Annotation of imach/src/imach.c, revision 1.203
1.203 ! brouard 1: /* $Id: imach.c,v 1.202 2015/09/22 19:45:16 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.203 ! brouard 4: Revision 1.202 2015/09/22 19:45:16 brouard
! 5: Summary: Adding some overall graph on contribution to likelihood. Might change
! 6:
1.202 brouard 7: Revision 1.201 2015/09/15 17:34:58 brouard
8: Summary: 0.98r0
9:
10: - Some new graphs like suvival functions
11: - Some bugs fixed like model=1+age+V2.
12:
1.201 brouard 13: Revision 1.200 2015/09/09 16:53:55 brouard
14: Summary: Big bug thanks to Flavia
15:
16: Even model=1+age+V2. did not work anymore
17:
1.200 brouard 18: Revision 1.199 2015/09/07 14:09:23 brouard
19: Summary: 0.98q6 changing default small png format for graph to vectorized svg.
20:
1.199 brouard 21: Revision 1.198 2015/09/03 07:14:39 brouard
22: Summary: 0.98q5 Flavia
23:
1.198 brouard 24: Revision 1.197 2015/09/01 18:24:39 brouard
25: *** empty log message ***
26:
1.197 brouard 27: Revision 1.196 2015/08/18 23:17:52 brouard
28: Summary: 0.98q5
29:
1.196 brouard 30: Revision 1.195 2015/08/18 16:28:39 brouard
31: Summary: Adding a hack for testing purpose
32:
33: After reading the title, ftol and model lines, if the comment line has
34: a q, starting with #q, the answer at the end of the run is quit. It
35: permits to run test files in batch with ctest. The former workaround was
36: $ echo q | imach foo.imach
37:
1.195 brouard 38: Revision 1.194 2015/08/18 13:32:00 brouard
39: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
40:
1.194 brouard 41: Revision 1.193 2015/08/04 07:17:42 brouard
42: Summary: 0.98q4
43:
1.193 brouard 44: Revision 1.192 2015/07/16 16:49:02 brouard
45: Summary: Fixing some outputs
46:
1.192 brouard 47: Revision 1.191 2015/07/14 10:00:33 brouard
48: Summary: Some fixes
49:
1.191 brouard 50: Revision 1.190 2015/05/05 08:51:13 brouard
51: Summary: Adding digits in output parameters (7 digits instead of 6)
52:
53: Fix 1+age+.
54:
1.190 brouard 55: Revision 1.189 2015/04/30 14:45:16 brouard
56: Summary: 0.98q2
57:
1.189 brouard 58: Revision 1.188 2015/04/30 08:27:53 brouard
59: *** empty log message ***
60:
1.188 brouard 61: Revision 1.187 2015/04/29 09:11:15 brouard
62: *** empty log message ***
63:
1.187 brouard 64: Revision 1.186 2015/04/23 12:01:52 brouard
65: Summary: V1*age is working now, version 0.98q1
66:
67: Some codes had been disabled in order to simplify and Vn*age was
68: working in the optimization phase, ie, giving correct MLE parameters,
69: but, as usual, outputs were not correct and program core dumped.
70:
1.186 brouard 71: Revision 1.185 2015/03/11 13:26:42 brouard
72: Summary: Inclusion of compile and links command line for Intel Compiler
73:
1.185 brouard 74: Revision 1.184 2015/03/11 11:52:39 brouard
75: Summary: Back from Windows 8. Intel Compiler
76:
1.184 brouard 77: Revision 1.183 2015/03/10 20:34:32 brouard
78: Summary: 0.98q0, trying with directest, mnbrak fixed
79:
80: We use directest instead of original Powell test; probably no
81: incidence on the results, but better justifications;
82: We fixed Numerical Recipes mnbrak routine which was wrong and gave
83: wrong results.
84:
1.183 brouard 85: Revision 1.182 2015/02/12 08:19:57 brouard
86: Summary: Trying to keep directest which seems simpler and more general
87: Author: Nicolas Brouard
88:
1.182 brouard 89: Revision 1.181 2015/02/11 23:22:24 brouard
90: Summary: Comments on Powell added
91:
92: Author:
93:
1.181 brouard 94: Revision 1.180 2015/02/11 17:33:45 brouard
95: Summary: Finishing move from main to function (hpijx and prevalence_limit)
96:
1.180 brouard 97: Revision 1.179 2015/01/04 09:57:06 brouard
98: Summary: back to OS/X
99:
1.179 brouard 100: Revision 1.178 2015/01/04 09:35:48 brouard
101: *** empty log message ***
102:
1.178 brouard 103: Revision 1.177 2015/01/03 18:40:56 brouard
104: Summary: Still testing ilc32 on OSX
105:
1.177 brouard 106: Revision 1.176 2015/01/03 16:45:04 brouard
107: *** empty log message ***
108:
1.176 brouard 109: Revision 1.175 2015/01/03 16:33:42 brouard
110: *** empty log message ***
111:
1.175 brouard 112: Revision 1.174 2015/01/03 16:15:49 brouard
113: Summary: Still in cross-compilation
114:
1.174 brouard 115: Revision 1.173 2015/01/03 12:06:26 brouard
116: Summary: trying to detect cross-compilation
117:
1.173 brouard 118: Revision 1.172 2014/12/27 12:07:47 brouard
119: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
120:
1.172 brouard 121: Revision 1.171 2014/12/23 13:26:59 brouard
122: Summary: Back from Visual C
123:
124: Still problem with utsname.h on Windows
125:
1.171 brouard 126: Revision 1.170 2014/12/23 11:17:12 brouard
127: Summary: Cleaning some \%% back to %%
128:
129: The escape was mandatory for a specific compiler (which one?), but too many warnings.
130:
1.170 brouard 131: Revision 1.169 2014/12/22 23:08:31 brouard
132: Summary: 0.98p
133:
134: Outputs some informations on compiler used, OS etc. Testing on different platforms.
135:
1.169 brouard 136: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 137: Summary: update
1.169 brouard 138:
1.168 brouard 139: Revision 1.167 2014/12/22 13:50:56 brouard
140: Summary: Testing uname and compiler version and if compiled 32 or 64
141:
142: Testing on Linux 64
143:
1.167 brouard 144: Revision 1.166 2014/12/22 11:40:47 brouard
145: *** empty log message ***
146:
1.166 brouard 147: Revision 1.165 2014/12/16 11:20:36 brouard
148: Summary: After compiling on Visual C
149:
150: * imach.c (Module): Merging 1.61 to 1.162
151:
1.165 brouard 152: Revision 1.164 2014/12/16 10:52:11 brouard
153: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
154:
155: * imach.c (Module): Merging 1.61 to 1.162
156:
1.164 brouard 157: Revision 1.163 2014/12/16 10:30:11 brouard
158: * imach.c (Module): Merging 1.61 to 1.162
159:
1.163 brouard 160: Revision 1.162 2014/09/25 11:43:39 brouard
161: Summary: temporary backup 0.99!
162:
1.162 brouard 163: Revision 1.1 2014/09/16 11:06:58 brouard
164: Summary: With some code (wrong) for nlopt
165:
166: Author:
167:
168: Revision 1.161 2014/09/15 20:41:41 brouard
169: Summary: Problem with macro SQR on Intel compiler
170:
1.161 brouard 171: Revision 1.160 2014/09/02 09:24:05 brouard
172: *** empty log message ***
173:
1.160 brouard 174: Revision 1.159 2014/09/01 10:34:10 brouard
175: Summary: WIN32
176: Author: Brouard
177:
1.159 brouard 178: Revision 1.158 2014/08/27 17:11:51 brouard
179: *** empty log message ***
180:
1.158 brouard 181: Revision 1.157 2014/08/27 16:26:55 brouard
182: Summary: Preparing windows Visual studio version
183: Author: Brouard
184:
185: In order to compile on Visual studio, time.h is now correct and time_t
186: and tm struct should be used. difftime should be used but sometimes I
187: just make the differences in raw time format (time(&now).
188: Trying to suppress #ifdef LINUX
189: Add xdg-open for __linux in order to open default browser.
190:
1.157 brouard 191: Revision 1.156 2014/08/25 20:10:10 brouard
192: *** empty log message ***
193:
1.156 brouard 194: Revision 1.155 2014/08/25 18:32:34 brouard
195: Summary: New compile, minor changes
196: Author: Brouard
197:
1.155 brouard 198: Revision 1.154 2014/06/20 17:32:08 brouard
199: Summary: Outputs now all graphs of convergence to period prevalence
200:
1.154 brouard 201: Revision 1.153 2014/06/20 16:45:46 brouard
202: Summary: If 3 live state, convergence to period prevalence on same graph
203: Author: Brouard
204:
1.153 brouard 205: Revision 1.152 2014/06/18 17:54:09 brouard
206: Summary: open browser, use gnuplot on same dir than imach if not found in the path
207:
1.152 brouard 208: Revision 1.151 2014/06/18 16:43:30 brouard
209: *** empty log message ***
210:
1.151 brouard 211: Revision 1.150 2014/06/18 16:42:35 brouard
212: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
213: Author: brouard
214:
1.150 brouard 215: Revision 1.149 2014/06/18 15:51:14 brouard
216: Summary: Some fixes in parameter files errors
217: Author: Nicolas Brouard
218:
1.149 brouard 219: Revision 1.148 2014/06/17 17:38:48 brouard
220: Summary: Nothing new
221: Author: Brouard
222:
223: Just a new packaging for OS/X version 0.98nS
224:
1.148 brouard 225: Revision 1.147 2014/06/16 10:33:11 brouard
226: *** empty log message ***
227:
1.147 brouard 228: Revision 1.146 2014/06/16 10:20:28 brouard
229: Summary: Merge
230: Author: Brouard
231:
232: Merge, before building revised version.
233:
1.146 brouard 234: Revision 1.145 2014/06/10 21:23:15 brouard
235: Summary: Debugging with valgrind
236: Author: Nicolas Brouard
237:
238: Lot of changes in order to output the results with some covariates
239: After the Edimburgh REVES conference 2014, it seems mandatory to
240: improve the code.
241: No more memory valgrind error but a lot has to be done in order to
242: continue the work of splitting the code into subroutines.
243: Also, decodemodel has been improved. Tricode is still not
244: optimal. nbcode should be improved. Documentation has been added in
245: the source code.
246:
1.144 brouard 247: Revision 1.143 2014/01/26 09:45:38 brouard
248: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
249:
250: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
251: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
252:
1.143 brouard 253: Revision 1.142 2014/01/26 03:57:36 brouard
254: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
255:
256: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
257:
1.142 brouard 258: Revision 1.141 2014/01/26 02:42:01 brouard
259: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
260:
1.141 brouard 261: Revision 1.140 2011/09/02 10:37:54 brouard
262: Summary: times.h is ok with mingw32 now.
263:
1.140 brouard 264: Revision 1.139 2010/06/14 07:50:17 brouard
265: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
266: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
267:
1.139 brouard 268: Revision 1.138 2010/04/30 18:19:40 brouard
269: *** empty log message ***
270:
1.138 brouard 271: Revision 1.137 2010/04/29 18:11:38 brouard
272: (Module): Checking covariates for more complex models
273: than V1+V2. A lot of change to be done. Unstable.
274:
1.137 brouard 275: Revision 1.136 2010/04/26 20:30:53 brouard
276: (Module): merging some libgsl code. Fixing computation
277: of likelione (using inter/intrapolation if mle = 0) in order to
278: get same likelihood as if mle=1.
279: Some cleaning of code and comments added.
280:
1.136 brouard 281: Revision 1.135 2009/10/29 15:33:14 brouard
282: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
283:
1.135 brouard 284: Revision 1.134 2009/10/29 13:18:53 brouard
285: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
286:
1.134 brouard 287: Revision 1.133 2009/07/06 10:21:25 brouard
288: just nforces
289:
1.133 brouard 290: Revision 1.132 2009/07/06 08:22:05 brouard
291: Many tings
292:
1.132 brouard 293: Revision 1.131 2009/06/20 16:22:47 brouard
294: Some dimensions resccaled
295:
1.131 brouard 296: Revision 1.130 2009/05/26 06:44:34 brouard
297: (Module): Max Covariate is now set to 20 instead of 8. A
298: lot of cleaning with variables initialized to 0. Trying to make
299: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
300:
1.130 brouard 301: Revision 1.129 2007/08/31 13:49:27 lievre
302: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
303:
1.129 lievre 304: Revision 1.128 2006/06/30 13:02:05 brouard
305: (Module): Clarifications on computing e.j
306:
1.128 brouard 307: Revision 1.127 2006/04/28 18:11:50 brouard
308: (Module): Yes the sum of survivors was wrong since
309: imach-114 because nhstepm was no more computed in the age
310: loop. Now we define nhstepma in the age loop.
311: (Module): In order to speed up (in case of numerous covariates) we
312: compute health expectancies (without variances) in a first step
313: and then all the health expectancies with variances or standard
314: deviation (needs data from the Hessian matrices) which slows the
315: computation.
316: In the future we should be able to stop the program is only health
317: expectancies and graph are needed without standard deviations.
318:
1.127 brouard 319: Revision 1.126 2006/04/28 17:23:28 brouard
320: (Module): Yes the sum of survivors was wrong since
321: imach-114 because nhstepm was no more computed in the age
322: loop. Now we define nhstepma in the age loop.
323: Version 0.98h
324:
1.126 brouard 325: Revision 1.125 2006/04/04 15:20:31 lievre
326: Errors in calculation of health expectancies. Age was not initialized.
327: Forecasting file added.
328:
329: Revision 1.124 2006/03/22 17:13:53 lievre
330: Parameters are printed with %lf instead of %f (more numbers after the comma).
331: The log-likelihood is printed in the log file
332:
333: Revision 1.123 2006/03/20 10:52:43 brouard
334: * imach.c (Module): <title> changed, corresponds to .htm file
335: name. <head> headers where missing.
336:
337: * imach.c (Module): Weights can have a decimal point as for
338: English (a comma might work with a correct LC_NUMERIC environment,
339: otherwise the weight is truncated).
340: Modification of warning when the covariates values are not 0 or
341: 1.
342: Version 0.98g
343:
344: Revision 1.122 2006/03/20 09:45:41 brouard
345: (Module): Weights can have a decimal point as for
346: English (a comma might work with a correct LC_NUMERIC environment,
347: otherwise the weight is truncated).
348: Modification of warning when the covariates values are not 0 or
349: 1.
350: Version 0.98g
351:
352: Revision 1.121 2006/03/16 17:45:01 lievre
353: * imach.c (Module): Comments concerning covariates added
354:
355: * imach.c (Module): refinements in the computation of lli if
356: status=-2 in order to have more reliable computation if stepm is
357: not 1 month. Version 0.98f
358:
359: Revision 1.120 2006/03/16 15:10:38 lievre
360: (Module): refinements in the computation of lli if
361: status=-2 in order to have more reliable computation if stepm is
362: not 1 month. Version 0.98f
363:
364: Revision 1.119 2006/03/15 17:42:26 brouard
365: (Module): Bug if status = -2, the loglikelihood was
366: computed as likelihood omitting the logarithm. Version O.98e
367:
368: Revision 1.118 2006/03/14 18:20:07 brouard
369: (Module): varevsij Comments added explaining the second
370: table of variances if popbased=1 .
371: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
372: (Module): Function pstamp added
373: (Module): Version 0.98d
374:
375: Revision 1.117 2006/03/14 17:16:22 brouard
376: (Module): varevsij Comments added explaining the second
377: table of variances if popbased=1 .
378: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
379: (Module): Function pstamp added
380: (Module): Version 0.98d
381:
382: Revision 1.116 2006/03/06 10:29:27 brouard
383: (Module): Variance-covariance wrong links and
384: varian-covariance of ej. is needed (Saito).
385:
386: Revision 1.115 2006/02/27 12:17:45 brouard
387: (Module): One freematrix added in mlikeli! 0.98c
388:
389: Revision 1.114 2006/02/26 12:57:58 brouard
390: (Module): Some improvements in processing parameter
391: filename with strsep.
392:
393: Revision 1.113 2006/02/24 14:20:24 brouard
394: (Module): Memory leaks checks with valgrind and:
395: datafile was not closed, some imatrix were not freed and on matrix
396: allocation too.
397:
398: Revision 1.112 2006/01/30 09:55:26 brouard
399: (Module): Back to gnuplot.exe instead of wgnuplot.exe
400:
401: Revision 1.111 2006/01/25 20:38:18 brouard
402: (Module): Lots of cleaning and bugs added (Gompertz)
403: (Module): Comments can be added in data file. Missing date values
404: can be a simple dot '.'.
405:
406: Revision 1.110 2006/01/25 00:51:50 brouard
407: (Module): Lots of cleaning and bugs added (Gompertz)
408:
409: Revision 1.109 2006/01/24 19:37:15 brouard
410: (Module): Comments (lines starting with a #) are allowed in data.
411:
412: Revision 1.108 2006/01/19 18:05:42 lievre
413: Gnuplot problem appeared...
414: To be fixed
415:
416: Revision 1.107 2006/01/19 16:20:37 brouard
417: Test existence of gnuplot in imach path
418:
419: Revision 1.106 2006/01/19 13:24:36 brouard
420: Some cleaning and links added in html output
421:
422: Revision 1.105 2006/01/05 20:23:19 lievre
423: *** empty log message ***
424:
425: Revision 1.104 2005/09/30 16:11:43 lievre
426: (Module): sump fixed, loop imx fixed, and simplifications.
427: (Module): If the status is missing at the last wave but we know
428: that the person is alive, then we can code his/her status as -2
429: (instead of missing=-1 in earlier versions) and his/her
430: contributions to the likelihood is 1 - Prob of dying from last
431: health status (= 1-p13= p11+p12 in the easiest case of somebody in
432: the healthy state at last known wave). Version is 0.98
433:
434: Revision 1.103 2005/09/30 15:54:49 lievre
435: (Module): sump fixed, loop imx fixed, and simplifications.
436:
437: Revision 1.102 2004/09/15 17:31:30 brouard
438: Add the possibility to read data file including tab characters.
439:
440: Revision 1.101 2004/09/15 10:38:38 brouard
441: Fix on curr_time
442:
443: Revision 1.100 2004/07/12 18:29:06 brouard
444: Add version for Mac OS X. Just define UNIX in Makefile
445:
446: Revision 1.99 2004/06/05 08:57:40 brouard
447: *** empty log message ***
448:
449: Revision 1.98 2004/05/16 15:05:56 brouard
450: New version 0.97 . First attempt to estimate force of mortality
451: directly from the data i.e. without the need of knowing the health
452: state at each age, but using a Gompertz model: log u =a + b*age .
453: This is the basic analysis of mortality and should be done before any
454: other analysis, in order to test if the mortality estimated from the
455: cross-longitudinal survey is different from the mortality estimated
456: from other sources like vital statistic data.
457:
458: The same imach parameter file can be used but the option for mle should be -3.
459:
1.133 brouard 460: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 461: former routines in order to include the new code within the former code.
462:
463: The output is very simple: only an estimate of the intercept and of
464: the slope with 95% confident intervals.
465:
466: Current limitations:
467: A) Even if you enter covariates, i.e. with the
468: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
469: B) There is no computation of Life Expectancy nor Life Table.
470:
471: Revision 1.97 2004/02/20 13:25:42 lievre
472: Version 0.96d. Population forecasting command line is (temporarily)
473: suppressed.
474:
475: Revision 1.96 2003/07/15 15:38:55 brouard
476: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
477: rewritten within the same printf. Workaround: many printfs.
478:
479: Revision 1.95 2003/07/08 07:54:34 brouard
480: * imach.c (Repository):
481: (Repository): Using imachwizard code to output a more meaningful covariance
482: matrix (cov(a12,c31) instead of numbers.
483:
484: Revision 1.94 2003/06/27 13:00:02 brouard
485: Just cleaning
486:
487: Revision 1.93 2003/06/25 16:33:55 brouard
488: (Module): On windows (cygwin) function asctime_r doesn't
489: exist so I changed back to asctime which exists.
490: (Module): Version 0.96b
491:
492: Revision 1.92 2003/06/25 16:30:45 brouard
493: (Module): On windows (cygwin) function asctime_r doesn't
494: exist so I changed back to asctime which exists.
495:
496: Revision 1.91 2003/06/25 15:30:29 brouard
497: * imach.c (Repository): Duplicated warning errors corrected.
498: (Repository): Elapsed time after each iteration is now output. It
499: helps to forecast when convergence will be reached. Elapsed time
500: is stamped in powell. We created a new html file for the graphs
501: concerning matrix of covariance. It has extension -cov.htm.
502:
503: Revision 1.90 2003/06/24 12:34:15 brouard
504: (Module): Some bugs corrected for windows. Also, when
505: mle=-1 a template is output in file "or"mypar.txt with the design
506: of the covariance matrix to be input.
507:
508: Revision 1.89 2003/06/24 12:30:52 brouard
509: (Module): Some bugs corrected for windows. Also, when
510: mle=-1 a template is output in file "or"mypar.txt with the design
511: of the covariance matrix to be input.
512:
513: Revision 1.88 2003/06/23 17:54:56 brouard
514: * 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.
515:
516: Revision 1.87 2003/06/18 12:26:01 brouard
517: Version 0.96
518:
519: Revision 1.86 2003/06/17 20:04:08 brouard
520: (Module): Change position of html and gnuplot routines and added
521: routine fileappend.
522:
523: Revision 1.85 2003/06/17 13:12:43 brouard
524: * imach.c (Repository): Check when date of death was earlier that
525: current date of interview. It may happen when the death was just
526: prior to the death. In this case, dh was negative and likelihood
527: was wrong (infinity). We still send an "Error" but patch by
528: assuming that the date of death was just one stepm after the
529: interview.
530: (Repository): Because some people have very long ID (first column)
531: we changed int to long in num[] and we added a new lvector for
532: memory allocation. But we also truncated to 8 characters (left
533: truncation)
534: (Repository): No more line truncation errors.
535:
536: Revision 1.84 2003/06/13 21:44:43 brouard
537: * imach.c (Repository): Replace "freqsummary" at a correct
538: place. It differs from routine "prevalence" which may be called
539: many times. Probs is memory consuming and must be used with
540: parcimony.
541: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
542:
543: Revision 1.83 2003/06/10 13:39:11 lievre
544: *** empty log message ***
545:
546: Revision 1.82 2003/06/05 15:57:20 brouard
547: Add log in imach.c and fullversion number is now printed.
548:
549: */
550: /*
551: Interpolated Markov Chain
552:
553: Short summary of the programme:
554:
555: This program computes Healthy Life Expectancies from
556: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
557: first survey ("cross") where individuals from different ages are
558: interviewed on their health status or degree of disability (in the
559: case of a health survey which is our main interest) -2- at least a
560: second wave of interviews ("longitudinal") which measure each change
561: (if any) in individual health status. Health expectancies are
562: computed from the time spent in each health state according to a
563: model. More health states you consider, more time is necessary to reach the
564: Maximum Likelihood of the parameters involved in the model. The
565: simplest model is the multinomial logistic model where pij is the
566: probability to be observed in state j at the second wave
567: conditional to be observed in state i at the first wave. Therefore
568: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
569: 'age' is age and 'sex' is a covariate. If you want to have a more
570: complex model than "constant and age", you should modify the program
571: where the markup *Covariates have to be included here again* invites
572: you to do it. More covariates you add, slower the
573: convergence.
574:
575: The advantage of this computer programme, compared to a simple
576: multinomial logistic model, is clear when the delay between waves is not
577: identical for each individual. Also, if a individual missed an
578: intermediate interview, the information is lost, but taken into
579: account using an interpolation or extrapolation.
580:
581: hPijx is the probability to be observed in state i at age x+h
582: conditional to the observed state i at age x. The delay 'h' can be
583: split into an exact number (nh*stepm) of unobserved intermediate
584: states. This elementary transition (by month, quarter,
585: semester or year) is modelled as a multinomial logistic. The hPx
586: matrix is simply the matrix product of nh*stepm elementary matrices
587: and the contribution of each individual to the likelihood is simply
588: hPijx.
589:
590: Also this programme outputs the covariance matrix of the parameters but also
591: of the life expectancies. It also computes the period (stable) prevalence.
592:
1.133 brouard 593: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
594: Institut national d'études démographiques, Paris.
1.126 brouard 595: This software have been partly granted by Euro-REVES, a concerted action
596: from the European Union.
597: It is copyrighted identically to a GNU software product, ie programme and
598: software can be distributed freely for non commercial use. Latest version
599: can be accessed at http://euroreves.ined.fr/imach .
600:
601: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
602: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
603:
604: **********************************************************************/
605: /*
606: main
607: read parameterfile
608: read datafile
609: concatwav
610: freqsummary
611: if (mle >= 1)
612: mlikeli
613: print results files
614: if mle==1
615: computes hessian
616: read end of parameter file: agemin, agemax, bage, fage, estepm
617: begin-prev-date,...
618: open gnuplot file
619: open html file
1.145 brouard 620: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
621: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
622: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
623: freexexit2 possible for memory heap.
624:
625: h Pij x | pij_nom ficrestpij
626: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
627: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
628: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
629:
630: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
631: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
632: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
633: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
634: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
635:
1.126 brouard 636: forecasting if prevfcast==1 prevforecast call prevalence()
637: health expectancies
638: Variance-covariance of DFLE
639: prevalence()
640: movingaverage()
641: varevsij()
642: if popbased==1 varevsij(,popbased)
643: total life expectancies
644: Variance of period (stable) prevalence
645: end
646: */
647:
1.187 brouard 648: /* #define DEBUG */
649: /* #define DEBUGBRENT */
1.203 ! brouard 650: /* #define DEBUGLINMIN */
! 651: /* #define DEBUGHESS */
! 652: #define DEBUGHESSIJ
! 653: /* #define LINMINORIGINAL /\* Don't use loop on scale in linmin (accepting nan)*\/ */
1.165 brouard 654: #define POWELL /* Instead of NLOPT */
1.192 brouard 655: #define POWELLF1F3 /* Skip test */
1.186 brouard 656: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
657: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 658:
659: #include <math.h>
660: #include <stdio.h>
661: #include <stdlib.h>
662: #include <string.h>
1.159 brouard 663:
664: #ifdef _WIN32
665: #include <io.h>
1.172 brouard 666: #include <windows.h>
667: #include <tchar.h>
1.159 brouard 668: #else
1.126 brouard 669: #include <unistd.h>
1.159 brouard 670: #endif
1.126 brouard 671:
672: #include <limits.h>
673: #include <sys/types.h>
1.171 brouard 674:
675: #if defined(__GNUC__)
676: #include <sys/utsname.h> /* Doesn't work on Windows */
677: #endif
678:
1.126 brouard 679: #include <sys/stat.h>
680: #include <errno.h>
1.159 brouard 681: /* extern int errno; */
1.126 brouard 682:
1.157 brouard 683: /* #ifdef LINUX */
684: /* #include <time.h> */
685: /* #include "timeval.h" */
686: /* #else */
687: /* #include <sys/time.h> */
688: /* #endif */
689:
1.126 brouard 690: #include <time.h>
691:
1.136 brouard 692: #ifdef GSL
693: #include <gsl/gsl_errno.h>
694: #include <gsl/gsl_multimin.h>
695: #endif
696:
1.167 brouard 697:
1.162 brouard 698: #ifdef NLOPT
699: #include <nlopt.h>
700: typedef struct {
701: double (* function)(double [] );
702: } myfunc_data ;
703: #endif
704:
1.126 brouard 705: /* #include <libintl.h> */
706: /* #define _(String) gettext (String) */
707:
1.141 brouard 708: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 709:
710: #define GNUPLOTPROGRAM "gnuplot"
711: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
712: #define FILENAMELENGTH 132
713:
714: #define GLOCK_ERROR_NOPATH -1 /* empty path */
715: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
716:
1.144 brouard 717: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
718: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 719:
720: #define NINTERVMAX 8
1.144 brouard 721: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
722: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
723: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.197 brouard 724: #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.126 brouard 725: #define MAXN 20000
1.144 brouard 726: #define YEARM 12. /**< Number of months per year */
1.126 brouard 727: #define AGESUP 130
728: #define AGEBASE 40
1.194 brouard 729: #define AGEOVERFLOW 1.e20
1.164 brouard 730: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 731: #ifdef _WIN32
732: #define DIRSEPARATOR '\\'
733: #define CHARSEPARATOR "\\"
734: #define ODIRSEPARATOR '/'
735: #else
1.126 brouard 736: #define DIRSEPARATOR '/'
737: #define CHARSEPARATOR "/"
738: #define ODIRSEPARATOR '\\'
739: #endif
740:
1.203 ! brouard 741: /* $Id: imach.c,v 1.202 2015/09/22 19:45:16 brouard Exp $ */
1.126 brouard 742: /* $State: Exp $ */
1.196 brouard 743: #include "version.h"
744: char version[]=__IMACH_VERSION__;
1.197 brouard 745: char copyright[]="September 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
1.203 ! brouard 746: char fullversion[]="$Revision: 1.202 $ $Date: 2015/09/22 19:45:16 $";
1.126 brouard 747: char strstart[80];
748: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 749: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 750: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 751: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
752: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
753: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
754: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
755: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
756: int cptcovprodnoage=0; /**< Number of covariate products without age */
757: int cptcoveff=0; /* Total number of covariates to vary for printing results */
758: int cptcov=0; /* Working variable */
1.126 brouard 759: int npar=NPARMAX;
760: int nlstate=2; /* Number of live states */
761: int ndeath=1; /* Number of dead states */
1.130 brouard 762: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.126 brouard 763: int popbased=0;
764:
765: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 766: int maxwav=0; /* Maxim number of waves */
767: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
768: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
769: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 770: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 771: int mle=1, weightopt=0;
1.126 brouard 772: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
773: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
774: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
775: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 776: int countcallfunc=0; /* Count the number of calls to func */
1.130 brouard 777: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 778: double **matprod2(); /* test */
1.126 brouard 779: double **oldm, **newm, **savm; /* Working pointers to matrices */
780: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.136 brouard 781: /*FILE *fic ; */ /* Used in readdata only */
782: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.126 brouard 783: FILE *ficlog, *ficrespow;
1.130 brouard 784: int globpr=0; /* Global variable for printing or not */
1.126 brouard 785: double fretone; /* Only one call to likelihood */
1.130 brouard 786: long ipmx=0; /* Number of contributions */
1.126 brouard 787: double sw; /* Sum of weights */
788: char filerespow[FILENAMELENGTH];
789: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
790: FILE *ficresilk;
791: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
792: FILE *ficresprobmorprev;
793: FILE *fichtm, *fichtmcov; /* Html File */
794: FILE *ficreseij;
795: char filerese[FILENAMELENGTH];
796: FILE *ficresstdeij;
797: char fileresstde[FILENAMELENGTH];
798: FILE *ficrescveij;
799: char filerescve[FILENAMELENGTH];
800: FILE *ficresvij;
801: char fileresv[FILENAMELENGTH];
802: FILE *ficresvpl;
803: char fileresvpl[FILENAMELENGTH];
804: char title[MAXLINE];
805: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
806: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
807: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
808: char command[FILENAMELENGTH];
809: int outcmd=0;
810:
811: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.202 brouard 812: char fileresu[FILENAMELENGTH]; /* fileres without r in front */
1.126 brouard 813: char filelog[FILENAMELENGTH]; /* Log file */
814: char filerest[FILENAMELENGTH];
815: char fileregp[FILENAMELENGTH];
816: char popfile[FILENAMELENGTH];
817:
818: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
819:
1.157 brouard 820: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
821: /* struct timezone tzp; */
822: /* extern int gettimeofday(); */
823: struct tm tml, *gmtime(), *localtime();
824:
825: extern time_t time();
826:
827: struct tm start_time, end_time, curr_time, last_time, forecast_time;
828: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
829: struct tm tm;
830:
1.126 brouard 831: char strcurr[80], strfor[80];
832:
833: char *endptr;
834: long lval;
835: double dval;
836:
837: #define NR_END 1
838: #define FREE_ARG char*
839: #define FTOL 1.0e-10
840:
841: #define NRANSI
842: #define ITMAX 200
843:
844: #define TOL 2.0e-4
845:
846: #define CGOLD 0.3819660
847: #define ZEPS 1.0e-10
848: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
849:
850: #define GOLD 1.618034
851: #define GLIMIT 100.0
852: #define TINY 1.0e-20
853:
854: static double maxarg1,maxarg2;
855: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
856: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
857:
858: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
859: #define rint(a) floor(a+0.5)
1.166 brouard 860: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 861: #define mytinydouble 1.0e-16
1.166 brouard 862: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
863: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
864: /* static double dsqrarg; */
865: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 866: static double sqrarg;
867: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
868: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
869: int agegomp= AGEGOMP;
870:
871: int imx;
872: int stepm=1;
873: /* Stepm, step in month: minimum step interpolation*/
874:
875: int estepm;
876: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
877:
878: int m,nb;
879: long *num;
1.197 brouard 880: int firstpass=0, lastpass=4,*cod, *cens;
1.192 brouard 881: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
882: covariate for which somebody answered excluding
883: undefined. Usually 2: 0 and 1. */
884: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
885: covariate for which somebody answered including
886: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 887: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
888: double **pmmij, ***probs;
889: double *ageexmed,*agecens;
890: double dateintmean=0;
891:
892: double *weight;
893: int **s; /* Status */
1.141 brouard 894: double *agedc;
1.145 brouard 895: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 896: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 897: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.141 brouard 898: double idx;
899: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.197 brouard 900: int *Tage;
1.145 brouard 901: int *Ndum; /** Freq of modality (tricode */
1.200 brouard 902: /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
1.141 brouard 903: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.126 brouard 904: double *lsurv, *lpop, *tpop;
905:
1.143 brouard 906: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
907: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 908:
909: /**************** split *************************/
910: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
911: {
912: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
913: the name of the file (name), its extension only (ext) and its first part of the name (finame)
914: */
915: char *ss; /* pointer */
1.186 brouard 916: int l1=0, l2=0; /* length counters */
1.126 brouard 917:
918: l1 = strlen(path ); /* length of path */
919: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
920: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
921: if ( ss == NULL ) { /* no directory, so determine current directory */
922: strcpy( name, path ); /* we got the fullname name because no directory */
923: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
924: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
925: /* get current working directory */
926: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 927: #ifdef WIN32
928: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
929: #else
930: if (getcwd(dirc, FILENAME_MAX) == NULL) {
931: #endif
1.126 brouard 932: return( GLOCK_ERROR_GETCWD );
933: }
934: /* got dirc from getcwd*/
935: printf(" DIRC = %s \n",dirc);
936: } else { /* strip direcotry from path */
937: ss++; /* after this, the filename */
938: l2 = strlen( ss ); /* length of filename */
939: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
940: strcpy( name, ss ); /* save file name */
941: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 942: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 943: printf(" DIRC2 = %s \n",dirc);
944: }
945: /* We add a separator at the end of dirc if not exists */
946: l1 = strlen( dirc ); /* length of directory */
947: if( dirc[l1-1] != DIRSEPARATOR ){
948: dirc[l1] = DIRSEPARATOR;
949: dirc[l1+1] = 0;
950: printf(" DIRC3 = %s \n",dirc);
951: }
952: ss = strrchr( name, '.' ); /* find last / */
953: if (ss >0){
954: ss++;
955: strcpy(ext,ss); /* save extension */
956: l1= strlen( name);
957: l2= strlen(ss)+1;
958: strncpy( finame, name, l1-l2);
959: finame[l1-l2]= 0;
960: }
961:
962: return( 0 ); /* we're done */
963: }
964:
965:
966: /******************************************/
967:
968: void replace_back_to_slash(char *s, char*t)
969: {
970: int i;
971: int lg=0;
972: i=0;
973: lg=strlen(t);
974: for(i=0; i<= lg; i++) {
975: (s[i] = t[i]);
976: if (t[i]== '\\') s[i]='/';
977: }
978: }
979:
1.132 brouard 980: char *trimbb(char *out, char *in)
1.137 brouard 981: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 982: char *s;
983: s=out;
984: while (*in != '\0'){
1.137 brouard 985: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 986: in++;
987: }
988: *out++ = *in++;
989: }
990: *out='\0';
991: return s;
992: }
993:
1.187 brouard 994: /* char *substrchaine(char *out, char *in, char *chain) */
995: /* { */
996: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
997: /* char *s, *t; */
998: /* t=in;s=out; */
999: /* while ((*in != *chain) && (*in != '\0')){ */
1000: /* *out++ = *in++; */
1001: /* } */
1002:
1003: /* /\* *in matches *chain *\/ */
1004: /* while ((*in++ == *chain++) && (*in != '\0')){ */
1005: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1006: /* } */
1007: /* in--; chain--; */
1008: /* while ( (*in != '\0')){ */
1009: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1010: /* *out++ = *in++; */
1011: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1012: /* } */
1013: /* *out='\0'; */
1014: /* out=s; */
1015: /* return out; */
1016: /* } */
1017: char *substrchaine(char *out, char *in, char *chain)
1018: {
1019: /* Substract chain 'chain' from 'in', return and output 'out' */
1020: /* in="V1+V1*age+age*age+V2", chain="age*age" */
1021:
1022: char *strloc;
1023:
1024: strcpy (out, in);
1025: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
1026: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
1027: if(strloc != NULL){
1028: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
1029: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
1030: /* strcpy (strloc, strloc +strlen(chain));*/
1031: }
1032: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
1033: return out;
1034: }
1035:
1036:
1.145 brouard 1037: char *cutl(char *blocc, char *alocc, char *in, char occ)
1038: {
1.187 brouard 1039: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 1040: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 1041: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 1042: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1043: */
1.160 brouard 1044: char *s, *t;
1.145 brouard 1045: t=in;s=in;
1046: while ((*in != occ) && (*in != '\0')){
1047: *alocc++ = *in++;
1048: }
1049: if( *in == occ){
1050: *(alocc)='\0';
1051: s=++in;
1052: }
1053:
1054: if (s == t) {/* occ not found */
1055: *(alocc-(in-s))='\0';
1056: in=s;
1057: }
1058: while ( *in != '\0'){
1059: *blocc++ = *in++;
1060: }
1061:
1062: *blocc='\0';
1063: return t;
1064: }
1.137 brouard 1065: char *cutv(char *blocc, char *alocc, char *in, char occ)
1066: {
1.187 brouard 1067: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1068: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1069: gives blocc="abcdef2ghi" and alocc="j".
