Annotation of imach/src/imach.c, revision 1.210
1.210 ! brouard 1: /* $Id: imach.c,v 1.209 2015/11/17 22:12:03 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.210 ! brouard 4: Revision 1.209 2015/11/17 22:12:03 brouard
! 5: Summary: Adding ftolpl parameter
! 6: Author: N Brouard
! 7:
! 8: We had difficulties to get smoothed confidence intervals. It was due
! 9: to the period prevalence which wasn't computed accurately. The inner
! 10: parameter ftolpl is now an outer parameter of the .imach parameter
! 11: file after estepm. If ftolpl is small 1.e-4 and estepm too,
! 12: computation are long.
! 13:
1.209 brouard 14: Revision 1.208 2015/11/17 14:31:57 brouard
15: Summary: temporary
16:
1.208 brouard 17: Revision 1.207 2015/10/27 17:36:57 brouard
18: *** empty log message ***
19:
1.207 brouard 20: Revision 1.206 2015/10/24 07:14:11 brouard
21: *** empty log message ***
22:
1.206 brouard 23: Revision 1.205 2015/10/23 15:50:53 brouard
24: Summary: 0.98r3 some clarification for graphs on likelihood contributions
25:
1.205 brouard 26: Revision 1.204 2015/10/01 16:20:26 brouard
27: Summary: Some new graphs of contribution to likelihood
28:
1.204 brouard 29: Revision 1.203 2015/09/30 17:45:14 brouard
30: Summary: looking at better estimation of the hessian
31:
32: Also a better criteria for convergence to the period prevalence And
33: therefore adding the number of years needed to converge. (The
34: prevalence in any alive state shold sum to one
35:
1.203 brouard 36: Revision 1.202 2015/09/22 19:45:16 brouard
37: Summary: Adding some overall graph on contribution to likelihood. Might change
38:
1.202 brouard 39: Revision 1.201 2015/09/15 17:34:58 brouard
40: Summary: 0.98r0
41:
42: - Some new graphs like suvival functions
43: - Some bugs fixed like model=1+age+V2.
44:
1.201 brouard 45: Revision 1.200 2015/09/09 16:53:55 brouard
46: Summary: Big bug thanks to Flavia
47:
48: Even model=1+age+V2. did not work anymore
49:
1.200 brouard 50: Revision 1.199 2015/09/07 14:09:23 brouard
51: Summary: 0.98q6 changing default small png format for graph to vectorized svg.
52:
1.199 brouard 53: Revision 1.198 2015/09/03 07:14:39 brouard
54: Summary: 0.98q5 Flavia
55:
1.198 brouard 56: Revision 1.197 2015/09/01 18:24:39 brouard
57: *** empty log message ***
58:
1.197 brouard 59: Revision 1.196 2015/08/18 23:17:52 brouard
60: Summary: 0.98q5
61:
1.196 brouard 62: Revision 1.195 2015/08/18 16:28:39 brouard
63: Summary: Adding a hack for testing purpose
64:
65: After reading the title, ftol and model lines, if the comment line has
66: a q, starting with #q, the answer at the end of the run is quit. It
67: permits to run test files in batch with ctest. The former workaround was
68: $ echo q | imach foo.imach
69:
1.195 brouard 70: Revision 1.194 2015/08/18 13:32:00 brouard
71: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
72:
1.194 brouard 73: Revision 1.193 2015/08/04 07:17:42 brouard
74: Summary: 0.98q4
75:
1.193 brouard 76: Revision 1.192 2015/07/16 16:49:02 brouard
77: Summary: Fixing some outputs
78:
1.192 brouard 79: Revision 1.191 2015/07/14 10:00:33 brouard
80: Summary: Some fixes
81:
1.191 brouard 82: Revision 1.190 2015/05/05 08:51:13 brouard
83: Summary: Adding digits in output parameters (7 digits instead of 6)
84:
85: Fix 1+age+.
86:
1.190 brouard 87: Revision 1.189 2015/04/30 14:45:16 brouard
88: Summary: 0.98q2
89:
1.189 brouard 90: Revision 1.188 2015/04/30 08:27:53 brouard
91: *** empty log message ***
92:
1.188 brouard 93: Revision 1.187 2015/04/29 09:11:15 brouard
94: *** empty log message ***
95:
1.187 brouard 96: Revision 1.186 2015/04/23 12:01:52 brouard
97: Summary: V1*age is working now, version 0.98q1
98:
99: Some codes had been disabled in order to simplify and Vn*age was
100: working in the optimization phase, ie, giving correct MLE parameters,
101: but, as usual, outputs were not correct and program core dumped.
102:
1.186 brouard 103: Revision 1.185 2015/03/11 13:26:42 brouard
104: Summary: Inclusion of compile and links command line for Intel Compiler
105:
1.185 brouard 106: Revision 1.184 2015/03/11 11:52:39 brouard
107: Summary: Back from Windows 8. Intel Compiler
108:
1.184 brouard 109: Revision 1.183 2015/03/10 20:34:32 brouard
110: Summary: 0.98q0, trying with directest, mnbrak fixed
111:
112: We use directest instead of original Powell test; probably no
113: incidence on the results, but better justifications;
114: We fixed Numerical Recipes mnbrak routine which was wrong and gave
115: wrong results.
116:
1.183 brouard 117: Revision 1.182 2015/02/12 08:19:57 brouard
118: Summary: Trying to keep directest which seems simpler and more general
119: Author: Nicolas Brouard
120:
1.182 brouard 121: Revision 1.181 2015/02/11 23:22:24 brouard
122: Summary: Comments on Powell added
123:
124: Author:
125:
1.181 brouard 126: Revision 1.180 2015/02/11 17:33:45 brouard
127: Summary: Finishing move from main to function (hpijx and prevalence_limit)
128:
1.180 brouard 129: Revision 1.179 2015/01/04 09:57:06 brouard
130: Summary: back to OS/X
131:
1.179 brouard 132: Revision 1.178 2015/01/04 09:35:48 brouard
133: *** empty log message ***
134:
1.178 brouard 135: Revision 1.177 2015/01/03 18:40:56 brouard
136: Summary: Still testing ilc32 on OSX
137:
1.177 brouard 138: Revision 1.176 2015/01/03 16:45:04 brouard
139: *** empty log message ***
140:
1.176 brouard 141: Revision 1.175 2015/01/03 16:33:42 brouard
142: *** empty log message ***
143:
1.175 brouard 144: Revision 1.174 2015/01/03 16:15:49 brouard
145: Summary: Still in cross-compilation
146:
1.174 brouard 147: Revision 1.173 2015/01/03 12:06:26 brouard
148: Summary: trying to detect cross-compilation
149:
1.173 brouard 150: Revision 1.172 2014/12/27 12:07:47 brouard
151: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
152:
1.172 brouard 153: Revision 1.171 2014/12/23 13:26:59 brouard
154: Summary: Back from Visual C
155:
156: Still problem with utsname.h on Windows
157:
1.171 brouard 158: Revision 1.170 2014/12/23 11:17:12 brouard
159: Summary: Cleaning some \%% back to %%
160:
161: The escape was mandatory for a specific compiler (which one?), but too many warnings.
162:
1.170 brouard 163: Revision 1.169 2014/12/22 23:08:31 brouard
164: Summary: 0.98p
165:
166: Outputs some informations on compiler used, OS etc. Testing on different platforms.
167:
1.169 brouard 168: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 169: Summary: update
1.169 brouard 170:
1.168 brouard 171: Revision 1.167 2014/12/22 13:50:56 brouard
172: Summary: Testing uname and compiler version and if compiled 32 or 64
173:
174: Testing on Linux 64
175:
1.167 brouard 176: Revision 1.166 2014/12/22 11:40:47 brouard
177: *** empty log message ***
178:
1.166 brouard 179: Revision 1.165 2014/12/16 11:20:36 brouard
180: Summary: After compiling on Visual C
181:
182: * imach.c (Module): Merging 1.61 to 1.162
183:
1.165 brouard 184: Revision 1.164 2014/12/16 10:52:11 brouard
185: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
186:
187: * imach.c (Module): Merging 1.61 to 1.162
188:
1.164 brouard 189: Revision 1.163 2014/12/16 10:30:11 brouard
190: * imach.c (Module): Merging 1.61 to 1.162
191:
1.163 brouard 192: Revision 1.162 2014/09/25 11:43:39 brouard
193: Summary: temporary backup 0.99!
194:
1.162 brouard 195: Revision 1.1 2014/09/16 11:06:58 brouard
196: Summary: With some code (wrong) for nlopt
197:
198: Author:
199:
200: Revision 1.161 2014/09/15 20:41:41 brouard
201: Summary: Problem with macro SQR on Intel compiler
202:
1.161 brouard 203: Revision 1.160 2014/09/02 09:24:05 brouard
204: *** empty log message ***
205:
1.160 brouard 206: Revision 1.159 2014/09/01 10:34:10 brouard
207: Summary: WIN32
208: Author: Brouard
209:
1.159 brouard 210: Revision 1.158 2014/08/27 17:11:51 brouard
211: *** empty log message ***
212:
1.158 brouard 213: Revision 1.157 2014/08/27 16:26:55 brouard
214: Summary: Preparing windows Visual studio version
215: Author: Brouard
216:
217: In order to compile on Visual studio, time.h is now correct and time_t
218: and tm struct should be used. difftime should be used but sometimes I
219: just make the differences in raw time format (time(&now).
220: Trying to suppress #ifdef LINUX
221: Add xdg-open for __linux in order to open default browser.
222:
1.157 brouard 223: Revision 1.156 2014/08/25 20:10:10 brouard
224: *** empty log message ***
225:
1.156 brouard 226: Revision 1.155 2014/08/25 18:32:34 brouard
227: Summary: New compile, minor changes
228: Author: Brouard
229:
1.155 brouard 230: Revision 1.154 2014/06/20 17:32:08 brouard
231: Summary: Outputs now all graphs of convergence to period prevalence
232:
1.154 brouard 233: Revision 1.153 2014/06/20 16:45:46 brouard
234: Summary: If 3 live state, convergence to period prevalence on same graph
235: Author: Brouard
236:
1.153 brouard 237: Revision 1.152 2014/06/18 17:54:09 brouard
238: Summary: open browser, use gnuplot on same dir than imach if not found in the path
239:
1.152 brouard 240: Revision 1.151 2014/06/18 16:43:30 brouard
241: *** empty log message ***
242:
1.151 brouard 243: Revision 1.150 2014/06/18 16:42:35 brouard
244: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
245: Author: brouard
246:
1.150 brouard 247: Revision 1.149 2014/06/18 15:51:14 brouard
248: Summary: Some fixes in parameter files errors
249: Author: Nicolas Brouard
250:
1.149 brouard 251: Revision 1.148 2014/06/17 17:38:48 brouard
252: Summary: Nothing new
253: Author: Brouard
254:
255: Just a new packaging for OS/X version 0.98nS
256:
1.148 brouard 257: Revision 1.147 2014/06/16 10:33:11 brouard
258: *** empty log message ***
259:
1.147 brouard 260: Revision 1.146 2014/06/16 10:20:28 brouard
261: Summary: Merge
262: Author: Brouard
263:
264: Merge, before building revised version.
265:
1.146 brouard 266: Revision 1.145 2014/06/10 21:23:15 brouard
267: Summary: Debugging with valgrind
268: Author: Nicolas Brouard
269:
270: Lot of changes in order to output the results with some covariates
271: After the Edimburgh REVES conference 2014, it seems mandatory to
272: improve the code.
273: No more memory valgrind error but a lot has to be done in order to
274: continue the work of splitting the code into subroutines.
275: Also, decodemodel has been improved. Tricode is still not
276: optimal. nbcode should be improved. Documentation has been added in
277: the source code.
278:
1.144 brouard 279: Revision 1.143 2014/01/26 09:45:38 brouard
280: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
281:
282: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
283: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
284:
1.143 brouard 285: Revision 1.142 2014/01/26 03:57:36 brouard
286: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
287:
288: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
289:
1.142 brouard 290: Revision 1.141 2014/01/26 02:42:01 brouard
291: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
292:
1.141 brouard 293: Revision 1.140 2011/09/02 10:37:54 brouard
294: Summary: times.h is ok with mingw32 now.
295:
1.140 brouard 296: Revision 1.139 2010/06/14 07:50:17 brouard
297: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
298: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
299:
1.139 brouard 300: Revision 1.138 2010/04/30 18:19:40 brouard
301: *** empty log message ***
302:
1.138 brouard 303: Revision 1.137 2010/04/29 18:11:38 brouard
304: (Module): Checking covariates for more complex models
305: than V1+V2. A lot of change to be done. Unstable.
306:
1.137 brouard 307: Revision 1.136 2010/04/26 20:30:53 brouard
308: (Module): merging some libgsl code. Fixing computation
309: of likelione (using inter/intrapolation if mle = 0) in order to
310: get same likelihood as if mle=1.
311: Some cleaning of code and comments added.
312:
1.136 brouard 313: Revision 1.135 2009/10/29 15:33:14 brouard
314: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
315:
1.135 brouard 316: Revision 1.134 2009/10/29 13:18:53 brouard
317: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
318:
1.134 brouard 319: Revision 1.133 2009/07/06 10:21:25 brouard
320: just nforces
321:
1.133 brouard 322: Revision 1.132 2009/07/06 08:22:05 brouard
323: Many tings
324:
1.132 brouard 325: Revision 1.131 2009/06/20 16:22:47 brouard
326: Some dimensions resccaled
327:
1.131 brouard 328: Revision 1.130 2009/05/26 06:44:34 brouard
329: (Module): Max Covariate is now set to 20 instead of 8. A
330: lot of cleaning with variables initialized to 0. Trying to make
331: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
332:
1.130 brouard 333: Revision 1.129 2007/08/31 13:49:27 lievre
334: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
335:
1.129 lievre 336: Revision 1.128 2006/06/30 13:02:05 brouard
337: (Module): Clarifications on computing e.j
338:
1.128 brouard 339: Revision 1.127 2006/04/28 18:11:50 brouard
340: (Module): Yes the sum of survivors was wrong since
341: imach-114 because nhstepm was no more computed in the age
342: loop. Now we define nhstepma in the age loop.
343: (Module): In order to speed up (in case of numerous covariates) we
344: compute health expectancies (without variances) in a first step
345: and then all the health expectancies with variances or standard
346: deviation (needs data from the Hessian matrices) which slows the
347: computation.
348: In the future we should be able to stop the program is only health
349: expectancies and graph are needed without standard deviations.
350:
1.127 brouard 351: Revision 1.126 2006/04/28 17:23:28 brouard
352: (Module): Yes the sum of survivors was wrong since
353: imach-114 because nhstepm was no more computed in the age
354: loop. Now we define nhstepma in the age loop.
355: Version 0.98h
356:
1.126 brouard 357: Revision 1.125 2006/04/04 15:20:31 lievre
358: Errors in calculation of health expectancies. Age was not initialized.
359: Forecasting file added.
360:
361: Revision 1.124 2006/03/22 17:13:53 lievre
362: Parameters are printed with %lf instead of %f (more numbers after the comma).
363: The log-likelihood is printed in the log file
364:
365: Revision 1.123 2006/03/20 10:52:43 brouard
366: * imach.c (Module): <title> changed, corresponds to .htm file
367: name. <head> headers where missing.
368:
369: * imach.c (Module): Weights can have a decimal point as for
370: English (a comma might work with a correct LC_NUMERIC environment,
371: otherwise the weight is truncated).
372: Modification of warning when the covariates values are not 0 or
373: 1.
374: Version 0.98g
375:
376: Revision 1.122 2006/03/20 09:45:41 brouard
377: (Module): Weights can have a decimal point as for
378: English (a comma might work with a correct LC_NUMERIC environment,
379: otherwise the weight is truncated).
380: Modification of warning when the covariates values are not 0 or
381: 1.
382: Version 0.98g
383:
384: Revision 1.121 2006/03/16 17:45:01 lievre
385: * imach.c (Module): Comments concerning covariates added
386:
387: * imach.c (Module): refinements in the computation of lli if
388: status=-2 in order to have more reliable computation if stepm is
389: not 1 month. Version 0.98f
390:
391: Revision 1.120 2006/03/16 15:10:38 lievre
392: (Module): refinements in the computation of lli if
393: status=-2 in order to have more reliable computation if stepm is
394: not 1 month. Version 0.98f
395:
396: Revision 1.119 2006/03/15 17:42:26 brouard
397: (Module): Bug if status = -2, the loglikelihood was
398: computed as likelihood omitting the logarithm. Version O.98e
399:
400: Revision 1.118 2006/03/14 18:20:07 brouard
401: (Module): varevsij Comments added explaining the second
402: table of variances if popbased=1 .
403: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
404: (Module): Function pstamp added
405: (Module): Version 0.98d
406:
407: Revision 1.117 2006/03/14 17:16:22 brouard
408: (Module): varevsij Comments added explaining the second
409: table of variances if popbased=1 .
410: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
411: (Module): Function pstamp added
412: (Module): Version 0.98d
413:
414: Revision 1.116 2006/03/06 10:29:27 brouard
415: (Module): Variance-covariance wrong links and
416: varian-covariance of ej. is needed (Saito).
417:
418: Revision 1.115 2006/02/27 12:17:45 brouard
419: (Module): One freematrix added in mlikeli! 0.98c
420:
421: Revision 1.114 2006/02/26 12:57:58 brouard
422: (Module): Some improvements in processing parameter
423: filename with strsep.
424:
425: Revision 1.113 2006/02/24 14:20:24 brouard
426: (Module): Memory leaks checks with valgrind and:
427: datafile was not closed, some imatrix were not freed and on matrix
428: allocation too.
429:
430: Revision 1.112 2006/01/30 09:55:26 brouard
431: (Module): Back to gnuplot.exe instead of wgnuplot.exe
432:
433: Revision 1.111 2006/01/25 20:38:18 brouard
434: (Module): Lots of cleaning and bugs added (Gompertz)
435: (Module): Comments can be added in data file. Missing date values
436: can be a simple dot '.'.
437:
438: Revision 1.110 2006/01/25 00:51:50 brouard
439: (Module): Lots of cleaning and bugs added (Gompertz)
440:
441: Revision 1.109 2006/01/24 19:37:15 brouard
442: (Module): Comments (lines starting with a #) are allowed in data.
443:
444: Revision 1.108 2006/01/19 18:05:42 lievre
445: Gnuplot problem appeared...
446: To be fixed
447:
448: Revision 1.107 2006/01/19 16:20:37 brouard
449: Test existence of gnuplot in imach path
450:
451: Revision 1.106 2006/01/19 13:24:36 brouard
452: Some cleaning and links added in html output
453:
454: Revision 1.105 2006/01/05 20:23:19 lievre
455: *** empty log message ***
456:
457: Revision 1.104 2005/09/30 16:11:43 lievre
458: (Module): sump fixed, loop imx fixed, and simplifications.
459: (Module): If the status is missing at the last wave but we know
460: that the person is alive, then we can code his/her status as -2
461: (instead of missing=-1 in earlier versions) and his/her
462: contributions to the likelihood is 1 - Prob of dying from last
463: health status (= 1-p13= p11+p12 in the easiest case of somebody in
464: the healthy state at last known wave). Version is 0.98
465:
466: Revision 1.103 2005/09/30 15:54:49 lievre
467: (Module): sump fixed, loop imx fixed, and simplifications.
468:
469: Revision 1.102 2004/09/15 17:31:30 brouard
470: Add the possibility to read data file including tab characters.
471:
472: Revision 1.101 2004/09/15 10:38:38 brouard
473: Fix on curr_time
474:
475: Revision 1.100 2004/07/12 18:29:06 brouard
476: Add version for Mac OS X. Just define UNIX in Makefile
477:
478: Revision 1.99 2004/06/05 08:57:40 brouard
479: *** empty log message ***
480:
481: Revision 1.98 2004/05/16 15:05:56 brouard
482: New version 0.97 . First attempt to estimate force of mortality
483: directly from the data i.e. without the need of knowing the health
484: state at each age, but using a Gompertz model: log u =a + b*age .
485: This is the basic analysis of mortality and should be done before any
486: other analysis, in order to test if the mortality estimated from the
487: cross-longitudinal survey is different from the mortality estimated
488: from other sources like vital statistic data.
489:
490: The same imach parameter file can be used but the option for mle should be -3.
491:
1.133 brouard 492: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 493: former routines in order to include the new code within the former code.
494:
495: The output is very simple: only an estimate of the intercept and of
496: the slope with 95% confident intervals.
497:
498: Current limitations:
499: A) Even if you enter covariates, i.e. with the
500: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
501: B) There is no computation of Life Expectancy nor Life Table.
502:
503: Revision 1.97 2004/02/20 13:25:42 lievre
504: Version 0.96d. Population forecasting command line is (temporarily)
505: suppressed.
506:
507: Revision 1.96 2003/07/15 15:38:55 brouard
508: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
509: rewritten within the same printf. Workaround: many printfs.
510:
511: Revision 1.95 2003/07/08 07:54:34 brouard
512: * imach.c (Repository):
513: (Repository): Using imachwizard code to output a more meaningful covariance
514: matrix (cov(a12,c31) instead of numbers.
515:
516: Revision 1.94 2003/06/27 13:00:02 brouard
517: Just cleaning
518:
519: Revision 1.93 2003/06/25 16:33:55 brouard
520: (Module): On windows (cygwin) function asctime_r doesn't
521: exist so I changed back to asctime which exists.
522: (Module): Version 0.96b
523:
524: Revision 1.92 2003/06/25 16:30:45 brouard
525: (Module): On windows (cygwin) function asctime_r doesn't
526: exist so I changed back to asctime which exists.
527:
528: Revision 1.91 2003/06/25 15:30:29 brouard
529: * imach.c (Repository): Duplicated warning errors corrected.
530: (Repository): Elapsed time after each iteration is now output. It
531: helps to forecast when convergence will be reached. Elapsed time
532: is stamped in powell. We created a new html file for the graphs
533: concerning matrix of covariance. It has extension -cov.htm.
534:
535: Revision 1.90 2003/06/24 12:34:15 brouard
536: (Module): Some bugs corrected for windows. Also, when
537: mle=-1 a template is output in file "or"mypar.txt with the design
538: of the covariance matrix to be input.
539:
540: Revision 1.89 2003/06/24 12:30:52 brouard
541: (Module): Some bugs corrected for windows. Also, when
542: mle=-1 a template is output in file "or"mypar.txt with the design
543: of the covariance matrix to be input.
544:
545: Revision 1.88 2003/06/23 17:54:56 brouard
546: * 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.
547:
548: Revision 1.87 2003/06/18 12:26:01 brouard
549: Version 0.96
550:
551: Revision 1.86 2003/06/17 20:04:08 brouard
552: (Module): Change position of html and gnuplot routines and added
553: routine fileappend.
554:
555: Revision 1.85 2003/06/17 13:12:43 brouard
556: * imach.c (Repository): Check when date of death was earlier that
557: current date of interview. It may happen when the death was just
558: prior to the death. In this case, dh was negative and likelihood
559: was wrong (infinity). We still send an "Error" but patch by
560: assuming that the date of death was just one stepm after the
561: interview.
562: (Repository): Because some people have very long ID (first column)
563: we changed int to long in num[] and we added a new lvector for
564: memory allocation. But we also truncated to 8 characters (left
565: truncation)
566: (Repository): No more line truncation errors.
567:
568: Revision 1.84 2003/06/13 21:44:43 brouard
569: * imach.c (Repository): Replace "freqsummary" at a correct
570: place. It differs from routine "prevalence" which may be called
571: many times. Probs is memory consuming and must be used with
572: parcimony.
573: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
574:
575: Revision 1.83 2003/06/10 13:39:11 lievre
576: *** empty log message ***
577:
578: Revision 1.82 2003/06/05 15:57:20 brouard
579: Add log in imach.c and fullversion number is now printed.
580:
581: */
582: /*
583: Interpolated Markov Chain
584:
585: Short summary of the programme:
586:
587: This program computes Healthy Life Expectancies from
588: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
589: first survey ("cross") where individuals from different ages are
590: interviewed on their health status or degree of disability (in the
591: case of a health survey which is our main interest) -2- at least a
592: second wave of interviews ("longitudinal") which measure each change
593: (if any) in individual health status. Health expectancies are
594: computed from the time spent in each health state according to a
595: model. More health states you consider, more time is necessary to reach the
596: Maximum Likelihood of the parameters involved in the model. The
597: simplest model is the multinomial logistic model where pij is the
598: probability to be observed in state j at the second wave
599: conditional to be observed in state i at the first wave. Therefore
600: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
601: 'age' is age and 'sex' is a covariate. If you want to have a more
602: complex model than "constant and age", you should modify the program
603: where the markup *Covariates have to be included here again* invites
604: you to do it. More covariates you add, slower the
605: convergence.
606:
607: The advantage of this computer programme, compared to a simple
608: multinomial logistic model, is clear when the delay between waves is not
609: identical for each individual. Also, if a individual missed an
610: intermediate interview, the information is lost, but taken into
611: account using an interpolation or extrapolation.
612:
613: hPijx is the probability to be observed in state i at age x+h
614: conditional to the observed state i at age x. The delay 'h' can be
615: split into an exact number (nh*stepm) of unobserved intermediate
616: states. This elementary transition (by month, quarter,
617: semester or year) is modelled as a multinomial logistic. The hPx
618: matrix is simply the matrix product of nh*stepm elementary matrices
619: and the contribution of each individual to the likelihood is simply
620: hPijx.
621:
622: Also this programme outputs the covariance matrix of the parameters but also
623: of the life expectancies. It also computes the period (stable) prevalence.
624:
1.133 brouard 625: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
626: Institut national d'études démographiques, Paris.
1.126 brouard 627: This software have been partly granted by Euro-REVES, a concerted action
628: from the European Union.
629: It is copyrighted identically to a GNU software product, ie programme and
630: software can be distributed freely for non commercial use. Latest version
631: can be accessed at http://euroreves.ined.fr/imach .
632:
633: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
634: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
635:
636: **********************************************************************/
637: /*
638: main
639: read parameterfile
640: read datafile
641: concatwav
642: freqsummary
643: if (mle >= 1)
644: mlikeli
645: print results files
646: if mle==1
647: computes hessian
648: read end of parameter file: agemin, agemax, bage, fage, estepm
649: begin-prev-date,...
650: open gnuplot file
651: open html file
1.145 brouard 652: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
653: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
654: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
655: freexexit2 possible for memory heap.
656:
657: h Pij x | pij_nom ficrestpij
658: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
659: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
660: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
661:
662: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
663: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
664: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
665: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
666: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
667:
1.126 brouard 668: forecasting if prevfcast==1 prevforecast call prevalence()
669: health expectancies
670: Variance-covariance of DFLE
671: prevalence()
672: movingaverage()
673: varevsij()
674: if popbased==1 varevsij(,popbased)
675: total life expectancies
676: Variance of period (stable) prevalence
677: end
678: */
679:
1.187 brouard 680: /* #define DEBUG */
681: /* #define DEBUGBRENT */
1.203 brouard 682: /* #define DEBUGLINMIN */
683: /* #define DEBUGHESS */
684: #define DEBUGHESSIJ
685: /* #define LINMINORIGINAL /\* Don't use loop on scale in linmin (accepting nan)*\/ */
1.165 brouard 686: #define POWELL /* Instead of NLOPT */
1.192 brouard 687: #define POWELLF1F3 /* Skip test */
1.186 brouard 688: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
689: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 690:
691: #include <math.h>
692: #include <stdio.h>
693: #include <stdlib.h>
694: #include <string.h>
1.159 brouard 695:
696: #ifdef _WIN32
697: #include <io.h>
1.172 brouard 698: #include <windows.h>
699: #include <tchar.h>
1.159 brouard 700: #else
1.126 brouard 701: #include <unistd.h>
1.159 brouard 702: #endif
1.126 brouard 703:
704: #include <limits.h>
705: #include <sys/types.h>
1.171 brouard 706:
707: #if defined(__GNUC__)
708: #include <sys/utsname.h> /* Doesn't work on Windows */
709: #endif
710:
1.126 brouard 711: #include <sys/stat.h>
712: #include <errno.h>
1.159 brouard 713: /* extern int errno; */
1.126 brouard 714:
1.157 brouard 715: /* #ifdef LINUX */
716: /* #include <time.h> */
717: /* #include "timeval.h" */
718: /* #else */
719: /* #include <sys/time.h> */
720: /* #endif */
721:
1.126 brouard 722: #include <time.h>
723:
1.136 brouard 724: #ifdef GSL
725: #include <gsl/gsl_errno.h>
726: #include <gsl/gsl_multimin.h>
727: #endif
728:
1.167 brouard 729:
1.162 brouard 730: #ifdef NLOPT
731: #include <nlopt.h>
732: typedef struct {
733: double (* function)(double [] );
734: } myfunc_data ;
735: #endif
736:
1.126 brouard 737: /* #include <libintl.h> */
738: /* #define _(String) gettext (String) */
739:
1.141 brouard 740: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 741:
742: #define GNUPLOTPROGRAM "gnuplot"
743: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
744: #define FILENAMELENGTH 132
745:
746: #define GLOCK_ERROR_NOPATH -1 /* empty path */
747: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
748:
1.144 brouard 749: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
750: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 751:
752: #define NINTERVMAX 8
1.144 brouard 753: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
754: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
755: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.197 brouard 756: #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.126 brouard 757: #define MAXN 20000
1.144 brouard 758: #define YEARM 12. /**< Number of months per year */
1.126 brouard 759: #define AGESUP 130
760: #define AGEBASE 40
1.194 brouard 761: #define AGEOVERFLOW 1.e20
1.164 brouard 762: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 763: #ifdef _WIN32
764: #define DIRSEPARATOR '\\'
765: #define CHARSEPARATOR "\\"
766: #define ODIRSEPARATOR '/'
767: #else
1.126 brouard 768: #define DIRSEPARATOR '/'
769: #define CHARSEPARATOR "/"
770: #define ODIRSEPARATOR '\\'
771: #endif
772:
1.210 ! brouard 773: /* $Id: imach.c,v 1.209 2015/11/17 22:12:03 brouard Exp $ */
1.126 brouard 774: /* $State: Exp $ */
1.196 brouard 775: #include "version.h"
776: char version[]=__IMACH_VERSION__;
1.204 brouard 777: char copyright[]="October 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
1.210 ! brouard 778: char fullversion[]="$Revision: 1.209 $ $Date: 2015/11/17 22:12:03 $";
1.126 brouard 779: char strstart[80];
780: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 781: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 782: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 783: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
784: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
785: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
786: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
787: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
788: int cptcovprodnoage=0; /**< Number of covariate products without age */
789: int cptcoveff=0; /* Total number of covariates to vary for printing results */
790: int cptcov=0; /* Working variable */
1.126 brouard 791: int npar=NPARMAX;
792: int nlstate=2; /* Number of live states */
793: int ndeath=1; /* Number of dead states */
1.130 brouard 794: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.126 brouard 795: int popbased=0;
796:
797: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 798: int maxwav=0; /* Maxim number of waves */
799: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
800: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
801: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 802: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 803: int mle=1, weightopt=0;
1.126 brouard 804: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
805: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
806: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
807: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 808: int countcallfunc=0; /* Count the number of calls to func */
1.130 brouard 809: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 810: double **matprod2(); /* test */
1.126 brouard 811: double **oldm, **newm, **savm; /* Working pointers to matrices */
812: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.136 brouard 813: /*FILE *fic ; */ /* Used in readdata only */
814: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.126 brouard 815: FILE *ficlog, *ficrespow;
1.130 brouard 816: int globpr=0; /* Global variable for printing or not */
1.126 brouard 817: double fretone; /* Only one call to likelihood */
1.130 brouard 818: long ipmx=0; /* Number of contributions */
1.126 brouard 819: double sw; /* Sum of weights */
820: char filerespow[FILENAMELENGTH];
821: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
822: FILE *ficresilk;
823: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
824: FILE *ficresprobmorprev;
825: FILE *fichtm, *fichtmcov; /* Html File */
826: FILE *ficreseij;
827: char filerese[FILENAMELENGTH];
828: FILE *ficresstdeij;
829: char fileresstde[FILENAMELENGTH];
830: FILE *ficrescveij;
831: char filerescve[FILENAMELENGTH];
832: FILE *ficresvij;
833: char fileresv[FILENAMELENGTH];
834: FILE *ficresvpl;
835: char fileresvpl[FILENAMELENGTH];
836: char title[MAXLINE];
837: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
838: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
839: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
840: char command[FILENAMELENGTH];
841: int outcmd=0;
842:
843: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.202 brouard 844: char fileresu[FILENAMELENGTH]; /* fileres without r in front */
1.126 brouard 845: char filelog[FILENAMELENGTH]; /* Log file */
846: char filerest[FILENAMELENGTH];
847: char fileregp[FILENAMELENGTH];
848: char popfile[FILENAMELENGTH];
849:
850: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
851:
1.157 brouard 852: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
853: /* struct timezone tzp; */
854: /* extern int gettimeofday(); */
855: struct tm tml, *gmtime(), *localtime();
856:
857: extern time_t time();
858:
859: struct tm start_time, end_time, curr_time, last_time, forecast_time;
860: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
861: struct tm tm;
862:
1.126 brouard 863: char strcurr[80], strfor[80];
864:
865: char *endptr;
866: long lval;
867: double dval;
868:
869: #define NR_END 1
870: #define FREE_ARG char*
871: #define FTOL 1.0e-10
872:
873: #define NRANSI
874: #define ITMAX 200
875:
876: #define TOL 2.0e-4
877:
878: #define CGOLD 0.3819660
879: #define ZEPS 1.0e-10
880: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
881:
882: #define GOLD 1.618034
883: #define GLIMIT 100.0
884: #define TINY 1.0e-20
885:
886: static double maxarg1,maxarg2;
887: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
888: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
889:
890: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
891: #define rint(a) floor(a+0.5)
1.166 brouard 892: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 893: #define mytinydouble 1.0e-16
1.166 brouard 894: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
895: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
896: /* static double dsqrarg; */
897: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 898: static double sqrarg;
899: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
900: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
901: int agegomp= AGEGOMP;
902:
903: int imx;
904: int stepm=1;
905: /* Stepm, step in month: minimum step interpolation*/
906:
907: int estepm;
908: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
909:
910: int m,nb;
911: long *num;
1.197 brouard 912: int firstpass=0, lastpass=4,*cod, *cens;
1.192 brouard 913: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
914: covariate for which somebody answered excluding
915: undefined. Usually 2: 0 and 1. */
916: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
917: covariate for which somebody answered including
918: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 919: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
920: double **pmmij, ***probs;
921: double *ageexmed,*agecens;
922: double dateintmean=0;
923:
924: double *weight;
925: int **s; /* Status */
1.141 brouard 926: double *agedc;
1.145 brouard 927: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 928: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 929: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.141 brouard 930: double idx;
931: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.197 brouard 932: int *Tage;
1.145 brouard 933: int *Ndum; /** Freq of modality (tricode */
1.200 brouard 934: /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
1.141 brouard 935: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.126 brouard 936: double *lsurv, *lpop, *tpop;
937:
1.143 brouard 938: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
939: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 940:
941: /**************** split *************************/
942: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
943: {
944: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
945: the name of the file (name), its extension only (ext) and its first part of the name (finame)
946: */
947: char *ss; /* pointer */
1.186 brouard 948: int l1=0, l2=0; /* length counters */
1.126 brouard 949:
950: l1 = strlen(path ); /* length of path */
951: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
952: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
953: if ( ss == NULL ) { /* no directory, so determine current directory */
954: strcpy( name, path ); /* we got the fullname name because no directory */
955: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
956: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
957: /* get current working directory */
958: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 959: #ifdef WIN32
960: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
961: #else
962: if (getcwd(dirc, FILENAME_MAX) == NULL) {
963: #endif
1.126 brouard 964: return( GLOCK_ERROR_GETCWD );
965: }
966: /* got dirc from getcwd*/
967: printf(" DIRC = %s \n",dirc);
1.205 brouard 968: } else { /* strip directory from path */
1.126 brouard 969: ss++; /* after this, the filename */
970: l2 = strlen( ss ); /* length of filename */
971: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
972: strcpy( name, ss ); /* save file name */
973: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 974: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 975: printf(" DIRC2 = %s \n",dirc);
976: }
977: /* We add a separator at the end of dirc if not exists */
978: l1 = strlen( dirc ); /* length of directory */
979: if( dirc[l1-1] != DIRSEPARATOR ){
980: dirc[l1] = DIRSEPARATOR;
981: dirc[l1+1] = 0;
982: printf(" DIRC3 = %s \n",dirc);
983: }
984: ss = strrchr( name, '.' ); /* find last / */
985: if (ss >0){
986: ss++;
987: strcpy(ext,ss); /* save extension */
988: l1= strlen( name);
989: l2= strlen(ss)+1;
990: strncpy( finame, name, l1-l2);
991: finame[l1-l2]= 0;
992: }
993:
994: return( 0 ); /* we're done */
995: }
996:
997:
998: /******************************************/
999:
1000: void replace_back_to_slash(char *s, char*t)
1001: {
1002: int i;
1003: int lg=0;
1004: i=0;
1005: lg=strlen(t);
1006: for(i=0; i<= lg; i++) {
1007: (s[i] = t[i]);
1008: if (t[i]== '\\') s[i]='/';
1009: }
1010: }
1011:
1.132 brouard 1012: char *trimbb(char *out, char *in)
1.137 brouard 1013: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 1014: char *s;
1015: s=out;
1016: while (*in != '\0'){
1.137 brouard 1017: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 1018: in++;
1019: }
1020: *out++ = *in++;
1021: }
1022: *out='\0';
1023: return s;
1024: }
1025:
1.187 brouard 1026: /* char *substrchaine(char *out, char *in, char *chain) */
1027: /* { */
1028: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
1029: /* char *s, *t; */
1030: /* t=in;s=out; */
1031: /* while ((*in != *chain) && (*in != '\0')){ */
1032: /* *out++ = *in++; */
1033: /* } */
1034:
1035: /* /\* *in matches *chain *\/ */
1036: /* while ((*in++ == *chain++) && (*in != '\0')){ */
1037: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1038: /* } */
1039: /* in--; chain--; */
1040: /* while ( (*in != '\0')){ */
1041: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1042: /* *out++ = *in++; */
1043: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1044: /* } */
1045: /* *out='\0'; */
1046: /* out=s; */
1047: /* return out; */
1048: /* } */
1049: char *substrchaine(char *out, char *in, char *chain)
1050: {
1051: /* Substract chain 'chain' from 'in', return and output 'out' */
1052: /* in="V1+V1*age+age*age+V2", chain="age*age" */
1053:
1054: char *strloc;
1055:
1056: strcpy (out, in);
1057: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
1058: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
1059: if(strloc != NULL){
1060: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
1061: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
1062: /* strcpy (strloc, strloc +strlen(chain));*/
1063: }
1064: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
1065: return out;
1066: }
1067:
1068:
1.145 brouard 1069: char *cutl(char *blocc, char *alocc, char *in, char occ)
1070: {
1.187 brouard 1071: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 1072: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 1073: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 1074: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1075: */
1.160 brouard 1076: char *s, *t;
1.145 brouard 1077: t=in;s=in;
1078: while ((*in != occ) && (*in != '\0')){
1079: *alocc++ = *in++;
1080: }
1081: if( *in == occ){
1082: *(alocc)='\0';
1083: s=++in;
1084: }
1085:
1086: if (s == t) {/* occ not found */
1087: *(alocc-(in-s))='\0';
1088: in=s;
1089: }
1090: while ( *in != '\0'){
1091: *blocc++ = *in++;
1092: }
1093:
1094: *blocc='\0';
1095: return t;
1096: }
1.137 brouard 1097: char *cutv(char *blocc, char *alocc, char *in, char occ)
1098: {
1.187 brouard 1099: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1100: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1101: gives blocc="abcdef2ghi" and alocc="j".
