Annotation of imach/src/imach.c, revision 1.187
1.187 ! brouard 1: /* $Id: imach.c,v 1.186 2015/04/23 12:01:52 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.187 ! brouard 4: Revision 1.186 2015/04/23 12:01:52 brouard
! 5: Summary: V1*age is working now, version 0.98q1
! 6:
! 7: Some codes had been disabled in order to simplify and Vn*age was
! 8: working in the optimization phase, ie, giving correct MLE parameters,
! 9: but, as usual, outputs were not correct and program core dumped.
! 10:
1.186 brouard 11: Revision 1.185 2015/03/11 13:26:42 brouard
12: Summary: Inclusion of compile and links command line for Intel Compiler
13:
1.185 brouard 14: Revision 1.184 2015/03/11 11:52:39 brouard
15: Summary: Back from Windows 8. Intel Compiler
16:
1.184 brouard 17: Revision 1.183 2015/03/10 20:34:32 brouard
18: Summary: 0.98q0, trying with directest, mnbrak fixed
19:
20: We use directest instead of original Powell test; probably no
21: incidence on the results, but better justifications;
22: We fixed Numerical Recipes mnbrak routine which was wrong and gave
23: wrong results.
24:
1.183 brouard 25: Revision 1.182 2015/02/12 08:19:57 brouard
26: Summary: Trying to keep directest which seems simpler and more general
27: Author: Nicolas Brouard
28:
1.182 brouard 29: Revision 1.181 2015/02/11 23:22:24 brouard
30: Summary: Comments on Powell added
31:
32: Author:
33:
1.181 brouard 34: Revision 1.180 2015/02/11 17:33:45 brouard
35: Summary: Finishing move from main to function (hpijx and prevalence_limit)
36:
1.180 brouard 37: Revision 1.179 2015/01/04 09:57:06 brouard
38: Summary: back to OS/X
39:
1.179 brouard 40: Revision 1.178 2015/01/04 09:35:48 brouard
41: *** empty log message ***
42:
1.178 brouard 43: Revision 1.177 2015/01/03 18:40:56 brouard
44: Summary: Still testing ilc32 on OSX
45:
1.177 brouard 46: Revision 1.176 2015/01/03 16:45:04 brouard
47: *** empty log message ***
48:
1.176 brouard 49: Revision 1.175 2015/01/03 16:33:42 brouard
50: *** empty log message ***
51:
1.175 brouard 52: Revision 1.174 2015/01/03 16:15:49 brouard
53: Summary: Still in cross-compilation
54:
1.174 brouard 55: Revision 1.173 2015/01/03 12:06:26 brouard
56: Summary: trying to detect cross-compilation
57:
1.173 brouard 58: Revision 1.172 2014/12/27 12:07:47 brouard
59: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
60:
1.172 brouard 61: Revision 1.171 2014/12/23 13:26:59 brouard
62: Summary: Back from Visual C
63:
64: Still problem with utsname.h on Windows
65:
1.171 brouard 66: Revision 1.170 2014/12/23 11:17:12 brouard
67: Summary: Cleaning some \%% back to %%
68:
69: The escape was mandatory for a specific compiler (which one?), but too many warnings.
70:
1.170 brouard 71: Revision 1.169 2014/12/22 23:08:31 brouard
72: Summary: 0.98p
73:
74: Outputs some informations on compiler used, OS etc. Testing on different platforms.
75:
1.169 brouard 76: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 77: Summary: update
1.169 brouard 78:
1.168 brouard 79: Revision 1.167 2014/12/22 13:50:56 brouard
80: Summary: Testing uname and compiler version and if compiled 32 or 64
81:
82: Testing on Linux 64
83:
1.167 brouard 84: Revision 1.166 2014/12/22 11:40:47 brouard
85: *** empty log message ***
86:
1.166 brouard 87: Revision 1.165 2014/12/16 11:20:36 brouard
88: Summary: After compiling on Visual C
89:
90: * imach.c (Module): Merging 1.61 to 1.162
91:
1.165 brouard 92: Revision 1.164 2014/12/16 10:52:11 brouard
93: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
94:
95: * imach.c (Module): Merging 1.61 to 1.162
96:
1.164 brouard 97: Revision 1.163 2014/12/16 10:30:11 brouard
98: * imach.c (Module): Merging 1.61 to 1.162
99:
1.163 brouard 100: Revision 1.162 2014/09/25 11:43:39 brouard
101: Summary: temporary backup 0.99!
102:
1.162 brouard 103: Revision 1.1 2014/09/16 11:06:58 brouard
104: Summary: With some code (wrong) for nlopt
105:
106: Author:
107:
108: Revision 1.161 2014/09/15 20:41:41 brouard
109: Summary: Problem with macro SQR on Intel compiler
110:
1.161 brouard 111: Revision 1.160 2014/09/02 09:24:05 brouard
112: *** empty log message ***
113:
1.160 brouard 114: Revision 1.159 2014/09/01 10:34:10 brouard
115: Summary: WIN32
116: Author: Brouard
117:
1.159 brouard 118: Revision 1.158 2014/08/27 17:11:51 brouard
119: *** empty log message ***
120:
1.158 brouard 121: Revision 1.157 2014/08/27 16:26:55 brouard
122: Summary: Preparing windows Visual studio version
123: Author: Brouard
124:
125: In order to compile on Visual studio, time.h is now correct and time_t
126: and tm struct should be used. difftime should be used but sometimes I
127: just make the differences in raw time format (time(&now).
128: Trying to suppress #ifdef LINUX
129: Add xdg-open for __linux in order to open default browser.
130:
1.157 brouard 131: Revision 1.156 2014/08/25 20:10:10 brouard
132: *** empty log message ***
133:
1.156 brouard 134: Revision 1.155 2014/08/25 18:32:34 brouard
135: Summary: New compile, minor changes
136: Author: Brouard
137:
1.155 brouard 138: Revision 1.154 2014/06/20 17:32:08 brouard
139: Summary: Outputs now all graphs of convergence to period prevalence
140:
1.154 brouard 141: Revision 1.153 2014/06/20 16:45:46 brouard
142: Summary: If 3 live state, convergence to period prevalence on same graph
143: Author: Brouard
144:
1.153 brouard 145: Revision 1.152 2014/06/18 17:54:09 brouard
146: Summary: open browser, use gnuplot on same dir than imach if not found in the path
147:
1.152 brouard 148: Revision 1.151 2014/06/18 16:43:30 brouard
149: *** empty log message ***
150:
1.151 brouard 151: Revision 1.150 2014/06/18 16:42:35 brouard
152: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
153: Author: brouard
154:
1.150 brouard 155: Revision 1.149 2014/06/18 15:51:14 brouard
156: Summary: Some fixes in parameter files errors
157: Author: Nicolas Brouard
158:
1.149 brouard 159: Revision 1.148 2014/06/17 17:38:48 brouard
160: Summary: Nothing new
161: Author: Brouard
162:
163: Just a new packaging for OS/X version 0.98nS
164:
1.148 brouard 165: Revision 1.147 2014/06/16 10:33:11 brouard
166: *** empty log message ***
167:
1.147 brouard 168: Revision 1.146 2014/06/16 10:20:28 brouard
169: Summary: Merge
170: Author: Brouard
171:
172: Merge, before building revised version.
173:
1.146 brouard 174: Revision 1.145 2014/06/10 21:23:15 brouard
175: Summary: Debugging with valgrind
176: Author: Nicolas Brouard
177:
178: Lot of changes in order to output the results with some covariates
179: After the Edimburgh REVES conference 2014, it seems mandatory to
180: improve the code.
181: No more memory valgrind error but a lot has to be done in order to
182: continue the work of splitting the code into subroutines.
183: Also, decodemodel has been improved. Tricode is still not
184: optimal. nbcode should be improved. Documentation has been added in
185: the source code.
186:
1.144 brouard 187: Revision 1.143 2014/01/26 09:45:38 brouard
188: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
189:
190: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
191: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
192:
1.143 brouard 193: Revision 1.142 2014/01/26 03:57:36 brouard
194: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
195:
196: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
197:
1.142 brouard 198: Revision 1.141 2014/01/26 02:42:01 brouard
199: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
200:
1.141 brouard 201: Revision 1.140 2011/09/02 10:37:54 brouard
202: Summary: times.h is ok with mingw32 now.
203:
1.140 brouard 204: Revision 1.139 2010/06/14 07:50:17 brouard
205: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
206: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
207:
1.139 brouard 208: Revision 1.138 2010/04/30 18:19:40 brouard
209: *** empty log message ***
210:
1.138 brouard 211: Revision 1.137 2010/04/29 18:11:38 brouard
212: (Module): Checking covariates for more complex models
213: than V1+V2. A lot of change to be done. Unstable.
214:
1.137 brouard 215: Revision 1.136 2010/04/26 20:30:53 brouard
216: (Module): merging some libgsl code. Fixing computation
217: of likelione (using inter/intrapolation if mle = 0) in order to
218: get same likelihood as if mle=1.
219: Some cleaning of code and comments added.
220:
1.136 brouard 221: Revision 1.135 2009/10/29 15:33:14 brouard
222: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
223:
1.135 brouard 224: Revision 1.134 2009/10/29 13:18:53 brouard
225: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
226:
1.134 brouard 227: Revision 1.133 2009/07/06 10:21:25 brouard
228: just nforces
229:
1.133 brouard 230: Revision 1.132 2009/07/06 08:22:05 brouard
231: Many tings
232:
1.132 brouard 233: Revision 1.131 2009/06/20 16:22:47 brouard
234: Some dimensions resccaled
235:
1.131 brouard 236: Revision 1.130 2009/05/26 06:44:34 brouard
237: (Module): Max Covariate is now set to 20 instead of 8. A
238: lot of cleaning with variables initialized to 0. Trying to make
239: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
240:
1.130 brouard 241: Revision 1.129 2007/08/31 13:49:27 lievre
242: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
243:
1.129 lievre 244: Revision 1.128 2006/06/30 13:02:05 brouard
245: (Module): Clarifications on computing e.j
246:
1.128 brouard 247: Revision 1.127 2006/04/28 18:11:50 brouard
248: (Module): Yes the sum of survivors was wrong since
249: imach-114 because nhstepm was no more computed in the age
250: loop. Now we define nhstepma in the age loop.
251: (Module): In order to speed up (in case of numerous covariates) we
252: compute health expectancies (without variances) in a first step
253: and then all the health expectancies with variances or standard
254: deviation (needs data from the Hessian matrices) which slows the
255: computation.
256: In the future we should be able to stop the program is only health
257: expectancies and graph are needed without standard deviations.
258:
1.127 brouard 259: Revision 1.126 2006/04/28 17:23:28 brouard
260: (Module): Yes the sum of survivors was wrong since
261: imach-114 because nhstepm was no more computed in the age
262: loop. Now we define nhstepma in the age loop.
263: Version 0.98h
264:
1.126 brouard 265: Revision 1.125 2006/04/04 15:20:31 lievre
266: Errors in calculation of health expectancies. Age was not initialized.
267: Forecasting file added.
268:
269: Revision 1.124 2006/03/22 17:13:53 lievre
270: Parameters are printed with %lf instead of %f (more numbers after the comma).
271: The log-likelihood is printed in the log file
272:
273: Revision 1.123 2006/03/20 10:52:43 brouard
274: * imach.c (Module): <title> changed, corresponds to .htm file
275: name. <head> headers where missing.
276:
277: * imach.c (Module): Weights can have a decimal point as for
278: English (a comma might work with a correct LC_NUMERIC environment,
279: otherwise the weight is truncated).
280: Modification of warning when the covariates values are not 0 or
281: 1.
282: Version 0.98g
283:
284: Revision 1.122 2006/03/20 09:45:41 brouard
285: (Module): Weights can have a decimal point as for
286: English (a comma might work with a correct LC_NUMERIC environment,
287: otherwise the weight is truncated).
288: Modification of warning when the covariates values are not 0 or
289: 1.
290: Version 0.98g
291:
292: Revision 1.121 2006/03/16 17:45:01 lievre
293: * imach.c (Module): Comments concerning covariates added
294:
295: * imach.c (Module): refinements in the computation of lli if
296: status=-2 in order to have more reliable computation if stepm is
297: not 1 month. Version 0.98f
298:
299: Revision 1.120 2006/03/16 15:10:38 lievre
300: (Module): refinements in the computation of lli if
301: status=-2 in order to have more reliable computation if stepm is
302: not 1 month. Version 0.98f
303:
304: Revision 1.119 2006/03/15 17:42:26 brouard
305: (Module): Bug if status = -2, the loglikelihood was
306: computed as likelihood omitting the logarithm. Version O.98e
307:
308: Revision 1.118 2006/03/14 18:20:07 brouard
309: (Module): varevsij Comments added explaining the second
310: table of variances if popbased=1 .
311: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
312: (Module): Function pstamp added
313: (Module): Version 0.98d
314:
315: Revision 1.117 2006/03/14 17:16:22 brouard
316: (Module): varevsij Comments added explaining the second
317: table of variances if popbased=1 .
318: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
319: (Module): Function pstamp added
320: (Module): Version 0.98d
321:
322: Revision 1.116 2006/03/06 10:29:27 brouard
323: (Module): Variance-covariance wrong links and
324: varian-covariance of ej. is needed (Saito).
325:
326: Revision 1.115 2006/02/27 12:17:45 brouard
327: (Module): One freematrix added in mlikeli! 0.98c
328:
329: Revision 1.114 2006/02/26 12:57:58 brouard
330: (Module): Some improvements in processing parameter
331: filename with strsep.
332:
333: Revision 1.113 2006/02/24 14:20:24 brouard
334: (Module): Memory leaks checks with valgrind and:
335: datafile was not closed, some imatrix were not freed and on matrix
336: allocation too.
337:
338: Revision 1.112 2006/01/30 09:55:26 brouard
339: (Module): Back to gnuplot.exe instead of wgnuplot.exe
340:
341: Revision 1.111 2006/01/25 20:38:18 brouard
342: (Module): Lots of cleaning and bugs added (Gompertz)
343: (Module): Comments can be added in data file. Missing date values
344: can be a simple dot '.'.
345:
346: Revision 1.110 2006/01/25 00:51:50 brouard
347: (Module): Lots of cleaning and bugs added (Gompertz)
348:
349: Revision 1.109 2006/01/24 19:37:15 brouard
350: (Module): Comments (lines starting with a #) are allowed in data.
351:
352: Revision 1.108 2006/01/19 18:05:42 lievre
353: Gnuplot problem appeared...
354: To be fixed
355:
356: Revision 1.107 2006/01/19 16:20:37 brouard
357: Test existence of gnuplot in imach path
358:
359: Revision 1.106 2006/01/19 13:24:36 brouard
360: Some cleaning and links added in html output
361:
362: Revision 1.105 2006/01/05 20:23:19 lievre
363: *** empty log message ***
364:
365: Revision 1.104 2005/09/30 16:11:43 lievre
366: (Module): sump fixed, loop imx fixed, and simplifications.
367: (Module): If the status is missing at the last wave but we know
368: that the person is alive, then we can code his/her status as -2
369: (instead of missing=-1 in earlier versions) and his/her
370: contributions to the likelihood is 1 - Prob of dying from last
371: health status (= 1-p13= p11+p12 in the easiest case of somebody in
372: the healthy state at last known wave). Version is 0.98
373:
374: Revision 1.103 2005/09/30 15:54:49 lievre
375: (Module): sump fixed, loop imx fixed, and simplifications.
376:
377: Revision 1.102 2004/09/15 17:31:30 brouard
378: Add the possibility to read data file including tab characters.
379:
380: Revision 1.101 2004/09/15 10:38:38 brouard
381: Fix on curr_time
382:
383: Revision 1.100 2004/07/12 18:29:06 brouard
384: Add version for Mac OS X. Just define UNIX in Makefile
385:
386: Revision 1.99 2004/06/05 08:57:40 brouard
387: *** empty log message ***
388:
389: Revision 1.98 2004/05/16 15:05:56 brouard
390: New version 0.97 . First attempt to estimate force of mortality
391: directly from the data i.e. without the need of knowing the health
392: state at each age, but using a Gompertz model: log u =a + b*age .
393: This is the basic analysis of mortality and should be done before any
394: other analysis, in order to test if the mortality estimated from the
395: cross-longitudinal survey is different from the mortality estimated
396: from other sources like vital statistic data.
397:
398: The same imach parameter file can be used but the option for mle should be -3.
399:
1.133 brouard 400: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 401: former routines in order to include the new code within the former code.
402:
403: The output is very simple: only an estimate of the intercept and of
404: the slope with 95% confident intervals.
405:
406: Current limitations:
407: A) Even if you enter covariates, i.e. with the
408: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
409: B) There is no computation of Life Expectancy nor Life Table.
410:
411: Revision 1.97 2004/02/20 13:25:42 lievre
412: Version 0.96d. Population forecasting command line is (temporarily)
413: suppressed.
414:
415: Revision 1.96 2003/07/15 15:38:55 brouard
416: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
417: rewritten within the same printf. Workaround: many printfs.
418:
419: Revision 1.95 2003/07/08 07:54:34 brouard
420: * imach.c (Repository):
421: (Repository): Using imachwizard code to output a more meaningful covariance
422: matrix (cov(a12,c31) instead of numbers.
423:
424: Revision 1.94 2003/06/27 13:00:02 brouard
425: Just cleaning
426:
427: Revision 1.93 2003/06/25 16:33:55 brouard
428: (Module): On windows (cygwin) function asctime_r doesn't
429: exist so I changed back to asctime which exists.
430: (Module): Version 0.96b
431:
432: Revision 1.92 2003/06/25 16:30:45 brouard
433: (Module): On windows (cygwin) function asctime_r doesn't
434: exist so I changed back to asctime which exists.
435:
436: Revision 1.91 2003/06/25 15:30:29 brouard
437: * imach.c (Repository): Duplicated warning errors corrected.
438: (Repository): Elapsed time after each iteration is now output. It
439: helps to forecast when convergence will be reached. Elapsed time
440: is stamped in powell. We created a new html file for the graphs
441: concerning matrix of covariance. It has extension -cov.htm.
442:
443: Revision 1.90 2003/06/24 12:34:15 brouard
444: (Module): Some bugs corrected for windows. Also, when
445: mle=-1 a template is output in file "or"mypar.txt with the design
446: of the covariance matrix to be input.
447:
448: Revision 1.89 2003/06/24 12:30:52 brouard
449: (Module): Some bugs corrected for windows. Also, when
450: mle=-1 a template is output in file "or"mypar.txt with the design
451: of the covariance matrix to be input.
452:
453: Revision 1.88 2003/06/23 17:54:56 brouard
454: * 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.
455:
456: Revision 1.87 2003/06/18 12:26:01 brouard
457: Version 0.96
458:
459: Revision 1.86 2003/06/17 20:04:08 brouard
460: (Module): Change position of html and gnuplot routines and added
461: routine fileappend.
462:
463: Revision 1.85 2003/06/17 13:12:43 brouard
464: * imach.c (Repository): Check when date of death was earlier that
465: current date of interview. It may happen when the death was just
466: prior to the death. In this case, dh was negative and likelihood
467: was wrong (infinity). We still send an "Error" but patch by
468: assuming that the date of death was just one stepm after the
469: interview.
470: (Repository): Because some people have very long ID (first column)
471: we changed int to long in num[] and we added a new lvector for
472: memory allocation. But we also truncated to 8 characters (left
473: truncation)
474: (Repository): No more line truncation errors.
475:
476: Revision 1.84 2003/06/13 21:44:43 brouard
477: * imach.c (Repository): Replace "freqsummary" at a correct
478: place. It differs from routine "prevalence" which may be called
479: many times. Probs is memory consuming and must be used with
480: parcimony.
481: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
482:
483: Revision 1.83 2003/06/10 13:39:11 lievre
484: *** empty log message ***
485:
486: Revision 1.82 2003/06/05 15:57:20 brouard
487: Add log in imach.c and fullversion number is now printed.
488:
489: */
490: /*
491: Interpolated Markov Chain
492:
493: Short summary of the programme:
494:
495: This program computes Healthy Life Expectancies from
496: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
497: first survey ("cross") where individuals from different ages are
498: interviewed on their health status or degree of disability (in the
499: case of a health survey which is our main interest) -2- at least a
500: second wave of interviews ("longitudinal") which measure each change
501: (if any) in individual health status. Health expectancies are
502: computed from the time spent in each health state according to a
503: model. More health states you consider, more time is necessary to reach the
504: Maximum Likelihood of the parameters involved in the model. The
505: simplest model is the multinomial logistic model where pij is the
506: probability to be observed in state j at the second wave
507: conditional to be observed in state i at the first wave. Therefore
508: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
509: 'age' is age and 'sex' is a covariate. If you want to have a more
510: complex model than "constant and age", you should modify the program
511: where the markup *Covariates have to be included here again* invites
512: you to do it. More covariates you add, slower the
513: convergence.
514:
515: The advantage of this computer programme, compared to a simple
516: multinomial logistic model, is clear when the delay between waves is not
517: identical for each individual. Also, if a individual missed an
518: intermediate interview, the information is lost, but taken into
519: account using an interpolation or extrapolation.
520:
521: hPijx is the probability to be observed in state i at age x+h
522: conditional to the observed state i at age x. The delay 'h' can be
523: split into an exact number (nh*stepm) of unobserved intermediate
524: states. This elementary transition (by month, quarter,
525: semester or year) is modelled as a multinomial logistic. The hPx
526: matrix is simply the matrix product of nh*stepm elementary matrices
527: and the contribution of each individual to the likelihood is simply
528: hPijx.
529:
530: Also this programme outputs the covariance matrix of the parameters but also
531: of the life expectancies. It also computes the period (stable) prevalence.
532:
1.133 brouard 533: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
534: Institut national d'études démographiques, Paris.
1.126 brouard 535: This software have been partly granted by Euro-REVES, a concerted action
536: from the European Union.
537: It is copyrighted identically to a GNU software product, ie programme and
538: software can be distributed freely for non commercial use. Latest version
539: can be accessed at http://euroreves.ined.fr/imach .
540:
541: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
542: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
543:
544: **********************************************************************/
545: /*
546: main
547: read parameterfile
548: read datafile
549: concatwav
550: freqsummary
551: if (mle >= 1)
552: mlikeli
553: print results files
554: if mle==1
555: computes hessian
556: read end of parameter file: agemin, agemax, bage, fage, estepm
557: begin-prev-date,...
558: open gnuplot file
559: open html file
1.145 brouard 560: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
561: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
562: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
563: freexexit2 possible for memory heap.
564:
565: h Pij x | pij_nom ficrestpij
566: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
567: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
568: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
569:
570: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
571: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
572: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
573: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
574: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
575:
1.126 brouard 576: forecasting if prevfcast==1 prevforecast call prevalence()
577: health expectancies
578: Variance-covariance of DFLE
579: prevalence()
580: movingaverage()
581: varevsij()
582: if popbased==1 varevsij(,popbased)
583: total life expectancies
584: Variance of period (stable) prevalence
585: end
586: */
587:
1.187 ! brouard 588: /* #define DEBUG */
! 589: /* #define DEBUGBRENT */
1.165 brouard 590: #define POWELL /* Instead of NLOPT */
1.186 brouard 591: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
592: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 593:
594: #include <math.h>
595: #include <stdio.h>
596: #include <stdlib.h>
597: #include <string.h>
1.159 brouard 598:
599: #ifdef _WIN32
600: #include <io.h>
1.172 brouard 601: #include <windows.h>
602: #include <tchar.h>
1.159 brouard 603: #else
1.126 brouard 604: #include <unistd.h>
1.159 brouard 605: #endif
1.126 brouard 606:
607: #include <limits.h>
608: #include <sys/types.h>
1.171 brouard 609:
610: #if defined(__GNUC__)
611: #include <sys/utsname.h> /* Doesn't work on Windows */
612: #endif
613:
1.126 brouard 614: #include <sys/stat.h>
615: #include <errno.h>
1.159 brouard 616: /* extern int errno; */
1.126 brouard 617:
1.157 brouard 618: /* #ifdef LINUX */
619: /* #include <time.h> */
620: /* #include "timeval.h" */
621: /* #else */
622: /* #include <sys/time.h> */
623: /* #endif */
624:
1.126 brouard 625: #include <time.h>
626:
1.136 brouard 627: #ifdef GSL
628: #include <gsl/gsl_errno.h>
629: #include <gsl/gsl_multimin.h>
630: #endif
631:
1.167 brouard 632:
1.162 brouard 633: #ifdef NLOPT
634: #include <nlopt.h>
635: typedef struct {
636: double (* function)(double [] );
637: } myfunc_data ;
638: #endif
639:
1.126 brouard 640: /* #include <libintl.h> */
641: /* #define _(String) gettext (String) */
642:
1.141 brouard 643: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 644:
645: #define GNUPLOTPROGRAM "gnuplot"
646: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
647: #define FILENAMELENGTH 132
648:
649: #define GLOCK_ERROR_NOPATH -1 /* empty path */
650: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
651:
1.144 brouard 652: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
653: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 654:
655: #define NINTERVMAX 8
1.144 brouard 656: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
657: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
658: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.145 brouard 659: #define codtabm(h,k) 1 & (h-1) >> (k-1) ;
1.126 brouard 660: #define MAXN 20000
1.144 brouard 661: #define YEARM 12. /**< Number of months per year */
1.126 brouard 662: #define AGESUP 130
663: #define AGEBASE 40
1.164 brouard 664: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 665: #ifdef _WIN32
666: #define DIRSEPARATOR '\\'
667: #define CHARSEPARATOR "\\"
668: #define ODIRSEPARATOR '/'
669: #else
1.126 brouard 670: #define DIRSEPARATOR '/'
671: #define CHARSEPARATOR "/"
672: #define ODIRSEPARATOR '\\'
673: #endif
674:
1.187 ! brouard 675: /* $Id: imach.c,v 1.186 2015/04/23 12:01:52 brouard Exp $ */
1.126 brouard 676: /* $State: Exp $ */
677:
1.186 brouard 678: 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";
1.187 ! brouard 679: char fullversion[]="$Revision: 1.186 $ $Date: 2015/04/23 12:01:52 $";
1.126 brouard 680: char strstart[80];
681: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 682: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 ! brouard 683: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 684: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
685: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
686: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
687: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
688: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
689: int cptcovprodnoage=0; /**< Number of covariate products without age */
690: int cptcoveff=0; /* Total number of covariates to vary for printing results */
691: int cptcov=0; /* Working variable */
1.126 brouard 692: int npar=NPARMAX;
693: int nlstate=2; /* Number of live states */
694: int ndeath=1; /* Number of dead states */
1.130 brouard 695: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.126 brouard 696: int popbased=0;
697:
698: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 699: int maxwav=0; /* Maxim number of waves */
700: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
701: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
702: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 703: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 704: int mle=1, weightopt=0;
1.126 brouard 705: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
706: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
707: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
708: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 709: int countcallfunc=0; /* Count the number of calls to func */
1.130 brouard 710: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 711: double **matprod2(); /* test */
1.126 brouard 712: double **oldm, **newm, **savm; /* Working pointers to matrices */
713: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.136 brouard 714: /*FILE *fic ; */ /* Used in readdata only */
715: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.126 brouard 716: FILE *ficlog, *ficrespow;
1.130 brouard 717: int globpr=0; /* Global variable for printing or not */
1.126 brouard 718: double fretone; /* Only one call to likelihood */
1.130 brouard 719: long ipmx=0; /* Number of contributions */
1.126 brouard 720: double sw; /* Sum of weights */
721: char filerespow[FILENAMELENGTH];
722: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
723: FILE *ficresilk;
724: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
725: FILE *ficresprobmorprev;
726: FILE *fichtm, *fichtmcov; /* Html File */
727: FILE *ficreseij;
728: char filerese[FILENAMELENGTH];
729: FILE *ficresstdeij;
730: char fileresstde[FILENAMELENGTH];
731: FILE *ficrescveij;
732: char filerescve[FILENAMELENGTH];
733: FILE *ficresvij;
734: char fileresv[FILENAMELENGTH];
735: FILE *ficresvpl;
736: char fileresvpl[FILENAMELENGTH];
737: char title[MAXLINE];
738: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
739: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
740: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
741: char command[FILENAMELENGTH];
742: int outcmd=0;
743:
744: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
745:
746: char filelog[FILENAMELENGTH]; /* Log file */
747: char filerest[FILENAMELENGTH];
748: char fileregp[FILENAMELENGTH];
749: char popfile[FILENAMELENGTH];
750:
751: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
752:
1.157 brouard 753: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
754: /* struct timezone tzp; */
755: /* extern int gettimeofday(); */
756: struct tm tml, *gmtime(), *localtime();
757:
758: extern time_t time();
759:
760: struct tm start_time, end_time, curr_time, last_time, forecast_time;
761: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
762: struct tm tm;
763:
1.126 brouard 764: char strcurr[80], strfor[80];
765:
766: char *endptr;
767: long lval;
768: double dval;
769:
770: #define NR_END 1
771: #define FREE_ARG char*
772: #define FTOL 1.0e-10
773:
774: #define NRANSI
775: #define ITMAX 200
776:
777: #define TOL 2.0e-4
778:
779: #define CGOLD 0.3819660
780: #define ZEPS 1.0e-10
781: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
782:
783: #define GOLD 1.618034
784: #define GLIMIT 100.0
785: #define TINY 1.0e-20
786:
787: static double maxarg1,maxarg2;
788: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
789: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
790:
791: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
792: #define rint(a) floor(a+0.5)
1.166 brouard 793: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 794: #define mytinydouble 1.0e-16
1.166 brouard 795: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
796: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
797: /* static double dsqrarg; */
798: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 799: static double sqrarg;
800: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
801: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
802: int agegomp= AGEGOMP;
803:
804: int imx;
805: int stepm=1;
806: /* Stepm, step in month: minimum step interpolation*/
807:
808: int estepm;
809: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
810:
811: int m,nb;
812: long *num;
813: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
814: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
815: double **pmmij, ***probs;
816: double *ageexmed,*agecens;
817: double dateintmean=0;
818:
819: double *weight;
820: int **s; /* Status */
1.141 brouard 821: double *agedc;
1.145 brouard 822: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 823: * covar=matrix(0,NCOVMAX,1,n);
1.187 ! brouard 824: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.141 brouard 825: double idx;
826: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.145 brouard 827: int *Ndum; /** Freq of modality (tricode */
1.141 brouard 828: int **codtab; /**< codtab=imatrix(1,100,1,10); */
829: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.126 brouard 830: double *lsurv, *lpop, *tpop;
831:
1.143 brouard 832: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
833: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 834:
835: /**************** split *************************/
836: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
837: {
838: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
839: the name of the file (name), its extension only (ext) and its first part of the name (finame)
840: */
841: char *ss; /* pointer */
1.186 brouard 842: int l1=0, l2=0; /* length counters */
1.126 brouard 843:
844: l1 = strlen(path ); /* length of path */
845: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
846: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
847: if ( ss == NULL ) { /* no directory, so determine current directory */
848: strcpy( name, path ); /* we got the fullname name because no directory */
849: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
850: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
851: /* get current working directory */
852: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 853: #ifdef WIN32
854: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
855: #else
856: if (getcwd(dirc, FILENAME_MAX) == NULL) {
857: #endif
1.126 brouard 858: return( GLOCK_ERROR_GETCWD );
859: }
860: /* got dirc from getcwd*/
861: printf(" DIRC = %s \n",dirc);
862: } else { /* strip direcotry from path */
863: ss++; /* after this, the filename */
864: l2 = strlen( ss ); /* length of filename */
865: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
866: strcpy( name, ss ); /* save file name */
867: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 868: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 869: printf(" DIRC2 = %s \n",dirc);
870: }
871: /* We add a separator at the end of dirc if not exists */
872: l1 = strlen( dirc ); /* length of directory */
873: if( dirc[l1-1] != DIRSEPARATOR ){
874: dirc[l1] = DIRSEPARATOR;
875: dirc[l1+1] = 0;
876: printf(" DIRC3 = %s \n",dirc);
877: }
878: ss = strrchr( name, '.' ); /* find last / */
879: if (ss >0){
880: ss++;
881: strcpy(ext,ss); /* save extension */
882: l1= strlen( name);
883: l2= strlen(ss)+1;
884: strncpy( finame, name, l1-l2);
885: finame[l1-l2]= 0;
886: }
887:
888: return( 0 ); /* we're done */
889: }
890:
891:
892: /******************************************/
893:
894: void replace_back_to_slash(char *s, char*t)
895: {
896: int i;
897: int lg=0;
898: i=0;
899: lg=strlen(t);
900: for(i=0; i<= lg; i++) {
901: (s[i] = t[i]);
902: if (t[i]== '\\') s[i]='/';
903: }
904: }
905:
1.132 brouard 906: char *trimbb(char *out, char *in)
1.137 brouard 907: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 908: char *s;
909: s=out;
910: while (*in != '\0'){
1.137 brouard 911: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 912: in++;
913: }
914: *out++ = *in++;
915: }
916: *out='\0';
917: return s;
918: }
919:
1.187 ! brouard 920: /* char *substrchaine(char *out, char *in, char *chain) */
! 921: /* { */
! 922: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
! 923: /* char *s, *t; */
! 924: /* t=in;s=out; */
! 925: /* while ((*in != *chain) && (*in != '\0')){ */
! 926: /* *out++ = *in++; */
! 927: /* } */
! 928:
! 929: /* /\* *in matches *chain *\/ */
! 930: /* while ((*in++ == *chain++) && (*in != '\0')){ */
! 931: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
! 932: /* } */
! 933: /* in--; chain--; */
! 934: /* while ( (*in != '\0')){ */
! 935: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
! 936: /* *out++ = *in++; */
! 937: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
! 938: /* } */
! 939: /* *out='\0'; */
! 940: /* out=s; */
! 941: /* return out; */
! 942: /* } */
! 943: char *substrchaine(char *out, char *in, char *chain)
! 944: {
! 945: /* Substract chain 'chain' from 'in', return and output 'out' */
! 946: /* in="V1+V1*age+age*age+V2", chain="age*age" */
! 947:
! 948: char *strloc;
! 949:
! 950: strcpy (out, in);
! 951: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
! 952: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
! 953: if(strloc != NULL){
! 954: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
! 955: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
! 956: /* strcpy (strloc, strloc +strlen(chain));*/
! 957: }
! 958: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
! 959: return out;
! 960: }
! 961:
! 962:
1.145 brouard 963: char *cutl(char *blocc, char *alocc, char *in, char occ)
964: {
1.187 ! brouard 965: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 966: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 ! brouard 967: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 968: If occ is not found blocc is null and alocc is equal to in. Returns blocc
969: */
1.160 brouard 970: char *s, *t;
1.145 brouard 971: t=in;s=in;
972: while ((*in != occ) && (*in != '\0')){
973: *alocc++ = *in++;
974: }
975: if( *in == occ){
976: *(alocc)='\0';
977: s=++in;
978: }
979:
980: if (s == t) {/* occ not found */
981: *(alocc-(in-s))='\0';
982: in=s;
983: }
984: while ( *in != '\0'){
985: *blocc++ = *in++;
986: }
987:
988: *blocc='\0';
989: return t;
990: }
1.137 brouard 991: char *cutv(char *blocc, char *alocc, char *in, char occ)
992: {
1.187 ! brouard 993: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 994: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
995: gives blocc="abcdef2ghi" and alocc="j".