1070: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1071: */
1072: char *s, *t;
1073: t=in;s=in;
1074: while (*in != '\0'){
1075: while( *in == occ){
1076: *blocc++ = *in++;
1077: s=in;
1078: }
1079: *blocc++ = *in++;
1080: }
1081: if (s == t) /* occ not found */
1082: *(blocc-(in-s))='\0';
1083: else
1084: *(blocc-(in-s)-1)='\0';
1085: in=s;
1086: while ( *in != '\0'){
1087: *alocc++ = *in++;
1088: }
1089:
1090: *alocc='\0';
1091: return s;
1092: }
1093:
1.126 brouard 1094: int nbocc(char *s, char occ)
1095: {
1096: int i,j=0;
1097: int lg=20;
1098: i=0;
1099: lg=strlen(s);
1100: for(i=0; i<= lg; i++) {
1101: if (s[i] == occ ) j++;
1102: }
1103: return j;
1104: }
1105:
1.137 brouard 1106: /* void cutv(char *u,char *v, char*t, char occ) */
1107: /* { */
1108: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1109: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1110: /* gives u="abcdef2ghi" and v="j" *\/ */
1111: /* int i,lg,j,p=0; */
1112: /* i=0; */
1113: /* lg=strlen(t); */
1114: /* for(j=0; j<=lg-1; j++) { */
1115: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1116: /* } */
1.126 brouard 1117:
1.137 brouard 1118: /* for(j=0; j<p; j++) { */
1119: /* (u[j] = t[j]); */
1120: /* } */
1121: /* u[p]='\0'; */
1.126 brouard 1122:
1.137 brouard 1123: /* for(j=0; j<= lg; j++) { */
1124: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1125: /* } */
1126: /* } */
1.126 brouard 1127:
1.160 brouard 1128: #ifdef _WIN32
1129: char * strsep(char **pp, const char *delim)
1130: {
1131: char *p, *q;
1132:
1133: if ((p = *pp) == NULL)
1134: return 0;
1135: if ((q = strpbrk (p, delim)) != NULL)
1136: {
1137: *pp = q + 1;
1138: *q = '\0';
1139: }
1140: else
1141: *pp = 0;
1142: return p;
1143: }
1144: #endif
1145:
1.126 brouard 1146: /********************** nrerror ********************/
1147:
1148: void nrerror(char error_text[])
1149: {
1150: fprintf(stderr,"ERREUR ...\n");
1151: fprintf(stderr,"%s\n",error_text);
1152: exit(EXIT_FAILURE);
1153: }
1154: /*********************** vector *******************/
1155: double *vector(int nl, int nh)
1156: {
1157: double *v;
1158: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1159: if (!v) nrerror("allocation failure in vector");
1160: return v-nl+NR_END;
1161: }
1162:
1163: /************************ free vector ******************/
1164: void free_vector(double*v, int nl, int nh)
1165: {
1166: free((FREE_ARG)(v+nl-NR_END));
1167: }
1168:
1169: /************************ivector *******************************/
1170: int *ivector(long nl,long nh)
1171: {
1172: int *v;
1173: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1174: if (!v) nrerror("allocation failure in ivector");
1175: return v-nl+NR_END;
1176: }
1177:
1178: /******************free ivector **************************/
1179: void free_ivector(int *v, long nl, long nh)
1180: {
1181: free((FREE_ARG)(v+nl-NR_END));
1182: }
1183:
1184: /************************lvector *******************************/
1185: long *lvector(long nl,long nh)
1186: {
1187: long *v;
1188: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1189: if (!v) nrerror("allocation failure in ivector");
1190: return v-nl+NR_END;
1191: }
1192:
1193: /******************free lvector **************************/
1194: void free_lvector(long *v, long nl, long nh)
1195: {
1196: free((FREE_ARG)(v+nl-NR_END));
1197: }
1198:
1199: /******************* imatrix *******************************/
1200: int **imatrix(long nrl, long nrh, long ncl, long nch)
1201: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1202: {
1203: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1204: int **m;
1205:
1206: /* allocate pointers to rows */
1207: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1208: if (!m) nrerror("allocation failure 1 in matrix()");
1209: m += NR_END;
1210: m -= nrl;
1211:
1212:
1213: /* allocate rows and set pointers to them */
1214: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1215: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1216: m[nrl] += NR_END;
1217: m[nrl] -= ncl;
1218:
1219: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1220:
1221: /* return pointer to array of pointers to rows */
1222: return m;
1223: }
1224:
1225: /****************** free_imatrix *************************/
1226: void free_imatrix(m,nrl,nrh,ncl,nch)
1227: int **m;
1228: long nch,ncl,nrh,nrl;
1229: /* free an int matrix allocated by imatrix() */
1230: {
1231: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1232: free((FREE_ARG) (m+nrl-NR_END));
1233: }
1234:
1235: /******************* matrix *******************************/
1236: double **matrix(long nrl, long nrh, long ncl, long nch)
1237: {
1238: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1239: double **m;
1240:
1241: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1242: if (!m) nrerror("allocation failure 1 in matrix()");
1243: m += NR_END;
1244: m -= nrl;
1245:
1246: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1247: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1248: m[nrl] += NR_END;
1249: m[nrl] -= ncl;
1250:
1251: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1252: return m;
1.145 brouard 1253: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1254: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1255: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1256: */
1257: }
1258:
1259: /*************************free matrix ************************/
1260: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1261: {
1262: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1263: free((FREE_ARG)(m+nrl-NR_END));
1264: }
1265:
1266: /******************* ma3x *******************************/
1267: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1268: {
1269: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1270: double ***m;
1271:
1272: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1273: if (!m) nrerror("allocation failure 1 in matrix()");
1274: m += NR_END;
1275: m -= nrl;
1276:
1277: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1278: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1279: m[nrl] += NR_END;
1280: m[nrl] -= ncl;
1281:
1282: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1283:
1284: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1285: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1286: m[nrl][ncl] += NR_END;
1287: m[nrl][ncl] -= nll;
1288: for (j=ncl+1; j<=nch; j++)
1289: m[nrl][j]=m[nrl][j-1]+nlay;
1290:
1291: for (i=nrl+1; i<=nrh; i++) {
1292: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1293: for (j=ncl+1; j<=nch; j++)
1294: m[i][j]=m[i][j-1]+nlay;
1295: }
1296: return m;
1297: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1298: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1299: */
1300: }
1301:
1302: /*************************free ma3x ************************/
1303: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1304: {
1305: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1306: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1307: free((FREE_ARG)(m+nrl-NR_END));
1308: }
1309:
1310: /*************** function subdirf ***********/
1311: char *subdirf(char fileres[])
1312: {
1313: /* Caution optionfilefiname is hidden */
1314: strcpy(tmpout,optionfilefiname);
1315: strcat(tmpout,"/"); /* Add to the right */
1316: strcat(tmpout,fileres);
1317: return tmpout;
1318: }
1319:
1320: /*************** function subdirf2 ***********/
1321: char *subdirf2(char fileres[], char *preop)
1322: {
1323:
1324: /* Caution optionfilefiname is hidden */
1325: strcpy(tmpout,optionfilefiname);
1326: strcat(tmpout,"/");
1327: strcat(tmpout,preop);
1328: strcat(tmpout,fileres);
1329: return tmpout;
1330: }
1331:
1332: /*************** function subdirf3 ***********/
1333: char *subdirf3(char fileres[], char *preop, char *preop2)
1334: {
1335:
1336: /* Caution optionfilefiname is hidden */
1337: strcpy(tmpout,optionfilefiname);
1338: strcat(tmpout,"/");
1339: strcat(tmpout,preop);
1340: strcat(tmpout,preop2);
1341: strcat(tmpout,fileres);
1342: return tmpout;
1343: }
1344:
1.162 brouard 1345: char *asc_diff_time(long time_sec, char ascdiff[])
1346: {
1347: long sec_left, days, hours, minutes;
1348: days = (time_sec) / (60*60*24);
1349: sec_left = (time_sec) % (60*60*24);
1350: hours = (sec_left) / (60*60) ;
1351: sec_left = (sec_left) %(60*60);
1352: minutes = (sec_left) /60;
1353: sec_left = (sec_left) % (60);
1354: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1355: return ascdiff;
1356: }
1357:
1.126 brouard 1358: /***************** f1dim *************************/
1359: extern int ncom;
1360: extern double *pcom,*xicom;
1361: extern double (*nrfunc)(double []);
1362:
1363: double f1dim(double x)
1364: {
1365: int j;
1366: double f;
1367: double *xt;
1368:
1369: xt=vector(1,ncom);
1370: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1371: f=(*nrfunc)(xt);
1372: free_vector(xt,1,ncom);
1373: return f;
1374: }
1375:
1376: /*****************brent *************************/
1377: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1378: {
1379: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1380: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1381: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1382: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1383: * returned function value.
1384: */
1.126 brouard 1385: int iter;
1386: double a,b,d,etemp;
1.159 brouard 1387: double fu=0,fv,fw,fx;
1.164 brouard 1388: double ftemp=0.;
1.126 brouard 1389: double p,q,r,tol1,tol2,u,v,w,x,xm;
1390: double e=0.0;
1391:
1392: a=(ax < cx ? ax : cx);
1393: b=(ax > cx ? ax : cx);
1394: x=w=v=bx;
1395: fw=fv=fx=(*f)(x);
1396: for (iter=1;iter<=ITMAX;iter++) {
1397: xm=0.5*(a+b);
1398: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1399: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1400: printf(".");fflush(stdout);
1401: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1402: #ifdef DEBUGBRENT
1.126 brouard 1403: 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);
1404: 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);
1405: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1406: #endif
1407: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1408: *xmin=x;
1409: return fx;
1410: }
1411: ftemp=fu;
1412: if (fabs(e) > tol1) {
1413: r=(x-w)*(fx-fv);
1414: q=(x-v)*(fx-fw);
1415: p=(x-v)*q-(x-w)*r;
1416: q=2.0*(q-r);
1417: if (q > 0.0) p = -p;
1418: q=fabs(q);
1419: etemp=e;
1420: e=d;
1421: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1422: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1423: else {
1424: d=p/q;
1425: u=x+d;
1426: if (u-a < tol2 || b-u < tol2)
1427: d=SIGN(tol1,xm-x);
1428: }
1429: } else {
1430: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1431: }
1432: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1433: fu=(*f)(u);
1434: if (fu <= fx) {
1435: if (u >= x) a=x; else b=x;
1436: SHFT(v,w,x,u)
1.183 brouard 1437: SHFT(fv,fw,fx,fu)
1438: } else {
1439: if (u < x) a=u; else b=u;
1440: if (fu <= fw || w == x) {
1441: v=w;
1442: w=u;
1443: fv=fw;
1444: fw=fu;
1445: } else if (fu <= fv || v == x || v == w) {
1446: v=u;
1447: fv=fu;
1448: }
1449: }
1.126 brouard 1450: }
1451: nrerror("Too many iterations in brent");
1452: *xmin=x;
1453: return fx;
1454: }
1455:
1456: /****************** mnbrak ***********************/
1457:
1458: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1459: double (*func)(double))
1.183 brouard 1460: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1461: the downhill direction (defined by the function as evaluated at the initial points) and returns
1462: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1463: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1464: */
1.126 brouard 1465: double ulim,u,r,q, dum;
1466: double fu;
1.187 brouard 1467:
1468: double scale=10.;
1469: int iterscale=0;
1470:
1471: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1472: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1473:
1474:
1475: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1476: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1477: /* *bx = *ax - (*ax - *bx)/scale; */
1478: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1479: /* } */
1480:
1.126 brouard 1481: if (*fb > *fa) {
1482: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1483: SHFT(dum,*fb,*fa,dum)
1484: }
1.126 brouard 1485: *cx=(*bx)+GOLD*(*bx-*ax);
1486: *fc=(*func)(*cx);
1.183 brouard 1487: #ifdef DEBUG
1488: printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1489: fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1490: #endif
1491: while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
1.126 brouard 1492: r=(*bx-*ax)*(*fb-*fc);
1493: q=(*bx-*cx)*(*fb-*fa);
1494: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 1495: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1496: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1497: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 1498: fu=(*func)(u);
1.163 brouard 1499: #ifdef DEBUG
1500: /* f(x)=A(x-u)**2+f(u) */
1501: double A, fparabu;
1502: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1503: fparabu= *fa - A*(*ax-u)*(*ax-u);
1504: 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);
1505: 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 1506: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1507: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1508: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1509: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 1510: #endif
1.184 brouard 1511: #ifdef MNBRAKORIGINAL
1.183 brouard 1512: #else
1.191 brouard 1513: /* if (fu > *fc) { */
1514: /* #ifdef DEBUG */
1515: /* printf("mnbrak4 fu > fc \n"); */
1516: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
1517: /* #endif */
1518: /* /\* 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 *\\/ *\/ */
1519: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
1520: /* dum=u; /\* Shifting c and u *\/ */
1521: /* u = *cx; */
1522: /* *cx = dum; */
1523: /* dum = fu; */
1524: /* fu = *fc; */
1525: /* *fc =dum; */
1526: /* } else { /\* end *\/ */
1527: /* #ifdef DEBUG */
1528: /* printf("mnbrak3 fu < fc \n"); */
1529: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
1530: /* #endif */
1531: /* dum=u; /\* Shifting c and u *\/ */
1532: /* u = *cx; */
1533: /* *cx = dum; */
1534: /* dum = fu; */
1535: /* fu = *fc; */
1536: /* *fc =dum; */
1537: /* } */
1.183 brouard 1538: #ifdef DEBUG
1.191 brouard 1539: printf("mnbrak34 fu < or >= fc \n");
1540: fprintf(ficlog, "mnbrak34 fu < fc\n");
1.183 brouard 1541: #endif
1.191 brouard 1542: dum=u; /* Shifting c and u */
1543: u = *cx;
1544: *cx = dum;
1545: dum = fu;
1546: fu = *fc;
1547: *fc =dum;
1.183 brouard 1548: #endif
1.162 brouard 1549: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 1550: #ifdef DEBUG
1551: printf("mnbrak2 u after c but before ulim\n");
1552: fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
1553: #endif
1.126 brouard 1554: fu=(*func)(u);
1555: if (fu < *fc) {
1.183 brouard 1556: #ifdef DEBUG
1557: printf("mnbrak2 u after c but before ulim AND fu < fc\n");
1558: fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
1559: #endif
1.126 brouard 1560: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1.183 brouard 1561: SHFT(*fb,*fc,fu,(*func)(u))
1562: }
1.162 brouard 1563: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 1564: #ifdef DEBUG
1565: printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1566: fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1567: #endif
1.126 brouard 1568: u=ulim;
1569: fu=(*func)(u);
1.183 brouard 1570: } else { /* u could be left to b (if r > q parabola has a maximum) */
1571: #ifdef DEBUG
1572: printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1573: fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1574: #endif
1.126 brouard 1575: u=(*cx)+GOLD*(*cx-*bx);
1576: fu=(*func)(u);
1.183 brouard 1577: } /* end tests */
1.126 brouard 1578: SHFT(*ax,*bx,*cx,u)
1.183 brouard 1579: SHFT(*fa,*fb,*fc,fu)
1580: #ifdef DEBUG
1581: 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);
1582: 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);
1583: #endif
1584: } /* 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 1585: }
1586:
1587: /*************** linmin ************************/
1.162 brouard 1588: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1589: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1590: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1591: the value of func at the returned location p . This is actually all accomplished by calling the
1592: routines mnbrak and brent .*/
1.126 brouard 1593: int ncom;
1594: double *pcom,*xicom;
1595: double (*nrfunc)(double []);
1596:
1597: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1598: {
1599: double brent(double ax, double bx, double cx,
1600: double (*f)(double), double tol, double *xmin);
1601: double f1dim(double x);
1602: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1603: double *fc, double (*func)(double));
1604: int j;
1605: double xx,xmin,bx,ax;
1606: double fx,fb,fa;
1.187 brouard 1607:
1.203 ! brouard 1608: #ifdef LINMINORIGINAL
! 1609: #else
! 1610: double scale=10., axs, xxs; /* Scale added for infinity */
! 1611: #endif
! 1612:
1.126 brouard 1613: ncom=n;
1614: pcom=vector(1,n);
1615: xicom=vector(1,n);
1616: nrfunc=func;
1617: for (j=1;j<=n;j++) {
1618: pcom[j]=p[j];
1.202 brouard 1619: xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
1.126 brouard 1620: }
1.187 brouard 1621:
1.203 ! brouard 1622: #ifdef LINMINORIGINAL
! 1623: xx=1.;
! 1624: #else
! 1625: axs=0.0;
! 1626: xxs=1.;
! 1627: do{
! 1628: xx= xxs;
! 1629: #endif
1.187 brouard 1630: ax=0.;
1631: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
1632: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
1633: /* 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)) */
1634: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
1635: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
1636: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
1637: /* 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]]*/
1.203 ! brouard 1638: #ifdef LINMINORIGINAL
! 1639: #else
! 1640: if (fx != fx){
! 1641: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
! 1642: printf("|");
! 1643: fprintf(ficlog,"|");
! 1644: #ifdef DEBUGLINMIN
! 1645: 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);
! 1646: #endif
! 1647: }
! 1648: }while(fx != fx);
! 1649: #endif
! 1650:
1.191 brouard 1651: #ifdef DEBUGLINMIN
1652: printf("\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n", ax,xx,bx,fa,fx,fb);
1.202 brouard 1653: fprintf(ficlog,"\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n", ax,xx,bx,fa,fx,fb);
1.191 brouard 1654: #endif
1.187 brouard 1655: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
1656: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
1657: /* fmin = f(p[j] + xmin * xi[j]) */
1658: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
1659: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 1660: #ifdef DEBUG
1661: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1662: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1663: #endif
1.191 brouard 1664: #ifdef DEBUGLINMIN
1665: printf("linmin end ");
1.202 brouard 1666: fprintf(ficlog,"linmin end ");
1.191 brouard 1667: #endif
1.126 brouard 1668: for (j=1;j<=n;j++) {
1.203 ! brouard 1669: #ifdef LINMINORIGINAL
! 1670: xi[j] *= xmin;
! 1671: #else
! 1672: #ifdef DEBUGLINMIN
! 1673: if(xxs <1.0)
! 1674: printf(" before xi[%d]=%12.8f", j,xi[j]);
! 1675: #endif
! 1676: xi[j] *= xmin*xxs; /* xi rescaled by xmin and number of loops: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
! 1677: #ifdef DEBUGLINMIN
! 1678: if(xxs <1.0)
! 1679: 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 );
! 1680: #endif
! 1681: #endif
1.187 brouard 1682: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 1683: }
1.191 brouard 1684: #ifdef DEBUGLINMIN
1.203 ! brouard 1685: printf("\n");
1.191 brouard 1686: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.202 brouard 1687: fprintf(ficlog,"Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.191 brouard 1688: for (j=1;j<=n;j++) {
1.202 brouard 1689: printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1690: fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1691: if(j % ncovmodel == 0){
1.191 brouard 1692: printf("\n");
1.202 brouard 1693: fprintf(ficlog,"\n");
1694: }
1.191 brouard 1695: }
1.203 ! brouard 1696: #else
1.191 brouard 1697: #endif
1.126 brouard 1698: free_vector(xicom,1,n);
1699: free_vector(pcom,1,n);
1700: }
1701:
1702:
1703: /*************** powell ************************/
1.162 brouard 1704: /*
1705: Minimization of a function func of n variables. Input consists of an initial starting point
1706: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1707: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1708: such that failure to decrease by more than this amount on one iteration signals doneness. On
1709: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1710: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1711: */
1.126 brouard 1712: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1713: double (*func)(double []))
1714: {
1715: void linmin(double p[], double xi[], int n, double *fret,
1716: double (*func)(double []));
1717: int i,ibig,j;
1718: double del,t,*pt,*ptt,*xit;
1.181 brouard 1719: double directest;
1.126 brouard 1720: double fp,fptt;
1721: double *xits;
1722: int niterf, itmp;
1723:
1724: pt=vector(1,n);
1725: ptt=vector(1,n);
1726: xit=vector(1,n);
1727: xits=vector(1,n);
1728: *fret=(*func)(p);
1729: for (j=1;j<=n;j++) pt[j]=p[j];
1.202 brouard 1730: rcurr_time = time(NULL);
1.126 brouard 1731: for (*iter=1;;++(*iter)) {
1.187 brouard 1732: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 1733: ibig=0;
1734: del=0.0;
1.157 brouard 1735: rlast_time=rcurr_time;
1736: /* (void) gettimeofday(&curr_time,&tzp); */
1737: rcurr_time = time(NULL);
1738: curr_time = *localtime(&rcurr_time);
1739: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1740: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1741: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 1742: for (i=1;i<=n;i++) {
1.126 brouard 1743: printf(" %d %.12f",i, p[i]);
1744: fprintf(ficlog," %d %.12lf",i, p[i]);
1745: fprintf(ficrespow," %.12lf", p[i]);
1746: }
1747: printf("\n");
1748: fprintf(ficlog,"\n");
1749: fprintf(ficrespow,"\n");fflush(ficrespow);
1750: if(*iter <=3){
1.157 brouard 1751: tml = *localtime(&rcurr_time);
1752: strcpy(strcurr,asctime(&tml));
1753: rforecast_time=rcurr_time;
1.126 brouard 1754: itmp = strlen(strcurr);
1755: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1756: strcurr[itmp-1]='\0';
1.162 brouard 1757: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 1758: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 1759: for(niterf=10;niterf<=30;niterf+=10){
1.157 brouard 1760: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1761: forecast_time = *localtime(&rforecast_time);
1762: strcpy(strfor,asctime(&forecast_time));
1.126 brouard 1763: itmp = strlen(strfor);
1764: if(strfor[itmp-1]=='\n')
1765: strfor[itmp-1]='\0';
1.157 brouard 1766: 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);
1767: 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 1768: }
1769: }
1.187 brouard 1770: for (i=1;i<=n;i++) { /* For each direction i */
1771: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 1772: fptt=(*fret);
1773: #ifdef DEBUG
1.203 ! brouard 1774: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
! 1775: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 1776: #endif
1.203 ! brouard 1777: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 1778: fprintf(ficlog,"%d",i);fflush(ficlog);
1.188 brouard 1779: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1780: /* Outputs are fret(new point p) p is updated and xit rescaled */
1781: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1782: /* because that direction will be replaced unless the gain del is small */
1783: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
1784: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
1785: /* with the new direction. */
1.126 brouard 1786: del=fabs(fptt-(*fret));
1787: ibig=i;
1788: }
1789: #ifdef DEBUG
1790: printf("%d %.12e",i,(*fret));
1791: fprintf(ficlog,"%d %.12e",i,(*fret));
1792: for (j=1;j<=n;j++) {
1793: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1794: printf(" x(%d)=%.12e",j,xit[j]);
1795: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1796: }
1797: for(j=1;j<=n;j++) {
1.162 brouard 1798: printf(" p(%d)=%.12e",j,p[j]);
1799: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 1800: }
1801: printf("\n");
1802: fprintf(ficlog,"\n");
1803: #endif
1.187 brouard 1804: } /* end loop on each direction i */
1805: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 1806: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 1807: /* New value of last point Pn is not computed, P(n-1) */
1.182 brouard 1808: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1.188 brouard 1809: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
1810: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
1811: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
1812: /* decreased of more than 3.84 */
1813: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
1814: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
1815: /* By adding 10 parameters more the gain should be 18.31 */
1816:
1817: /* Starting the program with initial values given by a former maximization will simply change */
1818: /* the scales of the directions and the directions, because the are reset to canonical directions */
1819: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
1820: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 1821: #ifdef DEBUG
1822: int k[2],l;
1823: k[0]=1;
1824: k[1]=-1;
1825: printf("Max: %.12e",(*func)(p));
1826: fprintf(ficlog,"Max: %.12e",(*func)(p));
1827: for (j=1;j<=n;j++) {
1828: printf(" %.12e",p[j]);
1829: fprintf(ficlog," %.12e",p[j]);
1830: }
1831: printf("\n");
1832: fprintf(ficlog,"\n");
1833: for(l=0;l<=1;l++) {
1834: for (j=1;j<=n;j++) {
1835: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1836: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1837: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1838: }
1839: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1840: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1841: }
1842: #endif
1843:
1844:
1845: free_vector(xit,1,n);
1846: free_vector(xits,1,n);
1847: free_vector(ptt,1,n);
1848: free_vector(pt,1,n);
1849: return;
1.192 brouard 1850: } /* enough precision */
1.126 brouard 1851: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1.181 brouard 1852: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 1853: ptt[j]=2.0*p[j]-pt[j];
1854: xit[j]=p[j]-pt[j];
1855: pt[j]=p[j];
1856: }
1.181 brouard 1857: fptt=(*func)(ptt); /* f_3 */
1.192 brouard 1858: #ifdef POWELLF1F3
1859: #else
1.161 brouard 1860: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 1861: #endif
1.162 brouard 1862: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 1863: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 1864: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1865: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1866: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.181 brouard 1867: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
1.161 brouard 1868: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.183 brouard 1869: #ifdef NRCORIGINAL
1870: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
1871: #else
1872: 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 1873: t= t- del*SQR(fp-fptt);
1.183 brouard 1874: #endif
1.202 brouard 1875: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
1.161 brouard 1876: #ifdef DEBUG
1.181 brouard 1877: 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);
1878: 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 1879: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1880: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1881: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1882: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1883: 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);
1884: 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);
1885: #endif
1.183 brouard 1886: #ifdef POWELLORIGINAL
1887: if (t < 0.0) { /* Then we use it for new direction */
1888: #else
1.182 brouard 1889: if (directest*t < 0.0) { /* Contradiction between both tests */
1.202 brouard 1890: printf("directest= %.12lf (if <0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
1.192 brouard 1891: printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1.202 brouard 1892: fprintf(ficlog,"directest= %.12lf (if <0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
1.192 brouard 1893: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1894: }
1.181 brouard 1895: if (directest < 0.0) { /* Then we use it for new direction */
1896: #endif
1.191 brouard 1897: #ifdef DEBUGLINMIN
1898: printf("Before linmin in direction P%d-P0\n",n);
1899: for (j=1;j<=n;j++) {
1.202 brouard 1900: printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1901: fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1902: if(j % ncovmodel == 0){
1.191 brouard 1903: printf("\n");
1.202 brouard 1904: fprintf(ficlog,"\n");
1905: }
1.191 brouard 1906: }
1907: #endif
1.187 brouard 1908: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.191 brouard 1909: #ifdef DEBUGLINMIN
1910: for (j=1;j<=n;j++) {
1911: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1.202 brouard 1912: fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1913: if(j % ncovmodel == 0){
1.191 brouard 1914: printf("\n");
1.202 brouard 1915: fprintf(ficlog,"\n");
1916: }
1.191 brouard 1917: }
1918: #endif
1.126 brouard 1919: for (j=1;j<=n;j++) {
1.181 brouard 1920: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
1921: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
1.126 brouard 1922: }
1.181 brouard 1923: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1924: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1.161 brouard 1925:
1.126 brouard 1926: #ifdef DEBUG
1.164 brouard 1927: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1928: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1.126 brouard 1929: for(j=1;j<=n;j++){
1930: printf(" %.12e",xit[j]);
1931: fprintf(ficlog," %.12e",xit[j]);
1932: }
1933: printf("\n");
1934: fprintf(ficlog,"\n");
1935: #endif
1.192 brouard 1936: } /* end of t or directest negative */
1937: #ifdef POWELLF1F3
1938: #else
1.162 brouard 1939: } /* end if (fptt < fp) */
1.192 brouard 1940: #endif
1941: } /* loop iteration */
1.126 brouard 1942: }
1943:
1944: /**** Prevalence limit (stable or period prevalence) ****************/
1945:
1.203 ! brouard 1946: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij)
1.126 brouard 1947: {
1948: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1.203 ! brouard 1949: matrix by transitions matrix until convergence is reached with precision ftolpl */
1.169 brouard 1950:
1.126 brouard 1951: int i, ii,j,k;
1952: double min, max, maxmin, maxmax,sumnew=0.;
1.145 brouard 1953: /* double **matprod2(); */ /* test */
1.131 brouard 1954: double **out, cov[NCOVMAX+1], **pmij();
1.126 brouard 1955: double **newm;
1.202 brouard 1956: double agefin, delaymax=100 ; /* Max number of years to converge */
1.203 ! brouard 1957: int ncvloop=0;
1.169 brouard 1958:
1.126 brouard 1959: for (ii=1;ii<=nlstate+ndeath;ii++)
1960: for (j=1;j<=nlstate+ndeath;j++){
1961: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1962: }
1.169 brouard 1963:
1964: cov[1]=1.;
1965:
1966: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.202 brouard 1967: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.126 brouard 1968: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1.202 brouard 1969: ncvloop++;
1.126 brouard 1970: newm=savm;
1971: /* Covariates have to be included here again */
1.138 brouard 1972: cov[2]=agefin;
1.187 brouard 1973: if(nagesqr==1)
1974: cov[3]= agefin*agefin;;
1.138 brouard 1975: for (k=1; k<=cptcovn;k++) {
1.200 brouard 1976: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1977: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
1.198 brouard 1978: /* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); */
1.138 brouard 1979: }
1.186 brouard 1980: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 1981: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
1982: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
1.186 brouard 1983: for (k=1; k<=cptcovprod;k++) /* Useless */
1.200 brouard 1984: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
1985: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
1.138 brouard 1986:
1987: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1988: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1989: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 1990: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1991: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.142 brouard 1992: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 1993:
1.126 brouard 1994: savm=oldm;
1995: oldm=newm;
1996: maxmax=0.;
1997: for(j=1;j<=nlstate;j++){
1998: min=1.;
1999: max=0.;
2000: for(i=1; i<=nlstate; i++) {
2001: sumnew=0;
2002: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
2003: prlim[i][j]= newm[i][j]/(1-sumnew);
2004: max=FMAX(max,prlim[i][j]);
2005: min=FMIN(min,prlim[i][j]);
1.202 brouard 2006: /* printf(" age= %d prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d max=%f min=%f\n", (int)age, i, j, i, j, prlim[i][j],(int)agefin, max, min); */
1.126 brouard 2007: }
1.203 ! brouard 2008: maxmin=(max-min)/(max+min)*2;
1.126 brouard 2009: maxmax=FMAX(maxmax,maxmin);
1.169 brouard 2010: } /* j loop */
1.203 ! brouard 2011: *ncvyear= (int)age- (int)agefin;
! 2012: /* printf("maxmax=%lf maxmin=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.126 brouard 2013: if(maxmax < ftolpl){
1.203 ! brouard 2014: /* printf("maxmax=%lf maxmin=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.126 brouard 2015: return prlim;
2016: }
1.169 brouard 2017: } /* age loop */
1.203 ! brouard 2018: printf("Warning: the stable prevalence at age %d did not converge with the required precision %g > ftolpl=%g. \n\
! 2019: Earliest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
! 2020: /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */
1.169 brouard 2021: return prlim; /* should not reach here */
1.126 brouard 2022: }
2023:
2024: /*************** transition probabilities ***************/
2025:
2026: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
2027: {
1.138 brouard 2028: /* According to parameters values stored in x and the covariate's values stored in cov,
2029: computes the probability to be observed in state j being in state i by appying the
2030: model to the ncovmodel covariates (including constant and age).
