
263: (Module): Yes the sum of survivors was wrong since
264: imach-114 because nhstepm was no more computed in the age
265: loop. Now we define nhstepma in the age loop.
266: Version 0.98h
267:
1.126 brouard 268: Revision 1.125 2006/04/04 15:20:31 lievre
269: Errors in calculation of health expectancies. Age was not initialized.
270: Forecasting file added.
271:
272: Revision 1.124 2006/03/22 17:13:53 lievre
273: Parameters are printed with %lf instead of %f (more numbers after the comma).
274: The log-likelihood is printed in the log file
275:
276: Revision 1.123 2006/03/20 10:52:43 brouard
277: * imach.c (Module): <title> changed, corresponds to .htm file
278: name. <head> headers where missing.
279:
280: * imach.c (Module): Weights can have a decimal point as for
281: English (a comma might work with a correct LC_NUMERIC environment,
282: otherwise the weight is truncated).
283: Modification of warning when the covariates values are not 0 or
284: 1.
285: Version 0.98g
286:
287: Revision 1.122 2006/03/20 09:45:41 brouard
288: (Module): Weights can have a decimal point as for
289: English (a comma might work with a correct LC_NUMERIC environment,
290: otherwise the weight is truncated).
291: Modification of warning when the covariates values are not 0 or
292: 1.
293: Version 0.98g
294:
295: Revision 1.121 2006/03/16 17:45:01 lievre
296: * imach.c (Module): Comments concerning covariates added
297:
298: * imach.c (Module): refinements in the computation of lli if
299: status=-2 in order to have more reliable computation if stepm is
300: not 1 month. Version 0.98f
301:
302: Revision 1.120 2006/03/16 15:10:38 lievre
303: (Module): refinements in the computation of lli if
304: status=-2 in order to have more reliable computation if stepm is
305: not 1 month. Version 0.98f
306:
307: Revision 1.119 2006/03/15 17:42:26 brouard
308: (Module): Bug if status = -2, the loglikelihood was
309: computed as likelihood omitting the logarithm. Version O.98e
310:
311: Revision 1.118 2006/03/14 18:20:07 brouard
312: (Module): varevsij Comments added explaining the second
313: table of variances if popbased=1 .
314: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
315: (Module): Function pstamp added
316: (Module): Version 0.98d
317:
318: Revision 1.117 2006/03/14 17:16:22 brouard
319: (Module): varevsij Comments added explaining the second
320: table of variances if popbased=1 .
321: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
322: (Module): Function pstamp added
323: (Module): Version 0.98d
324:
325: Revision 1.116 2006/03/06 10:29:27 brouard
326: (Module): Variance-covariance wrong links and
327: varian-covariance of ej. is needed (Saito).
328:
329: Revision 1.115 2006/02/27 12:17:45 brouard
330: (Module): One freematrix added in mlikeli! 0.98c
331:
332: Revision 1.114 2006/02/26 12:57:58 brouard
333: (Module): Some improvements in processing parameter
334: filename with strsep.
335:
336: Revision 1.113 2006/02/24 14:20:24 brouard
337: (Module): Memory leaks checks with valgrind and:
338: datafile was not closed, some imatrix were not freed and on matrix
339: allocation too.
340:
341: Revision 1.112 2006/01/30 09:55:26 brouard
342: (Module): Back to gnuplot.exe instead of wgnuplot.exe
343:
344: Revision 1.111 2006/01/25 20:38:18 brouard
345: (Module): Lots of cleaning and bugs added (Gompertz)
346: (Module): Comments can be added in data file. Missing date values
347: can be a simple dot '.'.
348:
349: Revision 1.110 2006/01/25 00:51:50 brouard
350: (Module): Lots of cleaning and bugs added (Gompertz)
351:
352: Revision 1.109 2006/01/24 19:37:15 brouard
353: (Module): Comments (lines starting with a #) are allowed in data.
354:
355: Revision 1.108 2006/01/19 18:05:42 lievre
356: Gnuplot problem appeared...
357: To be fixed
358:
359: Revision 1.107 2006/01/19 16:20:37 brouard
360: Test existence of gnuplot in imach path
361:
362: Revision 1.106 2006/01/19 13:24:36 brouard
363: Some cleaning and links added in html output
364:
365: Revision 1.105 2006/01/05 20:23:19 lievre
366: *** empty log message ***
367:
368: Revision 1.104 2005/09/30 16:11:43 lievre
369: (Module): sump fixed, loop imx fixed, and simplifications.
370: (Module): If the status is missing at the last wave but we know
371: that the person is alive, then we can code his/her status as -2
372: (instead of missing=-1 in earlier versions) and his/her
373: contributions to the likelihood is 1 - Prob of dying from last
374: health status (= 1-p13= p11+p12 in the easiest case of somebody in
375: the healthy state at last known wave). Version is 0.98
376:
377: Revision 1.103 2005/09/30 15:54:49 lievre
378: (Module): sump fixed, loop imx fixed, and simplifications.
379:
380: Revision 1.102 2004/09/15 17:31:30 brouard
381: Add the possibility to read data file including tab characters.
382:
383: Revision 1.101 2004/09/15 10:38:38 brouard
384: Fix on curr_time
385:
386: Revision 1.100 2004/07/12 18:29:06 brouard
387: Add version for Mac OS X. Just define UNIX in Makefile
388:
389: Revision 1.99 2004/06/05 08:57:40 brouard
390: *** empty log message ***
391:
392: Revision 1.98 2004/05/16 15:05:56 brouard
393: New version 0.97 . First attempt to estimate force of mortality
394: directly from the data i.e. without the need of knowing the health
395: state at each age, but using a Gompertz model: log u =a + b*age .
396: This is the basic analysis of mortality and should be done before any
397: other analysis, in order to test if the mortality estimated from the
398: cross-longitudinal survey is different from the mortality estimated
399: from other sources like vital statistic data.
400:
401: The same imach parameter file can be used but the option for mle should be -3.
402:
1.133 brouard 403: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 404: former routines in order to include the new code within the former code.
405:
406: The output is very simple: only an estimate of the intercept and of
407: the slope with 95% confident intervals.
408:
409: Current limitations:
410: A) Even if you enter covariates, i.e. with the
411: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
412: B) There is no computation of Life Expectancy nor Life Table.
413:
414: Revision 1.97 2004/02/20 13:25:42 lievre
415: Version 0.96d. Population forecasting command line is (temporarily)
416: suppressed.
417:
418: Revision 1.96 2003/07/15 15:38:55 brouard
419: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
420: rewritten within the same printf. Workaround: many printfs.
421:
422: Revision 1.95 2003/07/08 07:54:34 brouard
423: * imach.c (Repository):
424: (Repository): Using imachwizard code to output a more meaningful covariance
425: matrix (cov(a12,c31) instead of numbers.
426:
427: Revision 1.94 2003/06/27 13:00:02 brouard
428: Just cleaning
429:
430: Revision 1.93 2003/06/25 16:33:55 brouard
431: (Module): On windows (cygwin) function asctime_r doesn't
432: exist so I changed back to asctime which exists.
433: (Module): Version 0.96b
434:
435: Revision 1.92 2003/06/25 16:30:45 brouard
436: (Module): On windows (cygwin) function asctime_r doesn't
437: exist so I changed back to asctime which exists.
438:
439: Revision 1.91 2003/06/25 15:30:29 brouard
440: * imach.c (Repository): Duplicated warning errors corrected.
441: (Repository): Elapsed time after each iteration is now output. It
442: helps to forecast when convergence will be reached. Elapsed time
443: is stamped in powell. We created a new html file for the graphs
444: concerning matrix of covariance. It has extension -cov.htm.
445:
446: Revision 1.90 2003/06/24 12:34:15 brouard
447: (Module): Some bugs corrected for windows. Also, when
448: mle=-1 a template is output in file "or"mypar.txt with the design
449: of the covariance matrix to be input.
450:
451: Revision 1.89 2003/06/24 12:30:52 brouard
452: (Module): Some bugs corrected for windows. Also, when
453: mle=-1 a template is output in file "or"mypar.txt with the design
454: of the covariance matrix to be input.
455:
456: Revision 1.88 2003/06/23 17:54:56 brouard
457: * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
458:
459: Revision 1.87 2003/06/18 12:26:01 brouard
460: Version 0.96
461:
462: Revision 1.86 2003/06/17 20:04:08 brouard
463: (Module): Change position of html and gnuplot routines and added
464: routine fileappend.
465:
466: Revision 1.85 2003/06/17 13:12:43 brouard
467: * imach.c (Repository): Check when date of death was earlier that
468: current date of interview. It may happen when the death was just
469: prior to the death. In this case, dh was negative and likelihood
470: was wrong (infinity). We still send an "Error" but patch by
471: assuming that the date of death was just one stepm after the
472: interview.
473: (Repository): Because some people have very long ID (first column)
474: we changed int to long in num[] and we added a new lvector for
475: memory allocation. But we also truncated to 8 characters (left
476: truncation)
477: (Repository): No more line truncation errors.
478:
479: Revision 1.84 2003/06/13 21:44:43 brouard
480: * imach.c (Repository): Replace "freqsummary" at a correct
481: place. It differs from routine "prevalence" which may be called
482: many times. Probs is memory consuming and must be used with
483: parcimony.
484: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
485:
486: Revision 1.83 2003/06/10 13:39:11 lievre
487: *** empty log message ***
488:
489: Revision 1.82 2003/06/05 15:57:20 brouard
490: Add log in imach.c and fullversion number is now printed.
491:
492: */
493: /*
494: Interpolated Markov Chain
495:
496: Short summary of the programme:
497:
498: This program computes Healthy Life Expectancies from
499: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
500: first survey ("cross") where individuals from different ages are
501: interviewed on their health status or degree of disability (in the
502: case of a health survey which is our main interest) -2- at least a
503: second wave of interviews ("longitudinal") which measure each change
504: (if any) in individual health status. Health expectancies are
505: computed from the time spent in each health state according to a
506: model. More health states you consider, more time is necessary to reach the
507: Maximum Likelihood of the parameters involved in the model. The
508: simplest model is the multinomial logistic model where pij is the
509: probability to be observed in state j at the second wave
510: conditional to be observed in state i at the first wave. Therefore
511: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
512: 'age' is age and 'sex' is a covariate. If you want to have a more
513: complex model than "constant and age", you should modify the program
514: where the markup *Covariates have to be included here again* invites
515: you to do it. More covariates you add, slower the
516: convergence.
517:
518: The advantage of this computer programme, compared to a simple
519: multinomial logistic model, is clear when the delay between waves is not
520: identical for each individual. Also, if a individual missed an
521: intermediate interview, the information is lost, but taken into
522: account using an interpolation or extrapolation.
523:
524: hPijx is the probability to be observed in state i at age x+h
525: conditional to the observed state i at age x. The delay 'h' can be
526: split into an exact number (nh*stepm) of unobserved intermediate
527: states. This elementary transition (by month, quarter,
528: semester or year) is modelled as a multinomial logistic. The hPx
529: matrix is simply the matrix product of nh*stepm elementary matrices
530: and the contribution of each individual to the likelihood is simply
531: hPijx.
532:
533: Also this programme outputs the covariance matrix of the parameters but also
534: of the life expectancies. It also computes the period (stable) prevalence.
535:
1.133 brouard 536: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
537: Institut national d'études démographiques, Paris.
1.126 brouard 538: This software have been partly granted by Euro-REVES, a concerted action
539: from the European Union.
540: It is copyrighted identically to a GNU software product, ie programme and
541: software can be distributed freely for non commercial use. Latest version
542: can be accessed at http://euroreves.ined.fr/imach .
543:
544: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
545: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
546:
547: **********************************************************************/
548: /*
549: main
550: read parameterfile
551: read datafile
552: concatwav
553: freqsummary
554: if (mle >= 1)
555: mlikeli
556: print results files
557: if mle==1
558: computes hessian
559: read end of parameter file: agemin, agemax, bage, fage, estepm
560: begin-prev-date,...
561: open gnuplot file
562: open html file
1.145 brouard 563: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
564: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
565: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
566: freexexit2 possible for memory heap.
567:
568: h Pij x | pij_nom ficrestpij
569: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
570: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
571: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
572:
573: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
574: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
575: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
576: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
577: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
578:
1.126 brouard 579: forecasting if prevfcast==1 prevforecast call prevalence()
580: health expectancies
581: Variance-covariance of DFLE
582: prevalence()
583: movingaverage()
584: varevsij()
585: if popbased==1 varevsij(,popbased)
586: total life expectancies
587: Variance of period (stable) prevalence
588: end
589: */
590:
1.187 brouard 591: /* #define DEBUG */
592: /* #define DEBUGBRENT */
1.165 brouard 593: #define POWELL /* Instead of NLOPT */
1.186 brouard 594: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
595: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 596:
597: #include <math.h>
598: #include <stdio.h>
599: #include <stdlib.h>
600: #include <string.h>
1.159 brouard 601:
602: #ifdef _WIN32
603: #include <io.h>
1.172 brouard 604: #include <windows.h>
605: #include <tchar.h>
1.159 brouard 606: #else
1.126 brouard 607: #include <unistd.h>
1.159 brouard 608: #endif
1.126 brouard 609:
610: #include <limits.h>
611: #include <sys/types.h>
1.171 brouard 612:
613: #if defined(__GNUC__)
614: #include <sys/utsname.h> /* Doesn't work on Windows */
615: #endif
616:
1.126 brouard 617: #include <sys/stat.h>
618: #include <errno.h>
1.159 brouard 619: /* extern int errno; */
1.126 brouard 620:
1.157 brouard 621: /* #ifdef LINUX */
622: /* #include <time.h> */
623: /* #include "timeval.h" */
624: /* #else */
625: /* #include <sys/time.h> */
626: /* #endif */
627:
1.126 brouard 628: #include <time.h>
629:
1.136 brouard 630: #ifdef GSL
631: #include <gsl/gsl_errno.h>
632: #include <gsl/gsl_multimin.h>
633: #endif
634:
1.167 brouard 635:
1.162 brouard 636: #ifdef NLOPT
637: #include <nlopt.h>
638: typedef struct {
639: double (* function)(double [] );
640: } myfunc_data ;
641: #endif
642:
1.126 brouard 643: /* #include <libintl.h> */
644: /* #define _(String) gettext (String) */
645:
1.141 brouard 646: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 647:
648: #define GNUPLOTPROGRAM "gnuplot"
649: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
650: #define FILENAMELENGTH 132
651:
652: #define GLOCK_ERROR_NOPATH -1 /* empty path */
653: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
654:
1.144 brouard 655: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
656: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 657:
658: #define NINTERVMAX 8
1.144 brouard 659: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
660: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
661: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.145 brouard 662: #define codtabm(h,k) 1 & (h-1) >> (k-1) ;
1.126 brouard 663: #define MAXN 20000
1.144 brouard 664: #define YEARM 12. /**< Number of months per year */
1.126 brouard 665: #define AGESUP 130
666: #define AGEBASE 40
1.164 brouard 667: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 668: #ifdef _WIN32
669: #define DIRSEPARATOR '\\'
670: #define CHARSEPARATOR "\\"
671: #define ODIRSEPARATOR '/'
672: #else
1.126 brouard 673: #define DIRSEPARATOR '/'
674: #define CHARSEPARATOR "/"
675: #define ODIRSEPARATOR '\\'
676: #endif
677:
1.188 ! brouard 678: /* $Id: imach.c,v 1.187 2015/04/29 09:11:15 brouard Exp $ */
1.126 brouard 679: /* $State: Exp $ */
680:
1.186 brouard 681: char version[]="Imach version 0.98q1, April 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
1.188 ! brouard 682: char fullversion[]="$Revision: 1.187 $ $Date: 2015/04/29 09:11:15 $";
1.126 brouard 683: char strstart[80];
684: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 685: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 686: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 687: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
688: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
689: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
690: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
691: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
692: int cptcovprodnoage=0; /**< Number of covariate products without age */
693: int cptcoveff=0; /* Total number of covariates to vary for printing results */
694: int cptcov=0; /* Working variable */
1.126 brouard 695: int npar=NPARMAX;
696: int nlstate=2; /* Number of live states */
697: int ndeath=1; /* Number of dead states */
1.130 brouard 698: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.126 brouard 699: int popbased=0;
700:
701: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 702: int maxwav=0; /* Maxim number of waves */
703: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
704: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
705: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 706: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 707: int mle=1, weightopt=0;
1.126 brouard 708: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
709: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
710: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
711: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 712: int countcallfunc=0; /* Count the number of calls to func */
1.130 brouard 713: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 714: double **matprod2(); /* test */
1.126 brouard 715: double **oldm, **newm, **savm; /* Working pointers to matrices */
716: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.136 brouard 717: /*FILE *fic ; */ /* Used in readdata only */
718: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.126 brouard 719: FILE *ficlog, *ficrespow;
1.130 brouard 720: int globpr=0; /* Global variable for printing or not */
1.126 brouard 721: double fretone; /* Only one call to likelihood */
1.130 brouard 722: long ipmx=0; /* Number of contributions */
1.126 brouard 723: double sw; /* Sum of weights */
724: char filerespow[FILENAMELENGTH];
725: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
726: FILE *ficresilk;
727: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
728: FILE *ficresprobmorprev;
729: FILE *fichtm, *fichtmcov; /* Html File */
730: FILE *ficreseij;
731: char filerese[FILENAMELENGTH];
732: FILE *ficresstdeij;
733: char fileresstde[FILENAMELENGTH];
734: FILE *ficrescveij;
735: char filerescve[FILENAMELENGTH];
736: FILE *ficresvij;
737: char fileresv[FILENAMELENGTH];
738: FILE *ficresvpl;
739: char fileresvpl[FILENAMELENGTH];
740: char title[MAXLINE];
741: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
742: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
743: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
744: char command[FILENAMELENGTH];
745: int outcmd=0;
746:
747: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
748:
749: char filelog[FILENAMELENGTH]; /* Log file */
750: char filerest[FILENAMELENGTH];
751: char fileregp[FILENAMELENGTH];
752: char popfile[FILENAMELENGTH];
753:
754: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
755:
1.157 brouard 756: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
757: /* struct timezone tzp; */
758: /* extern int gettimeofday(); */
759: struct tm tml, *gmtime(), *localtime();
760:
761: extern time_t time();
762:
763: struct tm start_time, end_time, curr_time, last_time, forecast_time;
764: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
765: struct tm tm;
766:
1.126 brouard 767: char strcurr[80], strfor[80];
768:
769: char *endptr;
770: long lval;
771: double dval;
772:
773: #define NR_END 1
774: #define FREE_ARG char*
775: #define FTOL 1.0e-10
776:
777: #define NRANSI
778: #define ITMAX 200
779:
780: #define TOL 2.0e-4
781:
782: #define CGOLD 0.3819660
783: #define ZEPS 1.0e-10
784: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
785:
786: #define GOLD 1.618034
787: #define GLIMIT 100.0
788: #define TINY 1.0e-20
789:
790: static double maxarg1,maxarg2;
791: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
792: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
793:
794: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
795: #define rint(a) floor(a+0.5)
1.166 brouard 796: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 797: #define mytinydouble 1.0e-16
1.166 brouard 798: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
799: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
800: /* static double dsqrarg; */
801: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 802: static double sqrarg;
803: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
804: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
805: int agegomp= AGEGOMP;
806:
807: int imx;
808: int stepm=1;
809: /* Stepm, step in month: minimum step interpolation*/
810:
811: int estepm;
812: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
813:
814: int m,nb;
815: long *num;
816: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
817: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
818: double **pmmij, ***probs;
819: double *ageexmed,*agecens;
820: double dateintmean=0;
821:
822: double *weight;
823: int **s; /* Status */
1.141 brouard 824: double *agedc;
1.145 brouard 825: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 826: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 827: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.141 brouard 828: double idx;
829: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.145 brouard 830: int *Ndum; /** Freq of modality (tricode */
1.141 brouard 831: int **codtab; /**< codtab=imatrix(1,100,1,10); */
832: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.126 brouard 833: double *lsurv, *lpop, *tpop;
834:
1.143 brouard 835: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
836: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 837:
838: /**************** split *************************/
839: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
840: {
841: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
842: the name of the file (name), its extension only (ext) and its first part of the name (finame)
843: */
844: char *ss; /* pointer */
1.186 brouard 845: int l1=0, l2=0; /* length counters */
1.126 brouard 846:
847: l1 = strlen(path ); /* length of path */
848: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
849: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
850: if ( ss == NULL ) { /* no directory, so determine current directory */
851: strcpy( name, path ); /* we got the fullname name because no directory */
852: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
853: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
854: /* get current working directory */
855: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 856: #ifdef WIN32
857: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
858: #else
859: if (getcwd(dirc, FILENAME_MAX) == NULL) {
860: #endif
1.126 brouard 861: return( GLOCK_ERROR_GETCWD );
862: }
863: /* got dirc from getcwd*/
864: printf(" DIRC = %s \n",dirc);
865: } else { /* strip direcotry from path */
866: ss++; /* after this, the filename */
867: l2 = strlen( ss ); /* length of filename */
868: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
869: strcpy( name, ss ); /* save file name */
870: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 871: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 872: printf(" DIRC2 = %s \n",dirc);
873: }
874: /* We add a separator at the end of dirc if not exists */
875: l1 = strlen( dirc ); /* length of directory */
876: if( dirc[l1-1] != DIRSEPARATOR ){
877: dirc[l1] = DIRSEPARATOR;
878: dirc[l1+1] = 0;
879: printf(" DIRC3 = %s \n",dirc);
880: }
881: ss = strrchr( name, '.' ); /* find last / */
882: if (ss >0){
883: ss++;
884: strcpy(ext,ss); /* save extension */
885: l1= strlen( name);
886: l2= strlen(ss)+1;
887: strncpy( finame, name, l1-l2);
888: finame[l1-l2]= 0;
889: }
890:
891: return( 0 ); /* we're done */
892: }
893:
894:
895: /******************************************/
896:
897: void replace_back_to_slash(char *s, char*t)
898: {
899: int i;
900: int lg=0;
901: i=0;
902: lg=strlen(t);
903: for(i=0; i<= lg; i++) {
904: (s[i] = t[i]);
905: if (t[i]== '\\') s[i]='/';
906: }
907: }
908:
1.132 brouard 909: char *trimbb(char *out, char *in)
1.137 brouard 910: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 911: char *s;
912: s=out;
913: while (*in != '\0'){
1.137 brouard 914: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 915: in++;
916: }
917: *out++ = *in++;
918: }
919: *out='\0';
920: return s;
921: }
922:
1.187 brouard 923: /* char *substrchaine(char *out, char *in, char *chain) */
924: /* { */
925: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
926: /* char *s, *t; */
927: /* t=in;s=out; */
928: /* while ((*in != *chain) && (*in != '\0')){ */
929: /* *out++ = *in++; */
930: /* } */
931:
932: /* /\* *in matches *chain *\/ */
933: /* while ((*in++ == *chain++) && (*in != '\0')){ */
934: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
935: /* } */
936: /* in--; chain--; */
937: /* while ( (*in != '\0')){ */
938: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
939: /* *out++ = *in++; */
940: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
941: /* } */
942: /* *out='\0'; */
943: /* out=s; */
944: /* return out; */
945: /* } */
946: char *substrchaine(char *out, char *in, char *chain)
947: {
948: /* Substract chain 'chain' from 'in', return and output 'out' */
949: /* in="V1+V1*age+age*age+V2", chain="age*age" */
950:
951: char *strloc;
952:
953: strcpy (out, in);
954: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
955: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
956: if(strloc != NULL){
957: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
958: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
959: /* strcpy (strloc, strloc +strlen(chain));*/
960: }
961: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
962: return out;
963: }
964:
965:
1.145 brouard 966: char *cutl(char *blocc, char *alocc, char *in, char occ)
967: {
1.187 brouard 968: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 969: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 970: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 971: If occ is not found blocc is null and alocc is equal to in. Returns blocc
972: */
1.160 brouard 973: char *s, *t;
1.145 brouard 974: t=in;s=in;
975: while ((*in != occ) && (*in != '\0')){
976: *alocc++ = *in++;
977: }
978: if( *in == occ){
979: *(alocc)='\0';
980: s=++in;
981: }
982:
983: if (s == t) {/* occ not found */
984: *(alocc-(in-s))='\0';
985: in=s;
986: }
987: while ( *in != '\0'){
988: *blocc++ = *in++;
989: }
990:
991: *blocc='\0';
992: return t;
993: }
1.137 brouard 994: char *cutv(char *blocc, char *alocc, char *in, char occ)
995: {
1.187 brouard 996: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 997: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
998: gives blocc="abcdef2ghi" and alocc="j".
999: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1000: */
1001: char *s, *t;
1002: t=in;s=in;
1003: while (*in != '\0'){
1004: while( *in == occ){
1005: *blocc++ = *in++;
1006: s=in;
1007: }
1008: *blocc++ = *in++;
1009: }
1010: if (s == t) /* occ not found */
1011: *(blocc-(in-s))='\0';
1012: else
1013: *(blocc-(in-s)-1)='\0';
1014: in=s;
1015: while ( *in != '\0'){
1016: *alocc++ = *in++;
1017: }
1018:
1019: *alocc='\0';
1020: return s;
1021: }
1022:
1.126 brouard 1023: int nbocc(char *s, char occ)
1024: {
1025: int i,j=0;
1026: int lg=20;
1027: i=0;
1028: lg=strlen(s);
1029: for(i=0; i<= lg; i++) {
1030: if (s[i] == occ ) j++;
1031: }
1032: return j;
1033: }
1034:
1.137 brouard 1035: /* void cutv(char *u,char *v, char*t, char occ) */
1036: /* { */
1037: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1038: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1039: /* gives u="abcdef2ghi" and v="j" *\/ */
1040: /* int i,lg,j,p=0; */
1041: /* i=0; */
1042: /* lg=strlen(t); */
1043: /* for(j=0; j<=lg-1; j++) { */
1044: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1045: /* } */
1.126 brouard 1046:
1.137 brouard 1047: /* for(j=0; j<p; j++) { */
1048: /* (u[j] = t[j]); */
1049: /* } */
1050: /* u[p]='\0'; */
1.126 brouard 1051:
1.137 brouard 1052: /* for(j=0; j<= lg; j++) { */
1053: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1054: /* } */
1055: /* } */
1.126 brouard 1056:
1.160 brouard 1057: #ifdef _WIN32
1058: char * strsep(char **pp, const char *delim)
1059: {
1060: char *p, *q;
1061:
1062: if ((p = *pp) == NULL)
1063: return 0;
1064: if ((q = strpbrk (p, delim)) != NULL)
1065: {
1066: *pp = q + 1;
1067: *q = '\0';
1068: }
1069: else
1070: *pp = 0;
1071: return p;
1072: }
1073: #endif
1074:
1.126 brouard 1075: /********************** nrerror ********************/
1076:
1077: void nrerror(char error_text[])
1078: {
1079: fprintf(stderr,"ERREUR ...\n");
1080: fprintf(stderr,"%s\n",error_text);
1081: exit(EXIT_FAILURE);
1082: }
1083: /*********************** vector *******************/
1084: double *vector(int nl, int nh)
1085: {
1086: double *v;
1087: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1088: if (!v) nrerror("allocation failure in vector");
1089: return v-nl+NR_END;
1090: }
1091:
1092: /************************ free vector ******************/
1093: void free_vector(double*v, int nl, int nh)
1094: {
1095: free((FREE_ARG)(v+nl-NR_END));
1096: }
1097:
1098: /************************ivector *******************************/
1099: int *ivector(long nl,long nh)
1100: {
1101: int *v;
1102: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1103: if (!v) nrerror("allocation failure in ivector");
1104: return v-nl+NR_END;
1105: }
1106:
1107: /******************free ivector **************************/
1108: void free_ivector(int *v, long nl, long nh)
1109: {
1110: free((FREE_ARG)(v+nl-NR_END));
1111: }
1112:
1113: /************************lvector *******************************/
1114: long *lvector(long nl,long nh)
1115: {
1116: long *v;
1117: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1118: if (!v) nrerror("allocation failure in ivector");
1119: return v-nl+NR_END;
1120: }
1121:
1122: /******************free lvector **************************/
1123: void free_lvector(long *v, long nl, long nh)
1124: {
1125: free((FREE_ARG)(v+nl-NR_END));
1126: }
1127:
1128: /******************* imatrix *******************************/
1129: int **imatrix(long nrl, long nrh, long ncl, long nch)
1130: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1131: {
1132: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1133: int **m;
1134:
1135: /* allocate pointers to rows */
1136: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1137: if (!m) nrerror("allocation failure 1 in matrix()");
1138: m += NR_END;
1139: m -= nrl;
1140:
1141:
1142: /* allocate rows and set pointers to them */
1143: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1144: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1145: m[nrl] += NR_END;
1146: m[nrl] -= ncl;
1147:
1148: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1149:
1150: /* return pointer to array of pointers to rows */
1151: return m;
1152: }
1153:
1154: /****************** free_imatrix *************************/
1155: void free_imatrix(m,nrl,nrh,ncl,nch)
1156: int **m;
1157: long nch,ncl,nrh,nrl;
1158: /* free an int matrix allocated by imatrix() */
1159: {
1160: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1161: free((FREE_ARG) (m+nrl-NR_END));
1162: }
1163:
1164: /******************* matrix *******************************/
1165: double **matrix(long nrl, long nrh, long ncl, long nch)
1166: {
1167: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1168: double **m;
1169:
1170: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1171: if (!m) nrerror("allocation failure 1 in matrix()");
1172: m += NR_END;
1173: m -= nrl;
1174:
1175: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1176: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1177: m[nrl] += NR_END;
1178: m[nrl] -= ncl;
1179:
1180: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1181: return m;
1.145 brouard 1182: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1183: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1184: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1185: */
1186: }
1187:
1188: /*************************free matrix ************************/
1189: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1190: {
1191: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1192: free((FREE_ARG)(m+nrl-NR_END));
1193: }
1194:
1195: /******************* ma3x *******************************/
1196: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1197: {
1198: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1199: double ***m;
1200:
1201: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1202: if (!m) nrerror("allocation failure 1 in matrix()");
1203: m += NR_END;
1204: m -= nrl;
1205:
1206: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1207: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1208: m[nrl] += NR_END;
1209: m[nrl] -= ncl;
1210:
1211: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1212:
1213: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1214: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1215: m[nrl][ncl] += NR_END;
1216: m[nrl][ncl] -= nll;
1217: for (j=ncl+1; j<=nch; j++)
1218: m[nrl][j]=m[nrl][j-1]+nlay;
1219:
1220: for (i=nrl+1; i<=nrh; i++) {
1221: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1222: for (j=ncl+1; j<=nch; j++)
1223: m[i][j]=m[i][j-1]+nlay;
1224: }
1225: return m;
1226: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1227: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1228: */
1229: }
1230:
1231: /*************************free ma3x ************************/
1232: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1233: {
1234: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1235: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1236: free((FREE_ARG)(m+nrl-NR_END));
1237: }
1238:
1239: /*************** function subdirf ***********/
1240: char *subdirf(char fileres[])
1241: {
1242: /* Caution optionfilefiname is hidden */
1243: strcpy(tmpout,optionfilefiname);
1244: strcat(tmpout,"/"); /* Add to the right */
1245: strcat(tmpout,fileres);
1246: return tmpout;
1247: }
1248:
1249: /*************** function subdirf2 ***********/
1250: char *subdirf2(char fileres[], char *preop)
1251: {
1252:
1253: /* Caution optionfilefiname is hidden */
1254: strcpy(tmpout,optionfilefiname);
1255: strcat(tmpout,"/");
1256: strcat(tmpout,preop);
1257: strcat(tmpout,fileres);
1258: return tmpout;
1259: }
1260:
1261: /*************** function subdirf3 ***********/
1262: char *subdirf3(char fileres[], char *preop, char *preop2)
1263: {
1264:
1265: /* Caution optionfilefiname is hidden */
1266: strcpy(tmpout,optionfilefiname);
1267: strcat(tmpout,"/");
1268: strcat(tmpout,preop);
1269: strcat(tmpout,preop2);
1270: strcat(tmpout,fileres);
1271: return tmpout;
1272: }
1273:
1.162 brouard 1274: char *asc_diff_time(long time_sec, char ascdiff[])
1275: {
1276: long sec_left, days, hours, minutes;
1277: days = (time_sec) / (60*60*24);
1278: sec_left = (time_sec) % (60*60*24);
1279: hours = (sec_left) / (60*60) ;
1280: sec_left = (sec_left) %(60*60);
1281: minutes = (sec_left) /60;
1282: sec_left = (sec_left) % (60);
1283: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1284: return ascdiff;
1285: }
1286:
1.126 brouard 1287: /***************** f1dim *************************/
1288: extern int ncom;
1289: extern double *pcom,*xicom;
1290: extern double (*nrfunc)(double []);
1291:
1292: double f1dim(double x)
1293: {
1294: int j;
1295: double f;
1296: double *xt;
1297:
1298: xt=vector(1,ncom);
1299: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1300: f=(*nrfunc)(xt);
1301: free_vector(xt,1,ncom);
1302: return f;
1303: }
1304:
1305: /*****************brent *************************/
1306: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1307: {
1308: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1309: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1310: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1311: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1312: * returned function value.