1102: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1103: */
1104: char *s, *t;
1105: t=in;s=in;
1106: while (*in != '\0'){
1107: while( *in == occ){
1108: *blocc++ = *in++;
1109: s=in;
1110: }
1111: *blocc++ = *in++;
1112: }
1113: if (s == t) /* occ not found */
1114: *(blocc-(in-s))='\0';
1115: else
1116: *(blocc-(in-s)-1)='\0';
1117: in=s;
1118: while ( *in != '\0'){
1119: *alocc++ = *in++;
1120: }
1121:
1122: *alocc='\0';
1123: return s;
1124: }
1125:
1.126 brouard 1126: int nbocc(char *s, char occ)
1127: {
1128: int i,j=0;
1129: int lg=20;
1130: i=0;
1131: lg=strlen(s);
1132: for(i=0; i<= lg; i++) {
1133: if (s[i] == occ ) j++;
1134: }
1135: return j;
1136: }
1137:
1.137 brouard 1138: /* void cutv(char *u,char *v, char*t, char occ) */
1139: /* { */
1140: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1141: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1142: /* gives u="abcdef2ghi" and v="j" *\/ */
1143: /* int i,lg,j,p=0; */
1144: /* i=0; */
1145: /* lg=strlen(t); */
1146: /* for(j=0; j<=lg-1; j++) { */
1147: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1148: /* } */
1.126 brouard 1149:
1.137 brouard 1150: /* for(j=0; j<p; j++) { */
1151: /* (u[j] = t[j]); */
1152: /* } */
1153: /* u[p]='\0'; */
1.126 brouard 1154:
1.137 brouard 1155: /* for(j=0; j<= lg; j++) { */
1156: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1157: /* } */
1158: /* } */
1.126 brouard 1159:
1.160 brouard 1160: #ifdef _WIN32
1161: char * strsep(char **pp, const char *delim)
1162: {
1163: char *p, *q;
1164:
1165: if ((p = *pp) == NULL)
1166: return 0;
1167: if ((q = strpbrk (p, delim)) != NULL)
1168: {
1169: *pp = q + 1;
1170: *q = '\0';
1171: }
1172: else
1173: *pp = 0;
1174: return p;
1175: }
1176: #endif
1177:
1.126 brouard 1178: /********************** nrerror ********************/
1179:
1180: void nrerror(char error_text[])
1181: {
1182: fprintf(stderr,"ERREUR ...\n");
1183: fprintf(stderr,"%s\n",error_text);
1184: exit(EXIT_FAILURE);
1185: }
1186: /*********************** vector *******************/
1187: double *vector(int nl, int nh)
1188: {
1189: double *v;
1190: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1191: if (!v) nrerror("allocation failure in vector");
1192: return v-nl+NR_END;
1193: }
1194:
1195: /************************ free vector ******************/
1196: void free_vector(double*v, int nl, int nh)
1197: {
1198: free((FREE_ARG)(v+nl-NR_END));
1199: }
1200:
1201: /************************ivector *******************************/
1202: int *ivector(long nl,long nh)
1203: {
1204: int *v;
1205: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1206: if (!v) nrerror("allocation failure in ivector");
1207: return v-nl+NR_END;
1208: }
1209:
1210: /******************free ivector **************************/
1211: void free_ivector(int *v, long nl, long nh)
1212: {
1213: free((FREE_ARG)(v+nl-NR_END));
1214: }
1215:
1216: /************************lvector *******************************/
1217: long *lvector(long nl,long nh)
1218: {
1219: long *v;
1220: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1221: if (!v) nrerror("allocation failure in ivector");
1222: return v-nl+NR_END;
1223: }
1224:
1225: /******************free lvector **************************/
1226: void free_lvector(long *v, long nl, long nh)
1227: {
1228: free((FREE_ARG)(v+nl-NR_END));
1229: }
1230:
1231: /******************* imatrix *******************************/
1232: int **imatrix(long nrl, long nrh, long ncl, long nch)
1233: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1234: {
1235: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1236: int **m;
1237:
1238: /* allocate pointers to rows */
1239: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1240: if (!m) nrerror("allocation failure 1 in matrix()");
1241: m += NR_END;
1242: m -= nrl;
1243:
1244:
1245: /* allocate rows and set pointers to them */
1246: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
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:
1253: /* return pointer to array of pointers to rows */
1254: return m;
1255: }
1256:
1257: /****************** free_imatrix *************************/
1258: void free_imatrix(m,nrl,nrh,ncl,nch)
1259: int **m;
1260: long nch,ncl,nrh,nrl;
1261: /* free an int matrix allocated by imatrix() */
1262: {
1263: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1264: free((FREE_ARG) (m+nrl-NR_END));
1265: }
1266:
1267: /******************* matrix *******************************/
1268: double **matrix(long nrl, long nrh, long ncl, long nch)
1269: {
1270: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1271: double **m;
1272:
1273: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1274: if (!m) nrerror("allocation failure 1 in matrix()");
1275: m += NR_END;
1276: m -= nrl;
1277:
1278: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1279: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1280: m[nrl] += NR_END;
1281: m[nrl] -= ncl;
1282:
1283: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1284: return m;
1.145 brouard 1285: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1286: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1287: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1288: */
1289: }
1290:
1291: /*************************free matrix ************************/
1292: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1293: {
1294: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1295: free((FREE_ARG)(m+nrl-NR_END));
1296: }
1297:
1298: /******************* ma3x *******************************/
1299: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1300: {
1301: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1302: double ***m;
1303:
1304: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1305: if (!m) nrerror("allocation failure 1 in matrix()");
1306: m += NR_END;
1307: m -= nrl;
1308:
1309: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1310: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1311: m[nrl] += NR_END;
1312: m[nrl] -= ncl;
1313:
1314: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1315:
1316: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1317: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1318: m[nrl][ncl] += NR_END;
1319: m[nrl][ncl] -= nll;
1320: for (j=ncl+1; j<=nch; j++)
1321: m[nrl][j]=m[nrl][j-1]+nlay;
1322:
1323: for (i=nrl+1; i<=nrh; i++) {
1324: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1325: for (j=ncl+1; j<=nch; j++)
1326: m[i][j]=m[i][j-1]+nlay;
1327: }
1328: return m;
1329: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1330: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1331: */
1332: }
1333:
1334: /*************************free ma3x ************************/
1335: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1336: {
1337: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1338: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1339: free((FREE_ARG)(m+nrl-NR_END));
1340: }
1341:
1342: /*************** function subdirf ***********/
1343: char *subdirf(char fileres[])
1344: {
1345: /* Caution optionfilefiname is hidden */
1346: strcpy(tmpout,optionfilefiname);
1347: strcat(tmpout,"/"); /* Add to the right */
1348: strcat(tmpout,fileres);
1349: return tmpout;
1350: }
1351:
1352: /*************** function subdirf2 ***********/
1353: char *subdirf2(char fileres[], char *preop)
1354: {
1355:
1356: /* Caution optionfilefiname is hidden */
1357: strcpy(tmpout,optionfilefiname);
1358: strcat(tmpout,"/");
1359: strcat(tmpout,preop);
1360: strcat(tmpout,fileres);
1361: return tmpout;
1362: }
1363:
1364: /*************** function subdirf3 ***********/
1365: char *subdirf3(char fileres[], char *preop, char *preop2)
1366: {
1367:
1368: /* Caution optionfilefiname is hidden */
1369: strcpy(tmpout,optionfilefiname);
1370: strcat(tmpout,"/");
1371: strcat(tmpout,preop);
1372: strcat(tmpout,preop2);
1373: strcat(tmpout,fileres);
1374: return tmpout;
1375: }
1376:
1.162 brouard 1377: char *asc_diff_time(long time_sec, char ascdiff[])
1378: {
1379: long sec_left, days, hours, minutes;
1380: days = (time_sec) / (60*60*24);
1381: sec_left = (time_sec) % (60*60*24);
1382: hours = (sec_left) / (60*60) ;
1383: sec_left = (sec_left) %(60*60);
1384: minutes = (sec_left) /60;
1385: sec_left = (sec_left) % (60);
1386: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1387: return ascdiff;
1388: }
1389:
1.126 brouard 1390: /***************** f1dim *************************/
1391: extern int ncom;
1392: extern double *pcom,*xicom;
1393: extern double (*nrfunc)(double []);
1394:
1395: double f1dim(double x)
1396: {
1397: int j;
1398: double f;
1399: double *xt;
1400:
1401: xt=vector(1,ncom);
1402: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1403: f=(*nrfunc)(xt);
1404: free_vector(xt,1,ncom);
1405: return f;
1406: }
1407:
1408: /*****************brent *************************/
1409: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1410: {
1411: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1412: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1413: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1414: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1415: * returned function value.
1416: */
1.126 brouard 1417: int iter;
1418: double a,b,d,etemp;
1.159 brouard 1419: double fu=0,fv,fw,fx;
1.164 brouard 1420: double ftemp=0.;
1.126 brouard 1421: double p,q,r,tol1,tol2,u,v,w,x,xm;
1422: double e=0.0;
1423:
1424: a=(ax < cx ? ax : cx);
1425: b=(ax > cx ? ax : cx);
1426: x=w=v=bx;
1427: fw=fv=fx=(*f)(x);
1428: for (iter=1;iter<=ITMAX;iter++) {
1429: xm=0.5*(a+b);
1430: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1431: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1432: printf(".");fflush(stdout);
1433: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1434: #ifdef DEBUGBRENT
1.126 brouard 1435: 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);
1436: 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);
1437: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1438: #endif
1439: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1440: *xmin=x;
1441: return fx;
1442: }
1443: ftemp=fu;
1444: if (fabs(e) > tol1) {
1445: r=(x-w)*(fx-fv);
1446: q=(x-v)*(fx-fw);
1447: p=(x-v)*q-(x-w)*r;
1448: q=2.0*(q-r);
1449: if (q > 0.0) p = -p;
1450: q=fabs(q);
1451: etemp=e;
1452: e=d;
1453: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1454: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1455: else {
1456: d=p/q;
1457: u=x+d;
1458: if (u-a < tol2 || b-u < tol2)
1459: d=SIGN(tol1,xm-x);
1460: }
1461: } else {
1462: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1463: }
1464: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1465: fu=(*f)(u);
1466: if (fu <= fx) {
1467: if (u >= x) a=x; else b=x;
1468: SHFT(v,w,x,u)
1.183 brouard 1469: SHFT(fv,fw,fx,fu)
1470: } else {
1471: if (u < x) a=u; else b=u;
1472: if (fu <= fw || w == x) {
1473: v=w;
1474: w=u;
1475: fv=fw;
1476: fw=fu;
1477: } else if (fu <= fv || v == x || v == w) {
1478: v=u;
1479: fv=fu;
1480: }
1481: }
1.126 brouard 1482: }
1483: nrerror("Too many iterations in brent");
1484: *xmin=x;
1485: return fx;
1486: }
1487:
1488: /****************** mnbrak ***********************/
1489:
1490: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1491: double (*func)(double))
1.183 brouard 1492: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1493: the downhill direction (defined by the function as evaluated at the initial points) and returns
1494: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1495: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1496: */
1.126 brouard 1497: double ulim,u,r,q, dum;
1498: double fu;
1.187 brouard 1499:
1500: double scale=10.;
1501: int iterscale=0;
1502:
1503: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1504: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1505:
1506:
1507: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1508: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1509: /* *bx = *ax - (*ax - *bx)/scale; */
1510: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1511: /* } */
1512:
1.126 brouard 1513: if (*fb > *fa) {
1514: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1515: SHFT(dum,*fb,*fa,dum)
1516: }
1.126 brouard 1517: *cx=(*bx)+GOLD*(*bx-*ax);
1518: *fc=(*func)(*cx);
1.183 brouard 1519: #ifdef DEBUG
1520: printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1521: fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1522: #endif
1523: while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
1.126 brouard 1524: r=(*bx-*ax)*(*fb-*fc);
1525: q=(*bx-*cx)*(*fb-*fa);
1526: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 1527: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1528: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1529: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 1530: fu=(*func)(u);
1.163 brouard 1531: #ifdef DEBUG
1532: /* f(x)=A(x-u)**2+f(u) */
1533: double A, fparabu;
1534: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1535: fparabu= *fa - A*(*ax-u)*(*ax-u);
1536: 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);
1537: 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 1538: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1539: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1540: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1541: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 1542: #endif
1.184 brouard 1543: #ifdef MNBRAKORIGINAL
1.183 brouard 1544: #else
1.191 brouard 1545: /* if (fu > *fc) { */
1546: /* #ifdef DEBUG */
1547: /* printf("mnbrak4 fu > fc \n"); */
1548: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
1549: /* #endif */
1550: /* /\* 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 *\\/ *\/ */
1551: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
1552: /* dum=u; /\* Shifting c and u *\/ */
1553: /* u = *cx; */
1554: /* *cx = dum; */
1555: /* dum = fu; */
1556: /* fu = *fc; */
1557: /* *fc =dum; */
1558: /* } else { /\* end *\/ */
1559: /* #ifdef DEBUG */
1560: /* printf("mnbrak3 fu < fc \n"); */
1561: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
1562: /* #endif */
1563: /* dum=u; /\* Shifting c and u *\/ */
1564: /* u = *cx; */
1565: /* *cx = dum; */
1566: /* dum = fu; */
1567: /* fu = *fc; */
1568: /* *fc =dum; */
1569: /* } */
1.183 brouard 1570: #ifdef DEBUG
1.191 brouard 1571: printf("mnbrak34 fu < or >= fc \n");
1572: fprintf(ficlog, "mnbrak34 fu < fc\n");
1.183 brouard 1573: #endif
1.191 brouard 1574: dum=u; /* Shifting c and u */
1575: u = *cx;
1576: *cx = dum;
1577: dum = fu;
1578: fu = *fc;
1579: *fc =dum;
1.183 brouard 1580: #endif
1.162 brouard 1581: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 1582: #ifdef DEBUG
1583: printf("mnbrak2 u after c but before ulim\n");
1584: fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
1585: #endif
1.126 brouard 1586: fu=(*func)(u);
1587: if (fu < *fc) {
1.183 brouard 1588: #ifdef DEBUG
1589: printf("mnbrak2 u after c but before ulim AND fu < fc\n");
1590: fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
1591: #endif
1.126 brouard 1592: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1.183 brouard 1593: SHFT(*fb,*fc,fu,(*func)(u))
1594: }
1.162 brouard 1595: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 1596: #ifdef DEBUG
1597: printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1598: fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1599: #endif
1.126 brouard 1600: u=ulim;
1601: fu=(*func)(u);
1.183 brouard 1602: } else { /* u could be left to b (if r > q parabola has a maximum) */
1603: #ifdef DEBUG
1604: printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1605: fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1606: #endif
1.126 brouard 1607: u=(*cx)+GOLD*(*cx-*bx);
1608: fu=(*func)(u);
1.183 brouard 1609: } /* end tests */
1.126 brouard 1610: SHFT(*ax,*bx,*cx,u)
1.183 brouard 1611: SHFT(*fa,*fb,*fc,fu)
1612: #ifdef DEBUG
1613: 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);
1614: 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);
1615: #endif
1616: } /* 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 1617: }
1618:
1619: /*************** linmin ************************/
1.162 brouard 1620: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1621: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1622: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1623: the value of func at the returned location p . This is actually all accomplished by calling the
1624: routines mnbrak and brent .*/
1.126 brouard 1625: int ncom;
1626: double *pcom,*xicom;
1627: double (*nrfunc)(double []);
1628:
1629: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1630: {
1631: double brent(double ax, double bx, double cx,
1632: double (*f)(double), double tol, double *xmin);
1633: double f1dim(double x);
1634: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1635: double *fc, double (*func)(double));
1636: int j;
1637: double xx,xmin,bx,ax;
1638: double fx,fb,fa;
1.187 brouard 1639:
1.203 brouard 1640: #ifdef LINMINORIGINAL
1641: #else
1642: double scale=10., axs, xxs; /* Scale added for infinity */
1643: #endif
1644:
1.126 brouard 1645: ncom=n;
1646: pcom=vector(1,n);
1647: xicom=vector(1,n);
1648: nrfunc=func;
1649: for (j=1;j<=n;j++) {
1650: pcom[j]=p[j];
1.202 brouard 1651: xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
1.126 brouard 1652: }
1.187 brouard 1653:
1.203 brouard 1654: #ifdef LINMINORIGINAL
1655: xx=1.;
1656: #else
1657: axs=0.0;
1658: xxs=1.;
1659: do{
1660: xx= xxs;
1661: #endif
1.187 brouard 1662: ax=0.;
1663: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
1664: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
1665: /* 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)) */
1666: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
1667: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
1668: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
1669: /* 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 1670: #ifdef LINMINORIGINAL
1671: #else
1672: if (fx != fx){
1673: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
1674: printf("|");
1675: fprintf(ficlog,"|");
1676: #ifdef DEBUGLINMIN
1677: 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);
1678: #endif
1679: }
1680: }while(fx != fx);
1681: #endif
1682:
1.191 brouard 1683: #ifdef DEBUGLINMIN
1684: 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 1685: 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 1686: #endif
1.187 brouard 1687: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
1688: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
1689: /* fmin = f(p[j] + xmin * xi[j]) */
1690: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
1691: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 1692: #ifdef DEBUG
1693: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1694: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1695: #endif
1.191 brouard 1696: #ifdef DEBUGLINMIN
1697: printf("linmin end ");
1.202 brouard 1698: fprintf(ficlog,"linmin end ");
1.191 brouard 1699: #endif
1.126 brouard 1700: for (j=1;j<=n;j++) {
1.203 brouard 1701: #ifdef LINMINORIGINAL
1702: xi[j] *= xmin;
1703: #else
1704: #ifdef DEBUGLINMIN
1705: if(xxs <1.0)
1706: printf(" before xi[%d]=%12.8f", j,xi[j]);
1707: #endif
1708: 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) */
1709: #ifdef DEBUGLINMIN
1710: if(xxs <1.0)
1711: 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 );
1712: #endif
1713: #endif
1.187 brouard 1714: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 1715: }
1.191 brouard 1716: #ifdef DEBUGLINMIN
1.203 brouard 1717: printf("\n");
1.191 brouard 1718: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.202 brouard 1719: 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 1720: for (j=1;j<=n;j++) {
1.202 brouard 1721: printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1722: fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1723: if(j % ncovmodel == 0){
1.191 brouard 1724: printf("\n");
1.202 brouard 1725: fprintf(ficlog,"\n");
1726: }
1.191 brouard 1727: }
1.203 brouard 1728: #else
1.191 brouard 1729: #endif
1.126 brouard 1730: free_vector(xicom,1,n);
1731: free_vector(pcom,1,n);
1732: }
1733:
1734:
1735: /*************** powell ************************/
1.162 brouard 1736: /*
1737: Minimization of a function func of n variables. Input consists of an initial starting point
1738: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1739: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1740: such that failure to decrease by more than this amount on one iteration signals doneness. On
1741: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1742: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1743: */
1.126 brouard 1744: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1745: double (*func)(double []))
1746: {
1747: void linmin(double p[], double xi[], int n, double *fret,
1748: double (*func)(double []));
1749: int i,ibig,j;
1750: double del,t,*pt,*ptt,*xit;
1.181 brouard 1751: double directest;
1.126 brouard 1752: double fp,fptt;
1753: double *xits;
1754: int niterf, itmp;
1755:
1756: pt=vector(1,n);
1757: ptt=vector(1,n);
1758: xit=vector(1,n);
1759: xits=vector(1,n);
1760: *fret=(*func)(p);
1761: for (j=1;j<=n;j++) pt[j]=p[j];
1.202 brouard 1762: rcurr_time = time(NULL);
1.126 brouard 1763: for (*iter=1;;++(*iter)) {
1.187 brouard 1764: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 1765: ibig=0;
1766: del=0.0;
1.157 brouard 1767: rlast_time=rcurr_time;
1768: /* (void) gettimeofday(&curr_time,&tzp); */
1769: rcurr_time = time(NULL);
1770: curr_time = *localtime(&rcurr_time);
1771: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1772: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1773: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 1774: for (i=1;i<=n;i++) {
1.126 brouard 1775: printf(" %d %.12f",i, p[i]);
1776: fprintf(ficlog," %d %.12lf",i, p[i]);
1777: fprintf(ficrespow," %.12lf", p[i]);
1778: }
1779: printf("\n");
1780: fprintf(ficlog,"\n");
1781: fprintf(ficrespow,"\n");fflush(ficrespow);
1782: if(*iter <=3){
1.157 brouard 1783: tml = *localtime(&rcurr_time);
1784: strcpy(strcurr,asctime(&tml));
1785: rforecast_time=rcurr_time;
1.126 brouard 1786: itmp = strlen(strcurr);
1787: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1788: strcurr[itmp-1]='\0';
1.162 brouard 1789: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 1790: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 1791: for(niterf=10;niterf<=30;niterf+=10){
1.157 brouard 1792: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1793: forecast_time = *localtime(&rforecast_time);
1794: strcpy(strfor,asctime(&forecast_time));
1.126 brouard 1795: itmp = strlen(strfor);
1796: if(strfor[itmp-1]=='\n')
1797: strfor[itmp-1]='\0';
1.157 brouard 1798: 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);
1799: 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 1800: }
1801: }
1.187 brouard 1802: for (i=1;i<=n;i++) { /* For each direction i */
1803: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 1804: fptt=(*fret);
1805: #ifdef DEBUG
1.203 brouard 1806: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1807: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 1808: #endif
1.203 brouard 1809: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 1810: fprintf(ficlog,"%d",i);fflush(ficlog);
1.188 brouard 1811: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1812: /* Outputs are fret(new point p) p is updated and xit rescaled */
1813: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1814: /* because that direction will be replaced unless the gain del is small */
1815: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
1816: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
1817: /* with the new direction. */
1.126 brouard 1818: del=fabs(fptt-(*fret));
1819: ibig=i;
1820: }
1821: #ifdef DEBUG
1822: printf("%d %.12e",i,(*fret));
1823: fprintf(ficlog,"%d %.12e",i,(*fret));
1824: for (j=1;j<=n;j++) {
1825: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1826: printf(" x(%d)=%.12e",j,xit[j]);
1827: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1828: }
1829: for(j=1;j<=n;j++) {
1.162 brouard 1830: printf(" p(%d)=%.12e",j,p[j]);
1831: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 1832: }
1833: printf("\n");
1834: fprintf(ficlog,"\n");
1835: #endif
1.187 brouard 1836: } /* end loop on each direction i */
1837: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 1838: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 1839: /* New value of last point Pn is not computed, P(n-1) */
1.182 brouard 1840: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1.188 brouard 1841: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
1842: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
1843: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
1844: /* decreased of more than 3.84 */
1845: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
1846: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
1847: /* By adding 10 parameters more the gain should be 18.31 */
1848:
1849: /* Starting the program with initial values given by a former maximization will simply change */
1850: /* the scales of the directions and the directions, because the are reset to canonical directions */
1851: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
1852: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 1853: #ifdef DEBUG
1854: int k[2],l;
1855: k[0]=1;
1856: k[1]=-1;
1857: printf("Max: %.12e",(*func)(p));
1858: fprintf(ficlog,"Max: %.12e",(*func)(p));
1859: for (j=1;j<=n;j++) {
1860: printf(" %.12e",p[j]);
1861: fprintf(ficlog," %.12e",p[j]);
1862: }
1863: printf("\n");
1864: fprintf(ficlog,"\n");
1865: for(l=0;l<=1;l++) {
1866: for (j=1;j<=n;j++) {
1867: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1868: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1869: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1870: }
1871: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1872: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1873: }
1874: #endif
1875:
1876:
1877: free_vector(xit,1,n);
1878: free_vector(xits,1,n);
1879: free_vector(ptt,1,n);
1880: free_vector(pt,1,n);
1881: return;
1.192 brouard 1882: } /* enough precision */
1.126 brouard 1883: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1.181 brouard 1884: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 1885: ptt[j]=2.0*p[j]-pt[j];
1886: xit[j]=p[j]-pt[j];
1887: pt[j]=p[j];
1888: }
1.181 brouard 1889: fptt=(*func)(ptt); /* f_3 */
1.192 brouard 1890: #ifdef POWELLF1F3
1891: #else
1.161 brouard 1892: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 1893: #endif
1.162 brouard 1894: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 1895: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 1896: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1897: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1898: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.181 brouard 1899: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
1.161 brouard 1900: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.183 brouard 1901: #ifdef NRCORIGINAL
1902: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
1903: #else
1904: 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 1905: t= t- del*SQR(fp-fptt);
1.183 brouard 1906: #endif
1.202 brouard 1907: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
1.161 brouard 1908: #ifdef DEBUG
1.181 brouard 1909: 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);
1910: 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 1911: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1912: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1913: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1914: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1915: 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);
1916: 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);
1917: #endif
1.183 brouard 1918: #ifdef POWELLORIGINAL
1919: if (t < 0.0) { /* Then we use it for new direction */
1920: #else
1.182 brouard 1921: if (directest*t < 0.0) { /* Contradiction between both tests */
1.202 brouard 1922: 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 1923: 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 1924: 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 1925: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1926: }
1.181 brouard 1927: if (directest < 0.0) { /* Then we use it for new direction */
1928: #endif
1.191 brouard 1929: #ifdef DEBUGLINMIN
1930: printf("Before linmin in direction P%d-P0\n",n);
1931: for (j=1;j<=n;j++) {
1.202 brouard 1932: printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1933: fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1934: if(j % ncovmodel == 0){
1.191 brouard 1935: printf("\n");
1.202 brouard 1936: fprintf(ficlog,"\n");
1937: }
1.191 brouard 1938: }
1939: #endif
1.187 brouard 1940: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.191 brouard 1941: #ifdef DEBUGLINMIN
1942: for (j=1;j<=n;j++) {
1943: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1.202 brouard 1944: fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1945: if(j % ncovmodel == 0){
1.191 brouard 1946: printf("\n");
1.202 brouard 1947: fprintf(ficlog,"\n");
1948: }
1.191 brouard 1949: }
1950: #endif
1.126 brouard 1951: for (j=1;j<=n;j++) {
1.181 brouard 1952: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
1953: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
1.126 brouard 1954: }
1.181 brouard 1955: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1956: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1.161 brouard 1957:
1.126 brouard 1958: #ifdef DEBUG
1.164 brouard 1959: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1960: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1.126 brouard 1961: for(j=1;j<=n;j++){
1962: printf(" %.12e",xit[j]);
1963: fprintf(ficlog," %.12e",xit[j]);
1964: }
1965: printf("\n");
1966: fprintf(ficlog,"\n");
1967: #endif
1.192 brouard 1968: } /* end of t or directest negative */
1969: #ifdef POWELLF1F3
1970: #else
1.162 brouard 1971: } /* end if (fptt < fp) */
1.192 brouard 1972: #endif
1973: } /* loop iteration */
1.126 brouard 1974: }
1975:
1976: /**** Prevalence limit (stable or period prevalence) ****************/
1977:
1.203 brouard 1978: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij)
1.126 brouard 1979: {
1980: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1.203 brouard 1981: matrix by transitions matrix until convergence is reached with precision ftolpl */
1.206 brouard 1982: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
1983: /* Wx is row vector: population in state 1, population in state 2, population dead */
1984: /* or prevalence in state 1, prevalence in state 2, 0 */
1985: /* newm is the matrix after multiplications, its rows are identical at a factor */
1986: /* Initial matrix pimij */
1987: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
1988: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
1989: /* 0, 0 , 1} */
1990: /*
1991: * and after some iteration: */
1992: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
1993: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
1994: /* 0, 0 , 1} */
1995: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
1996: /* {0.51571254859325999, 0.4842874514067399, */
1997: /* 0.51326036147820708, 0.48673963852179264} */
1998: /* If we start from prlim again, prlim tends to a constant matrix */
1999:
1.126 brouard 2000: int i, ii,j,k;
1.209 brouard 2001: double *min, *max, *meandiff, maxmax,sumnew=0.;
1.145 brouard 2002: /* double **matprod2(); */ /* test */
1.131 brouard 2003: double **out, cov[NCOVMAX+1], **pmij();
1.126 brouard 2004: double **newm;
1.209 brouard 2005: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
1.203 brouard 2006: int ncvloop=0;
1.169 brouard 2007:
1.209 brouard 2008: min=vector(1,nlstate);
2009: max=vector(1,nlstate);
2010: meandiff=vector(1,nlstate);
2011:
1.126 brouard 2012: for (ii=1;ii<=nlstate+ndeath;ii++)
2013: for (j=1;j<=nlstate+ndeath;j++){
2014: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2015: }
1.169 brouard 2016:
2017: cov[1]=1.;
2018:
2019: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.202 brouard 2020: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.126 brouard 2021: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1.202 brouard 2022: ncvloop++;
1.126 brouard 2023: newm=savm;
2024: /* Covariates have to be included here again */
1.138 brouard 2025: cov[2]=agefin;
1.187 brouard 2026: if(nagesqr==1)
2027: cov[3]= agefin*agefin;;
1.138 brouard 2028: for (k=1; k<=cptcovn;k++) {
1.200 brouard 2029: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
2030: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
1.198 brouard 2031: /* 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 2032: }
1.186 brouard 2033: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 2034: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
2035: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
1.186 brouard 2036: for (k=1; k<=cptcovprod;k++) /* Useless */
1.200 brouard 2037: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
2038: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
1.138 brouard 2039:
2040: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2041: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2042: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 2043: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2044: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.142 brouard 2045: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 2046:
1.126 brouard 2047: savm=oldm;
2048: oldm=newm;
1.209 brouard 2049:
2050: for(j=1; j<=nlstate; j++){
2051: max[j]=0.;
2052: min[j]=1.;
2053: }
2054: for(i=1;i<=nlstate;i++){
2055: sumnew=0;
2056: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
2057: for(j=1; j<=nlstate; j++){
2058: prlim[i][j]= newm[i][j]/(1-sumnew);
2059: max[j]=FMAX(max[j],prlim[i][j]);
2060: min[j]=FMIN(min[j],prlim[i][j]);
2061: }
2062: }
2063:
1.126 brouard 2064: maxmax=0.;
1.209 brouard 2065: for(j=1; j<=nlstate; j++){
2066: meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
2067: maxmax=FMAX(maxmax,meandiff[j]);
2068: /* printf(" age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, j, meandiff[j],(int)agefin, j, max[j], j, min[j],maxmax); */
1.169 brouard 2069: } /* j loop */
1.203 brouard 2070: *ncvyear= (int)age- (int)agefin;
1.208 brouard 2071: /* printf("maxmax=%lf maxmin=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.126 brouard 2072: if(maxmax < ftolpl){
1.209 brouard 2073: /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
2074: free_vector(min,1,nlstate);
2075: free_vector(max,1,nlstate);
2076: free_vector(meandiff,1,nlstate);
1.126 brouard 2077: return prlim;
2078: }
1.169 brouard 2079: } /* age loop */
1.208 brouard 2080: /* After some age loop it doesn't converge */
1.209 brouard 2081: printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\
1.208 brouard 2082: Earliest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
1.209 brouard 2083: /* 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); */
2084: free_vector(min,1,nlstate);
2085: free_vector(max,1,nlstate);
2086: free_vector(meandiff,1,nlstate);
1.208 brouard 2087:
1.169 brouard 2088: return prlim; /* should not reach here */
1.126 brouard 2089: }
2090:
2091: /*************** transition probabilities ***************/
2092:
2093: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
2094: {
1.138 brouard 2095: /* According to parameters values stored in x and the covariate's values stored in cov,
2096: computes the probability to be observed in state j being in state i by appying the
2097: model to the ncovmodel covariates (including constant and age).