2031: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2032: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2033: ncth covariate in the global vector x is given by the formula:
2034: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2035: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2036: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2037: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
2038: Outputs ps[i][j] the probability to be observed in j being in j according to
2039: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
2040: */
2041: double s1, lnpijopii;
1.126 brouard 2042: /*double t34;*/
1.164 brouard 2043: int i,j, nc, ii, jj;
1.126 brouard 2044:
2045: for(i=1; i<= nlstate; i++){
2046: for(j=1; j<i;j++){
1.138 brouard 2047: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2048: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2049: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2050: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 2051: }
1.138 brouard 2052: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2053: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 2054: }
2055: for(j=i+1; j<=nlstate+ndeath;j++){
1.138 brouard 2056: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2057: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2058: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2059: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1.126 brouard 2060: }
1.138 brouard 2061: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1.126 brouard 2062: }
2063: }
2064:
2065: for(i=1; i<= nlstate; i++){
2066: s1=0;
1.131 brouard 2067: for(j=1; j<i; j++){
1.138 brouard 2068: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 2069: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2070: }
2071: for(j=i+1; j<=nlstate+ndeath; j++){
1.138 brouard 2072: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 2073: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2074: }
1.138 brouard 2075: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1.126 brouard 2076: ps[i][i]=1./(s1+1.);
1.138 brouard 2077: /* Computing other pijs */
1.126 brouard 2078: for(j=1; j<i; j++)
2079: ps[i][j]= exp(ps[i][j])*ps[i][i];
2080: for(j=i+1; j<=nlstate+ndeath; j++)
2081: ps[i][j]= exp(ps[i][j])*ps[i][i];
2082: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2083: } /* end i */
2084:
2085: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2086: for(jj=1; jj<= nlstate+ndeath; jj++){
2087: ps[ii][jj]=0;
2088: ps[ii][ii]=1;
2089: }
2090: }
2091:
1.145 brouard 2092:
2093: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2094: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2095: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2096: /* } */
2097: /* printf("\n "); */
2098: /* } */
2099: /* printf("\n ");printf("%lf ",cov[2]);*/
2100: /*
1.126 brouard 2101: for(i=1; i<= npar; i++) printf("%f ",x[i]);
2102: goto end;*/
2103: return ps;
2104: }
2105:
2106: /**************** Product of 2 matrices ******************/
2107:
1.145 brouard 2108: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 2109: {
2110: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
2111: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
2112: /* in, b, out are matrice of pointers which should have been initialized
2113: before: only the contents of out is modified. The function returns
2114: a pointer to pointers identical to out */
1.145 brouard 2115: int i, j, k;
1.126 brouard 2116: for(i=nrl; i<= nrh; i++)
1.145 brouard 2117: for(k=ncolol; k<=ncoloh; k++){
2118: out[i][k]=0.;
2119: for(j=ncl; j<=nch; j++)
2120: out[i][k] +=in[i][j]*b[j][k];
2121: }
1.126 brouard 2122: return out;
2123: }
2124:
2125:
2126: /************* Higher Matrix Product ***************/
2127:
2128: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
2129: {
2130: /* Computes the transition matrix starting at age 'age' over
2131: 'nhstepm*hstepm*stepm' months (i.e. until
2132: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2133: nhstepm*hstepm matrices.
2134: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2135: (typically every 2 years instead of every month which is too big
2136: for the memory).
2137: Model is determined by parameters x and covariates have to be
2138: included manually here.
2139:
2140: */
2141:
2142: int i, j, d, h, k;
1.131 brouard 2143: double **out, cov[NCOVMAX+1];
1.126 brouard 2144: double **newm;
1.187 brouard 2145: double agexact;
1.126 brouard 2146:
2147: /* Hstepm could be zero and should return the unit matrix */
2148: for (i=1;i<=nlstate+ndeath;i++)
2149: for (j=1;j<=nlstate+ndeath;j++){
2150: oldm[i][j]=(i==j ? 1.0 : 0.0);
2151: po[i][j][0]=(i==j ? 1.0 : 0.0);
2152: }
2153: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2154: for(h=1; h <=nhstepm; h++){
2155: for(d=1; d <=hstepm; d++){
2156: newm=savm;
2157: /* Covariates have to be included here again */
2158: cov[1]=1.;
1.187 brouard 2159: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
2160: cov[2]=agexact;
2161: if(nagesqr==1)
2162: cov[3]= agexact*agexact;
1.131 brouard 2163: for (k=1; k<=cptcovn;k++)
1.200 brouard 2164: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2165: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.186 brouard 2166: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
2167: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 2168: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2169: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
1.145 brouard 2170: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.200 brouard 2171: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
2172: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
1.126 brouard 2173:
2174:
2175: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2176: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
2177: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
2178: pmij(pmmij,cov,ncovmodel,x,nlstate));
2179: savm=oldm;
2180: oldm=newm;
2181: }
2182: for(i=1; i<=nlstate+ndeath; i++)
2183: for(j=1;j<=nlstate+ndeath;j++) {
2184: po[i][j][h]=newm[i][j];
1.128 brouard 2185: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 2186: }
1.128 brouard 2187: /*printf("h=%d ",h);*/
1.126 brouard 2188: } /* end h */
1.128 brouard 2189: /* printf("\n H=%d \n",h); */
1.126 brouard 2190: return po;
2191: }
2192:
1.162 brouard 2193: #ifdef NLOPT
2194: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
2195: double fret;
2196: double *xt;
2197: int j;
2198: myfunc_data *d2 = (myfunc_data *) pd;
2199: /* xt = (p1-1); */
2200: xt=vector(1,n);
2201: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
2202:
2203: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
2204: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
2205: printf("Function = %.12lf ",fret);
2206: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
2207: printf("\n");
2208: free_vector(xt,1,n);
2209: return fret;
2210: }
2211: #endif
1.126 brouard 2212:
2213: /*************** log-likelihood *************/
2214: double func( double *x)
2215: {
2216: int i, ii, j, k, mi, d, kk;
1.131 brouard 2217: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2218: double **out;
2219: double sw; /* Sum of weights */
2220: double lli; /* Individual log likelihood */
2221: int s1, s2;
2222: double bbh, survp;
2223: long ipmx;
1.187 brouard 2224: double agexact;
1.126 brouard 2225: /*extern weight */
2226: /* We are differentiating ll according to initial status */
2227: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2228: /*for(i=1;i<imx;i++)
2229: printf(" %d\n",s[4][i]);
2230: */
1.162 brouard 2231:
2232: ++countcallfunc;
2233:
1.126 brouard 2234: cov[1]=1.;
2235:
2236: for(k=1; k<=nlstate; k++) ll[k]=0.;
2237:
2238: if(mle==1){
2239: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.138 brouard 2240: /* Computes the values of the ncovmodel covariates of the model
2241: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
2242: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
2243: to be observed in j being in i according to the model.
2244: */
1.145 brouard 2245: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1.187 brouard 2246: cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.145 brouard 2247: }
1.137 brouard 2248: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1.138 brouard 2249: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1.137 brouard 2250: has been calculated etc */
1.126 brouard 2251: for(mi=1; mi<= wav[i]-1; mi++){
2252: for (ii=1;ii<=nlstate+ndeath;ii++)
2253: for (j=1;j<=nlstate+ndeath;j++){
2254: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2255: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2256: }
2257: for(d=0; d<dh[mi][i]; d++){
2258: newm=savm;
1.187 brouard 2259: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2260: cov[2]=agexact;
2261: if(nagesqr==1)
2262: cov[3]= agexact*agexact;
1.126 brouard 2263: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2264: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
1.126 brouard 2265: }
2266: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2267: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2268: savm=oldm;
2269: oldm=newm;
2270: } /* end mult */
2271:
2272: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
2273: /* But now since version 0.9 we anticipate for bias at large stepm.
2274: * If stepm is larger than one month (smallest stepm) and if the exact delay
2275: * (in months) between two waves is not a multiple of stepm, we rounded to
2276: * the nearest (and in case of equal distance, to the lowest) interval but now
2277: * we keep into memory the bias bh[mi][i] and also the previous matrix product
2278: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
2279: * probability in order to take into account the bias as a fraction of the way
2280: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
2281: * -stepm/2 to stepm/2 .
2282: * For stepm=1 the results are the same as for previous versions of Imach.
2283: * For stepm > 1 the results are less biased than in previous versions.
2284: */
2285: s1=s[mw[mi][i]][i];
2286: s2=s[mw[mi+1][i]][i];
2287: bbh=(double)bh[mi][i]/(double)stepm;
2288: /* bias bh is positive if real duration
2289: * is higher than the multiple of stepm and negative otherwise.
2290: */
2291: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
2292: if( s2 > nlstate){
2293: /* i.e. if s2 is a death state and if the date of death is known
2294: then the contribution to the likelihood is the probability to
2295: die between last step unit time and current step unit time,
2296: which is also equal to probability to die before dh
2297: minus probability to die before dh-stepm .
2298: In version up to 0.92 likelihood was computed
2299: as if date of death was unknown. Death was treated as any other
2300: health state: the date of the interview describes the actual state
2301: and not the date of a change in health state. The former idea was
2302: to consider that at each interview the state was recorded
2303: (healthy, disable or death) and IMaCh was corrected; but when we
2304: introduced the exact date of death then we should have modified
2305: the contribution of an exact death to the likelihood. This new
2306: contribution is smaller and very dependent of the step unit
2307: stepm. It is no more the probability to die between last interview
2308: and month of death but the probability to survive from last
2309: interview up to one month before death multiplied by the
2310: probability to die within a month. Thanks to Chris
2311: Jackson for correcting this bug. Former versions increased
2312: mortality artificially. The bad side is that we add another loop
2313: which slows down the processing. The difference can be up to 10%
2314: lower mortality.
2315: */
1.183 brouard 2316: /* If, at the beginning of the maximization mostly, the
2317: cumulative probability or probability to be dead is
2318: constant (ie = 1) over time d, the difference is equal to
2319: 0. out[s1][3] = savm[s1][3]: probability, being at state
2320: s1 at precedent wave, to be dead a month before current
2321: wave is equal to probability, being at state s1 at
2322: precedent wave, to be dead at mont of the current
2323: wave. Then the observed probability (that this person died)
2324: is null according to current estimated parameter. In fact,
2325: it should be very low but not zero otherwise the log go to
2326: infinity.
2327: */
2328: /* #ifdef INFINITYORIGINAL */
2329: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2330: /* #else */
2331: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
2332: /* lli=log(mytinydouble); */
2333: /* else */
2334: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2335: /* #endif */
2336: lli=log(out[s1][s2] - savm[s1][s2]);
1.126 brouard 2337:
2338: } else if (s2==-2) {
2339: for (j=1,survp=0. ; j<=nlstate; j++)
2340: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2341: /*survp += out[s1][j]; */
2342: lli= log(survp);
2343: }
2344:
2345: else if (s2==-4) {
2346: for (j=3,survp=0. ; j<=nlstate; j++)
2347: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2348: lli= log(survp);
2349: }
2350:
2351: else if (s2==-5) {
2352: for (j=1,survp=0. ; j<=2; j++)
2353: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2354: lli= log(survp);
2355: }
2356:
2357: else{
2358: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2359: /* 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 */
2360: }
2361: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
2362: /*if(lli ==000.0)*/
2363: /*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); */
2364: ipmx +=1;
2365: sw += weight[i];
2366: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.183 brouard 2367: /* if (lli < log(mytinydouble)){ */
2368: /* 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); */
2369: /* 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]); */
2370: /* } */
1.126 brouard 2371: } /* end of wave */
2372: } /* end of individual */
2373: } else if(mle==2){
2374: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2375: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2376: for(mi=1; mi<= wav[i]-1; mi++){
2377: for (ii=1;ii<=nlstate+ndeath;ii++)
2378: for (j=1;j<=nlstate+ndeath;j++){
2379: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2380: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2381: }
2382: for(d=0; d<=dh[mi][i]; d++){
2383: newm=savm;
1.187 brouard 2384: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2385: cov[2]=agexact;
2386: if(nagesqr==1)
2387: cov[3]= agexact*agexact;
1.126 brouard 2388: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2389: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2390: }
2391: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2392: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2393: savm=oldm;
2394: oldm=newm;
2395: } /* end mult */
2396:
2397: s1=s[mw[mi][i]][i];
2398: s2=s[mw[mi+1][i]][i];
2399: bbh=(double)bh[mi][i]/(double)stepm;
2400: 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 */
2401: ipmx +=1;
2402: sw += weight[i];
2403: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2404: } /* end of wave */
2405: } /* end of individual */
2406: } else if(mle==3){ /* exponential inter-extrapolation */
2407: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2408: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2409: for(mi=1; mi<= wav[i]-1; mi++){
2410: for (ii=1;ii<=nlstate+ndeath;ii++)
2411: for (j=1;j<=nlstate+ndeath;j++){
2412: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2413: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2414: }
2415: for(d=0; d<dh[mi][i]; d++){
2416: newm=savm;
1.187 brouard 2417: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2418: cov[2]=agexact;
2419: if(nagesqr==1)
2420: cov[3]= agexact*agexact;
1.126 brouard 2421: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2422: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2423: }
2424: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2425: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2426: savm=oldm;
2427: oldm=newm;
2428: } /* end mult */
2429:
2430: s1=s[mw[mi][i]][i];
2431: s2=s[mw[mi+1][i]][i];
2432: bbh=(double)bh[mi][i]/(double)stepm;
2433: 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 */
2434: ipmx +=1;
2435: sw += weight[i];
2436: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2437: } /* end of wave */
2438: } /* end of individual */
2439: }else if (mle==4){ /* ml=4 no inter-extrapolation */
2440: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2441: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2442: for(mi=1; mi<= wav[i]-1; mi++){
2443: for (ii=1;ii<=nlstate+ndeath;ii++)
2444: for (j=1;j<=nlstate+ndeath;j++){
2445: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2446: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2447: }
2448: for(d=0; d<dh[mi][i]; d++){
2449: newm=savm;
1.187 brouard 2450: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2451: cov[2]=agexact;
2452: if(nagesqr==1)
2453: cov[3]= agexact*agexact;
1.126 brouard 2454: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2455: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2456: }
2457:
2458: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2459: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2460: savm=oldm;
2461: oldm=newm;
2462: } /* end mult */
2463:
2464: s1=s[mw[mi][i]][i];
2465: s2=s[mw[mi+1][i]][i];
2466: if( s2 > nlstate){
2467: lli=log(out[s1][s2] - savm[s1][s2]);
2468: }else{
2469: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2470: }
2471: ipmx +=1;
2472: sw += weight[i];
2473: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2474: /* 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]); */
2475: } /* end of wave */
2476: } /* end of individual */
2477: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
2478: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2479: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2480: for(mi=1; mi<= wav[i]-1; mi++){
2481: for (ii=1;ii<=nlstate+ndeath;ii++)
2482: for (j=1;j<=nlstate+ndeath;j++){
2483: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2484: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2485: }
2486: for(d=0; d<dh[mi][i]; d++){
2487: newm=savm;
1.187 brouard 2488: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2489: cov[2]=agexact;
2490: if(nagesqr==1)
2491: cov[3]= agexact*agexact;
1.126 brouard 2492: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2493: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2494: }
2495:
2496: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2497: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2498: savm=oldm;
2499: oldm=newm;
2500: } /* end mult */
2501:
2502: s1=s[mw[mi][i]][i];
2503: s2=s[mw[mi+1][i]][i];
2504: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2505: ipmx +=1;
2506: sw += weight[i];
2507: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2508: /*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]);*/
2509: } /* end of wave */
2510: } /* end of individual */
2511: } /* End of if */
2512: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2513: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2514: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2515: return -l;
2516: }
2517:
2518: /*************** log-likelihood *************/
2519: double funcone( double *x)
2520: {
2521: /* Same as likeli but slower because of a lot of printf and if */
2522: int i, ii, j, k, mi, d, kk;
1.131 brouard 2523: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2524: double **out;
2525: double lli; /* Individual log likelihood */
2526: double llt;
2527: int s1, s2;
2528: double bbh, survp;
1.187 brouard 2529: double agexact;
1.126 brouard 2530: /*extern weight */
2531: /* We are differentiating ll according to initial status */
2532: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2533: /*for(i=1;i<imx;i++)
2534: printf(" %d\n",s[4][i]);
2535: */
2536: cov[1]=1.;
2537:
2538: for(k=1; k<=nlstate; k++) ll[k]=0.;
2539:
2540: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2541: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2542: for(mi=1; mi<= wav[i]-1; mi++){
2543: for (ii=1;ii<=nlstate+ndeath;ii++)
2544: for (j=1;j<=nlstate+ndeath;j++){
2545: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2546: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2547: }
2548: for(d=0; d<dh[mi][i]; d++){
2549: newm=savm;
1.187 brouard 2550: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2551: cov[2]=agexact;
2552: if(nagesqr==1)
2553: cov[3]= agexact*agexact;
1.126 brouard 2554: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2555: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2556: }
1.187 brouard 2557:
1.145 brouard 2558: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.126 brouard 2559: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2560: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1.145 brouard 2561: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2562: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
1.126 brouard 2563: savm=oldm;
2564: oldm=newm;
2565: } /* end mult */
2566:
2567: s1=s[mw[mi][i]][i];
2568: s2=s[mw[mi+1][i]][i];
2569: bbh=(double)bh[mi][i]/(double)stepm;
2570: /* bias is positive if real duration
2571: * is higher than the multiple of stepm and negative otherwise.
2572: */
2573: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2574: lli=log(out[s1][s2] - savm[s1][s2]);
2575: } else if (s2==-2) {
2576: for (j=1,survp=0. ; j<=nlstate; j++)
2577: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2578: lli= log(survp);
2579: }else if (mle==1){
2580: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2581: } else if(mle==2){
2582: 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 */
2583: } else if(mle==3){ /* exponential inter-extrapolation */
2584: 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 */
2585: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2586: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 2587: } else{ /* mle=0 back to 1 */
2588: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2589: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 2590: } /* End of if */
2591: ipmx +=1;
2592: sw += weight[i];
2593: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 2594: /*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 2595: if(globpr){
1.202 brouard 2596: fprintf(ficresilk,"%9ld %6.1f %6d %2d %2d %2d %2d %3d %11.6f %8.4f\
1.126 brouard 2597: %11.6f %11.6f %11.6f ", \
1.202 brouard 2598: num[i], agexact, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1.126 brouard 2599: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2600: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2601: llt +=ll[k]*gipmx/gsw;
2602: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2603: }
2604: fprintf(ficresilk," %10.6f\n", -llt);
2605: }
2606: } /* end of wave */
2607: } /* end of individual */
2608: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2609: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2610: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2611: if(globpr==0){ /* First time we count the contributions and weights */
2612: gipmx=ipmx;
2613: gsw=sw;
2614: }
2615: return -l;
2616: }
2617:
2618:
2619: /*************** function likelione ***********/
2620: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2621: {
2622: /* This routine should help understanding what is done with
2623: the selection of individuals/waves and
2624: to check the exact contribution to the likelihood.
2625: Plotting could be done.
2626: */
2627: int k;
2628:
2629: if(*globpri !=0){ /* Just counts and sums, no printings */
1.201 brouard 2630: strcpy(fileresilk,"ILK_");
1.202 brouard 2631: strcat(fileresilk,fileresu);
1.126 brouard 2632: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2633: printf("Problem with resultfile: %s\n", fileresilk);
2634: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2635: }
2636: 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");
1.202 brouard 2637: fprintf(ficresilk, "#num_i age i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1.126 brouard 2638: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2639: for(k=1; k<=nlstate; k++)
2640: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2641: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2642: }
2643:
2644: *fretone=(*funcone)(p);
2645: if(*globpri !=0){
2646: fclose(ficresilk);
1.202 brouard 2647: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle >= 1. You should at least run with mle >= 1 and starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
2648: fprintf(fichtm,"<br>- The first 3 individuals are drawn with lines. The function drawn is -2Log(L) in log scale: <a href=\"%s.png\">%s.png</a><br> \
2649: <img src=\"%s.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
2650: fflush(fichtm);
1.126 brouard 2651: }
2652: return;
2653: }
2654:
2655:
2656: /*********** Maximum Likelihood Estimation ***************/
2657:
2658: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2659: {
1.165 brouard 2660: int i,j, iter=0;
1.126 brouard 2661: double **xi;
2662: double fret;
2663: double fretone; /* Only one call to likelihood */
2664: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 2665:
2666: #ifdef NLOPT
2667: int creturn;
2668: nlopt_opt opt;
2669: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2670: double *lb;
2671: double minf; /* the minimum objective value, upon return */
2672: double * p1; /* Shifted parameters from 0 instead of 1 */
2673: myfunc_data dinst, *d = &dinst;
2674: #endif
2675:
2676:
1.126 brouard 2677: xi=matrix(1,npar,1,npar);
2678: for (i=1;i<=npar;i++)
2679: for (j=1;j<=npar;j++)
2680: xi[i][j]=(i==j ? 1.0 : 0.0);
2681: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.201 brouard 2682: strcpy(filerespow,"POW_");
1.126 brouard 2683: strcat(filerespow,fileres);
2684: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2685: printf("Problem with resultfile: %s\n", filerespow);
2686: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2687: }
2688: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2689: for (i=1;i<=nlstate;i++)
2690: for(j=1;j<=nlstate+ndeath;j++)
2691: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2692: fprintf(ficrespow,"\n");
1.162 brouard 2693: #ifdef POWELL
1.126 brouard 2694: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 2695: #endif
1.126 brouard 2696:
1.162 brouard 2697: #ifdef NLOPT
2698: #ifdef NEWUOA
2699: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2700: #else
2701: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2702: #endif
2703: lb=vector(0,npar-1);
2704: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2705: nlopt_set_lower_bounds(opt, lb);
2706: nlopt_set_initial_step1(opt, 0.1);
2707:
2708: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2709: d->function = func;
2710: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2711: nlopt_set_min_objective(opt, myfunc, d);
2712: nlopt_set_xtol_rel(opt, ftol);
2713: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2714: printf("nlopt failed! %d\n",creturn);
2715: }
2716: else {
2717: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2718: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2719: iter=1; /* not equal */
2720: }
2721: nlopt_destroy(opt);
2722: #endif
1.126 brouard 2723: free_matrix(xi,1,npar,1,npar);
2724: fclose(ficrespow);
1.203 ! brouard 2725: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
! 2726: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.180 brouard 2727: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 2728:
2729: }
2730:
2731: /**** Computes Hessian and covariance matrix ***/
1.203 ! brouard 2732: void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1.126 brouard 2733: {
2734: double **a,**y,*x,pd;
1.203 ! brouard 2735: /* double **hess; */
1.164 brouard 2736: int i, j;
1.126 brouard 2737: int *indx;
2738:
2739: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1.203 ! brouard 2740: double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
1.126 brouard 2741: void lubksb(double **a, int npar, int *indx, double b[]) ;
2742: void ludcmp(double **a, int npar, int *indx, double *d) ;
2743: double gompertz(double p[]);
1.203 ! brouard 2744: /* hess=matrix(1,npar,1,npar); */
1.126 brouard 2745:
2746: printf("\nCalculation of the hessian matrix. Wait...\n");
2747: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2748: for (i=1;i<=npar;i++){
1.203 ! brouard 2749: printf("%d-",i);fflush(stdout);
! 2750: fprintf(ficlog,"%d-",i);fflush(ficlog);
1.126 brouard 2751:
2752: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2753:
2754: /* printf(" %f ",p[i]);
2755: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2756: }
2757:
2758: for (i=1;i<=npar;i++) {
2759: for (j=1;j<=npar;j++) {
2760: if (j>i) {
1.203 ! brouard 2761: printf(".%d-%d",i,j);fflush(stdout);
! 2762: fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
! 2763: hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
1.126 brouard 2764:
2765: hess[j][i]=hess[i][j];
2766: /*printf(" %lf ",hess[i][j]);*/
2767: }
2768: }
2769: }
2770: printf("\n");
2771: fprintf(ficlog,"\n");
2772:
2773: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2774: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2775:
2776: a=matrix(1,npar,1,npar);
2777: y=matrix(1,npar,1,npar);
2778: x=vector(1,npar);
2779: indx=ivector(1,npar);
2780: for (i=1;i<=npar;i++)
2781: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2782: ludcmp(a,npar,indx,&pd);
2783:
2784: for (j=1;j<=npar;j++) {
2785: for (i=1;i<=npar;i++) x[i]=0;
2786: x[j]=1;
2787: lubksb(a,npar,indx,x);
2788: for (i=1;i<=npar;i++){
2789: matcov[i][j]=x[i];
2790: }
2791: }
2792:
2793: printf("\n#Hessian matrix#\n");
2794: fprintf(ficlog,"\n#Hessian matrix#\n");
2795: for (i=1;i<=npar;i++) {
2796: for (j=1;j<=npar;j++) {
1.203 ! brouard 2797: printf("%.6e ",hess[i][j]);
! 2798: fprintf(ficlog,"%.6e ",hess[i][j]);
1.126 brouard 2799: }
2800: printf("\n");
2801: fprintf(ficlog,"\n");
2802: }
2803:
1.203 ! brouard 2804: /* printf("\n#Covariance matrix#\n"); */
! 2805: /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
! 2806: /* for (i=1;i<=npar;i++) { */
! 2807: /* for (j=1;j<=npar;j++) { */
! 2808: /* printf("%.6e ",matcov[i][j]); */
! 2809: /* fprintf(ficlog,"%.6e ",matcov[i][j]); */
! 2810: /* } */
! 2811: /* printf("\n"); */
! 2812: /* fprintf(ficlog,"\n"); */
! 2813: /* } */
! 2814:
1.126 brouard 2815: /* Recompute Inverse */
1.203 ! brouard 2816: /* for (i=1;i<=npar;i++) */
! 2817: /* for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
! 2818: /* ludcmp(a,npar,indx,&pd); */
! 2819:
! 2820: /* printf("\n#Hessian matrix recomputed#\n"); */
! 2821:
! 2822: /* for (j=1;j<=npar;j++) { */
! 2823: /* for (i=1;i<=npar;i++) x[i]=0; */
! 2824: /* x[j]=1; */
! 2825: /* lubksb(a,npar,indx,x); */
! 2826: /* for (i=1;i<=npar;i++){ */
! 2827: /* y[i][j]=x[i]; */
! 2828: /* printf("%.3e ",y[i][j]); */
! 2829: /* fprintf(ficlog,"%.3e ",y[i][j]); */
! 2830: /* } */
! 2831: /* printf("\n"); */
! 2832: /* fprintf(ficlog,"\n"); */
! 2833: /* } */
! 2834:
! 2835: /* Verifying the inverse matrix */
! 2836: #ifdef DEBUGHESS
! 2837: y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
1.126 brouard 2838:
1.203 ! brouard 2839: printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
! 2840: fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
1.126 brouard 2841:
2842: for (j=1;j<=npar;j++) {
2843: for (i=1;i<=npar;i++){
1.203 ! brouard 2844: printf("%.2f ",y[i][j]);
! 2845: fprintf(ficlog,"%.2f ",y[i][j]);
1.126 brouard 2846: }
2847: printf("\n");
2848: fprintf(ficlog,"\n");
2849: }
1.203 ! brouard 2850: #endif
1.126 brouard 2851:
2852: free_matrix(a,1,npar,1,npar);
2853: free_matrix(y,1,npar,1,npar);
2854: free_vector(x,1,npar);
2855: free_ivector(indx,1,npar);
1.203 ! brouard 2856: /* free_matrix(hess,1,npar,1,npar); */
1.126 brouard 2857:
2858:
2859: }
2860:
2861: /*************** hessian matrix ****************/
2862: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.203 ! brouard 2863: { /* Around values of x, computes the function func and returns the scales delti and hessian */
1.126 brouard 2864: int i;
2865: int l=1, lmax=20;
1.203 ! brouard 2866: double k1,k2, res, fx;
1.132 brouard 2867: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 2868: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2869: int k=0,kmax=10;
2870: double l1;
2871:
2872: fx=func(x);
2873: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 2874: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 2875: l1=pow(10,l);
2876: delts=delt;
2877: for(k=1 ; k <kmax; k=k+1){
2878: delt = delta*(l1*k);
2879: p2[theta]=x[theta] +delt;
1.145 brouard 2880: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 2881: p2[theta]=x[theta]-delt;
2882: k2=func(p2)-fx;
2883: /*res= (k1-2.0*fx+k2)/delt/delt; */
1.203 ! brouard 2884: res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
1.126 brouard 2885:
1.203 ! brouard 2886: #ifdef DEBUGHESSII
1.126 brouard 2887: 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);
2888: 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);
2889: #endif
2890: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2891: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2892: k=kmax;
2893: }
2894: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 2895: k=kmax; l=lmax*10;
1.126 brouard 2896: }
2897: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2898: delts=delt;
2899: }
1.203 ! brouard 2900: } /* End loop k */
1.126 brouard 2901: }
2902: delti[theta]=delts;
2903: return res;
2904:
2905: }
2906:
1.203 ! brouard 2907: double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.126 brouard 2908: {
2909: int i;
1.164 brouard 2910: int l=1, lmax=20;
1.126 brouard 2911: double k1,k2,k3,k4,res,fx;
1.132 brouard 2912: double p2[MAXPARM+1];
1.203 ! brouard 2913: int k, kmax=1;
! 2914: double v1, v2, cv12, lc1, lc2;
! 2915:
1.126 brouard 2916: fx=func(x);
1.203 ! brouard 2917: for (k=1; k<=kmax; k=k+10) {
1.126 brouard 2918: for (i=1;i<=npar;i++) p2[i]=x[i];
1.203 ! brouard 2919: p2[thetai]=x[thetai]+delti[thetai]*k;
! 2920: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 2921: k1=func(p2)-fx;
2922:
1.203 ! brouard 2923: p2[thetai]=x[thetai]+delti[thetai]*k;
! 2924: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 2925: k2=func(p2)-fx;
2926:
1.203 ! brouard 2927: p2[thetai]=x[thetai]-delti[thetai]*k;
! 2928: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 2929: k3=func(p2)-fx;
2930:
1.203 ! brouard 2931: p2[thetai]=x[thetai]-delti[thetai]*k;
! 2932: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 2933: k4=func(p2)-fx;
1.203 ! brouard 2934: res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
! 2935: if(k1*k2*k3*k4 <0.){
! 2936: kmax=kmax+10;
! 2937: if(kmax >=10){
! 2938: printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol);
! 2939: fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol);
! 2940: 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);
! 2941: 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);
! 2942: }
! 2943: }
! 2944: #ifdef DEBUGHESSIJ
! 2945: v1=hess[thetai][thetai];
! 2946: v2=hess[thetaj][thetaj];
! 2947: cv12=res;
! 2948: /* Computing eigen value of Hessian matrix */
! 2949: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
! 2950: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
! 2951: if ((lc2 <0) || (lc1 <0) ){
! 2952: printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
! 2953: fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
! 2954: 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);
! 2955: 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);
! 2956: }
1.126 brouard 2957: #endif
2958: }
2959: return res;
2960: }
2961:
1.203 ! brouard 2962: /* Not done yet: Was supposed to fix if not exactly at the maximum */
! 2963: /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
! 2964: /* { */
! 2965: /* int i; */
! 2966: /* int l=1, lmax=20; */
! 2967: /* double k1,k2,k3,k4,res,fx; */
! 2968: /* double p2[MAXPARM+1]; */
! 2969: /* double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
! 2970: /* int k=0,kmax=10; */
! 2971: /* double l1; */
! 2972:
! 2973: /* fx=func(x); */
! 2974: /* for(l=0 ; l <=lmax; l++){ /\* Enlarging the zone around the Maximum *\/ */
! 2975: /* l1=pow(10,l); */
! 2976: /* delts=delt; */
! 2977: /* for(k=1 ; k <kmax; k=k+1){ */
! 2978: /* delt = delti*(l1*k); */
! 2979: /* for (i=1;i<=npar;i++) p2[i]=x[i]; */
! 2980: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
! 2981: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
! 2982: /* k1=func(p2)-fx; */
! 2983:
! 2984: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
! 2985: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
! 2986: /* k2=func(p2)-fx; */
! 2987:
! 2988: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
! 2989: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
! 2990: /* k3=func(p2)-fx; */
! 2991:
! 2992: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
! 2993: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
! 2994: /* k4=func(p2)-fx; */
! 2995: /* res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
! 2996: /* #ifdef DEBUGHESSIJ */
! 2997: /* 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); */
! 2998: /* 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); */
! 2999: /* #endif */
! 3000: /* if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
! 3001: /* k=kmax; */
! 3002: /* } */
! 3003: /* else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
! 3004: /* k=kmax; l=lmax*10; */
! 3005: /* } */
! 3006: /* else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ */
! 3007: /* delts=delt; */
! 3008: /* } */
! 3009: /* } /\* End loop k *\/ */
! 3010: /* } */
! 3011: /* delti[theta]=delts; */
! 3012: /* return res; */
! 3013: /* } */
! 3014:
! 3015:
1.126 brouard 3016: /************** Inverse of matrix **************/
3017: void ludcmp(double **a, int n, int *indx, double *d)
3018: {
3019: int i,imax,j,k;
3020: double big,dum,sum,temp;
3021: double *vv;
3022:
3023: vv=vector(1,n);
3024: *d=1.0;
3025: for (i=1;i<=n;i++) {
3026: big=0.0;
3027: for (j=1;j<=n;j++)
3028: if ((temp=fabs(a[i][j])) > big) big=temp;
3029: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
3030: vv[i]=1.0/big;
3031: }
3032: for (j=1;j<=n;j++) {
3033: for (i=1;i<j;i++) {
3034: sum=a[i][j];
3035: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
3036: a[i][j]=sum;
3037: }
3038: big=0.0;
3039: for (i=j;i<=n;i++) {
3040: sum=a[i][j];
3041: for (k=1;k<j;k++)
3042: sum -= a[i][k]*a[k][j];
3043: a[i][j]=sum;
3044: if ( (dum=vv[i]*fabs(sum)) >= big) {
3045: big=dum;
3046: imax=i;
3047: }
3048: }
3049: if (j != imax) {
3050: for (k=1;k<=n;k++) {
3051: dum=a[imax][k];
3052: a[imax][k]=a[j][k];
3053: a[j][k]=dum;
3054: }
3055: *d = -(*d);
3056: vv[imax]=vv[j];
3057: }
3058: indx[j]=imax;
3059: if (a[j][j] == 0.0) a[j][j]=TINY;
3060: if (j != n) {
3061: dum=1.0/(a[j][j]);
3062: for (i=j+1;i<=n;i++) a[i][j] *= dum;
3063: }
3064: }
3065: free_vector(vv,1,n); /* Doesn't work */
3066: ;
3067: }
3068:
3069: void lubksb(double **a, int n, int *indx, double b[])
3070: {
3071: int i,ii=0,ip,j;
3072: double sum;
3073:
3074: for (i=1;i<=n;i++) {
3075: ip=indx[i];
3076: sum=b[ip];
3077: b[ip]=b[i];
3078: if (ii)
3079: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
3080: else if (sum) ii=i;
3081: b[i]=sum;
3082: }
3083: for (i=n;i>=1;i--) {
3084: sum=b[i];
3085: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
3086: b[i]=sum/a[i][i];
3087: }
3088: }
3089:
3090: void pstamp(FILE *fichier)
3091: {
1.196 brouard 3092: fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126 brouard 3093: }
3094:
3095: /************ Frequencies ********************/
3096: 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[])
3097: { /* Some frequencies */
3098:
1.164 brouard 3099: int i, m, jk, j1, bool, z1,j;
1.126 brouard 3100: int first;
3101: double ***freq; /* Frequencies */
3102: double *pp, **prop;
3103: double pos,posprop, k2, dateintsum=0,k2cpt=0;
3104: char fileresp[FILENAMELENGTH];
3105:
3106: pp=vector(1,nlstate);
3107: prop=matrix(1,nlstate,iagemin,iagemax+3);
1.201 brouard 3108: strcpy(fileresp,"P_");
3109: strcat(fileresp,fileresu);
1.126 brouard 3110: if((ficresp=fopen(fileresp,"w"))==NULL) {
3111: printf("Problem with prevalence resultfile: %s\n", fileresp);
3112: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
3113: exit(0);
3114: }
3115: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
3116: j1=0;
3117:
3118: j=cptcoveff;
3119: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3120:
3121: first=1;
3122:
1.169 brouard 3123: /* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */
3124: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
3125: /* j1++; */
1.145 brouard 3126: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
1.126 brouard 3127: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
3128: scanf("%d", i);*/
3129: for (i=-5; i<=nlstate+ndeath; i++)
3130: for (jk=-5; jk<=nlstate+ndeath; jk++)
3131: for(m=iagemin; m <= iagemax+3; m++)
3132: freq[i][jk][m]=0;
1.143 brouard 3133:
3134: for (i=1; i<=nlstate; i++)
3135: for(m=iagemin; m <= iagemax+3; m++)
3136: prop[i][m]=0;
1.126 brouard 3137:
3138: dateintsum=0;
3139: k2cpt=0;
3140: for (i=1; i<=imx; i++) {
3141: bool=1;
1.144 brouard 3142: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
3143: for (z1=1; z1<=cptcoveff; z1++)
1.198 brouard 3144: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
1.145 brouard 3145: /* Tests if the value of each of the covariates of i is equal to filter j1 */
1.144 brouard 3146: bool=0;
1.198 brouard 3147: /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n",
3148: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
3149: j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
3150: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
1.144 brouard 3151: }
1.126 brouard 3152: }
1.144 brouard 3153:
1.126 brouard 3154: if (bool==1){
3155: for(m=firstpass; m<=lastpass; m++){
3156: k2=anint[m][i]+(mint[m][i]/12.);
3157: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
3158: if(agev[m][i]==0) agev[m][i]=iagemax+1;
3159: if(agev[m][i]==1) agev[m][i]=iagemax+2;
3160: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
3161: if (m<lastpass) {
3162: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
3163: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
3164: }
3165:
3166: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
3167: dateintsum=dateintsum+k2;
3168: k2cpt++;
3169: }
3170: /*}*/
3171: }
3172: }
1.145 brouard 3173: } /* end i */
1.126 brouard 3174:
3175: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
3176: pstamp(ficresp);
3177: if (cptcovn>0) {
3178: fprintf(ficresp, "\n#********** Variable ");
1.198 brouard 3179: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 3180: fprintf(ficresp, "**********\n#");
1.143 brouard 3181: fprintf(ficlog, "\n#********** Variable ");
1.198 brouard 3182: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.143 brouard 3183: fprintf(ficlog, "**********\n#");
1.126 brouard 3184: }
3185: for(i=1; i<=nlstate;i++)
3186: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
3187: fprintf(ficresp, "\n");
3188:
3189: for(i=iagemin; i <= iagemax+3; i++){
3190: if(i==iagemax+3){
3191: fprintf(ficlog,"Total");
3192: }else{
3193: if(first==1){
3194: first=0;
3195: printf("See log file for details...\n");
3196: }
3197: fprintf(ficlog,"Age %d", i);
3198: }
3199: for(jk=1; jk <=nlstate ; jk++){
3200: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
3201: pp[jk] += freq[jk][m][i];
3202: }
3203: for(jk=1; jk <=nlstate ; jk++){
3204: for(m=-1, pos=0; m <=0 ; m++)
3205: pos += freq[jk][m][i];
3206: if(pp[jk]>=1.e-10){
3207: if(first==1){
1.132 brouard 3208: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1.126 brouard 3209: }
3210: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
3211: }else{
3212: if(first==1)
3213: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3214: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3215: }
3216: }
3217:
3218: for(jk=1; jk <=nlstate ; jk++){
3219: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
3220: pp[jk] += freq[jk][m][i];
3221: }
3222: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
3223: pos += pp[jk];
3224: posprop += prop[jk][i];
3225: }
3226: for(jk=1; jk <=nlstate ; jk++){
3227: if(pos>=1.e-5){
3228: if(first==1)
3229: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3230: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3231: }else{
3232: if(first==1)
3233: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3234: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3235: }
3236: if( i <= iagemax){
3237: if(pos>=1.e-5){
3238: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
3239: /*probs[i][jk][j1]= pp[jk]/pos;*/
3240: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
3241: }
3242: else
3243: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
3244: }
3245: }
3246:
3247: for(jk=-1; jk <=nlstate+ndeath; jk++)
3248: for(m=-1; m <=nlstate+ndeath; m++)
3249: if(freq[jk][m][i] !=0 ) {
3250: if(first==1)
3251: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
3252: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
3253: }
3254: if(i <= iagemax)
3255: fprintf(ficresp,"\n");
3256: if(first==1)
3257: printf("Others in log...\n");
3258: fprintf(ficlog,"\n");
3259: }
1.145 brouard 3260: /*}*/
1.126 brouard 3261: }
3262: dateintmean=dateintsum/k2cpt;
3263:
3264: fclose(ficresp);
3265: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
3266: free_vector(pp,1,nlstate);
3267: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
3268: /* End of Freq */
3269: }
3270:
3271: /************ Prevalence ********************/
3272: 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)
3273: {
3274: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
3275: in each health status at the date of interview (if between dateprev1 and dateprev2).