996: If occ is not found blocc is null and alocc is equal to in. Returns alocc
997: */
998: char *s, *t;
999: t=in;s=in;
1000: while (*in != '\0'){
1001: while( *in == occ){
1002: *blocc++ = *in++;
1003: s=in;
1004: }
1005: *blocc++ = *in++;
1006: }
1007: if (s == t) /* occ not found */
1008: *(blocc-(in-s))='\0';
1009: else
1010: *(blocc-(in-s)-1)='\0';
1011: in=s;
1012: while ( *in != '\0'){
1013: *alocc++ = *in++;
1014: }
1015:
1016: *alocc='\0';
1017: return s;
1018: }
1019:
1.126 brouard 1020: int nbocc(char *s, char occ)
1021: {
1022: int i,j=0;
1023: int lg=20;
1024: i=0;
1025: lg=strlen(s);
1026: for(i=0; i<= lg; i++) {
1027: if (s[i] == occ ) j++;
1028: }
1029: return j;
1030: }
1031:
1.137 brouard 1032: /* void cutv(char *u,char *v, char*t, char occ) */
1033: /* { */
1034: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1035: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1036: /* gives u="abcdef2ghi" and v="j" *\/ */
1037: /* int i,lg,j,p=0; */
1038: /* i=0; */
1039: /* lg=strlen(t); */
1040: /* for(j=0; j<=lg-1; j++) { */
1041: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1042: /* } */
1.126 brouard 1043:
1.137 brouard 1044: /* for(j=0; j<p; j++) { */
1045: /* (u[j] = t[j]); */
1046: /* } */
1047: /* u[p]='\0'; */
1.126 brouard 1048:
1.137 brouard 1049: /* for(j=0; j<= lg; j++) { */
1050: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1051: /* } */
1052: /* } */
1.126 brouard 1053:
1.160 brouard 1054: #ifdef _WIN32
1055: char * strsep(char **pp, const char *delim)
1056: {
1057: char *p, *q;
1058:
1059: if ((p = *pp) == NULL)
1060: return 0;
1061: if ((q = strpbrk (p, delim)) != NULL)
1062: {
1063: *pp = q + 1;
1064: *q = '\0';
1065: }
1066: else
1067: *pp = 0;
1068: return p;
1069: }
1070: #endif
1071:
1.126 brouard 1072: /********************** nrerror ********************/
1073:
1074: void nrerror(char error_text[])
1075: {
1076: fprintf(stderr,"ERREUR ...\n");
1077: fprintf(stderr,"%s\n",error_text);
1078: exit(EXIT_FAILURE);
1079: }
1080: /*********************** vector *******************/
1081: double *vector(int nl, int nh)
1082: {
1083: double *v;
1084: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1085: if (!v) nrerror("allocation failure in vector");
1086: return v-nl+NR_END;
1087: }
1088:
1089: /************************ free vector ******************/
1090: void free_vector(double*v, int nl, int nh)
1091: {
1092: free((FREE_ARG)(v+nl-NR_END));
1093: }
1094:
1095: /************************ivector *******************************/
1096: int *ivector(long nl,long nh)
1097: {
1098: int *v;
1099: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1100: if (!v) nrerror("allocation failure in ivector");
1101: return v-nl+NR_END;
1102: }
1103:
1104: /******************free ivector **************************/
1105: void free_ivector(int *v, long nl, long nh)
1106: {
1107: free((FREE_ARG)(v+nl-NR_END));
1108: }
1109:
1110: /************************lvector *******************************/
1111: long *lvector(long nl,long nh)
1112: {
1113: long *v;
1114: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1115: if (!v) nrerror("allocation failure in ivector");
1116: return v-nl+NR_END;
1117: }
1118:
1119: /******************free lvector **************************/
1120: void free_lvector(long *v, long nl, long nh)
1121: {
1122: free((FREE_ARG)(v+nl-NR_END));
1123: }
1124:
1125: /******************* imatrix *******************************/
1126: int **imatrix(long nrl, long nrh, long ncl, long nch)
1127: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1128: {
1129: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1130: int **m;
1131:
1132: /* allocate pointers to rows */
1133: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1134: if (!m) nrerror("allocation failure 1 in matrix()");
1135: m += NR_END;
1136: m -= nrl;
1137:
1138:
1139: /* allocate rows and set pointers to them */
1140: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1141: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1142: m[nrl] += NR_END;
1143: m[nrl] -= ncl;
1144:
1145: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1146:
1147: /* return pointer to array of pointers to rows */
1148: return m;
1149: }
1150:
1151: /****************** free_imatrix *************************/
1152: void free_imatrix(m,nrl,nrh,ncl,nch)
1153: int **m;
1154: long nch,ncl,nrh,nrl;
1155: /* free an int matrix allocated by imatrix() */
1156: {
1157: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1158: free((FREE_ARG) (m+nrl-NR_END));
1159: }
1160:
1161: /******************* matrix *******************************/
1162: double **matrix(long nrl, long nrh, long ncl, long nch)
1163: {
1164: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1165: double **m;
1166:
1167: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1168: if (!m) nrerror("allocation failure 1 in matrix()");
1169: m += NR_END;
1170: m -= nrl;
1171:
1172: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1173: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1174: m[nrl] += NR_END;
1175: m[nrl] -= ncl;
1176:
1177: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1178: return m;
1.145 brouard 1179: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1180: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1181: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1182: */
1183: }
1184:
1185: /*************************free matrix ************************/
1186: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1187: {
1188: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1189: free((FREE_ARG)(m+nrl-NR_END));
1190: }
1191:
1192: /******************* ma3x *******************************/
1193: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1194: {
1195: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1196: double ***m;
1197:
1198: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1199: if (!m) nrerror("allocation failure 1 in matrix()");
1200: m += NR_END;
1201: m -= nrl;
1202:
1203: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1204: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1205: m[nrl] += NR_END;
1206: m[nrl] -= ncl;
1207:
1208: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1209:
1210: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1211: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1212: m[nrl][ncl] += NR_END;
1213: m[nrl][ncl] -= nll;
1214: for (j=ncl+1; j<=nch; j++)
1215: m[nrl][j]=m[nrl][j-1]+nlay;
1216:
1217: for (i=nrl+1; i<=nrh; i++) {
1218: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1219: for (j=ncl+1; j<=nch; j++)
1220: m[i][j]=m[i][j-1]+nlay;
1221: }
1222: return m;
1223: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1224: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1225: */
1226: }
1227:
1228: /*************************free ma3x ************************/
1229: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1230: {
1231: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1232: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1233: free((FREE_ARG)(m+nrl-NR_END));
1234: }
1235:
1236: /*************** function subdirf ***********/
1237: char *subdirf(char fileres[])
1238: {
1239: /* Caution optionfilefiname is hidden */
1240: strcpy(tmpout,optionfilefiname);
1241: strcat(tmpout,"/"); /* Add to the right */
1242: strcat(tmpout,fileres);
1243: return tmpout;
1244: }
1245:
1246: /*************** function subdirf2 ***********/
1247: char *subdirf2(char fileres[], char *preop)
1248: {
1249:
1250: /* Caution optionfilefiname is hidden */
1251: strcpy(tmpout,optionfilefiname);
1252: strcat(tmpout,"/");
1253: strcat(tmpout,preop);
1254: strcat(tmpout,fileres);
1255: return tmpout;
1256: }
1257:
1258: /*************** function subdirf3 ***********/
1259: char *subdirf3(char fileres[], char *preop, char *preop2)
1260: {
1261:
1262: /* Caution optionfilefiname is hidden */
1263: strcpy(tmpout,optionfilefiname);
1264: strcat(tmpout,"/");
1265: strcat(tmpout,preop);
1266: strcat(tmpout,preop2);
1267: strcat(tmpout,fileres);
1268: return tmpout;
1269: }
1270:
1.162 brouard 1271: char *asc_diff_time(long time_sec, char ascdiff[])
1272: {
1273: long sec_left, days, hours, minutes;
1274: days = (time_sec) / (60*60*24);
1275: sec_left = (time_sec) % (60*60*24);
1276: hours = (sec_left) / (60*60) ;
1277: sec_left = (sec_left) %(60*60);
1278: minutes = (sec_left) /60;
1279: sec_left = (sec_left) % (60);
1280: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1281: return ascdiff;
1282: }
1283:
1.126 brouard 1284: /***************** f1dim *************************/
1285: extern int ncom;
1286: extern double *pcom,*xicom;
1287: extern double (*nrfunc)(double []);
1288:
1289: double f1dim(double x)
1290: {
1291: int j;
1292: double f;
1293: double *xt;
1294:
1295: xt=vector(1,ncom);
1296: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1297: f=(*nrfunc)(xt);
1298: free_vector(xt,1,ncom);
1299: return f;
1300: }
1301:
1302: /*****************brent *************************/
1303: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 ! brouard 1304: {
! 1305: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
! 1306: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
! 1307: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
! 1308: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
! 1309: * returned function value.
! 1310: */
1.126 brouard 1311: int iter;
1312: double a,b,d,etemp;
1.159 brouard 1313: double fu=0,fv,fw,fx;
1.164 brouard 1314: double ftemp=0.;
1.126 brouard 1315: double p,q,r,tol1,tol2,u,v,w,x,xm;
1316: double e=0.0;
1317:
1318: a=(ax < cx ? ax : cx);
1319: b=(ax > cx ? ax : cx);
1320: x=w=v=bx;
1321: fw=fv=fx=(*f)(x);
1322: for (iter=1;iter<=ITMAX;iter++) {
1323: xm=0.5*(a+b);
1324: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1325: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1326: printf(".");fflush(stdout);
1327: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1328: #ifdef DEBUGBRENT
1.126 brouard 1329: 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);
1330: 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);
1331: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1332: #endif
1333: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1334: *xmin=x;
1335: return fx;
1336: }
1337: ftemp=fu;
1338: if (fabs(e) > tol1) {
1339: r=(x-w)*(fx-fv);
1340: q=(x-v)*(fx-fw);
1341: p=(x-v)*q-(x-w)*r;
1342: q=2.0*(q-r);
1343: if (q > 0.0) p = -p;
1344: q=fabs(q);
1345: etemp=e;
1346: e=d;
1347: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1348: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1349: else {
1350: d=p/q;
1351: u=x+d;
1352: if (u-a < tol2 || b-u < tol2)
1353: d=SIGN(tol1,xm-x);
1354: }
1355: } else {
1356: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1357: }
1358: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1359: fu=(*f)(u);
1360: if (fu <= fx) {
1361: if (u >= x) a=x; else b=x;
1362: SHFT(v,w,x,u)
1.183 brouard 1363: SHFT(fv,fw,fx,fu)
1364: } else {
1365: if (u < x) a=u; else b=u;
1366: if (fu <= fw || w == x) {
1367: v=w;
1368: w=u;
1369: fv=fw;
1370: fw=fu;
1371: } else if (fu <= fv || v == x || v == w) {
1372: v=u;
1373: fv=fu;
1374: }
1375: }
1.126 brouard 1376: }
1377: nrerror("Too many iterations in brent");
1378: *xmin=x;
1379: return fx;
1380: }
1381:
1382: /****************** mnbrak ***********************/
1383:
1384: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1385: double (*func)(double))
1.183 brouard 1386: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1387: the downhill direction (defined by the function as evaluated at the initial points) and returns
1388: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1389: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1390: */
1.126 brouard 1391: double ulim,u,r,q, dum;
1392: double fu;
1.187 ! brouard 1393:
! 1394: double scale=10.;
! 1395: int iterscale=0;
! 1396:
! 1397: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
! 1398: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
! 1399:
! 1400:
! 1401: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
! 1402: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
! 1403: /* *bx = *ax - (*ax - *bx)/scale; */
! 1404: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
! 1405: /* } */
! 1406:
1.126 brouard 1407: if (*fb > *fa) {
1408: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1409: SHFT(dum,*fb,*fa,dum)
1410: }
1.126 brouard 1411: *cx=(*bx)+GOLD*(*bx-*ax);
1412: *fc=(*func)(*cx);
1.183 brouard 1413: #ifdef DEBUG
1414: printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1415: fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1416: #endif
1417: while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
1.126 brouard 1418: r=(*bx-*ax)*(*fb-*fc);
1419: q=(*bx-*cx)*(*fb-*fa);
1420: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 1421: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1422: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1423: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 1424: fu=(*func)(u);
1.163 brouard 1425: #ifdef DEBUG
1426: /* f(x)=A(x-u)**2+f(u) */
1427: double A, fparabu;
1428: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1429: fparabu= *fa - A*(*ax-u)*(*ax-u);
1430: 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);
1431: 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 1432: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1433: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1434: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1435: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 1436: #endif
1.184 brouard 1437: #ifdef MNBRAKORIGINAL
1.183 brouard 1438: #else
1439: if (fu > *fc) {
1440: #ifdef DEBUG
1441: printf("mnbrak4 fu > fc \n");
1442: fprintf(ficlog, "mnbrak4 fu > fc\n");
1443: #endif
1444: /* 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 *\/ */
1445: /* SHFT(*fa,*fc,fu,*fc) /\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\/ */
1446: dum=u; /* Shifting c and u */
1447: u = *cx;
1448: *cx = dum;
1449: dum = fu;
1450: fu = *fc;
1451: *fc =dum;
1452: } else { /* end */
1453: #ifdef DEBUG
1454: printf("mnbrak3 fu < fc \n");
1455: fprintf(ficlog, "mnbrak3 fu < fc\n");
1456: #endif
1457: dum=u; /* Shifting c and u */
1458: u = *cx;
1459: *cx = dum;
1460: dum = fu;
1461: fu = *fc;
1462: *fc =dum;
1463: }
1464: #endif
1.162 brouard 1465: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 1466: #ifdef DEBUG
1467: printf("mnbrak2 u after c but before ulim\n");
1468: fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
1469: #endif
1.126 brouard 1470: fu=(*func)(u);
1471: if (fu < *fc) {
1.183 brouard 1472: #ifdef DEBUG
1473: printf("mnbrak2 u after c but before ulim AND fu < fc\n");
1474: fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
1475: #endif
1.126 brouard 1476: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1.183 brouard 1477: SHFT(*fb,*fc,fu,(*func)(u))
1478: }
1.162 brouard 1479: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 1480: #ifdef DEBUG
1481: printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1482: fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1483: #endif
1.126 brouard 1484: u=ulim;
1485: fu=(*func)(u);
1.183 brouard 1486: } else { /* u could be left to b (if r > q parabola has a maximum) */
1487: #ifdef DEBUG
1488: printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1489: fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1490: #endif
1.126 brouard 1491: u=(*cx)+GOLD*(*cx-*bx);
1492: fu=(*func)(u);
1.183 brouard 1493: } /* end tests */
1.126 brouard 1494: SHFT(*ax,*bx,*cx,u)
1.183 brouard 1495: SHFT(*fa,*fb,*fc,fu)
1496: #ifdef DEBUG
1497: 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);
1498: 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);
1499: #endif
1500: } /* 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 1501: }
1502:
1503: /*************** linmin ************************/
1.162 brouard 1504: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1505: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1506: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1507: the value of func at the returned location p . This is actually all accomplished by calling the
1508: routines mnbrak and brent .*/
1.126 brouard 1509: int ncom;
1510: double *pcom,*xicom;
1511: double (*nrfunc)(double []);
1512:
1513: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1514: {
1515: double brent(double ax, double bx, double cx,
1516: double (*f)(double), double tol, double *xmin);
1517: double f1dim(double x);
1518: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1519: double *fc, double (*func)(double));
1520: int j;
1521: double xx,xmin,bx,ax;
1522: double fx,fb,fa;
1.187 ! brouard 1523:
! 1524: double scale=10., axs, xxs, xxss; /* Scale added for infinity */
1.126 brouard 1525:
1526: ncom=n;
1527: pcom=vector(1,n);
1528: xicom=vector(1,n);
1529: nrfunc=func;
1530: for (j=1;j<=n;j++) {
1531: pcom[j]=p[j];
1532: xicom[j]=xi[j];
1533: }
1.187 ! brouard 1534:
! 1535: axs=0.0;
! 1536: xxss=1; /* 1 and using scale */
! 1537: xxs=1;
! 1538: do{
! 1539: ax=0.;
! 1540: xx= xxs;
! 1541: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
! 1542: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
! 1543: /* 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)) */
! 1544: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
! 1545: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
! 1546: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
! 1547: /* 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]]*/
! 1548: if (fx != fx){
! 1549: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
! 1550: 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);
! 1551: }
! 1552: }while(fx != fx);
! 1553:
! 1554: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
! 1555: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
! 1556: /* fmin = f(p[j] + xmin * xi[j]) */
! 1557: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
! 1558: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 1559: #ifdef DEBUG
1560: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1561: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1562: #endif
1.187 ! brouard 1563: printf("linmin end ");
1.126 brouard 1564: for (j=1;j<=n;j++) {
1.187 ! brouard 1565: printf(" before xi[%d]=%12.8f", j,xi[j]);
! 1566: xi[j] *= xmin; /* xi rescaled by xmin: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
! 1567: if(xxs <1.0)
! 1568: 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 );
! 1569: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 1570: }
1.187 ! brouard 1571: printf("\n");
1.126 brouard 1572: free_vector(xicom,1,n);
1573: free_vector(pcom,1,n);
1574: }
1575:
1576:
1577: /*************** powell ************************/
1.162 brouard 1578: /*
1579: Minimization of a function func of n variables. Input consists of an initial starting point
1580: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1581: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1582: such that failure to decrease by more than this amount on one iteration signals doneness. On
1583: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1584: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1585: */
1.126 brouard 1586: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1587: double (*func)(double []))
1588: {
1589: void linmin(double p[], double xi[], int n, double *fret,
1590: double (*func)(double []));
1591: int i,ibig,j;
1592: double del,t,*pt,*ptt,*xit;
1.181 brouard 1593: double directest;
1.126 brouard 1594: double fp,fptt;
1595: double *xits;
1596: int niterf, itmp;
1597:
1598: pt=vector(1,n);
1599: ptt=vector(1,n);
1600: xit=vector(1,n);
1601: xits=vector(1,n);
1602: *fret=(*func)(p);
1603: for (j=1;j<=n;j++) pt[j]=p[j];
1.157 brouard 1604: rcurr_time = time(NULL);
1.126 brouard 1605: for (*iter=1;;++(*iter)) {
1.187 ! brouard 1606: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 1607: ibig=0;
1608: del=0.0;
1.157 brouard 1609: rlast_time=rcurr_time;
1610: /* (void) gettimeofday(&curr_time,&tzp); */
1611: rcurr_time = time(NULL);
1612: curr_time = *localtime(&rcurr_time);
1613: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1614: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1615: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.126 brouard 1616: for (i=1;i<=n;i++) {
1617: printf(" %d %.12f",i, p[i]);
1618: fprintf(ficlog," %d %.12lf",i, p[i]);
1619: fprintf(ficrespow," %.12lf", p[i]);
1620: }
1621: printf("\n");
1622: fprintf(ficlog,"\n");
1623: fprintf(ficrespow,"\n");fflush(ficrespow);
1624: if(*iter <=3){
1.157 brouard 1625: tml = *localtime(&rcurr_time);
1626: strcpy(strcurr,asctime(&tml));
1627: rforecast_time=rcurr_time;
1.126 brouard 1628: itmp = strlen(strcurr);
1629: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1630: strcurr[itmp-1]='\0';
1.162 brouard 1631: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 1632: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 1633: for(niterf=10;niterf<=30;niterf+=10){
1.157 brouard 1634: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1635: forecast_time = *localtime(&rforecast_time);
1636: strcpy(strfor,asctime(&forecast_time));
1.126 brouard 1637: itmp = strlen(strfor);
1638: if(strfor[itmp-1]=='\n')
1639: strfor[itmp-1]='\0';
1.157 brouard 1640: 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);
1641: 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 1642: }
1643: }
1.187 ! brouard 1644: for (i=1;i<=n;i++) { /* For each direction i */
! 1645: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 1646: fptt=(*fret);
1647: #ifdef DEBUG
1.164 brouard 1648: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1649: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 1650: #endif
1.187 ! brouard 1651: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 1652: fprintf(ficlog,"%d",i);fflush(ficlog);
1.187 ! brouard 1653: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input. Outputs are fret(new point p) p is updated and xit rescaled */
1.181 brouard 1654: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions
1655: because that direction will be replaced unless the gain del is small
1656: in comparison with the 'probable' gain, mu^2, with the last average direction.
1657: Unless the n directions are conjugate some gain in the determinant may be obtained
1658: with the new direction.
1659: */
1.126 brouard 1660: del=fabs(fptt-(*fret));
1661: ibig=i;
1662: }
1663: #ifdef DEBUG
1664: printf("%d %.12e",i,(*fret));
1665: fprintf(ficlog,"%d %.12e",i,(*fret));
1666: for (j=1;j<=n;j++) {
1667: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1668: printf(" x(%d)=%.12e",j,xit[j]);
1669: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1670: }
1671: for(j=1;j<=n;j++) {
1.162 brouard 1672: printf(" p(%d)=%.12e",j,p[j]);
1673: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 1674: }
1675: printf("\n");
1676: fprintf(ficlog,"\n");
1677: #endif
1.187 ! brouard 1678: } /* end loop on each direction i */
! 1679: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
! 1680: /* But p and xit have been updated at the end of linmin and do not produce *fret any more! */
! 1681: /* New value of last point Pn is not computed, P(n-1) */
1.182 brouard 1682: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1.126 brouard 1683: #ifdef DEBUG
1684: int k[2],l;
1685: k[0]=1;
1686: k[1]=-1;
1687: printf("Max: %.12e",(*func)(p));
1688: fprintf(ficlog,"Max: %.12e",(*func)(p));
1689: for (j=1;j<=n;j++) {
1690: printf(" %.12e",p[j]);
1691: fprintf(ficlog," %.12e",p[j]);
1692: }
1693: printf("\n");
1694: fprintf(ficlog,"\n");
1695: for(l=0;l<=1;l++) {
1696: for (j=1;j<=n;j++) {
1697: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1698: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1699: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1700: }
1701: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1702: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1703: }
1704: #endif
1705:
1706:
1707: free_vector(xit,1,n);
1708: free_vector(xits,1,n);
1709: free_vector(ptt,1,n);
1710: free_vector(pt,1,n);
1711: return;
1712: }
1713: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1.181 brouard 1714: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 1715: ptt[j]=2.0*p[j]-pt[j];
1716: xit[j]=p[j]-pt[j];
1717: pt[j]=p[j];
1718: }
1.181 brouard 1719: fptt=(*func)(ptt); /* f_3 */
1.161 brouard 1720: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.162 brouard 1721: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 1722: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 1723: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1724: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1725: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.181 brouard 1726: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
1.161 brouard 1727: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.183 brouard 1728: #ifdef NRCORIGINAL
1729: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
1730: #else
1731: 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 1732: t= t- del*SQR(fp-fptt);
1.183 brouard 1733: #endif
1.182 brouard 1734: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
1.161 brouard 1735: #ifdef DEBUG
1.181 brouard 1736: 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);
1737: 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 1738: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1739: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1740: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1741: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1742: 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);
1743: 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);
1744: #endif
1.183 brouard 1745: #ifdef POWELLORIGINAL
1746: if (t < 0.0) { /* Then we use it for new direction */
1747: #else
1.182 brouard 1748: if (directest*t < 0.0) { /* Contradiction between both tests */
1.184 brouard 1749: printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
1.182 brouard 1750: 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 1751: fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
1.182 brouard 1752: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1753: }
1.181 brouard 1754: if (directest < 0.0) { /* Then we use it for new direction */
1755: #endif
1.187 ! brouard 1756: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.126 brouard 1757: for (j=1;j<=n;j++) {
1.181 brouard 1758: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
1759: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
1.126 brouard 1760: }
1.181 brouard 1761: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1762: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1.161 brouard 1763:
1.126 brouard 1764: #ifdef DEBUG
1.164 brouard 1765: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1766: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1.126 brouard 1767: for(j=1;j<=n;j++){
1768: printf(" %.12e",xit[j]);
1769: fprintf(ficlog," %.12e",xit[j]);
1770: }
1771: printf("\n");
1772: fprintf(ficlog,"\n");
1773: #endif
1.162 brouard 1774: } /* end of t negative */
1775: } /* end if (fptt < fp) */
1.126 brouard 1776: }
1777: }
1778:
1779: /**** Prevalence limit (stable or period prevalence) ****************/
1780:
1781: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1782: {
1783: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1784: matrix by transitions matrix until convergence is reached */
1.169 brouard 1785:
1.126 brouard 1786: int i, ii,j,k;
1787: double min, max, maxmin, maxmax,sumnew=0.;
1.145 brouard 1788: /* double **matprod2(); */ /* test */
1.131 brouard 1789: double **out, cov[NCOVMAX+1], **pmij();
1.126 brouard 1790: double **newm;
1791: double agefin, delaymax=50 ; /* Max number of years to converge */
1.169 brouard 1792:
1.126 brouard 1793: for (ii=1;ii<=nlstate+ndeath;ii++)
1794: for (j=1;j<=nlstate+ndeath;j++){
1795: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1796: }
1.169 brouard 1797:
1798: cov[1]=1.;
1799:
1800: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.126 brouard 1801: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1802: newm=savm;
1803: /* Covariates have to be included here again */
1.138 brouard 1804: cov[2]=agefin;
1.187 ! brouard 1805: if(nagesqr==1)
! 1806: cov[3]= agefin*agefin;;
1.138 brouard 1807: for (k=1; k<=cptcovn;k++) {
1.187 ! brouard 1808: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.145 brouard 1809: /*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 1810: }
1.186 brouard 1811: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.187 ! brouard 1812: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]*cov[2];
1.186 brouard 1813: for (k=1; k<=cptcovprod;k++) /* Useless */
1.187 ! brouard 1814: 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 1815:
1816: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1817: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1818: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 1819: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1820: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.142 brouard 1821: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 1822:
1.126 brouard 1823: savm=oldm;
1824: oldm=newm;
1825: maxmax=0.;
1826: for(j=1;j<=nlstate;j++){
1827: min=1.;
1828: max=0.;
1829: for(i=1; i<=nlstate; i++) {
1830: sumnew=0;
1831: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1832: prlim[i][j]= newm[i][j]/(1-sumnew);
1.145 brouard 1833: /*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 1834: max=FMAX(max,prlim[i][j]);
1835: min=FMIN(min,prlim[i][j]);
1836: }
1837: maxmin=max-min;
1838: maxmax=FMAX(maxmax,maxmin);
1.169 brouard 1839: } /* j loop */
1.126 brouard 1840: if(maxmax < ftolpl){
1841: return prlim;
1842: }
1.169 brouard 1843: } /* age loop */
1844: return prlim; /* should not reach here */
1.126 brouard 1845: }
1846:
1847: /*************** transition probabilities ***************/
1848:
1849: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1850: {
1.138 brouard 1851: /* According to parameters values stored in x and the covariate's values stored in cov,
1852: computes the probability to be observed in state j being in state i by appying the
1853: model to the ncovmodel covariates (including constant and age).