1313: */
1.126 brouard 1314: int iter;
1315: double a,b,d,etemp;
1.159 brouard 1316: double fu=0,fv,fw,fx;
1.164 brouard 1317: double ftemp=0.;
1.126 brouard 1318: double p,q,r,tol1,tol2,u,v,w,x,xm;
1319: double e=0.0;
1320:
1321: a=(ax < cx ? ax : cx);
1322: b=(ax > cx ? ax : cx);
1323: x=w=v=bx;
1324: fw=fv=fx=(*f)(x);
1325: for (iter=1;iter<=ITMAX;iter++) {
1326: xm=0.5*(a+b);
1327: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1328: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1329: printf(".");fflush(stdout);
1330: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1331: #ifdef DEBUGBRENT
1.126 brouard 1332: printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
1333: fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
1334: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1335: #endif
1336: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1337: *xmin=x;
1338: return fx;
1339: }
1340: ftemp=fu;
1341: if (fabs(e) > tol1) {
1342: r=(x-w)*(fx-fv);
1343: q=(x-v)*(fx-fw);
1344: p=(x-v)*q-(x-w)*r;
1345: q=2.0*(q-r);
1346: if (q > 0.0) p = -p;
1347: q=fabs(q);
1348: etemp=e;
1349: e=d;
1350: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1351: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1352: else {
1353: d=p/q;
1354: u=x+d;
1355: if (u-a < tol2 || b-u < tol2)
1356: d=SIGN(tol1,xm-x);
1357: }
1358: } else {
1359: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1360: }
1361: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1362: fu=(*f)(u);
1363: if (fu <= fx) {
1364: if (u >= x) a=x; else b=x;
1365: SHFT(v,w,x,u)
1.183 brouard 1366: SHFT(fv,fw,fx,fu)
1367: } else {
1368: if (u < x) a=u; else b=u;
1369: if (fu <= fw || w == x) {
1370: v=w;
1371: w=u;
1372: fv=fw;
1373: fw=fu;
1374: } else if (fu <= fv || v == x || v == w) {
1375: v=u;
1376: fv=fu;
1377: }
1378: }
1.126 brouard 1379: }
1380: nrerror("Too many iterations in brent");
1381: *xmin=x;
1382: return fx;
1383: }
1384:
1385: /****************** mnbrak ***********************/
1386:
1387: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1388: double (*func)(double))
1.183 brouard 1389: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1390: the downhill direction (defined by the function as evaluated at the initial points) and returns
1391: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1392: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1393: */
1.126 brouard 1394: double ulim,u,r,q, dum;
1395: double fu;
1.187 brouard 1396:
1397: double scale=10.;
1398: int iterscale=0;
1399:
1400: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1401: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1402:
1403:
1404: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1405: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1406: /* *bx = *ax - (*ax - *bx)/scale; */
1407: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1408: /* } */
1409:
1.126 brouard 1410: if (*fb > *fa) {
1411: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1412: SHFT(dum,*fb,*fa,dum)
1413: }
1.126 brouard 1414: *cx=(*bx)+GOLD*(*bx-*ax);
1415: *fc=(*func)(*cx);
1.183 brouard 1416: #ifdef DEBUG
1417: printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1418: fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1419: #endif
1420: while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
1.126 brouard 1421: r=(*bx-*ax)*(*fb-*fc);
1422: q=(*bx-*cx)*(*fb-*fa);
1423: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 1424: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1425: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1426: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 1427: fu=(*func)(u);
1.163 brouard 1428: #ifdef DEBUG
1429: /* f(x)=A(x-u)**2+f(u) */
1430: double A, fparabu;
1431: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1432: fparabu= *fa - A*(*ax-u)*(*ax-u);
1433: printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
1434: fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
1.183 brouard 1435: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1436: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1437: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1438: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 1439: #endif
1.184 brouard 1440: #ifdef MNBRAKORIGINAL
1.183 brouard 1441: #else
1442: if (fu > *fc) {
1443: #ifdef DEBUG
1444: printf("mnbrak4 fu > fc \n");
1445: fprintf(ficlog, "mnbrak4 fu > fc\n");
1446: #endif
1447: /* SHFT(u,*cx,*cx,u) /\* ie a=c, c=u and u=c; in that case, next SHFT(a,b,c,u) will give a=b=b, b=c=u, c=u=c and *\/ */
1448: /* SHFT(*fa,*fc,fu,*fc) /\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\/ */
1449: dum=u; /* Shifting c and u */
1450: u = *cx;
1451: *cx = dum;
1452: dum = fu;
1453: fu = *fc;
1454: *fc =dum;
1455: } else { /* end */
1456: #ifdef DEBUG
1457: printf("mnbrak3 fu < fc \n");
1458: fprintf(ficlog, "mnbrak3 fu < fc\n");
1459: #endif
1460: dum=u; /* Shifting c and u */
1461: u = *cx;
1462: *cx = dum;
1463: dum = fu;
1464: fu = *fc;
1465: *fc =dum;
1466: }
1467: #endif
1.162 brouard 1468: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 1469: #ifdef DEBUG
1470: printf("mnbrak2 u after c but before ulim\n");
1471: fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
1472: #endif
1.126 brouard 1473: fu=(*func)(u);
1474: if (fu < *fc) {
1.183 brouard 1475: #ifdef DEBUG
1476: printf("mnbrak2 u after c but before ulim AND fu < fc\n");
1477: fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
1478: #endif
1.126 brouard 1479: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1.183 brouard 1480: SHFT(*fb,*fc,fu,(*func)(u))
1481: }
1.162 brouard 1482: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 1483: #ifdef DEBUG
1484: printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1485: fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1486: #endif
1.126 brouard 1487: u=ulim;
1488: fu=(*func)(u);
1.183 brouard 1489: } else { /* u could be left to b (if r > q parabola has a maximum) */
1490: #ifdef DEBUG
1491: printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1492: fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1493: #endif
1.126 brouard 1494: u=(*cx)+GOLD*(*cx-*bx);
1495: fu=(*func)(u);
1.183 brouard 1496: } /* end tests */
1.126 brouard 1497: SHFT(*ax,*bx,*cx,u)
1.183 brouard 1498: SHFT(*fa,*fb,*fc,fu)
1499: #ifdef DEBUG
1500: printf("mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
1501: fprintf(ficlog, "mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
1502: #endif
1503: } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
1.126 brouard 1504: }
1505:
1506: /*************** linmin ************************/
1.162 brouard 1507: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1508: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1509: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1510: the value of func at the returned location p . This is actually all accomplished by calling the
1511: routines mnbrak and brent .*/
1.126 brouard 1512: int ncom;
1513: double *pcom,*xicom;
1514: double (*nrfunc)(double []);
1515:
1516: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1517: {
1518: double brent(double ax, double bx, double cx,
1519: double (*f)(double), double tol, double *xmin);
1520: double f1dim(double x);
1521: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1522: double *fc, double (*func)(double));
1523: int j;
1524: double xx,xmin,bx,ax;
1525: double fx,fb,fa;
1.187 brouard 1526:
1527: double scale=10., axs, xxs, xxss; /* Scale added for infinity */
1.126 brouard 1528:
1529: ncom=n;
1530: pcom=vector(1,n);
1531: xicom=vector(1,n);
1532: nrfunc=func;
1533: for (j=1;j<=n;j++) {
1534: pcom[j]=p[j];
1535: xicom[j]=xi[j];
1536: }
1.187 brouard 1537:
1538: axs=0.0;
1539: xxss=1; /* 1 and using scale */
1540: xxs=1;
1541: do{
1542: ax=0.;
1543: xx= xxs;
1544: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
1545: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
1546: /* xt[x,j]=pcom[j]+x*xicom[j] f(ax) = f(xt(a,j=1,n)) = f(p(j) + 0 * xi(j)) and f(xx) = f(xt(x, j=1,n)) = f(p(j) + 1 * xi(j)) */
1547: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
1548: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
1549: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
1550: /* Find a bracket a,x,b in direction n=xi ie xicom, order may change. Scale is [0:xxs*xi[j]] et non plus [0:xi[j]]*/
1551: if (fx != fx){
1552: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
1553: printf("\nLinmin NAN : input [axs=%lf:xxs=%lf], mnbrak outputs fx=%lf <(fb=%lf and fa=%lf) with xx=%lf in [ax=%lf:bx=%lf] \n", axs, xxs, fx,fb, fa, xx, ax, bx);
1554: }
1555: }while(fx != fx);
1556:
1557: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
1558: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
1559: /* fmin = f(p[j] + xmin * xi[j]) */
1560: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
1561: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 1562: #ifdef DEBUG
1563: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1564: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1565: #endif
1.187 brouard 1566: printf("linmin end ");
1.126 brouard 1567: for (j=1;j<=n;j++) {
1.188 ! brouard 1568: /* printf(" before xi[%d]=%12.8f", j,xi[j]); */
1.187 brouard 1569: xi[j] *= xmin; /* xi rescaled by xmin: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
1570: if(xxs <1.0)
1571: printf(" after xi[%d]=%12.8f, xmin=%12.8f, ax=%12.8f, xx=%12.8f, bx=%12.8f, xxs=%12.8f", j,xi[j], xmin, ax, xx, bx,xxs );
1572: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 1573: }
1.187 brouard 1574: printf("\n");
1.188 ! brouard 1575: printf("Comparing last *frec(xmin)=%12.8f from Brent and frec(0.)=%12.8f \n", (*func)(p));
1.126 brouard 1576: free_vector(xicom,1,n);
1577: free_vector(pcom,1,n);
1578: }
1579:
1580:
1581: /*************** powell ************************/
1.162 brouard 1582: /*
1583: Minimization of a function func of n variables. Input consists of an initial starting point
1584: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1585: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1586: such that failure to decrease by more than this amount on one iteration signals doneness. On
1587: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1588: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1589: */
1.126 brouard 1590: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1591: double (*func)(double []))
1592: {
1593: void linmin(double p[], double xi[], int n, double *fret,
1594: double (*func)(double []));
1595: int i,ibig,j;
1596: double del,t,*pt,*ptt,*xit;
1.181 brouard 1597: double directest;
1.126 brouard 1598: double fp,fptt;
1599: double *xits;
1600: int niterf, itmp;
1601:
1602: pt=vector(1,n);
1603: ptt=vector(1,n);
1604: xit=vector(1,n);
1605: xits=vector(1,n);
1606: *fret=(*func)(p);
1607: for (j=1;j<=n;j++) pt[j]=p[j];
1.157 brouard 1608: rcurr_time = time(NULL);
1.126 brouard 1609: for (*iter=1;;++(*iter)) {
1.187 brouard 1610: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 1611: ibig=0;
1612: del=0.0;
1.157 brouard 1613: rlast_time=rcurr_time;
1614: /* (void) gettimeofday(&curr_time,&tzp); */
1615: rcurr_time = time(NULL);
1616: curr_time = *localtime(&rcurr_time);
1617: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1618: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1619: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.126 brouard 1620: for (i=1;i<=n;i++) {
1621: printf(" %d %.12f",i, p[i]);
1622: fprintf(ficlog," %d %.12lf",i, p[i]);
1623: fprintf(ficrespow," %.12lf", p[i]);
1624: }
1625: printf("\n");
1626: fprintf(ficlog,"\n");
1627: fprintf(ficrespow,"\n");fflush(ficrespow);
1628: if(*iter <=3){
1.157 brouard 1629: tml = *localtime(&rcurr_time);
1630: strcpy(strcurr,asctime(&tml));
1631: rforecast_time=rcurr_time;
1.126 brouard 1632: itmp = strlen(strcurr);
1633: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1634: strcurr[itmp-1]='\0';
1.162 brouard 1635: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 1636: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 1637: for(niterf=10;niterf<=30;niterf+=10){
1.157 brouard 1638: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1639: forecast_time = *localtime(&rforecast_time);
1640: strcpy(strfor,asctime(&forecast_time));
1.126 brouard 1641: itmp = strlen(strfor);
1642: if(strfor[itmp-1]=='\n')
1643: strfor[itmp-1]='\0';
1.157 brouard 1644: 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);
1645: 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 1646: }
1647: }
1.187 brouard 1648: for (i=1;i<=n;i++) { /* For each direction i */
1649: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 1650: fptt=(*fret);
1651: #ifdef DEBUG
1.164 brouard 1652: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1653: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 1654: #endif
1.187 brouard 1655: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 1656: fprintf(ficlog,"%d",i);fflush(ficlog);
1.188 ! brouard 1657: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
! 1658: /* Outputs are fret(new point p) p is updated and xit rescaled */
! 1659: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
! 1660: /* because that direction will be replaced unless the gain del is small */
! 1661: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
! 1662: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
! 1663: /* with the new direction. */
1.126 brouard 1664: del=fabs(fptt-(*fret));
1665: ibig=i;
1666: }
1667: #ifdef DEBUG
1668: printf("%d %.12e",i,(*fret));
1669: fprintf(ficlog,"%d %.12e",i,(*fret));
1670: for (j=1;j<=n;j++) {
1671: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1672: printf(" x(%d)=%.12e",j,xit[j]);
1673: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1674: }
1675: for(j=1;j<=n;j++) {
1.162 brouard 1676: printf(" p(%d)=%.12e",j,p[j]);
1677: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 1678: }
1679: printf("\n");
1680: fprintf(ficlog,"\n");
1681: #endif
1.187 brouard 1682: } /* end loop on each direction i */
1683: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 ! brouard 1684: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 1685: /* New value of last point Pn is not computed, P(n-1) */
1.182 brouard 1686: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1.188 ! brouard 1687: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
! 1688: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
! 1689: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
! 1690: /* decreased of more than 3.84 */
! 1691: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
! 1692: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
! 1693: /* By adding 10 parameters more the gain should be 18.31 */
! 1694:
! 1695: /* Starting the program with initial values given by a former maximization will simply change */
! 1696: /* the scales of the directions and the directions, because the are reset to canonical directions */
! 1697: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
! 1698: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 1699: #ifdef DEBUG
1700: int k[2],l;
1701: k[0]=1;
1702: k[1]=-1;
1703: printf("Max: %.12e",(*func)(p));
1704: fprintf(ficlog,"Max: %.12e",(*func)(p));
1705: for (j=1;j<=n;j++) {
1706: printf(" %.12e",p[j]);
1707: fprintf(ficlog," %.12e",p[j]);
1708: }
1709: printf("\n");
1710: fprintf(ficlog,"\n");
1711: for(l=0;l<=1;l++) {
1712: for (j=1;j<=n;j++) {
1713: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1714: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1715: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1716: }
1717: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1718: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1719: }
1720: #endif
1721:
1722:
1723: free_vector(xit,1,n);
1724: free_vector(xits,1,n);
1725: free_vector(ptt,1,n);
1726: free_vector(pt,1,n);
1727: return;
1728: }
1729: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1.181 brouard 1730: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 1731: ptt[j]=2.0*p[j]-pt[j];
1732: xit[j]=p[j]-pt[j];
1733: pt[j]=p[j];
1734: }
1.181 brouard 1735: fptt=(*func)(ptt); /* f_3 */
1.161 brouard 1736: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.162 brouard 1737: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 1738: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 1739: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1740: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1741: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.181 brouard 1742: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
1.161 brouard 1743: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.183 brouard 1744: #ifdef NRCORIGINAL
1745: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
1746: #else
1747: 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 1748: t= t- del*SQR(fp-fptt);
1.183 brouard 1749: #endif
1.182 brouard 1750: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
1.161 brouard 1751: #ifdef DEBUG
1.181 brouard 1752: 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);
1753: 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 1754: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1755: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1756: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1757: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1758: 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);
1759: 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);
1760: #endif
1.183 brouard 1761: #ifdef POWELLORIGINAL
1762: if (t < 0.0) { /* Then we use it for new direction */
1763: #else
1.182 brouard 1764: if (directest*t < 0.0) { /* Contradiction between both tests */
1.184 brouard 1765: printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
1.182 brouard 1766: 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 1767: fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
1.182 brouard 1768: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1769: }
1.181 brouard 1770: if (directest < 0.0) { /* Then we use it for new direction */
1771: #endif
1.187 brouard 1772: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.126 brouard 1773: for (j=1;j<=n;j++) {
1.181 brouard 1774: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
1775: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
1.126 brouard 1776: }
1.181 brouard 1777: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1778: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1.161 brouard 1779:
1.126 brouard 1780: #ifdef DEBUG
1.164 brouard 1781: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1782: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1.126 brouard 1783: for(j=1;j<=n;j++){
1784: printf(" %.12e",xit[j]);
1785: fprintf(ficlog," %.12e",xit[j]);
1786: }
1787: printf("\n");
1788: fprintf(ficlog,"\n");
1789: #endif
1.162 brouard 1790: } /* end of t negative */
1791: } /* end if (fptt < fp) */
1.126 brouard 1792: }
1793: }
1794:
1795: /**** Prevalence limit (stable or period prevalence) ****************/
1796:
1797: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1798: {
1799: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1800: matrix by transitions matrix until convergence is reached */
1.169 brouard 1801:
1.126 brouard 1802: int i, ii,j,k;
1803: double min, max, maxmin, maxmax,sumnew=0.;
1.145 brouard 1804: /* double **matprod2(); */ /* test */
1.131 brouard 1805: double **out, cov[NCOVMAX+1], **pmij();
1.126 brouard 1806: double **newm;
1807: double agefin, delaymax=50 ; /* Max number of years to converge */
1.169 brouard 1808:
1.126 brouard 1809: for (ii=1;ii<=nlstate+ndeath;ii++)
1810: for (j=1;j<=nlstate+ndeath;j++){
1811: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1812: }
1.169 brouard 1813:
1814: cov[1]=1.;
1815:
1816: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.126 brouard 1817: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1818: newm=savm;
1819: /* Covariates have to be included here again */
1.138 brouard 1820: cov[2]=agefin;
1.187 brouard 1821: if(nagesqr==1)
1822: cov[3]= agefin*agefin;;
1.138 brouard 1823: for (k=1; k<=cptcovn;k++) {
1.187 brouard 1824: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.145 brouard 1825: /*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 1826: }
1.186 brouard 1827: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.187 brouard 1828: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]*cov[2];
1.186 brouard 1829: for (k=1; k<=cptcovprod;k++) /* Useless */
1.187 brouard 1830: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1.138 brouard 1831:
1832: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1833: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1834: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 1835: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1836: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.142 brouard 1837: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 1838:
1.126 brouard 1839: savm=oldm;
1840: oldm=newm;
1841: maxmax=0.;
1842: for(j=1;j<=nlstate;j++){
1843: min=1.;
1844: max=0.;
1845: for(i=1; i<=nlstate; i++) {
1846: sumnew=0;
1847: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1848: prlim[i][j]= newm[i][j]/(1-sumnew);
1.145 brouard 1849: /*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 1850: max=FMAX(max,prlim[i][j]);
1851: min=FMIN(min,prlim[i][j]);
1852: }
1853: maxmin=max-min;
1854: maxmax=FMAX(maxmax,maxmin);
1.169 brouard 1855: } /* j loop */
1.126 brouard 1856: if(maxmax < ftolpl){
1857: return prlim;
1858: }
1.169 brouard 1859: } /* age loop */
1860: return prlim; /* should not reach here */
1.126 brouard 1861: }
1862:
1863: /*************** transition probabilities ***************/
1864:
1865: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1866: {
1.138 brouard 1867: /* According to parameters values stored in x and the covariate's values stored in cov,
1868: computes the probability to be observed in state j being in state i by appying the
1869: model to the ncovmodel covariates (including constant and age).
1870: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1871: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1872: ncth covariate in the global vector x is given by the formula:
1873: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1874: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1875: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1876: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1877: Outputs ps[i][j] the probability to be observed in j being in j according to
1878: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1879: */
1880: double s1, lnpijopii;
1.126 brouard 1881: /*double t34;*/
1.164 brouard 1882: int i,j, nc, ii, jj;
1.126 brouard 1883:
1884: for(i=1; i<= nlstate; i++){
1885: for(j=1; j<i;j++){
1.138 brouard 1886: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1887: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1888: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1889: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 1890: }
1.138 brouard 1891: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1892: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 1893: }
1894: for(j=i+1; j<=nlstate+ndeath;j++){
1.138 brouard 1895: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1896: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
1897: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
1898: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1.126 brouard 1899: }
1.138 brouard 1900: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1.126 brouard 1901: }
1902: }
1903:
1904: for(i=1; i<= nlstate; i++){
1905: s1=0;
1.131 brouard 1906: for(j=1; j<i; j++){
1.138 brouard 1907: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 1908: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1909: }
1910: for(j=i+1; j<=nlstate+ndeath; j++){
1.138 brouard 1911: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 1912: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1913: }
1.138 brouard 1914: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1.126 brouard 1915: ps[i][i]=1./(s1+1.);
1.138 brouard 1916: /* Computing other pijs */
1.126 brouard 1917: for(j=1; j<i; j++)
1918: ps[i][j]= exp(ps[i][j])*ps[i][i];
1919: for(j=i+1; j<=nlstate+ndeath; j++)
1920: ps[i][j]= exp(ps[i][j])*ps[i][i];
1921: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1922: } /* end i */
1923:
1924: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1925: for(jj=1; jj<= nlstate+ndeath; jj++){
1926: ps[ii][jj]=0;
1927: ps[ii][ii]=1;
1928: }
1929: }
1930:
1.145 brouard 1931:
1932: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1933: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1934: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
1935: /* } */
1936: /* printf("\n "); */
1937: /* } */
1938: /* printf("\n ");printf("%lf ",cov[2]);*/
1939: /*
1.126 brouard 1940: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1941: goto end;*/
1942: return ps;
1943: }
1944:
1945: /**************** Product of 2 matrices ******************/
1946:
1.145 brouard 1947: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 1948: {
1949: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1950: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1951: /* in, b, out are matrice of pointers which should have been initialized
1952: before: only the contents of out is modified. The function returns
1953: a pointer to pointers identical to out */
1.145 brouard 1954: int i, j, k;
1.126 brouard 1955: for(i=nrl; i<= nrh; i++)
1.145 brouard 1956: for(k=ncolol; k<=ncoloh; k++){
1957: out[i][k]=0.;
1958: for(j=ncl; j<=nch; j++)
1959: out[i][k] +=in[i][j]*b[j][k];
1960: }
1.126 brouard 1961: return out;
1962: }
1963:
1964:
1965: /************* Higher Matrix Product ***************/
1966:
1967: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1968: {
1969: /* Computes the transition matrix starting at age 'age' over
1970: 'nhstepm*hstepm*stepm' months (i.e. until
1971: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1972: nhstepm*hstepm matrices.
1973: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1974: (typically every 2 years instead of every month which is too big
1975: for the memory).
1976: Model is determined by parameters x and covariates have to be
1977: included manually here.
1978:
1979: */
1980:
1981: int i, j, d, h, k;
1.131 brouard 1982: double **out, cov[NCOVMAX+1];
1.126 brouard 1983: double **newm;
1.187 brouard 1984: double agexact;
1.126 brouard 1985:
1986: /* Hstepm could be zero and should return the unit matrix */
1987: for (i=1;i<=nlstate+ndeath;i++)
1988: for (j=1;j<=nlstate+ndeath;j++){
1989: oldm[i][j]=(i==j ? 1.0 : 0.0);
1990: po[i][j][0]=(i==j ? 1.0 : 0.0);
1991: }
1992: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1993: for(h=1; h <=nhstepm; h++){
1994: for(d=1; d <=hstepm; d++){
1995: newm=savm;
1996: /* Covariates have to be included here again */
1997: cov[1]=1.;
1.187 brouard 1998: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1999: cov[2]=agexact;
2000: if(nagesqr==1)
2001: cov[3]= agexact*agexact;
1.131 brouard 2002: for (k=1; k<=cptcovn;k++)
1.187 brouard 2003: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.186 brouard 2004: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
2005: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.187 brouard 2006: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
1.145 brouard 2007: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.187 brouard 2008: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1.126 brouard 2009:
2010:
2011: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2012: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
2013: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
2014: pmij(pmmij,cov,ncovmodel,x,nlstate));
2015: savm=oldm;
2016: oldm=newm;
2017: }
2018: for(i=1; i<=nlstate+ndeath; i++)
2019: for(j=1;j<=nlstate+ndeath;j++) {
2020: po[i][j][h]=newm[i][j];
1.128 brouard 2021: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 2022: }
1.128 brouard 2023: /*printf("h=%d ",h);*/
1.126 brouard 2024: } /* end h */
1.128 brouard 2025: /* printf("\n H=%d \n",h); */
1.126 brouard 2026: return po;
2027: }
2028:
1.162 brouard 2029: #ifdef NLOPT
2030: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
2031: double fret;
2032: double *xt;
2033: int j;
2034: myfunc_data *d2 = (myfunc_data *) pd;
2035: /* xt = (p1-1); */
2036: xt=vector(1,n);
2037: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
2038:
2039: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
2040: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
2041: printf("Function = %.12lf ",fret);
2042: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
2043: printf("\n");
2044: free_vector(xt,1,n);
2045: return fret;
2046: }
2047: #endif
1.126 brouard 2048:
2049: /*************** log-likelihood *************/
2050: double func( double *x)
2051: {
2052: int i, ii, j, k, mi, d, kk;
1.131 brouard 2053: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2054: double **out;
2055: double sw; /* Sum of weights */
2056: double lli; /* Individual log likelihood */
2057: int s1, s2;
2058: double bbh, survp;
2059: long ipmx;
1.187 brouard 2060: double agexact;
1.126 brouard 2061: /*extern weight */
2062: /* We are differentiating ll according to initial status */
2063: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2064: /*for(i=1;i<imx;i++)
2065: printf(" %d\n",s[4][i]);
2066: */
1.162 brouard 2067:
2068: ++countcallfunc;
2069:
1.126 brouard 2070: cov[1]=1.;
2071:
2072: for(k=1; k<=nlstate; k++) ll[k]=0.;
2073:
2074: if(mle==1){
2075: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.138 brouard 2076: /* Computes the values of the ncovmodel covariates of the model
2077: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
2078: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
2079: to be observed in j being in i according to the model.