3276: We still use firstpass and lastpass as another selection.
3277: */
3278:
1.164 brouard 3279: int i, m, jk, j1, bool, z1,j;
3280:
3281: double **prop;
3282: double posprop;
1.126 brouard 3283: double y2; /* in fractional years */
3284: int iagemin, iagemax;
1.145 brouard 3285: int first; /** to stop verbosity which is redirected to log file */
1.126 brouard 3286:
3287: iagemin= (int) agemin;
3288: iagemax= (int) agemax;
3289: /*pp=vector(1,nlstate);*/
3290: prop=matrix(1,nlstate,iagemin,iagemax+3);
3291: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
3292: j1=0;
3293:
1.145 brouard 3294: /*j=cptcoveff;*/
1.126 brouard 3295: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3296:
1.145 brouard 3297: first=1;
3298: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
3299: /*for(i1=1; i1<=ncodemax[k1];i1++){
3300: j1++;*/
1.126 brouard 3301:
3302: for (i=1; i<=nlstate; i++)
3303: for(m=iagemin; m <= iagemax+3; m++)
3304: prop[i][m]=0.0;
3305:
3306: for (i=1; i<=imx; i++) { /* Each individual */
3307: bool=1;
3308: if (cptcovn>0) {
3309: for (z1=1; z1<=cptcoveff; z1++)
1.198 brouard 3310: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])
1.126 brouard 3311: bool=0;
3312: }
3313: if (bool==1) {
3314: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
3315: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
3316: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
3317: if(agev[m][i]==0) agev[m][i]=iagemax+1;
3318: if(agev[m][i]==1) agev[m][i]=iagemax+2;
3319: 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);
3320: if (s[m][i]>0 && s[m][i]<=nlstate) {
3321: /*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]]);*/
3322: prop[s[m][i]][(int)agev[m][i]] += weight[i];
3323: prop[s[m][i]][iagemax+3] += weight[i];
3324: }
3325: }
3326: } /* end selection of waves */
3327: }
3328: }
3329: for(i=iagemin; i <= iagemax+3; i++){
3330: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
3331: posprop += prop[jk][i];
3332: }
1.145 brouard 3333:
1.126 brouard 3334: for(jk=1; jk <=nlstate ; jk++){
3335: if( i <= iagemax){
3336: if(posprop>=1.e-5){
3337: probs[i][jk][j1]= prop[jk][i]/posprop;
1.145 brouard 3338: } else{
3339: if(first==1){
3340: first=0;
3341: 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]);
3342: }
3343: }
1.126 brouard 3344: }
3345: }/* end jk */
3346: }/* end i */
1.145 brouard 3347: /*} *//* end i1 */
3348: } /* end j1 */
1.126 brouard 3349:
3350: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
3351: /*free_vector(pp,1,nlstate);*/
3352: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
3353: } /* End of prevalence */
3354:
3355: /************* Waves Concatenation ***************/
3356:
3357: 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)
3358: {
3359: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
3360: Death is a valid wave (if date is known).
3361: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
3362: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3363: and mw[mi+1][i]. dh depends on stepm.
3364: */
3365:
3366: int i, mi, m;
3367: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
3368: double sum=0., jmean=0.;*/
3369: int first;
3370: int j, k=0,jk, ju, jl;
3371: double sum=0.;
3372: first=0;
1.164 brouard 3373: jmin=100000;
1.126 brouard 3374: jmax=-1;
3375: jmean=0.;
3376: for(i=1; i<=imx; i++){
3377: mi=0;
3378: m=firstpass;
3379: while(s[m][i] <= nlstate){
3380: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
3381: mw[++mi][i]=m;
3382: if(m >=lastpass)
3383: break;
3384: else
3385: m++;
3386: }/* end while */
3387: if (s[m][i] > nlstate){
3388: mi++; /* Death is another wave */
3389: /* if(mi==0) never been interviewed correctly before death */
3390: /* Only death is a correct wave */
3391: mw[mi][i]=m;
3392: }
3393:
3394: wav[i]=mi;
3395: if(mi==0){
3396: nbwarn++;
3397: if(first==0){
3398: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
3399: first=1;
3400: }
3401: if(first==1){
3402: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
3403: }
3404: } /* end mi==0 */
3405: } /* End individuals */
3406:
3407: for(i=1; i<=imx; i++){
3408: for(mi=1; mi<wav[i];mi++){
3409: if (stepm <=0)
3410: dh[mi][i]=1;
3411: else{
3412: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
3413: if (agedc[i] < 2*AGESUP) {
3414: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
3415: if(j==0) j=1; /* Survives at least one month after exam */
3416: else if(j<0){
3417: nberr++;
3418: 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]);
3419: j=1; /* Temporary Dangerous patch */
3420: 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);
3421: 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]);
3422: 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);
3423: }
3424: k=k+1;
3425: if (j >= jmax){
3426: jmax=j;
3427: ijmax=i;
3428: }
3429: if (j <= jmin){
3430: jmin=j;
3431: ijmin=i;
3432: }
3433: sum=sum+j;
3434: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
3435: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
3436: }
3437: }
3438: else{
3439: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
3440: /* 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]); */
3441:
3442: k=k+1;
3443: if (j >= jmax) {
3444: jmax=j;
3445: ijmax=i;
3446: }
3447: else if (j <= jmin){
3448: jmin=j;
3449: ijmin=i;
3450: }
3451: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
3452: /*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]);*/
3453: if(j<0){
3454: nberr++;
3455: 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]);
3456: 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]);
3457: }
3458: sum=sum+j;
3459: }
3460: jk= j/stepm;
3461: jl= j -jk*stepm;
3462: ju= j -(jk+1)*stepm;
3463: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
3464: if(jl==0){
3465: dh[mi][i]=jk;
3466: bh[mi][i]=0;
3467: }else{ /* We want a negative bias in order to only have interpolation ie
1.136 brouard 3468: * to avoid the price of an extra matrix product in likelihood */
1.126 brouard 3469: dh[mi][i]=jk+1;
3470: bh[mi][i]=ju;
3471: }
3472: }else{
3473: if(jl <= -ju){
3474: dh[mi][i]=jk;
3475: bh[mi][i]=jl; /* bias is positive if real duration
3476: * is higher than the multiple of stepm and negative otherwise.
3477: */
3478: }
3479: else{
3480: dh[mi][i]=jk+1;
3481: bh[mi][i]=ju;
3482: }
3483: if(dh[mi][i]==0){
3484: dh[mi][i]=1; /* At least one step */
3485: bh[mi][i]=ju; /* At least one step */
3486: /* 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);*/
3487: }
3488: } /* end if mle */
3489: }
3490: } /* end wave */
3491: }
3492: jmean=sum/k;
3493: 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 3494: 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 3495: }
3496:
3497: /*********** Tricode ****************************/
1.145 brouard 3498: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 3499: {
1.144 brouard 3500: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
3501: /* 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 3502: * Boring subroutine which should only output nbcode[Tvar[j]][k]
1.145 brouard 3503: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
1.169 brouard 3504: * nbcode[Tvar[j]][1]=
1.144 brouard 3505: */
1.130 brouard 3506:
1.145 brouard 3507: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 3508: int modmaxcovj=0; /* Modality max of covariates j */
1.145 brouard 3509: int cptcode=0; /* Modality max of covariates j */
3510: int modmincovj=0; /* Modality min of covariates j */
3511:
3512:
1.126 brouard 3513: cptcoveff=0;
3514:
1.144 brouard 3515: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 3516:
1.145 brouard 3517: /* Loop on covariates without age and products */
1.186 brouard 3518: for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
1.192 brouard 3519: for (k=-1; k < maxncov; k++) Ndum[k]=0;
1.186 brouard 3520: for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
1.136 brouard 3521: modality of this covariate Vj*/
1.145 brouard 3522: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
3523: * If product of Vn*Vm, still boolean *:
3524: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
3525: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
3526: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
1.136 brouard 3527: modality of the nth covariate of individual i. */
1.145 brouard 3528: if (ij > modmaxcovj)
3529: modmaxcovj=ij;
3530: else if (ij < modmincovj)
3531: modmincovj=ij;
3532: if ((ij < -1) && (ij > NCOVMAX)){
3533: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
3534: exit(1);
3535: }else
1.136 brouard 3536: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
1.145 brouard 3537: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
1.126 brouard 3538: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.136 brouard 3539: /* getting the maximum value of the modality of the covariate
3540: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
3541: female is 1, then modmaxcovj=1.*/
1.192 brouard 3542: } /* end for loop on individuals i */
1.145 brouard 3543: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
1.192 brouard 3544: fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
1.145 brouard 3545: cptcode=modmaxcovj;
1.137 brouard 3546: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
1.145 brouard 3547: /*for (i=0; i<=cptcode; i++) {*/
1.192 brouard 3548: for (k=modmincovj; k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
3549: printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
3550: fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
3551: if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
3552: if( k != -1){
3553: ncodemax[j]++; /* ncodemax[j]= Number of modalities of the j th
3554: covariate for which somebody answered excluding
3555: undefined. Usually 2: 0 and 1. */
3556: }
3557: ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
3558: covariate for which somebody answered including
3559: undefined. Usually 3: -1, 0 and 1. */
1.145 brouard 3560: }
3561: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
3562: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
1.131 brouard 3563: } /* Ndum[-1] number of undefined modalities */
1.126 brouard 3564:
1.136 brouard 3565: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
1.186 brouard 3566: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
3567: 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 3568: modmincovj=3; modmaxcovj = 7;
1.186 brouard 3569: There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
3570: which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
3571: defining two dummy variables: variables V1_1 and V1_2.
1.145 brouard 3572: nbcode[Tvar[j]][ij]=k;
3573: nbcode[Tvar[j]][1]=0;
3574: nbcode[Tvar[j]][2]=1;
3575: nbcode[Tvar[j]][3]=2;
1.197 brouard 3576: To be continued (not working yet).
1.145 brouard 3577: */
1.197 brouard 3578: ij=0; /* ij is similar to i but can jump over null modalities */
3579: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
3580: if (Ndum[i] == 0) { /* If nobody responded to this modality k */
1.192 brouard 3581: break;
3582: }
3583: ij++;
1.197 brouard 3584: nbcode[Tvar[j]][ij]=i; /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality.*/
1.192 brouard 3585: cptcode = ij; /* New max modality for covar j */
3586: } /* end of loop on modality i=-1 to 1 or more */
3587:
3588: /* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
3589: /* /\*recode from 0 *\/ */
3590: /* k is a modality. If we have model=V1+V1*sex */
3591: /* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
3592: /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
3593: /* } */
3594: /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
3595: /* if (ij > ncodemax[j]) { */
3596: /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
3597: /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
3598: /* break; */
3599: /* } */
3600: /* } /\* end of loop on modality k *\/ */
1.137 brouard 3601: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
3602:
1.145 brouard 3603: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.137 brouard 3604:
1.187 brouard 3605: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
1.145 brouard 3606: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
3607: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
1.187 brouard 3608: Ndum[ij]++; /* Might be supersed V1 + V1*age */
1.145 brouard 3609: }
1.126 brouard 3610:
1.192 brouard 3611: ij=0;
1.145 brouard 3612: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
3613: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
1.126 brouard 3614: if((Ndum[i]!=0) && (i<=ncovcol)){
1.192 brouard 3615: ij++;
1.145 brouard 3616: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
3617: Tvaraff[ij]=i; /*For printing (unclear) */
1.192 brouard 3618: }else{
3619: /* Tvaraff[ij]=0; */
3620: }
1.126 brouard 3621: }
1.192 brouard 3622: /* ij--; */
1.144 brouard 3623: cptcoveff=ij; /*Number of total covariates*/
1.145 brouard 3624:
1.126 brouard 3625: }
3626:
1.145 brouard 3627:
1.126 brouard 3628: /*********** Health Expectancies ****************/
3629:
1.127 brouard 3630: 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 3631:
3632: {
3633: /* Health expectancies, no variances */
1.164 brouard 3634: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 3635: int nhstepma, nstepma; /* Decreasing with age */
3636: double age, agelim, hf;
3637: double ***p3mat;
3638: double eip;
3639:
3640: pstamp(ficreseij);
3641: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3642: fprintf(ficreseij,"# Age");
3643: for(i=1; i<=nlstate;i++){
3644: for(j=1; j<=nlstate;j++){
3645: fprintf(ficreseij," e%1d%1d ",i,j);
3646: }
3647: fprintf(ficreseij," e%1d. ",i);
3648: }
3649: fprintf(ficreseij,"\n");
3650:
3651:
3652: if(estepm < stepm){
3653: printf ("Problem %d lower than %d\n",estepm, stepm);
3654: }
3655: else hstepm=estepm;
3656: /* We compute the life expectancy from trapezoids spaced every estepm months
3657: * This is mainly to measure the difference between two models: for example
3658: * if stepm=24 months pijx are given only every 2 years and by summing them
3659: * we are calculating an estimate of the Life Expectancy assuming a linear
3660: * progression in between and thus overestimating or underestimating according
3661: * to the curvature of the survival function. If, for the same date, we
3662: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3663: * to compare the new estimate of Life expectancy with the same linear
3664: * hypothesis. A more precise result, taking into account a more precise
3665: * curvature will be obtained if estepm is as small as stepm. */
3666:
3667: /* For example we decided to compute the life expectancy with the smallest unit */
3668: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3669: nhstepm is the number of hstepm from age to agelim
3670: nstepm is the number of stepm from age to agelin.
3671: Look at hpijx to understand the reason of that which relies in memory size
3672: and note for a fixed period like estepm months */
3673: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3674: survival function given by stepm (the optimization length). Unfortunately it
3675: means that if the survival funtion is printed only each two years of age and if
3676: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3677: results. So we changed our mind and took the option of the best precision.
3678: */
3679: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3680:
3681: agelim=AGESUP;
3682: /* If stepm=6 months */
3683: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3684: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3685:
3686: /* nhstepm age range expressed in number of stepm */
3687: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3688: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3689: /* if (stepm >= YEARM) hstepm=1;*/
3690: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3691: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3692:
3693: for (age=bage; age<=fage; age ++){
3694: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3695: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3696: /* if (stepm >= YEARM) hstepm=1;*/
3697: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3698:
3699: /* If stepm=6 months */
3700: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3701: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3702:
3703: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3704:
3705: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3706:
3707: printf("%d|",(int)age);fflush(stdout);
3708: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3709:
3710: /* Computing expectancies */
3711: for(i=1; i<=nlstate;i++)
3712: for(j=1; j<=nlstate;j++)
3713: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3714: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3715:
3716: /* 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]);*/
3717:
3718: }
3719:
3720: fprintf(ficreseij,"%3.0f",age );
3721: for(i=1; i<=nlstate;i++){
3722: eip=0;
3723: for(j=1; j<=nlstate;j++){
3724: eip +=eij[i][j][(int)age];
3725: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3726: }
3727: fprintf(ficreseij,"%9.4f", eip );
3728: }
3729: fprintf(ficreseij,"\n");
3730:
3731: }
3732: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3733: printf("\n");
3734: fprintf(ficlog,"\n");
3735:
3736: }
3737:
1.127 brouard 3738: 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 3739:
3740: {
3741: /* Covariances of health expectancies eij and of total life expectancies according
3742: to initial status i, ei. .
3743: */
3744: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3745: int nhstepma, nstepma; /* Decreasing with age */
3746: double age, agelim, hf;
3747: double ***p3matp, ***p3matm, ***varhe;
3748: double **dnewm,**doldm;
3749: double *xp, *xm;
3750: double **gp, **gm;
3751: double ***gradg, ***trgradg;
3752: int theta;
3753:
3754: double eip, vip;
3755:
3756: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
3757: xp=vector(1,npar);
3758: xm=vector(1,npar);
3759: dnewm=matrix(1,nlstate*nlstate,1,npar);
3760: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3761:
3762: pstamp(ficresstdeij);
3763: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3764: fprintf(ficresstdeij,"# Age");
3765: for(i=1; i<=nlstate;i++){
3766: for(j=1; j<=nlstate;j++)
3767: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3768: fprintf(ficresstdeij," e%1d. ",i);
3769: }
3770: fprintf(ficresstdeij,"\n");
3771:
3772: pstamp(ficrescveij);
3773: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3774: fprintf(ficrescveij,"# Age");
3775: for(i=1; i<=nlstate;i++)
3776: for(j=1; j<=nlstate;j++){
3777: cptj= (j-1)*nlstate+i;
3778: for(i2=1; i2<=nlstate;i2++)
3779: for(j2=1; j2<=nlstate;j2++){
3780: cptj2= (j2-1)*nlstate+i2;
3781: if(cptj2 <= cptj)
3782: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3783: }
3784: }
3785: fprintf(ficrescveij,"\n");
3786:
3787: if(estepm < stepm){
3788: printf ("Problem %d lower than %d\n",estepm, stepm);
3789: }
3790: else hstepm=estepm;
3791: /* We compute the life expectancy from trapezoids spaced every estepm months
3792: * This is mainly to measure the difference between two models: for example
3793: * if stepm=24 months pijx are given only every 2 years and by summing them
3794: * we are calculating an estimate of the Life Expectancy assuming a linear
3795: * progression in between and thus overestimating or underestimating according
3796: * to the curvature of the survival function. If, for the same date, we
3797: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3798: * to compare the new estimate of Life expectancy with the same linear
3799: * hypothesis. A more precise result, taking into account a more precise
3800: * curvature will be obtained if estepm is as small as stepm. */
3801:
3802: /* For example we decided to compute the life expectancy with the smallest unit */
3803: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3804: nhstepm is the number of hstepm from age to agelim
3805: nstepm is the number of stepm from age to agelin.
3806: Look at hpijx to understand the reason of that which relies in memory size
3807: and note for a fixed period like estepm months */
3808: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3809: survival function given by stepm (the optimization length). Unfortunately it
3810: means that if the survival funtion is printed only each two years of age and if
3811: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3812: results. So we changed our mind and took the option of the best precision.
3813: */
3814: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3815:
3816: /* If stepm=6 months */
3817: /* nhstepm age range expressed in number of stepm */
3818: agelim=AGESUP;
3819: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3820: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3821: /* if (stepm >= YEARM) hstepm=1;*/
3822: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3823:
3824: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3825: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3826: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3827: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3828: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3829: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3830:
3831: for (age=bage; age<=fage; age ++){
3832: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3833: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3834: /* if (stepm >= YEARM) hstepm=1;*/
3835: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3836:
3837: /* If stepm=6 months */
3838: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3839: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3840:
3841: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3842:
3843: /* Computing Variances of health expectancies */
3844: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3845: decrease memory allocation */
3846: for(theta=1; theta <=npar; theta++){
3847: for(i=1; i<=npar; i++){
3848: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3849: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3850: }
3851: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3852: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3853:
3854: for(j=1; j<= nlstate; j++){
3855: for(i=1; i<=nlstate; i++){
3856: for(h=0; h<=nhstepm-1; h++){
3857: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3858: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3859: }
3860: }
3861: }
3862:
3863: for(ij=1; ij<= nlstate*nlstate; ij++)
3864: for(h=0; h<=nhstepm-1; h++){
3865: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3866: }
3867: }/* End theta */
3868:
3869:
3870: for(h=0; h<=nhstepm-1; h++)
3871: for(j=1; j<=nlstate*nlstate;j++)
3872: for(theta=1; theta <=npar; theta++)
3873: trgradg[h][j][theta]=gradg[h][theta][j];
3874:
3875:
3876: for(ij=1;ij<=nlstate*nlstate;ij++)
3877: for(ji=1;ji<=nlstate*nlstate;ji++)
3878: varhe[ij][ji][(int)age] =0.;
3879:
3880: printf("%d|",(int)age);fflush(stdout);
3881: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3882: for(h=0;h<=nhstepm-1;h++){
3883: for(k=0;k<=nhstepm-1;k++){
3884: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3885: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3886: for(ij=1;ij<=nlstate*nlstate;ij++)
3887: for(ji=1;ji<=nlstate*nlstate;ji++)
3888: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3889: }
3890: }
3891:
3892: /* Computing expectancies */
3893: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3894: for(i=1; i<=nlstate;i++)
3895: for(j=1; j<=nlstate;j++)
3896: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3897: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3898:
3899: /* 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]);*/
3900:
3901: }
3902:
3903: fprintf(ficresstdeij,"%3.0f",age );
3904: for(i=1; i<=nlstate;i++){
3905: eip=0.;
3906: vip=0.;
3907: for(j=1; j<=nlstate;j++){
3908: eip += eij[i][j][(int)age];
3909: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3910: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3911: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3912: }
3913: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3914: }
3915: fprintf(ficresstdeij,"\n");
3916:
3917: fprintf(ficrescveij,"%3.0f",age );
3918: for(i=1; i<=nlstate;i++)
3919: for(j=1; j<=nlstate;j++){
3920: cptj= (j-1)*nlstate+i;
3921: for(i2=1; i2<=nlstate;i2++)
3922: for(j2=1; j2<=nlstate;j2++){
3923: cptj2= (j2-1)*nlstate+i2;
3924: if(cptj2 <= cptj)
3925: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3926: }
3927: }
3928: fprintf(ficrescveij,"\n");
3929:
3930: }
3931: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3932: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3933: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3934: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3935: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3936: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3937: printf("\n");
3938: fprintf(ficlog,"\n");
3939:
3940: free_vector(xm,1,npar);
3941: free_vector(xp,1,npar);
3942: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3943: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3944: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3945: }
3946:
3947: /************ Variance ******************/
1.203 ! brouard 3948: 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 *ncvyear, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
1.126 brouard 3949: {
3950: /* Variance of health expectancies */
3951: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3952: /* double **newm;*/
1.169 brouard 3953: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
3954:
3955: int movingaverage();
1.126 brouard 3956: double **dnewm,**doldm;
3957: double **dnewmp,**doldmp;
3958: int i, j, nhstepm, hstepm, h, nstepm ;
1.164 brouard 3959: int k;
1.126 brouard 3960: double *xp;
3961: double **gp, **gm; /* for var eij */
3962: double ***gradg, ***trgradg; /*for var eij */
3963: double **gradgp, **trgradgp; /* for var p point j */
3964: double *gpp, *gmp; /* for var p point j */
3965: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3966: double ***p3mat;
3967: double age,agelim, hf;
3968: double ***mobaverage;
3969: int theta;
3970: char digit[4];
3971: char digitp[25];
3972:
3973: char fileresprobmorprev[FILENAMELENGTH];
3974:
3975: if(popbased==1){
3976: if(mobilav!=0)
1.201 brouard 3977: strcpy(digitp,"-POPULBASED-MOBILAV_");
3978: else strcpy(digitp,"-POPULBASED-NOMOBIL_");
1.126 brouard 3979: }
3980: else
1.201 brouard 3981: strcpy(digitp,"-STABLBASED_");
1.126 brouard 3982:
3983: if (mobilav!=0) {
3984: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3985: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3986: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3987: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3988: }
3989: }
3990:
1.201 brouard 3991: strcpy(fileresprobmorprev,"PRMORPREV-");
1.126 brouard 3992: sprintf(digit,"%-d",ij);
3993: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3994: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3995: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
1.202 brouard 3996: strcat(fileresprobmorprev,fileresu);
1.126 brouard 3997: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3998: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3999: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
4000: }
4001: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
4002:
4003: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
4004: pstamp(ficresprobmorprev);
4005: 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);
4006: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
4007: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
4008: fprintf(ficresprobmorprev," p.%-d SE",j);
4009: for(i=1; i<=nlstate;i++)
4010: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
4011: }
4012: fprintf(ficresprobmorprev,"\n");
4013: fprintf(ficgp,"\n# Routine varevsij");
1.200 brouard 4014: fprintf(ficgp,"\nunset title \n");
4015: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
1.126 brouard 4016: 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");
4017: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
4018: /* } */
4019: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4020: pstamp(ficresvij);
4021: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
4022: if(popbased==1)
1.128 brouard 4023: 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 4024: else
4025: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
4026: fprintf(ficresvij,"# Age");
4027: for(i=1; i<=nlstate;i++)
4028: for(j=1; j<=nlstate;j++)
4029: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
4030: fprintf(ficresvij,"\n");
4031:
4032: xp=vector(1,npar);
4033: dnewm=matrix(1,nlstate,1,npar);
4034: doldm=matrix(1,nlstate,1,nlstate);
4035: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
4036: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4037:
4038: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
4039: gpp=vector(nlstate+1,nlstate+ndeath);
4040: gmp=vector(nlstate+1,nlstate+ndeath);
4041: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
4042:
4043: if(estepm < stepm){
4044: printf ("Problem %d lower than %d\n",estepm, stepm);
4045: }
4046: else hstepm=estepm;
4047: /* For example we decided to compute the life expectancy with the smallest unit */
4048: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
4049: nhstepm is the number of hstepm from age to agelim
4050: nstepm is the number of stepm from age to agelin.
1.128 brouard 4051: Look at function hpijx to understand why (it is linked to memory size questions) */
1.126 brouard 4052: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
4053: survival function given by stepm (the optimization length). Unfortunately it
4054: means that if the survival funtion is printed every two years of age and if
4055: you sum them up and add 1 year (area under the trapezoids) you won't get the same
4056: results. So we changed our mind and took the option of the best precision.
4057: */
4058: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
4059: agelim = AGESUP;
4060: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
4061: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4062: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
4063: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4064: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
4065: gp=matrix(0,nhstepm,1,nlstate);
4066: gm=matrix(0,nhstepm,1,nlstate);
4067:
4068:
4069: for(theta=1; theta <=npar; theta++){
4070: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
4071: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4072: }
4073: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1.203 ! brouard 4074: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear,ij);
1.126 brouard 4075:
4076: if (popbased==1) {
4077: if(mobilav ==0){
4078: for(i=1; i<=nlstate;i++)
4079: prlim[i][i]=probs[(int)age][i][ij];
4080: }else{ /* mobilav */
4081: for(i=1; i<=nlstate;i++)
4082: prlim[i][i]=mobaverage[(int)age][i][ij];
4083: }
4084: }
4085:
4086: for(j=1; j<= nlstate; j++){
4087: for(h=0; h<=nhstepm; h++){
4088: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
4089: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
4090: }
4091: }
4092: /* This for computing probability of death (h=1 means
4093: computed over hstepm matrices product = hstepm*stepm months)
4094: as a weighted average of prlim.
4095: */
4096: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4097: for(i=1,gpp[j]=0.; i<= nlstate; i++)
4098: gpp[j] += prlim[i][i]*p3mat[i][j][1];
4099: }
4100: /* end probability of death */
4101:
4102: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
4103: xp[i] = x[i] - (i==theta ?delti[theta]:0);
4104: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1.203 ! brouard 4105: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear, ij);
1.126 brouard 4106:
4107: if (popbased==1) {
4108: if(mobilav ==0){
4109: for(i=1; i<=nlstate;i++)
4110: prlim[i][i]=probs[(int)age][i][ij];
4111: }else{ /* mobilav */
4112: for(i=1; i<=nlstate;i++)
4113: prlim[i][i]=mobaverage[(int)age][i][ij];
4114: }
4115: }
4116:
1.128 brouard 4117: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
1.126 brouard 4118: for(h=0; h<=nhstepm; h++){
4119: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
4120: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
4121: }
4122: }
4123: /* This for computing probability of death (h=1 means
4124: computed over hstepm matrices product = hstepm*stepm months)
4125: as a weighted average of prlim.