1854: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1855: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1856: ncth covariate in the global vector x is given by the formula:
1857: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1858: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1859: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1860: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1861: Outputs ps[i][j] the probability to be observed in j being in j according to
1862: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1863: */
1864: double s1, lnpijopii;
1.126 brouard 1865: /*double t34;*/
1.164 brouard 1866: int i,j, nc, ii, jj;
1.126 brouard 1867:
1868: for(i=1; i<= nlstate; i++){
1869: for(j=1; j<i;j++){
1.138 brouard 1870: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1871: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1872: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1873: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 1874: }
1.138 brouard 1875: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1876: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 1877: }
1878: for(j=i+1; j<=nlstate+ndeath;j++){
1.138 brouard 1879: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1880: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
1881: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
1882: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1.126 brouard 1883: }
1.138 brouard 1884: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1.126 brouard 1885: }
1886: }
1887:
1888: for(i=1; i<= nlstate; i++){
1889: s1=0;
1.131 brouard 1890: for(j=1; j<i; j++){
1.138 brouard 1891: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 1892: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1893: }
1894: for(j=i+1; j<=nlstate+ndeath; j++){
1.138 brouard 1895: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 1896: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1897: }
1.138 brouard 1898: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1.126 brouard 1899: ps[i][i]=1./(s1+1.);
1.138 brouard 1900: /* Computing other pijs */
1.126 brouard 1901: for(j=1; j<i; j++)
1902: ps[i][j]= exp(ps[i][j])*ps[i][i];
1903: for(j=i+1; j<=nlstate+ndeath; j++)
1904: ps[i][j]= exp(ps[i][j])*ps[i][i];
1905: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1906: } /* end i */
1907:
1908: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1909: for(jj=1; jj<= nlstate+ndeath; jj++){
1910: ps[ii][jj]=0;
1911: ps[ii][ii]=1;
1912: }
1913: }
1914:
1.145 brouard 1915:
1916: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1917: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1918: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
1919: /* } */
1920: /* printf("\n "); */
1921: /* } */
1922: /* printf("\n ");printf("%lf ",cov[2]);*/
1923: /*
1.126 brouard 1924: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1925: goto end;*/
1926: return ps;
1927: }
1928:
1929: /**************** Product of 2 matrices ******************/
1930:
1.145 brouard 1931: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 1932: {
1933: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1934: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1935: /* in, b, out are matrice of pointers which should have been initialized
1936: before: only the contents of out is modified. The function returns
1937: a pointer to pointers identical to out */
1.145 brouard 1938: int i, j, k;
1.126 brouard 1939: for(i=nrl; i<= nrh; i++)
1.145 brouard 1940: for(k=ncolol; k<=ncoloh; k++){
1941: out[i][k]=0.;
1942: for(j=ncl; j<=nch; j++)
1943: out[i][k] +=in[i][j]*b[j][k];
1944: }
1.126 brouard 1945: return out;
1946: }
1947:
1948:
1949: /************* Higher Matrix Product ***************/
1950:
1951: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1952: {
1953: /* Computes the transition matrix starting at age 'age' over
1954: 'nhstepm*hstepm*stepm' months (i.e. until
1955: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1956: nhstepm*hstepm matrices.
1957: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1958: (typically every 2 years instead of every month which is too big
1959: for the memory).
1960: Model is determined by parameters x and covariates have to be
1961: included manually here.
1962:
1963: */
1964:
1965: int i, j, d, h, k;
1.131 brouard 1966: double **out, cov[NCOVMAX+1];
1.126 brouard 1967: double **newm;
1.187 ! brouard 1968: double agexact;
1.126 brouard 1969:
1970: /* Hstepm could be zero and should return the unit matrix */
1971: for (i=1;i<=nlstate+ndeath;i++)
1972: for (j=1;j<=nlstate+ndeath;j++){
1973: oldm[i][j]=(i==j ? 1.0 : 0.0);
1974: po[i][j][0]=(i==j ? 1.0 : 0.0);
1975: }
1976: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1977: for(h=1; h <=nhstepm; h++){
1978: for(d=1; d <=hstepm; d++){
1979: newm=savm;
1980: /* Covariates have to be included here again */
1981: cov[1]=1.;
1.187 ! brouard 1982: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
! 1983: cov[2]=agexact;
! 1984: if(nagesqr==1)
! 1985: cov[3]= agexact*agexact;
1.131 brouard 1986: for (k=1; k<=cptcovn;k++)
1.187 ! brouard 1987: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.186 brouard 1988: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
1989: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.187 ! brouard 1990: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
1.145 brouard 1991: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.187 ! brouard 1992: 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 1993:
1994:
1995: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1996: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1997: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1998: pmij(pmmij,cov,ncovmodel,x,nlstate));
1999: savm=oldm;
2000: oldm=newm;
2001: }
2002: for(i=1; i<=nlstate+ndeath; i++)
2003: for(j=1;j<=nlstate+ndeath;j++) {
2004: po[i][j][h]=newm[i][j];
1.128 brouard 2005: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 2006: }
1.128 brouard 2007: /*printf("h=%d ",h);*/
1.126 brouard 2008: } /* end h */
1.128 brouard 2009: /* printf("\n H=%d \n",h); */
1.126 brouard 2010: return po;
2011: }
2012:
1.162 brouard 2013: #ifdef NLOPT
2014: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
2015: double fret;
2016: double *xt;
2017: int j;
2018: myfunc_data *d2 = (myfunc_data *) pd;
2019: /* xt = (p1-1); */
2020: xt=vector(1,n);
2021: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
2022:
2023: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
2024: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
2025: printf("Function = %.12lf ",fret);
2026: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
2027: printf("\n");
2028: free_vector(xt,1,n);
2029: return fret;
2030: }
2031: #endif
1.126 brouard 2032:
2033: /*************** log-likelihood *************/
2034: double func( double *x)
2035: {
2036: int i, ii, j, k, mi, d, kk;
1.131 brouard 2037: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2038: double **out;
2039: double sw; /* Sum of weights */
2040: double lli; /* Individual log likelihood */
2041: int s1, s2;
2042: double bbh, survp;
2043: long ipmx;
1.187 ! brouard 2044: double agexact;
1.126 brouard 2045: /*extern weight */
2046: /* We are differentiating ll according to initial status */
2047: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2048: /*for(i=1;i<imx;i++)
2049: printf(" %d\n",s[4][i]);
2050: */
1.162 brouard 2051:
2052: ++countcallfunc;
2053:
1.126 brouard 2054: cov[1]=1.;
2055:
2056: for(k=1; k<=nlstate; k++) ll[k]=0.;
2057:
2058: if(mle==1){
2059: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.138 brouard 2060: /* Computes the values of the ncovmodel covariates of the model
2061: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
2062: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
2063: to be observed in j being in i according to the model.
2064: */
1.145 brouard 2065: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1.187 ! brouard 2066: cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.145 brouard 2067: }
1.137 brouard 2068: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1.138 brouard 2069: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1.137 brouard 2070: has been calculated etc */
1.126 brouard 2071: for(mi=1; mi<= wav[i]-1; mi++){
2072: for (ii=1;ii<=nlstate+ndeath;ii++)
2073: for (j=1;j<=nlstate+ndeath;j++){
2074: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2075: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2076: }
2077: for(d=0; d<dh[mi][i]; d++){
2078: newm=savm;
1.187 ! brouard 2079: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
! 2080: cov[2]=agexact;
! 2081: if(nagesqr==1)
! 2082: cov[3]= agexact*agexact;
1.126 brouard 2083: for (kk=1; kk<=cptcovage;kk++) {
1.187 ! brouard 2084: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
1.126 brouard 2085: }
2086: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2087: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2088: savm=oldm;
2089: oldm=newm;
2090: } /* end mult */
2091:
2092: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
2093: /* But now since version 0.9 we anticipate for bias at large stepm.
2094: * If stepm is larger than one month (smallest stepm) and if the exact delay
2095: * (in months) between two waves is not a multiple of stepm, we rounded to
2096: * the nearest (and in case of equal distance, to the lowest) interval but now
2097: * we keep into memory the bias bh[mi][i] and also the previous matrix product
2098: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
2099: * probability in order to take into account the bias as a fraction of the way
2100: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
2101: * -stepm/2 to stepm/2 .
2102: * For stepm=1 the results are the same as for previous versions of Imach.
2103: * For stepm > 1 the results are less biased than in previous versions.
2104: */
2105: s1=s[mw[mi][i]][i];
2106: s2=s[mw[mi+1][i]][i];
2107: bbh=(double)bh[mi][i]/(double)stepm;
2108: /* bias bh is positive if real duration
2109: * is higher than the multiple of stepm and negative otherwise.
2110: */
2111: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
2112: if( s2 > nlstate){
2113: /* i.e. if s2 is a death state and if the date of death is known
2114: then the contribution to the likelihood is the probability to
2115: die between last step unit time and current step unit time,
2116: which is also equal to probability to die before dh
2117: minus probability to die before dh-stepm .
2118: In version up to 0.92 likelihood was computed
2119: as if date of death was unknown. Death was treated as any other
2120: health state: the date of the interview describes the actual state
2121: and not the date of a change in health state. The former idea was
2122: to consider that at each interview the state was recorded
2123: (healthy, disable or death) and IMaCh was corrected; but when we
2124: introduced the exact date of death then we should have modified
2125: the contribution of an exact death to the likelihood. This new
2126: contribution is smaller and very dependent of the step unit
2127: stepm. It is no more the probability to die between last interview
2128: and month of death but the probability to survive from last
2129: interview up to one month before death multiplied by the
2130: probability to die within a month. Thanks to Chris
2131: Jackson for correcting this bug. Former versions increased
2132: mortality artificially. The bad side is that we add another loop
2133: which slows down the processing. The difference can be up to 10%
2134: lower mortality.
2135: */
1.183 brouard 2136: /* If, at the beginning of the maximization mostly, the
2137: cumulative probability or probability to be dead is
2138: constant (ie = 1) over time d, the difference is equal to
2139: 0. out[s1][3] = savm[s1][3]: probability, being at state
2140: s1 at precedent wave, to be dead a month before current
2141: wave is equal to probability, being at state s1 at
2142: precedent wave, to be dead at mont of the current
2143: wave. Then the observed probability (that this person died)
2144: is null according to current estimated parameter. In fact,
2145: it should be very low but not zero otherwise the log go to
2146: infinity.
2147: */
2148: /* #ifdef INFINITYORIGINAL */
2149: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2150: /* #else */
2151: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
2152: /* lli=log(mytinydouble); */
2153: /* else */
2154: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2155: /* #endif */
2156: lli=log(out[s1][s2] - savm[s1][s2]);
1.126 brouard 2157:
2158: } else if (s2==-2) {
2159: for (j=1,survp=0. ; j<=nlstate; j++)
2160: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2161: /*survp += out[s1][j]; */
2162: lli= log(survp);
2163: }
2164:
2165: else if (s2==-4) {
2166: for (j=3,survp=0. ; j<=nlstate; j++)
2167: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2168: lli= log(survp);
2169: }
2170:
2171: else if (s2==-5) {
2172: for (j=1,survp=0. ; j<=2; j++)
2173: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2174: lli= log(survp);
2175: }
2176:
2177: else{
2178: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2179: /* 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 */
2180: }
2181: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
2182: /*if(lli ==000.0)*/
2183: /*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); */
2184: ipmx +=1;
2185: sw += weight[i];
2186: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.183 brouard 2187: /* if (lli < log(mytinydouble)){ */
2188: /* 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); */
2189: /* 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]); */
2190: /* } */
1.126 brouard 2191: } /* end of wave */
2192: } /* end of individual */
2193: } else if(mle==2){
2194: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 ! brouard 2195: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2196: for(mi=1; mi<= wav[i]-1; mi++){
2197: for (ii=1;ii<=nlstate+ndeath;ii++)
2198: for (j=1;j<=nlstate+ndeath;j++){
2199: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2200: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2201: }
2202: for(d=0; d<=dh[mi][i]; d++){
2203: newm=savm;
1.187 ! brouard 2204: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
! 2205: cov[2]=agexact;
! 2206: if(nagesqr==1)
! 2207: cov[3]= agexact*agexact;
1.126 brouard 2208: for (kk=1; kk<=cptcovage;kk++) {
1.187 ! brouard 2209: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2210: }
2211: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2212: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2213: savm=oldm;
2214: oldm=newm;
2215: } /* end mult */
2216:
2217: s1=s[mw[mi][i]][i];
2218: s2=s[mw[mi+1][i]][i];
2219: bbh=(double)bh[mi][i]/(double)stepm;
2220: 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 */
2221: ipmx +=1;
2222: sw += weight[i];
2223: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2224: } /* end of wave */
2225: } /* end of individual */
2226: } else if(mle==3){ /* exponential inter-extrapolation */
2227: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 ! brouard 2228: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2229: for(mi=1; mi<= wav[i]-1; mi++){
2230: for (ii=1;ii<=nlstate+ndeath;ii++)
2231: for (j=1;j<=nlstate+ndeath;j++){
2232: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2233: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2234: }
2235: for(d=0; d<dh[mi][i]; d++){
2236: newm=savm;
1.187 ! brouard 2237: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
! 2238: cov[2]=agexact;
! 2239: if(nagesqr==1)
! 2240: cov[3]= agexact*agexact;
1.126 brouard 2241: for (kk=1; kk<=cptcovage;kk++) {
1.187 ! brouard 2242: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2243: }
2244: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2245: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2246: savm=oldm;
2247: oldm=newm;
2248: } /* end mult */
2249:
2250: s1=s[mw[mi][i]][i];
2251: s2=s[mw[mi+1][i]][i];
2252: bbh=(double)bh[mi][i]/(double)stepm;
2253: 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 */
2254: ipmx +=1;
2255: sw += weight[i];
2256: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2257: } /* end of wave */
2258: } /* end of individual */
2259: }else if (mle==4){ /* ml=4 no inter-extrapolation */
2260: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 ! brouard 2261: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2262: for(mi=1; mi<= wav[i]-1; mi++){
2263: for (ii=1;ii<=nlstate+ndeath;ii++)
2264: for (j=1;j<=nlstate+ndeath;j++){
2265: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2266: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2267: }
2268: for(d=0; d<dh[mi][i]; d++){
2269: newm=savm;
1.187 ! brouard 2270: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
! 2271: cov[2]=agexact;
! 2272: if(nagesqr==1)
! 2273: cov[3]= agexact*agexact;
1.126 brouard 2274: for (kk=1; kk<=cptcovage;kk++) {
1.187 ! brouard 2275: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2276: }
2277:
2278: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2279: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2280: savm=oldm;
2281: oldm=newm;
2282: } /* end mult */
2283:
2284: s1=s[mw[mi][i]][i];
2285: s2=s[mw[mi+1][i]][i];
2286: if( s2 > nlstate){
2287: lli=log(out[s1][s2] - savm[s1][s2]);
2288: }else{
2289: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2290: }
2291: ipmx +=1;
2292: sw += weight[i];
2293: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2294: /* 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]); */
2295: } /* end of wave */
2296: } /* end of individual */
2297: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
2298: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 ! brouard 2299: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2300: for(mi=1; mi<= wav[i]-1; mi++){
2301: for (ii=1;ii<=nlstate+ndeath;ii++)
2302: for (j=1;j<=nlstate+ndeath;j++){
2303: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2304: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2305: }
2306: for(d=0; d<dh[mi][i]; d++){
2307: newm=savm;
1.187 ! brouard 2308: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
! 2309: cov[2]=agexact;
! 2310: if(nagesqr==1)
! 2311: cov[3]= agexact*agexact;
1.126 brouard 2312: for (kk=1; kk<=cptcovage;kk++) {
1.187 ! brouard 2313: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2314: }
2315:
2316: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2317: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2318: savm=oldm;
2319: oldm=newm;
2320: } /* end mult */
2321:
2322: s1=s[mw[mi][i]][i];
2323: s2=s[mw[mi+1][i]][i];
2324: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2325: ipmx +=1;
2326: sw += weight[i];
2327: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2328: /*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]);*/
2329: } /* end of wave */
2330: } /* end of individual */
2331: } /* End of if */
2332: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2333: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2334: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2335: return -l;
2336: }
2337:
2338: /*************** log-likelihood *************/
2339: double funcone( double *x)
2340: {
2341: /* Same as likeli but slower because of a lot of printf and if */
2342: int i, ii, j, k, mi, d, kk;
1.131 brouard 2343: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2344: double **out;
2345: double lli; /* Individual log likelihood */
2346: double llt;
2347: int s1, s2;
2348: double bbh, survp;
1.187 ! brouard 2349: double agexact;
1.126 brouard 2350: /*extern weight */
2351: /* We are differentiating ll according to initial status */
2352: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2353: /*for(i=1;i<imx;i++)
2354: printf(" %d\n",s[4][i]);
2355: */
2356: cov[1]=1.;
2357:
2358: for(k=1; k<=nlstate; k++) ll[k]=0.;
2359:
2360: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 ! brouard 2361: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2362: for(mi=1; mi<= wav[i]-1; mi++){
2363: for (ii=1;ii<=nlstate+ndeath;ii++)
2364: for (j=1;j<=nlstate+ndeath;j++){
2365: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2366: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2367: }
2368: for(d=0; d<dh[mi][i]; d++){
2369: newm=savm;
1.187 ! brouard 2370: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
! 2371: cov[2]=agexact;
! 2372: if(nagesqr==1)
! 2373: cov[3]= agexact*agexact;
1.126 brouard 2374: for (kk=1; kk<=cptcovage;kk++) {
1.187 ! brouard 2375: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2376: }
1.187 ! brouard 2377:
1.145 brouard 2378: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.126 brouard 2379: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2380: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1.145 brouard 2381: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2382: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
1.126 brouard 2383: savm=oldm;
2384: oldm=newm;
2385: } /* end mult */
2386:
2387: s1=s[mw[mi][i]][i];
2388: s2=s[mw[mi+1][i]][i];
2389: bbh=(double)bh[mi][i]/(double)stepm;
2390: /* bias is positive if real duration
2391: * is higher than the multiple of stepm and negative otherwise.
2392: */
2393: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2394: lli=log(out[s1][s2] - savm[s1][s2]);
2395: } else if (s2==-2) {
2396: for (j=1,survp=0. ; j<=nlstate; j++)
2397: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2398: lli= log(survp);
2399: }else if (mle==1){
2400: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2401: } else if(mle==2){
2402: 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 */
2403: } else if(mle==3){ /* exponential inter-extrapolation */
2404: 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 */
2405: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2406: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 2407: } else{ /* mle=0 back to 1 */
2408: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2409: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 2410: } /* End of if */
2411: ipmx +=1;
2412: sw += weight[i];
2413: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 2414: /*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 2415: if(globpr){
1.141 brouard 2416: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
1.126 brouard 2417: %11.6f %11.6f %11.6f ", \
2418: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
2419: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2420: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2421: llt +=ll[k]*gipmx/gsw;
2422: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2423: }
2424: fprintf(ficresilk," %10.6f\n", -llt);
2425: }
2426: } /* end of wave */
2427: } /* end of individual */
2428: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2429: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2430: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2431: if(globpr==0){ /* First time we count the contributions and weights */
2432: gipmx=ipmx;
2433: gsw=sw;
2434: }
2435: return -l;
2436: }
2437:
2438:
2439: /*************** function likelione ***********/
2440: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2441: {
2442: /* This routine should help understanding what is done with
2443: the selection of individuals/waves and
2444: to check the exact contribution to the likelihood.
2445: Plotting could be done.
2446: */
2447: int k;
2448:
2449: if(*globpri !=0){ /* Just counts and sums, no printings */
2450: strcpy(fileresilk,"ilk");
2451: strcat(fileresilk,fileres);
2452: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2453: printf("Problem with resultfile: %s\n", fileresilk);
2454: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2455: }
2456: 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");
2457: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
2458: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2459: for(k=1; k<=nlstate; k++)
2460: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2461: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2462: }
2463:
2464: *fretone=(*funcone)(p);
2465: if(*globpri !=0){
2466: fclose(ficresilk);
2467: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
2468: fflush(fichtm);
2469: }
2470: return;
2471: }
2472:
2473:
2474: /*********** Maximum Likelihood Estimation ***************/
2475:
2476: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2477: {
1.165 brouard 2478: int i,j, iter=0;
1.126 brouard 2479: double **xi;
2480: double fret;
2481: double fretone; /* Only one call to likelihood */
2482: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 2483:
2484: #ifdef NLOPT
2485: int creturn;
2486: nlopt_opt opt;
2487: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2488: double *lb;
2489: double minf; /* the minimum objective value, upon return */
2490: double * p1; /* Shifted parameters from 0 instead of 1 */
2491: myfunc_data dinst, *d = &dinst;
2492: #endif
2493:
2494:
1.126 brouard 2495: xi=matrix(1,npar,1,npar);
2496: for (i=1;i<=npar;i++)
2497: for (j=1;j<=npar;j++)
2498: xi[i][j]=(i==j ? 1.0 : 0.0);
2499: printf("Powell\n"); fprintf(ficlog,"Powell\n");
2500: strcpy(filerespow,"pow");
2501: strcat(filerespow,fileres);
2502: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2503: printf("Problem with resultfile: %s\n", filerespow);
2504: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2505: }
2506: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2507: for (i=1;i<=nlstate;i++)
2508: for(j=1;j<=nlstate+ndeath;j++)
2509: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2510: fprintf(ficrespow,"\n");
1.162 brouard 2511: #ifdef POWELL
1.126 brouard 2512: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 2513: #endif
1.126 brouard 2514:
1.162 brouard 2515: #ifdef NLOPT
2516: #ifdef NEWUOA
2517: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2518: #else
2519: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2520: #endif
2521: lb=vector(0,npar-1);
2522: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2523: nlopt_set_lower_bounds(opt, lb);
2524: nlopt_set_initial_step1(opt, 0.1);
2525:
2526: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2527: d->function = func;
2528: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2529: nlopt_set_min_objective(opt, myfunc, d);
2530: nlopt_set_xtol_rel(opt, ftol);
2531: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2532: printf("nlopt failed! %d\n",creturn);
2533: }
2534: else {
2535: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2536: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2537: iter=1; /* not equal */
2538: }
2539: nlopt_destroy(opt);
2540: #endif
1.126 brouard 2541: free_matrix(xi,1,npar,1,npar);
2542: fclose(ficrespow);
1.180 brouard 2543: printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2544: fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2545: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 2546:
2547: }
2548:
2549: /**** Computes Hessian and covariance matrix ***/
2550: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
2551: {
2552: double **a,**y,*x,pd;
2553: double **hess;
1.164 brouard 2554: int i, j;
1.126 brouard 2555: int *indx;
2556:
2557: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
2558: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
2559: void lubksb(double **a, int npar, int *indx, double b[]) ;
2560: void ludcmp(double **a, int npar, int *indx, double *d) ;
2561: double gompertz(double p[]);
2562: hess=matrix(1,npar,1,npar);
2563:
2564: printf("\nCalculation of the hessian matrix. Wait...\n");
2565: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2566: for (i=1;i<=npar;i++){
2567: printf("%d",i);fflush(stdout);
2568: fprintf(ficlog,"%d",i);fflush(ficlog);
2569:
2570: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2571:
2572: /* printf(" %f ",p[i]);
2573: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2574: }
2575:
2576: for (i=1;i<=npar;i++) {
2577: for (j=1;j<=npar;j++) {
2578: if (j>i) {
2579: printf(".%d%d",i,j);fflush(stdout);
2580: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
2581: hess[i][j]=hessij(p,delti,i,j,func,npar);
2582:
2583: hess[j][i]=hess[i][j];
2584: /*printf(" %lf ",hess[i][j]);*/
2585: }
2586: }
2587: }
2588: printf("\n");
2589: fprintf(ficlog,"\n");
2590:
2591: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2592: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2593:
2594: a=matrix(1,npar,1,npar);
2595: y=matrix(1,npar,1,npar);
2596: x=vector(1,npar);
2597: indx=ivector(1,npar);
2598: for (i=1;i<=npar;i++)
2599: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2600: ludcmp(a,npar,indx,&pd);
2601:
2602: for (j=1;j<=npar;j++) {
2603: for (i=1;i<=npar;i++) x[i]=0;
2604: x[j]=1;
2605: lubksb(a,npar,indx,x);
2606: for (i=1;i<=npar;i++){
2607: matcov[i][j]=x[i];
2608: }
2609: }
2610:
2611: printf("\n#Hessian matrix#\n");
2612: fprintf(ficlog,"\n#Hessian matrix#\n");
2613: for (i=1;i<=npar;i++) {
2614: for (j=1;j<=npar;j++) {
2615: printf("%.3e ",hess[i][j]);
2616: fprintf(ficlog,"%.3e ",hess[i][j]);
2617: }
2618: printf("\n");
2619: fprintf(ficlog,"\n");
2620: }
2621:
2622: /* Recompute Inverse */
2623: for (i=1;i<=npar;i++)
2624: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
2625: ludcmp(a,npar,indx,&pd);
2626:
2627: /* printf("\n#Hessian matrix recomputed#\n");
2628:
2629: for (j=1;j<=npar;j++) {
2630: for (i=1;i<=npar;i++) x[i]=0;
2631: x[j]=1;
2632: lubksb(a,npar,indx,x);
2633: for (i=1;i<=npar;i++){
2634: y[i][j]=x[i];
2635: printf("%.3e ",y[i][j]);
2636: fprintf(ficlog,"%.3e ",y[i][j]);
2637: }
2638: printf("\n");
2639: fprintf(ficlog,"\n");
2640: }
2641: */
2642:
2643: free_matrix(a,1,npar,1,npar);
2644: free_matrix(y,1,npar,1,npar);
2645: free_vector(x,1,npar);
2646: free_ivector(indx,1,npar);
2647: free_matrix(hess,1,npar,1,npar);
2648:
2649:
2650: }
2651:
2652: /*************** hessian matrix ****************/
2653: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2654: {
2655: int i;
2656: int l=1, lmax=20;
2657: double k1,k2;
1.132 brouard 2658: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 2659: double res;
2660: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2661: double fx;
2662: int k=0,kmax=10;
2663: double l1;
2664:
2665: fx=func(x);
2666: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 2667: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 2668: l1=pow(10,l);
2669: delts=delt;
2670: for(k=1 ; k <kmax; k=k+1){
2671: delt = delta*(l1*k);
2672: p2[theta]=x[theta] +delt;
1.145 brouard 2673: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 2674: p2[theta]=x[theta]-delt;
2675: k2=func(p2)-fx;
2676: /*res= (k1-2.0*fx+k2)/delt/delt; */
2677: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2678:
1.132 brouard 2679: #ifdef DEBUGHESS
1.126 brouard 2680: 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);
2681: 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);
2682: #endif
2683: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2684: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2685: k=kmax;
2686: }
2687: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 2688: k=kmax; l=lmax*10;
1.126 brouard 2689: }
2690: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2691: delts=delt;
2692: }
2693: }
2694: }
2695: delti[theta]=delts;
2696: return res;
2697:
2698: }
2699:
2700: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2701: {
2702: int i;
1.164 brouard 2703: int l=1, lmax=20;
1.126 brouard 2704: double k1,k2,k3,k4,res,fx;
1.132 brouard 2705: double p2[MAXPARM+1];
1.126 brouard 2706: int k;
2707:
2708: fx=func(x);
2709: for (k=1; k<=2; k++) {
2710: for (i=1;i<=npar;i++) p2[i]=x[i];
2711: p2[thetai]=x[thetai]+delti[thetai]/k;
2712: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2713: k1=func(p2)-fx;
2714:
2715: p2[thetai]=x[thetai]+delti[thetai]/k;
2716: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2717: k2=func(p2)-fx;
2718:
2719: p2[thetai]=x[thetai]-delti[thetai]/k;
2720: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2721: k3=func(p2)-fx;
2722:
2723: p2[thetai]=x[thetai]-delti[thetai]/k;
2724: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2725: k4=func(p2)-fx;
2726: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2727: #ifdef DEBUG
2728: 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);
2729: 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);
2730: #endif
2731: }
2732: return res;
2733: }
2734:
2735: /************** Inverse of matrix **************/
2736: void ludcmp(double **a, int n, int *indx, double *d)
2737: {
2738: int i,imax,j,k;
2739: double big,dum,sum,temp;
2740: double *vv;
2741:
2742: vv=vector(1,n);
2743: *d=1.0;
2744: for (i=1;i<=n;i++) {
2745: big=0.0;
2746: for (j=1;j<=n;j++)
2747: if ((temp=fabs(a[i][j])) > big) big=temp;
2748: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2749: vv[i]=1.0/big;
2750: }
2751: for (j=1;j<=n;j++) {
2752: for (i=1;i<j;i++) {
2753: sum=a[i][j];
2754: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2755: a[i][j]=sum;
2756: }
2757: big=0.0;
2758: for (i=j;i<=n;i++) {
2759: sum=a[i][j];
2760: for (k=1;k<j;k++)
2761: sum -= a[i][k]*a[k][j];
2762: a[i][j]=sum;
2763: if ( (dum=vv[i]*fabs(sum)) >= big) {
2764: big=dum;
2765: imax=i;
2766: }
2767: }
2768: if (j != imax) {
2769: for (k=1;k<=n;k++) {
2770: dum=a[imax][k];
2771: a[imax][k]=a[j][k];
2772: a[j][k]=dum;
2773: }
2774: *d = -(*d);
2775: vv[imax]=vv[j];
2776: }
2777: indx[j]=imax;
2778: if (a[j][j] == 0.0) a[j][j]=TINY;
2779: if (j != n) {
2780: dum=1.0/(a[j][j]);
2781: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2782: }
2783: }
2784: free_vector(vv,1,n); /* Doesn't work */
2785: ;
2786: }
2787:
2788: void lubksb(double **a, int n, int *indx, double b[])
2789: {
2790: int i,ii=0,ip,j;
2791: double sum;
2792:
2793: for (i=1;i<=n;i++) {
2794: ip=indx[i];
2795: sum=b[ip];
2796: b[ip]=b[i];
2797: if (ii)
2798: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2799: else if (sum) ii=i;
2800: b[i]=sum;
2801: }
2802: for (i=n;i>=1;i--) {
2803: sum=b[i];
2804: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2805: b[i]=sum/a[i][i];
2806: }
2807: }
2808:
2809: void pstamp(FILE *fichier)
2810: {
2811: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2812: }
2813:
2814: /************ Frequencies ********************/
2815: 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[])
2816: { /* Some frequencies */
2817:
1.164 brouard 2818: int i, m, jk, j1, bool, z1,j;
1.126 brouard 2819: int first;
2820: double ***freq; /* Frequencies */
2821: double *pp, **prop;
2822: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2823: char fileresp[FILENAMELENGTH];
2824:
2825: pp=vector(1,nlstate);
2826: prop=matrix(1,nlstate,iagemin,iagemax+3);
2827: strcpy(fileresp,"p");
2828: strcat(fileresp,fileres);
2829: if((ficresp=fopen(fileresp,"w"))==NULL) {
2830: printf("Problem with prevalence resultfile: %s\n", fileresp);
2831: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2832: exit(0);
2833: }
2834: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2835: j1=0;
2836:
2837: j=cptcoveff;
2838: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2839:
2840: first=1;
2841:
1.169 brouard 2842: /* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */
2843: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
2844: /* j1++; */
1.145 brouard 2845: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
1.126 brouard 2846: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2847: scanf("%d", i);*/
2848: for (i=-5; i<=nlstate+ndeath; i++)
2849: for (jk=-5; jk<=nlstate+ndeath; jk++)
2850: for(m=iagemin; m <= iagemax+3; m++)
2851: freq[i][jk][m]=0;
1.143 brouard 2852:
2853: for (i=1; i<=nlstate; i++)
2854: for(m=iagemin; m <= iagemax+3; m++)
2855: prop[i][m]=0;
1.126 brouard 2856:
2857: dateintsum=0;
2858: k2cpt=0;
2859: for (i=1; i<=imx; i++) {
2860: bool=1;
1.144 brouard 2861: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
2862: for (z1=1; z1<=cptcoveff; z1++)
2863: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
1.145 brouard 2864: /* Tests if the value of each of the covariates of i is equal to filter j1 */
1.144 brouard 2865: bool=0;
1.145 brouard 2866: /* 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",
2867: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
2868: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
1.144 brouard 2869: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
2870: }
1.126 brouard 2871: }
1.144 brouard 2872:
1.126 brouard 2873: if (bool==1){
2874: for(m=firstpass; m<=lastpass; m++){
2875: k2=anint[m][i]+(mint[m][i]/12.);
2876: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2877: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2878: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2879: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2880: if (m<lastpass) {
2881: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2882: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2883: }
2884:
2885: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2886: dateintsum=dateintsum+k2;
2887: k2cpt++;
2888: }
2889: /*}*/
2890: }
2891: }
1.145 brouard 2892: } /* end i */
1.126 brouard 2893:
2894: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2895: pstamp(ficresp);
2896: if (cptcovn>0) {
2897: fprintf(ficresp, "\n#********** Variable ");
2898: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2899: fprintf(ficresp, "**********\n#");
1.143 brouard 2900: fprintf(ficlog, "\n#********** Variable ");
2901: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2902: fprintf(ficlog, "**********\n#");
1.126 brouard 2903: }
2904: for(i=1; i<=nlstate;i++)
2905: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2906: fprintf(ficresp, "\n");
2907:
2908: for(i=iagemin; i <= iagemax+3; i++){
2909: if(i==iagemax+3){
2910: fprintf(ficlog,"Total");
2911: }else{
2912: if(first==1){
2913: first=0;
2914: printf("See log file for details...\n");
2915: }
2916: fprintf(ficlog,"Age %d", i);
2917: }
2918: for(jk=1; jk <=nlstate ; jk++){
2919: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2920: pp[jk] += freq[jk][m][i];
2921: }
2922: for(jk=1; jk <=nlstate ; jk++){
2923: for(m=-1, pos=0; m <=0 ; m++)
2924: pos += freq[jk][m][i];
2925: if(pp[jk]>=1.e-10){
2926: if(first==1){
1.132 brouard 2927: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1.126 brouard 2928: }
2929: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2930: }else{
2931: if(first==1)
2932: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2933: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2934: }
2935: }
2936:
2937: for(jk=1; jk <=nlstate ; jk++){
2938: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2939: pp[jk] += freq[jk][m][i];
2940: }
2941: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2942: pos += pp[jk];
2943: posprop += prop[jk][i];
2944: }
2945: for(jk=1; jk <=nlstate ; jk++){
2946: if(pos>=1.e-5){
2947: if(first==1)
2948: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2949: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2950: }else{
2951: if(first==1)
2952: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2953: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2954: }
2955: if( i <= iagemax){
2956: if(pos>=1.e-5){
2957: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2958: /*probs[i][jk][j1]= pp[jk]/pos;*/
2959: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2960: }
2961: else
2962: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2963: }
2964: }
2965:
2966: for(jk=-1; jk <=nlstate+ndeath; jk++)
2967: for(m=-1; m <=nlstate+ndeath; m++)
2968: if(freq[jk][m][i] !=0 ) {
2969: if(first==1)
2970: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2971: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2972: }
2973: if(i <= iagemax)
2974: fprintf(ficresp,"\n");
2975: if(first==1)
2976: printf("Others in log...\n");
2977: fprintf(ficlog,"\n");
2978: }
1.145 brouard 2979: /*}*/
1.126 brouard 2980: }
2981: dateintmean=dateintsum/k2cpt;
2982:
2983: fclose(ficresp);
2984: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2985: free_vector(pp,1,nlstate);
2986: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2987: /* End of Freq */
2988: }
2989:
2990: /************ Prevalence ********************/
2991: 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)
2992: {
2993: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2994: in each health status at the date of interview (if between dateprev1 and dateprev2).