2080: */
1.145 brouard 2081: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1.187 brouard 2082: cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.145 brouard 2083: }
1.137 brouard 2084: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1.138 brouard 2085: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1.137 brouard 2086: has been calculated etc */
1.126 brouard 2087: for(mi=1; mi<= wav[i]-1; mi++){
2088: for (ii=1;ii<=nlstate+ndeath;ii++)
2089: for (j=1;j<=nlstate+ndeath;j++){
2090: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2091: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2092: }
2093: for(d=0; d<dh[mi][i]; d++){
2094: newm=savm;
1.187 brouard 2095: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2096: cov[2]=agexact;
2097: if(nagesqr==1)
2098: cov[3]= agexact*agexact;
1.126 brouard 2099: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2100: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
1.126 brouard 2101: }
2102: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2103: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2104: savm=oldm;
2105: oldm=newm;
2106: } /* end mult */
2107:
2108: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
2109: /* But now since version 0.9 we anticipate for bias at large stepm.
2110: * If stepm is larger than one month (smallest stepm) and if the exact delay
2111: * (in months) between two waves is not a multiple of stepm, we rounded to
2112: * the nearest (and in case of equal distance, to the lowest) interval but now
2113: * we keep into memory the bias bh[mi][i] and also the previous matrix product
2114: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
2115: * probability in order to take into account the bias as a fraction of the way
2116: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
2117: * -stepm/2 to stepm/2 .
2118: * For stepm=1 the results are the same as for previous versions of Imach.
2119: * For stepm > 1 the results are less biased than in previous versions.
2120: */
2121: s1=s[mw[mi][i]][i];
2122: s2=s[mw[mi+1][i]][i];
2123: bbh=(double)bh[mi][i]/(double)stepm;
2124: /* bias bh is positive if real duration
2125: * is higher than the multiple of stepm and negative otherwise.
2126: */
2127: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
2128: if( s2 > nlstate){
2129: /* i.e. if s2 is a death state and if the date of death is known
2130: then the contribution to the likelihood is the probability to
2131: die between last step unit time and current step unit time,
2132: which is also equal to probability to die before dh
2133: minus probability to die before dh-stepm .
2134: In version up to 0.92 likelihood was computed
2135: as if date of death was unknown. Death was treated as any other
2136: health state: the date of the interview describes the actual state
2137: and not the date of a change in health state. The former idea was
2138: to consider that at each interview the state was recorded
2139: (healthy, disable or death) and IMaCh was corrected; but when we
2140: introduced the exact date of death then we should have modified
2141: the contribution of an exact death to the likelihood. This new
2142: contribution is smaller and very dependent of the step unit
2143: stepm. It is no more the probability to die between last interview
2144: and month of death but the probability to survive from last
2145: interview up to one month before death multiplied by the
2146: probability to die within a month. Thanks to Chris
2147: Jackson for correcting this bug. Former versions increased
2148: mortality artificially. The bad side is that we add another loop
2149: which slows down the processing. The difference can be up to 10%
2150: lower mortality.
2151: */
1.183 brouard 2152: /* If, at the beginning of the maximization mostly, the
2153: cumulative probability or probability to be dead is
2154: constant (ie = 1) over time d, the difference is equal to
2155: 0. out[s1][3] = savm[s1][3]: probability, being at state
2156: s1 at precedent wave, to be dead a month before current
2157: wave is equal to probability, being at state s1 at
2158: precedent wave, to be dead at mont of the current
2159: wave. Then the observed probability (that this person died)
2160: is null according to current estimated parameter. In fact,
2161: it should be very low but not zero otherwise the log go to
2162: infinity.
2163: */
2164: /* #ifdef INFINITYORIGINAL */
2165: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2166: /* #else */
2167: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
2168: /* lli=log(mytinydouble); */
2169: /* else */
2170: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2171: /* #endif */
2172: lli=log(out[s1][s2] - savm[s1][s2]);
1.126 brouard 2173:
2174: } else if (s2==-2) {
2175: for (j=1,survp=0. ; j<=nlstate; j++)
2176: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2177: /*survp += out[s1][j]; */
2178: lli= log(survp);
2179: }
2180:
2181: else if (s2==-4) {
2182: for (j=3,survp=0. ; j<=nlstate; j++)
2183: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2184: lli= log(survp);
2185: }
2186:
2187: else if (s2==-5) {
2188: for (j=1,survp=0. ; j<=2; j++)
2189: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2190: lli= log(survp);
2191: }
2192:
2193: else{
2194: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2195: /* 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 */
2196: }
2197: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
2198: /*if(lli ==000.0)*/
2199: /*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); */
2200: ipmx +=1;
2201: sw += weight[i];
2202: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.183 brouard 2203: /* if (lli < log(mytinydouble)){ */
2204: /* 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); */
2205: /* 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]); */
2206: /* } */
1.126 brouard 2207: } /* end of wave */
2208: } /* end of individual */
2209: } else if(mle==2){
2210: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2211: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2212: for(mi=1; mi<= wav[i]-1; mi++){
2213: for (ii=1;ii<=nlstate+ndeath;ii++)
2214: for (j=1;j<=nlstate+ndeath;j++){
2215: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2216: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2217: }
2218: for(d=0; d<=dh[mi][i]; d++){
2219: newm=savm;
1.187 brouard 2220: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2221: cov[2]=agexact;
2222: if(nagesqr==1)
2223: cov[3]= agexact*agexact;
1.126 brouard 2224: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2225: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2226: }
2227: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2228: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2229: savm=oldm;
2230: oldm=newm;
2231: } /* end mult */
2232:
2233: s1=s[mw[mi][i]][i];
2234: s2=s[mw[mi+1][i]][i];
2235: bbh=(double)bh[mi][i]/(double)stepm;
2236: 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 */
2237: ipmx +=1;
2238: sw += weight[i];
2239: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2240: } /* end of wave */
2241: } /* end of individual */
2242: } else if(mle==3){ /* exponential inter-extrapolation */
2243: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2244: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2245: for(mi=1; mi<= wav[i]-1; mi++){
2246: for (ii=1;ii<=nlstate+ndeath;ii++)
2247: for (j=1;j<=nlstate+ndeath;j++){
2248: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2249: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2250: }
2251: for(d=0; d<dh[mi][i]; d++){
2252: newm=savm;
1.187 brouard 2253: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2254: cov[2]=agexact;
2255: if(nagesqr==1)
2256: cov[3]= agexact*agexact;
1.126 brouard 2257: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2258: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2259: }
2260: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2261: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2262: savm=oldm;
2263: oldm=newm;
2264: } /* end mult */
2265:
2266: s1=s[mw[mi][i]][i];
2267: s2=s[mw[mi+1][i]][i];
2268: bbh=(double)bh[mi][i]/(double)stepm;
2269: 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 */
2270: ipmx +=1;
2271: sw += weight[i];
2272: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2273: } /* end of wave */
2274: } /* end of individual */
2275: }else if (mle==4){ /* ml=4 no inter-extrapolation */
2276: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2277: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2278: for(mi=1; mi<= wav[i]-1; mi++){
2279: for (ii=1;ii<=nlstate+ndeath;ii++)
2280: for (j=1;j<=nlstate+ndeath;j++){
2281: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2282: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2283: }
2284: for(d=0; d<dh[mi][i]; d++){
2285: newm=savm;
1.187 brouard 2286: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2287: cov[2]=agexact;
2288: if(nagesqr==1)
2289: cov[3]= agexact*agexact;
1.126 brouard 2290: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2291: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2292: }
2293:
2294: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2295: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2296: savm=oldm;
2297: oldm=newm;
2298: } /* end mult */
2299:
2300: s1=s[mw[mi][i]][i];
2301: s2=s[mw[mi+1][i]][i];
2302: if( s2 > nlstate){
2303: lli=log(out[s1][s2] - savm[s1][s2]);
2304: }else{
2305: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2306: }
2307: ipmx +=1;
2308: sw += weight[i];
2309: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2310: /* 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]); */
2311: } /* end of wave */
2312: } /* end of individual */
2313: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
2314: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2315: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2316: for(mi=1; mi<= wav[i]-1; mi++){
2317: for (ii=1;ii<=nlstate+ndeath;ii++)
2318: for (j=1;j<=nlstate+ndeath;j++){
2319: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2320: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2321: }
2322: for(d=0; d<dh[mi][i]; d++){
2323: newm=savm;
1.187 brouard 2324: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2325: cov[2]=agexact;
2326: if(nagesqr==1)
2327: cov[3]= agexact*agexact;
1.126 brouard 2328: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2329: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2330: }
2331:
2332: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2333: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2334: savm=oldm;
2335: oldm=newm;
2336: } /* end mult */
2337:
2338: s1=s[mw[mi][i]][i];
2339: s2=s[mw[mi+1][i]][i];
2340: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2341: ipmx +=1;
2342: sw += weight[i];
2343: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2344: /*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]);*/
2345: } /* end of wave */
2346: } /* end of individual */
2347: } /* End of if */
2348: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2349: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2350: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2351: return -l;
2352: }
2353:
2354: /*************** log-likelihood *************/
2355: double funcone( double *x)
2356: {
2357: /* Same as likeli but slower because of a lot of printf and if */
2358: int i, ii, j, k, mi, d, kk;
1.131 brouard 2359: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2360: double **out;
2361: double lli; /* Individual log likelihood */
2362: double llt;
2363: int s1, s2;
2364: double bbh, survp;
1.187 brouard 2365: double agexact;
1.126 brouard 2366: /*extern weight */
2367: /* We are differentiating ll according to initial status */
2368: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2369: /*for(i=1;i<imx;i++)
2370: printf(" %d\n",s[4][i]);
2371: */
2372: cov[1]=1.;
2373:
2374: for(k=1; k<=nlstate; k++) ll[k]=0.;
2375:
2376: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2377: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2378: for(mi=1; mi<= wav[i]-1; mi++){
2379: for (ii=1;ii<=nlstate+ndeath;ii++)
2380: for (j=1;j<=nlstate+ndeath;j++){
2381: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2382: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2383: }
2384: for(d=0; d<dh[mi][i]; d++){
2385: newm=savm;
1.187 brouard 2386: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2387: cov[2]=agexact;
2388: if(nagesqr==1)
2389: cov[3]= agexact*agexact;
1.126 brouard 2390: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2391: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2392: }
1.187 brouard 2393:
1.145 brouard 2394: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.126 brouard 2395: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2396: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1.145 brouard 2397: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2398: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
1.126 brouard 2399: savm=oldm;
2400: oldm=newm;
2401: } /* end mult */
2402:
2403: s1=s[mw[mi][i]][i];
2404: s2=s[mw[mi+1][i]][i];
2405: bbh=(double)bh[mi][i]/(double)stepm;
2406: /* bias is positive if real duration
2407: * is higher than the multiple of stepm and negative otherwise.
2408: */
2409: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2410: lli=log(out[s1][s2] - savm[s1][s2]);
2411: } else if (s2==-2) {
2412: for (j=1,survp=0. ; j<=nlstate; j++)
2413: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2414: lli= log(survp);
2415: }else if (mle==1){
2416: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2417: } else if(mle==2){
2418: 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 */
2419: } else if(mle==3){ /* exponential inter-extrapolation */
2420: 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 */
2421: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2422: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 2423: } else{ /* mle=0 back to 1 */
2424: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2425: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 2426: } /* End of if */
2427: ipmx +=1;
2428: sw += weight[i];
2429: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 2430: /*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 2431: if(globpr){
1.141 brouard 2432: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
1.126 brouard 2433: %11.6f %11.6f %11.6f ", \
2434: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
2435: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2436: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2437: llt +=ll[k]*gipmx/gsw;
2438: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2439: }
2440: fprintf(ficresilk," %10.6f\n", -llt);
2441: }
2442: } /* end of wave */
2443: } /* end of individual */
2444: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2445: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2446: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2447: if(globpr==0){ /* First time we count the contributions and weights */
2448: gipmx=ipmx;
2449: gsw=sw;
2450: }
2451: return -l;
2452: }
2453:
2454:
2455: /*************** function likelione ***********/
2456: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2457: {
2458: /* This routine should help understanding what is done with
2459: the selection of individuals/waves and
2460: to check the exact contribution to the likelihood.
2461: Plotting could be done.
2462: */
2463: int k;
2464:
2465: if(*globpri !=0){ /* Just counts and sums, no printings */
2466: strcpy(fileresilk,"ilk");
2467: strcat(fileresilk,fileres);
2468: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2469: printf("Problem with resultfile: %s\n", fileresilk);
2470: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2471: }
2472: 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");
2473: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
2474: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2475: for(k=1; k<=nlstate; k++)
2476: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2477: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2478: }
2479:
2480: *fretone=(*funcone)(p);
2481: if(*globpri !=0){
2482: fclose(ficresilk);
2483: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
2484: fflush(fichtm);
2485: }
2486: return;
2487: }
2488:
2489:
2490: /*********** Maximum Likelihood Estimation ***************/
2491:
2492: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2493: {
1.165 brouard 2494: int i,j, iter=0;
1.126 brouard 2495: double **xi;
2496: double fret;
2497: double fretone; /* Only one call to likelihood */
2498: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 2499:
2500: #ifdef NLOPT
2501: int creturn;
2502: nlopt_opt opt;
2503: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2504: double *lb;
2505: double minf; /* the minimum objective value, upon return */
2506: double * p1; /* Shifted parameters from 0 instead of 1 */
2507: myfunc_data dinst, *d = &dinst;
2508: #endif
2509:
2510:
1.126 brouard 2511: xi=matrix(1,npar,1,npar);
2512: for (i=1;i<=npar;i++)
2513: for (j=1;j<=npar;j++)
2514: xi[i][j]=(i==j ? 1.0 : 0.0);
2515: printf("Powell\n"); fprintf(ficlog,"Powell\n");
2516: strcpy(filerespow,"pow");
2517: strcat(filerespow,fileres);
2518: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2519: printf("Problem with resultfile: %s\n", filerespow);
2520: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2521: }
2522: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2523: for (i=1;i<=nlstate;i++)
2524: for(j=1;j<=nlstate+ndeath;j++)
2525: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2526: fprintf(ficrespow,"\n");
1.162 brouard 2527: #ifdef POWELL
1.126 brouard 2528: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 2529: #endif
1.126 brouard 2530:
1.162 brouard 2531: #ifdef NLOPT
2532: #ifdef NEWUOA
2533: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2534: #else
2535: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2536: #endif
2537: lb=vector(0,npar-1);
2538: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2539: nlopt_set_lower_bounds(opt, lb);
2540: nlopt_set_initial_step1(opt, 0.1);
2541:
2542: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2543: d->function = func;
2544: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2545: nlopt_set_min_objective(opt, myfunc, d);
2546: nlopt_set_xtol_rel(opt, ftol);
2547: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2548: printf("nlopt failed! %d\n",creturn);
2549: }
2550: else {
2551: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2552: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2553: iter=1; /* not equal */
2554: }
2555: nlopt_destroy(opt);
2556: #endif
1.126 brouard 2557: free_matrix(xi,1,npar,1,npar);
2558: fclose(ficrespow);
1.180 brouard 2559: printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2560: fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2561: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 2562:
2563: }
2564:
2565: /**** Computes Hessian and covariance matrix ***/
2566: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
2567: {
2568: double **a,**y,*x,pd;
2569: double **hess;
1.164 brouard 2570: int i, j;
1.126 brouard 2571: int *indx;
2572:
2573: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
2574: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
2575: void lubksb(double **a, int npar, int *indx, double b[]) ;
2576: void ludcmp(double **a, int npar, int *indx, double *d) ;
2577: double gompertz(double p[]);
2578: hess=matrix(1,npar,1,npar);
2579:
2580: printf("\nCalculation of the hessian matrix. Wait...\n");
2581: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2582: for (i=1;i<=npar;i++){
2583: printf("%d",i);fflush(stdout);
2584: fprintf(ficlog,"%d",i);fflush(ficlog);
2585:
2586: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2587:
2588: /* printf(" %f ",p[i]);
2589: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2590: }
2591:
2592: for (i=1;i<=npar;i++) {
2593: for (j=1;j<=npar;j++) {
2594: if (j>i) {
2595: printf(".%d%d",i,j);fflush(stdout);
2596: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
2597: hess[i][j]=hessij(p,delti,i,j,func,npar);
2598:
2599: hess[j][i]=hess[i][j];
2600: /*printf(" %lf ",hess[i][j]);*/
2601: }
2602: }
2603: }
2604: printf("\n");
2605: fprintf(ficlog,"\n");
2606:
2607: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2608: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2609:
2610: a=matrix(1,npar,1,npar);
2611: y=matrix(1,npar,1,npar);
2612: x=vector(1,npar);
2613: indx=ivector(1,npar);
2614: for (i=1;i<=npar;i++)
2615: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2616: ludcmp(a,npar,indx,&pd);
2617:
2618: for (j=1;j<=npar;j++) {
2619: for (i=1;i<=npar;i++) x[i]=0;
2620: x[j]=1;
2621: lubksb(a,npar,indx,x);
2622: for (i=1;i<=npar;i++){
2623: matcov[i][j]=x[i];
2624: }
2625: }
2626:
2627: printf("\n#Hessian matrix#\n");
2628: fprintf(ficlog,"\n#Hessian matrix#\n");
2629: for (i=1;i<=npar;i++) {
2630: for (j=1;j<=npar;j++) {
2631: printf("%.3e ",hess[i][j]);
2632: fprintf(ficlog,"%.3e ",hess[i][j]);
2633: }
2634: printf("\n");
2635: fprintf(ficlog,"\n");
2636: }
2637:
2638: /* Recompute Inverse */
2639: for (i=1;i<=npar;i++)
2640: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
2641: ludcmp(a,npar,indx,&pd);
2642:
2643: /* printf("\n#Hessian matrix recomputed#\n");
2644:
2645: for (j=1;j<=npar;j++) {
2646: for (i=1;i<=npar;i++) x[i]=0;
2647: x[j]=1;
2648: lubksb(a,npar,indx,x);
2649: for (i=1;i<=npar;i++){
2650: y[i][j]=x[i];
2651: printf("%.3e ",y[i][j]);
2652: fprintf(ficlog,"%.3e ",y[i][j]);
2653: }
2654: printf("\n");
2655: fprintf(ficlog,"\n");
2656: }
2657: */
2658:
2659: free_matrix(a,1,npar,1,npar);
2660: free_matrix(y,1,npar,1,npar);
2661: free_vector(x,1,npar);
2662: free_ivector(indx,1,npar);
2663: free_matrix(hess,1,npar,1,npar);
2664:
2665:
2666: }
2667:
2668: /*************** hessian matrix ****************/
2669: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2670: {
2671: int i;
2672: int l=1, lmax=20;
2673: double k1,k2;
1.132 brouard 2674: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 2675: double res;
2676: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2677: double fx;
2678: int k=0,kmax=10;
2679: double l1;
2680:
2681: fx=func(x);
2682: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 2683: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 2684: l1=pow(10,l);
2685: delts=delt;
2686: for(k=1 ; k <kmax; k=k+1){
2687: delt = delta*(l1*k);
2688: p2[theta]=x[theta] +delt;
1.145 brouard 2689: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 2690: p2[theta]=x[theta]-delt;
2691: k2=func(p2)-fx;
2692: /*res= (k1-2.0*fx+k2)/delt/delt; */
2693: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2694:
1.132 brouard 2695: #ifdef DEBUGHESS
1.126 brouard 2696: 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);
2697: 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);
2698: #endif
2699: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2700: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2701: k=kmax;
2702: }
2703: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 2704: k=kmax; l=lmax*10;
1.126 brouard 2705: }
2706: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2707: delts=delt;
2708: }
2709: }
2710: }
2711: delti[theta]=delts;
2712: return res;
2713:
2714: }
2715:
2716: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2717: {
2718: int i;
1.164 brouard 2719: int l=1, lmax=20;
1.126 brouard 2720: double k1,k2,k3,k4,res,fx;
1.132 brouard 2721: double p2[MAXPARM+1];
1.126 brouard 2722: int k;
2723:
2724: fx=func(x);
2725: for (k=1; k<=2; k++) {
2726: for (i=1;i<=npar;i++) p2[i]=x[i];
2727: p2[thetai]=x[thetai]+delti[thetai]/k;
2728: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2729: k1=func(p2)-fx;
2730:
2731: p2[thetai]=x[thetai]+delti[thetai]/k;
2732: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2733: k2=func(p2)-fx;
2734:
2735: p2[thetai]=x[thetai]-delti[thetai]/k;
2736: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2737: k3=func(p2)-fx;
2738:
2739: p2[thetai]=x[thetai]-delti[thetai]/k;
2740: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2741: k4=func(p2)-fx;
2742: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2743: #ifdef DEBUG
2744: 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);
2745: 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);
2746: #endif
2747: }
2748: return res;
2749: }
2750:
2751: /************** Inverse of matrix **************/
2752: void ludcmp(double **a, int n, int *indx, double *d)
2753: {
2754: int i,imax,j,k;
2755: double big,dum,sum,temp;
2756: double *vv;
2757:
2758: vv=vector(1,n);
2759: *d=1.0;
2760: for (i=1;i<=n;i++) {
2761: big=0.0;
2762: for (j=1;j<=n;j++)
2763: if ((temp=fabs(a[i][j])) > big) big=temp;
2764: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2765: vv[i]=1.0/big;
2766: }
2767: for (j=1;j<=n;j++) {
2768: for (i=1;i<j;i++) {
2769: sum=a[i][j];
2770: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2771: a[i][j]=sum;
2772: }
2773: big=0.0;
2774: for (i=j;i<=n;i++) {
2775: sum=a[i][j];
2776: for (k=1;k<j;k++)
2777: sum -= a[i][k]*a[k][j];
2778: a[i][j]=sum;
2779: if ( (dum=vv[i]*fabs(sum)) >= big) {
2780: big=dum;
2781: imax=i;
2782: }
2783: }
2784: if (j != imax) {
2785: for (k=1;k<=n;k++) {
2786: dum=a[imax][k];
2787: a[imax][k]=a[j][k];
2788: a[j][k]=dum;
2789: }
2790: *d = -(*d);
2791: vv[imax]=vv[j];
2792: }
2793: indx[j]=imax;
2794: if (a[j][j] == 0.0) a[j][j]=TINY;
2795: if (j != n) {
2796: dum=1.0/(a[j][j]);
2797: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2798: }
2799: }
2800: free_vector(vv,1,n); /* Doesn't work */
2801: ;
2802: }
2803:
2804: void lubksb(double **a, int n, int *indx, double b[])
2805: {
2806: int i,ii=0,ip,j;
2807: double sum;
2808:
2809: for (i=1;i<=n;i++) {
2810: ip=indx[i];
2811: sum=b[ip];
2812: b[ip]=b[i];
2813: if (ii)
2814: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2815: else if (sum) ii=i;
2816: b[i]=sum;
2817: }
2818: for (i=n;i>=1;i--) {
2819: sum=b[i];
2820: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2821: b[i]=sum/a[i][i];
2822: }
2823: }
2824:
2825: void pstamp(FILE *fichier)
2826: {
2827: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2828: }
2829:
2830: /************ Frequencies ********************/
2831: 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[])
2832: { /* Some frequencies */
2833:
1.164 brouard 2834: int i, m, jk, j1, bool, z1,j;
1.126 brouard 2835: int first;
2836: double ***freq; /* Frequencies */
2837: double *pp, **prop;
2838: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2839: char fileresp[FILENAMELENGTH];
2840:
2841: pp=vector(1,nlstate);
2842: prop=matrix(1,nlstate,iagemin,iagemax+3);
2843: strcpy(fileresp,"p");
2844: strcat(fileresp,fileres);
2845: if((ficresp=fopen(fileresp,"w"))==NULL) {
2846: printf("Problem with prevalence resultfile: %s\n", fileresp);
2847: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2848: exit(0);
2849: }
2850: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2851: j1=0;
2852:
2853: j=cptcoveff;
2854: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2855:
2856: first=1;
2857:
1.169 brouard 2858: /* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */
2859: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
2860: /* j1++; */
1.145 brouard 2861: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
1.126 brouard 2862: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2863: scanf("%d", i);*/
2864: for (i=-5; i<=nlstate+ndeath; i++)
2865: for (jk=-5; jk<=nlstate+ndeath; jk++)
2866: for(m=iagemin; m <= iagemax+3; m++)
2867: freq[i][jk][m]=0;
1.143 brouard 2868:
2869: for (i=1; i<=nlstate; i++)
2870: for(m=iagemin; m <= iagemax+3; m++)
2871: prop[i][m]=0;
1.126 brouard 2872:
2873: dateintsum=0;
2874: k2cpt=0;
2875: for (i=1; i<=imx; i++) {
2876: bool=1;
1.144 brouard 2877: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
2878: for (z1=1; z1<=cptcoveff; z1++)
2879: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
1.145 brouard 2880: /* Tests if the value of each of the covariates of i is equal to filter j1 */
1.144 brouard 2881: bool=0;
1.145 brouard 2882: /* 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",
2883: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
2884: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
1.144 brouard 2885: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
2886: }
1.126 brouard 2887: }
1.144 brouard 2888:
1.126 brouard 2889: if (bool==1){
2890: for(m=firstpass; m<=lastpass; m++){
2891: k2=anint[m][i]+(mint[m][i]/12.);
2892: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2893: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2894: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2895: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2896: if (m<lastpass) {
2897: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2898: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2899: }
2900:
2901: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2902: dateintsum=dateintsum+k2;
2903: k2cpt++;
2904: }
2905: /*}*/
2906: }
2907: }
1.145 brouard 2908: } /* end i */
1.126 brouard 2909:
2910: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2911: pstamp(ficresp);
2912: if (cptcovn>0) {
2913: fprintf(ficresp, "\n#********** Variable ");
2914: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2915: fprintf(ficresp, "**********\n#");
1.143 brouard 2916: fprintf(ficlog, "\n#********** Variable ");
2917: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2918: fprintf(ficlog, "**********\n#");
1.126 brouard 2919: }
2920: for(i=1; i<=nlstate;i++)
2921: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2922: fprintf(ficresp, "\n");
2923:
2924: for(i=iagemin; i <= iagemax+3; i++){
2925: if(i==iagemax+3){
2926: fprintf(ficlog,"Total");
2927: }else{
2928: if(first==1){
2929: first=0;
2930: printf("See log file for details...\n");
2931: }
2932: fprintf(ficlog,"Age %d", i);
2933: }
2934: for(jk=1; jk <=nlstate ; jk++){
2935: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2936: pp[jk] += freq[jk][m][i];
2937: }
2938: for(jk=1; jk <=nlstate ; jk++){
2939: for(m=-1, pos=0; m <=0 ; m++)
2940: pos += freq[jk][m][i];
2941: if(pp[jk]>=1.e-10){
2942: if(first==1){
1.132 brouard 2943: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1.126 brouard 2944: }
2945: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2946: }else{
2947: if(first==1)
2948: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2949: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2950: }
2951: }
2952:
2953: for(jk=1; jk <=nlstate ; jk++){
2954: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2955: pp[jk] += freq[jk][m][i];
2956: }
2957: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2958: pos += pp[jk];
2959: posprop += prop[jk][i];
2960: }
2961: for(jk=1; jk <=nlstate ; jk++){
2962: if(pos>=1.e-5){
2963: if(first==1)
2964: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2965: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2966: }else{
2967: if(first==1)
2968: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2969: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2970: }
2971: if( i <= iagemax){
2972: if(pos>=1.e-5){
2973: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2974: /*probs[i][jk][j1]= pp[jk]/pos;*/
2975: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2976: }
2977: else
2978: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2979: }
2980: }
2981:
2982: for(jk=-1; jk <=nlstate+ndeath; jk++)
2983: for(m=-1; m <=nlstate+ndeath; m++)
2984: if(freq[jk][m][i] !=0 ) {
2985: if(first==1)
2986: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2987: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2988: }
2989: if(i <= iagemax)
2990: fprintf(ficresp,"\n");
2991: if(first==1)
2992: printf("Others in log...\n");
2993: fprintf(ficlog,"\n");
2994: }
1.145 brouard 2995: /*}*/
1.126 brouard 2996: }
2997: dateintmean=dateintsum/k2cpt;
2998:
2999: fclose(ficresp);
3000: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
3001: free_vector(pp,1,nlstate);
3002: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
3003: /* End of Freq */
3004: }
3005:
3006: /************ Prevalence ********************/
3007: 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)
3008: {
3009: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
3010: in each health status at the date of interview (if between dateprev1 and dateprev2).