2098: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2099: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2100: ncth covariate in the global vector x is given by the formula:
2101: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2102: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2103: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2104: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
2105: Outputs ps[i][j] the probability to be observed in j being in j according to
2106: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
2107: */
2108: double s1, lnpijopii;
1.126 brouard 2109: /*double t34;*/
1.164 brouard 2110: int i,j, nc, ii, jj;
1.126 brouard 2111:
2112: for(i=1; i<= nlstate; i++){
2113: for(j=1; j<i;j++){
1.138 brouard 2114: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2115: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2116: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2117: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 2118: }
1.138 brouard 2119: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2120: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 2121: }
2122: for(j=i+1; j<=nlstate+ndeath;j++){
1.138 brouard 2123: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2124: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2125: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2126: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1.126 brouard 2127: }
1.138 brouard 2128: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1.126 brouard 2129: }
2130: }
2131:
2132: for(i=1; i<= nlstate; i++){
2133: s1=0;
1.131 brouard 2134: for(j=1; j<i; j++){
1.138 brouard 2135: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 2136: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2137: }
2138: for(j=i+1; j<=nlstate+ndeath; j++){
1.138 brouard 2139: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 2140: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2141: }
1.138 brouard 2142: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1.126 brouard 2143: ps[i][i]=1./(s1+1.);
1.138 brouard 2144: /* Computing other pijs */
1.126 brouard 2145: for(j=1; j<i; j++)
2146: ps[i][j]= exp(ps[i][j])*ps[i][i];
2147: for(j=i+1; j<=nlstate+ndeath; j++)
2148: ps[i][j]= exp(ps[i][j])*ps[i][i];
2149: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2150: } /* end i */
2151:
2152: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2153: for(jj=1; jj<= nlstate+ndeath; jj++){
2154: ps[ii][jj]=0;
2155: ps[ii][ii]=1;
2156: }
2157: }
2158:
1.145 brouard 2159:
2160: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2161: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2162: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2163: /* } */
2164: /* printf("\n "); */
2165: /* } */
2166: /* printf("\n ");printf("%lf ",cov[2]);*/
2167: /*
1.126 brouard 2168: for(i=1; i<= npar; i++) printf("%f ",x[i]);
2169: goto end;*/
2170: return ps;
2171: }
2172:
2173: /**************** Product of 2 matrices ******************/
2174:
1.145 brouard 2175: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 2176: {
2177: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
2178: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
2179: /* in, b, out are matrice of pointers which should have been initialized
2180: before: only the contents of out is modified. The function returns
2181: a pointer to pointers identical to out */
1.145 brouard 2182: int i, j, k;
1.126 brouard 2183: for(i=nrl; i<= nrh; i++)
1.145 brouard 2184: for(k=ncolol; k<=ncoloh; k++){
2185: out[i][k]=0.;
2186: for(j=ncl; j<=nch; j++)
2187: out[i][k] +=in[i][j]*b[j][k];
2188: }
1.126 brouard 2189: return out;
2190: }
2191:
2192:
2193: /************* Higher Matrix Product ***************/
2194:
2195: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
2196: {
2197: /* Computes the transition matrix starting at age 'age' over
2198: 'nhstepm*hstepm*stepm' months (i.e. until
2199: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2200: nhstepm*hstepm matrices.
2201: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2202: (typically every 2 years instead of every month which is too big
2203: for the memory).
2204: Model is determined by parameters x and covariates have to be
2205: included manually here.
2206:
2207: */
2208:
2209: int i, j, d, h, k;
1.131 brouard 2210: double **out, cov[NCOVMAX+1];
1.126 brouard 2211: double **newm;
1.187 brouard 2212: double agexact;
1.126 brouard 2213:
2214: /* Hstepm could be zero and should return the unit matrix */
2215: for (i=1;i<=nlstate+ndeath;i++)
2216: for (j=1;j<=nlstate+ndeath;j++){
2217: oldm[i][j]=(i==j ? 1.0 : 0.0);
2218: po[i][j][0]=(i==j ? 1.0 : 0.0);
2219: }
2220: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2221: for(h=1; h <=nhstepm; h++){
2222: for(d=1; d <=hstepm; d++){
2223: newm=savm;
2224: /* Covariates have to be included here again */
2225: cov[1]=1.;
1.187 brouard 2226: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
2227: cov[2]=agexact;
2228: if(nagesqr==1)
2229: cov[3]= agexact*agexact;
1.131 brouard 2230: for (k=1; k<=cptcovn;k++)
1.200 brouard 2231: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2232: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.186 brouard 2233: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
2234: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 2235: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2236: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
1.145 brouard 2237: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.200 brouard 2238: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
2239: /* 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 2240:
2241:
2242: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2243: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
2244: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
2245: pmij(pmmij,cov,ncovmodel,x,nlstate));
2246: savm=oldm;
2247: oldm=newm;
2248: }
2249: for(i=1; i<=nlstate+ndeath; i++)
2250: for(j=1;j<=nlstate+ndeath;j++) {
2251: po[i][j][h]=newm[i][j];
1.128 brouard 2252: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 2253: }
1.128 brouard 2254: /*printf("h=%d ",h);*/
1.126 brouard 2255: } /* end h */
1.128 brouard 2256: /* printf("\n H=%d \n",h); */
1.126 brouard 2257: return po;
2258: }
2259:
1.162 brouard 2260: #ifdef NLOPT
2261: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
2262: double fret;
2263: double *xt;
2264: int j;
2265: myfunc_data *d2 = (myfunc_data *) pd;
2266: /* xt = (p1-1); */
2267: xt=vector(1,n);
2268: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
2269:
2270: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
2271: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
2272: printf("Function = %.12lf ",fret);
2273: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
2274: printf("\n");
2275: free_vector(xt,1,n);
2276: return fret;
2277: }
2278: #endif
1.126 brouard 2279:
2280: /*************** log-likelihood *************/
2281: double func( double *x)
2282: {
2283: int i, ii, j, k, mi, d, kk;
1.131 brouard 2284: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2285: double **out;
2286: double sw; /* Sum of weights */
2287: double lli; /* Individual log likelihood */
2288: int s1, s2;
2289: double bbh, survp;
2290: long ipmx;
1.187 brouard 2291: double agexact;
1.126 brouard 2292: /*extern weight */
2293: /* We are differentiating ll according to initial status */
2294: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2295: /*for(i=1;i<imx;i++)
2296: printf(" %d\n",s[4][i]);
2297: */
1.162 brouard 2298:
2299: ++countcallfunc;
2300:
1.126 brouard 2301: cov[1]=1.;
2302:
2303: for(k=1; k<=nlstate; k++) ll[k]=0.;
2304:
2305: if(mle==1){
2306: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.138 brouard 2307: /* Computes the values of the ncovmodel covariates of the model
2308: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
2309: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
2310: to be observed in j being in i according to the model.
2311: */
1.145 brouard 2312: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1.187 brouard 2313: cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.145 brouard 2314: }
1.137 brouard 2315: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1.138 brouard 2316: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1.137 brouard 2317: has been calculated etc */
1.126 brouard 2318: for(mi=1; mi<= wav[i]-1; mi++){
2319: for (ii=1;ii<=nlstate+ndeath;ii++)
2320: for (j=1;j<=nlstate+ndeath;j++){
2321: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2322: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2323: }
2324: for(d=0; d<dh[mi][i]; d++){
2325: newm=savm;
1.187 brouard 2326: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2327: cov[2]=agexact;
2328: if(nagesqr==1)
2329: cov[3]= agexact*agexact;
1.126 brouard 2330: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2331: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
1.126 brouard 2332: }
2333: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2334: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2335: savm=oldm;
2336: oldm=newm;
2337: } /* end mult */
2338:
2339: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
2340: /* But now since version 0.9 we anticipate for bias at large stepm.
2341: * If stepm is larger than one month (smallest stepm) and if the exact delay
2342: * (in months) between two waves is not a multiple of stepm, we rounded to
2343: * the nearest (and in case of equal distance, to the lowest) interval but now
2344: * we keep into memory the bias bh[mi][i] and also the previous matrix product
2345: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
2346: * probability in order to take into account the bias as a fraction of the way
2347: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
2348: * -stepm/2 to stepm/2 .
2349: * For stepm=1 the results are the same as for previous versions of Imach.
2350: * For stepm > 1 the results are less biased than in previous versions.
2351: */
2352: s1=s[mw[mi][i]][i];
2353: s2=s[mw[mi+1][i]][i];
2354: bbh=(double)bh[mi][i]/(double)stepm;
2355: /* bias bh is positive if real duration
2356: * is higher than the multiple of stepm and negative otherwise.
2357: */
2358: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
2359: if( s2 > nlstate){
2360: /* i.e. if s2 is a death state and if the date of death is known
2361: then the contribution to the likelihood is the probability to
2362: die between last step unit time and current step unit time,
2363: which is also equal to probability to die before dh
2364: minus probability to die before dh-stepm .
2365: In version up to 0.92 likelihood was computed
2366: as if date of death was unknown. Death was treated as any other
2367: health state: the date of the interview describes the actual state
2368: and not the date of a change in health state. The former idea was
2369: to consider that at each interview the state was recorded
2370: (healthy, disable or death) and IMaCh was corrected; but when we
2371: introduced the exact date of death then we should have modified
2372: the contribution of an exact death to the likelihood. This new
2373: contribution is smaller and very dependent of the step unit
2374: stepm. It is no more the probability to die between last interview
2375: and month of death but the probability to survive from last
2376: interview up to one month before death multiplied by the
2377: probability to die within a month. Thanks to Chris
2378: Jackson for correcting this bug. Former versions increased
2379: mortality artificially. The bad side is that we add another loop
2380: which slows down the processing. The difference can be up to 10%
2381: lower mortality.
2382: */
1.183 brouard 2383: /* If, at the beginning of the maximization mostly, the
2384: cumulative probability or probability to be dead is
2385: constant (ie = 1) over time d, the difference is equal to
2386: 0. out[s1][3] = savm[s1][3]: probability, being at state
2387: s1 at precedent wave, to be dead a month before current
2388: wave is equal to probability, being at state s1 at
2389: precedent wave, to be dead at mont of the current
2390: wave. Then the observed probability (that this person died)
2391: is null according to current estimated parameter. In fact,
2392: it should be very low but not zero otherwise the log go to
2393: infinity.
2394: */
2395: /* #ifdef INFINITYORIGINAL */
2396: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2397: /* #else */
2398: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
2399: /* lli=log(mytinydouble); */
2400: /* else */
2401: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2402: /* #endif */
2403: lli=log(out[s1][s2] - savm[s1][s2]);
1.126 brouard 2404:
2405: } else if (s2==-2) {
2406: for (j=1,survp=0. ; j<=nlstate; j++)
2407: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2408: /*survp += out[s1][j]; */
2409: lli= log(survp);
2410: }
2411:
2412: else if (s2==-4) {
2413: for (j=3,survp=0. ; j<=nlstate; j++)
2414: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2415: lli= log(survp);
2416: }
2417:
2418: else if (s2==-5) {
2419: for (j=1,survp=0. ; j<=2; j++)
2420: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2421: lli= log(survp);
2422: }
2423:
2424: else{
2425: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2426: /* 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 */
2427: }
2428: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
2429: /*if(lli ==000.0)*/
2430: /*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); */
2431: ipmx +=1;
2432: sw += weight[i];
2433: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.183 brouard 2434: /* if (lli < log(mytinydouble)){ */
2435: /* 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); */
2436: /* 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]); */
2437: /* } */
1.126 brouard 2438: } /* end of wave */
2439: } /* end of individual */
2440: } else if(mle==2){
2441: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2442: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2443: for(mi=1; mi<= wav[i]-1; mi++){
2444: for (ii=1;ii<=nlstate+ndeath;ii++)
2445: for (j=1;j<=nlstate+ndeath;j++){
2446: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2447: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2448: }
2449: for(d=0; d<=dh[mi][i]; d++){
2450: newm=savm;
1.187 brouard 2451: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2452: cov[2]=agexact;
2453: if(nagesqr==1)
2454: cov[3]= agexact*agexact;
1.126 brouard 2455: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2456: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 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: bbh=(double)bh[mi][i]/(double)stepm;
2467: 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 */
2468: ipmx +=1;
2469: sw += weight[i];
2470: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2471: } /* end of wave */
2472: } /* end of individual */
2473: } else if(mle==3){ /* exponential inter-extrapolation */
2474: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2475: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2476: for(mi=1; mi<= wav[i]-1; mi++){
2477: for (ii=1;ii<=nlstate+ndeath;ii++)
2478: for (j=1;j<=nlstate+ndeath;j++){
2479: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2480: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2481: }
2482: for(d=0; d<dh[mi][i]; d++){
2483: newm=savm;
1.187 brouard 2484: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2485: cov[2]=agexact;
2486: if(nagesqr==1)
2487: cov[3]= agexact*agexact;
1.126 brouard 2488: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2489: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2490: }
2491: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2492: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2493: savm=oldm;
2494: oldm=newm;
2495: } /* end mult */
2496:
2497: s1=s[mw[mi][i]][i];
2498: s2=s[mw[mi+1][i]][i];
2499: bbh=(double)bh[mi][i]/(double)stepm;
2500: 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 */
2501: ipmx +=1;
2502: sw += weight[i];
2503: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2504: } /* end of wave */
2505: } /* end of individual */
2506: }else if (mle==4){ /* ml=4 no inter-extrapolation */
2507: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2508: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2509: for(mi=1; mi<= wav[i]-1; mi++){
2510: for (ii=1;ii<=nlstate+ndeath;ii++)
2511: for (j=1;j<=nlstate+ndeath;j++){
2512: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2513: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2514: }
2515: for(d=0; d<dh[mi][i]; d++){
2516: newm=savm;
1.187 brouard 2517: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2518: cov[2]=agexact;
2519: if(nagesqr==1)
2520: cov[3]= agexact*agexact;
1.126 brouard 2521: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2522: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2523: }
2524:
2525: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2526: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2527: savm=oldm;
2528: oldm=newm;
2529: } /* end mult */
2530:
2531: s1=s[mw[mi][i]][i];
2532: s2=s[mw[mi+1][i]][i];
2533: if( s2 > nlstate){
2534: lli=log(out[s1][s2] - savm[s1][s2]);
2535: }else{
2536: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2537: }
2538: ipmx +=1;
2539: sw += weight[i];
2540: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2541: /* 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]); */
2542: } /* end of wave */
2543: } /* end of individual */
2544: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
2545: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2546: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2547: for(mi=1; mi<= wav[i]-1; mi++){
2548: for (ii=1;ii<=nlstate+ndeath;ii++)
2549: for (j=1;j<=nlstate+ndeath;j++){
2550: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2551: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2552: }
2553: for(d=0; d<dh[mi][i]; d++){
2554: newm=savm;
1.187 brouard 2555: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2556: cov[2]=agexact;
2557: if(nagesqr==1)
2558: cov[3]= agexact*agexact;
1.126 brouard 2559: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2560: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2561: }
2562:
2563: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2564: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2565: savm=oldm;
2566: oldm=newm;
2567: } /* end mult */
2568:
2569: s1=s[mw[mi][i]][i];
2570: s2=s[mw[mi+1][i]][i];
2571: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2572: ipmx +=1;
2573: sw += weight[i];
2574: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2575: /*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]);*/
2576: } /* end of wave */
2577: } /* end of individual */
2578: } /* End of if */
2579: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2580: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2581: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2582: return -l;
2583: }
2584:
2585: /*************** log-likelihood *************/
2586: double funcone( double *x)
2587: {
2588: /* Same as likeli but slower because of a lot of printf and if */
2589: int i, ii, j, k, mi, d, kk;
1.131 brouard 2590: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2591: double **out;
2592: double lli; /* Individual log likelihood */
2593: double llt;
2594: int s1, s2;
2595: double bbh, survp;
1.187 brouard 2596: double agexact;
1.126 brouard 2597: /*extern weight */
2598: /* We are differentiating ll according to initial status */
2599: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2600: /*for(i=1;i<imx;i++)
2601: printf(" %d\n",s[4][i]);
2602: */
2603: cov[1]=1.;
2604:
2605: for(k=1; k<=nlstate; k++) ll[k]=0.;
2606:
2607: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2608: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2609: for(mi=1; mi<= wav[i]-1; mi++){
2610: for (ii=1;ii<=nlstate+ndeath;ii++)
2611: for (j=1;j<=nlstate+ndeath;j++){
2612: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2613: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2614: }
2615: for(d=0; d<dh[mi][i]; d++){
2616: newm=savm;
1.187 brouard 2617: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2618: cov[2]=agexact;
2619: if(nagesqr==1)
2620: cov[3]= agexact*agexact;
1.126 brouard 2621: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2622: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2623: }
1.187 brouard 2624:
1.145 brouard 2625: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.126 brouard 2626: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2627: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1.145 brouard 2628: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2629: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
1.126 brouard 2630: savm=oldm;
2631: oldm=newm;
2632: } /* end mult */
2633:
2634: s1=s[mw[mi][i]][i];
2635: s2=s[mw[mi+1][i]][i];
2636: bbh=(double)bh[mi][i]/(double)stepm;
2637: /* bias is positive if real duration
2638: * is higher than the multiple of stepm and negative otherwise.
2639: */
2640: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2641: lli=log(out[s1][s2] - savm[s1][s2]);
2642: } else if (s2==-2) {
2643: for (j=1,survp=0. ; j<=nlstate; j++)
2644: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2645: lli= log(survp);
2646: }else if (mle==1){
2647: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2648: } else if(mle==2){
2649: 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 */
2650: } else if(mle==3){ /* exponential inter-extrapolation */
2651: 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 */
2652: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2653: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 2654: } else{ /* mle=0 back to 1 */
2655: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2656: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 2657: } /* End of if */
2658: ipmx +=1;
2659: sw += weight[i];
2660: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 2661: /*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 2662: if(globpr){
1.205 brouard 2663: fprintf(ficresilk,"%9ld %6.1f %6d %2d %2d %2d %2d %3d %11.6f %8.4f %8.3f\
1.126 brouard 2664: %11.6f %11.6f %11.6f ", \
1.205 brouard 2665: num[i], agexact, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
1.126 brouard 2666: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2667: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2668: llt +=ll[k]*gipmx/gsw;
2669: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2670: }
2671: fprintf(ficresilk," %10.6f\n", -llt);
2672: }
2673: } /* end of wave */
2674: } /* end of individual */
2675: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2676: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2677: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2678: if(globpr==0){ /* First time we count the contributions and weights */
2679: gipmx=ipmx;
2680: gsw=sw;
2681: }
2682: return -l;
2683: }
2684:
2685:
2686: /*************** function likelione ***********/
2687: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2688: {
2689: /* This routine should help understanding what is done with
2690: the selection of individuals/waves and
2691: to check the exact contribution to the likelihood.
2692: Plotting could be done.
2693: */
2694: int k;
2695:
2696: if(*globpri !=0){ /* Just counts and sums, no printings */
1.201 brouard 2697: strcpy(fileresilk,"ILK_");
1.202 brouard 2698: strcat(fileresilk,fileresu);
1.126 brouard 2699: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2700: printf("Problem with resultfile: %s\n", fileresilk);
2701: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2702: }
1.205 brouard 2703: fprintf(ficresilk, "#individual(line's_record) count age s1 s2 wave# effective_wave# number_of_matrices_product pij weight weight/gpw -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
1.207 brouard 2704: fprintf(ficresilk, "#num_i age i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
1.126 brouard 2705: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2706: for(k=1; k<=nlstate; k++)
2707: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2708: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2709: }
2710:
2711: *fretone=(*funcone)(p);
2712: if(*globpri !=0){
2713: fclose(ficresilk);
1.205 brouard 2714: if (mle ==0)
2715: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
2716: else if(mle >=1)
2717: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
2718: fprintf(fichtm," You should at least run with mle >= 1 to get 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));
1.207 brouard 2719:
1.208 brouard 2720:
2721: for (k=1; k<= nlstate ; k++) {
2722: fprintf(fichtm,"<br>- Probability p%dj by origin %d and destination j <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \
2723: <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
2724: }
1.207 brouard 2725: fprintf(fichtm,"<br>- The function drawn is -2Log(L) in Log scale: by state of origin <a href=\"%s-ori.png\">%s-ori.png</a><br> \
1.204 brouard 2726: <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 2727: fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
1.204 brouard 2728: <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 2729: fflush(fichtm);
1.205 brouard 2730: }
1.126 brouard 2731: return;
2732: }
2733:
2734:
2735: /*********** Maximum Likelihood Estimation ***************/
2736:
2737: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2738: {
1.165 brouard 2739: int i,j, iter=0;
1.126 brouard 2740: double **xi;
2741: double fret;
2742: double fretone; /* Only one call to likelihood */
2743: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 2744:
2745: #ifdef NLOPT
2746: int creturn;
2747: nlopt_opt opt;
2748: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2749: double *lb;
2750: double minf; /* the minimum objective value, upon return */
2751: double * p1; /* Shifted parameters from 0 instead of 1 */
2752: myfunc_data dinst, *d = &dinst;
2753: #endif
2754:
2755:
1.126 brouard 2756: xi=matrix(1,npar,1,npar);
2757: for (i=1;i<=npar;i++)
2758: for (j=1;j<=npar;j++)
2759: xi[i][j]=(i==j ? 1.0 : 0.0);
2760: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.201 brouard 2761: strcpy(filerespow,"POW_");
1.126 brouard 2762: strcat(filerespow,fileres);
2763: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2764: printf("Problem with resultfile: %s\n", filerespow);
2765: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2766: }
2767: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2768: for (i=1;i<=nlstate;i++)
2769: for(j=1;j<=nlstate+ndeath;j++)
2770: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2771: fprintf(ficrespow,"\n");
1.162 brouard 2772: #ifdef POWELL
1.126 brouard 2773: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 2774: #endif
1.126 brouard 2775:
1.162 brouard 2776: #ifdef NLOPT
2777: #ifdef NEWUOA
2778: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2779: #else
2780: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2781: #endif
2782: lb=vector(0,npar-1);
2783: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2784: nlopt_set_lower_bounds(opt, lb);
2785: nlopt_set_initial_step1(opt, 0.1);
2786:
2787: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2788: d->function = func;
2789: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2790: nlopt_set_min_objective(opt, myfunc, d);
2791: nlopt_set_xtol_rel(opt, ftol);
2792: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2793: printf("nlopt failed! %d\n",creturn);
2794: }
2795: else {
2796: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2797: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2798: iter=1; /* not equal */
2799: }
2800: nlopt_destroy(opt);
2801: #endif
1.126 brouard 2802: free_matrix(xi,1,npar,1,npar);
2803: fclose(ficrespow);
1.203 brouard 2804: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2805: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.180 brouard 2806: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 2807:
2808: }
2809:
2810: /**** Computes Hessian and covariance matrix ***/
1.203 brouard 2811: void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1.126 brouard 2812: {
2813: double **a,**y,*x,pd;
1.203 brouard 2814: /* double **hess; */
1.164 brouard 2815: int i, j;
1.126 brouard 2816: int *indx;
2817:
2818: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1.203 brouard 2819: double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
1.126 brouard 2820: void lubksb(double **a, int npar, int *indx, double b[]) ;
2821: void ludcmp(double **a, int npar, int *indx, double *d) ;
2822: double gompertz(double p[]);
1.203 brouard 2823: /* hess=matrix(1,npar,1,npar); */
1.126 brouard 2824:
2825: printf("\nCalculation of the hessian matrix. Wait...\n");
2826: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2827: for (i=1;i<=npar;i++){
1.203 brouard 2828: printf("%d-",i);fflush(stdout);
2829: fprintf(ficlog,"%d-",i);fflush(ficlog);
1.126 brouard 2830:
2831: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2832:
2833: /* printf(" %f ",p[i]);
2834: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2835: }
2836:
2837: for (i=1;i<=npar;i++) {
2838: for (j=1;j<=npar;j++) {
2839: if (j>i) {
1.203 brouard 2840: printf(".%d-%d",i,j);fflush(stdout);
2841: fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
2842: hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
1.126 brouard 2843:
2844: hess[j][i]=hess[i][j];
2845: /*printf(" %lf ",hess[i][j]);*/
2846: }
2847: }
2848: }
2849: printf("\n");
2850: fprintf(ficlog,"\n");
2851:
2852: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2853: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2854:
2855: a=matrix(1,npar,1,npar);
2856: y=matrix(1,npar,1,npar);
2857: x=vector(1,npar);
2858: indx=ivector(1,npar);
2859: for (i=1;i<=npar;i++)
2860: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2861: ludcmp(a,npar,indx,&pd);
2862:
2863: for (j=1;j<=npar;j++) {
2864: for (i=1;i<=npar;i++) x[i]=0;
2865: x[j]=1;
2866: lubksb(a,npar,indx,x);
2867: for (i=1;i<=npar;i++){
2868: matcov[i][j]=x[i];
2869: }
2870: }
2871:
2872: printf("\n#Hessian matrix#\n");
2873: fprintf(ficlog,"\n#Hessian matrix#\n");
2874: for (i=1;i<=npar;i++) {
2875: for (j=1;j<=npar;j++) {
1.203 brouard 2876: printf("%.6e ",hess[i][j]);
2877: fprintf(ficlog,"%.6e ",hess[i][j]);
1.126 brouard 2878: }
2879: printf("\n");
2880: fprintf(ficlog,"\n");
2881: }
2882:
1.203 brouard 2883: /* printf("\n#Covariance matrix#\n"); */
2884: /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
2885: /* for (i=1;i<=npar;i++) { */
2886: /* for (j=1;j<=npar;j++) { */
2887: /* printf("%.6e ",matcov[i][j]); */
2888: /* fprintf(ficlog,"%.6e ",matcov[i][j]); */
2889: /* } */
2890: /* printf("\n"); */
2891: /* fprintf(ficlog,"\n"); */
2892: /* } */
2893:
1.126 brouard 2894: /* Recompute Inverse */
1.203 brouard 2895: /* for (i=1;i<=npar;i++) */
2896: /* for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
2897: /* ludcmp(a,npar,indx,&pd); */
2898:
2899: /* printf("\n#Hessian matrix recomputed#\n"); */
2900:
2901: /* for (j=1;j<=npar;j++) { */
2902: /* for (i=1;i<=npar;i++) x[i]=0; */
2903: /* x[j]=1; */
2904: /* lubksb(a,npar,indx,x); */
2905: /* for (i=1;i<=npar;i++){ */
2906: /* y[i][j]=x[i]; */
2907: /* printf("%.3e ",y[i][j]); */
2908: /* fprintf(ficlog,"%.3e ",y[i][j]); */
2909: /* } */
2910: /* printf("\n"); */
2911: /* fprintf(ficlog,"\n"); */
2912: /* } */
2913:
2914: /* Verifying the inverse matrix */
2915: #ifdef DEBUGHESS
2916: y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
1.126 brouard 2917:
1.203 brouard 2918: printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
2919: fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
1.126 brouard 2920:
2921: for (j=1;j<=npar;j++) {
2922: for (i=1;i<=npar;i++){
1.203 brouard 2923: printf("%.2f ",y[i][j]);
2924: fprintf(ficlog,"%.2f ",y[i][j]);
1.126 brouard 2925: }
2926: printf("\n");
2927: fprintf(ficlog,"\n");
2928: }
1.203 brouard 2929: #endif
1.126 brouard 2930:
2931: free_matrix(a,1,npar,1,npar);
2932: free_matrix(y,1,npar,1,npar);
2933: free_vector(x,1,npar);
2934: free_ivector(indx,1,npar);
1.203 brouard 2935: /* free_matrix(hess,1,npar,1,npar); */
1.126 brouard 2936:
2937:
2938: }
2939:
2940: /*************** hessian matrix ****************/
2941: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.203 brouard 2942: { /* Around values of x, computes the function func and returns the scales delti and hessian */
1.126 brouard 2943: int i;
2944: int l=1, lmax=20;
1.203 brouard 2945: double k1,k2, res, fx;
1.132 brouard 2946: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 2947: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2948: int k=0,kmax=10;
2949: double l1;
2950:
2951: fx=func(x);
2952: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 2953: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 2954: l1=pow(10,l);
2955: delts=delt;
2956: for(k=1 ; k <kmax; k=k+1){
2957: delt = delta*(l1*k);
2958: p2[theta]=x[theta] +delt;
1.145 brouard 2959: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 2960: p2[theta]=x[theta]-delt;
2961: k2=func(p2)-fx;
2962: /*res= (k1-2.0*fx+k2)/delt/delt; */
1.203 brouard 2963: res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
1.126 brouard 2964:
1.203 brouard 2965: #ifdef DEBUGHESSII
1.126 brouard 2966: 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);
2967: 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);
2968: #endif