2995: We still use firstpass and lastpass as another selection.
2996: */
2997:
1.164 brouard 2998: int i, m, jk, j1, bool, z1,j;
2999:
3000: double **prop;
3001: double posprop;
1.126 brouard 3002: double y2; /* in fractional years */
3003: int iagemin, iagemax;
1.145 brouard 3004: int first; /** to stop verbosity which is redirected to log file */
1.126 brouard 3005:
3006: iagemin= (int) agemin;
3007: iagemax= (int) agemax;
3008: /*pp=vector(1,nlstate);*/
3009: prop=matrix(1,nlstate,iagemin,iagemax+3);
3010: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
3011: j1=0;
3012:
1.145 brouard 3013: /*j=cptcoveff;*/
1.126 brouard 3014: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3015:
1.145 brouard 3016: first=1;
3017: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
3018: /*for(i1=1; i1<=ncodemax[k1];i1++){
3019: j1++;*/
1.126 brouard 3020:
3021: for (i=1; i<=nlstate; i++)
3022: for(m=iagemin; m <= iagemax+3; m++)
3023: prop[i][m]=0.0;
3024:
3025: for (i=1; i<=imx; i++) { /* Each individual */
3026: bool=1;
3027: if (cptcovn>0) {
3028: for (z1=1; z1<=cptcoveff; z1++)
3029: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
3030: bool=0;
3031: }
3032: if (bool==1) {
3033: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
3034: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
3035: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
3036: if(agev[m][i]==0) agev[m][i]=iagemax+1;
3037: if(agev[m][i]==1) agev[m][i]=iagemax+2;
3038: 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);
3039: if (s[m][i]>0 && s[m][i]<=nlstate) {
3040: /*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]]);*/
3041: prop[s[m][i]][(int)agev[m][i]] += weight[i];
3042: prop[s[m][i]][iagemax+3] += weight[i];
3043: }
3044: }
3045: } /* end selection of waves */
3046: }
3047: }
3048: for(i=iagemin; i <= iagemax+3; i++){
3049: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
3050: posprop += prop[jk][i];
3051: }
1.145 brouard 3052:
1.126 brouard 3053: for(jk=1; jk <=nlstate ; jk++){
3054: if( i <= iagemax){
3055: if(posprop>=1.e-5){
3056: probs[i][jk][j1]= prop[jk][i]/posprop;
1.145 brouard 3057: } else{
3058: if(first==1){
3059: first=0;
3060: 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]);
3061: }
3062: }
1.126 brouard 3063: }
3064: }/* end jk */
3065: }/* end i */
1.145 brouard 3066: /*} *//* end i1 */
3067: } /* end j1 */
1.126 brouard 3068:
3069: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
3070: /*free_vector(pp,1,nlstate);*/
3071: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
3072: } /* End of prevalence */
3073:
3074: /************* Waves Concatenation ***************/
3075:
3076: 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)
3077: {
3078: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
3079: Death is a valid wave (if date is known).
3080: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
3081: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3082: and mw[mi+1][i]. dh depends on stepm.
3083: */
3084:
3085: int i, mi, m;
3086: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
3087: double sum=0., jmean=0.;*/
3088: int first;
3089: int j, k=0,jk, ju, jl;
3090: double sum=0.;
3091: first=0;
1.164 brouard 3092: jmin=100000;
1.126 brouard 3093: jmax=-1;
3094: jmean=0.;
3095: for(i=1; i<=imx; i++){
3096: mi=0;
3097: m=firstpass;
3098: while(s[m][i] <= nlstate){
3099: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
3100: mw[++mi][i]=m;
3101: if(m >=lastpass)
3102: break;
3103: else
3104: m++;
3105: }/* end while */
3106: if (s[m][i] > nlstate){
3107: mi++; /* Death is another wave */
3108: /* if(mi==0) never been interviewed correctly before death */
3109: /* Only death is a correct wave */
3110: mw[mi][i]=m;
3111: }
3112:
3113: wav[i]=mi;
3114: if(mi==0){
3115: nbwarn++;
3116: if(first==0){
3117: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
3118: first=1;
3119: }
3120: if(first==1){
3121: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
3122: }
3123: } /* end mi==0 */
3124: } /* End individuals */
3125:
3126: for(i=1; i<=imx; i++){
3127: for(mi=1; mi<wav[i];mi++){
3128: if (stepm <=0)
3129: dh[mi][i]=1;
3130: else{
3131: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
3132: if (agedc[i] < 2*AGESUP) {
3133: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
3134: if(j==0) j=1; /* Survives at least one month after exam */
3135: else if(j<0){
3136: nberr++;
3137: 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]);
3138: j=1; /* Temporary Dangerous patch */
3139: 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);
3140: 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]);
3141: 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);
3142: }
3143: k=k+1;
3144: if (j >= jmax){
3145: jmax=j;
3146: ijmax=i;
3147: }
3148: if (j <= jmin){
3149: jmin=j;
3150: ijmin=i;
3151: }
3152: sum=sum+j;
3153: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
3154: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
3155: }
3156: }
3157: else{
3158: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
3159: /* 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]); */
3160:
3161: k=k+1;
3162: if (j >= jmax) {
3163: jmax=j;
3164: ijmax=i;
3165: }
3166: else if (j <= jmin){
3167: jmin=j;
3168: ijmin=i;
3169: }
3170: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
3171: /*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]);*/
3172: if(j<0){
3173: nberr++;
3174: 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]);
3175: 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]);
3176: }
3177: sum=sum+j;
3178: }
3179: jk= j/stepm;
3180: jl= j -jk*stepm;
3181: ju= j -(jk+1)*stepm;
3182: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
3183: if(jl==0){
3184: dh[mi][i]=jk;
3185: bh[mi][i]=0;
3186: }else{ /* We want a negative bias in order to only have interpolation ie
1.136 brouard 3187: * to avoid the price of an extra matrix product in likelihood */
1.126 brouard 3188: dh[mi][i]=jk+1;
3189: bh[mi][i]=ju;
3190: }
3191: }else{
3192: if(jl <= -ju){
3193: dh[mi][i]=jk;
3194: bh[mi][i]=jl; /* bias is positive if real duration
3195: * is higher than the multiple of stepm and negative otherwise.
3196: */
3197: }
3198: else{
3199: dh[mi][i]=jk+1;
3200: bh[mi][i]=ju;
3201: }
3202: if(dh[mi][i]==0){
3203: dh[mi][i]=1; /* At least one step */
3204: bh[mi][i]=ju; /* At least one step */
3205: /* 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);*/
3206: }
3207: } /* end if mle */
3208: }
3209: } /* end wave */
3210: }
3211: jmean=sum/k;
3212: 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 3213: 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 3214: }
3215:
3216: /*********** Tricode ****************************/
1.145 brouard 3217: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 3218: {
1.144 brouard 3219: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
3220: /* 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 3221: * Boring subroutine which should only output nbcode[Tvar[j]][k]
1.145 brouard 3222: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
1.169 brouard 3223: * nbcode[Tvar[j]][1]=
1.144 brouard 3224: */
1.130 brouard 3225:
1.145 brouard 3226: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 3227: int modmaxcovj=0; /* Modality max of covariates j */
1.145 brouard 3228: int cptcode=0; /* Modality max of covariates j */
3229: int modmincovj=0; /* Modality min of covariates j */
3230:
3231:
1.126 brouard 3232: cptcoveff=0;
3233:
1.145 brouard 3234: for (k=-1; k < maxncov; k++) Ndum[k]=0;
1.144 brouard 3235: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 3236:
1.145 brouard 3237: /* Loop on covariates without age and products */
1.186 brouard 3238: for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
3239: for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
1.136 brouard 3240: modality of this covariate Vj*/
1.145 brouard 3241: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
3242: * If product of Vn*Vm, still boolean *:
3243: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
3244: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
3245: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
1.136 brouard 3246: modality of the nth covariate of individual i. */
1.145 brouard 3247: if (ij > modmaxcovj)
3248: modmaxcovj=ij;
3249: else if (ij < modmincovj)
3250: modmincovj=ij;
3251: if ((ij < -1) && (ij > NCOVMAX)){
3252: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
3253: exit(1);
3254: }else
1.136 brouard 3255: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
1.145 brouard 3256: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
1.126 brouard 3257: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.136 brouard 3258: /* getting the maximum value of the modality of the covariate
3259: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
3260: female is 1, then modmaxcovj=1.*/
1.187 ! brouard 3261: } /* end for loop on individuals */
1.145 brouard 3262: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
3263: cptcode=modmaxcovj;
1.137 brouard 3264: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
1.145 brouard 3265: /*for (i=0; i<=cptcode; i++) {*/
3266: for (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
1.187 ! brouard 3267: printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], i, Ndum[i]);
1.145 brouard 3268: if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
3269: ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
3270: }
3271: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
3272: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
1.131 brouard 3273: } /* Ndum[-1] number of undefined modalities */
1.126 brouard 3274:
1.136 brouard 3275: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
1.186 brouard 3276: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
3277: 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 3278: modmincovj=3; modmaxcovj = 7;
1.186 brouard 3279: There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
3280: which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
3281: defining two dummy variables: variables V1_1 and V1_2.
1.145 brouard 3282: nbcode[Tvar[j]][ij]=k;
3283: nbcode[Tvar[j]][1]=0;
3284: nbcode[Tvar[j]][2]=1;
3285: nbcode[Tvar[j]][3]=2;
3286: */
3287: ij=1; /* ij is similar to i but can jumps over null modalities */
3288: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
3289: for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
3290: /*recode from 0 */
1.131 brouard 3291: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
1.186 brouard 3292: nbcode[Tvar[j]][ij]=k; /* stores the modality k in an array nbcode.
1.131 brouard 3293: k is a modality. If we have model=V1+V1*sex
3294: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
1.126 brouard 3295: ij++;
3296: }
3297: if (ij > ncodemax[j]) break;
1.137 brouard 3298: } /* end of loop on */
3299: } /* end of loop on modality */
3300: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
3301:
1.145 brouard 3302: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.137 brouard 3303:
1.187 ! brouard 3304: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
1.145 brouard 3305: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
3306: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
1.187 ! brouard 3307: Ndum[ij]++; /* Might be supersed V1 + V1*age */
1.145 brouard 3308: }
1.126 brouard 3309:
3310: ij=1;
1.145 brouard 3311: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
3312: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
1.126 brouard 3313: if((Ndum[i]!=0) && (i<=ncovcol)){
1.145 brouard 3314: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
3315: Tvaraff[ij]=i; /*For printing (unclear) */
1.126 brouard 3316: ij++;
1.145 brouard 3317: }else
3318: Tvaraff[ij]=0;
1.126 brouard 3319: }
1.131 brouard 3320: ij--;
1.144 brouard 3321: cptcoveff=ij; /*Number of total covariates*/
1.145 brouard 3322:
1.126 brouard 3323: }
3324:
1.145 brouard 3325:
1.126 brouard 3326: /*********** Health Expectancies ****************/
3327:
1.127 brouard 3328: 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 3329:
3330: {
3331: /* Health expectancies, no variances */
1.164 brouard 3332: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 3333: int nhstepma, nstepma; /* Decreasing with age */
3334: double age, agelim, hf;
3335: double ***p3mat;
3336: double eip;
3337:
3338: pstamp(ficreseij);
3339: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3340: fprintf(ficreseij,"# Age");
3341: for(i=1; i<=nlstate;i++){
3342: for(j=1; j<=nlstate;j++){
3343: fprintf(ficreseij," e%1d%1d ",i,j);
3344: }
3345: fprintf(ficreseij," e%1d. ",i);
3346: }
3347: fprintf(ficreseij,"\n");
3348:
3349:
3350: if(estepm < stepm){
3351: printf ("Problem %d lower than %d\n",estepm, stepm);
3352: }
3353: else hstepm=estepm;
3354: /* We compute the life expectancy from trapezoids spaced every estepm months
3355: * This is mainly to measure the difference between two models: for example
3356: * if stepm=24 months pijx are given only every 2 years and by summing them
3357: * we are calculating an estimate of the Life Expectancy assuming a linear
3358: * progression in between and thus overestimating or underestimating according
3359: * to the curvature of the survival function. If, for the same date, we
3360: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3361: * to compare the new estimate of Life expectancy with the same linear
3362: * hypothesis. A more precise result, taking into account a more precise
3363: * curvature will be obtained if estepm is as small as stepm. */
3364:
3365: /* For example we decided to compute the life expectancy with the smallest unit */
3366: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3367: nhstepm is the number of hstepm from age to agelim
3368: nstepm is the number of stepm from age to agelin.
3369: Look at hpijx to understand the reason of that which relies in memory size
3370: and note for a fixed period like estepm months */
3371: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3372: survival function given by stepm (the optimization length). Unfortunately it
3373: means that if the survival funtion is printed only each two years of age and if
3374: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3375: results. So we changed our mind and took the option of the best precision.
3376: */
3377: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3378:
3379: agelim=AGESUP;
3380: /* If stepm=6 months */
3381: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3382: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3383:
3384: /* nhstepm age range expressed in number of stepm */
3385: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3386: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3387: /* if (stepm >= YEARM) hstepm=1;*/
3388: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3389: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3390:
3391: for (age=bage; age<=fage; age ++){
3392: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3393: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3394: /* if (stepm >= YEARM) hstepm=1;*/
3395: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3396:
3397: /* If stepm=6 months */
3398: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3399: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3400:
3401: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3402:
3403: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3404:
3405: printf("%d|",(int)age);fflush(stdout);
3406: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3407:
3408: /* Computing expectancies */
3409: for(i=1; i<=nlstate;i++)
3410: for(j=1; j<=nlstate;j++)
3411: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3412: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3413:
3414: /* 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]);*/
3415:
3416: }
3417:
3418: fprintf(ficreseij,"%3.0f",age );
3419: for(i=1; i<=nlstate;i++){
3420: eip=0;
3421: for(j=1; j<=nlstate;j++){
3422: eip +=eij[i][j][(int)age];
3423: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3424: }
3425: fprintf(ficreseij,"%9.4f", eip );
3426: }
3427: fprintf(ficreseij,"\n");
3428:
3429: }
3430: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3431: printf("\n");
3432: fprintf(ficlog,"\n");
3433:
3434: }
3435:
1.127 brouard 3436: 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 3437:
3438: {
3439: /* Covariances of health expectancies eij and of total life expectancies according
3440: to initial status i, ei. .
3441: */
3442: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3443: int nhstepma, nstepma; /* Decreasing with age */
3444: double age, agelim, hf;
3445: double ***p3matp, ***p3matm, ***varhe;
3446: double **dnewm,**doldm;
3447: double *xp, *xm;
3448: double **gp, **gm;
3449: double ***gradg, ***trgradg;
3450: int theta;
3451:
3452: double eip, vip;
3453:
3454: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
3455: xp=vector(1,npar);
3456: xm=vector(1,npar);
3457: dnewm=matrix(1,nlstate*nlstate,1,npar);
3458: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3459:
3460: pstamp(ficresstdeij);
3461: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3462: fprintf(ficresstdeij,"# Age");
3463: for(i=1; i<=nlstate;i++){
3464: for(j=1; j<=nlstate;j++)
3465: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3466: fprintf(ficresstdeij," e%1d. ",i);
3467: }
3468: fprintf(ficresstdeij,"\n");
3469:
3470: pstamp(ficrescveij);
3471: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3472: fprintf(ficrescveij,"# Age");
3473: for(i=1; i<=nlstate;i++)
3474: for(j=1; j<=nlstate;j++){
3475: cptj= (j-1)*nlstate+i;
3476: for(i2=1; i2<=nlstate;i2++)
3477: for(j2=1; j2<=nlstate;j2++){
3478: cptj2= (j2-1)*nlstate+i2;
3479: if(cptj2 <= cptj)
3480: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3481: }
3482: }
3483: fprintf(ficrescveij,"\n");
3484:
3485: if(estepm < stepm){
3486: printf ("Problem %d lower than %d\n",estepm, stepm);
3487: }
3488: else hstepm=estepm;
3489: /* We compute the life expectancy from trapezoids spaced every estepm months
3490: * This is mainly to measure the difference between two models: for example
3491: * if stepm=24 months pijx are given only every 2 years and by summing them
3492: * we are calculating an estimate of the Life Expectancy assuming a linear
3493: * progression in between and thus overestimating or underestimating according
3494: * to the curvature of the survival function. If, for the same date, we
3495: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3496: * to compare the new estimate of Life expectancy with the same linear
3497: * hypothesis. A more precise result, taking into account a more precise
3498: * curvature will be obtained if estepm is as small as stepm. */
3499:
3500: /* For example we decided to compute the life expectancy with the smallest unit */
3501: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3502: nhstepm is the number of hstepm from age to agelim
3503: nstepm is the number of stepm from age to agelin.
3504: Look at hpijx to understand the reason of that which relies in memory size
3505: and note for a fixed period like estepm months */
3506: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3507: survival function given by stepm (the optimization length). Unfortunately it
3508: means that if the survival funtion is printed only each two years of age and if
3509: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3510: results. So we changed our mind and took the option of the best precision.
3511: */
3512: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3513:
3514: /* If stepm=6 months */
3515: /* nhstepm age range expressed in number of stepm */
3516: agelim=AGESUP;
3517: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3518: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3519: /* if (stepm >= YEARM) hstepm=1;*/
3520: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3521:
3522: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3523: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3524: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3525: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3526: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3527: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3528:
3529: for (age=bage; age<=fage; age ++){
3530: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3531: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3532: /* if (stepm >= YEARM) hstepm=1;*/
3533: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3534:
3535: /* If stepm=6 months */
3536: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3537: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3538:
3539: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3540:
3541: /* Computing Variances of health expectancies */
3542: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3543: decrease memory allocation */
3544: for(theta=1; theta <=npar; theta++){
3545: for(i=1; i<=npar; i++){
3546: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3547: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3548: }
3549: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3550: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3551:
3552: for(j=1; j<= nlstate; j++){
3553: for(i=1; i<=nlstate; i++){
3554: for(h=0; h<=nhstepm-1; h++){
3555: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3556: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3557: }
3558: }
3559: }
3560:
3561: for(ij=1; ij<= nlstate*nlstate; ij++)
3562: for(h=0; h<=nhstepm-1; h++){
3563: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3564: }
3565: }/* End theta */
3566:
3567:
3568: for(h=0; h<=nhstepm-1; h++)
3569: for(j=1; j<=nlstate*nlstate;j++)
3570: for(theta=1; theta <=npar; theta++)
3571: trgradg[h][j][theta]=gradg[h][theta][j];
3572:
3573:
3574: for(ij=1;ij<=nlstate*nlstate;ij++)
3575: for(ji=1;ji<=nlstate*nlstate;ji++)
3576: varhe[ij][ji][(int)age] =0.;
3577:
3578: printf("%d|",(int)age);fflush(stdout);
3579: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3580: for(h=0;h<=nhstepm-1;h++){
3581: for(k=0;k<=nhstepm-1;k++){
3582: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3583: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3584: for(ij=1;ij<=nlstate*nlstate;ij++)
3585: for(ji=1;ji<=nlstate*nlstate;ji++)
3586: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3587: }
3588: }
3589:
3590: /* Computing expectancies */
3591: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3592: for(i=1; i<=nlstate;i++)
3593: for(j=1; j<=nlstate;j++)
3594: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3595: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3596:
3597: /* 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]);*/
3598:
3599: }
3600:
3601: fprintf(ficresstdeij,"%3.0f",age );
3602: for(i=1; i<=nlstate;i++){
3603: eip=0.;
3604: vip=0.;
3605: for(j=1; j<=nlstate;j++){
3606: eip += eij[i][j][(int)age];
3607: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3608: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3609: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3610: }
3611: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3612: }
3613: fprintf(ficresstdeij,"\n");
3614:
3615: fprintf(ficrescveij,"%3.0f",age );
3616: for(i=1; i<=nlstate;i++)
3617: for(j=1; j<=nlstate;j++){
3618: cptj= (j-1)*nlstate+i;
3619: for(i2=1; i2<=nlstate;i2++)
3620: for(j2=1; j2<=nlstate;j2++){
3621: cptj2= (j2-1)*nlstate+i2;
3622: if(cptj2 <= cptj)
3623: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3624: }
3625: }
3626: fprintf(ficrescveij,"\n");
3627:
3628: }
3629: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3630: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3631: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3632: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3633: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3634: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3635: printf("\n");
3636: fprintf(ficlog,"\n");
3637:
3638: free_vector(xm,1,npar);
3639: free_vector(xp,1,npar);
3640: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3641: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3642: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3643: }
3644:
3645: /************ Variance ******************/
3646: 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[])
3647: {
3648: /* Variance of health expectancies */
3649: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3650: /* double **newm;*/
1.169 brouard 3651: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
3652:
3653: int movingaverage();
1.126 brouard 3654: double **dnewm,**doldm;
3655: double **dnewmp,**doldmp;
3656: int i, j, nhstepm, hstepm, h, nstepm ;
1.164 brouard 3657: int k;
1.126 brouard 3658: double *xp;
3659: double **gp, **gm; /* for var eij */
3660: double ***gradg, ***trgradg; /*for var eij */
3661: double **gradgp, **trgradgp; /* for var p point j */
3662: double *gpp, *gmp; /* for var p point j */
3663: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3664: double ***p3mat;
3665: double age,agelim, hf;
3666: double ***mobaverage;
3667: int theta;
3668: char digit[4];
3669: char digitp[25];
3670:
3671: char fileresprobmorprev[FILENAMELENGTH];
3672:
3673: if(popbased==1){
3674: if(mobilav!=0)
3675: strcpy(digitp,"-populbased-mobilav-");
3676: else strcpy(digitp,"-populbased-nomobil-");
3677: }
3678: else
3679: strcpy(digitp,"-stablbased-");
3680:
3681: if (mobilav!=0) {
3682: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3683: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3684: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3685: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3686: }
3687: }
3688:
3689: strcpy(fileresprobmorprev,"prmorprev");
3690: sprintf(digit,"%-d",ij);
3691: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3692: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3693: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
3694: strcat(fileresprobmorprev,fileres);
3695: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3696: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3697: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3698: }
3699: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3700:
3701: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3702: pstamp(ficresprobmorprev);
3703: 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);
3704: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3705: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3706: fprintf(ficresprobmorprev," p.%-d SE",j);
3707: for(i=1; i<=nlstate;i++)
3708: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3709: }
3710: fprintf(ficresprobmorprev,"\n");
3711: fprintf(ficgp,"\n# Routine varevsij");
3712: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
3713: 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");
3714: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3715: /* } */
3716: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3717: pstamp(ficresvij);
3718: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3719: if(popbased==1)
1.128 brouard 3720: 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 3721: else
3722: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3723: fprintf(ficresvij,"# Age");
3724: for(i=1; i<=nlstate;i++)
3725: for(j=1; j<=nlstate;j++)
3726: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3727: fprintf(ficresvij,"\n");
3728:
3729: xp=vector(1,npar);
3730: dnewm=matrix(1,nlstate,1,npar);
3731: doldm=matrix(1,nlstate,1,nlstate);
3732: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3733: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3734:
3735: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3736: gpp=vector(nlstate+1,nlstate+ndeath);
3737: gmp=vector(nlstate+1,nlstate+ndeath);
3738: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3739:
3740: if(estepm < stepm){
3741: printf ("Problem %d lower than %d\n",estepm, stepm);
3742: }
3743: else hstepm=estepm;
3744: /* For example we decided to compute the life expectancy with the smallest unit */
3745: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3746: nhstepm is the number of hstepm from age to agelim
3747: nstepm is the number of stepm from age to agelin.
1.128 brouard 3748: Look at function hpijx to understand why (it is linked to memory size questions) */
1.126 brouard 3749: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3750: survival function given by stepm (the optimization length). Unfortunately it
3751: means that if the survival funtion is printed every two years of age and if
3752: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3753: results. So we changed our mind and took the option of the best precision.