4126: */
4127: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4128: for(i=1,gmp[j]=0.; i<= nlstate; i++)
4129: gmp[j] += prlim[i][i]*p3mat[i][j][1];
4130: }
4131: /* end probability of death */
4132:
4133: for(j=1; j<= nlstate; j++) /* vareij */
4134: for(h=0; h<=nhstepm; h++){
4135: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
4136: }
4137:
4138: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
4139: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
4140: }
4141:
4142: } /* End theta */
4143:
4144: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
4145:
4146: for(h=0; h<=nhstepm; h++) /* veij */
4147: for(j=1; j<=nlstate;j++)
4148: for(theta=1; theta <=npar; theta++)
4149: trgradg[h][j][theta]=gradg[h][theta][j];
4150:
4151: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
4152: for(theta=1; theta <=npar; theta++)
4153: trgradgp[j][theta]=gradgp[theta][j];
4154:
4155:
4156: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
4157: for(i=1;i<=nlstate;i++)
4158: for(j=1;j<=nlstate;j++)
4159: vareij[i][j][(int)age] =0.;
4160:
4161: for(h=0;h<=nhstepm;h++){
4162: for(k=0;k<=nhstepm;k++){
4163: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
4164: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
4165: for(i=1;i<=nlstate;i++)
4166: for(j=1;j<=nlstate;j++)
4167: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
4168: }
4169: }
4170:
4171: /* pptj */
4172: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
4173: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
4174: for(j=nlstate+1;j<=nlstate+ndeath;j++)
4175: for(i=nlstate+1;i<=nlstate+ndeath;i++)
4176: varppt[j][i]=doldmp[j][i];
4177: /* end ppptj */
4178: /* x centered again */
4179: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
1.203 ! brouard 4180: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyear,ij);
1.126 brouard 4181:
4182: if (popbased==1) {
4183: if(mobilav ==0){
4184: for(i=1; i<=nlstate;i++)
4185: prlim[i][i]=probs[(int)age][i][ij];
4186: }else{ /* mobilav */
4187: for(i=1; i<=nlstate;i++)
4188: prlim[i][i]=mobaverage[(int)age][i][ij];
4189: }
4190: }
4191:
4192: /* This for computing probability of death (h=1 means
4193: computed over hstepm (estepm) matrices product = hstepm*stepm months)
4194: as a weighted average of prlim.
4195: */
4196: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4197: for(i=1,gmp[j]=0.;i<= nlstate; i++)
4198: gmp[j] += prlim[i][i]*p3mat[i][j][1];
4199: }
4200: /* end probability of death */
4201:
4202: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
4203: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
4204: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
4205: for(i=1; i<=nlstate;i++){
4206: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
4207: }
4208: }
4209: fprintf(ficresprobmorprev,"\n");
4210:
4211: fprintf(ficresvij,"%.0f ",age );
4212: for(i=1; i<=nlstate;i++)
4213: for(j=1; j<=nlstate;j++){
4214: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
4215: }
4216: fprintf(ficresvij,"\n");
4217: free_matrix(gp,0,nhstepm,1,nlstate);
4218: free_matrix(gm,0,nhstepm,1,nlstate);
4219: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
4220: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
4221: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4222: } /* End age */
4223: free_vector(gpp,nlstate+1,nlstate+ndeath);
4224: free_vector(gmp,nlstate+1,nlstate+ndeath);
4225: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
4226: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.199 brouard 4227: /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
4228: fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
1.126 brouard 4229: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
1.131 brouard 4230: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.201 brouard 4231: fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 4232: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
4233: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
4234: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.145 brouard 4235: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
1.170 brouard 4236: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
1.145 brouard 4237: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
1.126 brouard 4238: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
1.201 brouard 4239: fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.svg\"> <br>\n", estepm,subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.199 brouard 4240: /* 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.svg\"> <br>\n", stepm,YEARM,digitp,digit);
1.126 brouard 4241: */
1.199 brouard 4242: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
1.201 brouard 4243: fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 4244:
4245: free_vector(xp,1,npar);
4246: free_matrix(doldm,1,nlstate,1,nlstate);
4247: free_matrix(dnewm,1,nlstate,1,npar);
4248: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4249: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
4250: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4251: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4252: fclose(ficresprobmorprev);
4253: fflush(ficgp);
4254: fflush(fichtm);
4255: } /* end varevsij */
4256:
4257: /************ Variance of prevlim ******************/
1.203 ! brouard 4258: 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 *ncvyear, int ij, char strstart[])
1.126 brouard 4259: {
4260: /* Variance of prevalence limit */
4261: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 4262:
1.126 brouard 4263: double **dnewm,**doldm;
4264: int i, j, nhstepm, hstepm;
4265: double *xp;
4266: double *gp, *gm;
4267: double **gradg, **trgradg;
4268: double age,agelim;
4269: int theta;
4270:
4271: pstamp(ficresvpl);
4272: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
4273: fprintf(ficresvpl,"# Age");
4274: for(i=1; i<=nlstate;i++)
4275: fprintf(ficresvpl," %1d-%1d",i,i);
4276: fprintf(ficresvpl,"\n");
4277:
4278: xp=vector(1,npar);
4279: dnewm=matrix(1,nlstate,1,npar);
4280: doldm=matrix(1,nlstate,1,nlstate);
4281:
4282: hstepm=1*YEARM; /* Every year of age */
4283: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
4284: agelim = AGESUP;
4285: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
4286: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4287: if (stepm >= YEARM) hstepm=1;
4288: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4289: gradg=matrix(1,npar,1,nlstate);
4290: gp=vector(1,nlstate);
4291: gm=vector(1,nlstate);
4292:
4293: for(theta=1; theta <=npar; theta++){
4294: for(i=1; i<=npar; i++){ /* Computes gradient */
4295: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4296: }
1.203 ! brouard 4297: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear,ij);
1.126 brouard 4298: for(i=1;i<=nlstate;i++)
4299: gp[i] = prlim[i][i];
4300:
4301: for(i=1; i<=npar; i++) /* Computes gradient */
4302: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.203 ! brouard 4303: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear,ij);
1.126 brouard 4304: for(i=1;i<=nlstate;i++)
4305: gm[i] = prlim[i][i];
4306:
4307: for(i=1;i<=nlstate;i++)
4308: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
4309: } /* End theta */
4310:
4311: trgradg =matrix(1,nlstate,1,npar);
4312:
4313: for(j=1; j<=nlstate;j++)
4314: for(theta=1; theta <=npar; theta++)
4315: trgradg[j][theta]=gradg[theta][j];
4316:
4317: for(i=1;i<=nlstate;i++)
4318: varpl[i][(int)age] =0.;
4319: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
4320: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
4321: for(i=1;i<=nlstate;i++)
4322: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
4323:
4324: fprintf(ficresvpl,"%.0f ",age );
4325: for(i=1; i<=nlstate;i++)
4326: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
4327: fprintf(ficresvpl,"\n");
4328: free_vector(gp,1,nlstate);
4329: free_vector(gm,1,nlstate);
4330: free_matrix(gradg,1,npar,1,nlstate);
4331: free_matrix(trgradg,1,nlstate,1,npar);
4332: } /* End age */
4333:
4334: free_vector(xp,1,npar);
4335: free_matrix(doldm,1,nlstate,1,npar);
4336: free_matrix(dnewm,1,nlstate,1,nlstate);
4337:
4338: }
4339:
4340: /************ Variance of one-step probabilities ******************/
4341: 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[])
4342: {
1.164 brouard 4343: int i, j=0, k1, l1, tj;
1.126 brouard 4344: int k2, l2, j1, z1;
1.164 brouard 4345: int k=0, l;
1.145 brouard 4346: int first=1, first1, first2;
1.126 brouard 4347: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
4348: double **dnewm,**doldm;
4349: double *xp;
4350: double *gp, *gm;
4351: double **gradg, **trgradg;
4352: double **mu;
1.164 brouard 4353: double age, cov[NCOVMAX+1];
1.126 brouard 4354: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
4355: int theta;
4356: char fileresprob[FILENAMELENGTH];
4357: char fileresprobcov[FILENAMELENGTH];
4358: char fileresprobcor[FILENAMELENGTH];
4359: double ***varpij;
4360:
1.201 brouard 4361: strcpy(fileresprob,"PROB_");
1.126 brouard 4362: strcat(fileresprob,fileres);
4363: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
4364: printf("Problem with resultfile: %s\n", fileresprob);
4365: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
4366: }
1.201 brouard 4367: strcpy(fileresprobcov,"PROBCOV_");
1.202 brouard 4368: strcat(fileresprobcov,fileresu);
1.126 brouard 4369: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
4370: printf("Problem with resultfile: %s\n", fileresprobcov);
4371: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
4372: }
1.201 brouard 4373: strcpy(fileresprobcor,"PROBCOR_");
1.202 brouard 4374: strcat(fileresprobcor,fileresu);
1.126 brouard 4375: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
4376: printf("Problem with resultfile: %s\n", fileresprobcor);
4377: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
4378: }
4379: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4380: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4381: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4382: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4383: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4384: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4385: pstamp(ficresprob);
4386: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
4387: fprintf(ficresprob,"# Age");
4388: pstamp(ficresprobcov);
4389: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
4390: fprintf(ficresprobcov,"# Age");
4391: pstamp(ficresprobcor);
4392: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
4393: fprintf(ficresprobcor,"# Age");
4394:
4395:
4396: for(i=1; i<=nlstate;i++)
4397: for(j=1; j<=(nlstate+ndeath);j++){
4398: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
4399: fprintf(ficresprobcov," p%1d-%1d ",i,j);
4400: fprintf(ficresprobcor," p%1d-%1d ",i,j);
4401: }
4402: /* fprintf(ficresprob,"\n");
4403: fprintf(ficresprobcov,"\n");
4404: fprintf(ficresprobcor,"\n");
4405: */
1.131 brouard 4406: xp=vector(1,npar);
1.126 brouard 4407: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4408: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4409: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
4410: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
4411: first=1;
4412: fprintf(ficgp,"\n# Routine varprob");
4413: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
4414: fprintf(fichtm,"\n");
4415:
1.200 brouard 4416: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back.</li>\n",optionfilehtmcov);
1.197 brouard 4417: fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov);
4418: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
1.126 brouard 4419: and drawn. It helps understanding how is the covariance between two incidences.\
4420: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
4421: 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. \
4422: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
4423: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
4424: standard deviations wide on each axis. <br>\
4425: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
4426: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
4427: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
4428:
4429: cov[1]=1;
1.145 brouard 4430: /* tj=cptcoveff; */
4431: tj = (int) pow(2,cptcoveff);
1.126 brouard 4432: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
4433: j1=0;
1.145 brouard 4434: for(j1=1; j1<=tj;j1++){
4435: /*for(i1=1; i1<=ncodemax[t];i1++){ */
4436: /*j1++;*/
1.126 brouard 4437: if (cptcovn>0) {
4438: fprintf(ficresprob, "\n#********** Variable ");
1.198 brouard 4439: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4440: fprintf(ficresprob, "**********\n#\n");
4441: fprintf(ficresprobcov, "\n#********** Variable ");
1.198 brouard 4442: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4443: fprintf(ficresprobcov, "**********\n#\n");
4444:
4445: fprintf(ficgp, "\n#********** Variable ");
1.198 brouard 4446: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4447: fprintf(ficgp, "**********\n#\n");
4448:
4449:
4450: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.198 brouard 4451: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4452: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
4453:
4454: fprintf(ficresprobcor, "\n#********** Variable ");
1.198 brouard 4455: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4456: fprintf(ficresprobcor, "**********\n#");
4457: }
4458:
1.145 brouard 4459: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
4460: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4461: gp=vector(1,(nlstate)*(nlstate+ndeath));
4462: gm=vector(1,(nlstate)*(nlstate+ndeath));
1.126 brouard 4463: for (age=bage; age<=fage; age ++){
4464: cov[2]=age;
1.187 brouard 4465: if(nagesqr==1)
4466: cov[3]= age*age;
1.126 brouard 4467: for (k=1; k<=cptcovn;k++) {
1.200 brouard 4468: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
4469: /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
1.145 brouard 4470: * 1 1 1 1 1
4471: * 2 2 1 1 1
4472: * 3 1 2 1 1
4473: */
4474: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
1.126 brouard 4475: }
1.186 brouard 4476: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 4477: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
1.126 brouard 4478: for (k=1; k<=cptcovprod;k++)
1.200 brouard 4479: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.126 brouard 4480:
4481:
4482: for(theta=1; theta <=npar; theta++){
4483: for(i=1; i<=npar; i++)
4484: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
4485:
4486: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4487:
4488: k=0;
4489: for(i=1; i<= (nlstate); i++){
4490: for(j=1; j<=(nlstate+ndeath);j++){
4491: k=k+1;
4492: gp[k]=pmmij[i][j];
4493: }
4494: }
4495:
4496: for(i=1; i<=npar; i++)
4497: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
4498:
4499: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4500: k=0;
4501: for(i=1; i<=(nlstate); i++){
4502: for(j=1; j<=(nlstate+ndeath);j++){
4503: k=k+1;
4504: gm[k]=pmmij[i][j];
4505: }
4506: }
4507:
4508: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
4509: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
4510: }
4511:
4512: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
4513: for(theta=1; theta <=npar; theta++)
4514: trgradg[j][theta]=gradg[theta][j];
4515:
4516: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
4517: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
4518:
4519: pmij(pmmij,cov,ncovmodel,x,nlstate);
4520:
4521: k=0;
4522: for(i=1; i<=(nlstate); i++){
4523: for(j=1; j<=(nlstate+ndeath);j++){
4524: k=k+1;
4525: mu[k][(int) age]=pmmij[i][j];
4526: }
4527: }
4528: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
4529: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
4530: varpij[i][j][(int)age] = doldm[i][j];
4531:
4532: /*printf("\n%d ",(int)age);
4533: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4534: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4535: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4536: }*/
4537:
4538: fprintf(ficresprob,"\n%d ",(int)age);
4539: fprintf(ficresprobcov,"\n%d ",(int)age);
4540: fprintf(ficresprobcor,"\n%d ",(int)age);
4541:
4542: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
4543: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
4544: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4545: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
4546: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
4547: }
4548: i=0;
4549: for (k=1; k<=(nlstate);k++){
4550: for (l=1; l<=(nlstate+ndeath);l++){
1.145 brouard 4551: i++;
1.126 brouard 4552: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
4553: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
4554: for (j=1; j<=i;j++){
1.145 brouard 4555: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
1.126 brouard 4556: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
4557: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
4558: }
4559: }
4560: }/* end of loop for state */
4561: } /* end of loop for age */
1.145 brouard 4562: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
4563: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
4564: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4565: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4566:
1.126 brouard 4567: /* Confidence intervalle of pij */
4568: /*
1.131 brouard 4569: fprintf(ficgp,"\nunset parametric;unset label");
1.126 brouard 4570: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
4571: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
4572: 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);
4573: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
4574: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
4575: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
4576: */
4577:
4578: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
1.145 brouard 4579: first1=1;first2=2;
1.126 brouard 4580: for (k2=1; k2<=(nlstate);k2++){
4581: for (l2=1; l2<=(nlstate+ndeath);l2++){
4582: if(l2==k2) continue;
4583: j=(k2-1)*(nlstate+ndeath)+l2;
4584: for (k1=1; k1<=(nlstate);k1++){
4585: for (l1=1; l1<=(nlstate+ndeath);l1++){
4586: if(l1==k1) continue;
4587: i=(k1-1)*(nlstate+ndeath)+l1;
4588: if(i<=j) continue;
4589: for (age=bage; age<=fage; age ++){
4590: if ((int)age %5==0){
4591: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
4592: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
4593: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
4594: mu1=mu[i][(int) age]/stepm*YEARM ;
4595: mu2=mu[j][(int) age]/stepm*YEARM;
4596: c12=cv12/sqrt(v1*v2);
4597: /* Computing eigen value of matrix of covariance */
4598: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4599: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
1.135 brouard 4600: if ((lc2 <0) || (lc1 <0) ){
1.145 brouard 4601: if(first2==1){
4602: first1=0;
4603: 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);
4604: }
4605: 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);
4606: /* lc1=fabs(lc1); */ /* If we want to have them positive */
4607: /* lc2=fabs(lc2); */
1.135 brouard 4608: }
4609:
1.126 brouard 4610: /* Eigen vectors */
4611: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
4612: /*v21=sqrt(1.-v11*v11); *//* error */
4613: v21=(lc1-v1)/cv12*v11;
4614: v12=-v21;
4615: v22=v11;
4616: tnalp=v21/v11;
4617: if(first1==1){
4618: first1=0;
4619: 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);
4620: }
4621: 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);
4622: /*printf(fignu*/
4623: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
4624: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
4625: if(first==1){
4626: first=0;
1.200 brouard 4627: fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
1.126 brouard 4628: fprintf(ficgp,"\nset parametric;unset label");
4629: 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);
1.199 brouard 4630: fprintf(ficgp,"\nset ter svg size 640, 480");
1.126 brouard 4631: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.201 brouard 4632: :<a href=\"%s_%d%1d%1d-%1d%1d.svg\">\
4633: %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
4634: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,\
4635: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
4636: fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
1.126 brouard 4637: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
1.201 brouard 4638: fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
1.126 brouard 4639: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4640: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4641: 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",\
4642: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4643: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4644: }else{
4645: first=0;
4646: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4647: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4648: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4649: 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",\
4650: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4651: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4652: }/* if first */
4653: } /* age mod 5 */
4654: } /* end loop age */
1.201 brouard 4655: fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
1.126 brouard 4656: first=1;
4657: } /*l12 */
4658: } /* k12 */
4659: } /*l1 */
4660: }/* k1 */
1.169 brouard 4661: /* } */ /* loop covariates */
1.126 brouard 4662: }
4663: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4664: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4665: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4666: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4667: free_vector(xp,1,npar);
4668: fclose(ficresprob);
4669: fclose(ficresprobcov);
4670: fclose(ficresprobcor);
4671: fflush(ficgp);
4672: fflush(fichtmcov);
4673: }
4674:
4675:
4676: /******************* Printing html file ***********/
1.201 brouard 4677: void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 4678: int lastpass, int stepm, int weightopt, char model[],\
4679: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
4680: int popforecast, int estepm ,\
4681: double jprev1, double mprev1,double anprev1, \
4682: double jprev2, double mprev2,double anprev2){
4683: int jj1, k1, i1, cpt;
4684:
4685: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4686: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4687: </ul>");
4688: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
4689: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
1.201 brouard 4690: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
1.126 brouard 4691: fprintf(fichtm,"\
4692: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
1.201 brouard 4693: stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
1.126 brouard 4694: fprintf(fichtm,"\
4695: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4696: subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
1.126 brouard 4697: fprintf(fichtm,"\
1.128 brouard 4698: - (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 4699: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4700: estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
1.126 brouard 4701: fprintf(fichtm,"\
4702: - Population projections by age and states: \
1.201 brouard 4703: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
1.126 brouard 4704:
4705: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4706:
1.145 brouard 4707: m=pow(2,cptcoveff);
1.126 brouard 4708: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4709:
4710: jj1=0;
4711: for(k1=1; k1<=m;k1++){
1.192 brouard 4712: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
1.126 brouard 4713: jj1++;
4714: if (cptcovn > 0) {
4715: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.192 brouard 4716: for (cpt=1; cpt<=cptcoveff;cpt++){
1.198 brouard 4717: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
4718: printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
1.192 brouard 4719: }
1.126 brouard 4720: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4721: }
1.201 brouard 4722: /* aij, bij */
4723: fprintf(fichtm,"<br>- Logit model, for example: logit(pij)=log(pij/pii)= aij+ bij age + V1 age + etc. as a function of age: <a href=\"%s_%d-1.svg\">%s_%d-1.svg</a><br> \
4724: <img src=\"%s_%d-1.svg\">",subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.126 brouard 4725: /* Pij */
1.202 brouard 4726: fprintf(fichtm,"<br>\n- Pij or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2.svg\">%s_%d-2.svg</a><br> \
1.201 brouard 4727: <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.126 brouard 4728: /* Quasi-incidences */
1.201 brouard 4729: fprintf(fichtm,"<br>\n- Iij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
4730: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too,\
4731: incidence (rates) are the limit when h tends to zero of the ratio of the probability hPij \
4732: divided by h: hPij/h : <a href=\"%s_%d-3.svg\">%s_%d-3.svg</a><br> \
4733: <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
4734: /* Survival functions (period) in state j */
4735: for(cpt=1; cpt<=nlstate;cpt++){
4736: fprintf(fichtm,"<br>\n- Survival functions in state %d. Or probability to survive in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> \
4737: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);
4738: }
4739: /* State specific survival functions (period) */
4740: for(cpt=1; cpt<=nlstate;cpt++){
4741: fprintf(fichtm,"<br>\n- Survival functions from state %d in any different live states and total.\
4742: Or probability to survive in various states (1 to %d) being in state %d at different ages.\
4743: <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> <img src=\"%s_%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1);
4744: }
4745: /* Period (stable) prevalence in each health state */
4746: for(cpt=1; cpt<=nlstate;cpt++){
4747: fprintf(fichtm,"<br>\n- 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.svg\">%s%d_%d.svg</a><br> \
4748: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);
4749: }
1.126 brouard 4750: for(cpt=1; cpt<=nlstate;cpt++) {
1.201 brouard 4751: 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) (or area under each survival functions): <a href=\"%s%d%d.svg\">%s%d%d.svg</a> <br> \
4752: <img src=\"%s_%d%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1);
1.126 brouard 4753: }
1.192 brouard 4754: /* } /\* end i1 *\/ */
1.126 brouard 4755: }/* End k1 */
4756: fprintf(fichtm,"</ul>");
4757:
4758: fprintf(fichtm,"\
4759: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 brouard 4760: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
1.203 ! brouard 4761: - 95%% confidence intervals and Wald tests of the estimated parameters are in the log file if optimization has been done (mle != 0).<br> \
1.197 brouard 4762: But because parameters are usually highly correlated (a higher incidence of disability \
4763: and a higher incidence of recovery can give very close observed transition) it might \
4764: be very useful to look not only at linear confidence intervals estimated from the \
4765: variances but at the covariance matrix. And instead of looking at the estimated coefficients \
4766: (parameters) of the logistic regression, it might be more meaningful to visualize the \
4767: covariance matrix of the one-step probabilities. \
4768: See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
1.126 brouard 4769:
1.193 brouard 4770: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4771: subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
1.126 brouard 4772: fprintf(fichtm,"\
4773: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4774: subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
1.126 brouard 4775:
4776: fprintf(fichtm,"\
4777: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4778: subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
1.126 brouard 4779: fprintf(fichtm,"\
4780: - 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): \
4781: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 4782: estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
1.126 brouard 4783: fprintf(fichtm,"\
4784: - (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): \
4785: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 4786: estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
1.126 brouard 4787: fprintf(fichtm,"\
1.128 brouard 4788: - 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",
1.201 brouard 4789: estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
1.126 brouard 4790: fprintf(fichtm,"\
1.128 brouard 4791: - 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",
1.201 brouard 4792: estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
1.126 brouard 4793: fprintf(fichtm,"\
4794: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
1.201 brouard 4795: subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
1.126 brouard 4796:
4797: /* if(popforecast==1) fprintf(fichtm,"\n */
4798: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4799: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4800: /* <br>",fileres,fileres,fileres,fileres); */
4801: /* else */
4802: /* 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); */
4803: fflush(fichtm);
4804: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4805:
1.145 brouard 4806: m=pow(2,cptcoveff);
1.126 brouard 4807: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4808:
4809: jj1=0;
4810: for(k1=1; k1<=m;k1++){
1.192 brouard 4811: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
1.126 brouard 4812: jj1++;
4813: if (cptcovn > 0) {
4814: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4815: for (cpt=1; cpt<=cptcoveff;cpt++)
1.198 brouard 4816: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
1.126 brouard 4817: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4818: }
4819: for(cpt=1; cpt<=nlstate;cpt++) {
4820: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
1.199 brouard 4821: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.svg <br>\
1.201 brouard 4822: <img src=\"%s_%d-%d.svg\">",cpt,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1);
1.126 brouard 4823: }
4824: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 4825: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4826: true period expectancies (those weighted with period prevalences are also\
4827: drawn in addition to the population based expectancies computed using\
1.201 brouard 4828: observed and cahotic prevalences: %s_%d.svg<br>\
4829: <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
1.192 brouard 4830: /* } /\* end i1 *\/ */
1.126 brouard 4831: }/* End k1 */
4832: fprintf(fichtm,"</ul>");
4833: fflush(fichtm);
4834: }
4835:
4836: /******************* Gnuplot file **************/
1.201 brouard 4837: void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 4838:
4839: char dirfileres[132],optfileres[132];
1.164 brouard 4840: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
1.130 brouard 4841: int ng=0;
1.201 brouard 4842: int vpopbased;
1.126 brouard 4843: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4844: /* printf("Problem with file %s",optionfilegnuplot); */
4845: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4846: /* } */
4847:
4848: /*#ifdef windows */
4849: fprintf(ficgp,"cd \"%s\" \n",pathc);
4850: /*#endif */
4851: m=pow(2,cptcoveff);
4852:
1.202 brouard 4853: /* Contribution to likelihood */
4854: /* Plot the probability implied in the likelihood */
4855: fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
4856: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
4857: /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
4858: fprintf(ficgp,"\nset ter png size 640, 480");
4859: /* good for mle=4 plot by number of matrix products.
4860: replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
4861: /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */
4862: /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
4863: fprintf(ficgp,"\nset out \"%s.png\";",subdirf2(optionfilefiname,"ILK_"));
4864: fprintf(ficgp,"\nplot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk));
4865: fprintf(ficgp,"\nreplot \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk));
1.203 ! brouard 4866: fprintf(ficgp,"\nset out;unset log\n");
1.202 brouard 4867: /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
4868:
1.126 brouard 4869: strcpy(dirfileres,optionfilefiname);
4870: strcpy(optfileres,"vpl");
4871: /* 1eme*/
1.201 brouard 4872: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files\n");
1.126 brouard 4873: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.145 brouard 4874: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
1.201 brouard 4875: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
4876: fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
1.126 brouard 4877: fprintf(ficgp,"set xlabel \"Age\" \n\
4878: set ylabel \"Probability\" \n\
1.199 brouard 4879: set ter svg size 640, 480\n\
1.201 brouard 4880: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
1.126 brouard 4881:
4882: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4883: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4884: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4885: }
1.201 brouard 4886: fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
1.126 brouard 4887: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4888: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4889: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4890: }
1.201 brouard 4891: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
1.126 brouard 4892: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4893: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4894: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4895: }
1.201 brouard 4896: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
4897: fprintf(ficgp,"\nset out \n");
4898: } /* k1 */
4899: } /* cpt */
1.126 brouard 4900: /*2 eme*/
1.153 brouard 4901: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
1.126 brouard 4902: for (k1=1; k1<= m ; k1 ++) {
1.201 brouard 4903: fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
4904: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
4905: if(vpopbased==0)
4906: fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
4907: else
4908: fprintf(ficgp,"\nreplot ");
4909: for (i=1; i<= nlstate+1 ; i ++) {
4910: k=2*i;
4911: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1, vpopbased);
4912: for (j=1; j<= nlstate+1 ; j ++) {
4913: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4914: else fprintf(ficgp," %%*lf (%%*lf)");
4915: }
4916: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
4917: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
4918: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
4919: for (j=1; j<= nlstate+1 ; j ++) {
4920: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4921: else fprintf(ficgp," %%*lf (%%*lf)");
4922: }
4923: fprintf(ficgp,"\" t\"\" w l lt 0,");
4924: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
4925: for (j=1; j<= nlstate+1 ; j ++) {
4926: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4927: else fprintf(ficgp," %%*lf (%%*lf)");
4928: }
4929: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4930: else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
4931: } /* state */
4932: } /* vpopbased */
4933: fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
4934: } /* k1 */
1.126 brouard 4935: /*3eme*/
4936:
4937: for (k1=1; k1<= m ; k1 ++) {
4938: for (cpt=1; cpt<= nlstate ; cpt ++) {
4939: /* k=2+nlstate*(2*cpt-2); */
4940: k=2+(nlstate+1)*(cpt-1);
1.201 brouard 4941: fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
1.199 brouard 4942: fprintf(ficgp,"set ter svg size 640, 480\n\
1.201 brouard 4943: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
1.126 brouard 4944: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4945: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4946: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4947: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4948: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4949: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4950:
4951: */
4952: for (i=1; i< nlstate ; i ++) {
1.201 brouard 4953: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+i,cpt,i+1);
1.126 brouard 4954: /* 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);*/
4955:
4956: }
1.201 brouard 4957: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+nlstate,cpt);
1.126 brouard 4958: }
4959: }
4960:
1.201 brouard 4961: /* Survival functions (period) from state i in state j by initial state i */
4962: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
4963: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
4964: k=3;
4965: fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'lij' files, cov=%d state=%d",k1, cpt);
4966: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
4967: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
4968: set ter svg size 640, 480\n\
4969: unset log y\n\
4970: plot [%.f:%.f] ", ageminpar, agemaxpar);
4971: for (i=1; i<= nlstate ; i ++){
4972: if(i==1)
4973: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
4974: else
4975: fprintf(ficgp,", '' ");
4976: l=(nlstate+ndeath)*(i-1)+1;
4977: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
4978: for (j=2; j<= nlstate+ndeath ; j ++)
4979: fprintf(ficgp,"+$%d",k+l+j-1);
4980: fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
4981: } /* nlstate */
4982: fprintf(ficgp,"\nset out\n");
4983: } /* end cpt state*/
4984: } /* end covariate */
4985:
4986: /* Survival functions (period) from state i in state j by final state j */
1.202 brouard 4987: for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
1.201 brouard 4988: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
4989: k=3;
4990: fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);
4991: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
4992: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
4993: set ter svg size 640, 480\n\
4994: unset log y\n\
4995: plot [%.f:%.f] ", ageminpar, agemaxpar);
4996: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
4997: if(j==1)
4998: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
4999: else
5000: fprintf(ficgp,", '' ");
5001: l=(nlstate+ndeath)*(cpt-1) +j;
5002: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
5003: /* for (i=2; i<= nlstate+ndeath ; i ++) */
5004: /* fprintf(ficgp,"+$%d",k+l+i-1); */
5005: fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
5006: } /* nlstate */
5007: fprintf(ficgp,", '' ");
5008: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
5009: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
5010: l=(nlstate+ndeath)*(cpt-1) +j;
5011: if(j < nlstate)
5012: fprintf(ficgp,"$%d +",k+l);
5013: else
5014: fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
5015: }
5016: fprintf(ficgp,"\nset out\n");
5017: } /* end cpt state*/
5018: } /* end covariate */
5019:
1.202 brouard 5020: /* CV preval stable (period) for each covariate */
5021: for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
1.153 brouard 5022: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.126 brouard 5023: k=3;
1.153 brouard 5024: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
1.201 brouard 5025: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
1.126 brouard 5026: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.199 brouard 5027: set ter svg size 640, 480\n\
1.126 brouard 5028: unset log y\n\
1.153 brouard 5029: plot [%.f:%.f] ", ageminpar, agemaxpar);
5030: for (i=1; i<= nlstate ; i ++){
5031: if(i==1)
1.201 brouard 5032: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
1.153 brouard 5033: else
5034: fprintf(ficgp,", '' ");
1.154 brouard 5035: l=(nlstate+ndeath)*(i-1)+1;
5036: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
1.201 brouard 5037: for (j=2; j<= nlstate ; j ++)
5038: fprintf(ficgp,"+$%d",k+l+j-1);
1.153 brouard 5039: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
5040: } /* nlstate */
1.201 brouard 5041: fprintf(ficgp,"\nset out\n");
1.153 brouard 5042: } /* end cpt state*/
5043: } /* end covariate */
1.201 brouard 5044:
1.126 brouard 5045: /* proba elementaires */
1.187 brouard 5046: fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
1.126 brouard 5047: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 5048: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 5049: for(k=1; k <=(nlstate+ndeath); k++){
5050: if (k != i) {
1.187 brouard 5051: fprintf(ficgp,"# current state %d\n",k);
1.126 brouard 5052: for(j=1; j <=ncovmodel; j++){
1.187 brouard 5053: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
1.126 brouard 5054: jk++;
5055: }
1.187 brouard 5056: fprintf(ficgp,"\n");
1.126 brouard 5057: }
5058: }
5059: }
1.187 brouard 5060: fprintf(ficgp,"##############\n#\n");
5061:
1.145 brouard 5062: /*goto avoid;*/
1.200 brouard 5063: fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");
1.187 brouard 5064: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
5065: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
5066: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
5067: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
5068: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
5069: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
5070: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
5071: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
5072: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
5073: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
5074: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
5075: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
5076: fprintf(ficgp,"#\n");
1.201 brouard 5077: for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
1.187 brouard 5078: fprintf(ficgp,"# ng=%d\n",ng);
5079: fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);
1.126 brouard 5080: for(jk=1; jk <=m; jk++) {
1.187 brouard 5081: fprintf(ficgp,"# jk=%d\n",jk);
1.201 brouard 5082: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
5083: fprintf(ficgp,"\nset ter svg size 640, 480 ");
5084: if (ng==1){
5085: fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
5086: fprintf(ficgp,"\nunset log y");
5087: }else if (ng==2){
5088: fprintf(ficgp,"\nset ylabel \"Probability\"\n");
5089: fprintf(ficgp,"\nset log y");
5090: }else if (ng==3){
1.126 brouard 5091: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
1.201 brouard 5092: fprintf(ficgp,"\nset log y");
5093: }else
5094: fprintf(ficgp,"\nunset title ");
5095: fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar);
1.126 brouard 5096: i=1;
5097: for(k2=1; k2<=nlstate; k2++) {
5098: k3=i;
5099: for(k=1; k<=(nlstate+ndeath); k++) {
5100: if (k != k2){
1.201 brouard 5101: switch( ng) {
5102: case 1:
1.187 brouard 5103: if(nagesqr==0)
1.201 brouard 5104: fprintf(ficgp," p%d+p%d*x",i,i+1);
1.187 brouard 5105: else /* nagesqr =1 */
1.201 brouard 5106: fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
5107: break;
5108: case 2: /* ng=2 */
1.187 brouard 5109: if(nagesqr==0)
5110: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
5111: else /* nagesqr =1 */
1.201 brouard 5112: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
5113: break;
5114: case 3:
5115: if(nagesqr==0)
5116: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
5117: else /* nagesqr =1 */
5118: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
5119: break;
5120: }
1.141 brouard 5121: ij=1;/* To be checked else nbcode[0][0] wrong */
1.187 brouard 5122: for(j=3; j <=ncovmodel-nagesqr; j++) {
1.197 brouard 5123: /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
5124: if(ij <=cptcovage) { /* Bug valgrind */
5125: if((j-2)==Tage[ij]) { /* Bug valgrind */
1.200 brouard 5126: fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
5127: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
1.197 brouard 5128: ij++;
5129: }
1.186 brouard 5130: }
5131: else
1.198 brouard 5132: fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
1.126 brouard 5133: }
1.201 brouard 5134: if(ng != 1){
5135: fprintf(ficgp,")/(1");
1.126 brouard 5136:
1.201 brouard 5137: for(k1=1; k1 <=nlstate; k1++){
5138: if(nagesqr==0)
5139: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
5140: else /* nagesqr =1 */
5141: 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);
5142:
5143: ij=1;
5144: for(j=3; j <=ncovmodel-nagesqr; j++){
5145: if(ij <=cptcovage) { /* Bug valgrind */
5146: if((j-2)==Tage[ij]) { /* Bug valgrind */
5147: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
5148: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
5149: ij++;
5150: }
1.197 brouard 5151: }
1.201 brouard 5152: else
5153: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
1.186 brouard 5154: }
1.201 brouard 5155: fprintf(ficgp,")");
1.126 brouard 5156: }
5157: fprintf(ficgp,")");
1.201 brouard 5158: if(ng ==2)
5159: fprintf(ficgp," t \"p%d%d\" ", k2,k);
5160: else /* ng= 3 */
5161: fprintf(ficgp," t \"i%d%d\" ", k2,k);
5162: }else{ /* end ng <> 1 */
5163: fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
1.126 brouard 5164: }
5165: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
5166: i=i+ncovmodel;
5167: }
5168: } /* end k */
5169: } /* end k2 */
1.201 brouard 5170: fprintf(ficgp,"\n set out\n");
1.126 brouard 5171: } /* end jk */
5172: } /* end ng */
1.164 brouard 5173: /* avoid: */
1.126 brouard 5174: fflush(ficgp);
5175: } /* end gnuplot */
5176:
5177:
5178: /*************** Moving average **************/
5179: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
5180:
5181: int i, cpt, cptcod;
5182: int modcovmax =1;
5183: int mobilavrange, mob;
5184: double age;
5185:
5186: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
5187: a covariate has 2 modalities */
5188: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
5189:
5190: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
5191: if(mobilav==1) mobilavrange=5; /* default */
5192: else mobilavrange=mobilav;
5193: for (age=bage; age<=fage; age++)
5194: for (i=1; i<=nlstate;i++)
5195: for (cptcod=1;cptcod<=modcovmax;cptcod++)
5196: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
5197: /* We keep the original values on the extreme ages bage, fage and for
5198: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
5199: we use a 5 terms etc. until the borders are no more concerned.