3011: We still use firstpass and lastpass as another selection.
3012: */
3013:
1.164 brouard 3014: int i, m, jk, j1, bool, z1,j;
3015:
3016: double **prop;
3017: double posprop;
1.126 brouard 3018: double y2; /* in fractional years */
3019: int iagemin, iagemax;
1.145 brouard 3020: int first; /** to stop verbosity which is redirected to log file */
1.126 brouard 3021:
3022: iagemin= (int) agemin;
3023: iagemax= (int) agemax;
3024: /*pp=vector(1,nlstate);*/
3025: prop=matrix(1,nlstate,iagemin,iagemax+3);
3026: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
3027: j1=0;
3028:
1.145 brouard 3029: /*j=cptcoveff;*/
1.126 brouard 3030: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3031:
1.145 brouard 3032: first=1;
3033: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
3034: /*for(i1=1; i1<=ncodemax[k1];i1++){
3035: j1++;*/
1.126 brouard 3036:
3037: for (i=1; i<=nlstate; i++)
3038: for(m=iagemin; m <= iagemax+3; m++)
3039: prop[i][m]=0.0;
3040:
3041: for (i=1; i<=imx; i++) { /* Each individual */
3042: bool=1;
3043: if (cptcovn>0) {
3044: for (z1=1; z1<=cptcoveff; z1++)
3045: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
3046: bool=0;
3047: }
3048: if (bool==1) {
3049: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
3050: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
3051: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
3052: if(agev[m][i]==0) agev[m][i]=iagemax+1;
3053: if(agev[m][i]==1) agev[m][i]=iagemax+2;
3054: 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);
3055: if (s[m][i]>0 && s[m][i]<=nlstate) {
3056: /*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]]);*/
3057: prop[s[m][i]][(int)agev[m][i]] += weight[i];
3058: prop[s[m][i]][iagemax+3] += weight[i];
3059: }
3060: }
3061: } /* end selection of waves */
3062: }
3063: }
3064: for(i=iagemin; i <= iagemax+3; i++){
3065: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
3066: posprop += prop[jk][i];
3067: }
1.145 brouard 3068:
1.126 brouard 3069: for(jk=1; jk <=nlstate ; jk++){
3070: if( i <= iagemax){
3071: if(posprop>=1.e-5){
3072: probs[i][jk][j1]= prop[jk][i]/posprop;
1.145 brouard 3073: } else{
3074: if(first==1){
3075: first=0;
3076: 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]);
3077: }
3078: }
1.126 brouard 3079: }
3080: }/* end jk */
3081: }/* end i */
1.145 brouard 3082: /*} *//* end i1 */
3083: } /* end j1 */
1.126 brouard 3084:
3085: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
3086: /*free_vector(pp,1,nlstate);*/
3087: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
3088: } /* End of prevalence */
3089:
3090: /************* Waves Concatenation ***************/
3091:
3092: 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)
3093: {
3094: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
3095: Death is a valid wave (if date is known).
3096: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
3097: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3098: and mw[mi+1][i]. dh depends on stepm.
3099: */
3100:
3101: int i, mi, m;
3102: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
3103: double sum=0., jmean=0.;*/
3104: int first;
3105: int j, k=0,jk, ju, jl;
3106: double sum=0.;
3107: first=0;
1.164 brouard 3108: jmin=100000;
1.126 brouard 3109: jmax=-1;
3110: jmean=0.;
3111: for(i=1; i<=imx; i++){
3112: mi=0;
3113: m=firstpass;
3114: while(s[m][i] <= nlstate){
3115: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
3116: mw[++mi][i]=m;
3117: if(m >=lastpass)
3118: break;
3119: else
3120: m++;
3121: }/* end while */
3122: if (s[m][i] > nlstate){
3123: mi++; /* Death is another wave */
3124: /* if(mi==0) never been interviewed correctly before death */
3125: /* Only death is a correct wave */
3126: mw[mi][i]=m;
3127: }
3128:
3129: wav[i]=mi;
3130: if(mi==0){
3131: nbwarn++;
3132: if(first==0){
3133: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
3134: first=1;
3135: }
3136: if(first==1){
3137: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
3138: }
3139: } /* end mi==0 */
3140: } /* End individuals */
3141:
3142: for(i=1; i<=imx; i++){
3143: for(mi=1; mi<wav[i];mi++){
3144: if (stepm <=0)
3145: dh[mi][i]=1;
3146: else{
3147: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
3148: if (agedc[i] < 2*AGESUP) {
3149: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
3150: if(j==0) j=1; /* Survives at least one month after exam */
3151: else if(j<0){
3152: nberr++;
3153: 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]);
3154: j=1; /* Temporary Dangerous patch */
3155: 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);
3156: 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]);
3157: 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);
3158: }
3159: k=k+1;
3160: if (j >= jmax){
3161: jmax=j;
3162: ijmax=i;
3163: }
3164: if (j <= jmin){
3165: jmin=j;
3166: ijmin=i;
3167: }
3168: sum=sum+j;
3169: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
3170: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
3171: }
3172: }
3173: else{
3174: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
3175: /* 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]); */
3176:
3177: k=k+1;
3178: if (j >= jmax) {
3179: jmax=j;
3180: ijmax=i;
3181: }
3182: else if (j <= jmin){
3183: jmin=j;
3184: ijmin=i;
3185: }
3186: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
3187: /*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]);*/
3188: if(j<0){
3189: nberr++;
3190: 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]);
3191: 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]);
3192: }
3193: sum=sum+j;
3194: }
3195: jk= j/stepm;
3196: jl= j -jk*stepm;
3197: ju= j -(jk+1)*stepm;
3198: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
3199: if(jl==0){
3200: dh[mi][i]=jk;
3201: bh[mi][i]=0;
3202: }else{ /* We want a negative bias in order to only have interpolation ie
1.136 brouard 3203: * to avoid the price of an extra matrix product in likelihood */
1.126 brouard 3204: dh[mi][i]=jk+1;
3205: bh[mi][i]=ju;
3206: }
3207: }else{
3208: if(jl <= -ju){
3209: dh[mi][i]=jk;
3210: bh[mi][i]=jl; /* bias is positive if real duration
3211: * is higher than the multiple of stepm and negative otherwise.
3212: */
3213: }
3214: else{
3215: dh[mi][i]=jk+1;
3216: bh[mi][i]=ju;
3217: }
3218: if(dh[mi][i]==0){
3219: dh[mi][i]=1; /* At least one step */
3220: bh[mi][i]=ju; /* At least one step */
3221: /* 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);*/
3222: }
3223: } /* end if mle */
3224: }
3225: } /* end wave */
3226: }
3227: jmean=sum/k;
3228: 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 3229: 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 3230: }
3231:
3232: /*********** Tricode ****************************/
1.145 brouard 3233: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 3234: {
1.144 brouard 3235: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
3236: /* 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 3237: * Boring subroutine which should only output nbcode[Tvar[j]][k]
1.145 brouard 3238: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
1.169 brouard 3239: * nbcode[Tvar[j]][1]=
1.144 brouard 3240: */
1.130 brouard 3241:
1.145 brouard 3242: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 3243: int modmaxcovj=0; /* Modality max of covariates j */
1.145 brouard 3244: int cptcode=0; /* Modality max of covariates j */
3245: int modmincovj=0; /* Modality min of covariates j */
3246:
3247:
1.126 brouard 3248: cptcoveff=0;
3249:
1.145 brouard 3250: for (k=-1; k < maxncov; k++) Ndum[k]=0;
1.144 brouard 3251: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 3252:
1.145 brouard 3253: /* Loop on covariates without age and products */
1.186 brouard 3254: for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
3255: for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
1.136 brouard 3256: modality of this covariate Vj*/
1.145 brouard 3257: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
3258: * If product of Vn*Vm, still boolean *:
3259: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
3260: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
3261: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
1.136 brouard 3262: modality of the nth covariate of individual i. */
1.145 brouard 3263: if (ij > modmaxcovj)
3264: modmaxcovj=ij;
3265: else if (ij < modmincovj)
3266: modmincovj=ij;
3267: if ((ij < -1) && (ij > NCOVMAX)){
3268: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
3269: exit(1);
3270: }else
1.136 brouard 3271: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
1.145 brouard 3272: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
1.126 brouard 3273: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.136 brouard 3274: /* getting the maximum value of the modality of the covariate
3275: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
3276: female is 1, then modmaxcovj=1.*/
1.187 brouard 3277: } /* end for loop on individuals */
1.145 brouard 3278: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
3279: cptcode=modmaxcovj;
1.137 brouard 3280: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
1.145 brouard 3281: /*for (i=0; i<=cptcode; i++) {*/
3282: for (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
1.187 brouard 3283: printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], i, Ndum[i]);
1.145 brouard 3284: if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
3285: ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
3286: }
3287: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
3288: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
1.131 brouard 3289: } /* Ndum[-1] number of undefined modalities */
1.126 brouard 3290:
1.136 brouard 3291: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
1.186 brouard 3292: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
3293: If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125;
1.145 brouard 3294: modmincovj=3; modmaxcovj = 7;
1.186 brouard 3295: There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
3296: which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
3297: defining two dummy variables: variables V1_1 and V1_2.
1.145 brouard 3298: nbcode[Tvar[j]][ij]=k;
3299: nbcode[Tvar[j]][1]=0;
3300: nbcode[Tvar[j]][2]=1;
3301: nbcode[Tvar[j]][3]=2;
3302: */
3303: ij=1; /* ij is similar to i but can jumps over null modalities */
3304: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
3305: for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
3306: /*recode from 0 */
1.131 brouard 3307: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
1.186 brouard 3308: nbcode[Tvar[j]][ij]=k; /* stores the modality k in an array nbcode.
1.131 brouard 3309: k is a modality. If we have model=V1+V1*sex
3310: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
1.126 brouard 3311: ij++;
3312: }
3313: if (ij > ncodemax[j]) break;
1.137 brouard 3314: } /* end of loop on */
3315: } /* end of loop on modality */
3316: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
3317:
1.145 brouard 3318: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.137 brouard 3319:
1.187 brouard 3320: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
1.145 brouard 3321: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
3322: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
1.187 brouard 3323: Ndum[ij]++; /* Might be supersed V1 + V1*age */
1.145 brouard 3324: }
1.126 brouard 3325:
3326: ij=1;
1.145 brouard 3327: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
3328: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
1.126 brouard 3329: if((Ndum[i]!=0) && (i<=ncovcol)){
1.145 brouard 3330: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
3331: Tvaraff[ij]=i; /*For printing (unclear) */
1.126 brouard 3332: ij++;
1.145 brouard 3333: }else
3334: Tvaraff[ij]=0;
1.126 brouard 3335: }
1.131 brouard 3336: ij--;
1.144 brouard 3337: cptcoveff=ij; /*Number of total covariates*/
1.145 brouard 3338:
1.126 brouard 3339: }
3340:
1.145 brouard 3341:
1.126 brouard 3342: /*********** Health Expectancies ****************/
3343:
1.127 brouard 3344: 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 3345:
3346: {
3347: /* Health expectancies, no variances */
1.164 brouard 3348: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 3349: int nhstepma, nstepma; /* Decreasing with age */
3350: double age, agelim, hf;
3351: double ***p3mat;
3352: double eip;
3353:
3354: pstamp(ficreseij);
3355: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3356: fprintf(ficreseij,"# Age");
3357: for(i=1; i<=nlstate;i++){
3358: for(j=1; j<=nlstate;j++){
3359: fprintf(ficreseij," e%1d%1d ",i,j);
3360: }
3361: fprintf(ficreseij," e%1d. ",i);
3362: }
3363: fprintf(ficreseij,"\n");
3364:
3365:
3366: if(estepm < stepm){
3367: printf ("Problem %d lower than %d\n",estepm, stepm);
3368: }
3369: else hstepm=estepm;
3370: /* We compute the life expectancy from trapezoids spaced every estepm months
3371: * This is mainly to measure the difference between two models: for example
3372: * if stepm=24 months pijx are given only every 2 years and by summing them
3373: * we are calculating an estimate of the Life Expectancy assuming a linear
3374: * progression in between and thus overestimating or underestimating according
3375: * to the curvature of the survival function. If, for the same date, we
3376: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3377: * to compare the new estimate of Life expectancy with the same linear
3378: * hypothesis. A more precise result, taking into account a more precise
3379: * curvature will be obtained if estepm is as small as stepm. */
3380:
3381: /* For example we decided to compute the life expectancy with the smallest unit */
3382: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3383: nhstepm is the number of hstepm from age to agelim
3384: nstepm is the number of stepm from age to agelin.
3385: Look at hpijx to understand the reason of that which relies in memory size
3386: and note for a fixed period like estepm months */
3387: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3388: survival function given by stepm (the optimization length). Unfortunately it
3389: means that if the survival funtion is printed only each two years of age and if
3390: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3391: results. So we changed our mind and took the option of the best precision.
3392: */
3393: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3394:
3395: agelim=AGESUP;
3396: /* If stepm=6 months */
3397: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3398: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3399:
3400: /* nhstepm age range expressed in number of stepm */
3401: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3402: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3403: /* if (stepm >= YEARM) hstepm=1;*/
3404: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3405: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3406:
3407: for (age=bage; age<=fage; age ++){
3408: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3409: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3410: /* if (stepm >= YEARM) hstepm=1;*/
3411: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3412:
3413: /* If stepm=6 months */
3414: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3415: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3416:
3417: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3418:
3419: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3420:
3421: printf("%d|",(int)age);fflush(stdout);
3422: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3423:
3424: /* Computing expectancies */
3425: for(i=1; i<=nlstate;i++)
3426: for(j=1; j<=nlstate;j++)
3427: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3428: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3429:
3430: /* 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]);*/
3431:
3432: }
3433:
3434: fprintf(ficreseij,"%3.0f",age );
3435: for(i=1; i<=nlstate;i++){
3436: eip=0;
3437: for(j=1; j<=nlstate;j++){
3438: eip +=eij[i][j][(int)age];
3439: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3440: }
3441: fprintf(ficreseij,"%9.4f", eip );
3442: }
3443: fprintf(ficreseij,"\n");
3444:
3445: }
3446: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3447: printf("\n");
3448: fprintf(ficlog,"\n");
3449:
3450: }
3451:
1.127 brouard 3452: 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 3453:
3454: {
3455: /* Covariances of health expectancies eij and of total life expectancies according
3456: to initial status i, ei. .
3457: */
3458: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3459: int nhstepma, nstepma; /* Decreasing with age */
3460: double age, agelim, hf;
3461: double ***p3matp, ***p3matm, ***varhe;
3462: double **dnewm,**doldm;
3463: double *xp, *xm;
3464: double **gp, **gm;
3465: double ***gradg, ***trgradg;
3466: int theta;
3467:
3468: double eip, vip;
3469:
3470: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
3471: xp=vector(1,npar);
3472: xm=vector(1,npar);
3473: dnewm=matrix(1,nlstate*nlstate,1,npar);
3474: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3475:
3476: pstamp(ficresstdeij);
3477: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3478: fprintf(ficresstdeij,"# Age");
3479: for(i=1; i<=nlstate;i++){
3480: for(j=1; j<=nlstate;j++)
3481: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3482: fprintf(ficresstdeij," e%1d. ",i);
3483: }
3484: fprintf(ficresstdeij,"\n");
3485:
3486: pstamp(ficrescveij);
3487: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3488: fprintf(ficrescveij,"# Age");
3489: for(i=1; i<=nlstate;i++)
3490: for(j=1; j<=nlstate;j++){
3491: cptj= (j-1)*nlstate+i;
3492: for(i2=1; i2<=nlstate;i2++)
3493: for(j2=1; j2<=nlstate;j2++){
3494: cptj2= (j2-1)*nlstate+i2;
3495: if(cptj2 <= cptj)
3496: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3497: }
3498: }
3499: fprintf(ficrescveij,"\n");
3500:
3501: if(estepm < stepm){
3502: printf ("Problem %d lower than %d\n",estepm, stepm);
3503: }
3504: else hstepm=estepm;
3505: /* We compute the life expectancy from trapezoids spaced every estepm months
3506: * This is mainly to measure the difference between two models: for example
3507: * if stepm=24 months pijx are given only every 2 years and by summing them
3508: * we are calculating an estimate of the Life Expectancy assuming a linear
3509: * progression in between and thus overestimating or underestimating according
3510: * to the curvature of the survival function. If, for the same date, we
3511: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3512: * to compare the new estimate of Life expectancy with the same linear
3513: * hypothesis. A more precise result, taking into account a more precise
3514: * curvature will be obtained if estepm is as small as stepm. */
3515:
3516: /* For example we decided to compute the life expectancy with the smallest unit */
3517: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3518: nhstepm is the number of hstepm from age to agelim
3519: nstepm is the number of stepm from age to agelin.
3520: Look at hpijx to understand the reason of that which relies in memory size
3521: and note for a fixed period like estepm months */
3522: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3523: survival function given by stepm (the optimization length). Unfortunately it
3524: means that if the survival funtion is printed only each two years of age and if
3525: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3526: results. So we changed our mind and took the option of the best precision.
3527: */
3528: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3529:
3530: /* If stepm=6 months */
3531: /* nhstepm age range expressed in number of stepm */
3532: agelim=AGESUP;
3533: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3534: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3535: /* if (stepm >= YEARM) hstepm=1;*/
3536: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3537:
3538: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3539: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3540: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3541: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3542: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3543: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3544:
3545: for (age=bage; age<=fage; age ++){
3546: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3547: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3548: /* if (stepm >= YEARM) hstepm=1;*/
3549: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3550:
3551: /* If stepm=6 months */
3552: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3553: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3554:
3555: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3556:
3557: /* Computing Variances of health expectancies */
3558: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3559: decrease memory allocation */
3560: for(theta=1; theta <=npar; theta++){
3561: for(i=1; i<=npar; i++){
3562: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3563: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3564: }
3565: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3566: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3567:
3568: for(j=1; j<= nlstate; j++){
3569: for(i=1; i<=nlstate; i++){
3570: for(h=0; h<=nhstepm-1; h++){
3571: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3572: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3573: }
3574: }
3575: }
3576:
3577: for(ij=1; ij<= nlstate*nlstate; ij++)
3578: for(h=0; h<=nhstepm-1; h++){
3579: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3580: }
3581: }/* End theta */
3582:
3583:
3584: for(h=0; h<=nhstepm-1; h++)
3585: for(j=1; j<=nlstate*nlstate;j++)
3586: for(theta=1; theta <=npar; theta++)
3587: trgradg[h][j][theta]=gradg[h][theta][j];
3588:
3589:
3590: for(ij=1;ij<=nlstate*nlstate;ij++)
3591: for(ji=1;ji<=nlstate*nlstate;ji++)
3592: varhe[ij][ji][(int)age] =0.;
3593:
3594: printf("%d|",(int)age);fflush(stdout);
3595: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3596: for(h=0;h<=nhstepm-1;h++){
3597: for(k=0;k<=nhstepm-1;k++){
3598: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3599: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3600: for(ij=1;ij<=nlstate*nlstate;ij++)
3601: for(ji=1;ji<=nlstate*nlstate;ji++)
3602: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3603: }
3604: }
3605:
3606: /* Computing expectancies */
3607: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3608: for(i=1; i<=nlstate;i++)
3609: for(j=1; j<=nlstate;j++)
3610: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3611: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3612:
3613: /* 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]);*/
3614:
3615: }
3616:
3617: fprintf(ficresstdeij,"%3.0f",age );
3618: for(i=1; i<=nlstate;i++){
3619: eip=0.;
3620: vip=0.;
3621: for(j=1; j<=nlstate;j++){
3622: eip += eij[i][j][(int)age];
3623: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3624: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3625: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3626: }
3627: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3628: }
3629: fprintf(ficresstdeij,"\n");
3630:
3631: fprintf(ficrescveij,"%3.0f",age );
3632: for(i=1; i<=nlstate;i++)
3633: for(j=1; j<=nlstate;j++){
3634: cptj= (j-1)*nlstate+i;
3635: for(i2=1; i2<=nlstate;i2++)
3636: for(j2=1; j2<=nlstate;j2++){
3637: cptj2= (j2-1)*nlstate+i2;
3638: if(cptj2 <= cptj)
3639: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3640: }
3641: }
3642: fprintf(ficrescveij,"\n");
3643:
3644: }
3645: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3646: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3647: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3648: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3649: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3650: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3651: printf("\n");
3652: fprintf(ficlog,"\n");
3653:
3654: free_vector(xm,1,npar);
3655: free_vector(xp,1,npar);
3656: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3657: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3658: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3659: }
3660:
3661: /************ Variance ******************/
3662: 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[])
3663: {
3664: /* Variance of health expectancies */
3665: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3666: /* double **newm;*/
1.169 brouard 3667: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
3668:
3669: int movingaverage();
1.126 brouard 3670: double **dnewm,**doldm;
3671: double **dnewmp,**doldmp;
3672: int i, j, nhstepm, hstepm, h, nstepm ;
1.164 brouard 3673: int k;
1.126 brouard 3674: double *xp;
3675: double **gp, **gm; /* for var eij */
3676: double ***gradg, ***trgradg; /*for var eij */
3677: double **gradgp, **trgradgp; /* for var p point j */
3678: double *gpp, *gmp; /* for var p point j */
3679: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3680: double ***p3mat;
3681: double age,agelim, hf;
3682: double ***mobaverage;
3683: int theta;
3684: char digit[4];
3685: char digitp[25];
3686:
3687: char fileresprobmorprev[FILENAMELENGTH];
3688:
3689: if(popbased==1){
3690: if(mobilav!=0)
3691: strcpy(digitp,"-populbased-mobilav-");
3692: else strcpy(digitp,"-populbased-nomobil-");
3693: }
3694: else
3695: strcpy(digitp,"-stablbased-");
3696:
3697: if (mobilav!=0) {
3698: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3699: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3700: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3701: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3702: }
3703: }
3704:
3705: strcpy(fileresprobmorprev,"prmorprev");
3706: sprintf(digit,"%-d",ij);
3707: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3708: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3709: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
3710: strcat(fileresprobmorprev,fileres);
3711: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3712: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3713: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3714: }
3715: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3716:
3717: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3718: pstamp(ficresprobmorprev);
3719: 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);
3720: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3721: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3722: fprintf(ficresprobmorprev," p.%-d SE",j);
3723: for(i=1; i<=nlstate;i++)
3724: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3725: }
3726: fprintf(ficresprobmorprev,"\n");
3727: fprintf(ficgp,"\n# Routine varevsij");
3728: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
3729: 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");
3730: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3731: /* } */
3732: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3733: pstamp(ficresvij);
3734: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3735: if(popbased==1)
1.128 brouard 3736: 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 3737: else
3738: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3739: fprintf(ficresvij,"# Age");
3740: for(i=1; i<=nlstate;i++)
3741: for(j=1; j<=nlstate;j++)
3742: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3743: fprintf(ficresvij,"\n");
3744:
3745: xp=vector(1,npar);
3746: dnewm=matrix(1,nlstate,1,npar);
3747: doldm=matrix(1,nlstate,1,nlstate);
3748: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3749: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3750:
3751: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3752: gpp=vector(nlstate+1,nlstate+ndeath);
3753: gmp=vector(nlstate+1,nlstate+ndeath);
3754: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3755:
3756: if(estepm < stepm){
3757: printf ("Problem %d lower than %d\n",estepm, stepm);
3758: }
3759: else hstepm=estepm;
3760: /* For example we decided to compute the life expectancy with the smallest unit */
3761: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3762: nhstepm is the number of hstepm from age to agelim
3763: nstepm is the number of stepm from age to agelin.
1.128 brouard 3764: Look at function hpijx to understand why (it is linked to memory size questions) */
1.126 brouard 3765: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3766: survival function given by stepm (the optimization length). Unfortunately it
3767: means that if the survival funtion is printed every two years of age and if
3768: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3769: results. So we changed our mind and took the option of the best precision.
3770: */
3771: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3772: agelim = AGESUP;
3773: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3774: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3775: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3776: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3777: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3778: gp=matrix(0,nhstepm,1,nlstate);
3779: gm=matrix(0,nhstepm,1,nlstate);
3780:
3781:
3782: for(theta=1; theta <=npar; theta++){
3783: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3784: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3785: }
3786: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3787: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3788:
3789: if (popbased==1) {
3790: if(mobilav ==0){
3791: for(i=1; i<=nlstate;i++)
3792: prlim[i][i]=probs[(int)age][i][ij];
3793: }else{ /* mobilav */
3794: for(i=1; i<=nlstate;i++)
3795: prlim[i][i]=mobaverage[(int)age][i][ij];
3796: }
3797: }
3798:
3799: for(j=1; j<= nlstate; j++){
3800: for(h=0; h<=nhstepm; h++){
3801: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3802: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3803: }
3804: }
3805: /* This for computing probability of death (h=1 means
3806: computed over hstepm matrices product = hstepm*stepm months)
3807: as a weighted average of prlim.
3808: */
3809: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3810: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3811: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3812: }
3813: /* end probability of death */
3814:
3815: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3816: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3817: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3818: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3819:
3820: if (popbased==1) {
3821: if(mobilav ==0){
3822: for(i=1; i<=nlstate;i++)
3823: prlim[i][i]=probs[(int)age][i][ij];
3824: }else{ /* mobilav */
3825: for(i=1; i<=nlstate;i++)
3826: prlim[i][i]=mobaverage[(int)age][i][ij];
3827: }
3828: }
3829:
1.128 brouard 3830: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
1.126 brouard 3831: for(h=0; h<=nhstepm; h++){
3832: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3833: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3834: }
3835: }
3836: /* This for computing probability of death (h=1 means
3837: computed over hstepm matrices product = hstepm*stepm months)
3838: as a weighted average of prlim.
3839: */
3840: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3841: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3842: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3843: }
3844: /* end probability of death */
3845:
3846: for(j=1; j<= nlstate; j++) /* vareij */
3847: for(h=0; h<=nhstepm; h++){
3848: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3849: }
3850:
3851: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3852: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3853: }
3854:
3855: } /* End theta */
3856:
3857: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3858:
3859: for(h=0; h<=nhstepm; h++) /* veij */
3860: for(j=1; j<=nlstate;j++)
3861: for(theta=1; theta <=npar; theta++)
3862: trgradg[h][j][theta]=gradg[h][theta][j];
3863:
3864: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3865: for(theta=1; theta <=npar; theta++)
3866: trgradgp[j][theta]=gradgp[theta][j];
3867:
3868:
3869: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3870: for(i=1;i<=nlstate;i++)
3871: for(j=1;j<=nlstate;j++)
3872: vareij[i][j][(int)age] =0.;
3873:
3874: for(h=0;h<=nhstepm;h++){
3875: for(k=0;k<=nhstepm;k++){
3876: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3877: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3878: for(i=1;i<=nlstate;i++)
3879: for(j=1;j<=nlstate;j++)
3880: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3881: }
3882: }
3883:
3884: /* pptj */
3885: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3886: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3887: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3888: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3889: varppt[j][i]=doldmp[j][i];
3890: /* end ppptj */
3891: /* x centered again */
3892: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3893: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3894:
3895: if (popbased==1) {
3896: if(mobilav ==0){
3897: for(i=1; i<=nlstate;i++)
3898: prlim[i][i]=probs[(int)age][i][ij];
3899: }else{ /* mobilav */
3900: for(i=1; i<=nlstate;i++)
3901: prlim[i][i]=mobaverage[(int)age][i][ij];
3902: }
3903: }
3904:
3905: /* This for computing probability of death (h=1 means
3906: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3907: as a weighted average of prlim.