2969: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2970: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2971: k=kmax;
2972: }
2973: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 2974: k=kmax; l=lmax*10;
1.126 brouard 2975: }
2976: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2977: delts=delt;
2978: }
1.203 brouard 2979: } /* End loop k */
1.126 brouard 2980: }
2981: delti[theta]=delts;
2982: return res;
2983:
2984: }
2985:
1.203 brouard 2986: double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.126 brouard 2987: {
2988: int i;
1.164 brouard 2989: int l=1, lmax=20;
1.126 brouard 2990: double k1,k2,k3,k4,res,fx;
1.132 brouard 2991: double p2[MAXPARM+1];
1.203 brouard 2992: int k, kmax=1;
2993: double v1, v2, cv12, lc1, lc2;
1.208 brouard 2994:
2995: int firstime=0;
1.203 brouard 2996:
1.126 brouard 2997: fx=func(x);
1.203 brouard 2998: for (k=1; k<=kmax; k=k+10) {
1.126 brouard 2999: for (i=1;i<=npar;i++) p2[i]=x[i];
1.203 brouard 3000: p2[thetai]=x[thetai]+delti[thetai]*k;
3001: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 3002: k1=func(p2)-fx;
3003:
1.203 brouard 3004: p2[thetai]=x[thetai]+delti[thetai]*k;
3005: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 3006: k2=func(p2)-fx;
3007:
1.203 brouard 3008: p2[thetai]=x[thetai]-delti[thetai]*k;
3009: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 3010: k3=func(p2)-fx;
3011:
1.203 brouard 3012: p2[thetai]=x[thetai]-delti[thetai]*k;
3013: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 3014: k4=func(p2)-fx;
1.203 brouard 3015: res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
3016: if(k1*k2*k3*k4 <0.){
1.208 brouard 3017: firstime=1;
1.203 brouard 3018: kmax=kmax+10;
1.208 brouard 3019: }
3020: if(kmax >=10 || firstime ==1){
1.203 brouard 3021: printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol);
3022: fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol);
3023: 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);
3024: 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);
3025: }
3026: #ifdef DEBUGHESSIJ
3027: v1=hess[thetai][thetai];
3028: v2=hess[thetaj][thetaj];
3029: cv12=res;
3030: /* Computing eigen value of Hessian matrix */
3031: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3032: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3033: if ((lc2 <0) || (lc1 <0) ){
3034: printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
3035: fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
3036: 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);
3037: 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);
3038: }
1.126 brouard 3039: #endif
3040: }
3041: return res;
3042: }
3043:
1.203 brouard 3044: /* Not done yet: Was supposed to fix if not exactly at the maximum */
3045: /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
3046: /* { */
3047: /* int i; */
3048: /* int l=1, lmax=20; */
3049: /* double k1,k2,k3,k4,res,fx; */
3050: /* double p2[MAXPARM+1]; */
3051: /* double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
3052: /* int k=0,kmax=10; */
3053: /* double l1; */
3054:
3055: /* fx=func(x); */
3056: /* for(l=0 ; l <=lmax; l++){ /\* Enlarging the zone around the Maximum *\/ */
3057: /* l1=pow(10,l); */
3058: /* delts=delt; */
3059: /* for(k=1 ; k <kmax; k=k+1){ */
3060: /* delt = delti*(l1*k); */
3061: /* for (i=1;i<=npar;i++) p2[i]=x[i]; */
3062: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3063: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3064: /* k1=func(p2)-fx; */
3065:
3066: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3067: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3068: /* k2=func(p2)-fx; */
3069:
3070: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3071: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3072: /* k3=func(p2)-fx; */
3073:
3074: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3075: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3076: /* k4=func(p2)-fx; */
3077: /* res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
3078: /* #ifdef DEBUGHESSIJ */
3079: /* 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); */
3080: /* 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); */
3081: /* #endif */
3082: /* if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
3083: /* k=kmax; */
3084: /* } */
3085: /* else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
3086: /* k=kmax; l=lmax*10; */
3087: /* } */
3088: /* else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ */
3089: /* delts=delt; */
3090: /* } */
3091: /* } /\* End loop k *\/ */
3092: /* } */
3093: /* delti[theta]=delts; */
3094: /* return res; */
3095: /* } */
3096:
3097:
1.126 brouard 3098: /************** Inverse of matrix **************/
3099: void ludcmp(double **a, int n, int *indx, double *d)
3100: {
3101: int i,imax,j,k;
3102: double big,dum,sum,temp;
3103: double *vv;
3104:
3105: vv=vector(1,n);
3106: *d=1.0;
3107: for (i=1;i<=n;i++) {
3108: big=0.0;
3109: for (j=1;j<=n;j++)
3110: if ((temp=fabs(a[i][j])) > big) big=temp;
3111: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
3112: vv[i]=1.0/big;
3113: }
3114: for (j=1;j<=n;j++) {
3115: for (i=1;i<j;i++) {
3116: sum=a[i][j];
3117: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
3118: a[i][j]=sum;
3119: }
3120: big=0.0;
3121: for (i=j;i<=n;i++) {
3122: sum=a[i][j];
3123: for (k=1;k<j;k++)
3124: sum -= a[i][k]*a[k][j];
3125: a[i][j]=sum;
3126: if ( (dum=vv[i]*fabs(sum)) >= big) {
3127: big=dum;
3128: imax=i;
3129: }
3130: }
3131: if (j != imax) {
3132: for (k=1;k<=n;k++) {
3133: dum=a[imax][k];
3134: a[imax][k]=a[j][k];
3135: a[j][k]=dum;
3136: }
3137: *d = -(*d);
3138: vv[imax]=vv[j];
3139: }
3140: indx[j]=imax;
3141: if (a[j][j] == 0.0) a[j][j]=TINY;
3142: if (j != n) {
3143: dum=1.0/(a[j][j]);
3144: for (i=j+1;i<=n;i++) a[i][j] *= dum;
3145: }
3146: }
3147: free_vector(vv,1,n); /* Doesn't work */
3148: ;
3149: }
3150:
3151: void lubksb(double **a, int n, int *indx, double b[])
3152: {
3153: int i,ii=0,ip,j;
3154: double sum;
3155:
3156: for (i=1;i<=n;i++) {
3157: ip=indx[i];
3158: sum=b[ip];
3159: b[ip]=b[i];
3160: if (ii)
3161: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
3162: else if (sum) ii=i;
3163: b[i]=sum;
3164: }
3165: for (i=n;i>=1;i--) {
3166: sum=b[i];
3167: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
3168: b[i]=sum/a[i][i];
3169: }
3170: }
3171:
3172: void pstamp(FILE *fichier)
3173: {
1.196 brouard 3174: fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126 brouard 3175: }
3176:
3177: /************ Frequencies ********************/
3178: 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[])
3179: { /* Some frequencies */
3180:
1.164 brouard 3181: int i, m, jk, j1, bool, z1,j;
1.126 brouard 3182: int first;
3183: double ***freq; /* Frequencies */
3184: double *pp, **prop;
3185: double pos,posprop, k2, dateintsum=0,k2cpt=0;
3186: char fileresp[FILENAMELENGTH];
3187:
3188: pp=vector(1,nlstate);
3189: prop=matrix(1,nlstate,iagemin,iagemax+3);
1.201 brouard 3190: strcpy(fileresp,"P_");
3191: strcat(fileresp,fileresu);
1.126 brouard 3192: if((ficresp=fopen(fileresp,"w"))==NULL) {
3193: printf("Problem with prevalence resultfile: %s\n", fileresp);
3194: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
3195: exit(0);
3196: }
3197: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
3198: j1=0;
3199:
3200: j=cptcoveff;
3201: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3202:
3203: first=1;
3204:
1.169 brouard 3205: /* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */
3206: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
3207: /* j1++; */
1.145 brouard 3208: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
1.126 brouard 3209: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
3210: scanf("%d", i);*/
3211: for (i=-5; i<=nlstate+ndeath; i++)
3212: for (jk=-5; jk<=nlstate+ndeath; jk++)
3213: for(m=iagemin; m <= iagemax+3; m++)
3214: freq[i][jk][m]=0;
1.143 brouard 3215:
3216: for (i=1; i<=nlstate; i++)
3217: for(m=iagemin; m <= iagemax+3; m++)
3218: prop[i][m]=0;
1.126 brouard 3219:
3220: dateintsum=0;
3221: k2cpt=0;
3222: for (i=1; i<=imx; i++) {
3223: bool=1;
1.210 ! brouard 3224: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
1.144 brouard 3225: for (z1=1; z1<=cptcoveff; z1++)
1.198 brouard 3226: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
1.145 brouard 3227: /* Tests if the value of each of the covariates of i is equal to filter j1 */
1.144 brouard 3228: bool=0;
1.198 brouard 3229: /* 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",
3230: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
3231: j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
3232: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
1.144 brouard 3233: }
1.210 ! brouard 3234: } /* cptcovn > 0 */
1.144 brouard 3235:
1.126 brouard 3236: if (bool==1){
3237: for(m=firstpass; m<=lastpass; m++){
3238: k2=anint[m][i]+(mint[m][i]/12.);
3239: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
3240: if(agev[m][i]==0) agev[m][i]=iagemax+1;
3241: if(agev[m][i]==1) agev[m][i]=iagemax+2;
3242: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
3243: if (m<lastpass) {
3244: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
3245: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
3246: }
3247:
1.210 ! brouard 3248: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3)) && (anint[m][i]!=9999) && (mint[m][i]!=99)) {
1.126 brouard 3249: dateintsum=dateintsum+k2;
3250: k2cpt++;
1.210 ! brouard 3251: /* printf("i=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",i, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
1.126 brouard 3252: }
3253: /*}*/
1.210 ! brouard 3254: } /* end m */
! 3255: } /* end bool */
! 3256: } /* end i = 1 to imx */
1.126 brouard 3257:
3258: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
3259: pstamp(ficresp);
3260: if (cptcovn>0) {
3261: fprintf(ficresp, "\n#********** Variable ");
1.198 brouard 3262: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 3263: fprintf(ficresp, "**********\n#");
1.143 brouard 3264: fprintf(ficlog, "\n#********** Variable ");
1.198 brouard 3265: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.143 brouard 3266: fprintf(ficlog, "**********\n#");
1.126 brouard 3267: }
3268: for(i=1; i<=nlstate;i++)
3269: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
3270: fprintf(ficresp, "\n");
3271:
3272: for(i=iagemin; i <= iagemax+3; i++){
3273: if(i==iagemax+3){
3274: fprintf(ficlog,"Total");
3275: }else{
3276: if(first==1){
3277: first=0;
3278: printf("See log file for details...\n");
3279: }
3280: fprintf(ficlog,"Age %d", i);
3281: }
3282: for(jk=1; jk <=nlstate ; jk++){
3283: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
3284: pp[jk] += freq[jk][m][i];
3285: }
3286: for(jk=1; jk <=nlstate ; jk++){
3287: for(m=-1, pos=0; m <=0 ; m++)
3288: pos += freq[jk][m][i];
3289: if(pp[jk]>=1.e-10){
3290: if(first==1){
1.132 brouard 3291: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1.126 brouard 3292: }
3293: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
3294: }else{
3295: if(first==1)
3296: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3297: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3298: }
3299: }
3300:
3301: for(jk=1; jk <=nlstate ; jk++){
3302: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
3303: pp[jk] += freq[jk][m][i];
3304: }
3305: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
3306: pos += pp[jk];
3307: posprop += prop[jk][i];
3308: }
3309: for(jk=1; jk <=nlstate ; jk++){
3310: if(pos>=1.e-5){
3311: if(first==1)
3312: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3313: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3314: }else{
3315: if(first==1)
3316: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3317: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3318: }
3319: if( i <= iagemax){
3320: if(pos>=1.e-5){
3321: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
3322: /*probs[i][jk][j1]= pp[jk]/pos;*/
3323: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
3324: }
3325: else
3326: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
3327: }
3328: }
3329:
3330: for(jk=-1; jk <=nlstate+ndeath; jk++)
3331: for(m=-1; m <=nlstate+ndeath; m++)
3332: if(freq[jk][m][i] !=0 ) {
3333: if(first==1)
3334: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
3335: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
3336: }
3337: if(i <= iagemax)
3338: fprintf(ficresp,"\n");
3339: if(first==1)
3340: printf("Others in log...\n");
3341: fprintf(ficlog,"\n");
1.210 ! brouard 3342: } /* end loop i */
1.145 brouard 3343: /*}*/
1.210 ! brouard 3344: } /* end j1 */
1.126 brouard 3345: dateintmean=dateintsum/k2cpt;
3346:
3347: fclose(ficresp);
3348: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
3349: free_vector(pp,1,nlstate);
3350: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
3351: /* End of Freq */
3352: }
3353:
3354: /************ Prevalence ********************/
3355: 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)
3356: {
3357: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
3358: in each health status at the date of interview (if between dateprev1 and dateprev2).
3359: We still use firstpass and lastpass as another selection.
3360: */
3361:
1.164 brouard 3362: int i, m, jk, j1, bool, z1,j;
3363:
3364: double **prop;
3365: double posprop;
1.126 brouard 3366: double y2; /* in fractional years */
3367: int iagemin, iagemax;
1.145 brouard 3368: int first; /** to stop verbosity which is redirected to log file */
1.126 brouard 3369:
3370: iagemin= (int) agemin;
3371: iagemax= (int) agemax;
3372: /*pp=vector(1,nlstate);*/
3373: prop=matrix(1,nlstate,iagemin,iagemax+3);
3374: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
3375: j1=0;
3376:
1.145 brouard 3377: /*j=cptcoveff;*/
1.126 brouard 3378: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3379:
1.145 brouard 3380: first=1;
3381: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
3382: /*for(i1=1; i1<=ncodemax[k1];i1++){
3383: j1++;*/
1.126 brouard 3384:
3385: for (i=1; i<=nlstate; i++)
3386: for(m=iagemin; m <= iagemax+3; m++)
3387: prop[i][m]=0.0;
3388:
3389: for (i=1; i<=imx; i++) { /* Each individual */
3390: bool=1;
3391: if (cptcovn>0) {
3392: for (z1=1; z1<=cptcoveff; z1++)
1.198 brouard 3393: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])
1.126 brouard 3394: bool=0;
3395: }
3396: if (bool==1) {
3397: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
3398: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
3399: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
3400: if(agev[m][i]==0) agev[m][i]=iagemax+1;
3401: if(agev[m][i]==1) agev[m][i]=iagemax+2;
3402: 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);
3403: if (s[m][i]>0 && s[m][i]<=nlstate) {
3404: /*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]]);*/
3405: prop[s[m][i]][(int)agev[m][i]] += weight[i];
3406: prop[s[m][i]][iagemax+3] += weight[i];
3407: }
3408: }
3409: } /* end selection of waves */
3410: }
3411: }
3412: for(i=iagemin; i <= iagemax+3; i++){
3413: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
3414: posprop += prop[jk][i];
3415: }
1.145 brouard 3416:
1.126 brouard 3417: for(jk=1; jk <=nlstate ; jk++){
3418: if( i <= iagemax){
3419: if(posprop>=1.e-5){
3420: probs[i][jk][j1]= prop[jk][i]/posprop;
1.145 brouard 3421: } else{
3422: if(first==1){
3423: first=0;
3424: 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]);
3425: }
3426: }
1.126 brouard 3427: }
3428: }/* end jk */
3429: }/* end i */
1.145 brouard 3430: /*} *//* end i1 */
3431: } /* end j1 */
1.126 brouard 3432:
3433: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
3434: /*free_vector(pp,1,nlstate);*/
3435: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
3436: } /* End of prevalence */
3437:
3438: /************* Waves Concatenation ***************/
3439:
3440: 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)
3441: {
3442: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
3443: Death is a valid wave (if date is known).
3444: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
3445: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3446: and mw[mi+1][i]. dh depends on stepm.
3447: */
3448:
3449: int i, mi, m;
3450: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
3451: double sum=0., jmean=0.;*/
3452: int first;
3453: int j, k=0,jk, ju, jl;
3454: double sum=0.;
3455: first=0;
1.164 brouard 3456: jmin=100000;
1.126 brouard 3457: jmax=-1;
3458: jmean=0.;
3459: for(i=1; i<=imx; i++){
3460: mi=0;
3461: m=firstpass;
3462: while(s[m][i] <= nlstate){
3463: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
3464: mw[++mi][i]=m;
3465: if(m >=lastpass)
3466: break;
3467: else
3468: m++;
3469: }/* end while */
3470: if (s[m][i] > nlstate){
3471: mi++; /* Death is another wave */
3472: /* if(mi==0) never been interviewed correctly before death */
3473: /* Only death is a correct wave */
3474: mw[mi][i]=m;
3475: }
3476:
3477: wav[i]=mi;
3478: if(mi==0){
3479: nbwarn++;
3480: if(first==0){
3481: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
3482: first=1;
3483: }
3484: if(first==1){
3485: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
3486: }
3487: } /* end mi==0 */
3488: } /* End individuals */
3489:
3490: for(i=1; i<=imx; i++){
3491: for(mi=1; mi<wav[i];mi++){
3492: if (stepm <=0)
3493: dh[mi][i]=1;
3494: else{
3495: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
3496: if (agedc[i] < 2*AGESUP) {
3497: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
3498: if(j==0) j=1; /* Survives at least one month after exam */
3499: else if(j<0){
3500: nberr++;
3501: 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]);
3502: j=1; /* Temporary Dangerous patch */
3503: 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);
3504: 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]);
3505: 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);
3506: }
3507: k=k+1;
3508: if (j >= jmax){
3509: jmax=j;
3510: ijmax=i;
3511: }
3512: if (j <= jmin){
3513: jmin=j;
3514: ijmin=i;
3515: }
3516: sum=sum+j;
3517: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
3518: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
3519: }
3520: }
3521: else{
3522: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
3523: /* 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]); */
3524:
3525: k=k+1;
3526: if (j >= jmax) {
3527: jmax=j;
3528: ijmax=i;
3529: }
3530: else if (j <= jmin){
3531: jmin=j;
3532: ijmin=i;
3533: }
3534: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
3535: /*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]);*/
3536: if(j<0){
3537: nberr++;
3538: 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]);
3539: 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]);
3540: }
3541: sum=sum+j;
3542: }
3543: jk= j/stepm;
3544: jl= j -jk*stepm;
3545: ju= j -(jk+1)*stepm;
3546: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
3547: if(jl==0){
3548: dh[mi][i]=jk;
3549: bh[mi][i]=0;
3550: }else{ /* We want a negative bias in order to only have interpolation ie
1.136 brouard 3551: * to avoid the price of an extra matrix product in likelihood */
1.126 brouard 3552: dh[mi][i]=jk+1;
3553: bh[mi][i]=ju;
3554: }
3555: }else{
3556: if(jl <= -ju){
3557: dh[mi][i]=jk;
3558: bh[mi][i]=jl; /* bias is positive if real duration
3559: * is higher than the multiple of stepm and negative otherwise.
3560: */
3561: }
3562: else{
3563: dh[mi][i]=jk+1;
3564: bh[mi][i]=ju;
3565: }
3566: if(dh[mi][i]==0){
3567: dh[mi][i]=1; /* At least one step */
3568: bh[mi][i]=ju; /* At least one step */
3569: /* 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);*/
3570: }
3571: } /* end if mle */
3572: }
3573: } /* end wave */
3574: }
3575: jmean=sum/k;
3576: 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 3577: 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 3578: }
3579:
3580: /*********** Tricode ****************************/
1.145 brouard 3581: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 3582: {
1.144 brouard 3583: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
3584: /* 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 3585: * Boring subroutine which should only output nbcode[Tvar[j]][k]
1.145 brouard 3586: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
1.169 brouard 3587: * nbcode[Tvar[j]][1]=
1.144 brouard 3588: */
1.130 brouard 3589:
1.145 brouard 3590: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 3591: int modmaxcovj=0; /* Modality max of covariates j */
1.145 brouard 3592: int cptcode=0; /* Modality max of covariates j */
3593: int modmincovj=0; /* Modality min of covariates j */
3594:
3595:
1.126 brouard 3596: cptcoveff=0;
3597:
1.144 brouard 3598: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 3599:
1.145 brouard 3600: /* Loop on covariates without age and products */
1.186 brouard 3601: for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
1.192 brouard 3602: for (k=-1; k < maxncov; k++) Ndum[k]=0;
1.186 brouard 3603: for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
1.136 brouard 3604: modality of this covariate Vj*/
1.145 brouard 3605: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
3606: * If product of Vn*Vm, still boolean *:
3607: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
3608: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
3609: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
1.136 brouard 3610: modality of the nth covariate of individual i. */
1.145 brouard 3611: if (ij > modmaxcovj)
3612: modmaxcovj=ij;
3613: else if (ij < modmincovj)
3614: modmincovj=ij;
3615: if ((ij < -1) && (ij > NCOVMAX)){
3616: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
3617: exit(1);
3618: }else
1.136 brouard 3619: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
1.145 brouard 3620: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
1.126 brouard 3621: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.136 brouard 3622: /* getting the maximum value of the modality of the covariate
3623: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
3624: female is 1, then modmaxcovj=1.*/
1.192 brouard 3625: } /* end for loop on individuals i */
1.145 brouard 3626: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
1.192 brouard 3627: 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 3628: cptcode=modmaxcovj;
1.137 brouard 3629: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
1.145 brouard 3630: /*for (i=0; i<=cptcode; i++) {*/
1.192 brouard 3631: for (k=modmincovj; k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
3632: printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
3633: fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
3634: if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
3635: if( k != -1){
3636: ncodemax[j]++; /* ncodemax[j]= Number of modalities of the j th
3637: covariate for which somebody answered excluding
3638: undefined. Usually 2: 0 and 1. */
3639: }
3640: ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
3641: covariate for which somebody answered including
3642: undefined. Usually 3: -1, 0 and 1. */
1.145 brouard 3643: }
3644: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
3645: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
1.131 brouard 3646: } /* Ndum[-1] number of undefined modalities */
1.126 brouard 3647:
1.136 brouard 3648: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
1.186 brouard 3649: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
3650: 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 3651: modmincovj=3; modmaxcovj = 7;
1.186 brouard 3652: There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
3653: which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
3654: defining two dummy variables: variables V1_1 and V1_2.
1.145 brouard 3655: nbcode[Tvar[j]][ij]=k;
3656: nbcode[Tvar[j]][1]=0;
3657: nbcode[Tvar[j]][2]=1;
3658: nbcode[Tvar[j]][3]=2;
1.197 brouard 3659: To be continued (not working yet).
1.145 brouard 3660: */
1.197 brouard 3661: ij=0; /* ij is similar to i but can jump over null modalities */
3662: 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*/
3663: if (Ndum[i] == 0) { /* If nobody responded to this modality k */
1.192 brouard 3664: break;
3665: }
3666: ij++;
1.197 brouard 3667: 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 3668: cptcode = ij; /* New max modality for covar j */
3669: } /* end of loop on modality i=-1 to 1 or more */
3670:
3671: /* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
3672: /* /\*recode from 0 *\/ */
3673: /* k is a modality. If we have model=V1+V1*sex */
3674: /* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
3675: /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
3676: /* } */
3677: /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
3678: /* if (ij > ncodemax[j]) { */
3679: /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
3680: /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
3681: /* break; */
3682: /* } */
3683: /* } /\* end of loop on modality k *\/ */
1.137 brouard 3684: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
3685:
1.145 brouard 3686: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.137 brouard 3687:
1.187 brouard 3688: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
1.145 brouard 3689: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
3690: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
1.187 brouard 3691: Ndum[ij]++; /* Might be supersed V1 + V1*age */
1.145 brouard 3692: }
1.126 brouard 3693:
1.192 brouard 3694: ij=0;
1.145 brouard 3695: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
3696: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
1.126 brouard 3697: if((Ndum[i]!=0) && (i<=ncovcol)){
1.192 brouard 3698: ij++;
1.145 brouard 3699: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
3700: Tvaraff[ij]=i; /*For printing (unclear) */
1.192 brouard 3701: }else{
3702: /* Tvaraff[ij]=0; */
3703: }
1.126 brouard 3704: }
1.192 brouard 3705: /* ij--; */
1.144 brouard 3706: cptcoveff=ij; /*Number of total covariates*/
1.145 brouard 3707:
1.126 brouard 3708: }
3709:
1.145 brouard 3710:
1.126 brouard 3711: /*********** Health Expectancies ****************/
3712:
1.127 brouard 3713: 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 3714:
3715: {
3716: /* Health expectancies, no variances */
1.164 brouard 3717: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 3718: int nhstepma, nstepma; /* Decreasing with age */
3719: double age, agelim, hf;
3720: double ***p3mat;
3721: double eip;
3722:
3723: pstamp(ficreseij);
3724: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3725: fprintf(ficreseij,"# Age");
3726: for(i=1; i<=nlstate;i++){
3727: for(j=1; j<=nlstate;j++){
3728: fprintf(ficreseij," e%1d%1d ",i,j);
3729: }
3730: fprintf(ficreseij," e%1d. ",i);
3731: }
3732: fprintf(ficreseij,"\n");
3733:
3734:
3735: if(estepm < stepm){
3736: printf ("Problem %d lower than %d\n",estepm, stepm);
3737: }
3738: else hstepm=estepm;
3739: /* We compute the life expectancy from trapezoids spaced every estepm months
3740: * This is mainly to measure the difference between two models: for example
3741: * if stepm=24 months pijx are given only every 2 years and by summing them
3742: * we are calculating an estimate of the Life Expectancy assuming a linear
3743: * progression in between and thus overestimating or underestimating according
3744: * to the curvature of the survival function. If, for the same date, we
3745: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3746: * to compare the new estimate of Life expectancy with the same linear
3747: * hypothesis. A more precise result, taking into account a more precise
3748: * curvature will be obtained if estepm is as small as stepm. */
3749:
3750: /* For example we decided to compute the life expectancy with the smallest unit */
3751: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3752: nhstepm is the number of hstepm from age to agelim
3753: nstepm is the number of stepm from age to agelin.
3754: Look at hpijx to understand the reason of that which relies in memory size
3755: and note for a fixed period like estepm months */
3756: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3757: survival function given by stepm (the optimization length). Unfortunately it
3758: means that if the survival funtion is printed only each two years of age and if
3759: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3760: results. So we changed our mind and took the option of the best precision.
3761: */
3762: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3763:
3764: agelim=AGESUP;
3765: /* If stepm=6 months */
3766: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3767: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3768:
3769: /* nhstepm age range expressed in number of stepm */
3770: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3771: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3772: /* if (stepm >= YEARM) hstepm=1;*/
3773: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3774: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3775:
3776: for (age=bage; age<=fage; age ++){
3777: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3778: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3779: /* if (stepm >= YEARM) hstepm=1;*/
3780: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3781:
3782: /* If stepm=6 months */
3783: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3784: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3785:
3786: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3787:
3788: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3789:
3790: printf("%d|",(int)age);fflush(stdout);
3791: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3792:
3793: /* Computing expectancies */
3794: for(i=1; i<=nlstate;i++)
3795: for(j=1; j<=nlstate;j++)
3796: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3797: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3798:
3799: /* 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]);*/
3800:
3801: }
3802:
3803: fprintf(ficreseij,"%3.0f",age );
3804: for(i=1; i<=nlstate;i++){
3805: eip=0;
3806: for(j=1; j<=nlstate;j++){
3807: eip +=eij[i][j][(int)age];
3808: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3809: }
3810: fprintf(ficreseij,"%9.4f", eip );
3811: }
3812: fprintf(ficreseij,"\n");
3813:
3814: }
3815: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3816: printf("\n");
3817: fprintf(ficlog,"\n");
3818:
3819: }
3820:
1.127 brouard 3821: 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 3822:
3823: {
3824: /* Covariances of health expectancies eij and of total life expectancies according
3825: to initial status i, ei. .
3826: */
3827: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3828: int nhstepma, nstepma; /* Decreasing with age */
3829: double age, agelim, hf;
3830: double ***p3matp, ***p3matm, ***varhe;
3831: double **dnewm,**doldm;
3832: double *xp, *xm;
3833: double **gp, **gm;
3834: double ***gradg, ***trgradg;
3835: int theta;
3836:
3837: double eip, vip;
3838:
3839: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
3840: xp=vector(1,npar);
3841: xm=vector(1,npar);
3842: dnewm=matrix(1,nlstate*nlstate,1,npar);
3843: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3844:
3845: pstamp(ficresstdeij);
3846: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3847: fprintf(ficresstdeij,"# Age");
3848: for(i=1; i<=nlstate;i++){
3849: for(j=1; j<=nlstate;j++)
3850: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3851: fprintf(ficresstdeij," e%1d. ",i);
3852: }
3853: fprintf(ficresstdeij,"\n");
3854:
3855: pstamp(ficrescveij);
3856: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3857: fprintf(ficrescveij,"# Age");
3858: for(i=1; i<=nlstate;i++)
3859: for(j=1; j<=nlstate;j++){
3860: cptj= (j-1)*nlstate+i;
3861: for(i2=1; i2<=nlstate;i2++)
3862: for(j2=1; j2<=nlstate;j2++){
3863: cptj2= (j2-1)*nlstate+i2;
3864: if(cptj2 <= cptj)
3865: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3866: }
3867: }
3868: fprintf(ficrescveij,"\n");
3869:
3870: if(estepm < stepm){
3871: printf ("Problem %d lower than %d\n",estepm, stepm);
3872: }
3873: else hstepm=estepm;
3874: /* We compute the life expectancy from trapezoids spaced every estepm months
3875: * This is mainly to measure the difference between two models: for example
3876: * if stepm=24 months pijx are given only every 2 years and by summing them
3877: * we are calculating an estimate of the Life Expectancy assuming a linear
3878: * progression in between and thus overestimating or underestimating according
3879: * to the curvature of the survival function. If, for the same date, we
3880: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3881: * to compare the new estimate of Life expectancy with the same linear
3882: * hypothesis. A more precise result, taking into account a more precise
3883: * curvature will be obtained if estepm is as small as stepm. */
3884:
3885: /* For example we decided to compute the life expectancy with the smallest unit */
3886: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3887: nhstepm is the number of hstepm from age to agelim
3888: nstepm is the number of stepm from age to agelin.
3889: Look at hpijx to understand the reason of that which relies in memory size
3890: and note for a fixed period like estepm months */
3891: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3892: survival function given by stepm (the optimization length). Unfortunately it
3893: means that if the survival funtion is printed only each two years of age and if
3894: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3895: results. So we changed our mind and took the option of the best precision.