5200: */
5201: for (mob=3;mob <=mobilavrange;mob=mob+2){
5202: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
5203: for (i=1; i<=nlstate;i++){
5204: for (cptcod=1;cptcod<=modcovmax;cptcod++){
5205: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
5206: for (cpt=1;cpt<=(mob-1)/2;cpt++){
5207: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
5208: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
5209: }
5210: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
5211: }
5212: }
5213: }/* end age */
5214: }/* end mob */
5215: }else return -1;
5216: return 0;
5217: }/* End movingaverage */
5218:
5219:
5220: /************** Forecasting ******************/
1.169 brouard 5221: 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 5222: /* proj1, year, month, day of starting projection
5223: agemin, agemax range of age
5224: dateprev1 dateprev2 range of dates during which prevalence is computed
5225: anproj2 year of en of projection (same day and month as proj1).
5226: */
1.164 brouard 5227: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
1.126 brouard 5228: double agec; /* generic age */
5229: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
5230: double *popeffectif,*popcount;
5231: double ***p3mat;
5232: double ***mobaverage;
5233: char fileresf[FILENAMELENGTH];
5234:
5235: agelim=AGESUP;
5236: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5237:
1.201 brouard 5238: strcpy(fileresf,"F_");
5239: strcat(fileresf,fileresu);
1.126 brouard 5240: if((ficresf=fopen(fileresf,"w"))==NULL) {
5241: printf("Problem with forecast resultfile: %s\n", fileresf);
5242: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
5243: }
5244: printf("Computing forecasting: result on file '%s' \n", fileresf);
5245: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
5246:
5247: if (cptcoveff==0) ncodemax[cptcoveff]=1;
5248:
5249: if (mobilav!=0) {
5250: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5251: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
5252: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5253: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5254: }
5255: }
5256:
5257: stepsize=(int) (stepm+YEARM-1)/YEARM;
5258: if (stepm<=12) stepsize=1;
5259: if(estepm < stepm){
5260: printf ("Problem %d lower than %d\n",estepm, stepm);
5261: }
5262: else hstepm=estepm;
5263:
5264: hstepm=hstepm/stepm;
5265: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
5266: fractional in yp1 */
5267: anprojmean=yp;
5268: yp2=modf((yp1*12),&yp);
5269: mprojmean=yp;
5270: yp1=modf((yp2*30.5),&yp);
5271: jprojmean=yp;
5272: if(jprojmean==0) jprojmean=1;
5273: if(mprojmean==0) jprojmean=1;
5274:
5275: i1=cptcoveff;
5276: if (cptcovn < 1){i1=1;}
5277:
5278: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
5279:
5280: fprintf(ficresf,"#****** Routine prevforecast **\n");
5281:
5282: /* if (h==(int)(YEARM*yearp)){ */
5283: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
5284: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
5285: k=k+1;
5286: fprintf(ficresf,"\n#******");
5287: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 5288: fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 5289: }
5290: fprintf(ficresf,"******\n");
5291: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
5292: for(j=1; j<=nlstate+ndeath;j++){
5293: for(i=1; i<=nlstate;i++)
5294: fprintf(ficresf," p%d%d",i,j);
5295: fprintf(ficresf," p.%d",j);
5296: }
5297: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
5298: fprintf(ficresf,"\n");
5299: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
5300:
5301: for (agec=fage; agec>=(ageminpar-1); agec--){
5302: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
5303: nhstepm = nhstepm/hstepm;
5304: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5305: oldm=oldms;savm=savms;
5306: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
5307:
5308: for (h=0; h<=nhstepm; h++){
5309: if (h*hstepm/YEARM*stepm ==yearp) {
5310: fprintf(ficresf,"\n");
5311: for(j=1;j<=cptcoveff;j++)
1.198 brouard 5312: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 5313: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
5314: }
5315: for(j=1; j<=nlstate+ndeath;j++) {
5316: ppij=0.;
5317: for(i=1; i<=nlstate;i++) {
5318: if (mobilav==1)
5319: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
5320: else {
5321: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
5322: }
5323: if (h*hstepm/YEARM*stepm== yearp) {
5324: fprintf(ficresf," %.3f", p3mat[i][j][h]);
5325: }
5326: } /* end i */
5327: if (h*hstepm/YEARM*stepm==yearp) {
5328: fprintf(ficresf," %.3f", ppij);
5329: }
5330: }/* end j */
5331: } /* end h */
5332: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5333: } /* end agec */
5334: } /* end yearp */
5335: } /* end cptcod */
5336: } /* end cptcov */
5337:
5338: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5339:
5340: fclose(ficresf);
5341: }
5342:
5343: /************** Forecasting *****not tested NB*************/
1.169 brouard 5344: 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 5345:
5346: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
5347: int *popage;
5348: double calagedatem, agelim, kk1, kk2;
5349: double *popeffectif,*popcount;
5350: double ***p3mat,***tabpop,***tabpopprev;
5351: double ***mobaverage;
5352: char filerespop[FILENAMELENGTH];
5353:
5354: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5355: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5356: agelim=AGESUP;
5357: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
5358:
5359: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5360:
5361:
1.201 brouard 5362: strcpy(filerespop,"POP_");
5363: strcat(filerespop,fileresu);
1.126 brouard 5364: if((ficrespop=fopen(filerespop,"w"))==NULL) {
5365: printf("Problem with forecast resultfile: %s\n", filerespop);
5366: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
5367: }
5368: printf("Computing forecasting: result on file '%s' \n", filerespop);
5369: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
5370:
5371: if (cptcoveff==0) ncodemax[cptcoveff]=1;
5372:
5373: if (mobilav!=0) {
5374: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5375: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
5376: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5377: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5378: }
5379: }
5380:
5381: stepsize=(int) (stepm+YEARM-1)/YEARM;
5382: if (stepm<=12) stepsize=1;
5383:
5384: agelim=AGESUP;
5385:
5386: hstepm=1;
5387: hstepm=hstepm/stepm;
5388:
5389: if (popforecast==1) {
5390: if((ficpop=fopen(popfile,"r"))==NULL) {
5391: printf("Problem with population file : %s\n",popfile);exit(0);
5392: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
5393: }
5394: popage=ivector(0,AGESUP);
5395: popeffectif=vector(0,AGESUP);
5396: popcount=vector(0,AGESUP);
5397:
5398: i=1;
5399: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
5400:
5401: imx=i;
5402: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
5403: }
5404:
5405: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
5406: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
5407: k=k+1;
5408: fprintf(ficrespop,"\n#******");
5409: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 5410: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 5411: }
5412: fprintf(ficrespop,"******\n");
5413: fprintf(ficrespop,"# Age");
5414: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
5415: if (popforecast==1) fprintf(ficrespop," [Population]");
5416:
5417: for (cpt=0; cpt<=0;cpt++) {
5418: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5419:
5420: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5421: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5422: nhstepm = nhstepm/hstepm;
5423:
5424: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5425: oldm=oldms;savm=savms;
5426: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5427:
5428: for (h=0; h<=nhstepm; h++){
5429: if (h==(int) (calagedatem+YEARM*cpt)) {
5430: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5431: }
5432: for(j=1; j<=nlstate+ndeath;j++) {
5433: kk1=0.;kk2=0;
5434: for(i=1; i<=nlstate;i++) {
5435: if (mobilav==1)
5436: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
5437: else {
5438: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
5439: }
5440: }
5441: if (h==(int)(calagedatem+12*cpt)){
5442: tabpop[(int)(agedeb)][j][cptcod]=kk1;
5443: /*fprintf(ficrespop," %.3f", kk1);
5444: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
5445: }
5446: }
5447: for(i=1; i<=nlstate;i++){
5448: kk1=0.;
5449: for(j=1; j<=nlstate;j++){
5450: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
5451: }
5452: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
5453: }
5454:
5455: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
5456: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
5457: }
5458: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5459: }
5460: }
5461:
5462: /******/
5463:
5464: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
5465: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5466: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5467: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5468: nhstepm = nhstepm/hstepm;
5469:
5470: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5471: oldm=oldms;savm=savms;
5472: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5473: for (h=0; h<=nhstepm; h++){
5474: if (h==(int) (calagedatem+YEARM*cpt)) {
5475: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5476: }
5477: for(j=1; j<=nlstate+ndeath;j++) {
5478: kk1=0.;kk2=0;
5479: for(i=1; i<=nlstate;i++) {
5480: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
5481: }
5482: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
5483: }
5484: }
5485: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5486: }
5487: }
5488: }
5489: }
5490:
5491: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5492:
5493: if (popforecast==1) {
5494: free_ivector(popage,0,AGESUP);
5495: free_vector(popeffectif,0,AGESUP);
5496: free_vector(popcount,0,AGESUP);
5497: }
5498: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5499: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5500: fclose(ficrespop);
5501: } /* End of popforecast */
5502:
5503: int fileappend(FILE *fichier, char *optionfich)
5504: {
5505: if((fichier=fopen(optionfich,"a"))==NULL) {
5506: printf("Problem with file: %s\n", optionfich);
5507: fprintf(ficlog,"Problem with file: %s\n", optionfich);
5508: return (0);
5509: }
5510: fflush(fichier);
5511: return (1);
5512: }
5513:
5514:
5515: /**************** function prwizard **********************/
5516: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
5517: {
5518:
5519: /* Wizard to print covariance matrix template */
5520:
1.164 brouard 5521: char ca[32], cb[32];
5522: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 5523: int numlinepar;
5524:
5525: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5526: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5527: for(i=1; i <=nlstate; i++){
5528: jj=0;
5529: for(j=1; j <=nlstate+ndeath; j++){
5530: if(j==i) continue;
5531: jj++;
5532: /*ca[0]= k+'a'-1;ca[1]='\0';*/
5533: printf("%1d%1d",i,j);
5534: fprintf(ficparo,"%1d%1d",i,j);
5535: for(k=1; k<=ncovmodel;k++){
5536: /* printf(" %lf",param[i][j][k]); */
5537: /* fprintf(ficparo," %lf",param[i][j][k]); */
5538: printf(" 0.");
5539: fprintf(ficparo," 0.");
5540: }
5541: printf("\n");
5542: fprintf(ficparo,"\n");
5543: }
5544: }
5545: printf("# Scales (for hessian or gradient estimation)\n");
5546: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
5547: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
5548: for(i=1; i <=nlstate; i++){
5549: jj=0;
5550: for(j=1; j <=nlstate+ndeath; j++){
5551: if(j==i) continue;
5552: jj++;
5553: fprintf(ficparo,"%1d%1d",i,j);
5554: printf("%1d%1d",i,j);
5555: fflush(stdout);
5556: for(k=1; k<=ncovmodel;k++){
5557: /* printf(" %le",delti3[i][j][k]); */
5558: /* fprintf(ficparo," %le",delti3[i][j][k]); */
5559: printf(" 0.");
5560: fprintf(ficparo," 0.");
5561: }
5562: numlinepar++;
5563: printf("\n");
5564: fprintf(ficparo,"\n");
5565: }
5566: }
5567: printf("# Covariance matrix\n");
5568: /* # 121 Var(a12)\n\ */
5569: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5570: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5571: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5572: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5573: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5574: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5575: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5576: fflush(stdout);
5577: fprintf(ficparo,"# Covariance matrix\n");
5578: /* # 121 Var(a12)\n\ */
5579: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5580: /* # ...\n\ */
5581: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5582:
5583: for(itimes=1;itimes<=2;itimes++){
5584: jj=0;
5585: for(i=1; i <=nlstate; i++){
5586: for(j=1; j <=nlstate+ndeath; j++){
5587: if(j==i) continue;
5588: for(k=1; k<=ncovmodel;k++){
5589: jj++;
5590: ca[0]= k+'a'-1;ca[1]='\0';
5591: if(itimes==1){
5592: printf("#%1d%1d%d",i,j,k);
5593: fprintf(ficparo,"#%1d%1d%d",i,j,k);
5594: }else{
5595: printf("%1d%1d%d",i,j,k);
5596: fprintf(ficparo,"%1d%1d%d",i,j,k);
5597: /* printf(" %.5le",matcov[i][j]); */
5598: }
5599: ll=0;
5600: for(li=1;li <=nlstate; li++){
5601: for(lj=1;lj <=nlstate+ndeath; lj++){
5602: if(lj==li) continue;
5603: for(lk=1;lk<=ncovmodel;lk++){
5604: ll++;
5605: if(ll<=jj){
5606: cb[0]= lk +'a'-1;cb[1]='\0';
5607: if(ll<jj){
5608: if(itimes==1){
5609: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5610: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5611: }else{
5612: printf(" 0.");
5613: fprintf(ficparo," 0.");
5614: }
5615: }else{
5616: if(itimes==1){
5617: printf(" Var(%s%1d%1d)",ca,i,j);
5618: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
5619: }else{
5620: printf(" 0.");
5621: fprintf(ficparo," 0.");
5622: }
5623: }
5624: }
5625: } /* end lk */
5626: } /* end lj */
5627: } /* end li */
5628: printf("\n");
5629: fprintf(ficparo,"\n");
5630: numlinepar++;
5631: } /* end k*/
5632: } /*end j */
5633: } /* end i */
5634: } /* end itimes */
5635:
5636: } /* end of prwizard */
5637: /******************* Gompertz Likelihood ******************************/
5638: double gompertz(double x[])
5639: {
5640: double A,B,L=0.0,sump=0.,num=0.;
5641: int i,n=0; /* n is the size of the sample */
5642:
5643: for (i=0;i<=imx-1 ; i++) {
5644: sump=sump+weight[i];
5645: /* sump=sump+1;*/
5646: num=num+1;
5647: }
5648:
5649:
5650: /* for (i=0; i<=imx; i++)
5651: 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]);*/
5652:
5653: for (i=1;i<=imx ; i++)
5654: {
5655: if (cens[i] == 1 && wav[i]>1)
5656: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
5657:
5658: if (cens[i] == 0 && wav[i]>1)
5659: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
5660: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
5661:
5662: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5663: if (wav[i] > 1 ) { /* ??? */
5664: L=L+A*weight[i];
5665: /* 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]);*/
5666: }
5667: }
5668:
5669: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5670:
5671: return -2*L*num/sump;
5672: }
5673:
1.136 brouard 5674: #ifdef GSL
5675: /******************* Gompertz_f Likelihood ******************************/
5676: double gompertz_f(const gsl_vector *v, void *params)
5677: {
5678: double A,B,LL=0.0,sump=0.,num=0.;
5679: double *x= (double *) v->data;
5680: int i,n=0; /* n is the size of the sample */
5681:
5682: for (i=0;i<=imx-1 ; i++) {
5683: sump=sump+weight[i];
5684: /* sump=sump+1;*/
5685: num=num+1;
5686: }
5687:
5688:
5689: /* for (i=0; i<=imx; i++)
5690: 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]);*/
5691: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
5692: for (i=1;i<=imx ; i++)
5693: {
5694: if (cens[i] == 1 && wav[i]>1)
5695: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
5696:
5697: if (cens[i] == 0 && wav[i]>1)
5698: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
5699: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
5700:
5701: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5702: if (wav[i] > 1 ) { /* ??? */
5703: LL=LL+A*weight[i];
5704: /* 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]);*/
5705: }
5706: }
5707:
5708: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5709: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
5710:
5711: return -2*LL*num/sump;
5712: }
5713: #endif
5714:
1.126 brouard 5715: /******************* Printing html file ***********/
1.201 brouard 5716: void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 5717: int lastpass, int stepm, int weightopt, char model[],\
5718: int imx, double p[],double **matcov,double agemortsup){
5719: int i,k;
5720:
5721: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
5722: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
5723: for (i=1;i<=2;i++)
5724: 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]));
1.199 brouard 5725: fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
1.126 brouard 5726: fprintf(fichtm,"</ul>");
5727:
5728: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
5729:
5730: 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>");
5731:
5732: for (k=agegomp;k<(agemortsup-2);k++)
5733: 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]);
5734:
5735:
5736: fflush(fichtm);
5737: }
5738:
5739: /******************* Gnuplot file **************/
1.201 brouard 5740: void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 5741:
5742: char dirfileres[132],optfileres[132];
1.164 brouard 5743:
1.126 brouard 5744: int ng;
5745:
5746:
5747: /*#ifdef windows */
5748: fprintf(ficgp,"cd \"%s\" \n",pathc);
5749: /*#endif */
5750:
5751:
5752: strcpy(dirfileres,optionfilefiname);
5753: strcpy(optfileres,"vpl");
1.199 brouard 5754: fprintf(ficgp,"set out \"graphmort.svg\"\n ");
1.126 brouard 5755: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.199 brouard 5756: fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
1.145 brouard 5757: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 5758: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
5759:
5760: }
5761:
1.136 brouard 5762: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
5763: {
1.126 brouard 5764:
1.136 brouard 5765: /*-------- data file ----------*/
5766: FILE *fic;
5767: char dummy[]=" ";
1.164 brouard 5768: int i=0, j=0, n=0;
1.136 brouard 5769: int linei, month, year,iout;
5770: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 5771: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 5772: char *stratrunc;
5773: int lstra;
1.126 brouard 5774:
5775:
1.136 brouard 5776: if((fic=fopen(datafile,"r"))==NULL) {
1.195 brouard 5777: printf("Problem while opening datafile: %s\n", datafile);fflush(stdout);
5778: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);fflush(ficlog);return 1;
1.136 brouard 5779: }
1.126 brouard 5780:
1.136 brouard 5781: i=1;
5782: linei=0;
5783: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
5784: linei=linei+1;
5785: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
5786: if(line[j] == '\t')
5787: line[j] = ' ';
5788: }
5789: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
5790: ;
5791: };
5792: line[j+1]=0; /* Trims blanks at end of line */
5793: if(line[0]=='#'){
5794: fprintf(ficlog,"Comment line\n%s\n",line);
5795: printf("Comment line\n%s\n",line);
5796: continue;
5797: }
5798: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 5799: strcpy(line, linetmp);
1.136 brouard 5800:
1.126 brouard 5801:
1.136 brouard 5802: for (j=maxwav;j>=1;j--){
1.137 brouard 5803: cutv(stra, strb, line, ' ');
1.136 brouard 5804: if(strb[0]=='.') { /* Missing status */
5805: lval=-1;
5806: }else{
5807: errno=0;
5808: lval=strtol(strb,&endptr,10);
5809: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
5810: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5811: 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);
5812: 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 5813: return 1;
5814: }
5815: }
5816: s[j][i]=lval;
5817:
5818: strcpy(line,stra);
5819: cutv(stra, strb,line,' ');
1.169 brouard 5820: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5821: }
1.169 brouard 5822: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5823: month=99;
5824: year=9999;
5825: }else{
1.141 brouard 5826: 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);
5827: 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 5828: return 1;
5829: }
5830: anint[j][i]= (double) year;
5831: mint[j][i]= (double)month;
5832: strcpy(line,stra);
5833: } /* ENd Waves */
5834:
5835: cutv(stra, strb,line,' ');
1.169 brouard 5836: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5837: }
1.169 brouard 5838: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5839: month=99;
5840: year=9999;
5841: }else{
1.141 brouard 5842: 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);
5843: 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 5844: return 1;
5845: }
5846: andc[i]=(double) year;
5847: moisdc[i]=(double) month;
5848: strcpy(line,stra);
5849:
5850: cutv(stra, strb,line,' ');
1.169 brouard 5851: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5852: }
1.169 brouard 5853: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 5854: month=99;
5855: year=9999;
5856: }else{
1.141 brouard 5857: 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);
5858: 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 5859: return 1;
5860: }
5861: if (year==9999) {
1.141 brouard 5862: 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);
5863: 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 5864: return 1;
1.126 brouard 5865:
1.136 brouard 5866: }
5867: annais[i]=(double)(year);
5868: moisnais[i]=(double)(month);
5869: strcpy(line,stra);
5870:
5871: cutv(stra, strb,line,' ');
5872: errno=0;
5873: dval=strtod(strb,&endptr);
5874: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5875: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
5876: 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 5877: fflush(ficlog);
5878: return 1;
5879: }
5880: weight[i]=dval;
5881: strcpy(line,stra);
5882:
5883: for (j=ncovcol;j>=1;j--){
5884: cutv(stra, strb,line,' ');
5885: if(strb[0]=='.') { /* Missing status */
5886: lval=-1;
5887: }else{
5888: errno=0;
5889: lval=strtol(strb,&endptr,10);
5890: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5891: 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);
5892: 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 5893: return 1;
5894: }
5895: }
5896: if(lval <-1 || lval >1){
1.141 brouard 5897: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5898: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5899: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5900: For example, for multinomial values like 1, 2 and 3,\n \
5901: build V1=0 V2=0 for the reference value (1),\n \
5902: V1=1 V2=0 for (2) \n \
5903: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5904: output of IMaCh is often meaningless.\n \
5905: Exiting.\n",lval,linei, i,line,j);
1.141 brouard 5906: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5907: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5908: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5909: For example, for multinomial values like 1, 2 and 3,\n \
5910: build V1=0 V2=0 for the reference value (1),\n \
5911: V1=1 V2=0 for (2) \n \
5912: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5913: output of IMaCh is often meaningless.\n \
5914: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
5915: return 1;
5916: }
5917: covar[j][i]=(double)(lval);
5918: strcpy(line,stra);
5919: }
5920: lstra=strlen(stra);
5921:
5922: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
5923: stratrunc = &(stra[lstra-9]);
5924: num[i]=atol(stratrunc);
5925: }
5926: else
5927: num[i]=atol(stra);
5928: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
5929: 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;}*/
5930:
5931: i=i+1;
5932: } /* End loop reading data */
1.126 brouard 5933:
1.136 brouard 5934: *imax=i-1; /* Number of individuals */
5935: fclose(fic);
5936:
5937: return (0);
1.164 brouard 5938: /* endread: */
1.136 brouard 5939: printf("Exiting readdata: ");
5940: fclose(fic);
5941: return (1);
1.126 brouard 5942:
5943:
5944:
1.136 brouard 5945: }
1.145 brouard 5946: void removespace(char *str) {
5947: char *p1 = str, *p2 = str;
5948: do
5949: while (*p2 == ' ')
5950: p2++;
1.169 brouard 5951: while (*p1++ == *p2++);
1.145 brouard 5952: }
5953:
5954: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
1.187 brouard 5955: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
5956: * - nagesqr = 1 if age*age in the model, otherwise 0.
5957: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
5958: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
1.145 brouard 5959: * - cptcovage number of covariates with age*products =2
5960: * - cptcovs number of simple covariates
5961: * - 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
5962: * which is a new column after the 9 (ncovcol) variables.
5963: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
5964: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
5965: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
5966: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
5967: */
1.136 brouard 5968: {
1.145 brouard 5969: int i, j, k, ks;
1.164 brouard 5970: int j1, k1, k2;
1.136 brouard 5971: char modelsav[80];
1.145 brouard 5972: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 5973: char *strpt;
1.136 brouard 5974:
1.145 brouard 5975: /*removespace(model);*/
1.136 brouard 5976: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 5977: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 5978: if (strstr(model,"AGE") !=0){
1.192 brouard 5979: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
5980: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 5981: return 1;
5982: }
1.141 brouard 5983: if (strstr(model,"v") !=0){
5984: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
5985: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
5986: return 1;
5987: }
1.187 brouard 5988: strcpy(modelsav,model);
5989: if ((strpt=strstr(model,"age*age")) !=0){
5990: printf(" strpt=%s, model=%s\n",strpt, model);
5991: if(strpt != model){
5992: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 5993: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 5994: corresponding column of parameters.\n",model);
5995: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 5996: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 5997: corresponding column of parameters.\n",model); fflush(ficlog);
5998: return 1;
5999: }
6000:
6001: nagesqr=1;
6002: if (strstr(model,"+age*age") !=0)
6003: substrchaine(modelsav, model, "+age*age");
6004: else if (strstr(model,"age*age+") !=0)
6005: substrchaine(modelsav, model, "age*age+");
6006: else
6007: substrchaine(modelsav, model, "age*age");
6008: }else
6009: nagesqr=0;
6010: if (strlen(modelsav) >1){
6011: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
6012: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
6013: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2 */
6014: cptcovt= j+1; /* Number of total covariates in the model, not including
6015: * cst, age and age*age
6016: * V1+V1*age+ V3 + V3*V4+age*age=> 4*/
6017: /* including age products which are counted in cptcovage.
6018: * but the covariates which are products must be treated
6019: * separately: ncovn=4- 2=2 (V1+V3). */
6020: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
6021: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
6022:
6023:
6024: /* Design
6025: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
6026: * < ncovcol=8 >
6027: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
6028: * k= 1 2 3 4 5 6 7 8
6029: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
6030: * covar[k,i], value of kth covariate if not including age for individual i:
6031: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
6032: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
6033: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
6034: * Tage[++cptcovage]=k
6035: * if products, new covar are created after ncovcol with k1
6036: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
6037: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
6038: * 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
6039: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
6040: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
6041: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
6042: * < ncovcol=8 >
6043: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
6044: * k= 1 2 3 4 5 6 7 8 9 10 11 12
6045: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
6046: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
6047: * p Tprod[1]@2={ 6, 5}
6048: *p Tvard[1][1]@4= {7, 8, 5, 6}
6049: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
6050: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
6051: *How to reorganize?