3908: */
3909: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3910: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3911: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3912: }
3913: /* end probability of death */
3914:
3915: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3916: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3917: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3918: for(i=1; i<=nlstate;i++){
3919: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3920: }
3921: }
3922: fprintf(ficresprobmorprev,"\n");
3923:
3924: fprintf(ficresvij,"%.0f ",age );
3925: for(i=1; i<=nlstate;i++)
3926: for(j=1; j<=nlstate;j++){
3927: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3928: }
3929: fprintf(ficresvij,"\n");
3930: free_matrix(gp,0,nhstepm,1,nlstate);
3931: free_matrix(gm,0,nhstepm,1,nlstate);
3932: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3933: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3934: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3935: } /* End age */
3936: free_vector(gpp,nlstate+1,nlstate+ndeath);
3937: free_vector(gmp,nlstate+1,nlstate+ndeath);
3938: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3939: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.145 brouard 3940: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
1.126 brouard 3941: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
1.131 brouard 3942: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.126 brouard 3943: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3944: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3945: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.145 brouard 3946: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
1.170 brouard 3947: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
1.145 brouard 3948: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
1.126 brouard 3949: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3950: 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);
3951: /* 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);
3952: */
3953: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3954: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3955:
3956: free_vector(xp,1,npar);
3957: free_matrix(doldm,1,nlstate,1,nlstate);
3958: free_matrix(dnewm,1,nlstate,1,npar);
3959: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3960: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3961: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3962: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3963: fclose(ficresprobmorprev);
3964: fflush(ficgp);
3965: fflush(fichtm);
3966: } /* end varevsij */
3967:
3968: /************ Variance of prevlim ******************/
3969: 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[])
3970: {
3971: /* Variance of prevalence limit */
3972: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 3973:
1.126 brouard 3974: double **dnewm,**doldm;
3975: int i, j, nhstepm, hstepm;
3976: double *xp;
3977: double *gp, *gm;
3978: double **gradg, **trgradg;
3979: double age,agelim;
3980: int theta;
3981:
3982: pstamp(ficresvpl);
3983: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3984: fprintf(ficresvpl,"# Age");
3985: for(i=1; i<=nlstate;i++)
3986: fprintf(ficresvpl," %1d-%1d",i,i);
3987: fprintf(ficresvpl,"\n");
3988:
3989: xp=vector(1,npar);
3990: dnewm=matrix(1,nlstate,1,npar);
3991: doldm=matrix(1,nlstate,1,nlstate);
3992:
3993: hstepm=1*YEARM; /* Every year of age */
3994: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3995: agelim = AGESUP;
3996: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3997: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3998: if (stepm >= YEARM) hstepm=1;
3999: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4000: gradg=matrix(1,npar,1,nlstate);
4001: gp=vector(1,nlstate);
4002: gm=vector(1,nlstate);
4003:
4004: for(theta=1; theta <=npar; theta++){
4005: for(i=1; i<=npar; i++){ /* Computes gradient */
4006: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4007: }
4008: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
4009: for(i=1;i<=nlstate;i++)
4010: gp[i] = prlim[i][i];
4011:
4012: for(i=1; i<=npar; i++) /* Computes gradient */
4013: xp[i] = x[i] - (i==theta ?delti[theta]:0);
4014: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
4015: for(i=1;i<=nlstate;i++)
4016: gm[i] = prlim[i][i];
4017:
4018: for(i=1;i<=nlstate;i++)
4019: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
4020: } /* End theta */
4021:
4022: trgradg =matrix(1,nlstate,1,npar);
4023:
4024: for(j=1; j<=nlstate;j++)
4025: for(theta=1; theta <=npar; theta++)
4026: trgradg[j][theta]=gradg[theta][j];
4027:
4028: for(i=1;i<=nlstate;i++)
4029: varpl[i][(int)age] =0.;
4030: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
4031: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
4032: for(i=1;i<=nlstate;i++)
4033: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
4034:
4035: fprintf(ficresvpl,"%.0f ",age );
4036: for(i=1; i<=nlstate;i++)
4037: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
4038: fprintf(ficresvpl,"\n");
4039: free_vector(gp,1,nlstate);
4040: free_vector(gm,1,nlstate);
4041: free_matrix(gradg,1,npar,1,nlstate);
4042: free_matrix(trgradg,1,nlstate,1,npar);
4043: } /* End age */
4044:
4045: free_vector(xp,1,npar);
4046: free_matrix(doldm,1,nlstate,1,npar);
4047: free_matrix(dnewm,1,nlstate,1,nlstate);
4048:
4049: }
4050:
4051: /************ Variance of one-step probabilities ******************/
4052: 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[])
4053: {
1.164 brouard 4054: int i, j=0, k1, l1, tj;
1.126 brouard 4055: int k2, l2, j1, z1;
1.164 brouard 4056: int k=0, l;
1.145 brouard 4057: int first=1, first1, first2;
1.126 brouard 4058: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
4059: double **dnewm,**doldm;
4060: double *xp;
4061: double *gp, *gm;
4062: double **gradg, **trgradg;
4063: double **mu;
1.164 brouard 4064: double age, cov[NCOVMAX+1];
1.126 brouard 4065: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
4066: int theta;
4067: char fileresprob[FILENAMELENGTH];
4068: char fileresprobcov[FILENAMELENGTH];
4069: char fileresprobcor[FILENAMELENGTH];
4070: double ***varpij;
4071:
4072: strcpy(fileresprob,"prob");
4073: strcat(fileresprob,fileres);
4074: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
4075: printf("Problem with resultfile: %s\n", fileresprob);
4076: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
4077: }
4078: strcpy(fileresprobcov,"probcov");
4079: strcat(fileresprobcov,fileres);
4080: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
4081: printf("Problem with resultfile: %s\n", fileresprobcov);
4082: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
4083: }
4084: strcpy(fileresprobcor,"probcor");
4085: strcat(fileresprobcor,fileres);
4086: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
4087: printf("Problem with resultfile: %s\n", fileresprobcor);
4088: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
4089: }
4090: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4091: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4092: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4093: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4094: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4095: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4096: pstamp(ficresprob);
4097: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
4098: fprintf(ficresprob,"# Age");
4099: pstamp(ficresprobcov);
4100: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
4101: fprintf(ficresprobcov,"# Age");
4102: pstamp(ficresprobcor);
4103: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
4104: fprintf(ficresprobcor,"# Age");
4105:
4106:
4107: for(i=1; i<=nlstate;i++)
4108: for(j=1; j<=(nlstate+ndeath);j++){
4109: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
4110: fprintf(ficresprobcov," p%1d-%1d ",i,j);
4111: fprintf(ficresprobcor," p%1d-%1d ",i,j);
4112: }
4113: /* fprintf(ficresprob,"\n");
4114: fprintf(ficresprobcov,"\n");
4115: fprintf(ficresprobcor,"\n");
4116: */
1.131 brouard 4117: xp=vector(1,npar);
1.126 brouard 4118: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4119: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4120: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
4121: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
4122: first=1;
4123: fprintf(ficgp,"\n# Routine varprob");
4124: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
4125: fprintf(fichtm,"\n");
4126:
4127: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
4128: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
4129: file %s<br>\n",optionfilehtmcov);
4130: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
4131: and drawn. It helps understanding how is the covariance between two incidences.\
4132: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
4133: 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. \
4134: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
4135: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
4136: standard deviations wide on each axis. <br>\
4137: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
4138: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
4139: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
4140:
4141: cov[1]=1;
1.145 brouard 4142: /* tj=cptcoveff; */
4143: tj = (int) pow(2,cptcoveff);
1.126 brouard 4144: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
4145: j1=0;
1.145 brouard 4146: for(j1=1; j1<=tj;j1++){
4147: /*for(i1=1; i1<=ncodemax[t];i1++){ */
4148: /*j1++;*/
1.126 brouard 4149: if (cptcovn>0) {
4150: fprintf(ficresprob, "\n#********** Variable ");
4151: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4152: fprintf(ficresprob, "**********\n#\n");
4153: fprintf(ficresprobcov, "\n#********** Variable ");
4154: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4155: fprintf(ficresprobcov, "**********\n#\n");
4156:
4157: fprintf(ficgp, "\n#********** Variable ");
4158: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4159: fprintf(ficgp, "**********\n#\n");
4160:
4161:
4162: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
4163: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4164: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
4165:
4166: fprintf(ficresprobcor, "\n#********** Variable ");
4167: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4168: fprintf(ficresprobcor, "**********\n#");
4169: }
4170:
1.145 brouard 4171: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
4172: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4173: gp=vector(1,(nlstate)*(nlstate+ndeath));
4174: gm=vector(1,(nlstate)*(nlstate+ndeath));
1.126 brouard 4175: for (age=bage; age<=fage; age ++){
4176: cov[2]=age;
1.187 brouard 4177: if(nagesqr==1)
4178: cov[3]= age*age;
1.126 brouard 4179: for (k=1; k<=cptcovn;k++) {
1.187 brouard 4180: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
1.145 brouard 4181: * 1 1 1 1 1
4182: * 2 2 1 1 1
4183: * 3 1 2 1 1
4184: */
4185: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
1.126 brouard 4186: }
1.186 brouard 4187: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
4188: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
1.126 brouard 4189: for (k=1; k<=cptcovprod;k++)
1.187 brouard 4190: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1.126 brouard 4191:
4192:
4193: for(theta=1; theta <=npar; theta++){
4194: for(i=1; i<=npar; i++)
4195: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
4196:
4197: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4198:
4199: k=0;
4200: for(i=1; i<= (nlstate); i++){
4201: for(j=1; j<=(nlstate+ndeath);j++){
4202: k=k+1;
4203: gp[k]=pmmij[i][j];
4204: }
4205: }
4206:
4207: for(i=1; i<=npar; i++)
4208: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
4209:
4210: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4211: k=0;
4212: for(i=1; i<=(nlstate); i++){
4213: for(j=1; j<=(nlstate+ndeath);j++){
4214: k=k+1;
4215: gm[k]=pmmij[i][j];
4216: }
4217: }
4218:
4219: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
4220: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
4221: }
4222:
4223: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
4224: for(theta=1; theta <=npar; theta++)
4225: trgradg[j][theta]=gradg[theta][j];
4226:
4227: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
4228: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
4229:
4230: pmij(pmmij,cov,ncovmodel,x,nlstate);
4231:
4232: k=0;
4233: for(i=1; i<=(nlstate); i++){
4234: for(j=1; j<=(nlstate+ndeath);j++){
4235: k=k+1;
4236: mu[k][(int) age]=pmmij[i][j];
4237: }
4238: }
4239: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
4240: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
4241: varpij[i][j][(int)age] = doldm[i][j];
4242:
4243: /*printf("\n%d ",(int)age);
4244: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4245: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4246: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4247: }*/
4248:
4249: fprintf(ficresprob,"\n%d ",(int)age);
4250: fprintf(ficresprobcov,"\n%d ",(int)age);
4251: fprintf(ficresprobcor,"\n%d ",(int)age);
4252:
4253: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
4254: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
4255: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4256: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
4257: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
4258: }
4259: i=0;
4260: for (k=1; k<=(nlstate);k++){
4261: for (l=1; l<=(nlstate+ndeath);l++){
1.145 brouard 4262: i++;
1.126 brouard 4263: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
4264: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
4265: for (j=1; j<=i;j++){
1.145 brouard 4266: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
1.126 brouard 4267: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
4268: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
4269: }
4270: }
4271: }/* end of loop for state */
4272: } /* end of loop for age */
1.145 brouard 4273: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
4274: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
4275: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4276: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4277:
1.126 brouard 4278: /* Confidence intervalle of pij */
4279: /*
1.131 brouard 4280: fprintf(ficgp,"\nunset parametric;unset label");
1.126 brouard 4281: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
4282: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
4283: 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);
4284: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
4285: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
4286: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
4287: */
4288:
4289: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
1.145 brouard 4290: first1=1;first2=2;
1.126 brouard 4291: for (k2=1; k2<=(nlstate);k2++){
4292: for (l2=1; l2<=(nlstate+ndeath);l2++){
4293: if(l2==k2) continue;
4294: j=(k2-1)*(nlstate+ndeath)+l2;
4295: for (k1=1; k1<=(nlstate);k1++){
4296: for (l1=1; l1<=(nlstate+ndeath);l1++){
4297: if(l1==k1) continue;
4298: i=(k1-1)*(nlstate+ndeath)+l1;
4299: if(i<=j) continue;
4300: for (age=bage; age<=fage; age ++){
4301: if ((int)age %5==0){
4302: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
4303: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
4304: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
4305: mu1=mu[i][(int) age]/stepm*YEARM ;
4306: mu2=mu[j][(int) age]/stepm*YEARM;
4307: c12=cv12/sqrt(v1*v2);
4308: /* Computing eigen value of matrix of covariance */
4309: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4310: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
1.135 brouard 4311: if ((lc2 <0) || (lc1 <0) ){
1.145 brouard 4312: if(first2==1){
4313: first1=0;
4314: 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);
4315: }
4316: 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);
4317: /* lc1=fabs(lc1); */ /* If we want to have them positive */
4318: /* lc2=fabs(lc2); */
1.135 brouard 4319: }
4320:
1.126 brouard 4321: /* Eigen vectors */
4322: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
4323: /*v21=sqrt(1.-v11*v11); *//* error */
4324: v21=(lc1-v1)/cv12*v11;
4325: v12=-v21;
4326: v22=v11;
4327: tnalp=v21/v11;
4328: if(first1==1){
4329: first1=0;
4330: 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);
4331: }
4332: 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);
4333: /*printf(fignu*/
4334: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
4335: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
4336: if(first==1){
4337: first=0;
4338: fprintf(ficgp,"\nset parametric;unset label");
4339: 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 4340: fprintf(ficgp,"\nset ter png small size 320, 240");
1.126 brouard 4341: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
4342: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
4343: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
4344: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
4345: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4346: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4347: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
4348: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4349: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4350: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4351: 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",\
4352: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4353: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4354: }else{
4355: first=0;
4356: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4357: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4358: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4359: 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",\
4360: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4361: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4362: }/* if first */
4363: } /* age mod 5 */
4364: } /* end loop age */
4365: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4366: first=1;
4367: } /*l12 */
4368: } /* k12 */
4369: } /*l1 */
4370: }/* k1 */
1.169 brouard 4371: /* } */ /* loop covariates */
1.126 brouard 4372: }
4373: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4374: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4375: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4376: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4377: free_vector(xp,1,npar);
4378: fclose(ficresprob);
4379: fclose(ficresprobcov);
4380: fclose(ficresprobcor);
4381: fflush(ficgp);
4382: fflush(fichtmcov);
4383: }
4384:
4385:
4386: /******************* Printing html file ***********/
4387: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
4388: int lastpass, int stepm, int weightopt, char model[],\
4389: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
4390: int popforecast, int estepm ,\
4391: double jprev1, double mprev1,double anprev1, \
4392: double jprev2, double mprev2,double anprev2){
4393: int jj1, k1, i1, cpt;
4394:
4395: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4396: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4397: </ul>");
4398: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
4399: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
4400: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
4401: fprintf(fichtm,"\
4402: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
4403: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
4404: fprintf(fichtm,"\
4405: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
4406: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
4407: fprintf(fichtm,"\
1.128 brouard 4408: - (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 4409: <a href=\"%s\">%s</a> <br>\n",
4410: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
4411: fprintf(fichtm,"\
4412: - Population projections by age and states: \
4413: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
4414:
4415: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4416:
1.145 brouard 4417: m=pow(2,cptcoveff);
1.126 brouard 4418: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4419:
4420: jj1=0;
4421: for(k1=1; k1<=m;k1++){
4422: for(i1=1; i1<=ncodemax[k1];i1++){
4423: jj1++;
4424: if (cptcovn > 0) {
4425: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4426: for (cpt=1; cpt<=cptcoveff;cpt++)
4427: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4428: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4429: }
4430: /* Pij */
1.145 brouard 4431: 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> \
4432: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.126 brouard 4433: /* Quasi-incidences */
4434: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.145 brouard 4435: 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> \
4436: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.126 brouard 4437: /* Period (stable) prevalence in each health state */
1.154 brouard 4438: for(cpt=1; cpt<=nlstate;cpt++){
1.166 brouard 4439: 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> \
4440: <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 4441: }
4442: for(cpt=1; cpt<=nlstate;cpt++) {
1.154 brouard 4443: 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> \
4444: <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 4445: }
4446: } /* end i1 */
4447: }/* End k1 */
4448: fprintf(fichtm,"</ul>");
4449:
4450:
4451: fprintf(fichtm,"\
4452: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
4453: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
4454:
4455: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4456: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
4457: fprintf(fichtm,"\
4458: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4459: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
4460:
4461: fprintf(fichtm,"\
4462: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4463: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
4464: fprintf(fichtm,"\
4465: - 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): \
4466: <a href=\"%s\">%s</a> <br>\n</li>",
4467: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
4468: fprintf(fichtm,"\
4469: - (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): \
4470: <a href=\"%s\">%s</a> <br>\n</li>",
4471: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
4472: fprintf(fichtm,"\
1.128 brouard 4473: - 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 4474: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
4475: fprintf(fichtm,"\
1.128 brouard 4476: - 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",
4477: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
1.126 brouard 4478: fprintf(fichtm,"\
4479: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
4480: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
4481:
4482: /* if(popforecast==1) fprintf(fichtm,"\n */
4483: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4484: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4485: /* <br>",fileres,fileres,fileres,fileres); */
4486: /* else */
4487: /* 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); */
4488: fflush(fichtm);
4489: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4490:
1.145 brouard 4491: m=pow(2,cptcoveff);
1.126 brouard 4492: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4493:
4494: jj1=0;
4495: for(k1=1; k1<=m;k1++){
4496: for(i1=1; i1<=ncodemax[k1];i1++){
4497: jj1++;
4498: if (cptcovn > 0) {
4499: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4500: for (cpt=1; cpt<=cptcoveff;cpt++)
4501: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4502: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4503: }
4504: for(cpt=1; cpt<=nlstate;cpt++) {
4505: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
1.145 brouard 4506: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
4507: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
1.126 brouard 4508: }
4509: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 4510: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4511: true period expectancies (those weighted with period prevalences are also\
4512: drawn in addition to the population based expectancies computed using\
4513: observed and cahotic prevalences: %s%d.png<br>\
1.126 brouard 4514: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
4515: } /* end i1 */
4516: }/* End k1 */
4517: fprintf(fichtm,"</ul>");
4518: fflush(fichtm);
4519: }
4520:
4521: /******************* Gnuplot file **************/
4522: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4523:
4524: char dirfileres[132],optfileres[132];
1.164 brouard 4525: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
1.130 brouard 4526: int ng=0;
1.126 brouard 4527: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4528: /* printf("Problem with file %s",optionfilegnuplot); */
4529: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4530: /* } */
4531:
4532: /*#ifdef windows */
4533: fprintf(ficgp,"cd \"%s\" \n",pathc);
4534: /*#endif */
4535: m=pow(2,cptcoveff);
4536:
4537: strcpy(dirfileres,optionfilefiname);
4538: strcpy(optfileres,"vpl");
4539: /* 1eme*/
1.153 brouard 4540: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
1.126 brouard 4541: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.145 brouard 4542: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
4543: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
4544: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
1.126 brouard 4545: fprintf(ficgp,"set xlabel \"Age\" \n\
4546: set ylabel \"Probability\" \n\
1.145 brouard 4547: set ter png small size 320, 240\n\
1.170 brouard 4548: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126 brouard 4549:
4550: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4551: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4552: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4553: }
1.170 brouard 4554: 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 4555: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4556: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4557: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4558: }
1.170 brouard 4559: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126 brouard 4560: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4561: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4562: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4563: }
1.145 brouard 4564: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
1.126 brouard 4565: }
4566: }
4567: /*2 eme*/
1.153 brouard 4568: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
1.126 brouard 4569: for (k1=1; k1<= m ; k1 ++) {
4570: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
1.145 brouard 4571: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
1.126 brouard 4572:
4573: for (i=1; i<= nlstate+1 ; i ++) {
4574: k=2*i;
1.170 brouard 4575: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126 brouard 4576: for (j=1; j<= nlstate+1 ; j ++) {
1.170 brouard 4577: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4578: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4579: }
4580: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
4581: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
1.170 brouard 4582: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126 brouard 4583: for (j=1; j<= nlstate+1 ; j ++) {
1.170 brouard 4584: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4585: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4586: }
1.145 brouard 4587: fprintf(ficgp,"\" t\"\" w l lt 0,");
1.170 brouard 4588: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126 brouard 4589: for (j=1; j<= nlstate+1 ; j ++) {
1.170 brouard 4590: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4591: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4592: }
1.145 brouard 4593: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4594: else fprintf(ficgp,"\" t\"\" w l lt 0,");
1.126 brouard 4595: }
4596: }
4597:
4598: /*3eme*/
4599:
4600: for (k1=1; k1<= m ; k1 ++) {
4601: for (cpt=1; cpt<= nlstate ; cpt ++) {
4602: /* k=2+nlstate*(2*cpt-2); */
4603: k=2+(nlstate+1)*(cpt-1);
4604: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
1.145 brouard 4605: fprintf(ficgp,"set ter png small size 320, 240\n\
1.126 brouard 4606: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
4607: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4608: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4609: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4610: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4611: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4612: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4613:
4614: */
4615: for (i=1; i< nlstate ; i ++) {
4616: 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);
4617: /* 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);*/
4618:
4619: }
4620: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
4621: }
4622: }
4623:
4624: /* CV preval stable (period) */
1.153 brouard 4625: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
4626: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.126 brouard 4627: k=3;
1.153 brouard 4628: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
1.145 brouard 4629: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
1.126 brouard 4630: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.145 brouard 4631: set ter png small size 320, 240\n\
1.126 brouard 4632: unset log y\n\
1.153 brouard 4633: plot [%.f:%.f] ", ageminpar, agemaxpar);
4634: for (i=1; i<= nlstate ; i ++){
4635: if(i==1)
4636: fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
4637: else
4638: fprintf(ficgp,", '' ");
1.154 brouard 4639: l=(nlstate+ndeath)*(i-1)+1;
4640: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
1.153 brouard 4641: for (j=1; j<= (nlstate-1) ; j ++)
4642: fprintf(ficgp,"+$%d",k+l+j);
4643: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
4644: } /* nlstate */
4645: fprintf(ficgp,"\n");
4646: } /* end cpt state*/
4647: } /* end covariate */
1.126 brouard 4648:
4649: /* proba elementaires */
1.187 brouard 4650: fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
1.126 brouard 4651: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 4652: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 4653: for(k=1; k <=(nlstate+ndeath); k++){
4654: if (k != i) {
1.187 brouard 4655: fprintf(ficgp,"# current state %d\n",k);
1.126 brouard 4656: for(j=1; j <=ncovmodel; j++){
1.187 brouard 4657: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
1.126 brouard 4658: jk++;
4659: }
1.187 brouard 4660: fprintf(ficgp,"\n");
1.126 brouard 4661: }
4662: }
4663: }
1.187 brouard 4664: fprintf(ficgp,"##############\n#\n");
4665:
1.145 brouard 4666: /*goto avoid;*/
1.187 brouard 4667: fprintf(ficgp,"\n##############\n#Graphics of of probabilities or incidences\n#############\n");
4668: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
4669: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
4670: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
4671: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
4672: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
4673: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
4674: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
4675: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
4676: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
4677: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
4678: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
4679: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
4680: fprintf(ficgp,"#\n");
1.126 brouard 4681: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
1.187 brouard 4682: fprintf(ficgp,"# ng=%d\n",ng);
4683: fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);
1.126 brouard 4684: for(jk=1; jk <=m; jk++) {
1.187 brouard 4685: fprintf(ficgp,"# jk=%d\n",jk);
1.145 brouard 4686: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
1.126 brouard 4687: if (ng==2)
4688: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
4689: else
4690: fprintf(ficgp,"\nset title \"Probability\"\n");
1.145 brouard 4691: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
1.126 brouard 4692: i=1;
4693: for(k2=1; k2<=nlstate; k2++) {
4694: k3=i;
4695: for(k=1; k<=(nlstate+ndeath); k++) {
4696: if (k != k2){
4697: if(ng==2)
1.187 brouard 4698: if(nagesqr==0)
4699: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
4700: else /* nagesqr =1 */
4701: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
1.126 brouard 4702: else
1.187 brouard 4703: if(nagesqr==0)
4704: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
4705: else /* nagesqr =1 */
4706: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
1.141 brouard 4707: ij=1;/* To be checked else nbcode[0][0] wrong */
1.187 brouard 4708: for(j=3; j <=ncovmodel-nagesqr; j++) {
1.186 brouard 4709: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /* Bug valgrind */
1.187 brouard 4710: fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
1.186 brouard 4711: ij++;
4712: }
4713: else
1.187 brouard 4714: fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
1.126 brouard 4715: }
4716: fprintf(ficgp,")/(1");
4717:
1.187 brouard 4718: for(k1=1; k1 <=nlstate; k1++){
4719: if(nagesqr==0)
4720: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
4721: else /* nagesqr =1 */
4722: fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr);
4723:
1.126 brouard 4724: ij=1;
1.187 brouard 4725: for(j=3; j <=ncovmodel-nagesqr; j++){
1.186 brouard 4726: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
1.187 brouard 4727: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
1.186 brouard 4728: ij++;
4729: }
4730: else
1.187 brouard 4731: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
1.126 brouard 4732: }
4733: fprintf(ficgp,")");
4734: }
4735: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
4736: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
4737: i=i+ncovmodel;
4738: }
4739: } /* end k */
4740: } /* end k2 */
4741: } /* end jk */
4742: } /* end ng */
1.164 brouard 4743: /* avoid: */
1.126 brouard 4744: fflush(ficgp);
4745: } /* end gnuplot */
4746:
4747:
4748: /*************** Moving average **************/
4749: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
4750:
4751: int i, cpt, cptcod;
4752: int modcovmax =1;
4753: int mobilavrange, mob;
4754: double age;
4755:
4756: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
4757: a covariate has 2 modalities */
4758: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
4759:
4760: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
4761: if(mobilav==1) mobilavrange=5; /* default */
4762: else mobilavrange=mobilav;
4763: for (age=bage; age<=fage; age++)
4764: for (i=1; i<=nlstate;i++)
4765: for (cptcod=1;cptcod<=modcovmax;cptcod++)
4766: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
4767: /* We keep the original values on the extreme ages bage, fage and for
4768: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
4769: we use a 5 terms etc. until the borders are no more concerned.
4770: */
4771: for (mob=3;mob <=mobilavrange;mob=mob+2){
4772: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
4773: for (i=1; i<=nlstate;i++){
4774: for (cptcod=1;cptcod<=modcovmax;cptcod++){
4775: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
4776: for (cpt=1;cpt<=(mob-1)/2;cpt++){
4777: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
4778: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
4779: }
4780: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
4781: }
4782: }
4783: }/* end age */
4784: }/* end mob */
4785: }else return -1;
4786: return 0;
4787: }/* End movingaverage */
4788:
4789:
4790: /************** Forecasting ******************/
1.169 brouard 4791: 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 4792: /* proj1, year, month, day of starting projection
4793: agemin, agemax range of age
4794: dateprev1 dateprev2 range of dates during which prevalence is computed
4795: anproj2 year of en of projection (same day and month as proj1).