3896: */
3897: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3898:
3899: /* If stepm=6 months */
3900: /* nhstepm age range expressed in number of stepm */
3901: agelim=AGESUP;
3902: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3903: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3904: /* if (stepm >= YEARM) hstepm=1;*/
3905: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3906:
3907: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3908: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3909: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3910: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3911: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3912: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3913:
3914: for (age=bage; age<=fage; age ++){
3915: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3916: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3917: /* if (stepm >= YEARM) hstepm=1;*/
3918: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3919:
3920: /* If stepm=6 months */
3921: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3922: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3923:
3924: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3925:
3926: /* Computing Variances of health expectancies */
3927: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3928: decrease memory allocation */
3929: for(theta=1; theta <=npar; theta++){
3930: for(i=1; i<=npar; i++){
3931: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3932: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3933: }
3934: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3935: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3936:
3937: for(j=1; j<= nlstate; j++){
3938: for(i=1; i<=nlstate; i++){
3939: for(h=0; h<=nhstepm-1; h++){
3940: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3941: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3942: }
3943: }
3944: }
3945:
3946: for(ij=1; ij<= nlstate*nlstate; ij++)
3947: for(h=0; h<=nhstepm-1; h++){
3948: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3949: }
3950: }/* End theta */
3951:
3952:
3953: for(h=0; h<=nhstepm-1; h++)
3954: for(j=1; j<=nlstate*nlstate;j++)
3955: for(theta=1; theta <=npar; theta++)
3956: trgradg[h][j][theta]=gradg[h][theta][j];
3957:
3958:
3959: for(ij=1;ij<=nlstate*nlstate;ij++)
3960: for(ji=1;ji<=nlstate*nlstate;ji++)
3961: varhe[ij][ji][(int)age] =0.;
3962:
3963: printf("%d|",(int)age);fflush(stdout);
3964: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3965: for(h=0;h<=nhstepm-1;h++){
3966: for(k=0;k<=nhstepm-1;k++){
3967: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3968: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3969: for(ij=1;ij<=nlstate*nlstate;ij++)
3970: for(ji=1;ji<=nlstate*nlstate;ji++)
3971: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3972: }
3973: }
3974:
3975: /* Computing expectancies */
3976: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3977: for(i=1; i<=nlstate;i++)
3978: for(j=1; j<=nlstate;j++)
3979: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3980: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3981:
3982: /* 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]);*/
3983:
3984: }
3985:
3986: fprintf(ficresstdeij,"%3.0f",age );
3987: for(i=1; i<=nlstate;i++){
3988: eip=0.;
3989: vip=0.;
3990: for(j=1; j<=nlstate;j++){
3991: eip += eij[i][j][(int)age];
3992: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3993: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3994: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3995: }
3996: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3997: }
3998: fprintf(ficresstdeij,"\n");
3999:
4000: fprintf(ficrescveij,"%3.0f",age );
4001: for(i=1; i<=nlstate;i++)
4002: for(j=1; j<=nlstate;j++){
4003: cptj= (j-1)*nlstate+i;
4004: for(i2=1; i2<=nlstate;i2++)
4005: for(j2=1; j2<=nlstate;j2++){
4006: cptj2= (j2-1)*nlstate+i2;
4007: if(cptj2 <= cptj)
4008: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
4009: }
4010: }
4011: fprintf(ficrescveij,"\n");
4012:
4013: }
4014: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
4015: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
4016: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
4017: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
4018: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4019: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4020: printf("\n");
4021: fprintf(ficlog,"\n");
4022:
4023: free_vector(xm,1,npar);
4024: free_vector(xp,1,npar);
4025: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
4026: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
4027: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
4028: }
4029:
4030: /************ Variance ******************/
1.209 brouard 4031: 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 *ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
1.126 brouard 4032: {
4033: /* Variance of health expectancies */
4034: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
4035: /* double **newm;*/
1.169 brouard 4036: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
4037:
4038: int movingaverage();
1.126 brouard 4039: double **dnewm,**doldm;
4040: double **dnewmp,**doldmp;
4041: int i, j, nhstepm, hstepm, h, nstepm ;
1.164 brouard 4042: int k;
1.126 brouard 4043: double *xp;
4044: double **gp, **gm; /* for var eij */
4045: double ***gradg, ***trgradg; /*for var eij */
4046: double **gradgp, **trgradgp; /* for var p point j */
4047: double *gpp, *gmp; /* for var p point j */
4048: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
4049: double ***p3mat;
4050: double age,agelim, hf;
4051: double ***mobaverage;
4052: int theta;
4053: char digit[4];
4054: char digitp[25];
4055:
4056: char fileresprobmorprev[FILENAMELENGTH];
4057:
4058: if(popbased==1){
4059: if(mobilav!=0)
1.201 brouard 4060: strcpy(digitp,"-POPULBASED-MOBILAV_");
4061: else strcpy(digitp,"-POPULBASED-NOMOBIL_");
1.126 brouard 4062: }
4063: else
1.201 brouard 4064: strcpy(digitp,"-STABLBASED_");
1.126 brouard 4065:
4066: if (mobilav!=0) {
4067: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4068: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
4069: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4070: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4071: }
4072: }
4073:
1.201 brouard 4074: strcpy(fileresprobmorprev,"PRMORPREV-");
1.126 brouard 4075: sprintf(digit,"%-d",ij);
4076: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
4077: strcat(fileresprobmorprev,digit); /* Tvar to be done */
4078: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
1.202 brouard 4079: strcat(fileresprobmorprev,fileresu);
1.126 brouard 4080: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
4081: printf("Problem with resultfile: %s\n", fileresprobmorprev);
4082: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
4083: }
4084: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
4085: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
4086: pstamp(ficresprobmorprev);
4087: 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);
4088: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
4089: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
4090: fprintf(ficresprobmorprev," p.%-d SE",j);
4091: for(i=1; i<=nlstate;i++)
4092: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
4093: }
4094: fprintf(ficresprobmorprev,"\n");
1.208 brouard 4095:
1.126 brouard 4096: fprintf(ficgp,"\n# Routine varevsij");
1.200 brouard 4097: fprintf(ficgp,"\nunset title \n");
4098: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
1.126 brouard 4099: 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");
4100: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
4101: /* } */
4102: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4103: pstamp(ficresvij);
4104: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
4105: if(popbased==1)
1.128 brouard 4106: 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 4107: else
4108: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
4109: fprintf(ficresvij,"# Age");
4110: for(i=1; i<=nlstate;i++)
4111: for(j=1; j<=nlstate;j++)
4112: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
4113: fprintf(ficresvij,"\n");
4114:
4115: xp=vector(1,npar);
4116: dnewm=matrix(1,nlstate,1,npar);
4117: doldm=matrix(1,nlstate,1,nlstate);
4118: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
4119: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4120:
4121: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
4122: gpp=vector(nlstate+1,nlstate+ndeath);
4123: gmp=vector(nlstate+1,nlstate+ndeath);
4124: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
4125:
4126: if(estepm < stepm){
4127: printf ("Problem %d lower than %d\n",estepm, stepm);
4128: }
4129: else hstepm=estepm;
4130: /* For example we decided to compute the life expectancy with the smallest unit */
4131: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
4132: nhstepm is the number of hstepm from age to agelim
1.208 brouard 4133: nstepm is the number of stepm from age to agelim.
1.209 brouard 4134: Look at function hpijx to understand why because of memory size limitations,
1.208 brouard 4135: we decided (b) to get a life expectancy respecting the most precise curvature of the
1.126 brouard 4136: survival function given by stepm (the optimization length). Unfortunately it
4137: means that if the survival funtion is printed every two years of age and if
4138: you sum them up and add 1 year (area under the trapezoids) you won't get the same
4139: results. So we changed our mind and took the option of the best precision.
4140: */
4141: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
4142: agelim = AGESUP;
4143: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
4144: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4145: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
4146: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4147: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
4148: gp=matrix(0,nhstepm,1,nlstate);
4149: gm=matrix(0,nhstepm,1,nlstate);
4150:
4151:
4152: for(theta=1; theta <=npar; theta++){
4153: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
4154: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4155: }
1.209 brouard 4156:
4157: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
1.126 brouard 4158:
4159: if (popbased==1) {
4160: if(mobilav ==0){
4161: for(i=1; i<=nlstate;i++)
4162: prlim[i][i]=probs[(int)age][i][ij];
4163: }else{ /* mobilav */
4164: for(i=1; i<=nlstate;i++)
4165: prlim[i][i]=mobaverage[(int)age][i][ij];
4166: }
4167: }
4168:
1.209 brouard 4169: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); /* Returns p3mat[i][j][h] for h=1 to nhstepm */
1.126 brouard 4170: for(j=1; j<= nlstate; j++){
4171: for(h=0; h<=nhstepm; h++){
4172: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
4173: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
4174: }
4175: }
1.209 brouard 4176: /* Next for computing probability of death (h=1 means
1.126 brouard 4177: computed over hstepm matrices product = hstepm*stepm months)
4178: as a weighted average of prlim.
4179: */
4180: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4181: for(i=1,gpp[j]=0.; i<= nlstate; i++)
4182: gpp[j] += prlim[i][i]*p3mat[i][j][1];
4183: }
4184: /* end probability of death */
4185:
4186: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
4187: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.209 brouard 4188:
4189: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij);
1.126 brouard 4190:
4191: if (popbased==1) {
4192: if(mobilav ==0){
4193: for(i=1; i<=nlstate;i++)
4194: prlim[i][i]=probs[(int)age][i][ij];
4195: }else{ /* mobilav */
4196: for(i=1; i<=nlstate;i++)
4197: prlim[i][i]=mobaverage[(int)age][i][ij];
4198: }
4199: }
4200:
1.209 brouard 4201: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
4202:
1.128 brouard 4203: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
1.126 brouard 4204: for(h=0; h<=nhstepm; h++){
4205: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
4206: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
4207: }
4208: }
4209: /* This for computing probability of death (h=1 means
4210: computed over hstepm matrices product = hstepm*stepm months)
4211: as a weighted average of prlim.
4212: */
4213: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4214: for(i=1,gmp[j]=0.; i<= nlstate; i++)
4215: gmp[j] += prlim[i][i]*p3mat[i][j][1];
4216: }
4217: /* end probability of death */
4218:
4219: for(j=1; j<= nlstate; j++) /* vareij */
4220: for(h=0; h<=nhstepm; h++){
4221: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
4222: }
4223:
4224: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
4225: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
4226: }
4227:
4228: } /* End theta */
4229:
4230: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
4231:
4232: for(h=0; h<=nhstepm; h++) /* veij */
4233: for(j=1; j<=nlstate;j++)
4234: for(theta=1; theta <=npar; theta++)
4235: trgradg[h][j][theta]=gradg[h][theta][j];
4236:
4237: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
4238: for(theta=1; theta <=npar; theta++)
4239: trgradgp[j][theta]=gradgp[theta][j];
4240:
4241:
4242: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
4243: for(i=1;i<=nlstate;i++)
4244: for(j=1;j<=nlstate;j++)
4245: vareij[i][j][(int)age] =0.;
4246:
4247: for(h=0;h<=nhstepm;h++){
4248: for(k=0;k<=nhstepm;k++){
4249: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
4250: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
4251: for(i=1;i<=nlstate;i++)
4252: for(j=1;j<=nlstate;j++)
4253: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
4254: }
4255: }
4256:
4257: /* pptj */
4258: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
4259: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
4260: for(j=nlstate+1;j<=nlstate+ndeath;j++)
4261: for(i=nlstate+1;i<=nlstate+ndeath;i++)
4262: varppt[j][i]=doldmp[j][i];
4263: /* end ppptj */
4264: /* x centered again */
1.209 brouard 4265:
4266: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij);
1.126 brouard 4267:
4268: if (popbased==1) {
4269: if(mobilav ==0){
4270: for(i=1; i<=nlstate;i++)
4271: prlim[i][i]=probs[(int)age][i][ij];
4272: }else{ /* mobilav */
4273: for(i=1; i<=nlstate;i++)
4274: prlim[i][i]=mobaverage[(int)age][i][ij];
4275: }
4276: }
4277:
4278: /* This for computing probability of death (h=1 means
4279: computed over hstepm (estepm) matrices product = hstepm*stepm months)
4280: as a weighted average of prlim.
4281: */
1.209 brouard 4282: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
1.126 brouard 4283: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4284: for(i=1,gmp[j]=0.;i<= nlstate; i++)
4285: gmp[j] += prlim[i][i]*p3mat[i][j][1];
4286: }
4287: /* end probability of death */
4288:
4289: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
4290: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
4291: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
4292: for(i=1; i<=nlstate;i++){
4293: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
4294: }
4295: }
4296: fprintf(ficresprobmorprev,"\n");
4297:
4298: fprintf(ficresvij,"%.0f ",age );
4299: for(i=1; i<=nlstate;i++)
4300: for(j=1; j<=nlstate;j++){
4301: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
4302: }
4303: fprintf(ficresvij,"\n");
4304: free_matrix(gp,0,nhstepm,1,nlstate);
4305: free_matrix(gm,0,nhstepm,1,nlstate);
4306: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
4307: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
4308: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4309: } /* End age */
4310: free_vector(gpp,nlstate+1,nlstate+ndeath);
4311: free_vector(gmp,nlstate+1,nlstate+ndeath);
4312: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
4313: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.199 brouard 4314: /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
4315: fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
1.126 brouard 4316: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
1.131 brouard 4317: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.201 brouard 4318: fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 4319: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
4320: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
4321: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.145 brouard 4322: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
1.170 brouard 4323: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
1.145 brouard 4324: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
1.126 brouard 4325: 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 4326: 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 4327: /* 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 4328: */
1.199 brouard 4329: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
1.201 brouard 4330: fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 4331:
4332: free_vector(xp,1,npar);
4333: free_matrix(doldm,1,nlstate,1,nlstate);
4334: free_matrix(dnewm,1,nlstate,1,npar);
4335: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4336: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
4337: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4338: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4339: fclose(ficresprobmorprev);
4340: fflush(ficgp);
4341: fflush(fichtm);
4342: } /* end varevsij */
4343:
4344: /************ Variance of prevlim ******************/
1.209 brouard 4345: 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 *ncvyearp, int ij, char strstart[])
1.126 brouard 4346: {
1.205 brouard 4347: /* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
1.126 brouard 4348: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 4349:
1.126 brouard 4350: double **dnewm,**doldm;
4351: int i, j, nhstepm, hstepm;
4352: double *xp;
4353: double *gp, *gm;
4354: double **gradg, **trgradg;
1.208 brouard 4355: double **mgm, **mgp;
1.126 brouard 4356: double age,agelim;
4357: int theta;
4358:
4359: pstamp(ficresvpl);
4360: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
4361: fprintf(ficresvpl,"# Age");
4362: for(i=1; i<=nlstate;i++)
4363: fprintf(ficresvpl," %1d-%1d",i,i);
4364: fprintf(ficresvpl,"\n");
4365:
4366: xp=vector(1,npar);
4367: dnewm=matrix(1,nlstate,1,npar);
4368: doldm=matrix(1,nlstate,1,nlstate);
4369:
4370: hstepm=1*YEARM; /* Every year of age */
4371: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
4372: agelim = AGESUP;
4373: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
4374: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4375: if (stepm >= YEARM) hstepm=1;
4376: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4377: gradg=matrix(1,npar,1,nlstate);
1.208 brouard 4378: mgp=matrix(1,npar,1,nlstate);
4379: mgm=matrix(1,npar,1,nlstate);
1.126 brouard 4380: gp=vector(1,nlstate);
4381: gm=vector(1,nlstate);
4382:
4383: for(theta=1; theta <=npar; theta++){
4384: for(i=1; i<=npar; i++){ /* Computes gradient */
4385: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4386: }
1.209 brouard 4387: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
4388: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
4389: else
4390: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
1.208 brouard 4391: for(i=1;i<=nlstate;i++){
1.126 brouard 4392: gp[i] = prlim[i][i];
1.208 brouard 4393: mgp[theta][i] = prlim[i][i];
4394: }
1.126 brouard 4395: for(i=1; i<=npar; i++) /* Computes gradient */
4396: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.209 brouard 4397: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
4398: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
4399: else
4400: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
1.208 brouard 4401: for(i=1;i<=nlstate;i++){
1.126 brouard 4402: gm[i] = prlim[i][i];
1.208 brouard 4403: mgm[theta][i] = prlim[i][i];
4404: }
1.126 brouard 4405: for(i=1;i<=nlstate;i++)
4406: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1.209 brouard 4407: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
1.126 brouard 4408: } /* End theta */
4409:
4410: trgradg =matrix(1,nlstate,1,npar);
4411:
4412: for(j=1; j<=nlstate;j++)
4413: for(theta=1; theta <=npar; theta++)
4414: trgradg[j][theta]=gradg[theta][j];
1.209 brouard 4415: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
4416: /* printf("\nmgm mgp %d ",(int)age); */
4417: /* for(j=1; j<=nlstate;j++){ */
4418: /* printf(" %d ",j); */
4419: /* for(theta=1; theta <=npar; theta++) */
4420: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
4421: /* printf("\n "); */
4422: /* } */
4423: /* } */
4424: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
4425: /* printf("\n gradg %d ",(int)age); */
4426: /* for(j=1; j<=nlstate;j++){ */
4427: /* printf("%d ",j); */
4428: /* for(theta=1; theta <=npar; theta++) */
4429: /* printf("%d %lf ",theta,gradg[theta][j]); */
4430: /* printf("\n "); */
4431: /* } */
4432: /* } */
1.126 brouard 4433:
4434: for(i=1;i<=nlstate;i++)
4435: varpl[i][(int)age] =0.;
1.209 brouard 4436: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
1.205 brouard 4437: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
4438: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
4439: }else{
1.126 brouard 4440: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
4441: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 4442: }
1.126 brouard 4443: for(i=1;i<=nlstate;i++)
4444: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
4445:
4446: fprintf(ficresvpl,"%.0f ",age );
4447: for(i=1; i<=nlstate;i++)
4448: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
4449: fprintf(ficresvpl,"\n");
4450: free_vector(gp,1,nlstate);
4451: free_vector(gm,1,nlstate);
1.208 brouard 4452: free_matrix(mgm,1,npar,1,nlstate);
4453: free_matrix(mgp,1,npar,1,nlstate);
1.126 brouard 4454: free_matrix(gradg,1,npar,1,nlstate);
4455: free_matrix(trgradg,1,nlstate,1,npar);
4456: } /* End age */
4457:
4458: free_vector(xp,1,npar);
4459: free_matrix(doldm,1,nlstate,1,npar);
4460: free_matrix(dnewm,1,nlstate,1,nlstate);
4461:
4462: }
4463:
4464: /************ Variance of one-step probabilities ******************/
4465: 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[])
4466: {
1.164 brouard 4467: int i, j=0, k1, l1, tj;
1.126 brouard 4468: int k2, l2, j1, z1;
1.164 brouard 4469: int k=0, l;
1.145 brouard 4470: int first=1, first1, first2;
1.126 brouard 4471: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
4472: double **dnewm,**doldm;
4473: double *xp;
4474: double *gp, *gm;
4475: double **gradg, **trgradg;
4476: double **mu;
1.164 brouard 4477: double age, cov[NCOVMAX+1];
1.126 brouard 4478: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
4479: int theta;
4480: char fileresprob[FILENAMELENGTH];
4481: char fileresprobcov[FILENAMELENGTH];
4482: char fileresprobcor[FILENAMELENGTH];
4483: double ***varpij;
4484:
1.201 brouard 4485: strcpy(fileresprob,"PROB_");
1.126 brouard 4486: strcat(fileresprob,fileres);
4487: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
4488: printf("Problem with resultfile: %s\n", fileresprob);
4489: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
4490: }
1.201 brouard 4491: strcpy(fileresprobcov,"PROBCOV_");
1.202 brouard 4492: strcat(fileresprobcov,fileresu);
1.126 brouard 4493: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
4494: printf("Problem with resultfile: %s\n", fileresprobcov);
4495: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
4496: }
1.201 brouard 4497: strcpy(fileresprobcor,"PROBCOR_");
1.202 brouard 4498: strcat(fileresprobcor,fileresu);
1.126 brouard 4499: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
4500: printf("Problem with resultfile: %s\n", fileresprobcor);
4501: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
4502: }
4503: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4504: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4505: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4506: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4507: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4508: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4509: pstamp(ficresprob);
4510: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
4511: fprintf(ficresprob,"# Age");
4512: pstamp(ficresprobcov);
4513: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
4514: fprintf(ficresprobcov,"# Age");
4515: pstamp(ficresprobcor);
4516: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
4517: fprintf(ficresprobcor,"# Age");
4518:
4519:
4520: for(i=1; i<=nlstate;i++)
4521: for(j=1; j<=(nlstate+ndeath);j++){
4522: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
4523: fprintf(ficresprobcov," p%1d-%1d ",i,j);
4524: fprintf(ficresprobcor," p%1d-%1d ",i,j);
4525: }
4526: /* fprintf(ficresprob,"\n");
4527: fprintf(ficresprobcov,"\n");
4528: fprintf(ficresprobcor,"\n");
4529: */
1.131 brouard 4530: xp=vector(1,npar);
1.126 brouard 4531: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4532: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4533: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
4534: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
4535: first=1;
4536: fprintf(ficgp,"\n# Routine varprob");
4537: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
4538: fprintf(fichtm,"\n");
4539:
1.200 brouard 4540: 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 4541: 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);
4542: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
1.126 brouard 4543: and drawn. It helps understanding how is the covariance between two incidences.\
4544: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
4545: 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. \
4546: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
4547: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
4548: standard deviations wide on each axis. <br>\
4549: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
4550: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
4551: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
4552:
4553: cov[1]=1;
1.145 brouard 4554: /* tj=cptcoveff; */
4555: tj = (int) pow(2,cptcoveff);
1.126 brouard 4556: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
4557: j1=0;
1.145 brouard 4558: for(j1=1; j1<=tj;j1++){
4559: /*for(i1=1; i1<=ncodemax[t];i1++){ */
4560: /*j1++;*/
1.126 brouard 4561: if (cptcovn>0) {
4562: fprintf(ficresprob, "\n#********** Variable ");
1.198 brouard 4563: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4564: fprintf(ficresprob, "**********\n#\n");
4565: fprintf(ficresprobcov, "\n#********** Variable ");
1.198 brouard 4566: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4567: fprintf(ficresprobcov, "**********\n#\n");
4568:
4569: fprintf(ficgp, "\n#********** Variable ");
1.198 brouard 4570: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4571: fprintf(ficgp, "**********\n#\n");
4572:
4573:
4574: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.198 brouard 4575: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4576: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
4577:
4578: fprintf(ficresprobcor, "\n#********** Variable ");
1.198 brouard 4579: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4580: fprintf(ficresprobcor, "**********\n#");
4581: }
4582:
1.145 brouard 4583: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
4584: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4585: gp=vector(1,(nlstate)*(nlstate+ndeath));
4586: gm=vector(1,(nlstate)*(nlstate+ndeath));
1.126 brouard 4587: for (age=bage; age<=fage; age ++){
4588: cov[2]=age;
1.187 brouard 4589: if(nagesqr==1)
4590: cov[3]= age*age;
1.126 brouard 4591: for (k=1; k<=cptcovn;k++) {
1.200 brouard 4592: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
4593: /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
1.145 brouard 4594: * 1 1 1 1 1
4595: * 2 2 1 1 1
4596: * 3 1 2 1 1
4597: */
4598: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
1.126 brouard 4599: }
1.186 brouard 4600: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 4601: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
1.126 brouard 4602: for (k=1; k<=cptcovprod;k++)
1.200 brouard 4603: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.126 brouard 4604:
4605:
4606: for(theta=1; theta <=npar; theta++){
4607: for(i=1; i<=npar; i++)
4608: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
4609:
4610: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4611:
4612: k=0;
4613: for(i=1; i<= (nlstate); i++){
4614: for(j=1; j<=(nlstate+ndeath);j++){
4615: k=k+1;
4616: gp[k]=pmmij[i][j];
4617: }
4618: }
4619:
4620: for(i=1; i<=npar; i++)
4621: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
4622:
4623: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4624: k=0;
4625: for(i=1; i<=(nlstate); i++){
4626: for(j=1; j<=(nlstate+ndeath);j++){
4627: k=k+1;
4628: gm[k]=pmmij[i][j];
4629: }
4630: }
4631:
4632: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
4633: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
4634: }
4635:
4636: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
4637: for(theta=1; theta <=npar; theta++)
4638: trgradg[j][theta]=gradg[theta][j];
4639:
4640: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
4641: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
4642:
4643: pmij(pmmij,cov,ncovmodel,x,nlstate);
4644:
4645: k=0;
4646: for(i=1; i<=(nlstate); i++){
4647: for(j=1; j<=(nlstate+ndeath);j++){
4648: k=k+1;
4649: mu[k][(int) age]=pmmij[i][j];
4650: }
4651: }
4652: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
4653: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
4654: varpij[i][j][(int)age] = doldm[i][j];
4655:
4656: /*printf("\n%d ",(int)age);
4657: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4658: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4659: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4660: }*/
4661:
4662: fprintf(ficresprob,"\n%d ",(int)age);
4663: fprintf(ficresprobcov,"\n%d ",(int)age);
4664: fprintf(ficresprobcor,"\n%d ",(int)age);
4665:
4666: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
4667: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
4668: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4669: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
4670: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
4671: }
4672: i=0;
4673: for (k=1; k<=(nlstate);k++){
4674: for (l=1; l<=(nlstate+ndeath);l++){
1.145 brouard 4675: i++;
1.126 brouard 4676: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
4677: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
4678: for (j=1; j<=i;j++){
1.145 brouard 4679: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
1.126 brouard 4680: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
4681: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
4682: }
4683: }
4684: }/* end of loop for state */
4685: } /* end of loop for age */
1.145 brouard 4686: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
4687: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
4688: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4689: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4690:
1.126 brouard 4691: /* Confidence intervalle of pij */
4692: /*
1.131 brouard 4693: fprintf(ficgp,"\nunset parametric;unset label");
1.126 brouard 4694: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
4695: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
4696: 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);
4697: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
4698: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
4699: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
4700: */
4701:
4702: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
1.145 brouard 4703: first1=1;first2=2;
1.126 brouard 4704: for (k2=1; k2<=(nlstate);k2++){
4705: for (l2=1; l2<=(nlstate+ndeath);l2++){
4706: if(l2==k2) continue;
4707: j=(k2-1)*(nlstate+ndeath)+l2;
4708: for (k1=1; k1<=(nlstate);k1++){
4709: for (l1=1; l1<=(nlstate+ndeath);l1++){
4710: if(l1==k1) continue;
4711: i=(k1-1)*(nlstate+ndeath)+l1;
4712: if(i<=j) continue;
4713: for (age=bage; age<=fage; age ++){
4714: if ((int)age %5==0){
4715: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
4716: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
4717: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
4718: mu1=mu[i][(int) age]/stepm*YEARM ;
4719: mu2=mu[j][(int) age]/stepm*YEARM;
4720: c12=cv12/sqrt(v1*v2);
4721: /* Computing eigen value of matrix of covariance */
4722: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4723: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
1.135 brouard 4724: if ((lc2 <0) || (lc1 <0) ){
1.145 brouard 4725: if(first2==1){
4726: first1=0;
4727: 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);
4728: }
4729: 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);
4730: /* lc1=fabs(lc1); */ /* If we want to have them positive */
4731: /* lc2=fabs(lc2); */
1.135 brouard 4732: }
4733:
1.126 brouard 4734: /* Eigen vectors */
4735: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
4736: /*v21=sqrt(1.-v11*v11); *//* error */
4737: v21=(lc1-v1)/cv12*v11;
4738: v12=-v21;
4739: v22=v11;
4740: tnalp=v21/v11;
4741: if(first1==1){
4742: first1=0;
4743: 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);
4744: }
4745: 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);
4746: /*printf(fignu*/
4747: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
4748: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
4749: if(first==1){
4750: first=0;
1.200 brouard 4751: fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
1.126 brouard 4752: fprintf(ficgp,"\nset parametric;unset label");
4753: 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 4754: fprintf(ficgp,"\nset ter svg size 640, 480");
1.126 brouard 4755: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.201 brouard 4756: :<a href=\"%s_%d%1d%1d-%1d%1d.svg\">\
4757: %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
4758: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,\
4759: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
4760: fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
1.126 brouard 4761: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
1.201 brouard 4762: fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
1.126 brouard 4763: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4764: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4765: 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",\
4766: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4767: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4768: }else{
4769: first=0;
4770: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4771: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4772: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4773: 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",\
4774: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4775: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4776: }/* if first */
4777: } /* age mod 5 */
4778: } /* end loop age */
1.201 brouard 4779: 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 4780: first=1;
4781: } /*l12 */
4782: } /* k12 */
4783: } /*l1 */
4784: }/* k1 */
1.169 brouard 4785: /* } */ /* loop covariates */
1.126 brouard 4786: }
4787: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4788: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4789: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4790: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4791: free_vector(xp,1,npar);
4792: fclose(ficresprob);
4793: fclose(ficresprobcov);
4794: fclose(ficresprobcor);
4795: fflush(ficgp);
4796: fflush(fichtmcov);
4797: }
4798:
4799:
4800: /******************* Printing html file ***********/
1.201 brouard 4801: void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 4802: int lastpass, int stepm, int weightopt, char model[],\
4803: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
4804: int popforecast, int estepm ,\
4805: double jprev1, double mprev1,double anprev1, \
4806: double jprev2, double mprev2,double anprev2){
4807: int jj1, k1, i1, cpt;
4808:
4809: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4810: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4811: </ul>");
4812: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
4813: - 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 4814: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
1.126 brouard 4815: fprintf(fichtm,"\
4816: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
1.201 brouard 4817: stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
1.126 brouard 4818: fprintf(fichtm,"\
4819: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4820: subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
1.126 brouard 4821: fprintf(fichtm,"\
1.128 brouard 4822: - (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 4823: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4824: estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
1.126 brouard 4825: fprintf(fichtm,"\
4826: - Population projections by age and states: \
1.201 brouard 4827: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
1.126 brouard 4828:
4829: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4830:
1.145 brouard 4831: m=pow(2,cptcoveff);
1.126 brouard 4832: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4833:
4834: jj1=0;
4835: for(k1=1; k1<=m;k1++){
1.192 brouard 4836: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
1.126 brouard 4837: jj1++;
4838: if (cptcovn > 0) {
4839: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.192 brouard 4840: for (cpt=1; cpt<=cptcoveff;cpt++){
1.198 brouard 4841: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
4842: printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
1.192 brouard 4843: }
1.126 brouard 4844: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4845: }
1.201 brouard 4846: /* aij, bij */
4847: 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> \
4848: <img src=\"%s_%d-1.svg\">",subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.126 brouard 4849: /* Pij */
1.202 brouard 4850: 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 4851: <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.126 brouard 4852: /* Quasi-incidences */
1.201 brouard 4853: fprintf(fichtm,"<br>\n- Iij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
4854: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too,\
4855: incidence (rates) are the limit when h tends to zero of the ratio of the probability hPij \
4856: divided by h: hPij/h : <a href=\"%s_%d-3.svg\">%s_%d-3.svg</a><br> \
4857: <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
4858: /* Survival functions (period) in state j */
4859: for(cpt=1; cpt<=nlstate;cpt++){
4860: 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> \
4861: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);
4862: }
4863: /* State specific survival functions (period) */
4864: for(cpt=1; cpt<=nlstate;cpt++){
1.208 brouard 4865: fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
1.201 brouard 4866: Or probability to survive in various states (1 to %d) being in state %d at different ages.\
4867: <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);
4868: }
4869: /* Period (stable) prevalence in each health state */
4870: for(cpt=1; cpt<=nlstate;cpt++){
4871: 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> \
4872: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);
4873: }
1.126 brouard 4874: for(cpt=1; cpt<=nlstate;cpt++) {
1.205 brouard 4875: 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> \
1.201 brouard 4876: <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 4877: }
1.192 brouard 4878: /* } /\* end i1 *\/ */
1.126 brouard 4879: }/* End k1 */
4880: fprintf(fichtm,"</ul>");
4881:
4882: fprintf(fichtm,"\
4883: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 brouard 4884: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
1.203 brouard 4885: - 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 4886: But because parameters are usually highly correlated (a higher incidence of disability \
4887: and a higher incidence of recovery can give very close observed transition) it might \
4888: be very useful to look not only at linear confidence intervals estimated from the \
4889: variances but at the covariance matrix. And instead of looking at the estimated coefficients \
4890: (parameters) of the logistic regression, it might be more meaningful to visualize the \
4891: covariance matrix of the one-step probabilities. \
4892: See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
1.126 brouard 4893:
1.193 brouard 4894: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4895: subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
1.126 brouard 4896: fprintf(fichtm,"\
4897: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4898: subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
1.126 brouard 4899:
4900: fprintf(fichtm,"\
4901: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4902: subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
1.126 brouard 4903: fprintf(fichtm,"\
4904: - 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): \
4905: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 4906: estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
1.126 brouard 4907: fprintf(fichtm,"\
4908: - (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): \
4909: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 4910: estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
1.126 brouard 4911: fprintf(fichtm,"\
1.128 brouard 4912: - 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 4913: estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
1.126 brouard 4914: fprintf(fichtm,"\
1.128 brouard 4915: - 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 4916: estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
1.126 brouard 4917: fprintf(fichtm,"\
4918: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
1.201 brouard 4919: subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
1.126 brouard 4920:
4921: /* if(popforecast==1) fprintf(fichtm,"\n */
4922: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4923: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4924: /* <br>",fileres,fileres,fileres,fileres); */
4925: /* else */
4926: /* 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); */
4927: fflush(fichtm);
4928: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4929:
1.145 brouard 4930: m=pow(2,cptcoveff);
1.126 brouard 4931: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4932:
4933: jj1=0;
4934: for(k1=1; k1<=m;k1++){
1.192 brouard 4935: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
1.126 brouard 4936: jj1++;
4937: if (cptcovn > 0) {
4938: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4939: for (cpt=1; cpt<=cptcoveff;cpt++)
1.198 brouard 4940: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
1.126 brouard 4941: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4942: }
4943: for(cpt=1; cpt<=nlstate;cpt++) {
4944: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
1.205 brouard 4945: prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d%d.svg\"> %s_%d-%d.svg <br>\
4946: <img src=\"%s_%d-%d.svg\">",cpt,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1);
1.126 brouard 4947: }
4948: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 4949: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4950: true period expectancies (those weighted with period prevalences are also\
4951: drawn in addition to the population based expectancies computed using\
1.205 brouard 4952: observed and cahotic prevalences: <a href=\"%s_%d.svg\">%s_%d.svg<br>\
4953: <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
1.192 brouard 4954: /* } /\* end i1 *\/ */
1.126 brouard 4955: }/* End k1 */
4956: fprintf(fichtm,"</ul>");
4957: fflush(fichtm);
4958: }
4959:
4960: /******************* Gnuplot file **************/
1.201 brouard 4961: void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 4962:
4963: char dirfileres[132],optfileres[132];
1.164 brouard 4964: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
1.130 brouard 4965: int ng=0;
1.201 brouard 4966: int vpopbased;
1.126 brouard 4967: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4968: /* printf("Problem with file %s",optionfilegnuplot); */
4969: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4970: /* } */
4971:
4972: /*#ifdef windows */
4973: fprintf(ficgp,"cd \"%s\" \n",pathc);
4974: /*#endif */
4975: m=pow(2,cptcoveff);
4976:
1.210 ! brouard 4977: /* Projected Prevalences */
! 4978: /* plot "NAGI0w_V1V2_monthlyb2b-proj/F_NAGI0w_V1V2_monthlyb2b-proj.txt" u 6:((($1 == 1) && ($2==0) && ($3==2) &&($4==0))? $7/(1-$13):1/0) t 'p11' w line */
! 4979: /* replot "" u 6:((($1 == 1) && ($2==0) && ($3==2) &&($4==0))? $8/(1-$14):1/0) t 'p21' w line */
! 4980: /* replot "" u 6:((($1 == 1) && ($2==0) && ($3==2) &&($4==0)&&($9!=0))? $9/(1-$15):1/0) t 'p.1' w line */
! 4981:
1.202 brouard 4982: /* Contribution to likelihood */
4983: /* Plot the probability implied in the likelihood */
4984: fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
4985: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
4986: /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
1.205 brouard 4987: fprintf(ficgp,"\nset ter pngcairo size 640, 480");
1.204 brouard 4988: /* nice for mle=4 plot by number of matrix products.