6052: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
6053: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
6054: * {2, 1, 4, 8, 5, 6, 3, 7}
6055: * Struct []
6056: */
1.145 brouard 6057:
1.187 brouard 6058: /* This loop fills the array Tvar from the string 'model'.*/
6059: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
6060: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
6061: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
6062: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
6063: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
6064: /* k=1 Tvar[1]=2 (from V2) */
6065: /* k=5 Tvar[5] */
6066: /* for (k=1; k<=cptcovn;k++) { */
1.198 brouard 6067: /* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.187 brouard 6068: /* } */
1.198 brouard 6069: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
1.187 brouard 6070: /*
6071: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
6072: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
1.145 brouard 6073: Tvar[k]=0;
1.187 brouard 6074: cptcovage=0;
6075: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
6076: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
6077: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
6078: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
6079: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
6080: /*scanf("%d",i);*/
6081: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
6082: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
6083: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
6084: /* covar is not filled and then is empty */
6085: cptcovprod--;
6086: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
6087: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
6088: cptcovage++; /* Sums the number of covariates which include age as a product */
6089: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
6090: /*printf("stre=%s ", stre);*/
6091: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
6092: cptcovprod--;
6093: cutl(stre,strb,strc,'V');
6094: Tvar[k]=atoi(stre);
6095: cptcovage++;
6096: Tage[cptcovage]=k;
6097: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
6098: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
6099: cptcovn++;
6100: cptcovprodnoage++;k1++;
6101: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
6102: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
6103: because this model-covariate is a construction we invent a new column
6104: ncovcol + k1
6105: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
6106: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
6107: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
6108: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
6109: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
6110: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
6111: k2=k2+2;
6112: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
6113: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
6114: for (i=1; i<=lastobs;i++){
6115: /* Computes the new covariate which is a product of
6116: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
6117: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
6118: }
6119: } /* End age is not in the model */
6120: } /* End if model includes a product */
6121: else { /* no more sum */
6122: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
6123: /* scanf("%d",i);*/
6124: cutl(strd,strc,strb,'V');
6125: ks++; /**< Number of simple covariates */
1.145 brouard 6126: cptcovn++;
1.187 brouard 6127: Tvar[k]=atoi(strd);
6128: }
6129: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
6130: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
6131: scanf("%d",i);*/
6132: } /* end of loop + on total covariates */
6133: } /* end if strlen(modelsave == 0) age*age might exist */
6134: } /* end if strlen(model == 0) */
1.136 brouard 6135:
6136: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
6137: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
6138:
6139: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
6140: printf("cptcovprod=%d ", cptcovprod);
6141: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
6142:
6143: scanf("%d ",i);*/
6144:
6145:
1.137 brouard 6146: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 6147: /*endread:*/
1.136 brouard 6148: printf("Exiting decodemodel: ");
6149: return (1);
6150: }
6151:
1.169 brouard 6152: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.136 brouard 6153: {
6154: int i, m;
6155:
6156: for (i=1; i<=imx; i++) {
6157: for(m=2; (m<= maxwav); m++) {
6158: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
6159: anint[m][i]=9999;
6160: s[m][i]=-1;
6161: }
6162: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169 brouard 6163: *nberr = *nberr + 1;
6164: 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);
6165: 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 6166: s[m][i]=-1;
6167: }
6168: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 6169: (*nberr)++;
1.136 brouard 6170: 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]);
6171: 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]);
6172: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
6173: }
6174: }
6175: }
6176:
6177: for (i=1; i<=imx; i++) {
6178: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
6179: for(m=firstpass; (m<= lastpass); m++){
6180: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
6181: if (s[m][i] >= nlstate+1) {
1.169 brouard 6182: if(agedc[i]>0){
6183: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 6184: agev[m][i]=agedc[i];
6185: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 6186: }else {
1.136 brouard 6187: if ((int)andc[i]!=9999){
6188: nbwarn++;
6189: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
6190: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
6191: agev[m][i]=-1;
6192: }
6193: }
1.169 brouard 6194: } /* agedc > 0 */
1.136 brouard 6195: }
6196: else if(s[m][i] !=9){ /* Standard case, age in fractional
6197: years but with the precision of a month */
6198: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
6199: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
6200: agev[m][i]=1;
6201: else if(agev[m][i] < *agemin){
6202: *agemin=agev[m][i];
6203: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
6204: }
6205: else if(agev[m][i] >*agemax){
6206: *agemax=agev[m][i];
1.156 brouard 6207: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 6208: }
6209: /*agev[m][i]=anint[m][i]-annais[i];*/
6210: /* agev[m][i] = age[i]+2*m;*/
6211: }
6212: else { /* =9 */
6213: agev[m][i]=1;
6214: s[m][i]=-1;
6215: }
6216: }
6217: else /*= 0 Unknown */
6218: agev[m][i]=1;
6219: }
6220:
6221: }
6222: for (i=1; i<=imx; i++) {
6223: for(m=firstpass; (m<=lastpass); m++){
6224: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 6225: (*nberr)++;
1.136 brouard 6226: 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);
6227: 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);
6228: return 1;
6229: }
6230: }
6231: }
6232:
6233: /*for (i=1; i<=imx; i++){
6234: for (m=firstpass; (m<lastpass); m++){
6235: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
6236: }
6237:
6238: }*/
6239:
6240:
1.139 brouard 6241: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
6242: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 6243:
6244: return (0);
1.164 brouard 6245: /* endread:*/
1.136 brouard 6246: printf("Exiting calandcheckages: ");
6247: return (1);
6248: }
6249:
1.172 brouard 6250: #if defined(_MSC_VER)
6251: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
6252: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
6253: //#include "stdafx.h"
6254: //#include <stdio.h>
6255: //#include <tchar.h>
6256: //#include <windows.h>
6257: //#include <iostream>
6258: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
6259:
6260: LPFN_ISWOW64PROCESS fnIsWow64Process;
6261:
6262: BOOL IsWow64()
6263: {
6264: BOOL bIsWow64 = FALSE;
6265:
6266: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
6267: // (HANDLE, PBOOL);
6268:
6269: //LPFN_ISWOW64PROCESS fnIsWow64Process;
6270:
6271: HMODULE module = GetModuleHandle(_T("kernel32"));
6272: const char funcName[] = "IsWow64Process";
6273: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
6274: GetProcAddress(module, funcName);
6275:
6276: if (NULL != fnIsWow64Process)
6277: {
6278: if (!fnIsWow64Process(GetCurrentProcess(),
6279: &bIsWow64))
6280: //throw std::exception("Unknown error");
6281: printf("Unknown error\n");
6282: }
6283: return bIsWow64 != FALSE;
6284: }
6285: #endif
1.177 brouard 6286:
1.191 brouard 6287: void syscompilerinfo(int logged)
1.167 brouard 6288: {
6289: /* #include "syscompilerinfo.h"*/
1.185 brouard 6290: /* command line Intel compiler 32bit windows, XP compatible:*/
6291: /* /GS /W3 /Gy
6292: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
6293: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
6294: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 6295: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
6296: */
6297: /* 64 bits */
1.185 brouard 6298: /*
6299: /GS /W3 /Gy
6300: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
6301: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
6302: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
6303: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
6304: /* Optimization are useless and O3 is slower than O2 */
6305: /*
6306: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
6307: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
6308: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
6309: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
6310: */
1.186 brouard 6311: /* Link is */ /* /OUT:"visual studio
1.185 brouard 6312: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
6313: /PDB:"visual studio
6314: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
6315: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
6316: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
6317: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
6318: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
6319: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
6320: uiAccess='false'"
6321: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
6322: /NOLOGO /TLBID:1
6323: */
1.177 brouard 6324: #if defined __INTEL_COMPILER
1.178 brouard 6325: #if defined(__GNUC__)
6326: struct utsname sysInfo; /* For Intel on Linux and OS/X */
6327: #endif
1.177 brouard 6328: #elif defined(__GNUC__)
1.179 brouard 6329: #ifndef __APPLE__
1.174 brouard 6330: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 6331: #endif
1.177 brouard 6332: struct utsname sysInfo;
1.178 brouard 6333: int cross = CROSS;
6334: if (cross){
6335: printf("Cross-");
1.191 brouard 6336: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 6337: }
1.174 brouard 6338: #endif
6339:
1.171 brouard 6340: #include <stdint.h>
1.178 brouard 6341:
1.191 brouard 6342: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 6343: #if defined(__clang__)
1.191 brouard 6344: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 6345: #endif
6346: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 6347: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 6348: #endif
6349: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 6350: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 6351: #endif
6352: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 6353: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 6354: #endif
6355: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 6356: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 6357: #endif
6358: #if defined(_MSC_VER)
1.191 brouard 6359: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 6360: #endif
6361: #if defined(__PGI)
1.191 brouard 6362: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 6363: #endif
6364: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 6365: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 6366: #endif
1.191 brouard 6367: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 6368:
1.167 brouard 6369: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
6370: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
6371: // Windows (x64 and x86)
1.191 brouard 6372: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 6373: #elif __unix__ // all unices, not all compilers
6374: // Unix
1.191 brouard 6375: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 6376: #elif __linux__
6377: // linux
1.191 brouard 6378: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 6379: #elif __APPLE__
1.174 brouard 6380: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 6381: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 6382: #endif
6383:
6384: /* __MINGW32__ */
6385: /* __CYGWIN__ */
6386: /* __MINGW64__ */
6387: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
6388: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
6389: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
6390: /* _WIN64 // Defined for applications for Win64. */
6391: /* _M_X64 // Defined for compilations that target x64 processors. */
6392: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 6393:
1.167 brouard 6394: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 6395: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 6396: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 6397: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 6398: #else
1.191 brouard 6399: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 6400: #endif
6401:
1.169 brouard 6402: #if defined(__GNUC__)
6403: # if defined(__GNUC_PATCHLEVEL__)
6404: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
6405: + __GNUC_MINOR__ * 100 \
6406: + __GNUC_PATCHLEVEL__)
6407: # else
6408: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
6409: + __GNUC_MINOR__ * 100)
6410: # endif
1.174 brouard 6411: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 6412: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 6413:
6414: if (uname(&sysInfo) != -1) {
6415: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 6416: if(logged) fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.176 brouard 6417: }
6418: else
6419: perror("uname() error");
1.179 brouard 6420: //#ifndef __INTEL_COMPILER
6421: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 6422: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 6423: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 6424: #endif
1.169 brouard 6425: #endif
1.172 brouard 6426:
6427: // void main()
6428: // {
1.169 brouard 6429: #if defined(_MSC_VER)
1.174 brouard 6430: if (IsWow64()){
1.191 brouard 6431: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
6432: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 6433: }
6434: else{
1.191 brouard 6435: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
6436: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 6437: }
1.172 brouard 6438: // printf("\nPress Enter to continue...");
6439: // getchar();
6440: // }
6441:
1.169 brouard 6442: #endif
6443:
1.167 brouard 6444:
6445: }
1.136 brouard 6446:
1.203 ! brouard 6447: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyear){
1.180 brouard 6448: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6449: int i, j, k, i1 ;
1.202 brouard 6450: /* double ftolpl = 1.e-10; */
1.180 brouard 6451: double age, agebase, agelim;
1.203 ! brouard 6452: double tot;
1.180 brouard 6453:
1.202 brouard 6454: strcpy(filerespl,"PL_");
6455: strcat(filerespl,fileresu);
6456: if((ficrespl=fopen(filerespl,"w"))==NULL) {
6457: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6458: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6459: }
6460: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6461: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6462: pstamp(ficrespl);
1.203 ! brouard 6463: fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.202 brouard 6464: fprintf(ficrespl,"#Age ");
6465: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
6466: fprintf(ficrespl,"\n");
1.180 brouard 6467:
6468: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
6469:
6470: agebase=ageminpar;
6471: agelim=agemaxpar;
6472:
6473: i1=pow(2,cptcoveff);
6474: if (cptcovn < 1){i1=1;}
6475:
6476: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6477: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
6478: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6479: k=k+1;
6480: /* to clean */
1.198 brouard 6481: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
1.200 brouard 6482: fprintf(ficrespl,"#******");
6483: printf("#******");
6484: fprintf(ficlog,"#******");
1.180 brouard 6485: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 6486: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
6487: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
6488: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.180 brouard 6489: }
6490: fprintf(ficrespl,"******\n");
6491: printf("******\n");
6492: fprintf(ficlog,"******\n");
6493:
6494: fprintf(ficrespl,"#Age ");
6495: for(j=1;j<=cptcoveff;j++) {
1.200 brouard 6496: fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.180 brouard 6497: }
1.203 ! brouard 6498: for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);
! 6499: fprintf(ficrespl,"Total Years_to_converge\n");
1.180 brouard 6500:
6501: for (age=agebase; age<=agelim; age++){
6502: /* for (age=agebase; age<=agebase; age++){ */
1.203 ! brouard 6503: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyear, k);
1.180 brouard 6504: fprintf(ficrespl,"%.0f ",age );
6505: for(j=1;j<=cptcoveff;j++)
1.198 brouard 6506: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.203 ! brouard 6507: tot=0.;
! 6508: for(i=1; i<=nlstate;i++){
! 6509: tot += prlim[i][i];
1.180 brouard 6510: fprintf(ficrespl," %.5f", prlim[i][i]);
1.203 ! brouard 6511: }
! 6512: fprintf(ficrespl," %.3f %d\n", tot, *ncvyear);
1.180 brouard 6513: } /* Age */
6514: /* was end of cptcod */
6515: } /* cptcov */
1.184 brouard 6516: return 0;
1.180 brouard 6517: }
6518:
6519: int hPijx(double *p, int bage, int fage){
6520: /*------------- h Pij x at various ages ------------*/
6521:
6522: int stepsize;
6523: int agelim;
6524: int hstepm;
6525: int nhstepm;
6526: int h, i, i1, j, k;
6527:
6528: double agedeb;
6529: double ***p3mat;
6530:
1.201 brouard 6531: strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu);
1.180 brouard 6532: if((ficrespij=fopen(filerespij,"w"))==NULL) {
6533: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
6534: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
6535: }
6536: printf("Computing pij: result on file '%s' \n", filerespij);
6537: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
6538:
6539: stepsize=(int) (stepm+YEARM-1)/YEARM;
6540: /*if (stepm<=24) stepsize=2;*/
6541:
6542: agelim=AGESUP;
6543: hstepm=stepsize*YEARM; /* Every year of age */
6544: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
6545:
6546: /* hstepm=1; aff par mois*/
6547: pstamp(ficrespij);
6548: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
6549: i1= pow(2,cptcoveff);
1.183 brouard 6550: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
6551: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
6552: /* k=k+1; */
6553: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6554: fprintf(ficrespij,"\n#****** ");
6555: for(j=1;j<=cptcoveff;j++)
1.198 brouard 6556: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.183 brouard 6557: fprintf(ficrespij,"******\n");
6558:
6559: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
6560: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6561: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6562:
6563: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 6564:
1.183 brouard 6565: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6566: oldm=oldms;savm=savms;
6567: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
6568: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
6569: for(i=1; i<=nlstate;i++)
6570: for(j=1; j<=nlstate+ndeath;j++)
6571: fprintf(ficrespij," %1d-%1d",i,j);
6572: fprintf(ficrespij,"\n");
6573: for (h=0; h<=nhstepm; h++){
6574: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
6575: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 6576: for(i=1; i<=nlstate;i++)
6577: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 6578: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 6579: fprintf(ficrespij,"\n");
6580: }
1.183 brouard 6581: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6582: fprintf(ficrespij,"\n");
6583: }
1.180 brouard 6584: /*}*/
6585: }
1.184 brouard 6586: return 0;
1.180 brouard 6587: }
6588:
6589:
1.136 brouard 6590: /***********************************************/
6591: /**************** Main Program *****************/
6592: /***********************************************/
6593:
6594: int main(int argc, char *argv[])
6595: {
6596: #ifdef GSL
6597: const gsl_multimin_fminimizer_type *T;
6598: size_t iteri = 0, it;
6599: int rval = GSL_CONTINUE;
6600: int status = GSL_SUCCESS;
6601: double ssval;
6602: #endif
6603: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 6604: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
1.203 ! brouard 6605: int ncvyearnp=0;
! 6606: int *ncvyear=&ncvyearnp; /* Number of years needed for the period prevalence to converge */
1.164 brouard 6607: int jj, ll, li, lj, lk;
1.136 brouard 6608: int numlinepar=0; /* Current linenumber of parameter file */
1.197 brouard 6609: int num_filled;
1.136 brouard 6610: int itimes;
6611: int NDIM=2;
6612: int vpopbased=0;
6613:
1.164 brouard 6614: char ca[32], cb[32];
1.136 brouard 6615: /* FILE *fichtm; *//* Html File */
6616: /* FILE *ficgp;*/ /*Gnuplot File */
6617: struct stat info;
1.191 brouard 6618: double agedeb=0.;
1.194 brouard 6619:
6620: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.136 brouard 6621:
1.165 brouard 6622: double fret;
1.191 brouard 6623: double dum=0.; /* Dummy variable */
1.136 brouard 6624: double ***p3mat;
6625: double ***mobaverage;
1.164 brouard 6626:
6627: char line[MAXLINE];
1.197 brouard 6628: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
6629:
6630: char model[MAXLINE], modeltemp[MAXLINE];
1.136 brouard 6631: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 6632: char *tok, *val; /* pathtot */
1.136 brouard 6633: int firstobs=1, lastobs=10;
1.195 brouard 6634: int c, h , cpt, c2;
1.191 brouard 6635: int jl=0;
6636: int i1, j1, jk, stepsize=0;
1.194 brouard 6637: int count=0;
6638:
1.164 brouard 6639: int *tab;
1.136 brouard 6640: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
6641: int mobilav=0,popforecast=0;
1.191 brouard 6642: int hstepm=0, nhstepm=0;
1.136 brouard 6643: int agemortsup;
6644: float sumlpop=0.;
6645: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
6646: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
6647:
1.191 brouard 6648: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 6649: double ftolpl=FTOL;
6650: double **prlim;
6651: double ***param; /* Matrix of parameters */
6652: double *p;
6653: double **matcov; /* Matrix of covariance */
1.203 ! brouard 6654: double **hess; /* Hessian matrix */
1.136 brouard 6655: double ***delti3; /* Scale */
6656: double *delti; /* Scale */
6657: double ***eij, ***vareij;
6658: double **varpl; /* Variances of prevalence limits by age */
6659: double *epj, vepp;
1.164 brouard 6660:
1.136 brouard 6661: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
6662: double **ximort;
1.145 brouard 6663: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 6664: int *dcwave;
6665:
1.164 brouard 6666: char z[1]="c";
1.136 brouard 6667:
6668: /*char *strt;*/
6669: char strtend[80];
1.126 brouard 6670:
1.164 brouard 6671:
1.126 brouard 6672: /* setlocale (LC_ALL, ""); */
6673: /* bindtextdomain (PACKAGE, LOCALEDIR); */
6674: /* textdomain (PACKAGE); */
6675: /* setlocale (LC_CTYPE, ""); */
6676: /* setlocale (LC_MESSAGES, ""); */
6677:
6678: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 6679: rstart_time = time(NULL);
6680: /* (void) gettimeofday(&start_time,&tzp);*/
6681: start_time = *localtime(&rstart_time);
1.126 brouard 6682: curr_time=start_time;
1.157 brouard 6683: /*tml = *localtime(&start_time.tm_sec);*/
6684: /* strcpy(strstart,asctime(&tml)); */
6685: strcpy(strstart,asctime(&start_time));
1.126 brouard 6686:
6687: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 6688: /* tp.tm_sec = tp.tm_sec +86400; */
6689: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 6690: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
6691: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
6692: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 6693: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 6694: /* strt=asctime(&tmg); */
6695: /* printf("Time(after) =%s",strstart); */
6696: /* (void) time (&time_value);
6697: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
6698: * tm = *localtime(&time_value);
6699: * strstart=asctime(&tm);
6700: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
6701: */
6702:
6703: nberr=0; /* Number of errors and warnings */
6704: nbwarn=0;
1.184 brouard 6705: #ifdef WIN32
6706: _getcwd(pathcd, size);
6707: #else
1.126 brouard 6708: getcwd(pathcd, size);
1.184 brouard 6709: #endif
1.191 brouard 6710: syscompilerinfo(0);
1.196 brouard 6711: printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126 brouard 6712: if(argc <=1){
6713: printf("\nEnter the parameter file name: ");
6714: fgets(pathr,FILENAMELENGTH,stdin);
6715: i=strlen(pathr);
6716: if(pathr[i-1]=='\n')
6717: pathr[i-1]='\0';
1.156 brouard 6718: i=strlen(pathr);
6719: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
6720: pathr[i-1]='\0';
1.126 brouard 6721: for (tok = pathr; tok != NULL; ){
6722: printf("Pathr |%s|\n",pathr);
6723: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
6724: printf("val= |%s| pathr=%s\n",val,pathr);
6725: strcpy (pathtot, val);
6726: if(pathr[0] == '\0') break; /* Dirty */
6727: }
6728: }
6729: else{
6730: strcpy(pathtot,argv[1]);
6731: }
6732: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
6733: /*cygwin_split_path(pathtot,path,optionfile);
6734: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
6735: /* cutv(path,optionfile,pathtot,'\\');*/
6736:
6737: /* Split argv[0], imach program to get pathimach */
6738: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
6739: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6740: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6741: /* strcpy(pathimach,argv[0]); */
6742: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
6743: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
6744: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 6745: #ifdef WIN32
6746: _chdir(path); /* Can be a relative path */
6747: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
6748: #else
1.126 brouard 6749: chdir(path); /* Can be a relative path */
1.184 brouard 6750: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
6751: #endif
6752: printf("Current directory %s!\n",pathcd);
1.126 brouard 6753: strcpy(command,"mkdir ");
6754: strcat(command,optionfilefiname);
6755: if((outcmd=system(command)) != 0){
1.169 brouard 6756: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 6757: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
6758: /* fclose(ficlog); */
6759: /* exit(1); */
6760: }
6761: /* if((imk=mkdir(optionfilefiname))<0){ */
6762: /* perror("mkdir"); */
6763: /* } */
6764:
6765: /*-------- arguments in the command line --------*/
6766:
1.186 brouard 6767: /* Main Log file */
1.126 brouard 6768: strcat(filelog, optionfilefiname);
6769: strcat(filelog,".log"); /* */
6770: if((ficlog=fopen(filelog,"w"))==NULL) {
6771: printf("Problem with logfile %s\n",filelog);
6772: goto end;
6773: }
6774: fprintf(ficlog,"Log filename:%s\n",filelog);
1.197 brouard 6775: fprintf(ficlog,"Version %s %s",version,fullversion);
1.126 brouard 6776: fprintf(ficlog,"\nEnter the parameter file name: \n");
6777: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
6778: path=%s \n\
6779: optionfile=%s\n\
6780: optionfilext=%s\n\
1.156 brouard 6781: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 6782:
1.197 brouard 6783: syscompilerinfo(1);
1.167 brouard 6784:
1.126 brouard 6785: printf("Local time (at start):%s",strstart);
6786: fprintf(ficlog,"Local time (at start): %s",strstart);
6787: fflush(ficlog);
6788: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 6789: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 6790:
6791: /* */
6792: strcpy(fileres,"r");
6793: strcat(fileres, optionfilefiname);
1.201 brouard 6794: strcat(fileresu, optionfilefiname); /* Without r in front */
1.126 brouard 6795: strcat(fileres,".txt"); /* Other files have txt extension */
1.201 brouard 6796: strcat(fileresu,".txt"); /* Other files have txt extension */
1.126 brouard 6797:
1.186 brouard 6798: /* Main ---------arguments file --------*/
1.126 brouard 6799:
6800: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 6801: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
6802: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 6803: fflush(ficlog);
1.149 brouard 6804: /* goto end; */
6805: exit(70);
1.126 brouard 6806: }
6807:
6808:
6809:
6810: strcpy(filereso,"o");
1.201 brouard 6811: strcat(filereso,fileresu);
1.126 brouard 6812: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
6813: printf("Problem with Output resultfile: %s\n", filereso);
6814: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
6815: fflush(ficlog);
6816: goto end;
6817: }
6818:
6819: /* Reads comments: lines beginning with '#' */
6820: numlinepar=0;
1.197 brouard 6821:
6822: /* First parameter line */
6823: while(fgets(line, MAXLINE, ficpar)) {
6824: /* If line starts with a # it is a comment */
6825: if (line[0] == '#') {
6826: numlinepar++;
6827: fputs(line,stdout);
6828: fputs(line,ficparo);
6829: fputs(line,ficlog);
6830: continue;
6831: }else
6832: break;
6833: }
6834: if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
6835: title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
6836: if (num_filled != 5) {
6837: printf("Should be 5 parameters\n");
6838: }
1.126 brouard 6839: numlinepar++;
1.197 brouard 6840: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
6841: }
6842: /* Second parameter line */
6843: while(fgets(line, MAXLINE, ficpar)) {
6844: /* If line starts with a # it is a comment */
6845: if (line[0] == '#') {
6846: numlinepar++;
6847: fputs(line,stdout);
6848: fputs(line,ficparo);
6849: fputs(line,ficlog);
6850: continue;
6851: }else
6852: break;
6853: }
6854: if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
6855: &ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
6856: if (num_filled != 8) {
6857: printf("Not 8\n");
6858: }
6859: printf("ftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt);
1.126 brouard 6860: }
1.203 ! brouard 6861: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
! 6862: ftolpl=6.e-3; /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
1.197 brouard 6863: /* Third parameter line */
6864: while(fgets(line, MAXLINE, ficpar)) {
6865: /* If line starts with a # it is a comment */
6866: if (line[0] == '#') {
6867: numlinepar++;
6868: fputs(line,stdout);
6869: fputs(line,ficparo);
6870: fputs(line,ficlog);
6871: continue;
6872: }else
6873: break;
6874: }
1.201 brouard 6875: if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
6876: if (num_filled == 0)
6877: model[0]='\0';
6878: else if (num_filled != 1){
1.197 brouard 6879: printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
6880: fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
6881: model[0]='\0';
6882: goto end;
6883: }
6884: else{
6885: if (model[0]=='+'){
6886: for(i=1; i<=strlen(model);i++)
6887: modeltemp[i-1]=model[i];
1.201 brouard 6888: strcpy(model,modeltemp);
1.197 brouard 6889: }
6890: }
1.199 brouard 6891: /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
1.203 ! brouard 6892: printf("model=1+age+%s\n",model);fflush(stdout);
1.197 brouard 6893: }
6894: /* 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); */
6895: /* numlinepar=numlinepar+3; /\* In general *\/ */
6896: /* 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); */
1.203 ! brouard 6897: 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);
! 6898: 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 6899: fflush(ficlog);
1.190 brouard 6900: /* if(model[0]=='#'|| model[0]== '\0'){ */
6901: if(model[0]=='#'){
1.187 brouard 6902: printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
6903: 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
6904: 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \
6905: if(mle != -1){
6906: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
6907: exit(1);
6908: }
6909: }
1.126 brouard 6910: while((c=getc(ficpar))=='#' && c!= EOF){
6911: ungetc(c,ficpar);
6912: fgets(line, MAXLINE, ficpar);
6913: numlinepar++;
1.195 brouard 6914: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
6915: z[0]=line[1];
6916: }
6917: /* printf("****line [1] = %c \n",line[1]); */
1.141 brouard 6918: fputs(line, stdout);
6919: //puts(line);
1.126 brouard 6920: fputs(line,ficparo);
6921: fputs(line,ficlog);
6922: }
6923: ungetc(c,ficpar);
6924:
6925:
1.145 brouard 6926: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.136 brouard 6927: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
6928: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
6929: v1+v2*age+v2*v3 makes cptcovn = 3
6930: */
6931: if (strlen(model)>1)
1.187 brouard 6932: 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 6933: else
1.187 brouard 6934: ncovmodel=2; /* Constant and age */
1.133 brouard 6935: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
6936: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 6937: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
6938: 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);
6939: 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);
6940: fflush(stdout);
6941: fclose (ficlog);
6942: goto end;
6943: }
1.126 brouard 6944: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6945: delti=delti3[1][1];
6946: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
6947: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
6948: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 6949: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
6950: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 6951: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6952: fclose (ficparo);
6953: fclose (ficlog);
6954: goto end;
6955: exit(0);
6956: }
1.186 brouard 6957: else if(mle==-3) { /* Main Wizard */
1.126 brouard 6958: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 6959: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
6960: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 6961: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6962: matcov=matrix(1,npar,1,npar);
1.203 ! brouard 6963: hess=matrix(1,npar,1,npar);
1.126 brouard 6964: }
6965: else{
1.145 brouard 6966: /* Read guessed parameters */
1.126 brouard 6967: /* Reads comments: lines beginning with '#' */
6968: while((c=getc(ficpar))=='#' && c!= EOF){
6969: ungetc(c,ficpar);
6970: fgets(line, MAXLINE, ficpar);
6971: numlinepar++;
1.141 brouard 6972: fputs(line,stdout);
1.126 brouard 6973: fputs(line,ficparo);
6974: fputs(line,ficlog);
6975: }
6976: ungetc(c,ficpar);
6977:
6978: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6979: for(i=1; i <=nlstate; i++){
6980: j=0;
6981: for(jj=1; jj <=nlstate+ndeath; jj++){
6982: if(jj==i) continue;
6983: j++;
6984: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.193 brouard 6985: if ((i1 != i) || (j1 != jj)){
1.126 brouard 6986: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
6987: It might be a problem of design; if ncovcol and the model are correct\n \
6988: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
6989: exit(1);
6990: }
6991: fprintf(ficparo,"%1d%1d",i1,j1);
6992: if(mle==1)
1.193 brouard 6993: printf("%1d%1d",i,jj);
6994: fprintf(ficlog,"%1d%1d",i,jj);
1.126 brouard 6995: for(k=1; k<=ncovmodel;k++){
6996: fscanf(ficpar," %lf",¶m[i][j][k]);
6997: if(mle==1){
6998: printf(" %lf",param[i][j][k]);
6999: fprintf(ficlog," %lf",param[i][j][k]);
7000: }
7001: else
7002: fprintf(ficlog," %lf",param[i][j][k]);
7003: fprintf(ficparo," %lf",param[i][j][k]);
7004: }
7005: fscanf(ficpar,"\n");
7006: numlinepar++;
7007: if(mle==1)
7008: printf("\n");
7009: fprintf(ficlog,"\n");
7010: fprintf(ficparo,"\n");
7011: }
7012: }
7013: fflush(ficlog);
7014:
1.145 brouard 7015: /* Reads scales values */
1.126 brouard 7016: p=param[1][1];
7017:
7018: /* Reads comments: lines beginning with '#' */
7019: while((c=getc(ficpar))=='#' && c!= EOF){
7020: ungetc(c,ficpar);
7021: fgets(line, MAXLINE, ficpar);
7022: numlinepar++;
1.141 brouard 7023: fputs(line,stdout);
1.126 brouard 7024: fputs(line,ficparo);
7025: fputs(line,ficlog);
7026: }
7027: ungetc(c,ficpar);
7028:
7029: for(i=1; i <=nlstate; i++){
7030: for(j=1; j <=nlstate+ndeath-1; j++){
7031: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.164 brouard 7032: if ( (i1-i) * (j1-j) != 0){
1.126 brouard 7033: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
7034: exit(1);
7035: }
7036: printf("%1d%1d",i,j);
7037: fprintf(ficparo,"%1d%1d",i1,j1);
7038: fprintf(ficlog,"%1d%1d",i1,j1);
7039: for(k=1; k<=ncovmodel;k++){
7040: fscanf(ficpar,"%le",&delti3[i][j][k]);
7041: printf(" %le",delti3[i][j][k]);
7042: fprintf(ficparo," %le",delti3[i][j][k]);
7043: fprintf(ficlog," %le",delti3[i][j][k]);
7044: }
7045: fscanf(ficpar,"\n");
7046: numlinepar++;
7047: printf("\n");
7048: fprintf(ficparo,"\n");
7049: fprintf(ficlog,"\n");
7050: }
7051: }
7052: fflush(ficlog);
7053:
1.145 brouard 7054: /* Reads covariance matrix */
1.126 brouard 7055: delti=delti3[1][1];
7056:
7057:
7058: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
7059:
7060: /* Reads comments: lines beginning with '#' */
7061: while((c=getc(ficpar))=='#' && c!= EOF){
7062: ungetc(c,ficpar);
7063: fgets(line, MAXLINE, ficpar);
7064: numlinepar++;
1.141 brouard 7065: fputs(line,stdout);
1.126 brouard 7066: fputs(line,ficparo);
7067: fputs(line,ficlog);
7068: }
7069: ungetc(c,ficpar);
7070:
7071: matcov=matrix(1,npar,1,npar);
1.203 ! brouard 7072: hess=matrix(1,npar,1,npar);
1.131 brouard 7073: for(i=1; i <=npar; i++)
7074: for(j=1; j <=npar; j++) matcov[i][j]=0.;
7075:
1.194 brouard 7076: /* Scans npar lines */
1.126 brouard 7077: for(i=1; i <=npar; i++){
1.194 brouard 7078: count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk);
7079: if(count != 3){
7080: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
7081: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
7082: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
7083: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
7084: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
7085: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
7086: exit(1);
7087: }else
1.126 brouard 7088: if(mle==1)
1.194 brouard 7089: printf("%1d%1d%1d",i1,j1,jk);
7090: fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);
7091: fprintf(ficparo,"%1d%1d%1d",i1,j1,jk);
1.126 brouard 7092: for(j=1; j <=i; j++){
7093: fscanf(ficpar," %le",&matcov[i][j]);
7094: if(mle==1){
7095: printf(" %.5le",matcov[i][j]);
7096: }
7097: fprintf(ficlog," %.5le",matcov[i][j]);
7098: fprintf(ficparo," %.5le",matcov[i][j]);
7099: }
7100: fscanf(ficpar,"\n");
7101: numlinepar++;
7102: if(mle==1)
7103: printf("\n");
7104: fprintf(ficlog,"\n");
7105: fprintf(ficparo,"\n");
7106: }
1.194 brouard 7107: /* End of read covariance matrix npar lines */
1.126 brouard 7108: for(i=1; i <=npar; i++)
7109: for(j=i+1;j<=npar;j++)
7110: matcov[i][j]=matcov[j][i];
7111:
7112: if(mle==1)
7113: printf("\n");
7114: fprintf(ficlog,"\n");
7115:
7116: fflush(ficlog);
7117:
7118: /*-------- Rewriting parameter file ----------*/
7119: strcpy(rfileres,"r"); /* "Rparameterfile */
7120: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
7121: strcat(rfileres,"."); /* */
7122: strcat(rfileres,optionfilext); /* Other files have txt extension */
7123: if((ficres =fopen(rfileres,"w"))==NULL) {
1.201 brouard 7124: printf("Problem writing new parameter file: %s\n", rfileres);goto end;
7125: fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
1.126 brouard 7126: }
7127: fprintf(ficres,"#%s\n",version);
7128: } /* End of mle != -3 */
7129:
1.186 brouard 7130: /* Main data
7131: */
1.126 brouard 7132: n= lastobs;
7133: num=lvector(1,n);
7134: moisnais=vector(1,n);
7135: annais=vector(1,n);
7136: moisdc=vector(1,n);
7137: andc=vector(1,n);
7138: agedc=vector(1,n);
7139: cod=ivector(1,n);
7140: weight=vector(1,n);
7141: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
7142: mint=matrix(1,maxwav,1,n);
7143: anint=matrix(1,maxwav,1,n);
1.131 brouard 7144: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 7145: tab=ivector(1,NCOVMAX);
1.144 brouard 7146: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 7147: ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.126 brouard 7148:
1.136 brouard 7149: /* Reads data from file datafile */
7150: if (readdata(datafile, firstobs, lastobs, &imx)==1)
7151: goto end;
7152:
7153: /* Calculation of the number of parameters from char model */
1.137 brouard 7154: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
7155: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
7156: k=3 V4 Tvar[k=3]= 4 (from V4)
7157: k=2 V1 Tvar[k=2]= 1 (from V1)
7158: k=1 Tvar[1]=2 (from V2)
7159: */
7160: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
7161: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
7162: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
7163: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
7164: */