4796: */
1.164 brouard 4797: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
1.126 brouard 4798: double agec; /* generic age */
4799: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
4800: double *popeffectif,*popcount;
4801: double ***p3mat;
4802: double ***mobaverage;
4803: char fileresf[FILENAMELENGTH];
4804:
4805: agelim=AGESUP;
4806: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4807:
4808: strcpy(fileresf,"f");
4809: strcat(fileresf,fileres);
4810: if((ficresf=fopen(fileresf,"w"))==NULL) {
4811: printf("Problem with forecast resultfile: %s\n", fileresf);
4812: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
4813: }
4814: printf("Computing forecasting: result on file '%s' \n", fileresf);
4815: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
4816:
4817: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4818:
4819: if (mobilav!=0) {
4820: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4821: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4822: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4823: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4824: }
4825: }
4826:
4827: stepsize=(int) (stepm+YEARM-1)/YEARM;
4828: if (stepm<=12) stepsize=1;
4829: if(estepm < stepm){
4830: printf ("Problem %d lower than %d\n",estepm, stepm);
4831: }
4832: else hstepm=estepm;
4833:
4834: hstepm=hstepm/stepm;
4835: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
4836: fractional in yp1 */
4837: anprojmean=yp;
4838: yp2=modf((yp1*12),&yp);
4839: mprojmean=yp;
4840: yp1=modf((yp2*30.5),&yp);
4841: jprojmean=yp;
4842: if(jprojmean==0) jprojmean=1;
4843: if(mprojmean==0) jprojmean=1;
4844:
4845: i1=cptcoveff;
4846: if (cptcovn < 1){i1=1;}
4847:
4848: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4849:
4850: fprintf(ficresf,"#****** Routine prevforecast **\n");
4851:
4852: /* if (h==(int)(YEARM*yearp)){ */
4853: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4854: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4855: k=k+1;
4856: fprintf(ficresf,"\n#******");
4857: for(j=1;j<=cptcoveff;j++) {
4858: 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]]);
4859: }
4860: fprintf(ficresf,"******\n");
4861: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4862: for(j=1; j<=nlstate+ndeath;j++){
4863: for(i=1; i<=nlstate;i++)
4864: fprintf(ficresf," p%d%d",i,j);
4865: fprintf(ficresf," p.%d",j);
4866: }
4867: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4868: fprintf(ficresf,"\n");
4869: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4870:
4871: for (agec=fage; agec>=(ageminpar-1); agec--){
4872: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4873: nhstepm = nhstepm/hstepm;
4874: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4875: oldm=oldms;savm=savms;
4876: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4877:
4878: for (h=0; h<=nhstepm; h++){
4879: if (h*hstepm/YEARM*stepm ==yearp) {
4880: fprintf(ficresf,"\n");
4881: for(j=1;j<=cptcoveff;j++)
4882: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4883: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4884: }
4885: for(j=1; j<=nlstate+ndeath;j++) {
4886: ppij=0.;
4887: for(i=1; i<=nlstate;i++) {
4888: if (mobilav==1)
4889: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4890: else {
4891: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4892: }
4893: if (h*hstepm/YEARM*stepm== yearp) {
4894: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4895: }
4896: } /* end i */
4897: if (h*hstepm/YEARM*stepm==yearp) {
4898: fprintf(ficresf," %.3f", ppij);
4899: }
4900: }/* end j */
4901: } /* end h */
4902: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4903: } /* end agec */
4904: } /* end yearp */
4905: } /* end cptcod */
4906: } /* end cptcov */
4907:
4908: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4909:
4910: fclose(ficresf);
4911: }
4912:
4913: /************** Forecasting *****not tested NB*************/
1.169 brouard 4914: 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 4915:
4916: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4917: int *popage;
4918: double calagedatem, agelim, kk1, kk2;
4919: double *popeffectif,*popcount;
4920: double ***p3mat,***tabpop,***tabpopprev;
4921: double ***mobaverage;
4922: char filerespop[FILENAMELENGTH];
4923:
4924: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4925: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4926: agelim=AGESUP;
4927: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4928:
4929: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4930:
4931:
4932: strcpy(filerespop,"pop");
4933: strcat(filerespop,fileres);
4934: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4935: printf("Problem with forecast resultfile: %s\n", filerespop);
4936: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4937: }
4938: printf("Computing forecasting: result on file '%s' \n", filerespop);
4939: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4940:
4941: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4942:
4943: if (mobilav!=0) {
4944: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4945: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4946: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4947: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4948: }
4949: }
4950:
4951: stepsize=(int) (stepm+YEARM-1)/YEARM;
4952: if (stepm<=12) stepsize=1;
4953:
4954: agelim=AGESUP;
4955:
4956: hstepm=1;
4957: hstepm=hstepm/stepm;
4958:
4959: if (popforecast==1) {
4960: if((ficpop=fopen(popfile,"r"))==NULL) {
4961: printf("Problem with population file : %s\n",popfile);exit(0);
4962: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4963: }
4964: popage=ivector(0,AGESUP);
4965: popeffectif=vector(0,AGESUP);
4966: popcount=vector(0,AGESUP);
4967:
4968: i=1;
4969: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4970:
4971: imx=i;
4972: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4973: }
4974:
4975: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4976: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4977: k=k+1;
4978: fprintf(ficrespop,"\n#******");
4979: for(j=1;j<=cptcoveff;j++) {
4980: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4981: }
4982: fprintf(ficrespop,"******\n");
4983: fprintf(ficrespop,"# Age");
4984: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4985: if (popforecast==1) fprintf(ficrespop," [Population]");
4986:
4987: for (cpt=0; cpt<=0;cpt++) {
4988: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4989:
4990: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4991: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4992: nhstepm = nhstepm/hstepm;
4993:
4994: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4995: oldm=oldms;savm=savms;
4996: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4997:
4998: for (h=0; h<=nhstepm; h++){
4999: if (h==(int) (calagedatem+YEARM*cpt)) {
5000: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5001: }
5002: for(j=1; j<=nlstate+ndeath;j++) {
5003: kk1=0.;kk2=0;
5004: for(i=1; i<=nlstate;i++) {
5005: if (mobilav==1)
5006: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
5007: else {
5008: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
5009: }
5010: }
5011: if (h==(int)(calagedatem+12*cpt)){
5012: tabpop[(int)(agedeb)][j][cptcod]=kk1;
5013: /*fprintf(ficrespop," %.3f", kk1);
5014: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
5015: }
5016: }
5017: for(i=1; i<=nlstate;i++){
5018: kk1=0.;
5019: for(j=1; j<=nlstate;j++){
5020: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
5021: }
5022: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
5023: }
5024:
5025: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
5026: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
5027: }
5028: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5029: }
5030: }
5031:
5032: /******/
5033:
5034: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
5035: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5036: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5037: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5038: nhstepm = nhstepm/hstepm;
5039:
5040: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5041: oldm=oldms;savm=savms;
5042: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5043: for (h=0; h<=nhstepm; h++){
5044: if (h==(int) (calagedatem+YEARM*cpt)) {
5045: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5046: }
5047: for(j=1; j<=nlstate+ndeath;j++) {
5048: kk1=0.;kk2=0;
5049: for(i=1; i<=nlstate;i++) {
5050: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
5051: }
5052: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
5053: }
5054: }
5055: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5056: }
5057: }
5058: }
5059: }
5060:
5061: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5062:
5063: if (popforecast==1) {
5064: free_ivector(popage,0,AGESUP);
5065: free_vector(popeffectif,0,AGESUP);
5066: free_vector(popcount,0,AGESUP);
5067: }
5068: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5069: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5070: fclose(ficrespop);
5071: } /* End of popforecast */
5072:
5073: int fileappend(FILE *fichier, char *optionfich)
5074: {
5075: if((fichier=fopen(optionfich,"a"))==NULL) {
5076: printf("Problem with file: %s\n", optionfich);
5077: fprintf(ficlog,"Problem with file: %s\n", optionfich);
5078: return (0);
5079: }
5080: fflush(fichier);
5081: return (1);
5082: }
5083:
5084:
5085: /**************** function prwizard **********************/
5086: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
5087: {
5088:
5089: /* Wizard to print covariance matrix template */
5090:
1.164 brouard 5091: char ca[32], cb[32];
5092: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 5093: int numlinepar;
5094:
5095: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5096: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5097: for(i=1; i <=nlstate; i++){
5098: jj=0;
5099: for(j=1; j <=nlstate+ndeath; j++){
5100: if(j==i) continue;
5101: jj++;
5102: /*ca[0]= k+'a'-1;ca[1]='\0';*/
5103: printf("%1d%1d",i,j);
5104: fprintf(ficparo,"%1d%1d",i,j);
5105: for(k=1; k<=ncovmodel;k++){
5106: /* printf(" %lf",param[i][j][k]); */
5107: /* fprintf(ficparo," %lf",param[i][j][k]); */
5108: printf(" 0.");
5109: fprintf(ficparo," 0.");
5110: }
5111: printf("\n");
5112: fprintf(ficparo,"\n");
5113: }
5114: }
5115: printf("# Scales (for hessian or gradient estimation)\n");
5116: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
5117: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
5118: for(i=1; i <=nlstate; i++){
5119: jj=0;
5120: for(j=1; j <=nlstate+ndeath; j++){
5121: if(j==i) continue;
5122: jj++;
5123: fprintf(ficparo,"%1d%1d",i,j);
5124: printf("%1d%1d",i,j);
5125: fflush(stdout);
5126: for(k=1; k<=ncovmodel;k++){
5127: /* printf(" %le",delti3[i][j][k]); */
5128: /* fprintf(ficparo," %le",delti3[i][j][k]); */
5129: printf(" 0.");
5130: fprintf(ficparo," 0.");
5131: }
5132: numlinepar++;
5133: printf("\n");
5134: fprintf(ficparo,"\n");
5135: }
5136: }
5137: printf("# Covariance matrix\n");
5138: /* # 121 Var(a12)\n\ */
5139: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5140: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5141: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5142: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5143: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5144: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5145: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5146: fflush(stdout);
5147: fprintf(ficparo,"# Covariance matrix\n");
5148: /* # 121 Var(a12)\n\ */
5149: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5150: /* # ...\n\ */
5151: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5152:
5153: for(itimes=1;itimes<=2;itimes++){
5154: jj=0;
5155: for(i=1; i <=nlstate; i++){
5156: for(j=1; j <=nlstate+ndeath; j++){
5157: if(j==i) continue;
5158: for(k=1; k<=ncovmodel;k++){
5159: jj++;
5160: ca[0]= k+'a'-1;ca[1]='\0';
5161: if(itimes==1){
5162: printf("#%1d%1d%d",i,j,k);
5163: fprintf(ficparo,"#%1d%1d%d",i,j,k);
5164: }else{
5165: printf("%1d%1d%d",i,j,k);
5166: fprintf(ficparo,"%1d%1d%d",i,j,k);
5167: /* printf(" %.5le",matcov[i][j]); */
5168: }
5169: ll=0;
5170: for(li=1;li <=nlstate; li++){
5171: for(lj=1;lj <=nlstate+ndeath; lj++){
5172: if(lj==li) continue;
5173: for(lk=1;lk<=ncovmodel;lk++){
5174: ll++;
5175: if(ll<=jj){
5176: cb[0]= lk +'a'-1;cb[1]='\0';
5177: if(ll<jj){
5178: if(itimes==1){
5179: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5180: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5181: }else{
5182: printf(" 0.");
5183: fprintf(ficparo," 0.");
5184: }
5185: }else{
5186: if(itimes==1){
5187: printf(" Var(%s%1d%1d)",ca,i,j);
5188: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
5189: }else{
5190: printf(" 0.");
5191: fprintf(ficparo," 0.");
5192: }
5193: }
5194: }
5195: } /* end lk */
5196: } /* end lj */
5197: } /* end li */
5198: printf("\n");
5199: fprintf(ficparo,"\n");
5200: numlinepar++;
5201: } /* end k*/
5202: } /*end j */
5203: } /* end i */
5204: } /* end itimes */
5205:
5206: } /* end of prwizard */
5207: /******************* Gompertz Likelihood ******************************/
5208: double gompertz(double x[])
5209: {
5210: double A,B,L=0.0,sump=0.,num=0.;
5211: int i,n=0; /* n is the size of the sample */
5212:
5213: for (i=0;i<=imx-1 ; i++) {
5214: sump=sump+weight[i];
5215: /* sump=sump+1;*/
5216: num=num+1;
5217: }
5218:
5219:
5220: /* for (i=0; i<=imx; i++)
5221: 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]);*/
5222:
5223: for (i=1;i<=imx ; i++)
5224: {
5225: if (cens[i] == 1 && wav[i]>1)
5226: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
5227:
5228: if (cens[i] == 0 && wav[i]>1)
5229: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
5230: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
5231:
5232: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5233: if (wav[i] > 1 ) { /* ??? */
5234: L=L+A*weight[i];
5235: /* 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]);*/
5236: }
5237: }
5238:
5239: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5240:
5241: return -2*L*num/sump;
5242: }
5243:
1.136 brouard 5244: #ifdef GSL
5245: /******************* Gompertz_f Likelihood ******************************/
5246: double gompertz_f(const gsl_vector *v, void *params)
5247: {
5248: double A,B,LL=0.0,sump=0.,num=0.;
5249: double *x= (double *) v->data;
5250: int i,n=0; /* n is the size of the sample */
5251:
5252: for (i=0;i<=imx-1 ; i++) {
5253: sump=sump+weight[i];
5254: /* sump=sump+1;*/
5255: num=num+1;
5256: }
5257:
5258:
5259: /* for (i=0; i<=imx; i++)
5260: 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]);*/
5261: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
5262: for (i=1;i<=imx ; i++)
5263: {
5264: if (cens[i] == 1 && wav[i]>1)
5265: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
5266:
5267: if (cens[i] == 0 && wav[i]>1)
5268: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
5269: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
5270:
5271: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5272: if (wav[i] > 1 ) { /* ??? */
5273: LL=LL+A*weight[i];
5274: /* 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]);*/
5275: }
5276: }
5277:
5278: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5279: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
5280:
5281: return -2*LL*num/sump;
5282: }
5283: #endif
5284:
1.126 brouard 5285: /******************* Printing html file ***********/
5286: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
5287: int lastpass, int stepm, int weightopt, char model[],\
5288: int imx, double p[],double **matcov,double agemortsup){
5289: int i,k;
5290:
5291: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
5292: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
5293: for (i=1;i<=2;i++)
5294: 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]));
5295: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
5296: fprintf(fichtm,"</ul>");
5297:
5298: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
5299:
5300: 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>");
5301:
5302: for (k=agegomp;k<(agemortsup-2);k++)
5303: 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]);
5304:
5305:
5306: fflush(fichtm);
5307: }
5308:
5309: /******************* Gnuplot file **************/
5310: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
5311:
5312: char dirfileres[132],optfileres[132];
1.164 brouard 5313:
1.126 brouard 5314: int ng;
5315:
5316:
5317: /*#ifdef windows */
5318: fprintf(ficgp,"cd \"%s\" \n",pathc);
5319: /*#endif */
5320:
5321:
5322: strcpy(dirfileres,optionfilefiname);
5323: strcpy(optfileres,"vpl");
5324: fprintf(ficgp,"set out \"graphmort.png\"\n ");
5325: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.145 brouard 5326: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
5327: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 5328: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
5329:
5330: }
5331:
1.136 brouard 5332: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
5333: {
1.126 brouard 5334:
1.136 brouard 5335: /*-------- data file ----------*/
5336: FILE *fic;
5337: char dummy[]=" ";
1.164 brouard 5338: int i=0, j=0, n=0;
1.136 brouard 5339: int linei, month, year,iout;
5340: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 5341: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 5342: char *stratrunc;
5343: int lstra;
1.126 brouard 5344:
5345:
1.136 brouard 5346: if((fic=fopen(datafile,"r"))==NULL) {
5347: printf("Problem while opening datafile: %s\n", datafile);return 1;
5348: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
5349: }
1.126 brouard 5350:
1.136 brouard 5351: i=1;
5352: linei=0;
5353: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
5354: linei=linei+1;
5355: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
5356: if(line[j] == '\t')
5357: line[j] = ' ';
5358: }
5359: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
5360: ;
5361: };
5362: line[j+1]=0; /* Trims blanks at end of line */
5363: if(line[0]=='#'){
5364: fprintf(ficlog,"Comment line\n%s\n",line);
5365: printf("Comment line\n%s\n",line);
5366: continue;
5367: }
5368: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 5369: strcpy(line, linetmp);
1.136 brouard 5370:
1.126 brouard 5371:
1.136 brouard 5372: for (j=maxwav;j>=1;j--){
1.137 brouard 5373: cutv(stra, strb, line, ' ');
1.136 brouard 5374: if(strb[0]=='.') { /* Missing status */
5375: lval=-1;
5376: }else{
5377: errno=0;
5378: lval=strtol(strb,&endptr,10);
5379: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
5380: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5381: 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);
5382: 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 5383: return 1;
5384: }
5385: }
5386: s[j][i]=lval;
5387:
5388: strcpy(line,stra);
5389: cutv(stra, strb,line,' ');
1.169 brouard 5390: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5391: }
1.169 brouard 5392: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5393: month=99;
5394: year=9999;
5395: }else{
1.141 brouard 5396: 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);
5397: 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 5398: return 1;
5399: }
5400: anint[j][i]= (double) year;
5401: mint[j][i]= (double)month;
5402: strcpy(line,stra);
5403: } /* ENd Waves */
5404:
5405: cutv(stra, strb,line,' ');
1.169 brouard 5406: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5407: }
1.169 brouard 5408: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5409: month=99;
5410: year=9999;
5411: }else{
1.141 brouard 5412: 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);
5413: 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 5414: return 1;
5415: }
5416: andc[i]=(double) year;
5417: moisdc[i]=(double) month;
5418: strcpy(line,stra);
5419:
5420: cutv(stra, strb,line,' ');
1.169 brouard 5421: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5422: }
1.169 brouard 5423: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 5424: month=99;
5425: year=9999;
5426: }else{
1.141 brouard 5427: 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);
5428: 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 5429: return 1;
5430: }
5431: if (year==9999) {
1.141 brouard 5432: 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);
5433: 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 5434: return 1;
1.126 brouard 5435:
1.136 brouard 5436: }
5437: annais[i]=(double)(year);
5438: moisnais[i]=(double)(month);
5439: strcpy(line,stra);
5440:
5441: cutv(stra, strb,line,' ');
5442: errno=0;
5443: dval=strtod(strb,&endptr);
5444: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5445: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
5446: 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 5447: fflush(ficlog);
5448: return 1;
5449: }
5450: weight[i]=dval;
5451: strcpy(line,stra);
5452:
5453: for (j=ncovcol;j>=1;j--){
5454: cutv(stra, strb,line,' ');
5455: if(strb[0]=='.') { /* Missing status */
5456: lval=-1;
5457: }else{
5458: errno=0;
5459: lval=strtol(strb,&endptr,10);
5460: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5461: 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);
5462: 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 5463: return 1;
5464: }
5465: }
5466: if(lval <-1 || lval >1){
1.141 brouard 5467: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5468: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5469: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5470: For example, for multinomial values like 1, 2 and 3,\n \
5471: build V1=0 V2=0 for the reference value (1),\n \
5472: V1=1 V2=0 for (2) \n \
5473: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5474: output of IMaCh is often meaningless.\n \
5475: Exiting.\n",lval,linei, i,line,j);
1.141 brouard 5476: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5477: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5478: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5479: For example, for multinomial values like 1, 2 and 3,\n \
5480: build V1=0 V2=0 for the reference value (1),\n \
5481: V1=1 V2=0 for (2) \n \
5482: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5483: output of IMaCh is often meaningless.\n \
5484: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
5485: return 1;
5486: }
5487: covar[j][i]=(double)(lval);
5488: strcpy(line,stra);
5489: }
5490: lstra=strlen(stra);
5491:
5492: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
5493: stratrunc = &(stra[lstra-9]);
5494: num[i]=atol(stratrunc);
5495: }
5496: else
5497: num[i]=atol(stra);
5498: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
5499: 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;}*/
5500:
5501: i=i+1;
5502: } /* End loop reading data */
1.126 brouard 5503:
1.136 brouard 5504: *imax=i-1; /* Number of individuals */
5505: fclose(fic);
5506:
5507: return (0);
1.164 brouard 5508: /* endread: */
1.136 brouard 5509: printf("Exiting readdata: ");
5510: fclose(fic);
5511: return (1);
1.126 brouard 5512:
5513:
5514:
1.136 brouard 5515: }
1.145 brouard 5516: void removespace(char *str) {
5517: char *p1 = str, *p2 = str;
5518: do
5519: while (*p2 == ' ')
5520: p2++;
1.169 brouard 5521: while (*p1++ == *p2++);
1.145 brouard 5522: }
5523:
5524: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
1.187 brouard 5525: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
5526: * - nagesqr = 1 if age*age in the model, otherwise 0.
5527: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
5528: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
1.145 brouard 5529: * - cptcovage number of covariates with age*products =2
5530: * - cptcovs number of simple covariates
5531: * - 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
5532: * which is a new column after the 9 (ncovcol) variables.
5533: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
5534: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
5535: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
5536: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
5537: */
1.136 brouard 5538: {
1.145 brouard 5539: int i, j, k, ks;
1.164 brouard 5540: int j1, k1, k2;
1.136 brouard 5541: char modelsav[80];
1.145 brouard 5542: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 5543: char *strpt;
1.136 brouard 5544:
1.145 brouard 5545: /*removespace(model);*/
1.136 brouard 5546: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 5547: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 5548: if (strstr(model,"AGE") !=0){
1.187 brouard 5549: printf("Error. AGE must be in lower case 'age' model=1+age+%s ",model);
5550: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s ",model);fflush(ficlog);
1.136 brouard 5551: return 1;
5552: }
1.141 brouard 5553: if (strstr(model,"v") !=0){
5554: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
5555: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
5556: return 1;
5557: }
1.187 brouard 5558: strcpy(modelsav,model);
5559: if ((strpt=strstr(model,"age*age")) !=0){
5560: printf(" strpt=%s, model=%s\n",strpt, model);
5561: if(strpt != model){
5562: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
5563: 'model=1+age+age*age+V1' or 'model=1+age+age*age+V1+V1*age', please swap as well as \n \
5564: corresponding column of parameters.\n",model);
5565: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
5566: 'model=1+age+age*age+V1' or 'model=1+age+age*age+V1+V1*age', please swap as well as \n \
5567: corresponding column of parameters.\n",model); fflush(ficlog);
5568: return 1;
5569: }
5570:
5571: nagesqr=1;
5572: if (strstr(model,"+age*age") !=0)
5573: substrchaine(modelsav, model, "+age*age");
5574: else if (strstr(model,"age*age+") !=0)
5575: substrchaine(modelsav, model, "age*age+");
5576: else
5577: substrchaine(modelsav, model, "age*age");
5578: }else
5579: nagesqr=0;
5580: if (strlen(modelsav) >1){
5581: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
5582: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
5583: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2 */
5584: cptcovt= j+1; /* Number of total covariates in the model, not including
5585: * cst, age and age*age
5586: * V1+V1*age+ V3 + V3*V4+age*age=> 4*/
5587: /* including age products which are counted in cptcovage.
5588: * but the covariates which are products must be treated
5589: * separately: ncovn=4- 2=2 (V1+V3). */
5590: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
5591: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
5592:
5593:
5594: /* Design
5595: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
5596: * < ncovcol=8 >
5597: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
5598: * k= 1 2 3 4 5 6 7 8
5599: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
5600: * covar[k,i], value of kth covariate if not including age for individual i:
5601: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
5602: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
5603: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
5604: * Tage[++cptcovage]=k
5605: * if products, new covar are created after ncovcol with k1
5606: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
5607: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
5608: * 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
5609: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
5610: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
5611: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
5612: * < ncovcol=8 >
5613: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
5614: * k= 1 2 3 4 5 6 7 8 9 10 11 12
5615: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
5616: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5617: * p Tprod[1]@2={ 6, 5}
5618: *p Tvard[1][1]@4= {7, 8, 5, 6}
5619: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
5620: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
5621: *How to reorganize?