3754: */
3755: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3756: agelim = AGESUP;
3757: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3758: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3759: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3760: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3761: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3762: gp=matrix(0,nhstepm,1,nlstate);
3763: gm=matrix(0,nhstepm,1,nlstate);
3764:
3765:
3766: for(theta=1; theta <=npar; theta++){
3767: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3768: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3769: }
3770: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3771: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3772:
3773: if (popbased==1) {
3774: if(mobilav ==0){
3775: for(i=1; i<=nlstate;i++)
3776: prlim[i][i]=probs[(int)age][i][ij];
3777: }else{ /* mobilav */
3778: for(i=1; i<=nlstate;i++)
3779: prlim[i][i]=mobaverage[(int)age][i][ij];
3780: }
3781: }
3782:
3783: for(j=1; j<= nlstate; j++){
3784: for(h=0; h<=nhstepm; h++){
3785: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3786: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3787: }
3788: }
3789: /* This for computing probability of death (h=1 means
3790: computed over hstepm matrices product = hstepm*stepm months)
3791: as a weighted average of prlim.
3792: */
3793: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3794: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3795: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3796: }
3797: /* end probability of death */
3798:
3799: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3800: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3801: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3802: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3803:
3804: if (popbased==1) {
3805: if(mobilav ==0){
3806: for(i=1; i<=nlstate;i++)
3807: prlim[i][i]=probs[(int)age][i][ij];
3808: }else{ /* mobilav */
3809: for(i=1; i<=nlstate;i++)
3810: prlim[i][i]=mobaverage[(int)age][i][ij];
3811: }
3812: }
3813:
1.128 brouard 3814: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
1.126 brouard 3815: for(h=0; h<=nhstepm; h++){
3816: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3817: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3818: }
3819: }
3820: /* This for computing probability of death (h=1 means
3821: computed over hstepm matrices product = hstepm*stepm months)
3822: as a weighted average of prlim.
3823: */
3824: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3825: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3826: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3827: }
3828: /* end probability of death */
3829:
3830: for(j=1; j<= nlstate; j++) /* vareij */
3831: for(h=0; h<=nhstepm; h++){
3832: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3833: }
3834:
3835: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3836: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3837: }
3838:
3839: } /* End theta */
3840:
3841: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3842:
3843: for(h=0; h<=nhstepm; h++) /* veij */
3844: for(j=1; j<=nlstate;j++)
3845: for(theta=1; theta <=npar; theta++)
3846: trgradg[h][j][theta]=gradg[h][theta][j];
3847:
3848: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3849: for(theta=1; theta <=npar; theta++)
3850: trgradgp[j][theta]=gradgp[theta][j];
3851:
3852:
3853: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3854: for(i=1;i<=nlstate;i++)
3855: for(j=1;j<=nlstate;j++)
3856: vareij[i][j][(int)age] =0.;
3857:
3858: for(h=0;h<=nhstepm;h++){
3859: for(k=0;k<=nhstepm;k++){
3860: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3861: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3862: for(i=1;i<=nlstate;i++)
3863: for(j=1;j<=nlstate;j++)
3864: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3865: }
3866: }
3867:
3868: /* pptj */
3869: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3870: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3871: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3872: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3873: varppt[j][i]=doldmp[j][i];
3874: /* end ppptj */
3875: /* x centered again */
3876: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3877: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3878:
3879: if (popbased==1) {
3880: if(mobilav ==0){
3881: for(i=1; i<=nlstate;i++)
3882: prlim[i][i]=probs[(int)age][i][ij];
3883: }else{ /* mobilav */
3884: for(i=1; i<=nlstate;i++)
3885: prlim[i][i]=mobaverage[(int)age][i][ij];
3886: }
3887: }
3888:
3889: /* This for computing probability of death (h=1 means
3890: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3891: as a weighted average of prlim.
3892: */
3893: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3894: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3895: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3896: }
3897: /* end probability of death */
3898:
3899: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3900: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3901: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3902: for(i=1; i<=nlstate;i++){
3903: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3904: }
3905: }
3906: fprintf(ficresprobmorprev,"\n");
3907:
3908: fprintf(ficresvij,"%.0f ",age );
3909: for(i=1; i<=nlstate;i++)
3910: for(j=1; j<=nlstate;j++){
3911: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3912: }
3913: fprintf(ficresvij,"\n");
3914: free_matrix(gp,0,nhstepm,1,nlstate);
3915: free_matrix(gm,0,nhstepm,1,nlstate);
3916: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3917: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3918: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3919: } /* End age */
3920: free_vector(gpp,nlstate+1,nlstate+ndeath);
3921: free_vector(gmp,nlstate+1,nlstate+ndeath);
3922: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3923: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.145 brouard 3924: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
1.126 brouard 3925: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
1.131 brouard 3926: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.126 brouard 3927: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3928: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3929: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.145 brouard 3930: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
1.170 brouard 3931: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
1.145 brouard 3932: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
1.126 brouard 3933: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3934: 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);
3935: /* 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);
3936: */
3937: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3938: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3939:
3940: free_vector(xp,1,npar);
3941: free_matrix(doldm,1,nlstate,1,nlstate);
3942: free_matrix(dnewm,1,nlstate,1,npar);
3943: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3944: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3945: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3946: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3947: fclose(ficresprobmorprev);
3948: fflush(ficgp);
3949: fflush(fichtm);
3950: } /* end varevsij */
3951:
3952: /************ Variance of prevlim ******************/
3953: 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[])
3954: {
3955: /* Variance of prevalence limit */
3956: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 3957:
1.126 brouard 3958: double **dnewm,**doldm;
3959: int i, j, nhstepm, hstepm;
3960: double *xp;
3961: double *gp, *gm;
3962: double **gradg, **trgradg;
3963: double age,agelim;
3964: int theta;
3965:
3966: pstamp(ficresvpl);
3967: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3968: fprintf(ficresvpl,"# Age");
3969: for(i=1; i<=nlstate;i++)
3970: fprintf(ficresvpl," %1d-%1d",i,i);
3971: fprintf(ficresvpl,"\n");
3972:
3973: xp=vector(1,npar);
3974: dnewm=matrix(1,nlstate,1,npar);
3975: doldm=matrix(1,nlstate,1,nlstate);
3976:
3977: hstepm=1*YEARM; /* Every year of age */
3978: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3979: agelim = AGESUP;
3980: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3981: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3982: if (stepm >= YEARM) hstepm=1;
3983: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3984: gradg=matrix(1,npar,1,nlstate);
3985: gp=vector(1,nlstate);
3986: gm=vector(1,nlstate);
3987:
3988: for(theta=1; theta <=npar; theta++){
3989: for(i=1; i<=npar; i++){ /* Computes gradient */
3990: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3991: }
3992: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3993: for(i=1;i<=nlstate;i++)
3994: gp[i] = prlim[i][i];
3995:
3996: for(i=1; i<=npar; i++) /* Computes gradient */
3997: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3998: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3999: for(i=1;i<=nlstate;i++)
4000: gm[i] = prlim[i][i];
4001:
4002: for(i=1;i<=nlstate;i++)
4003: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
4004: } /* End theta */
4005:
4006: trgradg =matrix(1,nlstate,1,npar);
4007:
4008: for(j=1; j<=nlstate;j++)
4009: for(theta=1; theta <=npar; theta++)
4010: trgradg[j][theta]=gradg[theta][j];
4011:
4012: for(i=1;i<=nlstate;i++)
4013: varpl[i][(int)age] =0.;
4014: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
4015: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
4016: for(i=1;i<=nlstate;i++)
4017: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
4018:
4019: fprintf(ficresvpl,"%.0f ",age );
4020: for(i=1; i<=nlstate;i++)
4021: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
4022: fprintf(ficresvpl,"\n");
4023: free_vector(gp,1,nlstate);
4024: free_vector(gm,1,nlstate);
4025: free_matrix(gradg,1,npar,1,nlstate);
4026: free_matrix(trgradg,1,nlstate,1,npar);
4027: } /* End age */
4028:
4029: free_vector(xp,1,npar);
4030: free_matrix(doldm,1,nlstate,1,npar);
4031: free_matrix(dnewm,1,nlstate,1,nlstate);
4032:
4033: }
4034:
4035: /************ Variance of one-step probabilities ******************/
4036: 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[])
4037: {
1.164 brouard 4038: int i, j=0, k1, l1, tj;
1.126 brouard 4039: int k2, l2, j1, z1;
1.164 brouard 4040: int k=0, l;
1.145 brouard 4041: int first=1, first1, first2;
1.126 brouard 4042: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
4043: double **dnewm,**doldm;
4044: double *xp;
4045: double *gp, *gm;
4046: double **gradg, **trgradg;
4047: double **mu;
1.164 brouard 4048: double age, cov[NCOVMAX+1];
1.126 brouard 4049: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
4050: int theta;
4051: char fileresprob[FILENAMELENGTH];
4052: char fileresprobcov[FILENAMELENGTH];
4053: char fileresprobcor[FILENAMELENGTH];
4054: double ***varpij;
4055:
4056: strcpy(fileresprob,"prob");
4057: strcat(fileresprob,fileres);
4058: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
4059: printf("Problem with resultfile: %s\n", fileresprob);
4060: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
4061: }
4062: strcpy(fileresprobcov,"probcov");
4063: strcat(fileresprobcov,fileres);
4064: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
4065: printf("Problem with resultfile: %s\n", fileresprobcov);
4066: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
4067: }
4068: strcpy(fileresprobcor,"probcor");
4069: strcat(fileresprobcor,fileres);
4070: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
4071: printf("Problem with resultfile: %s\n", fileresprobcor);
4072: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
4073: }
4074: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4075: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4076: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4077: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4078: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4079: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4080: pstamp(ficresprob);
4081: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
4082: fprintf(ficresprob,"# Age");
4083: pstamp(ficresprobcov);
4084: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
4085: fprintf(ficresprobcov,"# Age");
4086: pstamp(ficresprobcor);
4087: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
4088: fprintf(ficresprobcor,"# Age");
4089:
4090:
4091: for(i=1; i<=nlstate;i++)
4092: for(j=1; j<=(nlstate+ndeath);j++){
4093: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
4094: fprintf(ficresprobcov," p%1d-%1d ",i,j);
4095: fprintf(ficresprobcor," p%1d-%1d ",i,j);
4096: }
4097: /* fprintf(ficresprob,"\n");
4098: fprintf(ficresprobcov,"\n");
4099: fprintf(ficresprobcor,"\n");
4100: */
1.131 brouard 4101: xp=vector(1,npar);
1.126 brouard 4102: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4103: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4104: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
4105: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
4106: first=1;
4107: fprintf(ficgp,"\n# Routine varprob");
4108: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
4109: fprintf(fichtm,"\n");
4110:
4111: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
4112: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
4113: file %s<br>\n",optionfilehtmcov);
4114: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
4115: and drawn. It helps understanding how is the covariance between two incidences.\
4116: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
4117: 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. \
4118: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
4119: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
4120: standard deviations wide on each axis. <br>\
4121: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
4122: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
4123: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
4124:
4125: cov[1]=1;
1.145 brouard 4126: /* tj=cptcoveff; */
4127: tj = (int) pow(2,cptcoveff);
1.126 brouard 4128: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
4129: j1=0;
1.145 brouard 4130: for(j1=1; j1<=tj;j1++){
4131: /*for(i1=1; i1<=ncodemax[t];i1++){ */
4132: /*j1++;*/
1.126 brouard 4133: if (cptcovn>0) {
4134: fprintf(ficresprob, "\n#********** Variable ");
4135: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4136: fprintf(ficresprob, "**********\n#\n");
4137: fprintf(ficresprobcov, "\n#********** Variable ");
4138: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4139: fprintf(ficresprobcov, "**********\n#\n");
4140:
4141: fprintf(ficgp, "\n#********** Variable ");
4142: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4143: fprintf(ficgp, "**********\n#\n");
4144:
4145:
4146: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
4147: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4148: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
4149:
4150: fprintf(ficresprobcor, "\n#********** Variable ");
4151: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4152: fprintf(ficresprobcor, "**********\n#");
4153: }
4154:
1.145 brouard 4155: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
4156: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4157: gp=vector(1,(nlstate)*(nlstate+ndeath));
4158: gm=vector(1,(nlstate)*(nlstate+ndeath));
1.126 brouard 4159: for (age=bage; age<=fage; age ++){
4160: cov[2]=age;
1.187 ! brouard 4161: if(nagesqr==1)
! 4162: cov[3]= age*age;
1.126 brouard 4163: for (k=1; k<=cptcovn;k++) {
1.187 ! brouard 4164: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
1.145 brouard 4165: * 1 1 1 1 1
4166: * 2 2 1 1 1
4167: * 3 1 2 1 1
4168: */
4169: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
1.126 brouard 4170: }
1.186 brouard 4171: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
4172: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
1.126 brouard 4173: for (k=1; k<=cptcovprod;k++)
1.187 ! brouard 4174: 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 4175:
4176:
4177: for(theta=1; theta <=npar; theta++){
4178: for(i=1; i<=npar; i++)
4179: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
4180:
4181: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4182:
4183: k=0;
4184: for(i=1; i<= (nlstate); i++){
4185: for(j=1; j<=(nlstate+ndeath);j++){
4186: k=k+1;
4187: gp[k]=pmmij[i][j];
4188: }
4189: }
4190:
4191: for(i=1; i<=npar; i++)
4192: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
4193:
4194: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4195: k=0;
4196: for(i=1; i<=(nlstate); i++){
4197: for(j=1; j<=(nlstate+ndeath);j++){
4198: k=k+1;
4199: gm[k]=pmmij[i][j];
4200: }
4201: }
4202:
4203: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
4204: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
4205: }
4206:
4207: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
4208: for(theta=1; theta <=npar; theta++)
4209: trgradg[j][theta]=gradg[theta][j];
4210:
4211: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
4212: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
4213:
4214: pmij(pmmij,cov,ncovmodel,x,nlstate);
4215:
4216: k=0;
4217: for(i=1; i<=(nlstate); i++){
4218: for(j=1; j<=(nlstate+ndeath);j++){
4219: k=k+1;
4220: mu[k][(int) age]=pmmij[i][j];
4221: }
4222: }
4223: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
4224: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
4225: varpij[i][j][(int)age] = doldm[i][j];
4226:
4227: /*printf("\n%d ",(int)age);
4228: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4229: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4230: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4231: }*/
4232:
4233: fprintf(ficresprob,"\n%d ",(int)age);
4234: fprintf(ficresprobcov,"\n%d ",(int)age);
4235: fprintf(ficresprobcor,"\n%d ",(int)age);
4236:
4237: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
4238: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
4239: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4240: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
4241: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
4242: }
4243: i=0;
4244: for (k=1; k<=(nlstate);k++){
4245: for (l=1; l<=(nlstate+ndeath);l++){
1.145 brouard 4246: i++;
1.126 brouard 4247: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
4248: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
4249: for (j=1; j<=i;j++){
1.145 brouard 4250: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
1.126 brouard 4251: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
4252: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
4253: }
4254: }
4255: }/* end of loop for state */
4256: } /* end of loop for age */
1.145 brouard 4257: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
4258: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
4259: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4260: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4261:
1.126 brouard 4262: /* Confidence intervalle of pij */
4263: /*
1.131 brouard 4264: fprintf(ficgp,"\nunset parametric;unset label");
1.126 brouard 4265: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
4266: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
4267: 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);
4268: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
4269: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
4270: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
4271: */
4272:
4273: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
1.145 brouard 4274: first1=1;first2=2;
1.126 brouard 4275: for (k2=1; k2<=(nlstate);k2++){
4276: for (l2=1; l2<=(nlstate+ndeath);l2++){
4277: if(l2==k2) continue;
4278: j=(k2-1)*(nlstate+ndeath)+l2;
4279: for (k1=1; k1<=(nlstate);k1++){
4280: for (l1=1; l1<=(nlstate+ndeath);l1++){
4281: if(l1==k1) continue;
4282: i=(k1-1)*(nlstate+ndeath)+l1;
4283: if(i<=j) continue;
4284: for (age=bage; age<=fage; age ++){
4285: if ((int)age %5==0){
4286: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
4287: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
4288: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
4289: mu1=mu[i][(int) age]/stepm*YEARM ;
4290: mu2=mu[j][(int) age]/stepm*YEARM;
4291: c12=cv12/sqrt(v1*v2);
4292: /* Computing eigen value of matrix of covariance */
4293: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4294: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
1.135 brouard 4295: if ((lc2 <0) || (lc1 <0) ){
1.145 brouard 4296: if(first2==1){
4297: first1=0;
4298: 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);
4299: }
4300: 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);
4301: /* lc1=fabs(lc1); */ /* If we want to have them positive */
4302: /* lc2=fabs(lc2); */
1.135 brouard 4303: }
4304:
1.126 brouard 4305: /* Eigen vectors */
4306: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
4307: /*v21=sqrt(1.-v11*v11); *//* error */
4308: v21=(lc1-v1)/cv12*v11;
4309: v12=-v21;
4310: v22=v11;
4311: tnalp=v21/v11;
4312: if(first1==1){
4313: first1=0;
4314: 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);
4315: }
4316: 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);
4317: /*printf(fignu*/
4318: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
4319: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
4320: if(first==1){
4321: first=0;
4322: fprintf(ficgp,"\nset parametric;unset label");
4323: 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 4324: fprintf(ficgp,"\nset ter png small size 320, 240");
1.126 brouard 4325: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
4326: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
4327: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
4328: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
4329: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4330: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4331: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
4332: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4333: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4334: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4335: 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",\
4336: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4337: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4338: }else{
4339: first=0;
4340: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4341: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4342: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4343: 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",\
4344: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4345: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4346: }/* if first */
4347: } /* age mod 5 */
4348: } /* end loop age */
4349: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4350: first=1;
4351: } /*l12 */
4352: } /* k12 */
4353: } /*l1 */
4354: }/* k1 */
1.169 brouard 4355: /* } */ /* loop covariates */
1.126 brouard 4356: }
4357: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4358: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4359: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4360: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4361: free_vector(xp,1,npar);
4362: fclose(ficresprob);
4363: fclose(ficresprobcov);
4364: fclose(ficresprobcor);
4365: fflush(ficgp);
4366: fflush(fichtmcov);
4367: }
4368:
4369:
4370: /******************* Printing html file ***********/
4371: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
4372: int lastpass, int stepm, int weightopt, char model[],\
4373: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
4374: int popforecast, int estepm ,\
4375: double jprev1, double mprev1,double anprev1, \
4376: double jprev2, double mprev2,double anprev2){
4377: int jj1, k1, i1, cpt;
4378:
4379: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4380: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4381: </ul>");
4382: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
4383: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
4384: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
4385: fprintf(fichtm,"\
4386: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
4387: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
4388: fprintf(fichtm,"\
4389: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
4390: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
4391: fprintf(fichtm,"\
1.128 brouard 4392: - (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 4393: <a href=\"%s\">%s</a> <br>\n",
4394: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
4395: fprintf(fichtm,"\
4396: - Population projections by age and states: \
4397: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
4398:
4399: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4400:
1.145 brouard 4401: m=pow(2,cptcoveff);
1.126 brouard 4402: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4403:
4404: jj1=0;
4405: for(k1=1; k1<=m;k1++){
4406: for(i1=1; i1<=ncodemax[k1];i1++){
4407: jj1++;
4408: if (cptcovn > 0) {
4409: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4410: for (cpt=1; cpt<=cptcoveff;cpt++)
4411: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4412: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4413: }
4414: /* Pij */
1.145 brouard 4415: 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> \
4416: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.126 brouard 4417: /* Quasi-incidences */
4418: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.145 brouard 4419: 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> \
4420: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.126 brouard 4421: /* Period (stable) prevalence in each health state */
1.154 brouard 4422: for(cpt=1; cpt<=nlstate;cpt++){
1.166 brouard 4423: 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> \
4424: <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 4425: }
4426: for(cpt=1; cpt<=nlstate;cpt++) {
1.154 brouard 4427: 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> \
4428: <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 4429: }
4430: } /* end i1 */
4431: }/* End k1 */
4432: fprintf(fichtm,"</ul>");
4433:
4434:
4435: fprintf(fichtm,"\
4436: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
4437: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
4438:
4439: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4440: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
4441: fprintf(fichtm,"\
4442: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4443: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
4444:
4445: fprintf(fichtm,"\
4446: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4447: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
4448: fprintf(fichtm,"\
4449: - 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): \
4450: <a href=\"%s\">%s</a> <br>\n</li>",
4451: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
4452: fprintf(fichtm,"\
4453: - (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): \
4454: <a href=\"%s\">%s</a> <br>\n</li>",
4455: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
4456: fprintf(fichtm,"\
1.128 brouard 4457: - 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 4458: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
4459: fprintf(fichtm,"\
1.128 brouard 4460: - 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",
4461: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
1.126 brouard 4462: fprintf(fichtm,"\
4463: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
4464: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
4465:
4466: /* if(popforecast==1) fprintf(fichtm,"\n */
4467: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4468: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4469: /* <br>",fileres,fileres,fileres,fileres); */
4470: /* else */
4471: /* 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); */
4472: fflush(fichtm);
4473: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4474:
1.145 brouard 4475: m=pow(2,cptcoveff);
1.126 brouard 4476: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4477:
4478: jj1=0;
4479: for(k1=1; k1<=m;k1++){
4480: for(i1=1; i1<=ncodemax[k1];i1++){
4481: jj1++;
4482: if (cptcovn > 0) {
4483: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4484: for (cpt=1; cpt<=cptcoveff;cpt++)
4485: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4486: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4487: }
4488: for(cpt=1; cpt<=nlstate;cpt++) {
4489: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
1.145 brouard 4490: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
4491: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
1.126 brouard 4492: }
4493: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 4494: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4495: true period expectancies (those weighted with period prevalences are also\
4496: drawn in addition to the population based expectancies computed using\
4497: observed and cahotic prevalences: %s%d.png<br>\
1.126 brouard 4498: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
4499: } /* end i1 */
4500: }/* End k1 */
4501: fprintf(fichtm,"</ul>");
4502: fflush(fichtm);
4503: }
4504:
4505: /******************* Gnuplot file **************/
4506: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4507:
4508: char dirfileres[132],optfileres[132];
1.164 brouard 4509: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
1.130 brouard 4510: int ng=0;
1.126 brouard 4511: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4512: /* printf("Problem with file %s",optionfilegnuplot); */
4513: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4514: /* } */
4515:
4516: /*#ifdef windows */
4517: fprintf(ficgp,"cd \"%s\" \n",pathc);
4518: /*#endif */
4519: m=pow(2,cptcoveff);
4520:
4521: strcpy(dirfileres,optionfilefiname);
4522: strcpy(optfileres,"vpl");
4523: /* 1eme*/
1.153 brouard 4524: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
1.126 brouard 4525: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.145 brouard 4526: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
4527: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
4528: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
1.126 brouard 4529: fprintf(ficgp,"set xlabel \"Age\" \n\
4530: set ylabel \"Probability\" \n\
1.145 brouard 4531: set ter png small size 320, 240\n\
1.170 brouard 4532: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126 brouard 4533:
4534: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4535: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4536: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4537: }
1.170 brouard 4538: 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 4539: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4540: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4541: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4542: }
1.170 brouard 4543: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126 brouard 4544: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4545: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4546: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4547: }
1.145 brouard 4548: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
1.126 brouard 4549: }
4550: }
4551: /*2 eme*/
1.153 brouard 4552: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
1.126 brouard 4553: for (k1=1; k1<= m ; k1 ++) {
4554: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
1.145 brouard 4555: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
1.126 brouard 4556:
4557: for (i=1; i<= nlstate+1 ; i ++) {
4558: k=2*i;
1.170 brouard 4559: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126 brouard 4560: for (j=1; j<= nlstate+1 ; j ++) {
1.170 brouard 4561: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4562: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4563: }
4564: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
4565: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
1.170 brouard 4566: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126 brouard 4567: for (j=1; j<= nlstate+1 ; j ++) {
1.170 brouard 4568: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4569: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4570: }
1.145 brouard 4571: fprintf(ficgp,"\" t\"\" w l lt 0,");
1.170 brouard 4572: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126 brouard 4573: for (j=1; j<= nlstate+1 ; j ++) {
1.170 brouard 4574: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4575: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4576: }
1.145 brouard 4577: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4578: else fprintf(ficgp,"\" t\"\" w l lt 0,");
1.126 brouard 4579: }
4580: }
4581:
4582: /*3eme*/
4583:
4584: for (k1=1; k1<= m ; k1 ++) {
4585: for (cpt=1; cpt<= nlstate ; cpt ++) {
4586: /* k=2+nlstate*(2*cpt-2); */
4587: k=2+(nlstate+1)*(cpt-1);
4588: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
1.145 brouard 4589: fprintf(ficgp,"set ter png small size 320, 240\n\
1.126 brouard 4590: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
4591: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4592: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4593: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4594: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4595: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4596: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4597:
4598: */
4599: for (i=1; i< nlstate ; i ++) {
4600: 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);
4601: /* 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);*/
4602:
4603: }
4604: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
4605: }
4606: }
4607:
4608: /* CV preval stable (period) */
1.153 brouard 4609: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
4610: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.126 brouard 4611: k=3;
1.153 brouard 4612: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
1.145 brouard 4613: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
1.126 brouard 4614: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.145 brouard 4615: set ter png small size 320, 240\n\
1.126 brouard 4616: unset log y\n\
1.153 brouard 4617: plot [%.f:%.f] ", ageminpar, agemaxpar);
4618: for (i=1; i<= nlstate ; i ++){
4619: if(i==1)
4620: fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
4621: else
4622: fprintf(ficgp,", '' ");
1.154 brouard 4623: l=(nlstate+ndeath)*(i-1)+1;
4624: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
1.153 brouard 4625: for (j=1; j<= (nlstate-1) ; j ++)
4626: fprintf(ficgp,"+$%d",k+l+j);
4627: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
4628: } /* nlstate */
4629: fprintf(ficgp,"\n");
4630: } /* end cpt state*/
4631: } /* end covariate */
1.126 brouard 4632:
4633: /* proba elementaires */
1.187 ! brouard 4634: fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
1.126 brouard 4635: for(i=1,jk=1; i <=nlstate; i++){
1.187 ! brouard 4636: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 4637: for(k=1; k <=(nlstate+ndeath); k++){
4638: if (k != i) {
1.187 ! brouard 4639: fprintf(ficgp,"# current state %d\n",k);
1.126 brouard 4640: for(j=1; j <=ncovmodel; j++){
1.187 ! brouard 4641: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
1.126 brouard 4642: jk++;
4643: }
1.187 ! brouard 4644: fprintf(ficgp,"\n");
1.126 brouard 4645: }
4646: }
4647: }
1.187 ! brouard 4648: fprintf(ficgp,"##############\n#\n");
! 4649:
1.145 brouard 4650: /*goto avoid;*/
1.187 ! brouard 4651: fprintf(ficgp,"\n##############\n#Graphics of of probabilities or incidences\n#############\n");
! 4652: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
! 4653: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
! 4654: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
! 4655: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
! 4656: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
! 4657: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
! 4658: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
! 4659: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
! 4660: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
! 4661: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
! 4662: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
! 4663: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
! 4664: fprintf(ficgp,"#\n");
1.126 brouard 4665: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
1.187 ! brouard 4666: fprintf(ficgp,"# ng=%d\n",ng);
! 4667: fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);
1.126 brouard 4668: for(jk=1; jk <=m; jk++) {
1.187 ! brouard 4669: fprintf(ficgp,"# jk=%d\n",jk);
1.145 brouard 4670: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
1.126 brouard 4671: if (ng==2)
4672: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
4673: else
4674: fprintf(ficgp,"\nset title \"Probability\"\n");
1.145 brouard 4675: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
1.126 brouard 4676: i=1;
4677: for(k2=1; k2<=nlstate; k2++) {
4678: k3=i;
4679: for(k=1; k<=(nlstate+ndeath); k++) {
4680: if (k != k2){
4681: if(ng==2)
1.187 ! brouard 4682: if(nagesqr==0)
! 4683: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
! 4684: else /* nagesqr =1 */
! 4685: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
1.126 brouard 4686: else
1.187 ! brouard 4687: if(nagesqr==0)
! 4688: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
! 4689: else /* nagesqr =1 */
! 4690: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
1.141 brouard 4691: ij=1;/* To be checked else nbcode[0][0] wrong */
1.187 ! brouard 4692: for(j=3; j <=ncovmodel-nagesqr; j++) {
1.186 brouard 4693: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /* Bug valgrind */
1.187 ! brouard 4694: fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
1.186 brouard 4695: ij++;
4696: }
4697: else
1.187 ! brouard 4698: fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
1.126 brouard 4699: }
4700: fprintf(ficgp,")/(1");
4701:
1.187 ! brouard 4702: for(k1=1; k1 <=nlstate; k1++){
! 4703: if(nagesqr==0)
! 4704: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
! 4705: else /* nagesqr =1 */
! 4706: 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);
! 4707:
1.126 brouard 4708: ij=1;
1.187 ! brouard 4709: for(j=3; j <=ncovmodel-nagesqr; j++){
1.186 brouard 4710: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
1.187 ! brouard 4711: 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 4712: ij++;
4713: }
4714: else
1.187 ! brouard 4715: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
1.126 brouard 4716: }
4717: fprintf(ficgp,")");
4718: }
4719: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
4720: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
4721: i=i+ncovmodel;
4722: }
4723: } /* end k */
4724: } /* end k2 */
4725: } /* end jk */
4726: } /* end ng */
1.164 brouard 4727: /* avoid: */
1.126 brouard 4728: fflush(ficgp);
4729: } /* end gnuplot */
4730:
4731:
4732: /*************** Moving average **************/
4733: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
4734:
4735: int i, cpt, cptcod;
4736: int modcovmax =1;
4737: int mobilavrange, mob;
4738: double age;
4739:
4740: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
4741: a covariate has 2 modalities */
4742: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
4743:
4744: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
4745: if(mobilav==1) mobilavrange=5; /* default */
4746: else mobilavrange=mobilav;
4747: for (age=bage; age<=fage; age++)
4748: for (i=1; i<=nlstate;i++)
4749: for (cptcod=1;cptcod<=modcovmax;cptcod++)
4750: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
4751: /* We keep the original values on the extreme ages bage, fage and for
4752: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
4753: we use a 5 terms etc. until the borders are no more concerned.
4754: */
4755: for (mob=3;mob <=mobilavrange;mob=mob+2){
4756: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
4757: for (i=1; i<=nlstate;i++){
4758: for (cptcod=1;cptcod<=modcovmax;cptcod++){
4759: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
4760: for (cpt=1;cpt<=(mob-1)/2;cpt++){
4761: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
4762: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
4763: }
4764: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
4765: }
4766: }
4767: }/* end age */
4768: }/* end mob */
4769: }else return -1;
4770: return 0;
4771: }/* End movingaverage */
4772:
4773:
4774: /************** Forecasting ******************/
1.169 brouard 4775: 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 4776: /* proj1, year, month, day of starting projection
4777: agemin, agemax range of age
4778: dateprev1 dateprev2 range of dates during which prevalence is computed
4779: anproj2 year of en of projection (same day and month as proj1).