1.202 brouard 4989: replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
4990: /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */
4991: /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
1.204 brouard 4992: fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
1.205 brouard 4993: fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$12):5 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",subdirf(fileresilk));
1.204 brouard 4994: fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
1.205 brouard 4995: fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$12):4 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk));
1.204 brouard 4996: for (i=1; i<= nlstate ; i ++) {
4997: fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
1.205 brouard 4998: fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk));
4999: fprintf(ficgp," u 2:($4 == %d && $5==%d ? $9 : 1/0):($11/4.):5 t \"p%d%d\" with points pointtype 7 ps variable lc variable \\\n",i,1,i,1);
1.204 brouard 5000: for (j=2; j<= nlstate+ndeath ; j ++) {
1.205 brouard 5001: fprintf(ficgp,",\\\n \"\" u 2:($4 == %d && $5==%d ? $9 : 1/0):($11/4.):5 t \"p%d%d\" with points pointtype 7 ps variable lc variable ",i,j,i,j);
1.204 brouard 5002: }
5003: fprintf(ficgp,";\nset out; unset ylabel;\n");
5004: }
5005: /* unset log; plot "rrtest1_sorted_4/ILK_rrtest1_sorted_4.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with points lc variable */
5006: /* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
5007: /* 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 5008: fprintf(ficgp,"\nset out;unset log\n");
1.202 brouard 5009: /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
5010:
1.126 brouard 5011: strcpy(dirfileres,optionfilefiname);
5012: strcpy(optfileres,"vpl");
5013: /* 1eme*/
1.201 brouard 5014: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files\n");
1.126 brouard 5015: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.145 brouard 5016: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
1.201 brouard 5017: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
5018: fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
1.126 brouard 5019: fprintf(ficgp,"set xlabel \"Age\" \n\
5020: set ylabel \"Probability\" \n\
1.199 brouard 5021: set ter svg size 640, 480\n\
1.201 brouard 5022: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
1.126 brouard 5023:
5024: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 5025: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
5026: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 5027: }
1.201 brouard 5028: 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 5029: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 5030: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
5031: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 5032: }
1.201 brouard 5033: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
1.126 brouard 5034: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 5035: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
5036: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 5037: }
1.201 brouard 5038: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
5039: fprintf(ficgp,"\nset out \n");
5040: } /* k1 */
5041: } /* cpt */
1.126 brouard 5042: /*2 eme*/
1.153 brouard 5043: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
1.126 brouard 5044: for (k1=1; k1<= m ; k1 ++) {
1.201 brouard 5045: fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
5046: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
5047: if(vpopbased==0)
5048: fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
5049: else
5050: fprintf(ficgp,"\nreplot ");
5051: for (i=1; i<= nlstate+1 ; i ++) {
5052: k=2*i;
5053: 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);
5054: for (j=1; j<= nlstate+1 ; j ++) {
5055: if (j==i) fprintf(ficgp," %%lf (%%lf)");
5056: else fprintf(ficgp," %%*lf (%%*lf)");
5057: }
5058: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
5059: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
5060: 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);
5061: for (j=1; j<= nlstate+1 ; j ++) {
5062: if (j==i) fprintf(ficgp," %%lf (%%lf)");
5063: else fprintf(ficgp," %%*lf (%%*lf)");
5064: }
5065: fprintf(ficgp,"\" t\"\" w l lt 0,");
5066: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
5067: for (j=1; j<= nlstate+1 ; j ++) {
5068: if (j==i) fprintf(ficgp," %%lf (%%lf)");
5069: else fprintf(ficgp," %%*lf (%%*lf)");
5070: }
5071: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
5072: else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
5073: } /* state */
5074: } /* vpopbased */
5075: fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
5076: } /* k1 */
1.126 brouard 5077: /*3eme*/
5078:
5079: for (k1=1; k1<= m ; k1 ++) {
5080: for (cpt=1; cpt<= nlstate ; cpt ++) {
5081: /* k=2+nlstate*(2*cpt-2); */
5082: k=2+(nlstate+1)*(cpt-1);
1.201 brouard 5083: fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
1.199 brouard 5084: fprintf(ficgp,"set ter svg size 640, 480\n\
1.201 brouard 5085: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
1.126 brouard 5086: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
5087: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
5088: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
5089: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
5090: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
5091: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
5092:
5093: */
5094: for (i=1; i< nlstate ; i ++) {
1.201 brouard 5095: 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 5096: /* 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);*/
5097:
5098: }
1.201 brouard 5099: 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 5100: }
5101: }
5102:
1.201 brouard 5103: /* Survival functions (period) from state i in state j by initial state i */
5104: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
5105: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
5106: k=3;
5107: fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'lij' files, cov=%d state=%d",k1, cpt);
5108: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
5109: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
5110: set ter svg size 640, 480\n\
5111: unset log y\n\
5112: plot [%.f:%.f] ", ageminpar, agemaxpar);
5113: for (i=1; i<= nlstate ; i ++){
5114: if(i==1)
5115: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
5116: else
5117: fprintf(ficgp,", '' ");
5118: l=(nlstate+ndeath)*(i-1)+1;
5119: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
5120: for (j=2; j<= nlstate+ndeath ; j ++)
5121: fprintf(ficgp,"+$%d",k+l+j-1);
5122: fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
5123: } /* nlstate */
5124: fprintf(ficgp,"\nset out\n");
5125: } /* end cpt state*/
5126: } /* end covariate */
5127:
5128: /* Survival functions (period) from state i in state j by final state j */
1.202 brouard 5129: for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
1.201 brouard 5130: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
5131: k=3;
5132: 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);
5133: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
5134: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
5135: set ter svg size 640, 480\n\
5136: unset log y\n\
5137: plot [%.f:%.f] ", ageminpar, agemaxpar);
5138: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
5139: if(j==1)
5140: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
5141: else
5142: fprintf(ficgp,", '' ");
5143: l=(nlstate+ndeath)*(cpt-1) +j;
5144: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
5145: /* for (i=2; i<= nlstate+ndeath ; i ++) */
5146: /* fprintf(ficgp,"+$%d",k+l+i-1); */
5147: fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
5148: } /* nlstate */
5149: fprintf(ficgp,", '' ");
5150: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
5151: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
5152: l=(nlstate+ndeath)*(cpt-1) +j;
5153: if(j < nlstate)
5154: fprintf(ficgp,"$%d +",k+l);
5155: else
5156: fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
5157: }
5158: fprintf(ficgp,"\nset out\n");
5159: } /* end cpt state*/
5160: } /* end covariate */
5161:
1.202 brouard 5162: /* CV preval stable (period) for each covariate */
5163: for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
1.153 brouard 5164: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.126 brouard 5165: k=3;
1.153 brouard 5166: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
1.201 brouard 5167: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
1.126 brouard 5168: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.199 brouard 5169: set ter svg size 640, 480\n\
1.126 brouard 5170: unset log y\n\
1.153 brouard 5171: plot [%.f:%.f] ", ageminpar, agemaxpar);
5172: for (i=1; i<= nlstate ; i ++){
5173: if(i==1)
1.201 brouard 5174: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
1.153 brouard 5175: else
5176: fprintf(ficgp,", '' ");
1.154 brouard 5177: l=(nlstate+ndeath)*(i-1)+1;
5178: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
1.201 brouard 5179: for (j=2; j<= nlstate ; j ++)
5180: fprintf(ficgp,"+$%d",k+l+j-1);
1.153 brouard 5181: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
5182: } /* nlstate */
1.201 brouard 5183: fprintf(ficgp,"\nset out\n");
1.153 brouard 5184: } /* end cpt state*/
5185: } /* end covariate */
1.201 brouard 5186:
1.126 brouard 5187: /* proba elementaires */
1.187 brouard 5188: fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
1.126 brouard 5189: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 5190: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 5191: for(k=1; k <=(nlstate+ndeath); k++){
5192: if (k != i) {
1.187 brouard 5193: fprintf(ficgp,"# current state %d\n",k);
1.126 brouard 5194: for(j=1; j <=ncovmodel; j++){
1.187 brouard 5195: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
1.126 brouard 5196: jk++;
5197: }
1.187 brouard 5198: fprintf(ficgp,"\n");
1.126 brouard 5199: }
5200: }
5201: }
1.187 brouard 5202: fprintf(ficgp,"##############\n#\n");
5203:
1.145 brouard 5204: /*goto avoid;*/
1.200 brouard 5205: fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");
1.187 brouard 5206: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
5207: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
5208: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
5209: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
5210: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
5211: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
5212: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
5213: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
5214: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
5215: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
5216: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
5217: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
5218: fprintf(ficgp,"#\n");
1.201 brouard 5219: for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
1.187 brouard 5220: fprintf(ficgp,"# ng=%d\n",ng);
5221: fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);
1.126 brouard 5222: for(jk=1; jk <=m; jk++) {
1.187 brouard 5223: fprintf(ficgp,"# jk=%d\n",jk);
1.201 brouard 5224: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
5225: fprintf(ficgp,"\nset ter svg size 640, 480 ");
5226: if (ng==1){
5227: fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
5228: fprintf(ficgp,"\nunset log y");
5229: }else if (ng==2){
5230: fprintf(ficgp,"\nset ylabel \"Probability\"\n");
5231: fprintf(ficgp,"\nset log y");
5232: }else if (ng==3){
1.126 brouard 5233: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
1.201 brouard 5234: fprintf(ficgp,"\nset log y");
5235: }else
5236: fprintf(ficgp,"\nunset title ");
5237: fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar);
1.126 brouard 5238: i=1;
5239: for(k2=1; k2<=nlstate; k2++) {
5240: k3=i;
5241: for(k=1; k<=(nlstate+ndeath); k++) {
5242: if (k != k2){
1.201 brouard 5243: switch( ng) {
5244: case 1:
1.187 brouard 5245: if(nagesqr==0)
1.201 brouard 5246: fprintf(ficgp," p%d+p%d*x",i,i+1);
1.187 brouard 5247: else /* nagesqr =1 */
1.201 brouard 5248: fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
5249: break;
5250: case 2: /* ng=2 */
1.187 brouard 5251: if(nagesqr==0)
5252: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
5253: else /* nagesqr =1 */
1.201 brouard 5254: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
5255: break;
5256: case 3:
5257: if(nagesqr==0)
5258: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
5259: else /* nagesqr =1 */
5260: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
5261: break;
5262: }
1.141 brouard 5263: ij=1;/* To be checked else nbcode[0][0] wrong */
1.187 brouard 5264: for(j=3; j <=ncovmodel-nagesqr; j++) {
1.197 brouard 5265: /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
5266: if(ij <=cptcovage) { /* Bug valgrind */
5267: if((j-2)==Tage[ij]) { /* Bug valgrind */
1.200 brouard 5268: fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
5269: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
1.197 brouard 5270: ij++;
5271: }
1.186 brouard 5272: }
5273: else
1.198 brouard 5274: fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
1.126 brouard 5275: }
1.201 brouard 5276: if(ng != 1){
5277: fprintf(ficgp,")/(1");
1.126 brouard 5278:
1.201 brouard 5279: for(k1=1; k1 <=nlstate; k1++){
5280: if(nagesqr==0)
5281: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
5282: else /* nagesqr =1 */
5283: 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);
5284:
5285: ij=1;
5286: for(j=3; j <=ncovmodel-nagesqr; j++){
5287: if(ij <=cptcovage) { /* Bug valgrind */
5288: if((j-2)==Tage[ij]) { /* Bug valgrind */
5289: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
5290: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
5291: ij++;
5292: }
1.197 brouard 5293: }
1.201 brouard 5294: else
5295: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
1.186 brouard 5296: }
1.201 brouard 5297: fprintf(ficgp,")");
1.126 brouard 5298: }
5299: fprintf(ficgp,")");
1.201 brouard 5300: if(ng ==2)
5301: fprintf(ficgp," t \"p%d%d\" ", k2,k);
5302: else /* ng= 3 */
5303: fprintf(ficgp," t \"i%d%d\" ", k2,k);
5304: }else{ /* end ng <> 1 */
5305: fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
1.126 brouard 5306: }
5307: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
5308: i=i+ncovmodel;
5309: }
5310: } /* end k */
5311: } /* end k2 */
1.201 brouard 5312: fprintf(ficgp,"\n set out\n");
1.126 brouard 5313: } /* end jk */
5314: } /* end ng */
1.164 brouard 5315: /* avoid: */
1.126 brouard 5316: fflush(ficgp);
5317: } /* end gnuplot */
5318:
5319:
5320: /*************** Moving average **************/
5321: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
5322:
5323: int i, cpt, cptcod;
5324: int modcovmax =1;
5325: int mobilavrange, mob;
5326: double age;
5327:
5328: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
5329: a covariate has 2 modalities */
5330: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
5331:
5332: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
5333: if(mobilav==1) mobilavrange=5; /* default */
5334: else mobilavrange=mobilav;
5335: for (age=bage; age<=fage; age++)
5336: for (i=1; i<=nlstate;i++)
5337: for (cptcod=1;cptcod<=modcovmax;cptcod++)
5338: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
5339: /* We keep the original values on the extreme ages bage, fage and for
5340: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
5341: we use a 5 terms etc. until the borders are no more concerned.
5342: */
5343: for (mob=3;mob <=mobilavrange;mob=mob+2){
5344: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
5345: for (i=1; i<=nlstate;i++){
5346: for (cptcod=1;cptcod<=modcovmax;cptcod++){
5347: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
5348: for (cpt=1;cpt<=(mob-1)/2;cpt++){
5349: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
5350: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
5351: }
5352: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
5353: }
5354: }
5355: }/* end age */
5356: }/* end mob */
5357: }else return -1;
5358: return 0;
5359: }/* End movingaverage */
5360:
5361:
5362: /************** Forecasting ******************/
1.169 brouard 5363: 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 5364: /* proj1, year, month, day of starting projection
5365: agemin, agemax range of age
5366: dateprev1 dateprev2 range of dates during which prevalence is computed
5367: anproj2 year of en of projection (same day and month as proj1).
5368: */
1.164 brouard 5369: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
1.126 brouard 5370: double agec; /* generic age */
5371: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
5372: double *popeffectif,*popcount;
5373: double ***p3mat;
5374: double ***mobaverage;
5375: char fileresf[FILENAMELENGTH];
5376:
5377: agelim=AGESUP;
5378: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5379:
1.201 brouard 5380: strcpy(fileresf,"F_");
5381: strcat(fileresf,fileresu);
1.126 brouard 5382: if((ficresf=fopen(fileresf,"w"))==NULL) {
5383: printf("Problem with forecast resultfile: %s\n", fileresf);
5384: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
5385: }
5386: printf("Computing forecasting: result on file '%s' \n", fileresf);
5387: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
5388:
5389: if (cptcoveff==0) ncodemax[cptcoveff]=1;
5390:
5391: if (mobilav!=0) {
5392: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5393: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
5394: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5395: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5396: }
5397: }
5398:
5399: stepsize=(int) (stepm+YEARM-1)/YEARM;
5400: if (stepm<=12) stepsize=1;
5401: if(estepm < stepm){
5402: printf ("Problem %d lower than %d\n",estepm, stepm);
5403: }
5404: else hstepm=estepm;
5405:
5406: hstepm=hstepm/stepm;
5407: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
5408: fractional in yp1 */
5409: anprojmean=yp;
5410: yp2=modf((yp1*12),&yp);
5411: mprojmean=yp;
5412: yp1=modf((yp2*30.5),&yp);
5413: jprojmean=yp;
5414: if(jprojmean==0) jprojmean=1;
5415: if(mprojmean==0) jprojmean=1;
5416:
5417: i1=cptcoveff;
5418: if (cptcovn < 1){i1=1;}
5419:
5420: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
5421:
5422: fprintf(ficresf,"#****** Routine prevforecast **\n");
5423:
5424: /* if (h==(int)(YEARM*yearp)){ */
5425: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
5426: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
5427: k=k+1;
5428: fprintf(ficresf,"\n#******");
5429: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 5430: 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 5431: }
5432: fprintf(ficresf,"******\n");
5433: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
5434: for(j=1; j<=nlstate+ndeath;j++){
5435: for(i=1; i<=nlstate;i++)
5436: fprintf(ficresf," p%d%d",i,j);
5437: fprintf(ficresf," p.%d",j);
5438: }
5439: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
5440: fprintf(ficresf,"\n");
5441: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
5442:
5443: for (agec=fage; agec>=(ageminpar-1); agec--){
5444: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
5445: nhstepm = nhstepm/hstepm;
5446: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5447: oldm=oldms;savm=savms;
5448: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
5449:
5450: for (h=0; h<=nhstepm; h++){
5451: if (h*hstepm/YEARM*stepm ==yearp) {
5452: fprintf(ficresf,"\n");
5453: for(j=1;j<=cptcoveff;j++)
1.198 brouard 5454: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 5455: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
5456: }
5457: for(j=1; j<=nlstate+ndeath;j++) {
5458: ppij=0.;
5459: for(i=1; i<=nlstate;i++) {
5460: if (mobilav==1)
5461: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
5462: else {
5463: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
5464: }
5465: if (h*hstepm/YEARM*stepm== yearp) {
5466: fprintf(ficresf," %.3f", p3mat[i][j][h]);
5467: }
5468: } /* end i */
5469: if (h*hstepm/YEARM*stepm==yearp) {
5470: fprintf(ficresf," %.3f", ppij);
5471: }
5472: }/* end j */
5473: } /* end h */
5474: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5475: } /* end agec */
5476: } /* end yearp */
5477: } /* end cptcod */
5478: } /* end cptcov */
5479:
5480: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5481:
5482: fclose(ficresf);
5483: }
5484:
5485: /************** Forecasting *****not tested NB*************/
1.169 brouard 5486: 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 5487:
5488: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
5489: int *popage;
5490: double calagedatem, agelim, kk1, kk2;
5491: double *popeffectif,*popcount;
5492: double ***p3mat,***tabpop,***tabpopprev;
5493: double ***mobaverage;
5494: char filerespop[FILENAMELENGTH];
5495:
5496: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5497: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5498: agelim=AGESUP;
5499: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
5500:
5501: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5502:
5503:
1.201 brouard 5504: strcpy(filerespop,"POP_");
5505: strcat(filerespop,fileresu);
1.126 brouard 5506: if((ficrespop=fopen(filerespop,"w"))==NULL) {
5507: printf("Problem with forecast resultfile: %s\n", filerespop);
5508: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
5509: }
5510: printf("Computing forecasting: result on file '%s' \n", filerespop);
5511: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
5512:
5513: if (cptcoveff==0) ncodemax[cptcoveff]=1;
5514:
5515: if (mobilav!=0) {
5516: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5517: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
5518: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5519: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5520: }
5521: }
5522:
5523: stepsize=(int) (stepm+YEARM-1)/YEARM;
5524: if (stepm<=12) stepsize=1;
5525:
5526: agelim=AGESUP;
5527:
5528: hstepm=1;
5529: hstepm=hstepm/stepm;
5530:
5531: if (popforecast==1) {
5532: if((ficpop=fopen(popfile,"r"))==NULL) {
5533: printf("Problem with population file : %s\n",popfile);exit(0);
5534: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
5535: }
5536: popage=ivector(0,AGESUP);
5537: popeffectif=vector(0,AGESUP);
5538: popcount=vector(0,AGESUP);
5539:
5540: i=1;
5541: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
5542:
5543: imx=i;
5544: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
5545: }
5546:
5547: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
5548: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
5549: k=k+1;
5550: fprintf(ficrespop,"\n#******");
5551: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 5552: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 5553: }
5554: fprintf(ficrespop,"******\n");
5555: fprintf(ficrespop,"# Age");
5556: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
5557: if (popforecast==1) fprintf(ficrespop," [Population]");
5558:
5559: for (cpt=0; cpt<=0;cpt++) {
5560: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5561:
5562: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5563: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5564: nhstepm = nhstepm/hstepm;
5565:
5566: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5567: oldm=oldms;savm=savms;
5568: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5569:
5570: for (h=0; h<=nhstepm; h++){
5571: if (h==(int) (calagedatem+YEARM*cpt)) {
5572: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5573: }
5574: for(j=1; j<=nlstate+ndeath;j++) {
5575: kk1=0.;kk2=0;
5576: for(i=1; i<=nlstate;i++) {
5577: if (mobilav==1)
5578: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
5579: else {
5580: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
5581: }
5582: }
5583: if (h==(int)(calagedatem+12*cpt)){
5584: tabpop[(int)(agedeb)][j][cptcod]=kk1;
5585: /*fprintf(ficrespop," %.3f", kk1);
5586: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
5587: }
5588: }
5589: for(i=1; i<=nlstate;i++){
5590: kk1=0.;
5591: for(j=1; j<=nlstate;j++){
5592: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
5593: }
5594: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
5595: }
5596:
5597: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
5598: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
5599: }
5600: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5601: }
5602: }
5603:
5604: /******/
5605:
5606: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
5607: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5608: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5609: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5610: nhstepm = nhstepm/hstepm;
5611:
5612: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5613: oldm=oldms;savm=savms;
5614: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5615: for (h=0; h<=nhstepm; h++){
5616: if (h==(int) (calagedatem+YEARM*cpt)) {
5617: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5618: }
5619: for(j=1; j<=nlstate+ndeath;j++) {
5620: kk1=0.;kk2=0;
5621: for(i=1; i<=nlstate;i++) {
5622: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
5623: }
5624: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
5625: }
5626: }
5627: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5628: }
5629: }
5630: }
5631: }
5632:
5633: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5634:
5635: if (popforecast==1) {
5636: free_ivector(popage,0,AGESUP);
5637: free_vector(popeffectif,0,AGESUP);
5638: free_vector(popcount,0,AGESUP);
5639: }
5640: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5641: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5642: fclose(ficrespop);
5643: } /* End of popforecast */
5644:
5645: int fileappend(FILE *fichier, char *optionfich)
5646: {
5647: if((fichier=fopen(optionfich,"a"))==NULL) {
5648: printf("Problem with file: %s\n", optionfich);
5649: fprintf(ficlog,"Problem with file: %s\n", optionfich);
5650: return (0);
5651: }
5652: fflush(fichier);
5653: return (1);
5654: }
5655:
5656:
5657: /**************** function prwizard **********************/
5658: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
5659: {
5660:
5661: /* Wizard to print covariance matrix template */
5662:
1.164 brouard 5663: char ca[32], cb[32];
5664: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 5665: int numlinepar;
5666:
5667: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5668: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5669: for(i=1; i <=nlstate; i++){
5670: jj=0;
5671: for(j=1; j <=nlstate+ndeath; j++){
5672: if(j==i) continue;
5673: jj++;
5674: /*ca[0]= k+'a'-1;ca[1]='\0';*/
5675: printf("%1d%1d",i,j);
5676: fprintf(ficparo,"%1d%1d",i,j);
5677: for(k=1; k<=ncovmodel;k++){
5678: /* printf(" %lf",param[i][j][k]); */
5679: /* fprintf(ficparo," %lf",param[i][j][k]); */
5680: printf(" 0.");
5681: fprintf(ficparo," 0.");
5682: }
5683: printf("\n");
5684: fprintf(ficparo,"\n");
5685: }
5686: }
5687: printf("# Scales (for hessian or gradient estimation)\n");
5688: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
5689: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
5690: for(i=1; i <=nlstate; i++){
5691: jj=0;
5692: for(j=1; j <=nlstate+ndeath; j++){
5693: if(j==i) continue;
5694: jj++;
5695: fprintf(ficparo,"%1d%1d",i,j);
5696: printf("%1d%1d",i,j);
5697: fflush(stdout);
5698: for(k=1; k<=ncovmodel;k++){
5699: /* printf(" %le",delti3[i][j][k]); */
5700: /* fprintf(ficparo," %le",delti3[i][j][k]); */
5701: printf(" 0.");
5702: fprintf(ficparo," 0.");
5703: }
5704: numlinepar++;
5705: printf("\n");
5706: fprintf(ficparo,"\n");
5707: }
5708: }
5709: printf("# Covariance matrix\n");
5710: /* # 121 Var(a12)\n\ */
5711: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5712: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5713: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5714: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5715: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5716: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5717: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5718: fflush(stdout);
5719: fprintf(ficparo,"# Covariance matrix\n");
5720: /* # 121 Var(a12)\n\ */
5721: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5722: /* # ...\n\ */
5723: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5724:
5725: for(itimes=1;itimes<=2;itimes++){
5726: jj=0;
5727: for(i=1; i <=nlstate; i++){
5728: for(j=1; j <=nlstate+ndeath; j++){
5729: if(j==i) continue;
5730: for(k=1; k<=ncovmodel;k++){
5731: jj++;
5732: ca[0]= k+'a'-1;ca[1]='\0';
5733: if(itimes==1){
5734: printf("#%1d%1d%d",i,j,k);
5735: fprintf(ficparo,"#%1d%1d%d",i,j,k);
5736: }else{
5737: printf("%1d%1d%d",i,j,k);
5738: fprintf(ficparo,"%1d%1d%d",i,j,k);
5739: /* printf(" %.5le",matcov[i][j]); */
5740: }
5741: ll=0;
5742: for(li=1;li <=nlstate; li++){
5743: for(lj=1;lj <=nlstate+ndeath; lj++){
5744: if(lj==li) continue;
5745: for(lk=1;lk<=ncovmodel;lk++){
5746: ll++;
5747: if(ll<=jj){
5748: cb[0]= lk +'a'-1;cb[1]='\0';
5749: if(ll<jj){
5750: if(itimes==1){
5751: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5752: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5753: }else{
5754: printf(" 0.");
5755: fprintf(ficparo," 0.");
5756: }
5757: }else{
5758: if(itimes==1){
5759: printf(" Var(%s%1d%1d)",ca,i,j);
5760: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
5761: }else{
5762: printf(" 0.");
5763: fprintf(ficparo," 0.");
5764: }
5765: }
5766: }
5767: } /* end lk */
5768: } /* end lj */
5769: } /* end li */
5770: printf("\n");
5771: fprintf(ficparo,"\n");
5772: numlinepar++;
5773: } /* end k*/
5774: } /*end j */
5775: } /* end i */
5776: } /* end itimes */
5777:
5778: } /* end of prwizard */
5779: /******************* Gompertz Likelihood ******************************/
5780: double gompertz(double x[])
5781: {
5782: double A,B,L=0.0,sump=0.,num=0.;
5783: int i,n=0; /* n is the size of the sample */
5784:
5785: for (i=0;i<=imx-1 ; i++) {
5786: sump=sump+weight[i];
5787: /* sump=sump+1;*/
5788: num=num+1;
5789: }
5790:
5791:
5792: /* for (i=0; i<=imx; i++)
5793: 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]);*/
5794:
5795: for (i=1;i<=imx ; i++)
5796: {
5797: if (cens[i] == 1 && wav[i]>1)
5798: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
5799:
5800: if (cens[i] == 0 && wav[i]>1)
5801: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
5802: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
5803:
5804: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5805: if (wav[i] > 1 ) { /* ??? */
5806: L=L+A*weight[i];
5807: /* 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]);*/
5808: }
5809: }
5810:
5811: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5812:
5813: return -2*L*num/sump;
5814: }
5815:
1.136 brouard 5816: #ifdef GSL
5817: /******************* Gompertz_f Likelihood ******************************/
5818: double gompertz_f(const gsl_vector *v, void *params)
5819: {
5820: double A,B,LL=0.0,sump=0.,num=0.;
5821: double *x= (double *) v->data;
5822: int i,n=0; /* n is the size of the sample */
5823:
5824: for (i=0;i<=imx-1 ; i++) {
5825: sump=sump+weight[i];
5826: /* sump=sump+1;*/
5827: num=num+1;
5828: }
5829:
5830:
5831: /* for (i=0; i<=imx; i++)
5832: 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]);*/
5833: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
5834: for (i=1;i<=imx ; i++)
5835: {
5836: if (cens[i] == 1 && wav[i]>1)
5837: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
5838:
5839: if (cens[i] == 0 && wav[i]>1)
5840: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
5841: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
5842:
5843: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5844: if (wav[i] > 1 ) { /* ??? */
5845: LL=LL+A*weight[i];
5846: /* 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]);*/
5847: }
5848: }
5849:
5850: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5851: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
5852:
5853: return -2*LL*num/sump;
5854: }
5855: #endif
5856:
1.126 brouard 5857: /******************* Printing html file ***********/
1.201 brouard 5858: void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 5859: int lastpass, int stepm, int weightopt, char model[],\
5860: int imx, double p[],double **matcov,double agemortsup){
5861: int i,k;
5862:
5863: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
5864: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
5865: for (i=1;i<=2;i++)
5866: 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 5867: fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
1.126 brouard 5868: fprintf(fichtm,"</ul>");
5869:
5870: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
5871:
5872: 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>");
5873:
5874: for (k=agegomp;k<(agemortsup-2);k++)
5875: 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]);
5876:
5877:
5878: fflush(fichtm);
5879: }
5880:
5881: /******************* Gnuplot file **************/
1.201 brouard 5882: void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 5883:
5884: char dirfileres[132],optfileres[132];
1.164 brouard 5885:
1.126 brouard 5886: int ng;
5887:
5888:
5889: /*#ifdef windows */
5890: fprintf(ficgp,"cd \"%s\" \n",pathc);
5891: /*#endif */
5892:
5893:
5894: strcpy(dirfileres,optionfilefiname);
5895: strcpy(optfileres,"vpl");
1.199 brouard 5896: fprintf(ficgp,"set out \"graphmort.svg\"\n ");
1.126 brouard 5897: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.199 brouard 5898: fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
1.145 brouard 5899: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 5900: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
5901:
5902: }
5903:
1.136 brouard 5904: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
5905: {
1.126 brouard 5906:
1.136 brouard 5907: /*-------- data file ----------*/
5908: FILE *fic;
5909: char dummy[]=" ";
1.164 brouard 5910: int i=0, j=0, n=0;
1.136 brouard 5911: int linei, month, year,iout;
5912: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 5913: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 5914: char *stratrunc;
5915: int lstra;
1.126 brouard 5916:
5917:
1.136 brouard 5918: if((fic=fopen(datafile,"r"))==NULL) {
1.195 brouard 5919: printf("Problem while opening datafile: %s\n", datafile);fflush(stdout);
5920: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);fflush(ficlog);return 1;
1.136 brouard 5921: }
1.126 brouard 5922:
1.136 brouard 5923: i=1;
5924: linei=0;
5925: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
5926: linei=linei+1;
5927: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
5928: if(line[j] == '\t')
5929: line[j] = ' ';
5930: }
5931: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
5932: ;
5933: };
5934: line[j+1]=0; /* Trims blanks at end of line */
5935: if(line[0]=='#'){
5936: fprintf(ficlog,"Comment line\n%s\n",line);
5937: printf("Comment line\n%s\n",line);
5938: continue;
5939: }
5940: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 5941: strcpy(line, linetmp);
1.136 brouard 5942:
1.126 brouard 5943:
1.136 brouard 5944: for (j=maxwav;j>=1;j--){
1.137 brouard 5945: cutv(stra, strb, line, ' ');
1.136 brouard 5946: if(strb[0]=='.') { /* Missing status */
5947: lval=-1;
5948: }else{
5949: errno=0;
5950: lval=strtol(strb,&endptr,10);
5951: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
5952: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5953: 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);
5954: 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 5955: return 1;
5956: }
5957: }
5958: s[j][i]=lval;
5959:
5960: strcpy(line,stra);
5961: cutv(stra, strb,line,' ');
1.169 brouard 5962: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5963: }
1.169 brouard 5964: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5965: month=99;
5966: year=9999;
5967: }else{
1.141 brouard 5968: 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);
5969: 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 5970: return 1;
5971: }
5972: anint[j][i]= (double) year;
5973: mint[j][i]= (double)month;
5974: strcpy(line,stra);
5975: } /* ENd Waves */
5976:
5977: cutv(stra, strb,line,' ');
1.169 brouard 5978: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5979: }
1.169 brouard 5980: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5981: month=99;
5982: year=9999;
5983: }else{
1.141 brouard 5984: 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);
5985: 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 5986: return 1;
5987: }
5988: andc[i]=(double) year;
5989: moisdc[i]=(double) month;
5990: strcpy(line,stra);
5991:
5992: cutv(stra, strb,line,' ');
1.169 brouard 5993: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5994: }
1.169 brouard 5995: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 5996: month=99;
5997: year=9999;
5998: }else{
1.141 brouard 5999: 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);
6000: 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 6001: return 1;
6002: }
6003: if (year==9999) {
1.141 brouard 6004: 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);
6005: 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 6006: return 1;
1.126 brouard 6007:
1.136 brouard 6008: }
6009: annais[i]=(double)(year);
6010: moisnais[i]=(double)(month);
6011: strcpy(line,stra);
6012:
6013: cutv(stra, strb,line,' ');
6014: errno=0;
6015: dval=strtod(strb,&endptr);
6016: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 6017: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
6018: 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 6019: fflush(ficlog);
6020: return 1;
6021: }
6022: weight[i]=dval;
6023: strcpy(line,stra);
6024:
6025: for (j=ncovcol;j>=1;j--){
6026: cutv(stra, strb,line,' ');
6027: if(strb[0]=='.') { /* Missing status */
6028: lval=-1;
6029: }else{
6030: errno=0;
6031: lval=strtol(strb,&endptr,10);
6032: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 6033: 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);
6034: 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 6035: return 1;
6036: }
6037: }
6038: if(lval <-1 || lval >1){
1.141 brouard 6039: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 6040: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
6041: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
6042: For example, for multinomial values like 1, 2 and 3,\n \
6043: build V1=0 V2=0 for the reference value (1),\n \
6044: V1=1 V2=0 for (2) \n \
6045: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
6046: output of IMaCh is often meaningless.\n \
6047: Exiting.\n",lval,linei, i,line,j);
1.141 brouard 6048: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 6049: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
6050: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
6051: For example, for multinomial values like 1, 2 and 3,\n \
6052: build V1=0 V2=0 for the reference value (1),\n \
6053: V1=1 V2=0 for (2) \n \
6054: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
6055: output of IMaCh is often meaningless.\n \
6056: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
6057: return 1;
6058: }
6059: covar[j][i]=(double)(lval);
6060: strcpy(line,stra);
6061: }
6062: lstra=strlen(stra);
6063:
6064: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
6065: stratrunc = &(stra[lstra-9]);
6066: num[i]=atol(stratrunc);
6067: }
6068: else
6069: num[i]=atol(stra);
6070: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
6071: 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;}*/
6072:
6073: i=i+1;
6074: } /* End loop reading data */
1.126 brouard 6075:
1.136 brouard 6076: *imax=i-1; /* Number of individuals */
6077: fclose(fic);
6078:
6079: return (0);
1.164 brouard 6080: /* endread: */
1.136 brouard 6081: printf("Exiting readdata: ");
6082: fclose(fic);
6083: return (1);
1.126 brouard 6084:
6085:
6086:
1.136 brouard 6087: }
1.145 brouard 6088: void removespace(char *str) {
6089: char *p1 = str, *p2 = str;
6090: do
6091: while (*p2 == ' ')
6092: p2++;
1.169 brouard 6093: while (*p1++ == *p2++);
1.145 brouard 6094: }
6095:
6096: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
1.187 brouard 6097: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
6098: * - nagesqr = 1 if age*age in the model, otherwise 0.