5622: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
5623: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5624: * {2, 1, 4, 8, 5, 6, 3, 7}
5625: * Struct []
5626: */
1.145 brouard 5627:
1.187 brouard 5628: /* This loop fills the array Tvar from the string 'model'.*/
5629: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
5630: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
5631: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
5632: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
5633: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
5634: /* k=1 Tvar[1]=2 (from V2) */
5635: /* k=5 Tvar[5] */
5636: /* for (k=1; k<=cptcovn;k++) { */
5637: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
5638: /* } */
5639: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2]; */
5640: /*
5641: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
5642: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
1.145 brouard 5643: Tvar[k]=0;
1.187 brouard 5644: cptcovage=0;
5645: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
5646: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5647: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
5648: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
5649: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5650: /*scanf("%d",i);*/
5651: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
5652: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
5653: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
5654: /* covar is not filled and then is empty */
5655: cptcovprod--;
5656: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
5657: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
5658: cptcovage++; /* Sums the number of covariates which include age as a product */
5659: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
5660: /*printf("stre=%s ", stre);*/
5661: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
5662: cptcovprod--;
5663: cutl(stre,strb,strc,'V');
5664: Tvar[k]=atoi(stre);
5665: cptcovage++;
5666: Tage[cptcovage]=k;
5667: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
5668: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
5669: cptcovn++;
5670: cptcovprodnoage++;k1++;
5671: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5672: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
5673: because this model-covariate is a construction we invent a new column
5674: ncovcol + k1
5675: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
5676: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
5677: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
5678: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
5679: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
5680: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
5681: k2=k2+2;
5682: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
5683: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
5684: for (i=1; i<=lastobs;i++){
5685: /* Computes the new covariate which is a product of
5686: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
5687: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
5688: }
5689: } /* End age is not in the model */
5690: } /* End if model includes a product */
5691: else { /* no more sum */
5692: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5693: /* scanf("%d",i);*/
5694: cutl(strd,strc,strb,'V');
5695: ks++; /**< Number of simple covariates */
1.145 brouard 5696: cptcovn++;
1.187 brouard 5697: Tvar[k]=atoi(strd);
5698: }
5699: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
5700: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5701: scanf("%d",i);*/
5702: } /* end of loop + on total covariates */
5703: } /* end if strlen(modelsave == 0) age*age might exist */
5704: } /* end if strlen(model == 0) */
1.136 brouard 5705:
5706: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5707: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5708:
5709: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5710: printf("cptcovprod=%d ", cptcovprod);
5711: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5712:
5713: scanf("%d ",i);*/
5714:
5715:
1.137 brouard 5716: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 5717: /*endread:*/
1.136 brouard 5718: printf("Exiting decodemodel: ");
5719: return (1);
5720: }
5721:
1.169 brouard 5722: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.136 brouard 5723: {
5724: int i, m;
5725:
5726: for (i=1; i<=imx; i++) {
5727: for(m=2; (m<= maxwav); m++) {
5728: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5729: anint[m][i]=9999;
5730: s[m][i]=-1;
5731: }
5732: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169 brouard 5733: *nberr = *nberr + 1;
5734: 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);
5735: 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 5736: s[m][i]=-1;
5737: }
5738: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 5739: (*nberr)++;
1.136 brouard 5740: 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]);
5741: 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]);
5742: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5743: }
5744: }
5745: }
5746:
5747: for (i=1; i<=imx; i++) {
5748: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5749: for(m=firstpass; (m<= lastpass); m++){
5750: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5751: if (s[m][i] >= nlstate+1) {
1.169 brouard 5752: if(agedc[i]>0){
5753: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 5754: agev[m][i]=agedc[i];
5755: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 5756: }else {
1.136 brouard 5757: if ((int)andc[i]!=9999){
5758: nbwarn++;
5759: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5760: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5761: agev[m][i]=-1;
5762: }
5763: }
1.169 brouard 5764: } /* agedc > 0 */
1.136 brouard 5765: }
5766: else if(s[m][i] !=9){ /* Standard case, age in fractional
5767: years but with the precision of a month */
5768: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5769: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5770: agev[m][i]=1;
5771: else if(agev[m][i] < *agemin){
5772: *agemin=agev[m][i];
5773: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
5774: }
5775: else if(agev[m][i] >*agemax){
5776: *agemax=agev[m][i];
1.156 brouard 5777: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 5778: }
5779: /*agev[m][i]=anint[m][i]-annais[i];*/
5780: /* agev[m][i] = age[i]+2*m;*/
5781: }
5782: else { /* =9 */
5783: agev[m][i]=1;
5784: s[m][i]=-1;
5785: }
5786: }
5787: else /*= 0 Unknown */
5788: agev[m][i]=1;
5789: }
5790:
5791: }
5792: for (i=1; i<=imx; i++) {
5793: for(m=firstpass; (m<=lastpass); m++){
5794: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 5795: (*nberr)++;
1.136 brouard 5796: 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);
5797: 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);
5798: return 1;
5799: }
5800: }
5801: }
5802:
5803: /*for (i=1; i<=imx; i++){
5804: for (m=firstpass; (m<lastpass); m++){
5805: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5806: }
5807:
5808: }*/
5809:
5810:
1.139 brouard 5811: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5812: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 5813:
5814: return (0);
1.164 brouard 5815: /* endread:*/
1.136 brouard 5816: printf("Exiting calandcheckages: ");
5817: return (1);
5818: }
5819:
1.172 brouard 5820: #if defined(_MSC_VER)
5821: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5822: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5823: //#include "stdafx.h"
5824: //#include <stdio.h>
5825: //#include <tchar.h>
5826: //#include <windows.h>
5827: //#include <iostream>
5828: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
5829:
5830: LPFN_ISWOW64PROCESS fnIsWow64Process;
5831:
5832: BOOL IsWow64()
5833: {
5834: BOOL bIsWow64 = FALSE;
5835:
5836: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
5837: // (HANDLE, PBOOL);
5838:
5839: //LPFN_ISWOW64PROCESS fnIsWow64Process;
5840:
5841: HMODULE module = GetModuleHandle(_T("kernel32"));
5842: const char funcName[] = "IsWow64Process";
5843: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
5844: GetProcAddress(module, funcName);
5845:
5846: if (NULL != fnIsWow64Process)
5847: {
5848: if (!fnIsWow64Process(GetCurrentProcess(),
5849: &bIsWow64))
5850: //throw std::exception("Unknown error");
5851: printf("Unknown error\n");
5852: }
5853: return bIsWow64 != FALSE;
5854: }
5855: #endif
1.177 brouard 5856:
1.169 brouard 5857: void syscompilerinfo()
1.167 brouard 5858: {
5859: /* #include "syscompilerinfo.h"*/
1.185 brouard 5860: /* command line Intel compiler 32bit windows, XP compatible:*/
5861: /* /GS /W3 /Gy
5862: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
5863: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
5864: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 5865: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
5866: */
5867: /* 64 bits */
1.185 brouard 5868: /*
5869: /GS /W3 /Gy
5870: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
5871: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
5872: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
5873: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
5874: /* Optimization are useless and O3 is slower than O2 */
5875: /*
5876: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
5877: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
5878: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
5879: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
5880: */
1.186 brouard 5881: /* Link is */ /* /OUT:"visual studio
1.185 brouard 5882: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
5883: /PDB:"visual studio
5884: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
5885: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
5886: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
5887: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
5888: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
5889: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
5890: uiAccess='false'"
5891: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
5892: /NOLOGO /TLBID:1
5893: */
1.177 brouard 5894: #if defined __INTEL_COMPILER
1.178 brouard 5895: #if defined(__GNUC__)
5896: struct utsname sysInfo; /* For Intel on Linux and OS/X */
5897: #endif
1.177 brouard 5898: #elif defined(__GNUC__)
1.179 brouard 5899: #ifndef __APPLE__
1.174 brouard 5900: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 5901: #endif
1.177 brouard 5902: struct utsname sysInfo;
1.178 brouard 5903: int cross = CROSS;
5904: if (cross){
5905: printf("Cross-");
5906: fprintf(ficlog, "Cross-");
5907: }
1.174 brouard 5908: #endif
5909:
1.171 brouard 5910: #include <stdint.h>
1.178 brouard 5911:
1.169 brouard 5912: printf("Compiled with:");fprintf(ficlog,"Compiled with:");
5913: #if defined(__clang__)
5914: printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
5915: #endif
5916: #if defined(__ICC) || defined(__INTEL_COMPILER)
5917: printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
5918: #endif
5919: #if defined(__GNUC__) || defined(__GNUG__)
5920: printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
5921: #endif
5922: #if defined(__HP_cc) || defined(__HP_aCC)
5923: printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
5924: #endif
5925: #if defined(__IBMC__) || defined(__IBMCPP__)
5926: printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
5927: #endif
5928: #if defined(_MSC_VER)
5929: printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
5930: #endif
5931: #if defined(__PGI)
5932: printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
5933: #endif
5934: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
5935: printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 5936: #endif
1.174 brouard 5937: printf(" for ");fprintf(ficlog," for ");
1.169 brouard 5938:
1.167 brouard 5939: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
5940: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
5941: // Windows (x64 and x86)
1.174 brouard 5942: printf("Windows (x64 and x86) ");fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 5943: #elif __unix__ // all unices, not all compilers
5944: // Unix
1.174 brouard 5945: printf("Unix ");fprintf(ficlog,"Unix ");
1.167 brouard 5946: #elif __linux__
5947: // linux
1.174 brouard 5948: printf("linux ");fprintf(ficlog,"linux ");
1.167 brouard 5949: #elif __APPLE__
1.174 brouard 5950: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
5951: printf("Mac OS ");fprintf(ficlog,"Mac OS ");
1.167 brouard 5952: #endif
5953:
5954: /* __MINGW32__ */
5955: /* __CYGWIN__ */
5956: /* __MINGW64__ */
5957: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
5958: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
5959: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
5960: /* _WIN64 // Defined for applications for Win64. */
5961: /* _M_X64 // Defined for compilations that target x64 processors. */
5962: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 5963:
1.167 brouard 5964: #if UINTPTR_MAX == 0xffffffff
1.174 brouard 5965: printf(" 32-bit"); fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 5966: #elif UINTPTR_MAX == 0xffffffffffffffff
1.174 brouard 5967: printf(" 64-bit"); fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 5968: #else
1.174 brouard 5969: printf(" wtf-bit"); fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 5970: #endif
5971:
1.169 brouard 5972: #if defined(__GNUC__)
5973: # if defined(__GNUC_PATCHLEVEL__)
5974: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
5975: + __GNUC_MINOR__ * 100 \
5976: + __GNUC_PATCHLEVEL__)
5977: # else
5978: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
5979: + __GNUC_MINOR__ * 100)
5980: # endif
1.174 brouard 5981: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
5982: fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 5983:
5984: if (uname(&sysInfo) != -1) {
5985: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
5986: fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
5987: }
5988: else
5989: perror("uname() error");
1.179 brouard 5990: //#ifndef __INTEL_COMPILER
5991: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 5992: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.179 brouard 5993: fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 5994: #endif
1.169 brouard 5995: #endif
1.172 brouard 5996:
5997: // void main()
5998: // {
1.169 brouard 5999: #if defined(_MSC_VER)
1.174 brouard 6000: if (IsWow64()){
1.176 brouard 6001: printf("The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
6002: fprintf(ficlog, "The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 6003: }
6004: else{
1.176 brouard 6005: printf("The process is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.178 brouard 6006: fprintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 6007: }
1.172 brouard 6008: // printf("\nPress Enter to continue...");
6009: // getchar();
6010: // }
6011:
1.169 brouard 6012: #endif
6013:
1.167 brouard 6014:
6015: }
1.136 brouard 6016:
1.180 brouard 6017: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){
6018: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6019: int i, j, k, i1 ;
6020: double ftolpl = 1.e-10;
6021: double age, agebase, agelim;
6022:
6023: strcpy(filerespl,"pl");
6024: strcat(filerespl,fileres);
6025: if((ficrespl=fopen(filerespl,"w"))==NULL) {
6026: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6027: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6028: }
6029: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6030: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6031: pstamp(ficrespl);
6032: fprintf(ficrespl,"# Period (stable) prevalence \n");
6033: fprintf(ficrespl,"#Age ");
6034: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
6035: fprintf(ficrespl,"\n");
6036:
6037: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
6038:
6039: agebase=ageminpar;
6040: agelim=agemaxpar;
6041:
6042: i1=pow(2,cptcoveff);
6043: if (cptcovn < 1){i1=1;}
6044:
6045: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6046: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
6047: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6048: k=k+1;
6049: /* to clean */
6050: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);
6051: fprintf(ficrespl,"\n#******");
6052: printf("\n#******");
6053: fprintf(ficlog,"\n#******");
6054: for(j=1;j<=cptcoveff;j++) {
6055: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6056: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6057: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6058: }
6059: fprintf(ficrespl,"******\n");
6060: printf("******\n");
6061: fprintf(ficlog,"******\n");
6062:
6063: fprintf(ficrespl,"#Age ");
6064: for(j=1;j<=cptcoveff;j++) {
6065: fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6066: }
6067: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
6068: fprintf(ficrespl,"\n");
6069:
6070: for (age=agebase; age<=agelim; age++){
6071: /* for (age=agebase; age<=agebase; age++){ */
6072: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6073: fprintf(ficrespl,"%.0f ",age );
6074: for(j=1;j<=cptcoveff;j++)
6075: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6076: for(i=1; i<=nlstate;i++)
6077: fprintf(ficrespl," %.5f", prlim[i][i]);
6078: fprintf(ficrespl,"\n");
6079: } /* Age */
6080: /* was end of cptcod */
6081: } /* cptcov */
1.184 brouard 6082: return 0;
1.180 brouard 6083: }
6084:
6085: int hPijx(double *p, int bage, int fage){
6086: /*------------- h Pij x at various ages ------------*/
6087:
6088: int stepsize;
6089: int agelim;
6090: int hstepm;
6091: int nhstepm;
6092: int h, i, i1, j, k;
6093:
6094: double agedeb;
6095: double ***p3mat;
6096:
6097: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
6098: if((ficrespij=fopen(filerespij,"w"))==NULL) {
6099: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
6100: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
6101: }
6102: printf("Computing pij: result on file '%s' \n", filerespij);
6103: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
6104:
6105: stepsize=(int) (stepm+YEARM-1)/YEARM;
6106: /*if (stepm<=24) stepsize=2;*/
6107:
6108: agelim=AGESUP;
6109: hstepm=stepsize*YEARM; /* Every year of age */
6110: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
6111:
6112: /* hstepm=1; aff par mois*/
6113: pstamp(ficrespij);
6114: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
6115: i1= pow(2,cptcoveff);
1.183 brouard 6116: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
6117: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
6118: /* k=k+1; */
6119: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6120: fprintf(ficrespij,"\n#****** ");
6121: for(j=1;j<=cptcoveff;j++)
6122: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6123: fprintf(ficrespij,"******\n");
6124:
6125: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
6126: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6127: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6128:
6129: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 6130:
1.183 brouard 6131: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6132: oldm=oldms;savm=savms;
6133: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
6134: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
6135: for(i=1; i<=nlstate;i++)
6136: for(j=1; j<=nlstate+ndeath;j++)
6137: fprintf(ficrespij," %1d-%1d",i,j);
6138: fprintf(ficrespij,"\n");
6139: for (h=0; h<=nhstepm; h++){
6140: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
6141: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 6142: for(i=1; i<=nlstate;i++)
6143: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 6144: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 6145: fprintf(ficrespij,"\n");
6146: }
1.183 brouard 6147: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6148: fprintf(ficrespij,"\n");
6149: }
1.180 brouard 6150: /*}*/
6151: }
1.184 brouard 6152: return 0;
1.180 brouard 6153: }
6154:
6155:
1.136 brouard 6156: /***********************************************/
6157: /**************** Main Program *****************/
6158: /***********************************************/
6159:
6160: int main(int argc, char *argv[])
6161: {
6162: #ifdef GSL
6163: const gsl_multimin_fminimizer_type *T;
6164: size_t iteri = 0, it;
6165: int rval = GSL_CONTINUE;
6166: int status = GSL_SUCCESS;
6167: double ssval;
6168: #endif
6169: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 6170: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
6171:
6172: int jj, ll, li, lj, lk;
1.136 brouard 6173: int numlinepar=0; /* Current linenumber of parameter file */
6174: int itimes;
6175: int NDIM=2;
6176: int vpopbased=0;
6177:
1.164 brouard 6178: char ca[32], cb[32];
1.136 brouard 6179: /* FILE *fichtm; *//* Html File */
6180: /* FILE *ficgp;*/ /*Gnuplot File */
6181: struct stat info;
1.164 brouard 6182: double agedeb;
1.136 brouard 6183: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
6184:
1.165 brouard 6185: double fret;
1.136 brouard 6186: double dum; /* Dummy variable */
6187: double ***p3mat;
6188: double ***mobaverage;
1.164 brouard 6189:
6190: char line[MAXLINE];
1.136 brouard 6191: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
6192: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 6193: char *tok, *val; /* pathtot */
1.136 brouard 6194: int firstobs=1, lastobs=10;
1.164 brouard 6195: int c, h , cpt;
6196: int jl;
6197: int i1, j1, jk, stepsize;
6198: int *tab;
1.136 brouard 6199: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
6200: int mobilav=0,popforecast=0;
6201: int hstepm, nhstepm;
6202: int agemortsup;
6203: float sumlpop=0.;
6204: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
6205: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
6206:
1.164 brouard 6207: double bage=0, fage=110, age, agelim, agebase;
1.136 brouard 6208: double ftolpl=FTOL;
6209: double **prlim;
6210: double ***param; /* Matrix of parameters */
6211: double *p;
6212: double **matcov; /* Matrix of covariance */
6213: double ***delti3; /* Scale */
6214: double *delti; /* Scale */
6215: double ***eij, ***vareij;
6216: double **varpl; /* Variances of prevalence limits by age */
6217: double *epj, vepp;
1.164 brouard 6218:
1.136 brouard 6219: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
6220: double **ximort;
1.145 brouard 6221: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 6222: int *dcwave;
6223:
1.164 brouard 6224: char z[1]="c";
1.136 brouard 6225:
6226: /*char *strt;*/
6227: char strtend[80];
1.126 brouard 6228:
1.164 brouard 6229:
1.126 brouard 6230: /* setlocale (LC_ALL, ""); */
6231: /* bindtextdomain (PACKAGE, LOCALEDIR); */
6232: /* textdomain (PACKAGE); */
6233: /* setlocale (LC_CTYPE, ""); */
6234: /* setlocale (LC_MESSAGES, ""); */
6235:
6236: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 6237: rstart_time = time(NULL);
6238: /* (void) gettimeofday(&start_time,&tzp);*/
6239: start_time = *localtime(&rstart_time);
1.126 brouard 6240: curr_time=start_time;
1.157 brouard 6241: /*tml = *localtime(&start_time.tm_sec);*/
6242: /* strcpy(strstart,asctime(&tml)); */
6243: strcpy(strstart,asctime(&start_time));
1.126 brouard 6244:
6245: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 6246: /* tp.tm_sec = tp.tm_sec +86400; */
6247: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 6248: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
6249: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
6250: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 6251: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 6252: /* strt=asctime(&tmg); */
6253: /* printf("Time(after) =%s",strstart); */
6254: /* (void) time (&time_value);
6255: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
6256: * tm = *localtime(&time_value);
6257: * strstart=asctime(&tm);
6258: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
6259: */
6260:
6261: nberr=0; /* Number of errors and warnings */
6262: nbwarn=0;
1.184 brouard 6263: #ifdef WIN32
6264: _getcwd(pathcd, size);
6265: #else
1.126 brouard 6266: getcwd(pathcd, size);
1.184 brouard 6267: #endif
1.126 brouard 6268:
6269: printf("\n%s\n%s",version,fullversion);
6270: if(argc <=1){
6271: printf("\nEnter the parameter file name: ");
6272: fgets(pathr,FILENAMELENGTH,stdin);
6273: i=strlen(pathr);
6274: if(pathr[i-1]=='\n')
6275: pathr[i-1]='\0';
1.156 brouard 6276: i=strlen(pathr);
6277: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
6278: pathr[i-1]='\0';
1.126 brouard 6279: for (tok = pathr; tok != NULL; ){
6280: printf("Pathr |%s|\n",pathr);
6281: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
6282: printf("val= |%s| pathr=%s\n",val,pathr);
6283: strcpy (pathtot, val);
6284: if(pathr[0] == '\0') break; /* Dirty */
6285: }
6286: }
6287: else{
6288: strcpy(pathtot,argv[1]);
6289: }
6290: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
6291: /*cygwin_split_path(pathtot,path,optionfile);
6292: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
6293: /* cutv(path,optionfile,pathtot,'\\');*/
6294:
6295: /* Split argv[0], imach program to get pathimach */
6296: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
6297: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6298: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6299: /* strcpy(pathimach,argv[0]); */
6300: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
6301: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
6302: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 6303: #ifdef WIN32
6304: _chdir(path); /* Can be a relative path */
6305: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
6306: #else
1.126 brouard 6307: chdir(path); /* Can be a relative path */
1.184 brouard 6308: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
6309: #endif
6310: printf("Current directory %s!\n",pathcd);
1.126 brouard 6311: strcpy(command,"mkdir ");
6312: strcat(command,optionfilefiname);
6313: if((outcmd=system(command)) != 0){
1.169 brouard 6314: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 6315: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
6316: /* fclose(ficlog); */
6317: /* exit(1); */
6318: }
6319: /* if((imk=mkdir(optionfilefiname))<0){ */
6320: /* perror("mkdir"); */
6321: /* } */
6322:
6323: /*-------- arguments in the command line --------*/
6324:
1.186 brouard 6325: /* Main Log file */
1.126 brouard 6326: strcat(filelog, optionfilefiname);
6327: strcat(filelog,".log"); /* */
6328: if((ficlog=fopen(filelog,"w"))==NULL) {
6329: printf("Problem with logfile %s\n",filelog);
6330: goto end;
6331: }
6332: fprintf(ficlog,"Log filename:%s\n",filelog);
6333: fprintf(ficlog,"\n%s\n%s",version,fullversion);
6334: fprintf(ficlog,"\nEnter the parameter file name: \n");
6335: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
6336: path=%s \n\
6337: optionfile=%s\n\
6338: optionfilext=%s\n\
1.156 brouard 6339: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 6340:
1.167 brouard 6341: syscompilerinfo();
6342:
1.126 brouard 6343: printf("Local time (at start):%s",strstart);
6344: fprintf(ficlog,"Local time (at start): %s",strstart);
6345: fflush(ficlog);
6346: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 6347: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 6348:
6349: /* */
6350: strcpy(fileres,"r");
6351: strcat(fileres, optionfilefiname);
6352: strcat(fileres,".txt"); /* Other files have txt extension */
6353:
1.186 brouard 6354: /* Main ---------arguments file --------*/
1.126 brouard 6355:
6356: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 6357: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
6358: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 6359: fflush(ficlog);
1.149 brouard 6360: /* goto end; */
6361: exit(70);
1.126 brouard 6362: }
6363:
6364:
6365:
6366: strcpy(filereso,"o");
6367: strcat(filereso,fileres);
6368: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
6369: printf("Problem with Output resultfile: %s\n", filereso);
6370: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
6371: fflush(ficlog);
6372: goto end;
6373: }
6374:
6375: /* Reads comments: lines beginning with '#' */
6376: numlinepar=0;
6377: while((c=getc(ficpar))=='#' && c!= EOF){
6378: ungetc(c,ficpar);
6379: fgets(line, MAXLINE, ficpar);
6380: numlinepar++;
1.141 brouard 6381: fputs(line,stdout);
1.126 brouard 6382: fputs(line,ficparo);
6383: fputs(line,ficlog);
6384: }
6385: ungetc(c,ficpar);
6386:
1.187 brouard 6387: fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
1.126 brouard 6388: numlinepar++;
1.187 brouard 6389: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
6390: if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the model */
6391: model[strlen(model)-1]='\0';
6392: fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
6393: fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
1.126 brouard 6394: fflush(ficlog);
1.187 brouard 6395: if(model[0]=='#'|| model[0]== '\0'){
6396: printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
6397: 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
6398: 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \
6399: if(mle != -1){
6400: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
6401: exit(1);
6402: }
6403: }
1.126 brouard 6404: while((c=getc(ficpar))=='#' && c!= EOF){
6405: ungetc(c,ficpar);
6406: fgets(line, MAXLINE, ficpar);
6407: numlinepar++;
1.141 brouard 6408: fputs(line, stdout);
6409: //puts(line);
1.126 brouard 6410: fputs(line,ficparo);
6411: fputs(line,ficlog);
6412: }
6413: ungetc(c,ficpar);
6414:
6415:
1.145 brouard 6416: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.136 brouard 6417: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
6418: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
6419: v1+v2*age+v2*v3 makes cptcovn = 3
6420: */
6421: if (strlen(model)>1)
1.187 brouard 6422: ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7,age*age makes 3*/
1.145 brouard 6423: else
1.187 brouard 6424: ncovmodel=2; /* Constant and age */
1.133 brouard 6425: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
6426: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 6427: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
6428: 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);
6429: 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);
6430: fflush(stdout);
6431: fclose (ficlog);
6432: goto end;
6433: }
1.126 brouard 6434: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6435: delti=delti3[1][1];
6436: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
6437: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
6438: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
6439: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
6440: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
6441: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6442: fclose (ficparo);
6443: fclose (ficlog);
6444: goto end;
6445: exit(0);
6446: }
1.186 brouard 6447: else if(mle==-3) { /* Main Wizard */
1.126 brouard 6448: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
6449: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
6450: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
6451: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6452: matcov=matrix(1,npar,1,npar);
6453: }
6454: else{
1.145 brouard 6455: /* Read guessed parameters */
1.126 brouard 6456: /* Reads comments: lines beginning with '#' */
6457: while((c=getc(ficpar))=='#' && c!= EOF){
6458: ungetc(c,ficpar);
6459: fgets(line, MAXLINE, ficpar);
6460: numlinepar++;
1.141 brouard 6461: fputs(line,stdout);
1.126 brouard 6462: fputs(line,ficparo);
6463: fputs(line,ficlog);
6464: }
6465: ungetc(c,ficpar);
6466:
6467: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6468: for(i=1; i <=nlstate; i++){
6469: j=0;
6470: for(jj=1; jj <=nlstate+ndeath; jj++){
6471: if(jj==i) continue;
6472: j++;
6473: fscanf(ficpar,"%1d%1d",&i1,&j1);
6474: if ((i1 != i) && (j1 != j)){
6475: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
6476: It might be a problem of design; if ncovcol and the model are correct\n \
6477: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
6478: exit(1);
6479: }
6480: fprintf(ficparo,"%1d%1d",i1,j1);
6481: if(mle==1)
6482: printf("%1d%1d",i,j);
6483: fprintf(ficlog,"%1d%1d",i,j);
6484: for(k=1; k<=ncovmodel;k++){
6485: fscanf(ficpar," %lf",¶m[i][j][k]);
6486: if(mle==1){
6487: printf(" %lf",param[i][j][k]);
6488: fprintf(ficlog," %lf",param[i][j][k]);
6489: }
6490: else
6491: fprintf(ficlog," %lf",param[i][j][k]);
6492: fprintf(ficparo," %lf",param[i][j][k]);
6493: }
6494: fscanf(ficpar,"\n");
6495: numlinepar++;
6496: if(mle==1)
6497: printf("\n");
6498: fprintf(ficlog,"\n");
6499: fprintf(ficparo,"\n");
6500: }
6501: }
6502: fflush(ficlog);
6503:
1.145 brouard 6504: /* Reads scales values */
1.126 brouard 6505: p=param[1][1];
6506:
6507: /* Reads comments: lines beginning with '#' */
6508: while((c=getc(ficpar))=='#' && c!= EOF){
6509: ungetc(c,ficpar);
6510: fgets(line, MAXLINE, ficpar);
6511: numlinepar++;
1.141 brouard 6512: fputs(line,stdout);
1.126 brouard 6513: fputs(line,ficparo);
6514: fputs(line,ficlog);
6515: }
6516: ungetc(c,ficpar);
6517:
6518: for(i=1; i <=nlstate; i++){
6519: for(j=1; j <=nlstate+ndeath-1; j++){
6520: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.164 brouard 6521: if ( (i1-i) * (j1-j) != 0){
1.126 brouard 6522: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
6523: exit(1);
6524: }
6525: printf("%1d%1d",i,j);
6526: fprintf(ficparo,"%1d%1d",i1,j1);
6527: fprintf(ficlog,"%1d%1d",i1,j1);
6528: for(k=1; k<=ncovmodel;k++){
6529: fscanf(ficpar,"%le",&delti3[i][j][k]);
6530: printf(" %le",delti3[i][j][k]);
6531: fprintf(ficparo," %le",delti3[i][j][k]);
6532: fprintf(ficlog," %le",delti3[i][j][k]);
6533: }
6534: fscanf(ficpar,"\n");
6535: numlinepar++;
6536: printf("\n");
6537: fprintf(ficparo,"\n");
6538: fprintf(ficlog,"\n");
6539: }
6540: }
6541: fflush(ficlog);
6542:
1.145 brouard 6543: /* Reads covariance matrix */
1.126 brouard 6544: delti=delti3[1][1];
6545:
6546:
6547: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
6548:
6549: /* Reads comments: lines beginning with '#' */
6550: while((c=getc(ficpar))=='#' && c!= EOF){
6551: ungetc(c,ficpar);
6552: fgets(line, MAXLINE, ficpar);
6553: numlinepar++;
1.141 brouard 6554: fputs(line,stdout);
1.126 brouard 6555: fputs(line,ficparo);
6556: fputs(line,ficlog);
6557: }
6558: ungetc(c,ficpar);
6559:
6560: matcov=matrix(1,npar,1,npar);
1.131 brouard 6561: for(i=1; i <=npar; i++)
6562: for(j=1; j <=npar; j++) matcov[i][j]=0.;
6563:
1.126 brouard 6564: for(i=1; i <=npar; i++){
1.145 brouard 6565: fscanf(ficpar,"%s",str);
1.126 brouard 6566: if(mle==1)
6567: printf("%s",str);
6568: fprintf(ficlog,"%s",str);
6569: fprintf(ficparo,"%s",str);
6570: for(j=1; j <=i; j++){
6571: fscanf(ficpar," %le",&matcov[i][j]);
6572: if(mle==1){
6573: printf(" %.5le",matcov[i][j]);
6574: }
6575: fprintf(ficlog," %.5le",matcov[i][j]);
6576: fprintf(ficparo," %.5le",matcov[i][j]);
6577: }
6578: fscanf(ficpar,"\n");
6579: numlinepar++;
6580: if(mle==1)
6581: printf("\n");
6582: fprintf(ficlog,"\n");
6583: fprintf(ficparo,"\n");
6584: }
6585: for(i=1; i <=npar; i++)
6586: for(j=i+1;j<=npar;j++)
6587: matcov[i][j]=matcov[j][i];
6588:
6589: if(mle==1)
6590: printf("\n");
6591: fprintf(ficlog,"\n");
6592:
6593: fflush(ficlog);
6594:
6595: /*-------- Rewriting parameter file ----------*/
6596: strcpy(rfileres,"r"); /* "Rparameterfile */
6597: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
6598: strcat(rfileres,"."); /* */
6599: strcat(rfileres,optionfilext); /* Other files have txt extension */
6600: if((ficres =fopen(rfileres,"w"))==NULL) {
6601: printf("Problem writing new parameter file: %s\n", fileres);goto end;
6602: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
6603: }
6604: fprintf(ficres,"#%s\n",version);
6605: } /* End of mle != -3 */
6606:
1.186 brouard 6607: /* Main data
6608: */
1.126 brouard 6609: n= lastobs;
6610: num=lvector(1,n);
6611: moisnais=vector(1,n);
6612: annais=vector(1,n);
6613: moisdc=vector(1,n);
6614: andc=vector(1,n);
6615: agedc=vector(1,n);
6616: cod=ivector(1,n);
6617: weight=vector(1,n);
6618: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
6619: mint=matrix(1,maxwav,1,n);
6620: anint=matrix(1,maxwav,1,n);
1.131 brouard 6621: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 6622: tab=ivector(1,NCOVMAX);
1.144 brouard 6623: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.126 brouard 6624:
1.136 brouard 6625: /* Reads data from file datafile */
6626: if (readdata(datafile, firstobs, lastobs, &imx)==1)
6627: goto end;
6628:
6629: /* Calculation of the number of parameters from char model */
1.137 brouard 6630: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
6631: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
6632: k=3 V4 Tvar[k=3]= 4 (from V4)
6633: k=2 V1 Tvar[k=2]= 1 (from V1)
6634: k=1 Tvar[1]=2 (from V2)
6635: */
6636: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
6637: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
6638: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
6639: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
6640: */
6641: /* For model-covariate k tells which data-covariate to use but
6642: because this model-covariate is a construction we invent a new column
6643: ncovcol + k1
6644: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
6645: Tvar[3=V1*V4]=4+1 etc */