4780: */
1.164 brouard 4781: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
1.126 brouard 4782: double agec; /* generic age */
4783: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
4784: double *popeffectif,*popcount;
4785: double ***p3mat;
4786: double ***mobaverage;
4787: char fileresf[FILENAMELENGTH];
4788:
4789: agelim=AGESUP;
4790: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4791:
4792: strcpy(fileresf,"f");
4793: strcat(fileresf,fileres);
4794: if((ficresf=fopen(fileresf,"w"))==NULL) {
4795: printf("Problem with forecast resultfile: %s\n", fileresf);
4796: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
4797: }
4798: printf("Computing forecasting: result on file '%s' \n", fileresf);
4799: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
4800:
4801: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4802:
4803: if (mobilav!=0) {
4804: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4805: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4806: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4807: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4808: }
4809: }
4810:
4811: stepsize=(int) (stepm+YEARM-1)/YEARM;
4812: if (stepm<=12) stepsize=1;
4813: if(estepm < stepm){
4814: printf ("Problem %d lower than %d\n",estepm, stepm);
4815: }
4816: else hstepm=estepm;
4817:
4818: hstepm=hstepm/stepm;
4819: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
4820: fractional in yp1 */
4821: anprojmean=yp;
4822: yp2=modf((yp1*12),&yp);
4823: mprojmean=yp;
4824: yp1=modf((yp2*30.5),&yp);
4825: jprojmean=yp;
4826: if(jprojmean==0) jprojmean=1;
4827: if(mprojmean==0) jprojmean=1;
4828:
4829: i1=cptcoveff;
4830: if (cptcovn < 1){i1=1;}
4831:
4832: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4833:
4834: fprintf(ficresf,"#****** Routine prevforecast **\n");
4835:
4836: /* if (h==(int)(YEARM*yearp)){ */
4837: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4838: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4839: k=k+1;
4840: fprintf(ficresf,"\n#******");
4841: for(j=1;j<=cptcoveff;j++) {
4842: 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]]);
4843: }
4844: fprintf(ficresf,"******\n");
4845: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4846: for(j=1; j<=nlstate+ndeath;j++){
4847: for(i=1; i<=nlstate;i++)
4848: fprintf(ficresf," p%d%d",i,j);
4849: fprintf(ficresf," p.%d",j);
4850: }
4851: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4852: fprintf(ficresf,"\n");
4853: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4854:
4855: for (agec=fage; agec>=(ageminpar-1); agec--){
4856: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4857: nhstepm = nhstepm/hstepm;
4858: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4859: oldm=oldms;savm=savms;
4860: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4861:
4862: for (h=0; h<=nhstepm; h++){
4863: if (h*hstepm/YEARM*stepm ==yearp) {
4864: fprintf(ficresf,"\n");
4865: for(j=1;j<=cptcoveff;j++)
4866: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4867: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4868: }
4869: for(j=1; j<=nlstate+ndeath;j++) {
4870: ppij=0.;
4871: for(i=1; i<=nlstate;i++) {
4872: if (mobilav==1)
4873: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4874: else {
4875: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4876: }
4877: if (h*hstepm/YEARM*stepm== yearp) {
4878: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4879: }
4880: } /* end i */
4881: if (h*hstepm/YEARM*stepm==yearp) {
4882: fprintf(ficresf," %.3f", ppij);
4883: }
4884: }/* end j */
4885: } /* end h */
4886: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4887: } /* end agec */
4888: } /* end yearp */
4889: } /* end cptcod */
4890: } /* end cptcov */
4891:
4892: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4893:
4894: fclose(ficresf);
4895: }
4896:
4897: /************** Forecasting *****not tested NB*************/
1.169 brouard 4898: 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 4899:
4900: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4901: int *popage;
4902: double calagedatem, agelim, kk1, kk2;
4903: double *popeffectif,*popcount;
4904: double ***p3mat,***tabpop,***tabpopprev;
4905: double ***mobaverage;
4906: char filerespop[FILENAMELENGTH];
4907:
4908: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4909: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4910: agelim=AGESUP;
4911: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4912:
4913: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4914:
4915:
4916: strcpy(filerespop,"pop");
4917: strcat(filerespop,fileres);
4918: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4919: printf("Problem with forecast resultfile: %s\n", filerespop);
4920: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4921: }
4922: printf("Computing forecasting: result on file '%s' \n", filerespop);
4923: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4924:
4925: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4926:
4927: if (mobilav!=0) {
4928: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4929: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4930: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4931: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4932: }
4933: }
4934:
4935: stepsize=(int) (stepm+YEARM-1)/YEARM;
4936: if (stepm<=12) stepsize=1;
4937:
4938: agelim=AGESUP;
4939:
4940: hstepm=1;
4941: hstepm=hstepm/stepm;
4942:
4943: if (popforecast==1) {
4944: if((ficpop=fopen(popfile,"r"))==NULL) {
4945: printf("Problem with population file : %s\n",popfile);exit(0);
4946: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4947: }
4948: popage=ivector(0,AGESUP);
4949: popeffectif=vector(0,AGESUP);
4950: popcount=vector(0,AGESUP);
4951:
4952: i=1;
4953: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4954:
4955: imx=i;
4956: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4957: }
4958:
4959: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4960: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4961: k=k+1;
4962: fprintf(ficrespop,"\n#******");
4963: for(j=1;j<=cptcoveff;j++) {
4964: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4965: }
4966: fprintf(ficrespop,"******\n");
4967: fprintf(ficrespop,"# Age");
4968: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4969: if (popforecast==1) fprintf(ficrespop," [Population]");
4970:
4971: for (cpt=0; cpt<=0;cpt++) {
4972: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4973:
4974: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4975: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4976: nhstepm = nhstepm/hstepm;
4977:
4978: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4979: oldm=oldms;savm=savms;
4980: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4981:
4982: for (h=0; h<=nhstepm; h++){
4983: if (h==(int) (calagedatem+YEARM*cpt)) {
4984: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4985: }
4986: for(j=1; j<=nlstate+ndeath;j++) {
4987: kk1=0.;kk2=0;
4988: for(i=1; i<=nlstate;i++) {
4989: if (mobilav==1)
4990: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4991: else {
4992: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4993: }
4994: }
4995: if (h==(int)(calagedatem+12*cpt)){
4996: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4997: /*fprintf(ficrespop," %.3f", kk1);
4998: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4999: }
5000: }
5001: for(i=1; i<=nlstate;i++){
5002: kk1=0.;
5003: for(j=1; j<=nlstate;j++){
5004: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
5005: }
5006: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
5007: }
5008:
5009: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
5010: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
5011: }
5012: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5013: }
5014: }
5015:
5016: /******/
5017:
5018: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
5019: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5020: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5021: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5022: nhstepm = nhstepm/hstepm;
5023:
5024: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5025: oldm=oldms;savm=savms;
5026: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5027: for (h=0; h<=nhstepm; h++){
5028: if (h==(int) (calagedatem+YEARM*cpt)) {
5029: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5030: }
5031: for(j=1; j<=nlstate+ndeath;j++) {
5032: kk1=0.;kk2=0;
5033: for(i=1; i<=nlstate;i++) {
5034: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
5035: }
5036: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
5037: }
5038: }
5039: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5040: }
5041: }
5042: }
5043: }
5044:
5045: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5046:
5047: if (popforecast==1) {
5048: free_ivector(popage,0,AGESUP);
5049: free_vector(popeffectif,0,AGESUP);
5050: free_vector(popcount,0,AGESUP);
5051: }
5052: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5053: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5054: fclose(ficrespop);
5055: } /* End of popforecast */
5056:
5057: int fileappend(FILE *fichier, char *optionfich)
5058: {
5059: if((fichier=fopen(optionfich,"a"))==NULL) {
5060: printf("Problem with file: %s\n", optionfich);
5061: fprintf(ficlog,"Problem with file: %s\n", optionfich);
5062: return (0);
5063: }
5064: fflush(fichier);
5065: return (1);
5066: }
5067:
5068:
5069: /**************** function prwizard **********************/
5070: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
5071: {
5072:
5073: /* Wizard to print covariance matrix template */
5074:
1.164 brouard 5075: char ca[32], cb[32];
5076: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 5077: int numlinepar;
5078:
5079: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5080: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5081: for(i=1; i <=nlstate; i++){
5082: jj=0;
5083: for(j=1; j <=nlstate+ndeath; j++){
5084: if(j==i) continue;
5085: jj++;
5086: /*ca[0]= k+'a'-1;ca[1]='\0';*/
5087: printf("%1d%1d",i,j);
5088: fprintf(ficparo,"%1d%1d",i,j);
5089: for(k=1; k<=ncovmodel;k++){
5090: /* printf(" %lf",param[i][j][k]); */
5091: /* fprintf(ficparo," %lf",param[i][j][k]); */
5092: printf(" 0.");
5093: fprintf(ficparo," 0.");
5094: }
5095: printf("\n");
5096: fprintf(ficparo,"\n");
5097: }
5098: }
5099: printf("# Scales (for hessian or gradient estimation)\n");
5100: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
5101: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
5102: for(i=1; i <=nlstate; i++){
5103: jj=0;
5104: for(j=1; j <=nlstate+ndeath; j++){
5105: if(j==i) continue;
5106: jj++;
5107: fprintf(ficparo,"%1d%1d",i,j);
5108: printf("%1d%1d",i,j);
5109: fflush(stdout);
5110: for(k=1; k<=ncovmodel;k++){
5111: /* printf(" %le",delti3[i][j][k]); */
5112: /* fprintf(ficparo," %le",delti3[i][j][k]); */
5113: printf(" 0.");
5114: fprintf(ficparo," 0.");
5115: }
5116: numlinepar++;
5117: printf("\n");
5118: fprintf(ficparo,"\n");
5119: }
5120: }
5121: printf("# Covariance matrix\n");
5122: /* # 121 Var(a12)\n\ */
5123: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5124: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5125: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5126: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5127: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5128: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5129: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5130: fflush(stdout);
5131: fprintf(ficparo,"# Covariance matrix\n");
5132: /* # 121 Var(a12)\n\ */
5133: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5134: /* # ...\n\ */
5135: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5136:
5137: for(itimes=1;itimes<=2;itimes++){
5138: jj=0;
5139: for(i=1; i <=nlstate; i++){
5140: for(j=1; j <=nlstate+ndeath; j++){
5141: if(j==i) continue;
5142: for(k=1; k<=ncovmodel;k++){
5143: jj++;
5144: ca[0]= k+'a'-1;ca[1]='\0';
5145: if(itimes==1){
5146: printf("#%1d%1d%d",i,j,k);
5147: fprintf(ficparo,"#%1d%1d%d",i,j,k);
5148: }else{
5149: printf("%1d%1d%d",i,j,k);
5150: fprintf(ficparo,"%1d%1d%d",i,j,k);
5151: /* printf(" %.5le",matcov[i][j]); */
5152: }
5153: ll=0;
5154: for(li=1;li <=nlstate; li++){
5155: for(lj=1;lj <=nlstate+ndeath; lj++){
5156: if(lj==li) continue;
5157: for(lk=1;lk<=ncovmodel;lk++){
5158: ll++;
5159: if(ll<=jj){
5160: cb[0]= lk +'a'-1;cb[1]='\0';
5161: if(ll<jj){
5162: if(itimes==1){
5163: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5164: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5165: }else{
5166: printf(" 0.");
5167: fprintf(ficparo," 0.");
5168: }
5169: }else{
5170: if(itimes==1){
5171: printf(" Var(%s%1d%1d)",ca,i,j);
5172: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
5173: }else{
5174: printf(" 0.");
5175: fprintf(ficparo," 0.");
5176: }
5177: }
5178: }
5179: } /* end lk */
5180: } /* end lj */
5181: } /* end li */
5182: printf("\n");
5183: fprintf(ficparo,"\n");
5184: numlinepar++;
5185: } /* end k*/
5186: } /*end j */
5187: } /* end i */
5188: } /* end itimes */
5189:
5190: } /* end of prwizard */
5191: /******************* Gompertz Likelihood ******************************/
5192: double gompertz(double x[])
5193: {
5194: double A,B,L=0.0,sump=0.,num=0.;
5195: int i,n=0; /* n is the size of the sample */
5196:
5197: for (i=0;i<=imx-1 ; i++) {
5198: sump=sump+weight[i];
5199: /* sump=sump+1;*/
5200: num=num+1;
5201: }
5202:
5203:
5204: /* for (i=0; i<=imx; i++)
5205: 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]);*/
5206:
5207: for (i=1;i<=imx ; i++)
5208: {
5209: if (cens[i] == 1 && wav[i]>1)
5210: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
5211:
5212: if (cens[i] == 0 && wav[i]>1)
5213: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
5214: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
5215:
5216: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5217: if (wav[i] > 1 ) { /* ??? */
5218: L=L+A*weight[i];
5219: /* 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]);*/
5220: }
5221: }
5222:
5223: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5224:
5225: return -2*L*num/sump;
5226: }
5227:
1.136 brouard 5228: #ifdef GSL
5229: /******************* Gompertz_f Likelihood ******************************/
5230: double gompertz_f(const gsl_vector *v, void *params)
5231: {
5232: double A,B,LL=0.0,sump=0.,num=0.;
5233: double *x= (double *) v->data;
5234: int i,n=0; /* n is the size of the sample */
5235:
5236: for (i=0;i<=imx-1 ; i++) {
5237: sump=sump+weight[i];
5238: /* sump=sump+1;*/
5239: num=num+1;
5240: }
5241:
5242:
5243: /* for (i=0; i<=imx; i++)
5244: 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]);*/
5245: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
5246: for (i=1;i<=imx ; i++)
5247: {
5248: if (cens[i] == 1 && wav[i]>1)
5249: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
5250:
5251: if (cens[i] == 0 && wav[i]>1)
5252: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
5253: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
5254:
5255: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5256: if (wav[i] > 1 ) { /* ??? */
5257: LL=LL+A*weight[i];
5258: /* 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]);*/
5259: }
5260: }
5261:
5262: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5263: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
5264:
5265: return -2*LL*num/sump;
5266: }
5267: #endif
5268:
1.126 brouard 5269: /******************* Printing html file ***********/
5270: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
5271: int lastpass, int stepm, int weightopt, char model[],\
5272: int imx, double p[],double **matcov,double agemortsup){
5273: int i,k;
5274:
5275: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
5276: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
5277: for (i=1;i<=2;i++)
5278: 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]));
5279: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
5280: fprintf(fichtm,"</ul>");
5281:
5282: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
5283:
5284: 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>");
5285:
5286: for (k=agegomp;k<(agemortsup-2);k++)
5287: 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]);
5288:
5289:
5290: fflush(fichtm);
5291: }
5292:
5293: /******************* Gnuplot file **************/
5294: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
5295:
5296: char dirfileres[132],optfileres[132];
1.164 brouard 5297:
1.126 brouard 5298: int ng;
5299:
5300:
5301: /*#ifdef windows */
5302: fprintf(ficgp,"cd \"%s\" \n",pathc);
5303: /*#endif */
5304:
5305:
5306: strcpy(dirfileres,optionfilefiname);
5307: strcpy(optfileres,"vpl");
5308: fprintf(ficgp,"set out \"graphmort.png\"\n ");
5309: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.145 brouard 5310: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
5311: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 5312: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
5313:
5314: }
5315:
1.136 brouard 5316: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
5317: {
1.126 brouard 5318:
1.136 brouard 5319: /*-------- data file ----------*/
5320: FILE *fic;
5321: char dummy[]=" ";
1.164 brouard 5322: int i=0, j=0, n=0;
1.136 brouard 5323: int linei, month, year,iout;
5324: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 5325: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 5326: char *stratrunc;
5327: int lstra;
1.126 brouard 5328:
5329:
1.136 brouard 5330: if((fic=fopen(datafile,"r"))==NULL) {
5331: printf("Problem while opening datafile: %s\n", datafile);return 1;
5332: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
5333: }
1.126 brouard 5334:
1.136 brouard 5335: i=1;
5336: linei=0;
5337: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
5338: linei=linei+1;
5339: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
5340: if(line[j] == '\t')
5341: line[j] = ' ';
5342: }
5343: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
5344: ;
5345: };
5346: line[j+1]=0; /* Trims blanks at end of line */
5347: if(line[0]=='#'){
5348: fprintf(ficlog,"Comment line\n%s\n",line);
5349: printf("Comment line\n%s\n",line);
5350: continue;
5351: }
5352: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 5353: strcpy(line, linetmp);
1.136 brouard 5354:
1.126 brouard 5355:
1.136 brouard 5356: for (j=maxwav;j>=1;j--){
1.137 brouard 5357: cutv(stra, strb, line, ' ');
1.136 brouard 5358: if(strb[0]=='.') { /* Missing status */
5359: lval=-1;
5360: }else{
5361: errno=0;
5362: lval=strtol(strb,&endptr,10);
5363: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
5364: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5365: 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);
5366: 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 5367: return 1;
5368: }
5369: }
5370: s[j][i]=lval;
5371:
5372: strcpy(line,stra);
5373: cutv(stra, strb,line,' ');
1.169 brouard 5374: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5375: }
1.169 brouard 5376: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5377: month=99;
5378: year=9999;
5379: }else{
1.141 brouard 5380: 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);
5381: 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 5382: return 1;
5383: }
5384: anint[j][i]= (double) year;
5385: mint[j][i]= (double)month;
5386: strcpy(line,stra);
5387: } /* ENd Waves */
5388:
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 death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
5397: 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 5398: return 1;
5399: }
5400: andc[i]=(double) year;
5401: moisdc[i]=(double) month;
5402: strcpy(line,stra);
5403:
5404: cutv(stra, strb,line,' ');
1.169 brouard 5405: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5406: }
1.169 brouard 5407: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 5408: month=99;
5409: year=9999;
5410: }else{
1.141 brouard 5411: 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);
5412: 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 5413: return 1;
5414: }
5415: if (year==9999) {
1.141 brouard 5416: 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);
5417: 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 5418: return 1;
1.126 brouard 5419:
1.136 brouard 5420: }
5421: annais[i]=(double)(year);
5422: moisnais[i]=(double)(month);
5423: strcpy(line,stra);
5424:
5425: cutv(stra, strb,line,' ');
5426: errno=0;
5427: dval=strtod(strb,&endptr);
5428: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5429: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
5430: 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 5431: fflush(ficlog);
5432: return 1;
5433: }
5434: weight[i]=dval;
5435: strcpy(line,stra);
5436:
5437: for (j=ncovcol;j>=1;j--){
5438: cutv(stra, strb,line,' ');
5439: if(strb[0]=='.') { /* Missing status */
5440: lval=-1;
5441: }else{
5442: errno=0;
5443: lval=strtol(strb,&endptr,10);
5444: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5445: 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);
5446: 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 5447: return 1;
5448: }
5449: }
5450: if(lval <-1 || lval >1){
1.141 brouard 5451: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5452: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5453: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5454: For example, for multinomial values like 1, 2 and 3,\n \
5455: build V1=0 V2=0 for the reference value (1),\n \
5456: V1=1 V2=0 for (2) \n \
5457: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5458: output of IMaCh is often meaningless.\n \
5459: Exiting.\n",lval,linei, i,line,j);
1.141 brouard 5460: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5461: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5462: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5463: For example, for multinomial values like 1, 2 and 3,\n \
5464: build V1=0 V2=0 for the reference value (1),\n \
5465: V1=1 V2=0 for (2) \n \
5466: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5467: output of IMaCh is often meaningless.\n \
5468: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
5469: return 1;
5470: }
5471: covar[j][i]=(double)(lval);
5472: strcpy(line,stra);
5473: }
5474: lstra=strlen(stra);
5475:
5476: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
5477: stratrunc = &(stra[lstra-9]);
5478: num[i]=atol(stratrunc);
5479: }
5480: else
5481: num[i]=atol(stra);
5482: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
5483: 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;}*/
5484:
5485: i=i+1;
5486: } /* End loop reading data */
1.126 brouard 5487:
1.136 brouard 5488: *imax=i-1; /* Number of individuals */
5489: fclose(fic);
5490:
5491: return (0);
1.164 brouard 5492: /* endread: */
1.136 brouard 5493: printf("Exiting readdata: ");
5494: fclose(fic);
5495: return (1);
1.126 brouard 5496:
5497:
5498:
1.136 brouard 5499: }
1.145 brouard 5500: void removespace(char *str) {
5501: char *p1 = str, *p2 = str;
5502: do
5503: while (*p2 == ' ')
5504: p2++;
1.169 brouard 5505: while (*p1++ == *p2++);
1.145 brouard 5506: }
5507:
5508: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
1.187 ! brouard 5509: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
! 5510: * - nagesqr = 1 if age*age in the model, otherwise 0.
! 5511: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
! 5512: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
1.145 brouard 5513: * - cptcovage number of covariates with age*products =2
5514: * - cptcovs number of simple covariates
5515: * - 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
5516: * which is a new column after the 9 (ncovcol) variables.
5517: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
5518: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
5519: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
5520: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
5521: */
1.136 brouard 5522: {
1.145 brouard 5523: int i, j, k, ks;
1.164 brouard 5524: int j1, k1, k2;
1.136 brouard 5525: char modelsav[80];
1.145 brouard 5526: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 ! brouard 5527: char *strpt;
1.136 brouard 5528:
1.145 brouard 5529: /*removespace(model);*/
1.136 brouard 5530: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 5531: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 5532: if (strstr(model,"AGE") !=0){
1.187 ! brouard 5533: printf("Error. AGE must be in lower case 'age' model=1+age+%s ",model);
! 5534: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s ",model);fflush(ficlog);
1.136 brouard 5535: return 1;
5536: }
1.141 brouard 5537: if (strstr(model,"v") !=0){
5538: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
5539: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
5540: return 1;
5541: }
1.187 ! brouard 5542: strcpy(modelsav,model);
! 5543: if ((strpt=strstr(model,"age*age")) !=0){
! 5544: printf(" strpt=%s, model=%s\n",strpt, model);
! 5545: if(strpt != model){
! 5546: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
! 5547: 'model=1+age+age*age+V1' or 'model=1+age+age*age+V1+V1*age', please swap as well as \n \
! 5548: corresponding column of parameters.\n",model);
! 5549: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
! 5550: 'model=1+age+age*age+V1' or 'model=1+age+age*age+V1+V1*age', please swap as well as \n \
! 5551: corresponding column of parameters.\n",model); fflush(ficlog);
! 5552: return 1;
! 5553: }
! 5554:
! 5555: nagesqr=1;
! 5556: if (strstr(model,"+age*age") !=0)
! 5557: substrchaine(modelsav, model, "+age*age");
! 5558: else if (strstr(model,"age*age+") !=0)
! 5559: substrchaine(modelsav, model, "age*age+");
! 5560: else
! 5561: substrchaine(modelsav, model, "age*age");
! 5562: }else
! 5563: nagesqr=0;
! 5564: if (strlen(modelsav) >1){
! 5565: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
! 5566: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
! 5567: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2 */
! 5568: cptcovt= j+1; /* Number of total covariates in the model, not including
! 5569: * cst, age and age*age
! 5570: * V1+V1*age+ V3 + V3*V4+age*age=> 4*/
! 5571: /* including age products which are counted in cptcovage.
! 5572: * but the covariates which are products must be treated
! 5573: * separately: ncovn=4- 2=2 (V1+V3). */
! 5574: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
! 5575: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
! 5576:
! 5577:
! 5578: /* Design
! 5579: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
! 5580: * < ncovcol=8 >
! 5581: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
! 5582: * k= 1 2 3 4 5 6 7 8
! 5583: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
! 5584: * covar[k,i], value of kth covariate if not including age for individual i:
! 5585: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
! 5586: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
! 5587: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
! 5588: * Tage[++cptcovage]=k
! 5589: * if products, new covar are created after ncovcol with k1
! 5590: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
! 5591: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
! 5592: * 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
! 5593: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
! 5594: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
! 5595: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
! 5596: * < ncovcol=8 >
! 5597: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
! 5598: * k= 1 2 3 4 5 6 7 8 9 10 11 12
! 5599: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
! 5600: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
! 5601: * p Tprod[1]@2={ 6, 5}
! 5602: *p Tvard[1][1]@4= {7, 8, 5, 6}
! 5603: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
! 5604: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
! 5605: *How to reorganize?