7165: /* For model-covariate k tells which data-covariate to use but
7166: because this model-covariate is a construction we invent a new column
7167: ncovcol + k1
7168: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
7169: Tvar[3=V1*V4]=4+1 etc */
1.145 brouard 7170: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
1.137 brouard 7171: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
7172: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
7173: */
1.145 brouard 7174: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
7175: 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 7176: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
7177: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 7178: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 7179: 4 covariates (3 plus signs)
7180: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
7181: */
1.136 brouard 7182:
1.186 brouard 7183: /* Main decodemodel */
7184:
1.187 brouard 7185:
1.136 brouard 7186: if(decodemodel(model, lastobs) == 1)
7187: goto end;
7188:
1.137 brouard 7189: if((double)(lastobs-imx)/(double)imx > 1.10){
7190: nbwarn++;
7191: 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);
7192: 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);
7193: }
1.136 brouard 7194: /* if(mle==1){*/
1.137 brouard 7195: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
7196: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 7197: }
7198:
7199: /*-calculation of age at interview from date of interview and age at death -*/
7200: agev=matrix(1,maxwav,1,imx);
7201:
7202: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
7203: goto end;
7204:
1.126 brouard 7205:
1.136 brouard 7206: agegomp=(int)agemin;
7207: free_vector(moisnais,1,n);
7208: free_vector(annais,1,n);
1.126 brouard 7209: /* free_matrix(mint,1,maxwav,1,n);
7210: free_matrix(anint,1,maxwav,1,n);*/
7211: free_vector(moisdc,1,n);
7212: free_vector(andc,1,n);
1.145 brouard 7213: /* */
7214:
1.126 brouard 7215: wav=ivector(1,imx);
7216: dh=imatrix(1,lastpass-firstpass+1,1,imx);
7217: bh=imatrix(1,lastpass-firstpass+1,1,imx);
7218: mw=imatrix(1,lastpass-firstpass+1,1,imx);
7219:
7220: /* Concatenates waves */
7221: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 brouard 7222: /* */
7223:
1.126 brouard 7224: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
7225:
7226: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
7227: ncodemax[1]=1;
1.145 brouard 7228: Ndum =ivector(-1,NCOVMAX);
1.187 brouard 7229: if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */
1.145 brouard 7230: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.186 brouard 7231: /* Nbcode gives the value of the lth modality of jth covariate, in
7232: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
7233: /* 1 to ncodemax[j] is the maximum value of this jth covariate */
1.145 brouard 7234:
1.200 brouard 7235: /* codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
1.198 brouard 7236: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
1.186 brouard 7237: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.145 brouard 7238: h=0;
7239:
7240:
7241: /*if (cptcovn > 0) */
1.126 brouard 7242:
1.145 brouard 7243:
1.126 brouard 7244: m=pow(2,cptcoveff);
7245:
1.144 brouard 7246: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.186 brouard 7247: * For k=4 covariates, h goes from 1 to 2**k
7248: * codtabm(h,k)= 1 & (h-1) >> (k-1) ;
7249: * h\k 1 2 3 4
1.143 brouard 7250: *______________________________
7251: * 1 i=1 1 i=1 1 i=1 1 i=1 1
7252: * 2 2 1 1 1
7253: * 3 i=2 1 2 1 1
7254: * 4 2 2 1 1
7255: * 5 i=3 1 i=2 1 2 1
7256: * 6 2 1 2 1
7257: * 7 i=4 1 2 2 1
7258: * 8 2 2 2 1
1.197 brouard 7259: * 9 i=5 1 i=3 1 i=2 1 2
7260: * 10 2 1 1 2
7261: * 11 i=6 1 2 1 2
7262: * 12 2 2 1 2
7263: * 13 i=7 1 i=4 1 2 2
7264: * 14 2 1 2 2
7265: * 15 i=8 1 2 2 2
7266: * 16 2 2 2 2
1.143 brouard 7267: */
1.202 brouard 7268: /* /\* for(h=1; h <=100 ;h++){ *\/ */
7269: /* /\* printf("h=%2d ", h); *\/ */
7270: /* /\* for(k=1; k <=10; k++){ *\/ */
7271: /* /\* printf("k=%d %d ",k,codtabm(h,k)); *\/ */
7272: /* /\* codtab[h][k]=codtabm(h,k); *\/ */
7273: /* /\* } *\/ */
7274: /* /\* printf("\n"); *\/ */
7275: /* } */
1.197 brouard 7276: /* for(k=1;k<=cptcoveff; k++){ /\* scans any effective covariate *\/ */
7277: /* 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 *\/ */
7278: /* for(j=1; j <= ncodemax[k]; j++){ /\* For each modality of this covariate ncodemax=2*\/ */
7279: /* for(cpt=1; cpt <=pow(2,k-1); cpt++){ /\* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 *\/ */
7280: /* h++; */
7281: /* if (h>m) */
7282: /* h=1; */
7283: /* codtab[h][k]=j; */
7284: /* /\* codtab[12][3]=1; *\/ */
7285: /* /\*codtab[h][Tvar[k]]=j;*\/ */
7286: /* /\* 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]]); *\/ */
7287: /* } */
7288: /* } */
7289: /* } */
7290: /* } */
1.126 brouard 7291: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
7292: codtab[1][2]=1;codtab[2][2]=2; */
1.197 brouard 7293: /* for(i=1; i <=m ;i++){ */
7294: /* for(k=1; k <=cptcovn; k++){ */
7295: /* printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); */
7296: /* } */
7297: /* printf("\n"); */
7298: /* } */
7299: /* scanf("%d",i);*/
1.145 brouard 7300:
7301: free_ivector(Ndum,-1,NCOVMAX);
7302:
7303:
1.126 brouard 7304:
1.186 brouard 7305: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 7306: strcpy(optionfilegnuplot,optionfilefiname);
7307: if(mle==-3)
1.201 brouard 7308: strcat(optionfilegnuplot,"-MORT_");
1.126 brouard 7309: strcat(optionfilegnuplot,".gp");
7310:
7311: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
7312: printf("Problem with file %s",optionfilegnuplot);
7313: }
7314: else{
7315: fprintf(ficgp,"\n# %s\n", version);
7316: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 7317: //fprintf(ficgp,"set missing 'NaNq'\n");
7318: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 7319: }
7320: /* fclose(ficgp);*/
1.186 brouard 7321:
7322:
7323: /* Initialisation of --------- index.htm --------*/
1.126 brouard 7324:
7325: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
7326: if(mle==-3)
1.201 brouard 7327: strcat(optionfilehtm,"-MORT_");
1.126 brouard 7328: strcat(optionfilehtm,".htm");
7329: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 7330: printf("Problem with %s \n",optionfilehtm);
7331: exit(0);
1.126 brouard 7332: }
7333:
7334: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
7335: strcat(optionfilehtmcov,"-cov.htm");
7336: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
7337: printf("Problem with %s \n",optionfilehtmcov), exit(0);
7338: }
7339: else{
7340: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
7341: <hr size=\"2\" color=\"#EC5E5E\"> \n\
7342: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
7343: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
7344: }
7345:
7346: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
7347: <hr size=\"2\" color=\"#EC5E5E\"> \n\
7348: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
7349: \n\
7350: <hr size=\"2\" color=\"#EC5E5E\">\
7351: <ul><li><h4>Parameter files</h4>\n\
7352: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
7353: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
7354: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
7355: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
7356: - Date and time at start: %s</ul>\n",\
7357: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
7358: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
7359: fileres,fileres,\
7360: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
7361: fflush(fichtm);
7362:
7363: strcpy(pathr,path);
7364: strcat(pathr,optionfilefiname);
1.184 brouard 7365: #ifdef WIN32
7366: _chdir(optionfilefiname); /* Move to directory named optionfile */
7367: #else
1.126 brouard 7368: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 7369: #endif
7370:
1.126 brouard 7371:
7372: /* Calculates basic frequencies. Computes observed prevalence at single age
7373: and prints on file fileres'p'. */
7374: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
7375:
7376: fprintf(fichtm,"\n");
7377: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
7378: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
7379: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
7380: imx,agemin,agemax,jmin,jmax,jmean);
7381: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7382: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7383: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7384: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7385: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
7386:
7387:
7388: /* For Powell, parameters are in a vector p[] starting at p[1]
7389: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
7390: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
7391:
7392: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 7393: /* For mortality only */
1.126 brouard 7394: if (mle==-3){
1.136 brouard 7395: ximort=matrix(1,NDIM,1,NDIM);
1.186 brouard 7396: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 7397: cens=ivector(1,n);
7398: ageexmed=vector(1,n);
7399: agecens=vector(1,n);
7400: dcwave=ivector(1,n);
7401:
7402: for (i=1; i<=imx; i++){
7403: dcwave[i]=-1;
7404: for (m=firstpass; m<=lastpass; m++)
7405: if (s[m][i]>nlstate) {
7406: dcwave[i]=m;
7407: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
7408: break;
7409: }
7410: }
7411:
7412: for (i=1; i<=imx; i++) {
7413: if (wav[i]>0){
7414: ageexmed[i]=agev[mw[1][i]][i];
7415: j=wav[i];
7416: agecens[i]=1.;
7417:
7418: if (ageexmed[i]> 1 && wav[i] > 0){
7419: agecens[i]=agev[mw[j][i]][i];
7420: cens[i]= 1;
7421: }else if (ageexmed[i]< 1)
7422: cens[i]= -1;
7423: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
7424: cens[i]=0 ;
7425: }
7426: else cens[i]=-1;
7427: }
7428:
7429: for (i=1;i<=NDIM;i++) {
7430: for (j=1;j<=NDIM;j++)
7431: ximort[i][j]=(i == j ? 1.0 : 0.0);
7432: }
7433:
1.145 brouard 7434: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 7435: /*printf("%lf %lf", p[1], p[2]);*/
7436:
7437:
1.136 brouard 7438: #ifdef GSL
7439: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 7440: #else
1.126 brouard 7441: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 7442: #endif
1.201 brouard 7443: strcpy(filerespow,"POW-MORT_");
7444: strcat(filerespow,fileresu);
1.126 brouard 7445: if((ficrespow=fopen(filerespow,"w"))==NULL) {
7446: printf("Problem with resultfile: %s\n", filerespow);
7447: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
7448: }
1.136 brouard 7449: #ifdef GSL
7450: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 7451: #else
1.126 brouard 7452: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 7453: #endif
1.126 brouard 7454: /* for (i=1;i<=nlstate;i++)
7455: for(j=1;j<=nlstate+ndeath;j++)
7456: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
7457: */
7458: fprintf(ficrespow,"\n");
1.136 brouard 7459: #ifdef GSL
7460: /* gsl starts here */
7461: T = gsl_multimin_fminimizer_nmsimplex;
7462: gsl_multimin_fminimizer *sfm = NULL;
7463: gsl_vector *ss, *x;
7464: gsl_multimin_function minex_func;
7465:
7466: /* Initial vertex size vector */
7467: ss = gsl_vector_alloc (NDIM);
7468:
7469: if (ss == NULL){
7470: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
7471: }
7472: /* Set all step sizes to 1 */
7473: gsl_vector_set_all (ss, 0.001);
7474:
7475: /* Starting point */
1.126 brouard 7476:
1.136 brouard 7477: x = gsl_vector_alloc (NDIM);
7478:
7479: if (x == NULL){
7480: gsl_vector_free(ss);
7481: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
7482: }
7483:
7484: /* Initialize method and iterate */
7485: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 7486: /* gsl_vector_set(x, 0, 0.0268); */
7487: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 7488: gsl_vector_set(x, 0, p[1]);
7489: gsl_vector_set(x, 1, p[2]);
7490:
7491: minex_func.f = &gompertz_f;
7492: minex_func.n = NDIM;
7493: minex_func.params = (void *)&p; /* ??? */
7494:
7495: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
7496: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
7497:
7498: printf("Iterations beginning .....\n\n");
7499: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
7500:
7501: iteri=0;
7502: while (rval == GSL_CONTINUE){
7503: iteri++;
7504: status = gsl_multimin_fminimizer_iterate(sfm);
7505:
7506: if (status) printf("error: %s\n", gsl_strerror (status));
7507: fflush(0);
7508:
7509: if (status)
7510: break;
7511:
7512: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
7513: ssval = gsl_multimin_fminimizer_size (sfm);
7514:
7515: if (rval == GSL_SUCCESS)
7516: printf ("converged to a local maximum at\n");
7517:
7518: printf("%5d ", iteri);
7519: for (it = 0; it < NDIM; it++){
7520: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
7521: }
7522: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
7523: }
7524:
7525: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
7526:
7527: gsl_vector_free(x); /* initial values */
7528: gsl_vector_free(ss); /* inital step size */
7529: for (it=0; it<NDIM; it++){
7530: p[it+1]=gsl_vector_get(sfm->x,it);
7531: fprintf(ficrespow," %.12lf", p[it]);
7532: }
7533: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
7534: #endif
7535: #ifdef POWELL
7536: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
7537: #endif
1.126 brouard 7538: fclose(ficrespow);
7539:
1.203 ! brouard 7540: hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz);
1.126 brouard 7541:
7542: for(i=1; i <=NDIM; i++)
7543: for(j=i+1;j<=NDIM;j++)
7544: matcov[i][j]=matcov[j][i];
7545:
7546: printf("\nCovariance matrix\n ");
1.203 ! brouard 7547: fprintf(ficlog,"\nCovariance matrix\n ");
1.126 brouard 7548: for(i=1; i <=NDIM; i++) {
7549: for(j=1;j<=NDIM;j++){
7550: printf("%f ",matcov[i][j]);
1.203 ! brouard 7551: fprintf(ficlog,"%f ",matcov[i][j]);
1.126 brouard 7552: }
1.203 ! brouard 7553: printf("\n "); fprintf(ficlog,"\n ");
1.126 brouard 7554: }
7555:
7556: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 brouard 7557: for (i=1;i<=NDIM;i++) {
1.126 brouard 7558: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 brouard 7559: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
7560: }
1.126 brouard 7561: lsurv=vector(1,AGESUP);
7562: lpop=vector(1,AGESUP);
7563: tpop=vector(1,AGESUP);
7564: lsurv[agegomp]=100000;
7565:
7566: for (k=agegomp;k<=AGESUP;k++) {
7567: agemortsup=k;
7568: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
7569: }
7570:
7571: for (k=agegomp;k<agemortsup;k++)
7572: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
7573:
7574: for (k=agegomp;k<agemortsup;k++){
7575: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
7576: sumlpop=sumlpop+lpop[k];
7577: }
7578:
7579: tpop[agegomp]=sumlpop;
7580: for (k=agegomp;k<(agemortsup-3);k++){
7581: /* tpop[k+1]=2;*/
7582: tpop[k+1]=tpop[k]-lpop[k];
7583: }
7584:
7585:
7586: printf("\nAge lx qx dx Lx Tx e(x)\n");
7587: for (k=agegomp;k<(agemortsup-2);k++)
7588: 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]);
7589:
7590:
7591: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 7592: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
7593: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7594: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7595: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7596: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7597: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7598: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7599: }else
1.201 brouard 7600: printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
7601: printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
1.126 brouard 7602: stepm, weightopt,\
7603: model,imx,p,matcov,agemortsup);
7604:
7605: free_vector(lsurv,1,AGESUP);
7606: free_vector(lpop,1,AGESUP);
7607: free_vector(tpop,1,AGESUP);
1.136 brouard 7608: #ifdef GSL
7609: free_ivector(cens,1,n);
7610: free_vector(agecens,1,n);
7611: free_ivector(dcwave,1,n);
7612: free_matrix(ximort,1,NDIM,1,NDIM);
7613: #endif
1.186 brouard 7614: } /* Endof if mle==-3 mortality only */
7615: /* Standard maximisation */
1.203 ! brouard 7616: else{ /* For mle !=- 3 */
1.132 brouard 7617: globpr=0;/* debug */
1.186 brouard 7618: /* Computes likelihood for initial parameters */
1.132 brouard 7619: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 7620: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7621: for (k=1; k<=npar;k++)
7622: printf(" %d %8.5f",k,p[k]);
7623: printf("\n");
1.186 brouard 7624: globpr=1; /* again, to print the contributions */
1.126 brouard 7625: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
7626: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7627: for (k=1; k<=npar;k++)
7628: printf(" %d %8.5f",k,p[k]);
7629: printf("\n");
1.186 brouard 7630: if(mle>=1){ /* Could be 1 or 2, Real Maximisation */
1.126 brouard 7631: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
7632: }
7633:
7634: /*--------- results files --------------*/
1.192 brouard 7635: 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 7636:
7637:
7638: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7639: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7640: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7641: for(i=1,jk=1; i <=nlstate; i++){
7642: for(k=1; k <=(nlstate+ndeath); k++){
7643: if (k != i) {
7644: printf("%d%d ",i,k);
7645: fprintf(ficlog,"%d%d ",i,k);
7646: fprintf(ficres,"%1d%1d ",i,k);
7647: for(j=1; j <=ncovmodel; j++){
1.190 brouard 7648: printf("%12.7f ",p[jk]);
7649: fprintf(ficlog,"%12.7f ",p[jk]);
7650: fprintf(ficres,"%12.7f ",p[jk]);
1.126 brouard 7651: jk++;
7652: }
7653: printf("\n");
7654: fprintf(ficlog,"\n");
7655: fprintf(ficres,"\n");
7656: }
7657: }
7658: }
1.203 ! brouard 7659: if(mle != 0){
! 7660: /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
1.126 brouard 7661: ftolhess=ftol; /* Usually correct */
1.203 ! brouard 7662: hesscov(matcov, hess, p, npar, delti, ftolhess, func);
! 7663: printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
! 7664: fprintf(ficlog, "Parameters, Wald tests and Wald-based confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W \n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
! 7665: for(i=1,jk=1; i <=nlstate; i++){
! 7666: for(k=1; k <=(nlstate+ndeath); k++){
! 7667: if (k != i) {
! 7668: printf("%d%d ",i,k);
! 7669: fprintf(ficlog,"%d%d ",i,k);
! 7670: for(j=1; j <=ncovmodel; j++){
! 7671: printf("%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
! 7672: fprintf(ficlog,"%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
! 7673: jk++;
! 7674: }
! 7675: printf("\n");
! 7676: fprintf(ficlog,"\n");
1.193 brouard 7677: }
7678: }
7679: }
1.203 ! brouard 7680: } /* end of hesscov and Wald tests */
1.193 brouard 7681:
1.203 ! brouard 7682: /* */
1.126 brouard 7683: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
7684: printf("# Scales (for hessian or gradient estimation)\n");
7685: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
7686: for(i=1,jk=1; i <=nlstate; i++){
7687: for(j=1; j <=nlstate+ndeath; j++){
7688: if (j!=i) {
7689: fprintf(ficres,"%1d%1d",i,j);
7690: printf("%1d%1d",i,j);
7691: fprintf(ficlog,"%1d%1d",i,j);
7692: for(k=1; k<=ncovmodel;k++){
7693: printf(" %.5e",delti[jk]);
7694: fprintf(ficlog," %.5e",delti[jk]);
7695: fprintf(ficres," %.5e",delti[jk]);
7696: jk++;
7697: }
7698: printf("\n");
7699: fprintf(ficlog,"\n");
7700: fprintf(ficres,"\n");
7701: }
7702: }
7703: }
7704:
7705: 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");
1.203 ! brouard 7706: if(mle >= 1) /* To big for the screen */
1.126 brouard 7707: 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");
7708: 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");
7709: /* # 121 Var(a12)\n\ */
7710: /* # 122 Cov(b12,a12) Var(b12)\n\ */
7711: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
7712: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
7713: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
7714: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
7715: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
7716: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
7717:
7718:
7719: /* Just to have a covariance matrix which will be more understandable
7720: even is we still don't want to manage dictionary of variables
7721: */
7722: for(itimes=1;itimes<=2;itimes++){
7723: jj=0;
7724: for(i=1; i <=nlstate; i++){
7725: for(j=1; j <=nlstate+ndeath; j++){
7726: if(j==i) continue;
7727: for(k=1; k<=ncovmodel;k++){
7728: jj++;
7729: ca[0]= k+'a'-1;ca[1]='\0';
7730: if(itimes==1){
7731: if(mle>=1)
7732: printf("#%1d%1d%d",i,j,k);
7733: fprintf(ficlog,"#%1d%1d%d",i,j,k);
7734: fprintf(ficres,"#%1d%1d%d",i,j,k);
7735: }else{
7736: if(mle>=1)
7737: printf("%1d%1d%d",i,j,k);
7738: fprintf(ficlog,"%1d%1d%d",i,j,k);
7739: fprintf(ficres,"%1d%1d%d",i,j,k);
7740: }
7741: ll=0;
7742: for(li=1;li <=nlstate; li++){
7743: for(lj=1;lj <=nlstate+ndeath; lj++){
7744: if(lj==li) continue;
7745: for(lk=1;lk<=ncovmodel;lk++){
7746: ll++;
7747: if(ll<=jj){
7748: cb[0]= lk +'a'-1;cb[1]='\0';
7749: if(ll<jj){
7750: if(itimes==1){
7751: if(mle>=1)
7752: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7753: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7754: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7755: }else{
7756: if(mle>=1)
7757: printf(" %.5e",matcov[jj][ll]);
7758: fprintf(ficlog," %.5e",matcov[jj][ll]);
7759: fprintf(ficres," %.5e",matcov[jj][ll]);
7760: }
7761: }else{
7762: if(itimes==1){
7763: if(mle>=1)
7764: printf(" Var(%s%1d%1d)",ca,i,j);
7765: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
7766: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
7767: }else{
7768: if(mle>=1)
1.203 ! brouard 7769: printf(" %.7e",matcov[jj][ll]);
! 7770: fprintf(ficlog," %.7e",matcov[jj][ll]);
! 7771: fprintf(ficres," %.7e",matcov[jj][ll]);
1.126 brouard 7772: }
7773: }
7774: }
7775: } /* end lk */
7776: } /* end lj */
7777: } /* end li */
7778: if(mle>=1)
7779: printf("\n");
7780: fprintf(ficlog,"\n");
7781: fprintf(ficres,"\n");
7782: numlinepar++;
7783: } /* end k*/
7784: } /*end j */
7785: } /* end i */
7786: } /* end itimes */
7787:
7788: fflush(ficlog);
7789: fflush(ficres);
7790:
7791: while((c=getc(ficpar))=='#' && c!= EOF){
7792: ungetc(c,ficpar);
7793: fgets(line, MAXLINE, ficpar);
1.141 brouard 7794: fputs(line,stdout);
1.126 brouard 7795: fputs(line,ficparo);
7796: }
7797: ungetc(c,ficpar);
7798:
7799: estepm=0;
7800: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
7801: if (estepm==0 || estepm < stepm) estepm=stepm;
7802: if (fage <= 2) {
7803: bage = ageminpar;
7804: fage = agemaxpar;
7805: }
7806:
7807: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
7808: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
7809: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
1.186 brouard 7810:
7811: /* Other stuffs, more or less useful */
1.126 brouard 7812: while((c=getc(ficpar))=='#' && c!= EOF){
7813: ungetc(c,ficpar);
7814: fgets(line, MAXLINE, ficpar);
1.141 brouard 7815: fputs(line,stdout);
1.126 brouard 7816: fputs(line,ficparo);
7817: }
7818: ungetc(c,ficpar);
7819:
7820: 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);
7821: 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);
7822: 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);
7823: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
7824: 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);
7825:
7826: while((c=getc(ficpar))=='#' && c!= EOF){
7827: ungetc(c,ficpar);
7828: fgets(line, MAXLINE, ficpar);
1.141 brouard 7829: fputs(line,stdout);
1.126 brouard 7830: fputs(line,ficparo);
7831: }
7832: ungetc(c,ficpar);
7833:
7834:
7835: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
7836: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
7837:
7838: fscanf(ficpar,"pop_based=%d\n",&popbased);
1.193 brouard 7839: fprintf(ficlog,"pop_based=%d\n",popbased);
1.126 brouard 7840: fprintf(ficparo,"pop_based=%d\n",popbased);
7841: fprintf(ficres,"pop_based=%d\n",popbased);
7842:
7843: while((c=getc(ficpar))=='#' && c!= EOF){
7844: ungetc(c,ficpar);
7845: fgets(line, MAXLINE, ficpar);
1.141 brouard 7846: fputs(line,stdout);
1.126 brouard 7847: fputs(line,ficparo);
7848: }
7849: ungetc(c,ficpar);
7850:
7851: 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);
7852: 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);
7853: 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);
7854: 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);
7855: 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);
7856: /* day and month of proj2 are not used but only year anproj2.*/
7857:
7858:
7859:
1.145 brouard 7860: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
7861: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 7862:
7863: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 7864: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
7865: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7866: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7867: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7868: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7869: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7870: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7871: }else
1.201 brouard 7872: printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.126 brouard 7873:
1.201 brouard 7874: printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt,\
1.126 brouard 7875: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
7876: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
7877:
7878: /*------------ free_vector -------------*/
7879: /* chdir(path); */
7880:
7881: free_ivector(wav,1,imx);
7882: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
7883: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
7884: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
7885: free_lvector(num,1,n);
7886: free_vector(agedc,1,n);
7887: /*free_matrix(covar,0,NCOVMAX,1,n);*/
7888: /*free_matrix(covar,1,NCOVMAX,1,n);*/
7889: fclose(ficparo);
7890: fclose(ficres);
7891:
7892:
1.186 brouard 7893: /* Other results (useful)*/
7894:
7895:
1.126 brouard 7896: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 7897: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
7898: prlim=matrix(1,nlstate,1,nlstate);
1.203 ! brouard 7899: prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, ncvyear);
1.126 brouard 7900: fclose(ficrespl);
7901:
1.145 brouard 7902: #ifdef FREEEXIT2
7903: #include "freeexit2.h"
7904: #endif
7905:
1.126 brouard 7906: /*------------- h Pij x at various ages ------------*/
1.180 brouard 7907: /*#include "hpijx.h"*/
7908: hPijx(p, bage, fage);
1.145 brouard 7909: fclose(ficrespij);
1.126 brouard 7910:
1.145 brouard 7911: /*-------------- Variance of one-step probabilities---*/
7912: k=1;
1.126 brouard 7913: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
7914:
7915:
7916: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7917: for(i=1;i<=AGESUP;i++)
7918: for(j=1;j<=NCOVMAX;j++)
7919: for(k=1;k<=NCOVMAX;k++)
7920: probs[i][j][k]=0.;
7921:
7922: /*---------- Forecasting ------------------*/
7923: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
7924: if(prevfcast==1){
7925: /* if(stepm ==1){*/
1.201 brouard 7926: prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.126 brouard 7927: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
7928: /* } */
7929: /* else{ */
7930: /* erreur=108; */
7931: /* 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); */
7932: /* 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); */
7933: /* } */
7934: }
1.186 brouard 7935:
7936: /* ------ Other prevalence ratios------------ */
1.126 brouard 7937:
1.127 brouard 7938: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
7939:
7940: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
7941: /* 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",\
7942: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
7943: */
1.126 brouard 7944:
1.127 brouard 7945: if (mobilav!=0) {
7946: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7947: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
7948: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
7949: printf(" Error in movingaverage mobilav=%d\n",mobilav);
7950: }
1.126 brouard 7951: }
7952:
7953:
1.127 brouard 7954: /*---------- Health expectancies, no variances ------------*/
7955:
1.201 brouard 7956: strcpy(filerese,"E_");
7957: strcat(filerese,fileresu);
1.126 brouard 7958: if((ficreseij=fopen(filerese,"w"))==NULL) {
7959: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
7960: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
7961: }
7962: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
7963: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.145 brouard 7964: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7965: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7966:
7967: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.127 brouard 7968: fprintf(ficreseij,"\n#****** ");
7969: for(j=1;j<=cptcoveff;j++) {
1.200 brouard 7970: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.127 brouard 7971: }
7972: fprintf(ficreseij,"******\n");
7973:
7974: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7975: oldm=oldms;savm=savms;
7976: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
7977:
7978: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.145 brouard 7979: /*}*/
1.127 brouard 7980: }
7981: fclose(ficreseij);
7982:
7983:
7984: /*---------- Health expectancies and variances ------------*/
7985:
7986:
1.201 brouard 7987: strcpy(filerest,"T_");
7988: strcat(filerest,fileresu);
1.127 brouard 7989: if((ficrest=fopen(filerest,"w"))==NULL) {
7990: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
7991: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
7992: }
7993: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
7994: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
7995:
1.126 brouard 7996:
1.201 brouard 7997: strcpy(fileresstde,"STDE_");
7998: strcat(fileresstde,fileresu);
1.126 brouard 7999: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
8000: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
8001: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
8002: }
8003: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
8004: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
8005:
1.201 brouard 8006: strcpy(filerescve,"CVE_");
8007: strcat(filerescve,fileresu);
1.126 brouard 8008: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
8009: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
8010: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
8011: }
8012: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
8013: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
8014:
1.201 brouard 8015: strcpy(fileresv,"V_");
8016: strcat(fileresv,fileresu);
1.126 brouard 8017: if((ficresvij=fopen(fileresv,"w"))==NULL) {
8018: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
8019: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
8020: }
8021: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
8022: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
8023:
1.145 brouard 8024: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
8025: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
8026:
8027: for (k=1; k <= (int) pow(2,cptcoveff); k++){
8028: fprintf(ficrest,"\n#****** ");
1.126 brouard 8029: for(j=1;j<=cptcoveff;j++)
1.200 brouard 8030: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 8031: fprintf(ficrest,"******\n");
8032:
8033: fprintf(ficresstdeij,"\n#****** ");
8034: fprintf(ficrescveij,"\n#****** ");
8035: for(j=1;j<=cptcoveff;j++) {
1.200 brouard 8036: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8037: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 8038: }
8039: fprintf(ficresstdeij,"******\n");
8040: fprintf(ficrescveij,"******\n");
8041:
8042: fprintf(ficresvij,"\n#****** ");
8043: for(j=1;j<=cptcoveff;j++)
1.200 brouard 8044: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 8045: fprintf(ficresvij,"******\n");
8046:
8047: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
8048: oldm=oldms;savm=savms;
1.127 brouard 8049: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
1.145 brouard 8050: /*
8051: */
8052: /* goto endfree; */
1.126 brouard 8053:
8054: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
8055: pstamp(ficrest);
1.145 brouard 8056:
8057:
1.128 brouard 8058: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.199 brouard 8059: oldm=oldms;savm=savms; /* ZZ Segmentation fault */
1.161 brouard 8060: cptcod= 0; /* To be deleted */
1.203 ! brouard 8061: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
1.145 brouard 8062: 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 8063: if(vpopbased==1)
8064: 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);
8065: else
8066: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
1.201 brouard 8067: fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
1.128 brouard 8068: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
8069: fprintf(ficrest,"\n");
1.199 brouard 8070: /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
1.128 brouard 8071: epj=vector(1,nlstate+1);
8072: for(age=bage; age <=fage ;age++){
1.203 ! brouard 8073: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyear, k); /*ZZ Is it the correct prevalim */
1.128 brouard 8074: if (vpopbased==1) {
8075: if(mobilav ==0){
8076: for(i=1; i<=nlstate;i++)
8077: prlim[i][i]=probs[(int)age][i][k];
8078: }else{ /* mobilav */
8079: for(i=1; i<=nlstate;i++)
8080: prlim[i][i]=mobaverage[(int)age][i][k];
8081: }
1.126 brouard 8082: }
8083:
1.201 brouard 8084: fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
1.199 brouard 8085: /* printf(" age %4.0f ",age); */
1.128 brouard 8086: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
8087: for(i=1, epj[j]=0.;i <=nlstate;i++) {
8088: epj[j] += prlim[i][i]*eij[i][j][(int)age];
1.199 brouard 8089: /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
8090: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
1.128 brouard 8091: }
8092: epj[nlstate+1] +=epj[j];
1.126 brouard 8093: }
1.199 brouard 8094: /* printf(" age %4.0f \n",age); */
1.126 brouard 8095:
1.128 brouard 8096: for(i=1, vepp=0.;i <=nlstate;i++)
8097: for(j=1;j <=nlstate;j++)
8098: vepp += vareij[i][j][(int)age];
8099: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
8100: for(j=1;j <=nlstate;j++){
8101: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
8102: }
8103: fprintf(ficrest,"\n");
1.126 brouard 8104: }
8105: }
8106: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
8107: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
8108: free_vector(epj,1,nlstate+1);
1.145 brouard 8109: /*}*/
1.126 brouard 8110: }
8111: free_vector(weight,1,n);
1.145 brouard 8112: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.126 brouard 8113: free_imatrix(s,1,maxwav+1,1,n);
8114: free_matrix(anint,1,maxwav,1,n);
8115: free_matrix(mint,1,maxwav,1,n);
8116: free_ivector(cod,1,n);
8117: free_ivector(tab,1,NCOVMAX);
8118: fclose(ficresstdeij);
8119: fclose(ficrescveij);
8120: fclose(ficresvij);
8121: fclose(ficrest);
8122: fclose(ficpar);
8123:
8124: /*------- Variance of period (stable) prevalence------*/
8125:
1.201 brouard 8126: strcpy(fileresvpl,"VPL_");
8127: strcat(fileresvpl,fileresu);
1.126 brouard 8128: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
8129: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
8130: exit(0);
8131: }
8132: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
8133:
1.145 brouard 8134: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
8135: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
8136:
8137: for (k=1; k <= (int) pow(2,cptcoveff); k++){
8138: fprintf(ficresvpl,"\n#****** ");
1.126 brouard 8139: for(j=1;j<=cptcoveff;j++)
1.200 brouard 8140: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 8141: fprintf(ficresvpl,"******\n");
8142:
8143: varpl=matrix(1,nlstate,(int) bage, (int) fage);
8144: oldm=oldms;savm=savms;
1.203 ! brouard 8145: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyear, k, strstart);
1.126 brouard 8146: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 8147: /*}*/
1.126 brouard 8148: }
8149:
8150: fclose(ficresvpl);
8151:
8152: /*---------- End : free ----------------*/
8153: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
8154: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
8155: } /* mle==-3 arrives here for freeing */
1.164 brouard 8156: /* endfree:*/
1.141 brouard 8157: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.126 brouard 8158: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
8159: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
8160: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
8161: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
8162: free_matrix(covar,0,NCOVMAX,1,n);
8163: free_matrix(matcov,1,npar,1,npar);
1.203 ! brouard 8164: free_matrix(hess,1,npar,1,npar);
1.126 brouard 8165: /*free_vector(delti,1,npar);*/
8166: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
8167: free_matrix(agev,1,maxwav,1,imx);
8168: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
8169:
1.145 brouard 8170: free_ivector(ncodemax,1,NCOVMAX);
1.192 brouard 8171: free_ivector(ncodemaxwundef,1,NCOVMAX);
1.145 brouard 8172: free_ivector(Tvar,1,NCOVMAX);
8173: free_ivector(Tprod,1,NCOVMAX);
8174: free_ivector(Tvaraff,1,NCOVMAX);
8175: free_ivector(Tage,1,NCOVMAX);
1.126 brouard 8176:
8177: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
1.200 brouard 8178: /* free_imatrix(codtab,1,100,1,10); */
1.126 brouard 8179: fflush(fichtm);
8180: fflush(ficgp);
8181:
8182:
8183: if((nberr >0) || (nbwarn>0)){
8184: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
8185: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
8186: }else{
8187: printf("End of Imach\n");
8188: fprintf(ficlog,"End of Imach\n");
8189: }
8190: printf("See log file on %s\n",filelog);
8191: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 8192: /*(void) gettimeofday(&end_time,&tzp);*/
8193: rend_time = time(NULL);
8194: end_time = *localtime(&rend_time);
8195: /* tml = *localtime(&end_time.tm_sec); */
8196: strcpy(strtend,asctime(&end_time));
1.126 brouard 8197: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
8198: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 8199: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.126 brouard 8200:
1.157 brouard 8201: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
8202: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
8203: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 8204: /* printf("Total time was %d uSec.\n", total_usecs);*/
8205: /* if(fileappend(fichtm,optionfilehtm)){ */
8206: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
8207: fclose(fichtm);
8208: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
8209: fclose(fichtmcov);
8210: fclose(ficgp);
8211: fclose(ficlog);
8212: /*------ End -----------*/
8213:
8214:
8215: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 8216: #ifdef WIN32
8217: if (_chdir(pathcd) != 0)
8218: printf("Can't move to directory %s!\n",path);
8219: if(_getcwd(pathcd,MAXLINE) > 0)
8220: #else
1.126 brouard 8221: if(chdir(pathcd) != 0)
1.184 brouard 8222: printf("Can't move to directory %s!\n", path);
8223: if (getcwd(pathcd, MAXLINE) > 0)
8224: #endif
1.126 brouard 8225: printf("Current directory %s!\n",pathcd);
8226: /*strcat(plotcmd,CHARSEPARATOR);*/
8227: sprintf(plotcmd,"gnuplot");
1.157 brouard 8228: #ifdef _WIN32
1.126 brouard 8229: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
8230: #endif
8231: if(!stat(plotcmd,&info)){
1.158 brouard 8232: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 8233: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 8234: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 8235: }else
8236: strcpy(pplotcmd,plotcmd);
1.157 brouard 8237: #ifdef __unix
1.126 brouard 8238: strcpy(plotcmd,GNUPLOTPROGRAM);
8239: if(!stat(plotcmd,&info)){
1.158 brouard 8240: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 8241: }else
8242: strcpy(pplotcmd,plotcmd);
8243: #endif
8244: }else
8245: strcpy(pplotcmd,plotcmd);
8246:
8247: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 8248: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 8249:
8250: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 8251: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 8252: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 8253: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 8254: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 8255: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 8256: }
1.158 brouard 8257: printf(" Successful, please wait...");
1.126 brouard 8258: while (z[0] != 'q') {
8259: /* chdir(path); */
1.154 brouard 8260: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 8261: scanf("%s",z);
8262: /* if (z[0] == 'c') system("./imach"); */
8263: if (z[0] == 'e') {
1.158 brouard 8264: #ifdef __APPLE__
1.152 brouard 8265: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 8266: #elif __linux
8267: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 8268: #else
1.152 brouard 8269: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 8270: #endif
8271: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
8272: system(pplotcmd);
1.126 brouard 8273: }
8274: else if (z[0] == 'g') system(plotcmd);
8275: else if (z[0] == 'q') exit(0);
8276: }
8277: end:
8278: while (z[0] != 'q') {
1.195 brouard 8279: printf("\nType q for exiting: "); fflush(stdout);
1.126 brouard 8280: scanf("%s",z);
8281: }
8282: }
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