1.145 brouard 6646: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
1.137 brouard 6647: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
6648: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
6649: */
1.145 brouard 6650: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
6651: 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 6652: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
6653: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 6654: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 6655: 4 covariates (3 plus signs)
6656: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
6657: */
1.136 brouard 6658:
1.186 brouard 6659: /* Main decodemodel */
6660:
1.187 brouard 6661:
1.136 brouard 6662: if(decodemodel(model, lastobs) == 1)
6663: goto end;
6664:
1.137 brouard 6665: if((double)(lastobs-imx)/(double)imx > 1.10){
6666: nbwarn++;
6667: 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);
6668: 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);
6669: }
1.136 brouard 6670: /* if(mle==1){*/
1.137 brouard 6671: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
6672: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 6673: }
6674:
6675: /*-calculation of age at interview from date of interview and age at death -*/
6676: agev=matrix(1,maxwav,1,imx);
6677:
6678: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
6679: goto end;
6680:
1.126 brouard 6681:
1.136 brouard 6682: agegomp=(int)agemin;
6683: free_vector(moisnais,1,n);
6684: free_vector(annais,1,n);
1.126 brouard 6685: /* free_matrix(mint,1,maxwav,1,n);
6686: free_matrix(anint,1,maxwav,1,n);*/
6687: free_vector(moisdc,1,n);
6688: free_vector(andc,1,n);
1.145 brouard 6689: /* */
6690:
1.126 brouard 6691: wav=ivector(1,imx);
6692: dh=imatrix(1,lastpass-firstpass+1,1,imx);
6693: bh=imatrix(1,lastpass-firstpass+1,1,imx);
6694: mw=imatrix(1,lastpass-firstpass+1,1,imx);
6695:
6696: /* Concatenates waves */
6697: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 brouard 6698: /* */
6699:
1.126 brouard 6700: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
6701:
6702: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
6703: ncodemax[1]=1;
1.145 brouard 6704: Ndum =ivector(-1,NCOVMAX);
1.187 brouard 6705: if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */
1.145 brouard 6706: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.186 brouard 6707: /* Nbcode gives the value of the lth modality of jth covariate, in
6708: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
6709: /* 1 to ncodemax[j] is the maximum value of this jth covariate */
1.145 brouard 6710:
6711: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
6712: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
1.186 brouard 6713: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.145 brouard 6714: h=0;
6715:
6716:
6717: /*if (cptcovn > 0) */
1.126 brouard 6718:
1.145 brouard 6719:
1.126 brouard 6720: m=pow(2,cptcoveff);
6721:
1.131 brouard 6722: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
1.143 brouard 6723: 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 */
6724: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
6725: 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 6726: h++;
1.141 brouard 6727: if (h>m)
1.136 brouard 6728: h=1;
1.144 brouard 6729: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.186 brouard 6730: * For k=4 covariates, h goes from 1 to 2**k
6731: * codtabm(h,k)= 1 & (h-1) >> (k-1) ;
6732: * h\k 1 2 3 4
1.143 brouard 6733: *______________________________
6734: * 1 i=1 1 i=1 1 i=1 1 i=1 1
6735: * 2 2 1 1 1
6736: * 3 i=2 1 2 1 1
6737: * 4 2 2 1 1
6738: * 5 i=3 1 i=2 1 2 1
6739: * 6 2 1 2 1
6740: * 7 i=4 1 2 2 1
6741: * 8 2 2 2 1
6742: * 9 i=5 1 i=3 1 i=2 1 1
6743: * 10 2 1 1 1
6744: * 11 i=6 1 2 1 1
6745: * 12 2 2 1 1
6746: * 13 i=7 1 i=4 1 2 1
6747: * 14 2 1 2 1
6748: * 15 i=8 1 2 2 1
6749: * 16 2 2 2 1
6750: */
1.141 brouard 6751: codtab[h][k]=j;
1.186 brouard 6752: /* codtab[12][3]=1; */
1.145 brouard 6753: /*codtab[h][Tvar[k]]=j;*/
1.130 brouard 6754: 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 6755: }
6756: }
6757: }
6758: }
6759: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
6760: codtab[1][2]=1;codtab[2][2]=2; */
6761: /* for(i=1; i <=m ;i++){
6762: for(k=1; k <=cptcovn; k++){
1.131 brouard 6763: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
1.126 brouard 6764: }
6765: printf("\n");
6766: }
6767: scanf("%d",i);*/
1.145 brouard 6768:
6769: free_ivector(Ndum,-1,NCOVMAX);
6770:
6771:
1.126 brouard 6772:
1.186 brouard 6773: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 6774: strcpy(optionfilegnuplot,optionfilefiname);
6775: if(mle==-3)
6776: strcat(optionfilegnuplot,"-mort");
6777: strcat(optionfilegnuplot,".gp");
6778:
6779: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
6780: printf("Problem with file %s",optionfilegnuplot);
6781: }
6782: else{
6783: fprintf(ficgp,"\n# %s\n", version);
6784: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 6785: //fprintf(ficgp,"set missing 'NaNq'\n");
6786: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 6787: }
6788: /* fclose(ficgp);*/
1.186 brouard 6789:
6790:
6791: /* Initialisation of --------- index.htm --------*/
1.126 brouard 6792:
6793: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
6794: if(mle==-3)
6795: strcat(optionfilehtm,"-mort");
6796: strcat(optionfilehtm,".htm");
6797: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 6798: printf("Problem with %s \n",optionfilehtm);
6799: exit(0);
1.126 brouard 6800: }
6801:
6802: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
6803: strcat(optionfilehtmcov,"-cov.htm");
6804: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
6805: printf("Problem with %s \n",optionfilehtmcov), exit(0);
6806: }
6807: else{
6808: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6809: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6810: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
6811: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
6812: }
6813:
6814: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6815: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6816: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
6817: \n\
6818: <hr size=\"2\" color=\"#EC5E5E\">\
6819: <ul><li><h4>Parameter files</h4>\n\
6820: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
6821: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
6822: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
6823: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
6824: - Date and time at start: %s</ul>\n",\
6825: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
6826: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
6827: fileres,fileres,\
6828: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
6829: fflush(fichtm);
6830:
6831: strcpy(pathr,path);
6832: strcat(pathr,optionfilefiname);
1.184 brouard 6833: #ifdef WIN32
6834: _chdir(optionfilefiname); /* Move to directory named optionfile */
6835: #else
1.126 brouard 6836: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 6837: #endif
6838:
1.126 brouard 6839:
6840: /* Calculates basic frequencies. Computes observed prevalence at single age
6841: and prints on file fileres'p'. */
6842: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
6843:
6844: fprintf(fichtm,"\n");
6845: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
6846: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
6847: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
6848: imx,agemin,agemax,jmin,jmax,jmean);
6849: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6850: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6851: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6852: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6853: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
6854:
6855:
6856: /* For Powell, parameters are in a vector p[] starting at p[1]
6857: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
6858: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
6859:
6860: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 6861: /* For mortality only */
1.126 brouard 6862: if (mle==-3){
1.136 brouard 6863: ximort=matrix(1,NDIM,1,NDIM);
1.186 brouard 6864: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 6865: cens=ivector(1,n);
6866: ageexmed=vector(1,n);
6867: agecens=vector(1,n);
6868: dcwave=ivector(1,n);
6869:
6870: for (i=1; i<=imx; i++){
6871: dcwave[i]=-1;
6872: for (m=firstpass; m<=lastpass; m++)
6873: if (s[m][i]>nlstate) {
6874: dcwave[i]=m;
6875: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
6876: break;
6877: }
6878: }
6879:
6880: for (i=1; i<=imx; i++) {
6881: if (wav[i]>0){
6882: ageexmed[i]=agev[mw[1][i]][i];
6883: j=wav[i];
6884: agecens[i]=1.;
6885:
6886: if (ageexmed[i]> 1 && wav[i] > 0){
6887: agecens[i]=agev[mw[j][i]][i];
6888: cens[i]= 1;
6889: }else if (ageexmed[i]< 1)
6890: cens[i]= -1;
6891: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
6892: cens[i]=0 ;
6893: }
6894: else cens[i]=-1;
6895: }
6896:
6897: for (i=1;i<=NDIM;i++) {
6898: for (j=1;j<=NDIM;j++)
6899: ximort[i][j]=(i == j ? 1.0 : 0.0);
6900: }
6901:
1.145 brouard 6902: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 6903: /*printf("%lf %lf", p[1], p[2]);*/
6904:
6905:
1.136 brouard 6906: #ifdef GSL
6907: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 6908: #else
1.126 brouard 6909: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 6910: #endif
1.126 brouard 6911: strcpy(filerespow,"pow-mort");
6912: strcat(filerespow,fileres);
6913: if((ficrespow=fopen(filerespow,"w"))==NULL) {
6914: printf("Problem with resultfile: %s\n", filerespow);
6915: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
6916: }
1.136 brouard 6917: #ifdef GSL
6918: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 6919: #else
1.126 brouard 6920: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 6921: #endif
1.126 brouard 6922: /* for (i=1;i<=nlstate;i++)
6923: for(j=1;j<=nlstate+ndeath;j++)
6924: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
6925: */
6926: fprintf(ficrespow,"\n");
1.136 brouard 6927: #ifdef GSL
6928: /* gsl starts here */
6929: T = gsl_multimin_fminimizer_nmsimplex;
6930: gsl_multimin_fminimizer *sfm = NULL;
6931: gsl_vector *ss, *x;
6932: gsl_multimin_function minex_func;
6933:
6934: /* Initial vertex size vector */
6935: ss = gsl_vector_alloc (NDIM);
6936:
6937: if (ss == NULL){
6938: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
6939: }
6940: /* Set all step sizes to 1 */
6941: gsl_vector_set_all (ss, 0.001);
6942:
6943: /* Starting point */
1.126 brouard 6944:
1.136 brouard 6945: x = gsl_vector_alloc (NDIM);
6946:
6947: if (x == NULL){
6948: gsl_vector_free(ss);
6949: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
6950: }
6951:
6952: /* Initialize method and iterate */
6953: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 6954: /* gsl_vector_set(x, 0, 0.0268); */
6955: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 6956: gsl_vector_set(x, 0, p[1]);
6957: gsl_vector_set(x, 1, p[2]);
6958:
6959: minex_func.f = &gompertz_f;
6960: minex_func.n = NDIM;
6961: minex_func.params = (void *)&p; /* ??? */
6962:
6963: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
6964: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
6965:
6966: printf("Iterations beginning .....\n\n");
6967: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
6968:
6969: iteri=0;
6970: while (rval == GSL_CONTINUE){
6971: iteri++;
6972: status = gsl_multimin_fminimizer_iterate(sfm);
6973:
6974: if (status) printf("error: %s\n", gsl_strerror (status));
6975: fflush(0);
6976:
6977: if (status)
6978: break;
6979:
6980: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
6981: ssval = gsl_multimin_fminimizer_size (sfm);
6982:
6983: if (rval == GSL_SUCCESS)
6984: printf ("converged to a local maximum at\n");
6985:
6986: printf("%5d ", iteri);
6987: for (it = 0; it < NDIM; it++){
6988: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
6989: }
6990: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
6991: }
6992:
6993: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
6994:
6995: gsl_vector_free(x); /* initial values */
6996: gsl_vector_free(ss); /* inital step size */
6997: for (it=0; it<NDIM; it++){
6998: p[it+1]=gsl_vector_get(sfm->x,it);
6999: fprintf(ficrespow," %.12lf", p[it]);
7000: }
7001: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
7002: #endif
7003: #ifdef POWELL
7004: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
7005: #endif
1.126 brouard 7006: fclose(ficrespow);
7007:
7008: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
7009:
7010: for(i=1; i <=NDIM; i++)
7011: for(j=i+1;j<=NDIM;j++)
7012: matcov[i][j]=matcov[j][i];
7013:
7014: printf("\nCovariance matrix\n ");
7015: for(i=1; i <=NDIM; i++) {
7016: for(j=1;j<=NDIM;j++){
7017: printf("%f ",matcov[i][j]);
7018: }
7019: printf("\n ");
7020: }
7021:
7022: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
7023: for (i=1;i<=NDIM;i++)
7024: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
7025:
7026: lsurv=vector(1,AGESUP);
7027: lpop=vector(1,AGESUP);
7028: tpop=vector(1,AGESUP);
7029: lsurv[agegomp]=100000;
7030:
7031: for (k=agegomp;k<=AGESUP;k++) {
7032: agemortsup=k;
7033: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
7034: }
7035:
7036: for (k=agegomp;k<agemortsup;k++)
7037: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
7038:
7039: for (k=agegomp;k<agemortsup;k++){
7040: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
7041: sumlpop=sumlpop+lpop[k];
7042: }
7043:
7044: tpop[agegomp]=sumlpop;
7045: for (k=agegomp;k<(agemortsup-3);k++){
7046: /* tpop[k+1]=2;*/
7047: tpop[k+1]=tpop[k]-lpop[k];
7048: }
7049:
7050:
7051: printf("\nAge lx qx dx Lx Tx e(x)\n");
7052: for (k=agegomp;k<(agemortsup-2);k++)
7053: 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]);
7054:
7055:
7056: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
7057: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
7058:
7059: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
7060: stepm, weightopt,\
7061: model,imx,p,matcov,agemortsup);
7062:
7063: free_vector(lsurv,1,AGESUP);
7064: free_vector(lpop,1,AGESUP);
7065: free_vector(tpop,1,AGESUP);
1.136 brouard 7066: #ifdef GSL
7067: free_ivector(cens,1,n);
7068: free_vector(agecens,1,n);
7069: free_ivector(dcwave,1,n);
7070: free_matrix(ximort,1,NDIM,1,NDIM);
7071: #endif
1.186 brouard 7072: } /* Endof if mle==-3 mortality only */
7073: /* Standard maximisation */
1.126 brouard 7074: else{ /* For mle >=1 */
1.132 brouard 7075: globpr=0;/* debug */
1.186 brouard 7076: /* Computes likelihood for initial parameters */
1.132 brouard 7077: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 7078: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7079: for (k=1; k<=npar;k++)
7080: printf(" %d %8.5f",k,p[k]);
7081: printf("\n");
1.186 brouard 7082: globpr=1; /* again, to print the contributions */
1.126 brouard 7083: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
7084: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7085: for (k=1; k<=npar;k++)
7086: printf(" %d %8.5f",k,p[k]);
7087: printf("\n");
1.186 brouard 7088: if(mle>=1){ /* Could be 1 or 2, Real Maximisation */
1.126 brouard 7089: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
7090: }
7091:
7092: /*--------- results files --------------*/
1.187 brouard 7093: fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
1.126 brouard 7094:
7095:
7096: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7097: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7098: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7099: for(i=1,jk=1; i <=nlstate; i++){
7100: for(k=1; k <=(nlstate+ndeath); k++){
7101: if (k != i) {
7102: printf("%d%d ",i,k);
7103: fprintf(ficlog,"%d%d ",i,k);
7104: fprintf(ficres,"%1d%1d ",i,k);
7105: for(j=1; j <=ncovmodel; j++){
7106: printf("%lf ",p[jk]);
7107: fprintf(ficlog,"%lf ",p[jk]);
7108: fprintf(ficres,"%lf ",p[jk]);
7109: jk++;
7110: }
7111: printf("\n");
7112: fprintf(ficlog,"\n");
7113: fprintf(ficres,"\n");
7114: }
7115: }
7116: }
7117: if(mle!=0){
7118: /* Computing hessian and covariance matrix */
7119: ftolhess=ftol; /* Usually correct */
7120: hesscov(matcov, p, npar, delti, ftolhess, func);
7121: }
7122: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
7123: printf("# Scales (for hessian or gradient estimation)\n");
7124: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
7125: for(i=1,jk=1; i <=nlstate; i++){
7126: for(j=1; j <=nlstate+ndeath; j++){
7127: if (j!=i) {
7128: fprintf(ficres,"%1d%1d",i,j);
7129: printf("%1d%1d",i,j);
7130: fprintf(ficlog,"%1d%1d",i,j);
7131: for(k=1; k<=ncovmodel;k++){
7132: printf(" %.5e",delti[jk]);
7133: fprintf(ficlog," %.5e",delti[jk]);
7134: fprintf(ficres," %.5e",delti[jk]);
7135: jk++;
7136: }
7137: printf("\n");
7138: fprintf(ficlog,"\n");
7139: fprintf(ficres,"\n");
7140: }
7141: }
7142: }
7143:
7144: 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");
7145: if(mle>=1)
7146: 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");
7147: 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");
7148: /* # 121 Var(a12)\n\ */
7149: /* # 122 Cov(b12,a12) Var(b12)\n\ */
7150: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
7151: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
7152: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
7153: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
7154: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
7155: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
7156:
7157:
7158: /* Just to have a covariance matrix which will be more understandable
7159: even is we still don't want to manage dictionary of variables
7160: */
7161: for(itimes=1;itimes<=2;itimes++){
7162: jj=0;
7163: for(i=1; i <=nlstate; i++){
7164: for(j=1; j <=nlstate+ndeath; j++){
7165: if(j==i) continue;
7166: for(k=1; k<=ncovmodel;k++){
7167: jj++;
7168: ca[0]= k+'a'-1;ca[1]='\0';
7169: if(itimes==1){
7170: if(mle>=1)
7171: printf("#%1d%1d%d",i,j,k);
7172: fprintf(ficlog,"#%1d%1d%d",i,j,k);
7173: fprintf(ficres,"#%1d%1d%d",i,j,k);
7174: }else{
7175: if(mle>=1)
7176: printf("%1d%1d%d",i,j,k);
7177: fprintf(ficlog,"%1d%1d%d",i,j,k);
7178: fprintf(ficres,"%1d%1d%d",i,j,k);
7179: }
7180: ll=0;
7181: for(li=1;li <=nlstate; li++){
7182: for(lj=1;lj <=nlstate+ndeath; lj++){
7183: if(lj==li) continue;
7184: for(lk=1;lk<=ncovmodel;lk++){
7185: ll++;
7186: if(ll<=jj){
7187: cb[0]= lk +'a'-1;cb[1]='\0';
7188: if(ll<jj){
7189: if(itimes==1){
7190: if(mle>=1)
7191: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7192: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7193: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7194: }else{
7195: if(mle>=1)
7196: printf(" %.5e",matcov[jj][ll]);
7197: fprintf(ficlog," %.5e",matcov[jj][ll]);
7198: fprintf(ficres," %.5e",matcov[jj][ll]);
7199: }
7200: }else{
7201: if(itimes==1){
7202: if(mle>=1)
7203: printf(" Var(%s%1d%1d)",ca,i,j);
7204: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
7205: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
7206: }else{
7207: if(mle>=1)
7208: printf(" %.5e",matcov[jj][ll]);
7209: fprintf(ficlog," %.5e",matcov[jj][ll]);
7210: fprintf(ficres," %.5e",matcov[jj][ll]);
7211: }
7212: }
7213: }
7214: } /* end lk */
7215: } /* end lj */
7216: } /* end li */
7217: if(mle>=1)
7218: printf("\n");
7219: fprintf(ficlog,"\n");
7220: fprintf(ficres,"\n");
7221: numlinepar++;
7222: } /* end k*/
7223: } /*end j */
7224: } /* end i */
7225: } /* end itimes */
7226:
7227: fflush(ficlog);
7228: fflush(ficres);
7229:
7230: while((c=getc(ficpar))=='#' && c!= EOF){
7231: ungetc(c,ficpar);
7232: fgets(line, MAXLINE, ficpar);
1.141 brouard 7233: fputs(line,stdout);
1.126 brouard 7234: fputs(line,ficparo);
7235: }
7236: ungetc(c,ficpar);
7237:
7238: estepm=0;
7239: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
7240: if (estepm==0 || estepm < stepm) estepm=stepm;
7241: if (fage <= 2) {
7242: bage = ageminpar;
7243: fage = agemaxpar;
7244: }
7245:
7246: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
7247: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
7248: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
1.186 brouard 7249:
7250: /* Other stuffs, more or less useful */
1.126 brouard 7251: while((c=getc(ficpar))=='#' && c!= EOF){
7252: ungetc(c,ficpar);
7253: fgets(line, MAXLINE, ficpar);
1.141 brouard 7254: fputs(line,stdout);
1.126 brouard 7255: fputs(line,ficparo);
7256: }
7257: ungetc(c,ficpar);
7258:
7259: 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);
7260: 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);
7261: 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);
7262: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
7263: 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);
7264:
7265: while((c=getc(ficpar))=='#' && c!= EOF){
7266: ungetc(c,ficpar);
7267: fgets(line, MAXLINE, ficpar);
1.141 brouard 7268: fputs(line,stdout);
1.126 brouard 7269: fputs(line,ficparo);
7270: }
7271: ungetc(c,ficpar);
7272:
7273:
7274: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
7275: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
7276:
7277: fscanf(ficpar,"pop_based=%d\n",&popbased);
7278: fprintf(ficparo,"pop_based=%d\n",popbased);
7279: fprintf(ficres,"pop_based=%d\n",popbased);
7280:
7281: while((c=getc(ficpar))=='#' && c!= EOF){
7282: ungetc(c,ficpar);
7283: fgets(line, MAXLINE, ficpar);
1.141 brouard 7284: fputs(line,stdout);
1.126 brouard 7285: fputs(line,ficparo);
7286: }
7287: ungetc(c,ficpar);
7288:
7289: 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);
7290: 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);
7291: 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);
7292: 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);
7293: 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);
7294: /* day and month of proj2 are not used but only year anproj2.*/
7295:
7296:
7297:
1.145 brouard 7298: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
7299: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 7300:
7301: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
7302: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
7303:
7304: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
7305: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
7306: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
7307:
7308: /*------------ free_vector -------------*/
7309: /* chdir(path); */
7310:
7311: free_ivector(wav,1,imx);
7312: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
7313: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
7314: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
7315: free_lvector(num,1,n);
7316: free_vector(agedc,1,n);
7317: /*free_matrix(covar,0,NCOVMAX,1,n);*/
7318: /*free_matrix(covar,1,NCOVMAX,1,n);*/
7319: fclose(ficparo);
7320: fclose(ficres);
7321:
7322:
1.186 brouard 7323: /* Other results (useful)*/
7324:
7325:
1.126 brouard 7326: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 7327: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
7328: prlim=matrix(1,nlstate,1,nlstate);
7329: prevalence_limit(p, prlim, ageminpar, agemaxpar);
1.126 brouard 7330: fclose(ficrespl);
7331:
1.145 brouard 7332: #ifdef FREEEXIT2
7333: #include "freeexit2.h"
7334: #endif
7335:
1.126 brouard 7336: /*------------- h Pij x at various ages ------------*/
1.180 brouard 7337: /*#include "hpijx.h"*/
7338: hPijx(p, bage, fage);
1.145 brouard 7339: fclose(ficrespij);
1.126 brouard 7340:
1.145 brouard 7341: /*-------------- Variance of one-step probabilities---*/
7342: k=1;
1.126 brouard 7343: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
7344:
7345:
7346: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7347: for(i=1;i<=AGESUP;i++)
7348: for(j=1;j<=NCOVMAX;j++)
7349: for(k=1;k<=NCOVMAX;k++)
7350: probs[i][j][k]=0.;
7351:
7352: /*---------- Forecasting ------------------*/
7353: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
7354: if(prevfcast==1){
7355: /* if(stepm ==1){*/
7356: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
7357: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
7358: /* } */
7359: /* else{ */
7360: /* erreur=108; */
7361: /* 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); */
7362: /* 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); */
7363: /* } */
7364: }
1.186 brouard 7365:
7366: /* ------ Other prevalence ratios------------ */
1.126 brouard 7367:
1.127 brouard 7368: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
7369:
7370: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
7371: /* 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",\
7372: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
7373: */
1.126 brouard 7374:
1.127 brouard 7375: if (mobilav!=0) {
7376: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7377: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
7378: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
7379: printf(" Error in movingaverage mobilav=%d\n",mobilav);
7380: }
1.126 brouard 7381: }
7382:
7383:
1.127 brouard 7384: /*---------- Health expectancies, no variances ------------*/
7385:
1.126 brouard 7386: strcpy(filerese,"e");
7387: strcat(filerese,fileres);
7388: if((ficreseij=fopen(filerese,"w"))==NULL) {
7389: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
7390: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
7391: }
7392: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
7393: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.145 brouard 7394: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7395: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7396:
7397: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.127 brouard 7398: fprintf(ficreseij,"\n#****** ");
7399: for(j=1;j<=cptcoveff;j++) {
7400: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7401: }
7402: fprintf(ficreseij,"******\n");
7403:
7404: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7405: oldm=oldms;savm=savms;
7406: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
7407:
7408: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.145 brouard 7409: /*}*/
1.127 brouard 7410: }
7411: fclose(ficreseij);
7412:
7413:
7414: /*---------- Health expectancies and variances ------------*/
7415:
7416:
7417: strcpy(filerest,"t");
7418: strcat(filerest,fileres);
7419: if((ficrest=fopen(filerest,"w"))==NULL) {
7420: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
7421: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
7422: }
7423: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
7424: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
7425:
1.126 brouard 7426:
7427: strcpy(fileresstde,"stde");
7428: strcat(fileresstde,fileres);
7429: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
7430: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
7431: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
7432: }
7433: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
7434: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
7435:
7436: strcpy(filerescve,"cve");
7437: strcat(filerescve,fileres);
7438: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
7439: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
7440: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
7441: }
7442: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
7443: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
7444:
7445: strcpy(fileresv,"v");
7446: strcat(fileresv,fileres);
7447: if((ficresvij=fopen(fileresv,"w"))==NULL) {
7448: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
7449: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
7450: }
7451: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
7452: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
7453:
1.145 brouard 7454: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7455: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7456:
7457: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7458: fprintf(ficrest,"\n#****** ");
1.126 brouard 7459: for(j=1;j<=cptcoveff;j++)
7460: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7461: fprintf(ficrest,"******\n");
7462:
7463: fprintf(ficresstdeij,"\n#****** ");
7464: fprintf(ficrescveij,"\n#****** ");
7465: for(j=1;j<=cptcoveff;j++) {
7466: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7467: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7468: }
7469: fprintf(ficresstdeij,"******\n");
7470: fprintf(ficrescveij,"******\n");
7471:
7472: fprintf(ficresvij,"\n#****** ");
7473: for(j=1;j<=cptcoveff;j++)
7474: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7475: fprintf(ficresvij,"******\n");
7476:
7477: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7478: oldm=oldms;savm=savms;
1.127 brouard 7479: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
1.145 brouard 7480: /*
7481: */
7482: /* goto endfree; */
1.126 brouard 7483:
7484: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7485: pstamp(ficrest);
1.145 brouard 7486:
7487:
1.128 brouard 7488: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.145 brouard 7489: oldm=oldms;savm=savms; /* Segmentation fault */
1.161 brouard 7490: cptcod= 0; /* To be deleted */
7491: 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 7492: 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 7493: if(vpopbased==1)
7494: 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);
7495: else
7496: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
7497: fprintf(ficrest,"# Age e.. (std) ");
7498: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
7499: fprintf(ficrest,"\n");
1.126 brouard 7500:
1.128 brouard 7501: epj=vector(1,nlstate+1);
7502: for(age=bage; age <=fage ;age++){
7503: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
7504: if (vpopbased==1) {
7505: if(mobilav ==0){
7506: for(i=1; i<=nlstate;i++)
7507: prlim[i][i]=probs[(int)age][i][k];
7508: }else{ /* mobilav */
7509: for(i=1; i<=nlstate;i++)
7510: prlim[i][i]=mobaverage[(int)age][i][k];
7511: }
1.126 brouard 7512: }
7513:
1.128 brouard 7514: fprintf(ficrest," %4.0f",age);
7515: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
7516: for(i=1, epj[j]=0.;i <=nlstate;i++) {
7517: epj[j] += prlim[i][i]*eij[i][j][(int)age];
7518: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
7519: }
7520: epj[nlstate+1] +=epj[j];
1.126 brouard 7521: }
7522:
1.128 brouard 7523: for(i=1, vepp=0.;i <=nlstate;i++)
7524: for(j=1;j <=nlstate;j++)
7525: vepp += vareij[i][j][(int)age];
7526: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
7527: for(j=1;j <=nlstate;j++){
7528: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
7529: }
7530: fprintf(ficrest,"\n");
1.126 brouard 7531: }
7532: }
7533: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
7534: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
7535: free_vector(epj,1,nlstate+1);
1.145 brouard 7536: /*}*/
1.126 brouard 7537: }
7538: free_vector(weight,1,n);
1.145 brouard 7539: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.126 brouard 7540: free_imatrix(s,1,maxwav+1,1,n);
7541: free_matrix(anint,1,maxwav,1,n);
7542: free_matrix(mint,1,maxwav,1,n);
7543: free_ivector(cod,1,n);
7544: free_ivector(tab,1,NCOVMAX);
7545: fclose(ficresstdeij);
7546: fclose(ficrescveij);
7547: fclose(ficresvij);
7548: fclose(ficrest);
7549: fclose(ficpar);
7550:
7551: /*------- Variance of period (stable) prevalence------*/
7552:
7553: strcpy(fileresvpl,"vpl");
7554: strcat(fileresvpl,fileres);
7555: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
7556: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
7557: exit(0);
7558: }
7559: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
7560:
1.145 brouard 7561: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7562: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7563:
7564: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7565: fprintf(ficresvpl,"\n#****** ");
1.126 brouard 7566: for(j=1;j<=cptcoveff;j++)
7567: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7568: fprintf(ficresvpl,"******\n");
7569:
7570: varpl=matrix(1,nlstate,(int) bage, (int) fage);
7571: oldm=oldms;savm=savms;
7572: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
7573: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 7574: /*}*/
1.126 brouard 7575: }
7576:
7577: fclose(ficresvpl);
7578:
7579: /*---------- End : free ----------------*/
7580: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7581: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7582: } /* mle==-3 arrives here for freeing */
1.164 brouard 7583: /* endfree:*/
1.141 brouard 7584: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.126 brouard 7585: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
7586: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
7587: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
7588: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
7589: free_matrix(covar,0,NCOVMAX,1,n);
7590: free_matrix(matcov,1,npar,1,npar);
7591: /*free_vector(delti,1,npar);*/
7592: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7593: free_matrix(agev,1,maxwav,1,imx);
7594: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7595:
1.145 brouard 7596: free_ivector(ncodemax,1,NCOVMAX);
7597: free_ivector(Tvar,1,NCOVMAX);
7598: free_ivector(Tprod,1,NCOVMAX);
7599: free_ivector(Tvaraff,1,NCOVMAX);
7600: free_ivector(Tage,1,NCOVMAX);
1.126 brouard 7601:
7602: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
7603: free_imatrix(codtab,1,100,1,10);
7604: fflush(fichtm);
7605: fflush(ficgp);
7606:
7607:
7608: if((nberr >0) || (nbwarn>0)){
7609: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
7610: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
7611: }else{
7612: printf("End of Imach\n");
7613: fprintf(ficlog,"End of Imach\n");
7614: }
7615: printf("See log file on %s\n",filelog);
7616: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 7617: /*(void) gettimeofday(&end_time,&tzp);*/
7618: rend_time = time(NULL);
7619: end_time = *localtime(&rend_time);
7620: /* tml = *localtime(&end_time.tm_sec); */
7621: strcpy(strtend,asctime(&end_time));
1.126 brouard 7622: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
7623: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 7624: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.126 brouard 7625:
1.157 brouard 7626: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
7627: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
7628: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 7629: /* printf("Total time was %d uSec.\n", total_usecs);*/
7630: /* if(fileappend(fichtm,optionfilehtm)){ */
7631: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7632: fclose(fichtm);
7633: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7634: fclose(fichtmcov);
7635: fclose(ficgp);
7636: fclose(ficlog);
7637: /*------ End -----------*/
7638:
7639:
7640: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 7641: #ifdef WIN32
7642: if (_chdir(pathcd) != 0)
7643: printf("Can't move to directory %s!\n",path);
7644: if(_getcwd(pathcd,MAXLINE) > 0)
7645: #else
1.126 brouard 7646: if(chdir(pathcd) != 0)
1.184 brouard 7647: printf("Can't move to directory %s!\n", path);
7648: if (getcwd(pathcd, MAXLINE) > 0)
7649: #endif
1.126 brouard 7650: printf("Current directory %s!\n",pathcd);
7651: /*strcat(plotcmd,CHARSEPARATOR);*/
7652: sprintf(plotcmd,"gnuplot");
1.157 brouard 7653: #ifdef _WIN32
1.126 brouard 7654: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
7655: #endif
7656: if(!stat(plotcmd,&info)){
1.158 brouard 7657: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 7658: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 7659: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 7660: }else
7661: strcpy(pplotcmd,plotcmd);
1.157 brouard 7662: #ifdef __unix
1.126 brouard 7663: strcpy(plotcmd,GNUPLOTPROGRAM);
7664: if(!stat(plotcmd,&info)){
1.158 brouard 7665: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 7666: }else
7667: strcpy(pplotcmd,plotcmd);
7668: #endif
7669: }else
7670: strcpy(pplotcmd,plotcmd);
7671:
7672: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 7673: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 7674:
7675: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 7676: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 7677: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 7678: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 7679: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 7680: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 7681: }
1.158 brouard 7682: printf(" Successful, please wait...");
1.126 brouard 7683: while (z[0] != 'q') {
7684: /* chdir(path); */
1.154 brouard 7685: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 7686: scanf("%s",z);
7687: /* if (z[0] == 'c') system("./imach"); */
7688: if (z[0] == 'e') {
1.158 brouard 7689: #ifdef __APPLE__
1.152 brouard 7690: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 7691: #elif __linux
7692: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 7693: #else
1.152 brouard 7694: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 7695: #endif
7696: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
7697: system(pplotcmd);
1.126 brouard 7698: }
7699: else if (z[0] == 'g') system(plotcmd);
7700: else if (z[0] == 'q') exit(0);
7701: }
7702: end:
7703: while (z[0] != 'q') {
7704: printf("\nType q for exiting: ");
7705: scanf("%s",z);
7706: }
7707: }
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