! 5606: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
! 5607: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
! 5608: * {2, 1, 4, 8, 5, 6, 3, 7}
! 5609: * Struct []
! 5610: */
1.145 brouard 5611:
1.187 ! brouard 5612: /* This loop fills the array Tvar from the string 'model'.*/
! 5613: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
! 5614: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
! 5615: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
! 5616: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
! 5617: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
! 5618: /* k=1 Tvar[1]=2 (from V2) */
! 5619: /* k=5 Tvar[5] */
! 5620: /* for (k=1; k<=cptcovn;k++) { */
! 5621: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
! 5622: /* } */
! 5623: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2]; */
! 5624: /*
! 5625: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
! 5626: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
1.145 brouard 5627: Tvar[k]=0;
1.187 ! brouard 5628: cptcovage=0;
! 5629: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
! 5630: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
! 5631: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
! 5632: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
! 5633: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
! 5634: /*scanf("%d",i);*/
! 5635: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
! 5636: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
! 5637: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
! 5638: /* covar is not filled and then is empty */
! 5639: cptcovprod--;
! 5640: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
! 5641: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
! 5642: cptcovage++; /* Sums the number of covariates which include age as a product */
! 5643: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
! 5644: /*printf("stre=%s ", stre);*/
! 5645: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
! 5646: cptcovprod--;
! 5647: cutl(stre,strb,strc,'V');
! 5648: Tvar[k]=atoi(stre);
! 5649: cptcovage++;
! 5650: Tage[cptcovage]=k;
! 5651: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
! 5652: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
! 5653: cptcovn++;
! 5654: cptcovprodnoage++;k1++;
! 5655: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
! 5656: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
! 5657: because this model-covariate is a construction we invent a new column
! 5658: ncovcol + k1
! 5659: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
! 5660: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
! 5661: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
! 5662: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
! 5663: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
! 5664: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
! 5665: k2=k2+2;
! 5666: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
! 5667: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
! 5668: for (i=1; i<=lastobs;i++){
! 5669: /* Computes the new covariate which is a product of
! 5670: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
! 5671: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
! 5672: }
! 5673: } /* End age is not in the model */
! 5674: } /* End if model includes a product */
! 5675: else { /* no more sum */
! 5676: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
! 5677: /* scanf("%d",i);*/
! 5678: cutl(strd,strc,strb,'V');
! 5679: ks++; /**< Number of simple covariates */
1.145 brouard 5680: cptcovn++;
1.187 ! brouard 5681: Tvar[k]=atoi(strd);
! 5682: }
! 5683: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
! 5684: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
! 5685: scanf("%d",i);*/
! 5686: } /* end of loop + on total covariates */
! 5687: } /* end if strlen(modelsave == 0) age*age might exist */
! 5688: } /* end if strlen(model == 0) */
1.136 brouard 5689:
5690: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5691: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5692:
5693: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5694: printf("cptcovprod=%d ", cptcovprod);
5695: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5696:
5697: scanf("%d ",i);*/
5698:
5699:
1.137 brouard 5700: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 5701: /*endread:*/
1.136 brouard 5702: printf("Exiting decodemodel: ");
5703: return (1);
5704: }
5705:
1.169 brouard 5706: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.136 brouard 5707: {
5708: int i, m;
5709:
5710: for (i=1; i<=imx; i++) {
5711: for(m=2; (m<= maxwav); m++) {
5712: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5713: anint[m][i]=9999;
5714: s[m][i]=-1;
5715: }
5716: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169 brouard 5717: *nberr = *nberr + 1;
5718: 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);
5719: 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 5720: s[m][i]=-1;
5721: }
5722: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 5723: (*nberr)++;
1.136 brouard 5724: 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]);
5725: 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]);
5726: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5727: }
5728: }
5729: }
5730:
5731: for (i=1; i<=imx; i++) {
5732: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5733: for(m=firstpass; (m<= lastpass); m++){
5734: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5735: if (s[m][i] >= nlstate+1) {
1.169 brouard 5736: if(agedc[i]>0){
5737: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 5738: agev[m][i]=agedc[i];
5739: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 5740: }else {
1.136 brouard 5741: if ((int)andc[i]!=9999){
5742: nbwarn++;
5743: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5744: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5745: agev[m][i]=-1;
5746: }
5747: }
1.169 brouard 5748: } /* agedc > 0 */
1.136 brouard 5749: }
5750: else if(s[m][i] !=9){ /* Standard case, age in fractional
5751: years but with the precision of a month */
5752: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5753: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5754: agev[m][i]=1;
5755: else if(agev[m][i] < *agemin){
5756: *agemin=agev[m][i];
5757: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
5758: }
5759: else if(agev[m][i] >*agemax){
5760: *agemax=agev[m][i];
1.156 brouard 5761: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 5762: }
5763: /*agev[m][i]=anint[m][i]-annais[i];*/
5764: /* agev[m][i] = age[i]+2*m;*/
5765: }
5766: else { /* =9 */
5767: agev[m][i]=1;
5768: s[m][i]=-1;
5769: }
5770: }
5771: else /*= 0 Unknown */
5772: agev[m][i]=1;
5773: }
5774:
5775: }
5776: for (i=1; i<=imx; i++) {
5777: for(m=firstpass; (m<=lastpass); m++){
5778: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 5779: (*nberr)++;
1.136 brouard 5780: 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);
5781: 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);
5782: return 1;
5783: }
5784: }
5785: }
5786:
5787: /*for (i=1; i<=imx; i++){
5788: for (m=firstpass; (m<lastpass); m++){
5789: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5790: }
5791:
5792: }*/
5793:
5794:
1.139 brouard 5795: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5796: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 5797:
5798: return (0);
1.164 brouard 5799: /* endread:*/
1.136 brouard 5800: printf("Exiting calandcheckages: ");
5801: return (1);
5802: }
5803:
1.172 brouard 5804: #if defined(_MSC_VER)
5805: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5806: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5807: //#include "stdafx.h"
5808: //#include <stdio.h>
5809: //#include <tchar.h>
5810: //#include <windows.h>
5811: //#include <iostream>
5812: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
5813:
5814: LPFN_ISWOW64PROCESS fnIsWow64Process;
5815:
5816: BOOL IsWow64()
5817: {
5818: BOOL bIsWow64 = FALSE;
5819:
5820: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
5821: // (HANDLE, PBOOL);
5822:
5823: //LPFN_ISWOW64PROCESS fnIsWow64Process;
5824:
5825: HMODULE module = GetModuleHandle(_T("kernel32"));
5826: const char funcName[] = "IsWow64Process";
5827: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
5828: GetProcAddress(module, funcName);
5829:
5830: if (NULL != fnIsWow64Process)
5831: {
5832: if (!fnIsWow64Process(GetCurrentProcess(),
5833: &bIsWow64))
5834: //throw std::exception("Unknown error");
5835: printf("Unknown error\n");
5836: }
5837: return bIsWow64 != FALSE;
5838: }
5839: #endif
1.177 brouard 5840:
1.169 brouard 5841: void syscompilerinfo()
1.167 brouard 5842: {
5843: /* #include "syscompilerinfo.h"*/
1.185 brouard 5844: /* command line Intel compiler 32bit windows, XP compatible:*/
5845: /* /GS /W3 /Gy
5846: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
5847: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
5848: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 5849: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
5850: */
5851: /* 64 bits */
1.185 brouard 5852: /*
5853: /GS /W3 /Gy
5854: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
5855: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
5856: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
5857: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
5858: /* Optimization are useless and O3 is slower than O2 */
5859: /*
5860: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
5861: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
5862: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
5863: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
5864: */
1.186 brouard 5865: /* Link is */ /* /OUT:"visual studio
1.185 brouard 5866: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
5867: /PDB:"visual studio
5868: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
5869: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
5870: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
5871: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
5872: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
5873: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
5874: uiAccess='false'"
5875: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
5876: /NOLOGO /TLBID:1
5877: */
1.177 brouard 5878: #if defined __INTEL_COMPILER
1.178 brouard 5879: #if defined(__GNUC__)
5880: struct utsname sysInfo; /* For Intel on Linux and OS/X */
5881: #endif
1.177 brouard 5882: #elif defined(__GNUC__)
1.179 brouard 5883: #ifndef __APPLE__
1.174 brouard 5884: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 5885: #endif
1.177 brouard 5886: struct utsname sysInfo;
1.178 brouard 5887: int cross = CROSS;
5888: if (cross){
5889: printf("Cross-");
5890: fprintf(ficlog, "Cross-");
5891: }
1.174 brouard 5892: #endif
5893:
1.171 brouard 5894: #include <stdint.h>
1.178 brouard 5895:
1.169 brouard 5896: printf("Compiled with:");fprintf(ficlog,"Compiled with:");
5897: #if defined(__clang__)
5898: printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
5899: #endif
5900: #if defined(__ICC) || defined(__INTEL_COMPILER)
5901: printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
5902: #endif
5903: #if defined(__GNUC__) || defined(__GNUG__)
5904: printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
5905: #endif
5906: #if defined(__HP_cc) || defined(__HP_aCC)
5907: printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
5908: #endif
5909: #if defined(__IBMC__) || defined(__IBMCPP__)
5910: printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
5911: #endif
5912: #if defined(_MSC_VER)
5913: printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
5914: #endif
5915: #if defined(__PGI)
5916: printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
5917: #endif
5918: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
5919: printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 5920: #endif
1.174 brouard 5921: printf(" for ");fprintf(ficlog," for ");
1.169 brouard 5922:
1.167 brouard 5923: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
5924: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
5925: // Windows (x64 and x86)
1.174 brouard 5926: printf("Windows (x64 and x86) ");fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 5927: #elif __unix__ // all unices, not all compilers
5928: // Unix
1.174 brouard 5929: printf("Unix ");fprintf(ficlog,"Unix ");
1.167 brouard 5930: #elif __linux__
5931: // linux
1.174 brouard 5932: printf("linux ");fprintf(ficlog,"linux ");
1.167 brouard 5933: #elif __APPLE__
1.174 brouard 5934: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
5935: printf("Mac OS ");fprintf(ficlog,"Mac OS ");
1.167 brouard 5936: #endif
5937:
5938: /* __MINGW32__ */
5939: /* __CYGWIN__ */
5940: /* __MINGW64__ */
5941: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
5942: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
5943: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
5944: /* _WIN64 // Defined for applications for Win64. */
5945: /* _M_X64 // Defined for compilations that target x64 processors. */
5946: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 5947:
1.167 brouard 5948: #if UINTPTR_MAX == 0xffffffff
1.174 brouard 5949: printf(" 32-bit"); fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 5950: #elif UINTPTR_MAX == 0xffffffffffffffff
1.174 brouard 5951: printf(" 64-bit"); fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 5952: #else
1.174 brouard 5953: printf(" wtf-bit"); fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 5954: #endif
5955:
1.169 brouard 5956: #if defined(__GNUC__)
5957: # if defined(__GNUC_PATCHLEVEL__)
5958: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
5959: + __GNUC_MINOR__ * 100 \
5960: + __GNUC_PATCHLEVEL__)
5961: # else
5962: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
5963: + __GNUC_MINOR__ * 100)
5964: # endif
1.174 brouard 5965: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
5966: fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 5967:
5968: if (uname(&sysInfo) != -1) {
5969: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
5970: fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
5971: }
5972: else
5973: perror("uname() error");
1.179 brouard 5974: //#ifndef __INTEL_COMPILER
5975: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 5976: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.179 brouard 5977: fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 5978: #endif
1.169 brouard 5979: #endif
1.172 brouard 5980:
5981: // void main()
5982: // {
1.169 brouard 5983: #if defined(_MSC_VER)
1.174 brouard 5984: if (IsWow64()){
1.176 brouard 5985: printf("The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
5986: fprintf(ficlog, "The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 5987: }
5988: else{
1.176 brouard 5989: printf("The process is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.178 brouard 5990: fprintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 5991: }
1.172 brouard 5992: // printf("\nPress Enter to continue...");
5993: // getchar();
5994: // }
5995:
1.169 brouard 5996: #endif
5997:
1.167 brouard 5998:
5999: }
1.136 brouard 6000:
1.180 brouard 6001: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){
6002: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6003: int i, j, k, i1 ;
6004: double ftolpl = 1.e-10;
6005: double age, agebase, agelim;
6006:
6007: strcpy(filerespl,"pl");
6008: strcat(filerespl,fileres);
6009: if((ficrespl=fopen(filerespl,"w"))==NULL) {
6010: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6011: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6012: }
6013: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6014: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6015: pstamp(ficrespl);
6016: fprintf(ficrespl,"# Period (stable) prevalence \n");
6017: fprintf(ficrespl,"#Age ");
6018: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
6019: fprintf(ficrespl,"\n");
6020:
6021: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
6022:
6023: agebase=ageminpar;
6024: agelim=agemaxpar;
6025:
6026: i1=pow(2,cptcoveff);
6027: if (cptcovn < 1){i1=1;}
6028:
6029: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6030: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
6031: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6032: k=k+1;
6033: /* to clean */
6034: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);
6035: fprintf(ficrespl,"\n#******");
6036: printf("\n#******");
6037: fprintf(ficlog,"\n#******");
6038: for(j=1;j<=cptcoveff;j++) {
6039: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6040: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6041: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6042: }
6043: fprintf(ficrespl,"******\n");
6044: printf("******\n");
6045: fprintf(ficlog,"******\n");
6046:
6047: fprintf(ficrespl,"#Age ");
6048: for(j=1;j<=cptcoveff;j++) {
6049: fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6050: }
6051: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
6052: fprintf(ficrespl,"\n");
6053:
6054: for (age=agebase; age<=agelim; age++){
6055: /* for (age=agebase; age<=agebase; age++){ */
6056: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6057: fprintf(ficrespl,"%.0f ",age );
6058: for(j=1;j<=cptcoveff;j++)
6059: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6060: for(i=1; i<=nlstate;i++)
6061: fprintf(ficrespl," %.5f", prlim[i][i]);
6062: fprintf(ficrespl,"\n");
6063: } /* Age */
6064: /* was end of cptcod */
6065: } /* cptcov */
1.184 brouard 6066: return 0;
1.180 brouard 6067: }
6068:
6069: int hPijx(double *p, int bage, int fage){
6070: /*------------- h Pij x at various ages ------------*/
6071:
6072: int stepsize;
6073: int agelim;
6074: int hstepm;
6075: int nhstepm;
6076: int h, i, i1, j, k;
6077:
6078: double agedeb;
6079: double ***p3mat;
6080:
6081: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
6082: if((ficrespij=fopen(filerespij,"w"))==NULL) {
6083: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
6084: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
6085: }
6086: printf("Computing pij: result on file '%s' \n", filerespij);
6087: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
6088:
6089: stepsize=(int) (stepm+YEARM-1)/YEARM;
6090: /*if (stepm<=24) stepsize=2;*/
6091:
6092: agelim=AGESUP;
6093: hstepm=stepsize*YEARM; /* Every year of age */
6094: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
6095:
6096: /* hstepm=1; aff par mois*/
6097: pstamp(ficrespij);
6098: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
6099: i1= pow(2,cptcoveff);
1.183 brouard 6100: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
6101: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
6102: /* k=k+1; */
6103: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6104: fprintf(ficrespij,"\n#****** ");
6105: for(j=1;j<=cptcoveff;j++)
6106: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6107: fprintf(ficrespij,"******\n");
6108:
6109: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
6110: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6111: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6112:
6113: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 6114:
1.183 brouard 6115: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6116: oldm=oldms;savm=savms;
6117: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
6118: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
6119: for(i=1; i<=nlstate;i++)
6120: for(j=1; j<=nlstate+ndeath;j++)
6121: fprintf(ficrespij," %1d-%1d",i,j);
6122: fprintf(ficrespij,"\n");
6123: for (h=0; h<=nhstepm; h++){
6124: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
6125: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 6126: for(i=1; i<=nlstate;i++)
6127: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 6128: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 6129: fprintf(ficrespij,"\n");
6130: }
1.183 brouard 6131: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6132: fprintf(ficrespij,"\n");
6133: }
1.180 brouard 6134: /*}*/
6135: }
1.184 brouard 6136: return 0;
1.180 brouard 6137: }
6138:
6139:
1.136 brouard 6140: /***********************************************/
6141: /**************** Main Program *****************/
6142: /***********************************************/
6143:
6144: int main(int argc, char *argv[])
6145: {
6146: #ifdef GSL
6147: const gsl_multimin_fminimizer_type *T;
6148: size_t iteri = 0, it;
6149: int rval = GSL_CONTINUE;
6150: int status = GSL_SUCCESS;
6151: double ssval;
6152: #endif
6153: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 6154: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
6155:
6156: int jj, ll, li, lj, lk;
1.136 brouard 6157: int numlinepar=0; /* Current linenumber of parameter file */
6158: int itimes;
6159: int NDIM=2;
6160: int vpopbased=0;
6161:
1.164 brouard 6162: char ca[32], cb[32];
1.136 brouard 6163: /* FILE *fichtm; *//* Html File */
6164: /* FILE *ficgp;*/ /*Gnuplot File */
6165: struct stat info;
1.164 brouard 6166: double agedeb;
1.136 brouard 6167: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
6168:
1.165 brouard 6169: double fret;
1.136 brouard 6170: double dum; /* Dummy variable */
6171: double ***p3mat;
6172: double ***mobaverage;
1.164 brouard 6173:
6174: char line[MAXLINE];
1.136 brouard 6175: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
6176: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 6177: char *tok, *val; /* pathtot */
1.136 brouard 6178: int firstobs=1, lastobs=10;
1.164 brouard 6179: int c, h , cpt;
6180: int jl;
6181: int i1, j1, jk, stepsize;
6182: int *tab;
1.136 brouard 6183: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
6184: int mobilav=0,popforecast=0;
6185: int hstepm, nhstepm;
6186: int agemortsup;
6187: float sumlpop=0.;
6188: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
6189: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
6190:
1.164 brouard 6191: double bage=0, fage=110, age, agelim, agebase;
1.136 brouard 6192: double ftolpl=FTOL;
6193: double **prlim;
6194: double ***param; /* Matrix of parameters */
6195: double *p;
6196: double **matcov; /* Matrix of covariance */
6197: double ***delti3; /* Scale */
6198: double *delti; /* Scale */
6199: double ***eij, ***vareij;
6200: double **varpl; /* Variances of prevalence limits by age */
6201: double *epj, vepp;
1.164 brouard 6202:
1.136 brouard 6203: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
6204: double **ximort;
1.145 brouard 6205: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 6206: int *dcwave;
6207:
1.164 brouard 6208: char z[1]="c";
1.136 brouard 6209:
6210: /*char *strt;*/
6211: char strtend[80];
1.126 brouard 6212:
1.164 brouard 6213:
1.126 brouard 6214: /* setlocale (LC_ALL, ""); */
6215: /* bindtextdomain (PACKAGE, LOCALEDIR); */
6216: /* textdomain (PACKAGE); */
6217: /* setlocale (LC_CTYPE, ""); */
6218: /* setlocale (LC_MESSAGES, ""); */
6219:
6220: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 6221: rstart_time = time(NULL);
6222: /* (void) gettimeofday(&start_time,&tzp);*/
6223: start_time = *localtime(&rstart_time);
1.126 brouard 6224: curr_time=start_time;
1.157 brouard 6225: /*tml = *localtime(&start_time.tm_sec);*/
6226: /* strcpy(strstart,asctime(&tml)); */
6227: strcpy(strstart,asctime(&start_time));
1.126 brouard 6228:
6229: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 6230: /* tp.tm_sec = tp.tm_sec +86400; */
6231: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 6232: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
6233: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
6234: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 6235: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 6236: /* strt=asctime(&tmg); */
6237: /* printf("Time(after) =%s",strstart); */
6238: /* (void) time (&time_value);
6239: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
6240: * tm = *localtime(&time_value);
6241: * strstart=asctime(&tm);
6242: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
6243: */
6244:
6245: nberr=0; /* Number of errors and warnings */
6246: nbwarn=0;
1.184 brouard 6247: #ifdef WIN32
6248: _getcwd(pathcd, size);
6249: #else
1.126 brouard 6250: getcwd(pathcd, size);
1.184 brouard 6251: #endif
1.126 brouard 6252:
6253: printf("\n%s\n%s",version,fullversion);
6254: if(argc <=1){
6255: printf("\nEnter the parameter file name: ");
6256: fgets(pathr,FILENAMELENGTH,stdin);
6257: i=strlen(pathr);
6258: if(pathr[i-1]=='\n')
6259: pathr[i-1]='\0';
1.156 brouard 6260: i=strlen(pathr);
6261: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
6262: pathr[i-1]='\0';
1.126 brouard 6263: for (tok = pathr; tok != NULL; ){
6264: printf("Pathr |%s|\n",pathr);
6265: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
6266: printf("val= |%s| pathr=%s\n",val,pathr);
6267: strcpy (pathtot, val);
6268: if(pathr[0] == '\0') break; /* Dirty */
6269: }
6270: }
6271: else{
6272: strcpy(pathtot,argv[1]);
6273: }
6274: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
6275: /*cygwin_split_path(pathtot,path,optionfile);
6276: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
6277: /* cutv(path,optionfile,pathtot,'\\');*/
6278:
6279: /* Split argv[0], imach program to get pathimach */
6280: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
6281: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6282: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6283: /* strcpy(pathimach,argv[0]); */
6284: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
6285: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
6286: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 6287: #ifdef WIN32
6288: _chdir(path); /* Can be a relative path */
6289: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
6290: #else
1.126 brouard 6291: chdir(path); /* Can be a relative path */
1.184 brouard 6292: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
6293: #endif
6294: printf("Current directory %s!\n",pathcd);
1.126 brouard 6295: strcpy(command,"mkdir ");
6296: strcat(command,optionfilefiname);
6297: if((outcmd=system(command)) != 0){
1.169 brouard 6298: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 6299: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
6300: /* fclose(ficlog); */
6301: /* exit(1); */
6302: }
6303: /* if((imk=mkdir(optionfilefiname))<0){ */
6304: /* perror("mkdir"); */
6305: /* } */
6306:
6307: /*-------- arguments in the command line --------*/
6308:
1.186 brouard 6309: /* Main Log file */
1.126 brouard 6310: strcat(filelog, optionfilefiname);
6311: strcat(filelog,".log"); /* */
6312: if((ficlog=fopen(filelog,"w"))==NULL) {
6313: printf("Problem with logfile %s\n",filelog);
6314: goto end;
6315: }
6316: fprintf(ficlog,"Log filename:%s\n",filelog);
6317: fprintf(ficlog,"\n%s\n%s",version,fullversion);
6318: fprintf(ficlog,"\nEnter the parameter file name: \n");
6319: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
6320: path=%s \n\
6321: optionfile=%s\n\
6322: optionfilext=%s\n\
1.156 brouard 6323: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 6324:
1.167 brouard 6325: syscompilerinfo();
6326:
1.126 brouard 6327: printf("Local time (at start):%s",strstart);
6328: fprintf(ficlog,"Local time (at start): %s",strstart);
6329: fflush(ficlog);
6330: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 6331: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 6332:
6333: /* */
6334: strcpy(fileres,"r");
6335: strcat(fileres, optionfilefiname);
6336: strcat(fileres,".txt"); /* Other files have txt extension */
6337:
1.186 brouard 6338: /* Main ---------arguments file --------*/
1.126 brouard 6339:
6340: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 6341: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
6342: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 6343: fflush(ficlog);
1.149 brouard 6344: /* goto end; */
6345: exit(70);
1.126 brouard 6346: }
6347:
6348:
6349:
6350: strcpy(filereso,"o");
6351: strcat(filereso,fileres);
6352: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
6353: printf("Problem with Output resultfile: %s\n", filereso);
6354: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
6355: fflush(ficlog);
6356: goto end;
6357: }
6358:
6359: /* Reads comments: lines beginning with '#' */
6360: numlinepar=0;
6361: while((c=getc(ficpar))=='#' && c!= EOF){
6362: ungetc(c,ficpar);
6363: fgets(line, MAXLINE, ficpar);
6364: numlinepar++;
1.141 brouard 6365: fputs(line,stdout);
1.126 brouard 6366: fputs(line,ficparo);
6367: fputs(line,ficlog);
6368: }
6369: ungetc(c,ficpar);
6370:
1.187 ! brouard 6371: 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 6372: numlinepar++;
1.187 ! brouard 6373: 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);
! 6374: if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the model */
! 6375: model[strlen(model)-1]='\0';
! 6376: 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);
! 6377: 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 6378: fflush(ficlog);
1.187 ! brouard 6379: if(model[0]=='#'|| model[0]== '\0'){
! 6380: printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
! 6381: 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
! 6382: 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \
! 6383: if(mle != -1){
! 6384: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
! 6385: exit(1);
! 6386: }
! 6387: }
1.126 brouard 6388: while((c=getc(ficpar))=='#' && c!= EOF){
6389: ungetc(c,ficpar);
6390: fgets(line, MAXLINE, ficpar);
6391: numlinepar++;
1.141 brouard 6392: fputs(line, stdout);
6393: //puts(line);
1.126 brouard 6394: fputs(line,ficparo);
6395: fputs(line,ficlog);
6396: }
6397: ungetc(c,ficpar);
6398:
6399:
1.145 brouard 6400: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.136 brouard 6401: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
6402: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
6403: v1+v2*age+v2*v3 makes cptcovn = 3
6404: */
6405: if (strlen(model)>1)
1.187 ! brouard 6406: 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 6407: else
1.187 ! brouard 6408: ncovmodel=2; /* Constant and age */
1.133 brouard 6409: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
6410: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 6411: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
6412: 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);
6413: 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);
6414: fflush(stdout);
6415: fclose (ficlog);
6416: goto end;
6417: }
1.126 brouard 6418: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6419: delti=delti3[1][1];
6420: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
6421: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
6422: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
6423: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
6424: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
6425: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6426: fclose (ficparo);
6427: fclose (ficlog);
6428: goto end;
6429: exit(0);
6430: }
1.186 brouard 6431: else if(mle==-3) { /* Main Wizard */
1.126 brouard 6432: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
6433: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
6434: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
6435: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6436: matcov=matrix(1,npar,1,npar);
6437: }
6438: else{
1.145 brouard 6439: /* Read guessed parameters */
1.126 brouard 6440: /* Reads comments: lines beginning with '#' */
6441: while((c=getc(ficpar))=='#' && c!= EOF){
6442: ungetc(c,ficpar);
6443: fgets(line, MAXLINE, ficpar);
6444: numlinepar++;
1.141 brouard 6445: fputs(line,stdout);
1.126 brouard 6446: fputs(line,ficparo);
6447: fputs(line,ficlog);
6448: }
6449: ungetc(c,ficpar);
6450:
6451: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6452: for(i=1; i <=nlstate; i++){
6453: j=0;
6454: for(jj=1; jj <=nlstate+ndeath; jj++){
6455: if(jj==i) continue;
6456: j++;
6457: fscanf(ficpar,"%1d%1d",&i1,&j1);
6458: if ((i1 != i) && (j1 != j)){
6459: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
6460: It might be a problem of design; if ncovcol and the model are correct\n \
6461: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
6462: exit(1);
6463: }
6464: fprintf(ficparo,"%1d%1d",i1,j1);
6465: if(mle==1)
6466: printf("%1d%1d",i,j);
6467: fprintf(ficlog,"%1d%1d",i,j);
6468: for(k=1; k<=ncovmodel;k++){
6469: fscanf(ficpar," %lf",¶m[i][j][k]);
6470: if(mle==1){
6471: printf(" %lf",param[i][j][k]);
6472: fprintf(ficlog," %lf",param[i][j][k]);
6473: }
6474: else
6475: fprintf(ficlog," %lf",param[i][j][k]);
6476: fprintf(ficparo," %lf",param[i][j][k]);
6477: }
6478: fscanf(ficpar,"\n");
6479: numlinepar++;
6480: if(mle==1)
6481: printf("\n");
6482: fprintf(ficlog,"\n");
6483: fprintf(ficparo,"\n");
6484: }
6485: }
6486: fflush(ficlog);
6487:
1.145 brouard 6488: /* Reads scales values */
1.126 brouard 6489: p=param[1][1];
6490:
6491: /* Reads comments: lines beginning with '#' */
6492: while((c=getc(ficpar))=='#' && c!= EOF){
6493: ungetc(c,ficpar);
6494: fgets(line, MAXLINE, ficpar);
6495: numlinepar++;
1.141 brouard 6496: fputs(line,stdout);
1.126 brouard 6497: fputs(line,ficparo);
6498: fputs(line,ficlog);
6499: }
6500: ungetc(c,ficpar);
6501:
6502: for(i=1; i <=nlstate; i++){
6503: for(j=1; j <=nlstate+ndeath-1; j++){
6504: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.164 brouard 6505: if ( (i1-i) * (j1-j) != 0){
1.126 brouard 6506: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
6507: exit(1);
6508: }
6509: printf("%1d%1d",i,j);
6510: fprintf(ficparo,"%1d%1d",i1,j1);
6511: fprintf(ficlog,"%1d%1d",i1,j1);
6512: for(k=1; k<=ncovmodel;k++){
6513: fscanf(ficpar,"%le",&delti3[i][j][k]);
6514: printf(" %le",delti3[i][j][k]);
6515: fprintf(ficparo," %le",delti3[i][j][k]);
6516: fprintf(ficlog," %le",delti3[i][j][k]);
6517: }
6518: fscanf(ficpar,"\n");
6519: numlinepar++;
6520: printf("\n");
6521: fprintf(ficparo,"\n");
6522: fprintf(ficlog,"\n");
6523: }
6524: }
6525: fflush(ficlog);
6526:
1.145 brouard 6527: /* Reads covariance matrix */
1.126 brouard 6528: delti=delti3[1][1];
6529:
6530:
6531: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
6532:
6533: /* Reads comments: lines beginning with '#' */
6534: while((c=getc(ficpar))=='#' && c!= EOF){
6535: ungetc(c,ficpar);
6536: fgets(line, MAXLINE, ficpar);
6537: numlinepar++;
1.141 brouard 6538: fputs(line,stdout);
1.126 brouard 6539: fputs(line,ficparo);
6540: fputs(line,ficlog);
6541: }
6542: ungetc(c,ficpar);
6543:
6544: matcov=matrix(1,npar,1,npar);
1.131 brouard 6545: for(i=1; i <=npar; i++)
6546: for(j=1; j <=npar; j++) matcov[i][j]=0.;
6547:
1.126 brouard 6548: for(i=1; i <=npar; i++){
1.145 brouard 6549: fscanf(ficpar,"%s",str);
1.126 brouard 6550: if(mle==1)
6551: printf("%s",str);
6552: fprintf(ficlog,"%s",str);
6553: fprintf(ficparo,"%s",str);
6554: for(j=1; j <=i; j++){
6555: fscanf(ficpar," %le",&matcov[i][j]);
6556: if(mle==1){
6557: printf(" %.5le",matcov[i][j]);
6558: }
6559: fprintf(ficlog," %.5le",matcov[i][j]);
6560: fprintf(ficparo," %.5le",matcov[i][j]);
6561: }
6562: fscanf(ficpar,"\n");
6563: numlinepar++;
6564: if(mle==1)
6565: printf("\n");
6566: fprintf(ficlog,"\n");
6567: fprintf(ficparo,"\n");
6568: }
6569: for(i=1; i <=npar; i++)
6570: for(j=i+1;j<=npar;j++)
6571: matcov[i][j]=matcov[j][i];
6572:
6573: if(mle==1)
6574: printf("\n");
6575: fprintf(ficlog,"\n");
6576:
6577: fflush(ficlog);
6578:
6579: /*-------- Rewriting parameter file ----------*/
6580: strcpy(rfileres,"r"); /* "Rparameterfile */
6581: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
6582: strcat(rfileres,"."); /* */
6583: strcat(rfileres,optionfilext); /* Other files have txt extension */
6584: if((ficres =fopen(rfileres,"w"))==NULL) {
6585: printf("Problem writing new parameter file: %s\n", fileres);goto end;
6586: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
6587: }
6588: fprintf(ficres,"#%s\n",version);
6589: } /* End of mle != -3 */
6590:
1.186 brouard 6591: /* Main data
6592: */
1.126 brouard 6593: n= lastobs;
6594: num=lvector(1,n);
6595: moisnais=vector(1,n);
6596: annais=vector(1,n);
6597: moisdc=vector(1,n);
6598: andc=vector(1,n);
6599: agedc=vector(1,n);
6600: cod=ivector(1,n);
6601: weight=vector(1,n);
6602: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
6603: mint=matrix(1,maxwav,1,n);
6604: anint=matrix(1,maxwav,1,n);
1.131 brouard 6605: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 6606: tab=ivector(1,NCOVMAX);
1.144 brouard 6607: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.126 brouard 6608:
1.136 brouard 6609: /* Reads data from file datafile */
6610: if (readdata(datafile, firstobs, lastobs, &imx)==1)
6611: goto end;
6612:
6613: /* Calculation of the number of parameters from char model */
1.137 brouard 6614: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
6615: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
6616: k=3 V4 Tvar[k=3]= 4 (from V4)
6617: k=2 V1 Tvar[k=2]= 1 (from V1)
6618: k=1 Tvar[1]=2 (from V2)
6619: */
6620: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
6621: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
6622: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
6623: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
6624: */
6625: /* For model-covariate k tells which data-covariate to use but