6099: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
6100: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
1.145 brouard 6101: * - cptcovage number of covariates with age*products =2
6102: * - cptcovs number of simple covariates
6103: * - 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
6104: * which is a new column after the 9 (ncovcol) variables.
6105: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
6106: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
6107: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
6108: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
6109: */
1.136 brouard 6110: {
1.145 brouard 6111: int i, j, k, ks;
1.164 brouard 6112: int j1, k1, k2;
1.136 brouard 6113: char modelsav[80];
1.145 brouard 6114: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 6115: char *strpt;
1.136 brouard 6116:
1.145 brouard 6117: /*removespace(model);*/
1.136 brouard 6118: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 6119: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 6120: if (strstr(model,"AGE") !=0){
1.192 brouard 6121: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
6122: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 6123: return 1;
6124: }
1.141 brouard 6125: if (strstr(model,"v") !=0){
6126: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
6127: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
6128: return 1;
6129: }
1.187 brouard 6130: strcpy(modelsav,model);
6131: if ((strpt=strstr(model,"age*age")) !=0){
6132: printf(" strpt=%s, model=%s\n",strpt, model);
6133: if(strpt != model){
6134: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 6135: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 6136: corresponding column of parameters.\n",model);
6137: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 6138: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 6139: corresponding column of parameters.\n",model); fflush(ficlog);
6140: return 1;
6141: }
6142:
6143: nagesqr=1;
6144: if (strstr(model,"+age*age") !=0)
6145: substrchaine(modelsav, model, "+age*age");
6146: else if (strstr(model,"age*age+") !=0)
6147: substrchaine(modelsav, model, "age*age+");
6148: else
6149: substrchaine(modelsav, model, "age*age");
6150: }else
6151: nagesqr=0;
6152: if (strlen(modelsav) >1){
6153: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
6154: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
6155: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2 */
6156: cptcovt= j+1; /* Number of total covariates in the model, not including
6157: * cst, age and age*age
6158: * V1+V1*age+ V3 + V3*V4+age*age=> 4*/
6159: /* including age products which are counted in cptcovage.
6160: * but the covariates which are products must be treated
6161: * separately: ncovn=4- 2=2 (V1+V3). */
6162: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
6163: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
6164:
6165:
6166: /* Design
6167: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
6168: * < ncovcol=8 >
6169: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
6170: * k= 1 2 3 4 5 6 7 8
6171: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
6172: * covar[k,i], value of kth covariate if not including age for individual i:
6173: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
6174: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
6175: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
6176: * Tage[++cptcovage]=k
6177: * if products, new covar are created after ncovcol with k1
6178: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
6179: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
6180: * 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
6181: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
6182: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
6183: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
6184: * < ncovcol=8 >
6185: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
6186: * k= 1 2 3 4 5 6 7 8 9 10 11 12
6187: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
6188: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
6189: * p Tprod[1]@2={ 6, 5}
6190: *p Tvard[1][1]@4= {7, 8, 5, 6}
6191: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
6192: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
6193: *How to reorganize?
6194: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
6195: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
6196: * {2, 1, 4, 8, 5, 6, 3, 7}
6197: * Struct []
6198: */
1.145 brouard 6199:
1.187 brouard 6200: /* This loop fills the array Tvar from the string 'model'.*/
6201: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
6202: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
6203: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
6204: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
6205: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
6206: /* k=1 Tvar[1]=2 (from V2) */
6207: /* k=5 Tvar[5] */
6208: /* for (k=1; k<=cptcovn;k++) { */
1.198 brouard 6209: /* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.187 brouard 6210: /* } */
1.198 brouard 6211: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
1.187 brouard 6212: /*
6213: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
6214: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
1.145 brouard 6215: Tvar[k]=0;
1.187 brouard 6216: cptcovage=0;
6217: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
6218: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
6219: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
6220: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
6221: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
6222: /*scanf("%d",i);*/
6223: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
6224: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
6225: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
6226: /* covar is not filled and then is empty */
6227: cptcovprod--;
6228: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
6229: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
6230: cptcovage++; /* Sums the number of covariates which include age as a product */
6231: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
6232: /*printf("stre=%s ", stre);*/
6233: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
6234: cptcovprod--;
6235: cutl(stre,strb,strc,'V');
6236: Tvar[k]=atoi(stre);
6237: cptcovage++;
6238: Tage[cptcovage]=k;
6239: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
6240: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
6241: cptcovn++;
6242: cptcovprodnoage++;k1++;
6243: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
6244: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
6245: because this model-covariate is a construction we invent a new column
6246: ncovcol + k1
6247: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
6248: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
6249: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
6250: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
6251: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
6252: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
6253: k2=k2+2;
6254: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
6255: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
6256: for (i=1; i<=lastobs;i++){
6257: /* Computes the new covariate which is a product of
6258: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
6259: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
6260: }
6261: } /* End age is not in the model */
6262: } /* End if model includes a product */
6263: else { /* no more sum */
6264: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
6265: /* scanf("%d",i);*/
6266: cutl(strd,strc,strb,'V');
6267: ks++; /**< Number of simple covariates */
1.145 brouard 6268: cptcovn++;
1.187 brouard 6269: Tvar[k]=atoi(strd);
6270: }
6271: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
6272: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
6273: scanf("%d",i);*/
6274: } /* end of loop + on total covariates */
6275: } /* end if strlen(modelsave == 0) age*age might exist */
6276: } /* end if strlen(model == 0) */
1.136 brouard 6277:
6278: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
6279: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
6280:
6281: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
6282: printf("cptcovprod=%d ", cptcovprod);
6283: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
6284:
6285: scanf("%d ",i);*/
6286:
6287:
1.137 brouard 6288: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 6289: /*endread:*/
1.136 brouard 6290: printf("Exiting decodemodel: ");
6291: return (1);
6292: }
6293:
1.169 brouard 6294: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.136 brouard 6295: {
6296: int i, m;
6297:
6298: for (i=1; i<=imx; i++) {
6299: for(m=2; (m<= maxwav); m++) {
6300: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
6301: anint[m][i]=9999;
6302: s[m][i]=-1;
6303: }
6304: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169 brouard 6305: *nberr = *nberr + 1;
6306: 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);
6307: 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 6308: s[m][i]=-1;
6309: }
6310: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 6311: (*nberr)++;
1.136 brouard 6312: 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]);
6313: 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]);
6314: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
6315: }
6316: }
6317: }
6318:
6319: for (i=1; i<=imx; i++) {
6320: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
6321: for(m=firstpass; (m<= lastpass); m++){
6322: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
6323: if (s[m][i] >= nlstate+1) {
1.169 brouard 6324: if(agedc[i]>0){
6325: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 6326: agev[m][i]=agedc[i];
6327: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 6328: }else {
1.136 brouard 6329: if ((int)andc[i]!=9999){
6330: nbwarn++;
6331: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
6332: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
6333: agev[m][i]=-1;
6334: }
6335: }
1.169 brouard 6336: } /* agedc > 0 */
1.136 brouard 6337: }
6338: else if(s[m][i] !=9){ /* Standard case, age in fractional
6339: years but with the precision of a month */
6340: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
6341: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
6342: agev[m][i]=1;
6343: else if(agev[m][i] < *agemin){
6344: *agemin=agev[m][i];
6345: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
6346: }
6347: else if(agev[m][i] >*agemax){
6348: *agemax=agev[m][i];
1.156 brouard 6349: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 6350: }
6351: /*agev[m][i]=anint[m][i]-annais[i];*/
6352: /* agev[m][i] = age[i]+2*m;*/
6353: }
6354: else { /* =9 */
6355: agev[m][i]=1;
6356: s[m][i]=-1;
6357: }
6358: }
6359: else /*= 0 Unknown */
6360: agev[m][i]=1;
6361: }
6362:
6363: }
6364: for (i=1; i<=imx; i++) {
6365: for(m=firstpass; (m<=lastpass); m++){
6366: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 6367: (*nberr)++;
1.136 brouard 6368: 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);
6369: 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);
6370: return 1;
6371: }
6372: }
6373: }
6374:
6375: /*for (i=1; i<=imx; i++){
6376: for (m=firstpass; (m<lastpass); m++){
6377: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
6378: }
6379:
6380: }*/
6381:
6382:
1.139 brouard 6383: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
6384: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 6385:
6386: return (0);
1.164 brouard 6387: /* endread:*/
1.136 brouard 6388: printf("Exiting calandcheckages: ");
6389: return (1);
6390: }
6391:
1.172 brouard 6392: #if defined(_MSC_VER)
6393: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
6394: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
6395: //#include "stdafx.h"
6396: //#include <stdio.h>
6397: //#include <tchar.h>
6398: //#include <windows.h>
6399: //#include <iostream>
6400: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
6401:
6402: LPFN_ISWOW64PROCESS fnIsWow64Process;
6403:
6404: BOOL IsWow64()
6405: {
6406: BOOL bIsWow64 = FALSE;
6407:
6408: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
6409: // (HANDLE, PBOOL);
6410:
6411: //LPFN_ISWOW64PROCESS fnIsWow64Process;
6412:
6413: HMODULE module = GetModuleHandle(_T("kernel32"));
6414: const char funcName[] = "IsWow64Process";
6415: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
6416: GetProcAddress(module, funcName);
6417:
6418: if (NULL != fnIsWow64Process)
6419: {
6420: if (!fnIsWow64Process(GetCurrentProcess(),
6421: &bIsWow64))
6422: //throw std::exception("Unknown error");
6423: printf("Unknown error\n");
6424: }
6425: return bIsWow64 != FALSE;
6426: }
6427: #endif
1.177 brouard 6428:
1.191 brouard 6429: void syscompilerinfo(int logged)
1.167 brouard 6430: {
6431: /* #include "syscompilerinfo.h"*/
1.185 brouard 6432: /* command line Intel compiler 32bit windows, XP compatible:*/
6433: /* /GS /W3 /Gy
6434: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
6435: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
6436: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 6437: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
6438: */
6439: /* 64 bits */
1.185 brouard 6440: /*
6441: /GS /W3 /Gy
6442: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
6443: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
6444: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
6445: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
6446: /* Optimization are useless and O3 is slower than O2 */
6447: /*
6448: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
6449: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
6450: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
6451: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
6452: */
1.186 brouard 6453: /* Link is */ /* /OUT:"visual studio
1.185 brouard 6454: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
6455: /PDB:"visual studio
6456: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
6457: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
6458: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
6459: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
6460: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
6461: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
6462: uiAccess='false'"
6463: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
6464: /NOLOGO /TLBID:1
6465: */
1.177 brouard 6466: #if defined __INTEL_COMPILER
1.178 brouard 6467: #if defined(__GNUC__)
6468: struct utsname sysInfo; /* For Intel on Linux and OS/X */
6469: #endif
1.177 brouard 6470: #elif defined(__GNUC__)
1.179 brouard 6471: #ifndef __APPLE__
1.174 brouard 6472: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 6473: #endif
1.177 brouard 6474: struct utsname sysInfo;
1.178 brouard 6475: int cross = CROSS;
6476: if (cross){
6477: printf("Cross-");
1.191 brouard 6478: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 6479: }
1.174 brouard 6480: #endif
6481:
1.171 brouard 6482: #include <stdint.h>
1.178 brouard 6483:
1.191 brouard 6484: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 6485: #if defined(__clang__)
1.191 brouard 6486: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 6487: #endif
6488: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 6489: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 6490: #endif
6491: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 6492: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 6493: #endif
6494: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 6495: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 6496: #endif
6497: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 6498: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 6499: #endif
6500: #if defined(_MSC_VER)
1.191 brouard 6501: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 6502: #endif
6503: #if defined(__PGI)
1.191 brouard 6504: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 6505: #endif
6506: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 6507: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 6508: #endif
1.191 brouard 6509: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 6510:
1.167 brouard 6511: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
6512: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
6513: // Windows (x64 and x86)
1.191 brouard 6514: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 6515: #elif __unix__ // all unices, not all compilers
6516: // Unix
1.191 brouard 6517: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 6518: #elif __linux__
6519: // linux
1.191 brouard 6520: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 6521: #elif __APPLE__
1.174 brouard 6522: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 6523: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 6524: #endif
6525:
6526: /* __MINGW32__ */
6527: /* __CYGWIN__ */
6528: /* __MINGW64__ */
6529: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
6530: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
6531: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
6532: /* _WIN64 // Defined for applications for Win64. */
6533: /* _M_X64 // Defined for compilations that target x64 processors. */
6534: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 6535:
1.167 brouard 6536: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 6537: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 6538: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 6539: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 6540: #else
1.191 brouard 6541: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 6542: #endif
6543:
1.169 brouard 6544: #if defined(__GNUC__)
6545: # if defined(__GNUC_PATCHLEVEL__)
6546: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
6547: + __GNUC_MINOR__ * 100 \
6548: + __GNUC_PATCHLEVEL__)
6549: # else
6550: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
6551: + __GNUC_MINOR__ * 100)
6552: # endif
1.174 brouard 6553: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 6554: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 6555:
6556: if (uname(&sysInfo) != -1) {
6557: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 6558: 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 6559: }
6560: else
6561: perror("uname() error");
1.179 brouard 6562: //#ifndef __INTEL_COMPILER
6563: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 6564: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 6565: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 6566: #endif
1.169 brouard 6567: #endif
1.172 brouard 6568:
6569: // void main()
6570: // {
1.169 brouard 6571: #if defined(_MSC_VER)
1.174 brouard 6572: if (IsWow64()){
1.191 brouard 6573: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
6574: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 6575: }
6576: else{
1.191 brouard 6577: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
6578: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 6579: }
1.172 brouard 6580: // printf("\nPress Enter to continue...");
6581: // getchar();
6582: // }
6583:
1.169 brouard 6584: #endif
6585:
1.167 brouard 6586:
6587: }
1.136 brouard 6588:
1.209 brouard 6589: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
1.180 brouard 6590: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6591: int i, j, k, i1 ;
1.202 brouard 6592: /* double ftolpl = 1.e-10; */
1.180 brouard 6593: double age, agebase, agelim;
1.203 brouard 6594: double tot;
1.180 brouard 6595:
1.202 brouard 6596: strcpy(filerespl,"PL_");
6597: strcat(filerespl,fileresu);
6598: if((ficrespl=fopen(filerespl,"w"))==NULL) {
6599: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6600: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6601: }
6602: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6603: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6604: pstamp(ficrespl);
1.203 brouard 6605: fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.202 brouard 6606: fprintf(ficrespl,"#Age ");
6607: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
6608: fprintf(ficrespl,"\n");
1.180 brouard 6609:
6610: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
6611:
6612: agebase=ageminpar;
6613: agelim=agemaxpar;
6614:
6615: i1=pow(2,cptcoveff);
6616: if (cptcovn < 1){i1=1;}
6617:
6618: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6619: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
6620: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6621: k=k+1;
6622: /* to clean */
1.198 brouard 6623: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
1.200 brouard 6624: fprintf(ficrespl,"#******");
6625: printf("#******");
6626: fprintf(ficlog,"#******");
1.180 brouard 6627: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 6628: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
6629: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
6630: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.180 brouard 6631: }
6632: fprintf(ficrespl,"******\n");
6633: printf("******\n");
6634: fprintf(ficlog,"******\n");
6635:
6636: fprintf(ficrespl,"#Age ");
6637: for(j=1;j<=cptcoveff;j++) {
1.200 brouard 6638: fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.180 brouard 6639: }
1.203 brouard 6640: for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);
6641: fprintf(ficrespl,"Total Years_to_converge\n");
1.180 brouard 6642:
6643: for (age=agebase; age<=agelim; age++){
6644: /* for (age=agebase; age<=agebase; age++){ */
1.209 brouard 6645: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k);
1.180 brouard 6646: fprintf(ficrespl,"%.0f ",age );
6647: for(j=1;j<=cptcoveff;j++)
1.198 brouard 6648: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.203 brouard 6649: tot=0.;
6650: for(i=1; i<=nlstate;i++){
6651: tot += prlim[i][i];
1.180 brouard 6652: fprintf(ficrespl," %.5f", prlim[i][i]);
1.203 brouard 6653: }
1.209 brouard 6654: fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
1.180 brouard 6655: } /* Age */
6656: /* was end of cptcod */
6657: } /* cptcov */
1.184 brouard 6658: return 0;
1.180 brouard 6659: }
6660:
6661: int hPijx(double *p, int bage, int fage){
6662: /*------------- h Pij x at various ages ------------*/
6663:
6664: int stepsize;
6665: int agelim;
6666: int hstepm;
6667: int nhstepm;
6668: int h, i, i1, j, k;
6669:
6670: double agedeb;
6671: double ***p3mat;
6672:
1.201 brouard 6673: strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu);
1.180 brouard 6674: if((ficrespij=fopen(filerespij,"w"))==NULL) {
6675: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
6676: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
6677: }
6678: printf("Computing pij: result on file '%s' \n", filerespij);
6679: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
6680:
6681: stepsize=(int) (stepm+YEARM-1)/YEARM;
6682: /*if (stepm<=24) stepsize=2;*/
6683:
6684: agelim=AGESUP;
6685: hstepm=stepsize*YEARM; /* Every year of age */
6686: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
6687:
6688: /* hstepm=1; aff par mois*/
6689: pstamp(ficrespij);
6690: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
6691: i1= pow(2,cptcoveff);
1.183 brouard 6692: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
6693: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
6694: /* k=k+1; */
6695: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6696: fprintf(ficrespij,"\n#****** ");
6697: for(j=1;j<=cptcoveff;j++)
1.198 brouard 6698: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.183 brouard 6699: fprintf(ficrespij,"******\n");
6700:
6701: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
6702: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6703: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6704:
6705: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 6706:
1.183 brouard 6707: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6708: oldm=oldms;savm=savms;
6709: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
6710: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
6711: for(i=1; i<=nlstate;i++)
6712: for(j=1; j<=nlstate+ndeath;j++)
6713: fprintf(ficrespij," %1d-%1d",i,j);
6714: fprintf(ficrespij,"\n");
6715: for (h=0; h<=nhstepm; h++){
6716: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
6717: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 6718: for(i=1; i<=nlstate;i++)
6719: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 6720: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 6721: fprintf(ficrespij,"\n");
6722: }
1.183 brouard 6723: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6724: fprintf(ficrespij,"\n");
6725: }
1.180 brouard 6726: /*}*/
6727: }
1.184 brouard 6728: return 0;
1.180 brouard 6729: }
6730:
6731:
1.136 brouard 6732: /***********************************************/
6733: /**************** Main Program *****************/
6734: /***********************************************/
6735:
6736: int main(int argc, char *argv[])
6737: {
6738: #ifdef GSL
6739: const gsl_multimin_fminimizer_type *T;
6740: size_t iteri = 0, it;
6741: int rval = GSL_CONTINUE;
6742: int status = GSL_SUCCESS;
6743: double ssval;
6744: #endif
6745: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 6746: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
1.209 brouard 6747: int ncvyear=0; /* Number of years needed for the period prevalence to converge */
1.164 brouard 6748: int jj, ll, li, lj, lk;
1.136 brouard 6749: int numlinepar=0; /* Current linenumber of parameter file */
1.197 brouard 6750: int num_filled;
1.136 brouard 6751: int itimes;
6752: int NDIM=2;
6753: int vpopbased=0;
6754:
1.164 brouard 6755: char ca[32], cb[32];
1.136 brouard 6756: /* FILE *fichtm; *//* Html File */
6757: /* FILE *ficgp;*/ /*Gnuplot File */
6758: struct stat info;
1.191 brouard 6759: double agedeb=0.;
1.194 brouard 6760:
6761: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.136 brouard 6762:
1.165 brouard 6763: double fret;
1.191 brouard 6764: double dum=0.; /* Dummy variable */
1.136 brouard 6765: double ***p3mat;
6766: double ***mobaverage;
1.164 brouard 6767:
6768: char line[MAXLINE];
1.197 brouard 6769: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
6770:
6771: char model[MAXLINE], modeltemp[MAXLINE];
1.136 brouard 6772: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 6773: char *tok, *val; /* pathtot */
1.136 brouard 6774: int firstobs=1, lastobs=10;
1.195 brouard 6775: int c, h , cpt, c2;
1.191 brouard 6776: int jl=0;
6777: int i1, j1, jk, stepsize=0;
1.194 brouard 6778: int count=0;
6779:
1.164 brouard 6780: int *tab;
1.136 brouard 6781: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
6782: int mobilav=0,popforecast=0;
1.191 brouard 6783: int hstepm=0, nhstepm=0;
1.136 brouard 6784: int agemortsup;
6785: float sumlpop=0.;
6786: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
6787: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
6788:
1.191 brouard 6789: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 6790: double ftolpl=FTOL;
6791: double **prlim;
6792: double ***param; /* Matrix of parameters */
6793: double *p;
6794: double **matcov; /* Matrix of covariance */
1.203 brouard 6795: double **hess; /* Hessian matrix */
1.136 brouard 6796: double ***delti3; /* Scale */
6797: double *delti; /* Scale */
6798: double ***eij, ***vareij;
6799: double **varpl; /* Variances of prevalence limits by age */
6800: double *epj, vepp;
1.164 brouard 6801:
1.136 brouard 6802: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
6803: double **ximort;
1.145 brouard 6804: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 6805: int *dcwave;
6806:
1.164 brouard 6807: char z[1]="c";
1.136 brouard 6808:
6809: /*char *strt;*/
6810: char strtend[80];
1.126 brouard 6811:
1.164 brouard 6812:
1.126 brouard 6813: /* setlocale (LC_ALL, ""); */
6814: /* bindtextdomain (PACKAGE, LOCALEDIR); */
6815: /* textdomain (PACKAGE); */
6816: /* setlocale (LC_CTYPE, ""); */
6817: /* setlocale (LC_MESSAGES, ""); */
6818:
6819: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 6820: rstart_time = time(NULL);
6821: /* (void) gettimeofday(&start_time,&tzp);*/
6822: start_time = *localtime(&rstart_time);
1.126 brouard 6823: curr_time=start_time;
1.157 brouard 6824: /*tml = *localtime(&start_time.tm_sec);*/
6825: /* strcpy(strstart,asctime(&tml)); */
6826: strcpy(strstart,asctime(&start_time));
1.126 brouard 6827:
6828: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 6829: /* tp.tm_sec = tp.tm_sec +86400; */
6830: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 6831: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
6832: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
6833: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 6834: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 6835: /* strt=asctime(&tmg); */
6836: /* printf("Time(after) =%s",strstart); */
6837: /* (void) time (&time_value);
6838: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
6839: * tm = *localtime(&time_value);
6840: * strstart=asctime(&tm);
6841: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
6842: */
6843:
6844: nberr=0; /* Number of errors and warnings */
6845: nbwarn=0;
1.184 brouard 6846: #ifdef WIN32
6847: _getcwd(pathcd, size);
6848: #else
1.126 brouard 6849: getcwd(pathcd, size);
1.184 brouard 6850: #endif
1.191 brouard 6851: syscompilerinfo(0);
1.196 brouard 6852: printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126 brouard 6853: if(argc <=1){
6854: printf("\nEnter the parameter file name: ");
1.205 brouard 6855: if(!fgets(pathr,FILENAMELENGTH,stdin)){
6856: printf("ERROR Empty parameter file name\n");
6857: goto end;
6858: }
1.126 brouard 6859: i=strlen(pathr);
6860: if(pathr[i-1]=='\n')
6861: pathr[i-1]='\0';
1.156 brouard 6862: i=strlen(pathr);
1.205 brouard 6863: if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
1.156 brouard 6864: pathr[i-1]='\0';
1.205 brouard 6865: }
6866: i=strlen(pathr);
6867: if( i==0 ){
6868: printf("ERROR Empty parameter file name\n");
6869: goto end;
6870: }
6871: for (tok = pathr; tok != NULL; ){
1.126 brouard 6872: printf("Pathr |%s|\n",pathr);
6873: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
6874: printf("val= |%s| pathr=%s\n",val,pathr);
6875: strcpy (pathtot, val);
6876: if(pathr[0] == '\0') break; /* Dirty */
6877: }
6878: }
6879: else{
6880: strcpy(pathtot,argv[1]);
6881: }
6882: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
6883: /*cygwin_split_path(pathtot,path,optionfile);
6884: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
6885: /* cutv(path,optionfile,pathtot,'\\');*/
6886:
6887: /* Split argv[0], imach program to get pathimach */
6888: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
6889: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6890: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6891: /* strcpy(pathimach,argv[0]); */
6892: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
6893: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
6894: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 6895: #ifdef WIN32
6896: _chdir(path); /* Can be a relative path */
6897: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
6898: #else
1.126 brouard 6899: chdir(path); /* Can be a relative path */
1.184 brouard 6900: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
6901: #endif
6902: printf("Current directory %s!\n",pathcd);
1.126 brouard 6903: strcpy(command,"mkdir ");
6904: strcat(command,optionfilefiname);
6905: if((outcmd=system(command)) != 0){
1.169 brouard 6906: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 6907: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
6908: /* fclose(ficlog); */
6909: /* exit(1); */
6910: }
6911: /* if((imk=mkdir(optionfilefiname))<0){ */
6912: /* perror("mkdir"); */
6913: /* } */
6914:
6915: /*-------- arguments in the command line --------*/
6916:
1.186 brouard 6917: /* Main Log file */
1.126 brouard 6918: strcat(filelog, optionfilefiname);
6919: strcat(filelog,".log"); /* */
6920: if((ficlog=fopen(filelog,"w"))==NULL) {
6921: printf("Problem with logfile %s\n",filelog);
6922: goto end;
6923: }
6924: fprintf(ficlog,"Log filename:%s\n",filelog);
1.197 brouard 6925: fprintf(ficlog,"Version %s %s",version,fullversion);
1.126 brouard 6926: fprintf(ficlog,"\nEnter the parameter file name: \n");
6927: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
6928: path=%s \n\
6929: optionfile=%s\n\
6930: optionfilext=%s\n\
1.156 brouard 6931: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 6932:
1.197 brouard 6933: syscompilerinfo(1);
1.167 brouard 6934:
1.126 brouard 6935: printf("Local time (at start):%s",strstart);
6936: fprintf(ficlog,"Local time (at start): %s",strstart);
6937: fflush(ficlog);
6938: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 6939: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 6940:
6941: /* */
6942: strcpy(fileres,"r");
6943: strcat(fileres, optionfilefiname);
1.201 brouard 6944: strcat(fileresu, optionfilefiname); /* Without r in front */
1.126 brouard 6945: strcat(fileres,".txt"); /* Other files have txt extension */
1.201 brouard 6946: strcat(fileresu,".txt"); /* Other files have txt extension */
1.126 brouard 6947:
1.186 brouard 6948: /* Main ---------arguments file --------*/
1.126 brouard 6949:
6950: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 6951: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
6952: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 6953: fflush(ficlog);
1.149 brouard 6954: /* goto end; */
6955: exit(70);
1.126 brouard 6956: }
6957:
6958:
6959:
6960: strcpy(filereso,"o");
1.201 brouard 6961: strcat(filereso,fileresu);
1.126 brouard 6962: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
6963: printf("Problem with Output resultfile: %s\n", filereso);
6964: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
6965: fflush(ficlog);
6966: goto end;
6967: }
6968:
6969: /* Reads comments: lines beginning with '#' */
6970: numlinepar=0;
1.197 brouard 6971:
6972: /* First parameter line */
6973: while(fgets(line, MAXLINE, ficpar)) {
6974: /* If line starts with a # it is a comment */
6975: if (line[0] == '#') {
6976: numlinepar++;
6977: fputs(line,stdout);
6978: fputs(line,ficparo);
6979: fputs(line,ficlog);
6980: continue;
6981: }else
6982: break;
6983: }
6984: if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
6985: title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
6986: if (num_filled != 5) {
6987: printf("Should be 5 parameters\n");
6988: }
1.126 brouard 6989: numlinepar++;
1.197 brouard 6990: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
6991: }
6992: /* Second parameter line */
6993: while(fgets(line, MAXLINE, ficpar)) {
6994: /* If line starts with a # it is a comment */
6995: if (line[0] == '#') {
6996: numlinepar++;
6997: fputs(line,stdout);
6998: fputs(line,ficparo);
6999: fputs(line,ficlog);
7000: continue;
7001: }else
7002: break;
7003: }
7004: if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
7005: &ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
7006: if (num_filled != 8) {
1.209 brouard 7007: printf("Not 8 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
7008: printf("but line=%s\n",line);
1.197 brouard 7009: }
7010: 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 7011: }
1.203 brouard 7012: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
1.209 brouard 7013: /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
1.197 brouard 7014: /* Third parameter line */
7015: while(fgets(line, MAXLINE, ficpar)) {
7016: /* If line starts with a # it is a comment */
7017: if (line[0] == '#') {
7018: numlinepar++;
7019: fputs(line,stdout);
7020: fputs(line,ficparo);
7021: fputs(line,ficlog);
7022: continue;
7023: }else
7024: break;
7025: }
1.201 brouard 7026: if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
7027: if (num_filled == 0)
7028: model[0]='\0';
7029: else if (num_filled != 1){
1.197 brouard 7030: printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
7031: fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
7032: model[0]='\0';
7033: goto end;
7034: }
7035: else{
7036: if (model[0]=='+'){
7037: for(i=1; i<=strlen(model);i++)
7038: modeltemp[i-1]=model[i];
1.201 brouard 7039: strcpy(model,modeltemp);
1.197 brouard 7040: }
7041: }
1.199 brouard 7042: /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
1.203 brouard 7043: printf("model=1+age+%s\n",model);fflush(stdout);
1.197 brouard 7044: }
7045: /* 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); */
7046: /* numlinepar=numlinepar+3; /\* In general *\/ */
7047: /* 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 7048: 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);