6626: because this model-covariate is a construction we invent a new column
6627: ncovcol + k1
6628: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
6629: Tvar[3=V1*V4]=4+1 etc */
1.145 brouard 6630: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
1.137 brouard 6631: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
6632: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
6633: */
1.145 brouard 6634: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
6635: 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 6636: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
6637: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 6638: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 6639: 4 covariates (3 plus signs)
6640: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
6641: */
1.136 brouard 6642:
1.186 brouard 6643: /* Main decodemodel */
6644:
1.187 ! brouard 6645:
1.136 brouard 6646: if(decodemodel(model, lastobs) == 1)
6647: goto end;
6648:
1.137 brouard 6649: if((double)(lastobs-imx)/(double)imx > 1.10){
6650: nbwarn++;
6651: 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);
6652: 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);
6653: }
1.136 brouard 6654: /* if(mle==1){*/
1.137 brouard 6655: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
6656: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 6657: }
6658:
6659: /*-calculation of age at interview from date of interview and age at death -*/
6660: agev=matrix(1,maxwav,1,imx);
6661:
6662: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
6663: goto end;
6664:
1.126 brouard 6665:
1.136 brouard 6666: agegomp=(int)agemin;
6667: free_vector(moisnais,1,n);
6668: free_vector(annais,1,n);
1.126 brouard 6669: /* free_matrix(mint,1,maxwav,1,n);
6670: free_matrix(anint,1,maxwav,1,n);*/
6671: free_vector(moisdc,1,n);
6672: free_vector(andc,1,n);
1.145 brouard 6673: /* */
6674:
1.126 brouard 6675: wav=ivector(1,imx);
6676: dh=imatrix(1,lastpass-firstpass+1,1,imx);
6677: bh=imatrix(1,lastpass-firstpass+1,1,imx);
6678: mw=imatrix(1,lastpass-firstpass+1,1,imx);
6679:
6680: /* Concatenates waves */
6681: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 brouard 6682: /* */
6683:
1.126 brouard 6684: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
6685:
6686: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
6687: ncodemax[1]=1;
1.145 brouard 6688: Ndum =ivector(-1,NCOVMAX);
1.187 ! brouard 6689: if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */
1.145 brouard 6690: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.186 brouard 6691: /* Nbcode gives the value of the lth modality of jth covariate, in
6692: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
6693: /* 1 to ncodemax[j] is the maximum value of this jth covariate */
1.145 brouard 6694:
6695: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
6696: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
1.186 brouard 6697: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.145 brouard 6698: h=0;
6699:
6700:
6701: /*if (cptcovn > 0) */
1.126 brouard 6702:
1.145 brouard 6703:
1.126 brouard 6704: m=pow(2,cptcoveff);
6705:
1.131 brouard 6706: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
1.143 brouard 6707: 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 */
6708: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
6709: 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 6710: h++;
1.141 brouard 6711: if (h>m)
1.136 brouard 6712: h=1;
1.144 brouard 6713: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.186 brouard 6714: * For k=4 covariates, h goes from 1 to 2**k
6715: * codtabm(h,k)= 1 & (h-1) >> (k-1) ;
6716: * h\k 1 2 3 4
1.143 brouard 6717: *______________________________
6718: * 1 i=1 1 i=1 1 i=1 1 i=1 1
6719: * 2 2 1 1 1
6720: * 3 i=2 1 2 1 1
6721: * 4 2 2 1 1
6722: * 5 i=3 1 i=2 1 2 1
6723: * 6 2 1 2 1
6724: * 7 i=4 1 2 2 1
6725: * 8 2 2 2 1
6726: * 9 i=5 1 i=3 1 i=2 1 1
6727: * 10 2 1 1 1
6728: * 11 i=6 1 2 1 1
6729: * 12 2 2 1 1
6730: * 13 i=7 1 i=4 1 2 1
6731: * 14 2 1 2 1
6732: * 15 i=8 1 2 2 1
6733: * 16 2 2 2 1
6734: */
1.141 brouard 6735: codtab[h][k]=j;
1.186 brouard 6736: /* codtab[12][3]=1; */
1.145 brouard 6737: /*codtab[h][Tvar[k]]=j;*/
1.130 brouard 6738: 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 6739: }
6740: }
6741: }
6742: }
6743: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
6744: codtab[1][2]=1;codtab[2][2]=2; */
6745: /* for(i=1; i <=m ;i++){
6746: for(k=1; k <=cptcovn; k++){
1.131 brouard 6747: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
1.126 brouard 6748: }
6749: printf("\n");
6750: }
6751: scanf("%d",i);*/
1.145 brouard 6752:
6753: free_ivector(Ndum,-1,NCOVMAX);
6754:
6755:
1.126 brouard 6756:
1.186 brouard 6757: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 6758: strcpy(optionfilegnuplot,optionfilefiname);
6759: if(mle==-3)
6760: strcat(optionfilegnuplot,"-mort");
6761: strcat(optionfilegnuplot,".gp");
6762:
6763: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
6764: printf("Problem with file %s",optionfilegnuplot);
6765: }
6766: else{
6767: fprintf(ficgp,"\n# %s\n", version);
6768: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 6769: //fprintf(ficgp,"set missing 'NaNq'\n");
6770: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 6771: }
6772: /* fclose(ficgp);*/
1.186 brouard 6773:
6774:
6775: /* Initialisation of --------- index.htm --------*/
1.126 brouard 6776:
6777: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
6778: if(mle==-3)
6779: strcat(optionfilehtm,"-mort");
6780: strcat(optionfilehtm,".htm");
6781: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 6782: printf("Problem with %s \n",optionfilehtm);
6783: exit(0);
1.126 brouard 6784: }
6785:
6786: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
6787: strcat(optionfilehtmcov,"-cov.htm");
6788: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
6789: printf("Problem with %s \n",optionfilehtmcov), exit(0);
6790: }
6791: else{
6792: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6793: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6794: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
6795: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
6796: }
6797:
6798: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6799: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6800: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
6801: \n\
6802: <hr size=\"2\" color=\"#EC5E5E\">\
6803: <ul><li><h4>Parameter files</h4>\n\
6804: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
6805: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
6806: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
6807: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
6808: - Date and time at start: %s</ul>\n",\
6809: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
6810: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
6811: fileres,fileres,\
6812: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
6813: fflush(fichtm);
6814:
6815: strcpy(pathr,path);
6816: strcat(pathr,optionfilefiname);
1.184 brouard 6817: #ifdef WIN32
6818: _chdir(optionfilefiname); /* Move to directory named optionfile */
6819: #else
1.126 brouard 6820: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 6821: #endif
6822:
1.126 brouard 6823:
6824: /* Calculates basic frequencies. Computes observed prevalence at single age
6825: and prints on file fileres'p'. */
6826: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
6827:
6828: fprintf(fichtm,"\n");
6829: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
6830: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
6831: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
6832: imx,agemin,agemax,jmin,jmax,jmean);
6833: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6834: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6835: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6836: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6837: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
6838:
6839:
6840: /* For Powell, parameters are in a vector p[] starting at p[1]
6841: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
6842: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
6843:
6844: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 6845: /* For mortality only */
1.126 brouard 6846: if (mle==-3){
1.136 brouard 6847: ximort=matrix(1,NDIM,1,NDIM);
1.186 brouard 6848: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 6849: cens=ivector(1,n);
6850: ageexmed=vector(1,n);
6851: agecens=vector(1,n);
6852: dcwave=ivector(1,n);
6853:
6854: for (i=1; i<=imx; i++){
6855: dcwave[i]=-1;
6856: for (m=firstpass; m<=lastpass; m++)
6857: if (s[m][i]>nlstate) {
6858: dcwave[i]=m;
6859: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
6860: break;
6861: }
6862: }
6863:
6864: for (i=1; i<=imx; i++) {
6865: if (wav[i]>0){
6866: ageexmed[i]=agev[mw[1][i]][i];
6867: j=wav[i];
6868: agecens[i]=1.;
6869:
6870: if (ageexmed[i]> 1 && wav[i] > 0){
6871: agecens[i]=agev[mw[j][i]][i];
6872: cens[i]= 1;
6873: }else if (ageexmed[i]< 1)
6874: cens[i]= -1;
6875: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
6876: cens[i]=0 ;
6877: }
6878: else cens[i]=-1;
6879: }
6880:
6881: for (i=1;i<=NDIM;i++) {
6882: for (j=1;j<=NDIM;j++)
6883: ximort[i][j]=(i == j ? 1.0 : 0.0);
6884: }
6885:
1.145 brouard 6886: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 6887: /*printf("%lf %lf", p[1], p[2]);*/
6888:
6889:
1.136 brouard 6890: #ifdef GSL
6891: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 6892: #else
1.126 brouard 6893: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 6894: #endif
1.126 brouard 6895: strcpy(filerespow,"pow-mort");
6896: strcat(filerespow,fileres);
6897: if((ficrespow=fopen(filerespow,"w"))==NULL) {
6898: printf("Problem with resultfile: %s\n", filerespow);
6899: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
6900: }
1.136 brouard 6901: #ifdef GSL
6902: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 6903: #else
1.126 brouard 6904: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 6905: #endif
1.126 brouard 6906: /* for (i=1;i<=nlstate;i++)
6907: for(j=1;j<=nlstate+ndeath;j++)
6908: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
6909: */
6910: fprintf(ficrespow,"\n");
1.136 brouard 6911: #ifdef GSL
6912: /* gsl starts here */
6913: T = gsl_multimin_fminimizer_nmsimplex;
6914: gsl_multimin_fminimizer *sfm = NULL;
6915: gsl_vector *ss, *x;
6916: gsl_multimin_function minex_func;
6917:
6918: /* Initial vertex size vector */
6919: ss = gsl_vector_alloc (NDIM);
6920:
6921: if (ss == NULL){
6922: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
6923: }
6924: /* Set all step sizes to 1 */
6925: gsl_vector_set_all (ss, 0.001);
6926:
6927: /* Starting point */
1.126 brouard 6928:
1.136 brouard 6929: x = gsl_vector_alloc (NDIM);
6930:
6931: if (x == NULL){
6932: gsl_vector_free(ss);
6933: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
6934: }
6935:
6936: /* Initialize method and iterate */
6937: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 6938: /* gsl_vector_set(x, 0, 0.0268); */
6939: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 6940: gsl_vector_set(x, 0, p[1]);
6941: gsl_vector_set(x, 1, p[2]);
6942:
6943: minex_func.f = &gompertz_f;
6944: minex_func.n = NDIM;
6945: minex_func.params = (void *)&p; /* ??? */
6946:
6947: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
6948: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
6949:
6950: printf("Iterations beginning .....\n\n");
6951: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
6952:
6953: iteri=0;
6954: while (rval == GSL_CONTINUE){
6955: iteri++;
6956: status = gsl_multimin_fminimizer_iterate(sfm);
6957:
6958: if (status) printf("error: %s\n", gsl_strerror (status));
6959: fflush(0);
6960:
6961: if (status)
6962: break;
6963:
6964: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
6965: ssval = gsl_multimin_fminimizer_size (sfm);
6966:
6967: if (rval == GSL_SUCCESS)
6968: printf ("converged to a local maximum at\n");
6969:
6970: printf("%5d ", iteri);
6971: for (it = 0; it < NDIM; it++){
6972: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
6973: }
6974: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
6975: }
6976:
6977: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
6978:
6979: gsl_vector_free(x); /* initial values */
6980: gsl_vector_free(ss); /* inital step size */
6981: for (it=0; it<NDIM; it++){
6982: p[it+1]=gsl_vector_get(sfm->x,it);
6983: fprintf(ficrespow," %.12lf", p[it]);
6984: }
6985: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
6986: #endif
6987: #ifdef POWELL
6988: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
6989: #endif
1.126 brouard 6990: fclose(ficrespow);
6991:
6992: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
6993:
6994: for(i=1; i <=NDIM; i++)
6995: for(j=i+1;j<=NDIM;j++)
6996: matcov[i][j]=matcov[j][i];
6997:
6998: printf("\nCovariance matrix\n ");
6999: for(i=1; i <=NDIM; i++) {
7000: for(j=1;j<=NDIM;j++){
7001: printf("%f ",matcov[i][j]);
7002: }
7003: printf("\n ");
7004: }
7005:
7006: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
7007: for (i=1;i<=NDIM;i++)
7008: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
7009:
7010: lsurv=vector(1,AGESUP);
7011: lpop=vector(1,AGESUP);
7012: tpop=vector(1,AGESUP);
7013: lsurv[agegomp]=100000;
7014:
7015: for (k=agegomp;k<=AGESUP;k++) {
7016: agemortsup=k;
7017: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
7018: }
7019:
7020: for (k=agegomp;k<agemortsup;k++)
7021: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
7022:
7023: for (k=agegomp;k<agemortsup;k++){
7024: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
7025: sumlpop=sumlpop+lpop[k];
7026: }
7027:
7028: tpop[agegomp]=sumlpop;
7029: for (k=agegomp;k<(agemortsup-3);k++){
7030: /* tpop[k+1]=2;*/
7031: tpop[k+1]=tpop[k]-lpop[k];
7032: }
7033:
7034:
7035: printf("\nAge lx qx dx Lx Tx e(x)\n");
7036: for (k=agegomp;k<(agemortsup-2);k++)
7037: 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]);
7038:
7039:
7040: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
7041: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
7042:
7043: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
7044: stepm, weightopt,\
7045: model,imx,p,matcov,agemortsup);
7046:
7047: free_vector(lsurv,1,AGESUP);
7048: free_vector(lpop,1,AGESUP);
7049: free_vector(tpop,1,AGESUP);
1.136 brouard 7050: #ifdef GSL
7051: free_ivector(cens,1,n);
7052: free_vector(agecens,1,n);
7053: free_ivector(dcwave,1,n);
7054: free_matrix(ximort,1,NDIM,1,NDIM);
7055: #endif
1.186 brouard 7056: } /* Endof if mle==-3 mortality only */
7057: /* Standard maximisation */
1.126 brouard 7058: else{ /* For mle >=1 */
1.132 brouard 7059: globpr=0;/* debug */
1.186 brouard 7060: /* Computes likelihood for initial parameters */
1.132 brouard 7061: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 7062: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7063: for (k=1; k<=npar;k++)
7064: printf(" %d %8.5f",k,p[k]);
7065: printf("\n");
1.186 brouard 7066: globpr=1; /* again, to print the contributions */
1.126 brouard 7067: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
7068: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7069: for (k=1; k<=npar;k++)
7070: printf(" %d %8.5f",k,p[k]);
7071: printf("\n");
1.186 brouard 7072: if(mle>=1){ /* Could be 1 or 2, Real Maximisation */
1.126 brouard 7073: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
7074: }
7075:
7076: /*--------- results files --------------*/
1.187 ! brouard 7077: 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 7078:
7079:
7080: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7081: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7082: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7083: for(i=1,jk=1; i <=nlstate; i++){
7084: for(k=1; k <=(nlstate+ndeath); k++){
7085: if (k != i) {
7086: printf("%d%d ",i,k);
7087: fprintf(ficlog,"%d%d ",i,k);
7088: fprintf(ficres,"%1d%1d ",i,k);
7089: for(j=1; j <=ncovmodel; j++){
7090: printf("%lf ",p[jk]);
7091: fprintf(ficlog,"%lf ",p[jk]);
7092: fprintf(ficres,"%lf ",p[jk]);
7093: jk++;
7094: }
7095: printf("\n");
7096: fprintf(ficlog,"\n");
7097: fprintf(ficres,"\n");
7098: }
7099: }
7100: }
7101: if(mle!=0){
7102: /* Computing hessian and covariance matrix */
7103: ftolhess=ftol; /* Usually correct */
7104: hesscov(matcov, p, npar, delti, ftolhess, func);
7105: }
7106: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
7107: printf("# Scales (for hessian or gradient estimation)\n");
7108: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
7109: for(i=1,jk=1; i <=nlstate; i++){
7110: for(j=1; j <=nlstate+ndeath; j++){
7111: if (j!=i) {
7112: fprintf(ficres,"%1d%1d",i,j);
7113: printf("%1d%1d",i,j);
7114: fprintf(ficlog,"%1d%1d",i,j);
7115: for(k=1; k<=ncovmodel;k++){
7116: printf(" %.5e",delti[jk]);
7117: fprintf(ficlog," %.5e",delti[jk]);
7118: fprintf(ficres," %.5e",delti[jk]);
7119: jk++;
7120: }
7121: printf("\n");
7122: fprintf(ficlog,"\n");
7123: fprintf(ficres,"\n");
7124: }
7125: }
7126: }
7127:
7128: 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");
7129: if(mle>=1)
7130: 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");
7131: 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");
7132: /* # 121 Var(a12)\n\ */
7133: /* # 122 Cov(b12,a12) Var(b12)\n\ */
7134: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
7135: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
7136: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
7137: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
7138: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
7139: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
7140:
7141:
7142: /* Just to have a covariance matrix which will be more understandable
7143: even is we still don't want to manage dictionary of variables
7144: */
7145: for(itimes=1;itimes<=2;itimes++){
7146: jj=0;
7147: for(i=1; i <=nlstate; i++){
7148: for(j=1; j <=nlstate+ndeath; j++){
7149: if(j==i) continue;
7150: for(k=1; k<=ncovmodel;k++){
7151: jj++;
7152: ca[0]= k+'a'-1;ca[1]='\0';
7153: if(itimes==1){
7154: if(mle>=1)
7155: printf("#%1d%1d%d",i,j,k);
7156: fprintf(ficlog,"#%1d%1d%d",i,j,k);
7157: fprintf(ficres,"#%1d%1d%d",i,j,k);
7158: }else{
7159: if(mle>=1)
7160: printf("%1d%1d%d",i,j,k);
7161: fprintf(ficlog,"%1d%1d%d",i,j,k);
7162: fprintf(ficres,"%1d%1d%d",i,j,k);
7163: }
7164: ll=0;
7165: for(li=1;li <=nlstate; li++){
7166: for(lj=1;lj <=nlstate+ndeath; lj++){
7167: if(lj==li) continue;
7168: for(lk=1;lk<=ncovmodel;lk++){
7169: ll++;
7170: if(ll<=jj){
7171: cb[0]= lk +'a'-1;cb[1]='\0';
7172: if(ll<jj){
7173: if(itimes==1){
7174: if(mle>=1)
7175: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7176: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7177: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7178: }else{
7179: if(mle>=1)
7180: printf(" %.5e",matcov[jj][ll]);
7181: fprintf(ficlog," %.5e",matcov[jj][ll]);
7182: fprintf(ficres," %.5e",matcov[jj][ll]);
7183: }
7184: }else{
7185: if(itimes==1){
7186: if(mle>=1)
7187: printf(" Var(%s%1d%1d)",ca,i,j);
7188: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
7189: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
7190: }else{
7191: if(mle>=1)
7192: printf(" %.5e",matcov[jj][ll]);
7193: fprintf(ficlog," %.5e",matcov[jj][ll]);
7194: fprintf(ficres," %.5e",matcov[jj][ll]);
7195: }
7196: }
7197: }
7198: } /* end lk */
7199: } /* end lj */
7200: } /* end li */
7201: if(mle>=1)
7202: printf("\n");
7203: fprintf(ficlog,"\n");
7204: fprintf(ficres,"\n");
7205: numlinepar++;
7206: } /* end k*/
7207: } /*end j */
7208: } /* end i */
7209: } /* end itimes */
7210:
7211: fflush(ficlog);
7212: fflush(ficres);
7213:
7214: while((c=getc(ficpar))=='#' && c!= EOF){
7215: ungetc(c,ficpar);
7216: fgets(line, MAXLINE, ficpar);
1.141 brouard 7217: fputs(line,stdout);
1.126 brouard 7218: fputs(line,ficparo);
7219: }
7220: ungetc(c,ficpar);
7221:
7222: estepm=0;
7223: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
7224: if (estepm==0 || estepm < stepm) estepm=stepm;
7225: if (fage <= 2) {
7226: bage = ageminpar;
7227: fage = agemaxpar;
7228: }
7229:
7230: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
7231: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
7232: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
1.186 brouard 7233:
7234: /* Other stuffs, more or less useful */
1.126 brouard 7235: while((c=getc(ficpar))=='#' && c!= EOF){
7236: ungetc(c,ficpar);
7237: fgets(line, MAXLINE, ficpar);
1.141 brouard 7238: fputs(line,stdout);
1.126 brouard 7239: fputs(line,ficparo);
7240: }
7241: ungetc(c,ficpar);
7242:
7243: 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);
7244: 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);
7245: 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);
7246: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
7247: fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
7248:
7249: while((c=getc(ficpar))=='#' && c!= EOF){
7250: ungetc(c,ficpar);
7251: fgets(line, MAXLINE, ficpar);
1.141 brouard 7252: fputs(line,stdout);
1.126 brouard 7253: fputs(line,ficparo);
7254: }
7255: ungetc(c,ficpar);
7256:
7257:
7258: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
7259: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
7260:
7261: fscanf(ficpar,"pop_based=%d\n",&popbased);
7262: fprintf(ficparo,"pop_based=%d\n",popbased);
7263: fprintf(ficres,"pop_based=%d\n",popbased);
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: 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);
7274: 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);
7275: 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);
7276: 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);
7277: 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);
7278: /* day and month of proj2 are not used but only year anproj2.*/
7279:
7280:
7281:
1.145 brouard 7282: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
7283: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 7284:
7285: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
7286: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
7287:
7288: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
7289: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
7290: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
7291:
7292: /*------------ free_vector -------------*/
7293: /* chdir(path); */
7294:
7295: free_ivector(wav,1,imx);
7296: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
7297: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
7298: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
7299: free_lvector(num,1,n);
7300: free_vector(agedc,1,n);
7301: /*free_matrix(covar,0,NCOVMAX,1,n);*/
7302: /*free_matrix(covar,1,NCOVMAX,1,n);*/
7303: fclose(ficparo);
7304: fclose(ficres);
7305:
7306:
1.186 brouard 7307: /* Other results (useful)*/
7308:
7309:
1.126 brouard 7310: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 7311: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
7312: prlim=matrix(1,nlstate,1,nlstate);
7313: prevalence_limit(p, prlim, ageminpar, agemaxpar);
1.126 brouard 7314: fclose(ficrespl);
7315:
1.145 brouard 7316: #ifdef FREEEXIT2
7317: #include "freeexit2.h"
7318: #endif
7319:
1.126 brouard 7320: /*------------- h Pij x at various ages ------------*/
1.180 brouard 7321: /*#include "hpijx.h"*/
7322: hPijx(p, bage, fage);
1.145 brouard 7323: fclose(ficrespij);
1.126 brouard 7324:
1.145 brouard 7325: /*-------------- Variance of one-step probabilities---*/
7326: k=1;
1.126 brouard 7327: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
7328:
7329:
7330: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7331: for(i=1;i<=AGESUP;i++)
7332: for(j=1;j<=NCOVMAX;j++)
7333: for(k=1;k<=NCOVMAX;k++)
7334: probs[i][j][k]=0.;
7335:
7336: /*---------- Forecasting ------------------*/
7337: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
7338: if(prevfcast==1){
7339: /* if(stepm ==1){*/
7340: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
7341: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
7342: /* } */
7343: /* else{ */
7344: /* erreur=108; */
7345: /* 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); */
7346: /* 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); */
7347: /* } */
7348: }
1.186 brouard 7349:
7350: /* ------ Other prevalence ratios------------ */
1.126 brouard 7351:
1.127 brouard 7352: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
7353:
7354: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
7355: /* 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",\
7356: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
7357: */
1.126 brouard 7358:
1.127 brouard 7359: if (mobilav!=0) {
7360: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7361: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
7362: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
7363: printf(" Error in movingaverage mobilav=%d\n",mobilav);
7364: }
1.126 brouard 7365: }
7366:
7367:
1.127 brouard 7368: /*---------- Health expectancies, no variances ------------*/
7369:
1.126 brouard 7370: strcpy(filerese,"e");
7371: strcat(filerese,fileres);
7372: if((ficreseij=fopen(filerese,"w"))==NULL) {
7373: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
7374: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
7375: }
7376: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
7377: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.145 brouard 7378: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7379: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7380:
7381: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.127 brouard 7382: fprintf(ficreseij,"\n#****** ");
7383: for(j=1;j<=cptcoveff;j++) {
7384: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7385: }
7386: fprintf(ficreseij,"******\n");
7387:
7388: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7389: oldm=oldms;savm=savms;
7390: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
7391:
7392: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.145 brouard 7393: /*}*/
1.127 brouard 7394: }
7395: fclose(ficreseij);
7396:
7397:
7398: /*---------- Health expectancies and variances ------------*/
7399:
7400:
7401: strcpy(filerest,"t");
7402: strcat(filerest,fileres);
7403: if((ficrest=fopen(filerest,"w"))==NULL) {
7404: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
7405: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
7406: }
7407: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
7408: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
7409:
1.126 brouard 7410:
7411: strcpy(fileresstde,"stde");
7412: strcat(fileresstde,fileres);
7413: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
7414: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
7415: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
7416: }
7417: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
7418: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
7419:
7420: strcpy(filerescve,"cve");
7421: strcat(filerescve,fileres);
7422: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
7423: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
7424: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
7425: }
7426: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
7427: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
7428:
7429: strcpy(fileresv,"v");
7430: strcat(fileresv,fileres);
7431: if((ficresvij=fopen(fileresv,"w"))==NULL) {
7432: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
7433: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
7434: }
7435: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
7436: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
7437:
1.145 brouard 7438: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7439: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7440:
7441: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7442: fprintf(ficrest,"\n#****** ");
1.126 brouard 7443: for(j=1;j<=cptcoveff;j++)
7444: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7445: fprintf(ficrest,"******\n");
7446:
7447: fprintf(ficresstdeij,"\n#****** ");
7448: fprintf(ficrescveij,"\n#****** ");
7449: for(j=1;j<=cptcoveff;j++) {
7450: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7451: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7452: }
7453: fprintf(ficresstdeij,"******\n");
7454: fprintf(ficrescveij,"******\n");
7455:
7456: fprintf(ficresvij,"\n#****** ");
7457: for(j=1;j<=cptcoveff;j++)
7458: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7459: fprintf(ficresvij,"******\n");
7460:
7461: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7462: oldm=oldms;savm=savms;
1.127 brouard 7463: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
1.145 brouard 7464: /*
7465: */
7466: /* goto endfree; */
1.126 brouard 7467:
7468: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7469: pstamp(ficrest);
1.145 brouard 7470:
7471:
1.128 brouard 7472: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.145 brouard 7473: oldm=oldms;savm=savms; /* Segmentation fault */
1.161 brouard 7474: cptcod= 0; /* To be deleted */
7475: 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 7476: 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 7477: if(vpopbased==1)
7478: 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);
7479: else
7480: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
7481: fprintf(ficrest,"# Age e.. (std) ");
7482: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
7483: fprintf(ficrest,"\n");
1.126 brouard 7484:
1.128 brouard 7485: epj=vector(1,nlstate+1);
7486: for(age=bage; age <=fage ;age++){
7487: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
7488: if (vpopbased==1) {
7489: if(mobilav ==0){
7490: for(i=1; i<=nlstate;i++)
7491: prlim[i][i]=probs[(int)age][i][k];
7492: }else{ /* mobilav */
7493: for(i=1; i<=nlstate;i++)
7494: prlim[i][i]=mobaverage[(int)age][i][k];
7495: }
1.126 brouard 7496: }
7497:
1.128 brouard 7498: fprintf(ficrest," %4.0f",age);
7499: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
7500: for(i=1, epj[j]=0.;i <=nlstate;i++) {
7501: epj[j] += prlim[i][i]*eij[i][j][(int)age];
7502: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
7503: }
7504: epj[nlstate+1] +=epj[j];
1.126 brouard 7505: }
7506:
1.128 brouard 7507: for(i=1, vepp=0.;i <=nlstate;i++)
7508: for(j=1;j <=nlstate;j++)
7509: vepp += vareij[i][j][(int)age];
7510: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
7511: for(j=1;j <=nlstate;j++){
7512: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
7513: }
7514: fprintf(ficrest,"\n");
1.126 brouard 7515: }
7516: }
7517: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
7518: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
7519: free_vector(epj,1,nlstate+1);
1.145 brouard 7520: /*}*/
1.126 brouard 7521: }
7522: free_vector(weight,1,n);
1.145 brouard 7523: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.126 brouard 7524: free_imatrix(s,1,maxwav+1,1,n);
7525: free_matrix(anint,1,maxwav,1,n);
7526: free_matrix(mint,1,maxwav,1,n);
7527: free_ivector(cod,1,n);
7528: free_ivector(tab,1,NCOVMAX);
7529: fclose(ficresstdeij);
7530: fclose(ficrescveij);
7531: fclose(ficresvij);
7532: fclose(ficrest);
7533: fclose(ficpar);
7534:
7535: /*------- Variance of period (stable) prevalence------*/
7536:
7537: strcpy(fileresvpl,"vpl");
7538: strcat(fileresvpl,fileres);
7539: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
7540: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
7541: exit(0);
7542: }
7543: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
7544:
1.145 brouard 7545: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7546: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7547:
7548: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7549: fprintf(ficresvpl,"\n#****** ");
1.126 brouard 7550: for(j=1;j<=cptcoveff;j++)
7551: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7552: fprintf(ficresvpl,"******\n");
7553:
7554: varpl=matrix(1,nlstate,(int) bage, (int) fage);
7555: oldm=oldms;savm=savms;
7556: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
7557: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 7558: /*}*/
1.126 brouard 7559: }
7560:
7561: fclose(ficresvpl);
7562:
7563: /*---------- End : free ----------------*/
7564: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7565: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7566: } /* mle==-3 arrives here for freeing */
1.164 brouard 7567: /* endfree:*/
1.141 brouard 7568: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.126 brouard 7569: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
7570: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
7571: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
7572: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
7573: free_matrix(covar,0,NCOVMAX,1,n);
7574: free_matrix(matcov,1,npar,1,npar);
7575: /*free_vector(delti,1,npar);*/
7576: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7577: free_matrix(agev,1,maxwav,1,imx);
7578: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7579:
1.145 brouard 7580: free_ivector(ncodemax,1,NCOVMAX);
7581: free_ivector(Tvar,1,NCOVMAX);
7582: free_ivector(Tprod,1,NCOVMAX);
7583: free_ivector(Tvaraff,1,NCOVMAX);
7584: free_ivector(Tage,1,NCOVMAX);
1.126 brouard 7585:
7586: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
7587: free_imatrix(codtab,1,100,1,10);
7588: fflush(fichtm);
7589: fflush(ficgp);
7590:
7591:
7592: if((nberr >0) || (nbwarn>0)){
7593: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
7594: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
7595: }else{
7596: printf("End of Imach\n");
7597: fprintf(ficlog,"End of Imach\n");
7598: }
7599: printf("See log file on %s\n",filelog);
7600: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 7601: /*(void) gettimeofday(&end_time,&tzp);*/
7602: rend_time = time(NULL);
7603: end_time = *localtime(&rend_time);
7604: /* tml = *localtime(&end_time.tm_sec); */
7605: strcpy(strtend,asctime(&end_time));
1.126 brouard 7606: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
7607: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 7608: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.126 brouard 7609:
1.157 brouard 7610: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
7611: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
7612: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 7613: /* printf("Total time was %d uSec.\n", total_usecs);*/
7614: /* if(fileappend(fichtm,optionfilehtm)){ */
7615: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7616: fclose(fichtm);
7617: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7618: fclose(fichtmcov);
7619: fclose(ficgp);
7620: fclose(ficlog);
7621: /*------ End -----------*/
7622:
7623:
7624: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 7625: #ifdef WIN32
7626: if (_chdir(pathcd) != 0)
7627: printf("Can't move to directory %s!\n",path);
7628: if(_getcwd(pathcd,MAXLINE) > 0)
7629: #else
1.126 brouard 7630: if(chdir(pathcd) != 0)
1.184 brouard 7631: printf("Can't move to directory %s!\n", path);
7632: if (getcwd(pathcd, MAXLINE) > 0)
7633: #endif
1.126 brouard 7634: printf("Current directory %s!\n",pathcd);
7635: /*strcat(plotcmd,CHARSEPARATOR);*/
7636: sprintf(plotcmd,"gnuplot");
1.157 brouard 7637: #ifdef _WIN32
1.126 brouard 7638: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
7639: #endif
7640: if(!stat(plotcmd,&info)){
1.158 brouard 7641: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 7642: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 7643: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 7644: }else
7645: strcpy(pplotcmd,plotcmd);
1.157 brouard 7646: #ifdef __unix
1.126 brouard 7647: strcpy(plotcmd,GNUPLOTPROGRAM);
7648: if(!stat(plotcmd,&info)){
1.158 brouard 7649: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 7650: }else
7651: strcpy(pplotcmd,plotcmd);
7652: #endif
7653: }else
7654: strcpy(pplotcmd,plotcmd);
7655:
7656: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 7657: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 7658:
7659: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 7660: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 7661: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 7662: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 7663: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 7664: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 7665: }
1.158 brouard 7666: printf(" Successful, please wait...");
1.126 brouard 7667: while (z[0] != 'q') {
7668: /* chdir(path); */
1.154 brouard 7669: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 7670: scanf("%s",z);
7671: /* if (z[0] == 'c') system("./imach"); */
7672: if (z[0] == 'e') {
1.158 brouard 7673: #ifdef __APPLE__
1.152 brouard 7674: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 7675: #elif __linux
7676: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 7677: #else
1.152 brouard 7678: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 7679: #endif
7680: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
7681: system(pplotcmd);
1.126 brouard 7682: }
7683: else if (z[0] == 'g') system(plotcmd);
7684: else if (z[0] == 'q') exit(0);
7685: }
7686: end:
7687: while (z[0] != 'q') {
7688: printf("\nType q for exiting: ");
7689: scanf("%s",z);
7690: }
7691: }
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