7049: 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 7050: fflush(ficlog);
1.190 brouard 7051: /* if(model[0]=='#'|| model[0]== '\0'){ */
7052: if(model[0]=='#'){
1.187 brouard 7053: printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
7054: 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
7055: 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \
7056: if(mle != -1){
7057: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
7058: exit(1);
7059: }
7060: }
1.126 brouard 7061: while((c=getc(ficpar))=='#' && c!= EOF){
7062: ungetc(c,ficpar);
7063: fgets(line, MAXLINE, ficpar);
7064: numlinepar++;
1.195 brouard 7065: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
7066: z[0]=line[1];
7067: }
7068: /* printf("****line [1] = %c \n",line[1]); */
1.141 brouard 7069: fputs(line, stdout);
7070: //puts(line);
1.126 brouard 7071: fputs(line,ficparo);
7072: fputs(line,ficlog);
7073: }
7074: ungetc(c,ficpar);
7075:
7076:
1.145 brouard 7077: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.136 brouard 7078: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
7079: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
7080: v1+v2*age+v2*v3 makes cptcovn = 3
7081: */
7082: if (strlen(model)>1)
1.187 brouard 7083: 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 7084: else
1.187 brouard 7085: ncovmodel=2; /* Constant and age */
1.133 brouard 7086: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
7087: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 7088: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
7089: 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);
7090: 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);
7091: fflush(stdout);
7092: fclose (ficlog);
7093: goto end;
7094: }
1.126 brouard 7095: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
7096: delti=delti3[1][1];
7097: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
7098: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
7099: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 7100: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
7101: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 7102: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7103: fclose (ficparo);
7104: fclose (ficlog);
7105: goto end;
7106: exit(0);
7107: }
1.186 brouard 7108: else if(mle==-3) { /* Main Wizard */
1.126 brouard 7109: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 7110: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
7111: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 7112: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
7113: matcov=matrix(1,npar,1,npar);
1.203 brouard 7114: hess=matrix(1,npar,1,npar);
1.126 brouard 7115: }
7116: else{
1.145 brouard 7117: /* Read guessed parameters */
1.126 brouard 7118: /* Reads comments: lines beginning with '#' */
7119: while((c=getc(ficpar))=='#' && c!= EOF){
7120: ungetc(c,ficpar);
7121: fgets(line, MAXLINE, ficpar);
7122: numlinepar++;
1.141 brouard 7123: fputs(line,stdout);
1.126 brouard 7124: fputs(line,ficparo);
7125: fputs(line,ficlog);
7126: }
7127: ungetc(c,ficpar);
7128:
7129: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
7130: for(i=1; i <=nlstate; i++){
7131: j=0;
7132: for(jj=1; jj <=nlstate+ndeath; jj++){
7133: if(jj==i) continue;
7134: j++;
7135: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.193 brouard 7136: if ((i1 != i) || (j1 != jj)){
1.126 brouard 7137: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
7138: It might be a problem of design; if ncovcol and the model are correct\n \
7139: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
7140: exit(1);
7141: }
7142: fprintf(ficparo,"%1d%1d",i1,j1);
7143: if(mle==1)
1.193 brouard 7144: printf("%1d%1d",i,jj);
7145: fprintf(ficlog,"%1d%1d",i,jj);
1.126 brouard 7146: for(k=1; k<=ncovmodel;k++){
7147: fscanf(ficpar," %lf",¶m[i][j][k]);
7148: if(mle==1){
7149: printf(" %lf",param[i][j][k]);
7150: fprintf(ficlog," %lf",param[i][j][k]);
7151: }
7152: else
7153: fprintf(ficlog," %lf",param[i][j][k]);
7154: fprintf(ficparo," %lf",param[i][j][k]);
7155: }
7156: fscanf(ficpar,"\n");
7157: numlinepar++;
7158: if(mle==1)
7159: printf("\n");
7160: fprintf(ficlog,"\n");
7161: fprintf(ficparo,"\n");
7162: }
7163: }
7164: fflush(ficlog);
7165:
1.145 brouard 7166: /* Reads scales values */
1.126 brouard 7167: p=param[1][1];
7168:
7169: /* Reads comments: lines beginning with '#' */
7170: while((c=getc(ficpar))=='#' && c!= EOF){
7171: ungetc(c,ficpar);
7172: fgets(line, MAXLINE, ficpar);
7173: numlinepar++;
1.141 brouard 7174: fputs(line,stdout);
1.126 brouard 7175: fputs(line,ficparo);
7176: fputs(line,ficlog);
7177: }
7178: ungetc(c,ficpar);
7179:
7180: for(i=1; i <=nlstate; i++){
7181: for(j=1; j <=nlstate+ndeath-1; j++){
7182: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.164 brouard 7183: if ( (i1-i) * (j1-j) != 0){
1.126 brouard 7184: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
7185: exit(1);
7186: }
7187: printf("%1d%1d",i,j);
7188: fprintf(ficparo,"%1d%1d",i1,j1);
7189: fprintf(ficlog,"%1d%1d",i1,j1);
7190: for(k=1; k<=ncovmodel;k++){
7191: fscanf(ficpar,"%le",&delti3[i][j][k]);
7192: printf(" %le",delti3[i][j][k]);
7193: fprintf(ficparo," %le",delti3[i][j][k]);
7194: fprintf(ficlog," %le",delti3[i][j][k]);
7195: }
7196: fscanf(ficpar,"\n");
7197: numlinepar++;
7198: printf("\n");
7199: fprintf(ficparo,"\n");
7200: fprintf(ficlog,"\n");
7201: }
7202: }
7203: fflush(ficlog);
7204:
1.145 brouard 7205: /* Reads covariance matrix */
1.126 brouard 7206: delti=delti3[1][1];
7207:
7208:
7209: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
7210:
7211: /* Reads comments: lines beginning with '#' */
7212: while((c=getc(ficpar))=='#' && c!= EOF){
7213: ungetc(c,ficpar);
7214: fgets(line, MAXLINE, ficpar);
7215: numlinepar++;
1.141 brouard 7216: fputs(line,stdout);
1.126 brouard 7217: fputs(line,ficparo);
7218: fputs(line,ficlog);
7219: }
7220: ungetc(c,ficpar);
7221:
7222: matcov=matrix(1,npar,1,npar);
1.203 brouard 7223: hess=matrix(1,npar,1,npar);
1.131 brouard 7224: for(i=1; i <=npar; i++)
7225: for(j=1; j <=npar; j++) matcov[i][j]=0.;
7226:
1.194 brouard 7227: /* Scans npar lines */
1.126 brouard 7228: for(i=1; i <=npar; i++){
1.194 brouard 7229: count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk);
7230: if(count != 3){
7231: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
7232: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
7233: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
7234: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
7235: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
7236: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
7237: exit(1);
7238: }else
1.126 brouard 7239: if(mle==1)
1.194 brouard 7240: printf("%1d%1d%1d",i1,j1,jk);
7241: fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);
7242: fprintf(ficparo,"%1d%1d%1d",i1,j1,jk);
1.126 brouard 7243: for(j=1; j <=i; j++){
7244: fscanf(ficpar," %le",&matcov[i][j]);
7245: if(mle==1){
7246: printf(" %.5le",matcov[i][j]);
7247: }
7248: fprintf(ficlog," %.5le",matcov[i][j]);
7249: fprintf(ficparo," %.5le",matcov[i][j]);
7250: }
7251: fscanf(ficpar,"\n");
7252: numlinepar++;
7253: if(mle==1)
7254: printf("\n");
7255: fprintf(ficlog,"\n");
7256: fprintf(ficparo,"\n");
7257: }
1.194 brouard 7258: /* End of read covariance matrix npar lines */
1.126 brouard 7259: for(i=1; i <=npar; i++)
7260: for(j=i+1;j<=npar;j++)
7261: matcov[i][j]=matcov[j][i];
7262:
7263: if(mle==1)
7264: printf("\n");
7265: fprintf(ficlog,"\n");
7266:
7267: fflush(ficlog);
7268:
7269: /*-------- Rewriting parameter file ----------*/
7270: strcpy(rfileres,"r"); /* "Rparameterfile */
7271: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
7272: strcat(rfileres,"."); /* */
7273: strcat(rfileres,optionfilext); /* Other files have txt extension */
7274: if((ficres =fopen(rfileres,"w"))==NULL) {
1.201 brouard 7275: printf("Problem writing new parameter file: %s\n", rfileres);goto end;
7276: fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
1.126 brouard 7277: }
7278: fprintf(ficres,"#%s\n",version);
7279: } /* End of mle != -3 */
7280:
1.186 brouard 7281: /* Main data
7282: */
1.126 brouard 7283: n= lastobs;
7284: num=lvector(1,n);
7285: moisnais=vector(1,n);
7286: annais=vector(1,n);
7287: moisdc=vector(1,n);
7288: andc=vector(1,n);
7289: agedc=vector(1,n);
7290: cod=ivector(1,n);
7291: weight=vector(1,n);
7292: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
7293: mint=matrix(1,maxwav,1,n);
7294: anint=matrix(1,maxwav,1,n);
1.131 brouard 7295: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 7296: tab=ivector(1,NCOVMAX);
1.144 brouard 7297: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 7298: 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 7299:
1.136 brouard 7300: /* Reads data from file datafile */
7301: if (readdata(datafile, firstobs, lastobs, &imx)==1)
7302: goto end;
7303:
7304: /* Calculation of the number of parameters from char model */
1.137 brouard 7305: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
7306: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
7307: k=3 V4 Tvar[k=3]= 4 (from V4)
7308: k=2 V1 Tvar[k=2]= 1 (from V1)
7309: k=1 Tvar[1]=2 (from V2)
7310: */
7311: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
7312: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
7313: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
7314: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
7315: */
7316: /* For model-covariate k tells which data-covariate to use but
7317: because this model-covariate is a construction we invent a new column
7318: ncovcol + k1
7319: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
7320: Tvar[3=V1*V4]=4+1 etc */
1.145 brouard 7321: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
1.137 brouard 7322: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
7323: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
7324: */
1.145 brouard 7325: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
7326: 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 7327: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
7328: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 7329: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 7330: 4 covariates (3 plus signs)
7331: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
7332: */
1.136 brouard 7333:
1.186 brouard 7334: /* Main decodemodel */
7335:
1.187 brouard 7336:
1.136 brouard 7337: if(decodemodel(model, lastobs) == 1)
7338: goto end;
7339:
1.137 brouard 7340: if((double)(lastobs-imx)/(double)imx > 1.10){
7341: nbwarn++;
7342: 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);
7343: 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);
7344: }
1.136 brouard 7345: /* if(mle==1){*/
1.137 brouard 7346: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
7347: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 7348: }
7349:
7350: /*-calculation of age at interview from date of interview and age at death -*/
7351: agev=matrix(1,maxwav,1,imx);
7352:
7353: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
7354: goto end;
7355:
1.126 brouard 7356:
1.136 brouard 7357: agegomp=(int)agemin;
7358: free_vector(moisnais,1,n);
7359: free_vector(annais,1,n);
1.126 brouard 7360: /* free_matrix(mint,1,maxwav,1,n);
7361: free_matrix(anint,1,maxwav,1,n);*/
7362: free_vector(moisdc,1,n);
7363: free_vector(andc,1,n);
1.145 brouard 7364: /* */
7365:
1.126 brouard 7366: wav=ivector(1,imx);
7367: dh=imatrix(1,lastpass-firstpass+1,1,imx);
7368: bh=imatrix(1,lastpass-firstpass+1,1,imx);
7369: mw=imatrix(1,lastpass-firstpass+1,1,imx);
7370:
7371: /* Concatenates waves */
7372: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 brouard 7373: /* */
7374:
1.126 brouard 7375: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
7376:
7377: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
7378: ncodemax[1]=1;
1.145 brouard 7379: Ndum =ivector(-1,NCOVMAX);
1.187 brouard 7380: if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */
1.145 brouard 7381: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.186 brouard 7382: /* Nbcode gives the value of the lth modality of jth covariate, in
7383: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
7384: /* 1 to ncodemax[j] is the maximum value of this jth covariate */
1.145 brouard 7385:
1.200 brouard 7386: /* codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
1.198 brouard 7387: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
1.186 brouard 7388: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.145 brouard 7389: h=0;
7390:
7391:
7392: /*if (cptcovn > 0) */
1.126 brouard 7393:
1.145 brouard 7394:
1.126 brouard 7395: m=pow(2,cptcoveff);
7396:
1.144 brouard 7397: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.186 brouard 7398: * For k=4 covariates, h goes from 1 to 2**k
7399: * codtabm(h,k)= 1 & (h-1) >> (k-1) ;
7400: * h\k 1 2 3 4
1.143 brouard 7401: *______________________________
7402: * 1 i=1 1 i=1 1 i=1 1 i=1 1
7403: * 2 2 1 1 1
7404: * 3 i=2 1 2 1 1
7405: * 4 2 2 1 1
7406: * 5 i=3 1 i=2 1 2 1
7407: * 6 2 1 2 1
7408: * 7 i=4 1 2 2 1
7409: * 8 2 2 2 1
1.197 brouard 7410: * 9 i=5 1 i=3 1 i=2 1 2
7411: * 10 2 1 1 2
7412: * 11 i=6 1 2 1 2
7413: * 12 2 2 1 2
7414: * 13 i=7 1 i=4 1 2 2
7415: * 14 2 1 2 2
7416: * 15 i=8 1 2 2 2
7417: * 16 2 2 2 2
1.143 brouard 7418: */
1.202 brouard 7419: /* /\* for(h=1; h <=100 ;h++){ *\/ */
7420: /* /\* printf("h=%2d ", h); *\/ */
7421: /* /\* for(k=1; k <=10; k++){ *\/ */
7422: /* /\* printf("k=%d %d ",k,codtabm(h,k)); *\/ */
7423: /* /\* codtab[h][k]=codtabm(h,k); *\/ */
7424: /* /\* } *\/ */
7425: /* /\* printf("\n"); *\/ */
7426: /* } */
1.197 brouard 7427: /* for(k=1;k<=cptcoveff; k++){ /\* scans any effective covariate *\/ */
7428: /* 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 *\/ */
7429: /* for(j=1; j <= ncodemax[k]; j++){ /\* For each modality of this covariate ncodemax=2*\/ */
7430: /* for(cpt=1; cpt <=pow(2,k-1); cpt++){ /\* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 *\/ */
7431: /* h++; */
7432: /* if (h>m) */
7433: /* h=1; */
7434: /* codtab[h][k]=j; */
7435: /* /\* codtab[12][3]=1; *\/ */
7436: /* /\*codtab[h][Tvar[k]]=j;*\/ */
7437: /* /\* 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]]); *\/ */
7438: /* } */
7439: /* } */
7440: /* } */
7441: /* } */
1.126 brouard 7442: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
7443: codtab[1][2]=1;codtab[2][2]=2; */
1.197 brouard 7444: /* for(i=1; i <=m ;i++){ */
7445: /* for(k=1; k <=cptcovn; k++){ */
7446: /* printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); */
7447: /* } */
7448: /* printf("\n"); */
7449: /* } */
7450: /* scanf("%d",i);*/
1.145 brouard 7451:
7452: free_ivector(Ndum,-1,NCOVMAX);
7453:
7454:
1.126 brouard 7455:
1.186 brouard 7456: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 7457: strcpy(optionfilegnuplot,optionfilefiname);
7458: if(mle==-3)
1.201 brouard 7459: strcat(optionfilegnuplot,"-MORT_");
1.126 brouard 7460: strcat(optionfilegnuplot,".gp");
7461:
7462: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
7463: printf("Problem with file %s",optionfilegnuplot);
7464: }
7465: else{
1.204 brouard 7466: fprintf(ficgp,"\n# IMaCh-%s\n", version);
1.126 brouard 7467: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 7468: //fprintf(ficgp,"set missing 'NaNq'\n");
7469: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 7470: }
7471: /* fclose(ficgp);*/
1.186 brouard 7472:
7473:
7474: /* Initialisation of --------- index.htm --------*/
1.126 brouard 7475:
7476: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
7477: if(mle==-3)
1.201 brouard 7478: strcat(optionfilehtm,"-MORT_");
1.126 brouard 7479: strcat(optionfilehtm,".htm");
7480: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 7481: printf("Problem with %s \n",optionfilehtm);
7482: exit(0);
1.126 brouard 7483: }
7484:
7485: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
7486: strcat(optionfilehtmcov,"-cov.htm");
7487: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
7488: printf("Problem with %s \n",optionfilehtmcov), exit(0);
7489: }
7490: else{
7491: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
7492: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 7493: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.126 brouard 7494: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
7495: }
7496:
1.204 brouard 7497: fprintf(fichtm,"<html><head>\n<head>\n<meta charset=\"utf-8\"/><meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\" />\n<title>IMaCh %s</title></head>\n <body><font size=\"7\"><a href=http:/euroreves.ined.fr/imach>IMaCh for Interpolated Markov Chain</a> </font><br>\n<font size=\"3\">Sponsored by Copyright (C) 2002-2015 <a href=http://www.ined.fr>INED</a>-EUROREVES-Institut de longévité-Japan Society for the Promotion of Sciences 日本学術振興会 (<a href=https://www.jsps.go.jp/english/e-grants/>Grant-in-Aid for Scientific Research 25293121</a>) - <a href=https://software.intel.com/en-us>Intel Software 2015</a></font><br> \
7498: <hr size=\"2\" color=\"#EC5E5E\"> \n\
7499: <font size=\"2\">IMaCh-%s <br> %s</font> \
1.126 brouard 7500: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 7501: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
1.126 brouard 7502: \n\
7503: <hr size=\"2\" color=\"#EC5E5E\">\
7504: <ul><li><h4>Parameter files</h4>\n\
7505: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
7506: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
7507: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
7508: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
7509: - Date and time at start: %s</ul>\n",\
7510: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
7511: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
7512: fileres,fileres,\
7513: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
7514: fflush(fichtm);
7515:
7516: strcpy(pathr,path);
7517: strcat(pathr,optionfilefiname);
1.184 brouard 7518: #ifdef WIN32
7519: _chdir(optionfilefiname); /* Move to directory named optionfile */
7520: #else
1.126 brouard 7521: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 7522: #endif
7523:
1.126 brouard 7524:
7525: /* Calculates basic frequencies. Computes observed prevalence at single age
7526: and prints on file fileres'p'. */
7527: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
7528:
7529: fprintf(fichtm,"\n");
7530: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
7531: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
7532: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
7533: imx,agemin,agemax,jmin,jmax,jmean);
7534: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7535: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7536: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7537: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7538: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
7539:
7540:
7541: /* For Powell, parameters are in a vector p[] starting at p[1]
7542: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
7543: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
7544:
7545: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 7546: /* For mortality only */
1.126 brouard 7547: if (mle==-3){
1.136 brouard 7548: ximort=matrix(1,NDIM,1,NDIM);
1.186 brouard 7549: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 7550: cens=ivector(1,n);
7551: ageexmed=vector(1,n);
7552: agecens=vector(1,n);
7553: dcwave=ivector(1,n);
7554:
7555: for (i=1; i<=imx; i++){
7556: dcwave[i]=-1;
7557: for (m=firstpass; m<=lastpass; m++)
7558: if (s[m][i]>nlstate) {
7559: dcwave[i]=m;
7560: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
7561: break;
7562: }
7563: }
7564:
7565: for (i=1; i<=imx; i++) {
7566: if (wav[i]>0){
7567: ageexmed[i]=agev[mw[1][i]][i];
7568: j=wav[i];
7569: agecens[i]=1.;
7570:
7571: if (ageexmed[i]> 1 && wav[i] > 0){
7572: agecens[i]=agev[mw[j][i]][i];
7573: cens[i]= 1;
7574: }else if (ageexmed[i]< 1)
7575: cens[i]= -1;
7576: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
7577: cens[i]=0 ;
7578: }
7579: else cens[i]=-1;
7580: }
7581:
7582: for (i=1;i<=NDIM;i++) {
7583: for (j=1;j<=NDIM;j++)
7584: ximort[i][j]=(i == j ? 1.0 : 0.0);
7585: }
7586:
1.145 brouard 7587: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 7588: /*printf("%lf %lf", p[1], p[2]);*/
7589:
7590:
1.136 brouard 7591: #ifdef GSL
7592: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 7593: #else
1.126 brouard 7594: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 7595: #endif
1.201 brouard 7596: strcpy(filerespow,"POW-MORT_");
7597: strcat(filerespow,fileresu);
1.126 brouard 7598: if((ficrespow=fopen(filerespow,"w"))==NULL) {
7599: printf("Problem with resultfile: %s\n", filerespow);
7600: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
7601: }
1.136 brouard 7602: #ifdef GSL
7603: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 7604: #else
1.126 brouard 7605: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 7606: #endif
1.126 brouard 7607: /* for (i=1;i<=nlstate;i++)
7608: for(j=1;j<=nlstate+ndeath;j++)
7609: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
7610: */
7611: fprintf(ficrespow,"\n");
1.136 brouard 7612: #ifdef GSL
7613: /* gsl starts here */
7614: T = gsl_multimin_fminimizer_nmsimplex;
7615: gsl_multimin_fminimizer *sfm = NULL;
7616: gsl_vector *ss, *x;
7617: gsl_multimin_function minex_func;
7618:
7619: /* Initial vertex size vector */
7620: ss = gsl_vector_alloc (NDIM);
7621:
7622: if (ss == NULL){
7623: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
7624: }
7625: /* Set all step sizes to 1 */
7626: gsl_vector_set_all (ss, 0.001);
7627:
7628: /* Starting point */
1.126 brouard 7629:
1.136 brouard 7630: x = gsl_vector_alloc (NDIM);
7631:
7632: if (x == NULL){
7633: gsl_vector_free(ss);
7634: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
7635: }
7636:
7637: /* Initialize method and iterate */
7638: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 7639: /* gsl_vector_set(x, 0, 0.0268); */
7640: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 7641: gsl_vector_set(x, 0, p[1]);
7642: gsl_vector_set(x, 1, p[2]);
7643:
7644: minex_func.f = &gompertz_f;
7645: minex_func.n = NDIM;
7646: minex_func.params = (void *)&p; /* ??? */
7647:
7648: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
7649: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
7650:
7651: printf("Iterations beginning .....\n\n");
7652: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
7653:
7654: iteri=0;
7655: while (rval == GSL_CONTINUE){
7656: iteri++;
7657: status = gsl_multimin_fminimizer_iterate(sfm);
7658:
7659: if (status) printf("error: %s\n", gsl_strerror (status));
7660: fflush(0);
7661:
7662: if (status)
7663: break;
7664:
7665: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
7666: ssval = gsl_multimin_fminimizer_size (sfm);
7667:
7668: if (rval == GSL_SUCCESS)
7669: printf ("converged to a local maximum at\n");
7670:
7671: printf("%5d ", iteri);
7672: for (it = 0; it < NDIM; it++){
7673: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
7674: }
7675: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
7676: }
7677:
7678: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
7679:
7680: gsl_vector_free(x); /* initial values */
7681: gsl_vector_free(ss); /* inital step size */
7682: for (it=0; it<NDIM; it++){
7683: p[it+1]=gsl_vector_get(sfm->x,it);
7684: fprintf(ficrespow," %.12lf", p[it]);
7685: }
7686: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
7687: #endif
7688: #ifdef POWELL
7689: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
7690: #endif
1.126 brouard 7691: fclose(ficrespow);
7692:
1.203 brouard 7693: hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz);
1.126 brouard 7694:
7695: for(i=1; i <=NDIM; i++)
7696: for(j=i+1;j<=NDIM;j++)
7697: matcov[i][j]=matcov[j][i];
7698:
7699: printf("\nCovariance matrix\n ");
1.203 brouard 7700: fprintf(ficlog,"\nCovariance matrix\n ");
1.126 brouard 7701: for(i=1; i <=NDIM; i++) {
7702: for(j=1;j<=NDIM;j++){
7703: printf("%f ",matcov[i][j]);
1.203 brouard 7704: fprintf(ficlog,"%f ",matcov[i][j]);
1.126 brouard 7705: }
1.203 brouard 7706: printf("\n "); fprintf(ficlog,"\n ");
1.126 brouard 7707: }
7708:
7709: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 brouard 7710: for (i=1;i<=NDIM;i++) {
1.126 brouard 7711: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 brouard 7712: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
7713: }
1.126 brouard 7714: lsurv=vector(1,AGESUP);
7715: lpop=vector(1,AGESUP);
7716: tpop=vector(1,AGESUP);
7717: lsurv[agegomp]=100000;
7718:
7719: for (k=agegomp;k<=AGESUP;k++) {
7720: agemortsup=k;
7721: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
7722: }
7723:
7724: for (k=agegomp;k<agemortsup;k++)
7725: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
7726:
7727: for (k=agegomp;k<agemortsup;k++){
7728: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
7729: sumlpop=sumlpop+lpop[k];
7730: }
7731:
7732: tpop[agegomp]=sumlpop;
7733: for (k=agegomp;k<(agemortsup-3);k++){
7734: /* tpop[k+1]=2;*/
7735: tpop[k+1]=tpop[k]-lpop[k];
7736: }
7737:
7738:
7739: printf("\nAge lx qx dx Lx Tx e(x)\n");
7740: for (k=agegomp;k<(agemortsup-2);k++)
7741: 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]);
7742:
7743:
7744: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 7745: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
7746: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7747: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7748: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7749: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7750: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7751: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7752: }else
1.201 brouard 7753: printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
7754: printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
1.126 brouard 7755: stepm, weightopt,\
7756: model,imx,p,matcov,agemortsup);
7757:
7758: free_vector(lsurv,1,AGESUP);
7759: free_vector(lpop,1,AGESUP);
7760: free_vector(tpop,1,AGESUP);
1.136 brouard 7761: #ifdef GSL
7762: free_ivector(cens,1,n);
7763: free_vector(agecens,1,n);
7764: free_ivector(dcwave,1,n);
7765: free_matrix(ximort,1,NDIM,1,NDIM);
7766: #endif
1.186 brouard 7767: } /* Endof if mle==-3 mortality only */
1.205 brouard 7768: /* Standard */
7769: else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
7770: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
7771: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
1.132 brouard 7772: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 7773: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7774: for (k=1; k<=npar;k++)
7775: printf(" %d %8.5f",k,p[k]);
7776: printf("\n");
1.205 brouard 7777: if(mle>=1){ /* Could be 1 or 2, Real Maximization */
7778: /* mlikeli uses func not funcone */
7779: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
7780: }
7781: if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
7782: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
7783: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
7784: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
7785: }
7786: globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
1.126 brouard 7787: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
7788: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7789: for (k=1; k<=npar;k++)
7790: printf(" %d %8.5f",k,p[k]);
7791: printf("\n");
7792:
7793: /*--------- results files --------------*/
1.192 brouard 7794: 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 7795:
7796:
7797: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7798: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7799: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7800: for(i=1,jk=1; i <=nlstate; i++){
7801: for(k=1; k <=(nlstate+ndeath); k++){
7802: if (k != i) {
7803: printf("%d%d ",i,k);
7804: fprintf(ficlog,"%d%d ",i,k);
7805: fprintf(ficres,"%1d%1d ",i,k);
7806: for(j=1; j <=ncovmodel; j++){
1.190 brouard 7807: printf("%12.7f ",p[jk]);
7808: fprintf(ficlog,"%12.7f ",p[jk]);
7809: fprintf(ficres,"%12.7f ",p[jk]);
1.126 brouard 7810: jk++;
7811: }
7812: printf("\n");
7813: fprintf(ficlog,"\n");
7814: fprintf(ficres,"\n");
7815: }
7816: }
7817: }
1.203 brouard 7818: if(mle != 0){
7819: /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
1.126 brouard 7820: ftolhess=ftol; /* Usually correct */
1.203 brouard 7821: hesscov(matcov, hess, p, npar, delti, ftolhess, func);
7822: 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");
7823: 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");
7824: for(i=1,jk=1; i <=nlstate; i++){
7825: for(k=1; k <=(nlstate+ndeath); k++){
7826: if (k != i) {
7827: printf("%d%d ",i,k);
7828: fprintf(ficlog,"%d%d ",i,k);
7829: for(j=1; j <=ncovmodel; j++){
7830: 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]));
7831: 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]));
7832: jk++;
7833: }
7834: printf("\n");
7835: fprintf(ficlog,"\n");
1.193 brouard 7836: }
7837: }
7838: }
1.203 brouard 7839: } /* end of hesscov and Wald tests */
1.193 brouard 7840:
1.203 brouard 7841: /* */
1.126 brouard 7842: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
7843: printf("# Scales (for hessian or gradient estimation)\n");
7844: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
7845: for(i=1,jk=1; i <=nlstate; i++){
7846: for(j=1; j <=nlstate+ndeath; j++){
7847: if (j!=i) {
7848: fprintf(ficres,"%1d%1d",i,j);
7849: printf("%1d%1d",i,j);
7850: fprintf(ficlog,"%1d%1d",i,j);
7851: for(k=1; k<=ncovmodel;k++){
7852: printf(" %.5e",delti[jk]);
7853: fprintf(ficlog," %.5e",delti[jk]);
7854: fprintf(ficres," %.5e",delti[jk]);
7855: jk++;
7856: }
7857: printf("\n");
7858: fprintf(ficlog,"\n");
7859: fprintf(ficres,"\n");
7860: }
7861: }
7862: }
7863:
7864: 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 7865: if(mle >= 1) /* To big for the screen */
1.126 brouard 7866: 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");
7867: 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");
7868: /* # 121 Var(a12)\n\ */
7869: /* # 122 Cov(b12,a12) Var(b12)\n\ */
7870: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
7871: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
7872: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
7873: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
7874: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
7875: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
7876:
7877:
7878: /* Just to have a covariance matrix which will be more understandable
7879: even is we still don't want to manage dictionary of variables
7880: */
7881: for(itimes=1;itimes<=2;itimes++){
7882: jj=0;
7883: for(i=1; i <=nlstate; i++){
7884: for(j=1; j <=nlstate+ndeath; j++){
7885: if(j==i) continue;
7886: for(k=1; k<=ncovmodel;k++){
7887: jj++;
7888: ca[0]= k+'a'-1;ca[1]='\0';
7889: if(itimes==1){
7890: if(mle>=1)
7891: printf("#%1d%1d%d",i,j,k);
7892: fprintf(ficlog,"#%1d%1d%d",i,j,k);
7893: fprintf(ficres,"#%1d%1d%d",i,j,k);
7894: }else{
7895: if(mle>=1)
7896: printf("%1d%1d%d",i,j,k);
7897: fprintf(ficlog,"%1d%1d%d",i,j,k);
7898: fprintf(ficres,"%1d%1d%d",i,j,k);
7899: }
7900: ll=0;
7901: for(li=1;li <=nlstate; li++){
7902: for(lj=1;lj <=nlstate+ndeath; lj++){
7903: if(lj==li) continue;
7904: for(lk=1;lk<=ncovmodel;lk++){
7905: ll++;
7906: if(ll<=jj){
7907: cb[0]= lk +'a'-1;cb[1]='\0';
7908: if(ll<jj){
7909: if(itimes==1){
7910: if(mle>=1)
7911: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7912: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7913: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7914: }else{
7915: if(mle>=1)
7916: printf(" %.5e",matcov[jj][ll]);
7917: fprintf(ficlog," %.5e",matcov[jj][ll]);
7918: fprintf(ficres," %.5e",matcov[jj][ll]);
7919: }
7920: }else{
7921: if(itimes==1){
7922: if(mle>=1)
7923: printf(" Var(%s%1d%1d)",ca,i,j);
7924: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
7925: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
7926: }else{
7927: if(mle>=1)
1.203 brouard 7928: printf(" %.7e",matcov[jj][ll]);
7929: fprintf(ficlog," %.7e",matcov[jj][ll]);
7930: fprintf(ficres," %.7e",matcov[jj][ll]);
1.126 brouard 7931: }
7932: }
7933: }
7934: } /* end lk */
7935: } /* end lj */
7936: } /* end li */
7937: if(mle>=1)
7938: printf("\n");
7939: fprintf(ficlog,"\n");
7940: fprintf(ficres,"\n");
7941: numlinepar++;
7942: } /* end k*/
7943: } /*end j */
7944: } /* end i */
7945: } /* end itimes */
7946:
7947: fflush(ficlog);
7948: fflush(ficres);
1.209 brouard 7949: while(fgets(line, MAXLINE, ficpar)) {
7950: /* If line starts with a # it is a comment */
7951: if (line[0] == '#') {
7952: numlinepar++;
1.141 brouard 7953: fputs(line,stdout);
1.126 brouard 7954: fputs(line,ficparo);
1.209 brouard 7955: fputs(line,ficlog);
7956: continue;
7957: }else
7958: break;
7959: }
7960:
7961: /* while((c=getc(ficpar))=='#' && c!= EOF){ */
7962: /* ungetc(c,ficpar); */
7963: /* fgets(line, MAXLINE, ficpar); */
7964: /* fputs(line,stdout); */
7965: /* fputs(line,ficparo); */
7966: /* } */
7967: /* ungetc(c,ficpar); */
1.126 brouard 7968:
7969: estepm=0;
1.209 brouard 7970: if((num_filled=sscanf(line,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm, &ftolpl)) !=EOF){
7971:
7972: if (num_filled != 6) {
7973: printf("Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n");
7974: printf("but line=%s\n",line);
7975: goto end;
7976: }
7977: printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
7978: }
7979: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
7980: /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
7981:
7982: /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
1.126 brouard 7983: if (estepm==0 || estepm < stepm) estepm=stepm;
7984: if (fage <= 2) {
7985: bage = ageminpar;
7986: fage = agemaxpar;
7987: }
7988:
7989: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
7990: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
7991: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
1.186 brouard 7992:
7993: /* Other stuffs, more or less useful */
1.126 brouard 7994: while((c=getc(ficpar))=='#' && c!= EOF){
7995: ungetc(c,ficpar);
7996: fgets(line, MAXLINE, ficpar);
1.141 brouard 7997: fputs(line,stdout);
1.126 brouard 7998: fputs(line,ficparo);
7999: }
8000: ungetc(c,ficpar);
8001:
8002: 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);
8003: 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);
8004: 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);
8005: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
8006: 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);
8007:
8008: while((c=getc(ficpar))=='#' && c!= EOF){
8009: ungetc(c,ficpar);
8010: fgets(line, MAXLINE, ficpar);
1.141 brouard 8011: fputs(line,stdout);
1.126 brouard 8012: fputs(line,ficparo);
8013: }
8014: ungetc(c,ficpar);
8015:
8016:
8017: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
8018: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
8019:
8020: fscanf(ficpar,"pop_based=%d\n",&popbased);
1.193 brouard 8021: fprintf(ficlog,"pop_based=%d\n",popbased);
1.126 brouard 8022: fprintf(ficparo,"pop_based=%d\n",popbased);
8023: fprintf(ficres,"pop_based=%d\n",popbased);
8024:
8025: while((c=getc(ficpar))=='#' && c!= EOF){
8026: ungetc(c,ficpar);
8027: fgets(line, MAXLINE, ficpar);
1.141 brouard 8028: fputs(line,stdout);
1.126 brouard 8029: fputs(line,ficparo);
8030: }
8031: ungetc(c,ficpar);
8032:
8033: 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);
8034: 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);
8035: 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);
8036: 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);
8037: 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);
8038: /* day and month of proj2 are not used but only year anproj2.*/
8039:
8040:
8041:
1.145 brouard 8042: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
8043: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 8044:
8045: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 8046: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
8047: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
8048: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
8049: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
8050: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
8051: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
8052: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
8053: }else
1.201 brouard 8054: printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.126 brouard 8055:
1.201 brouard 8056: printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt,\
1.126 brouard 8057: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
8058: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
8059:
8060: /*------------ free_vector -------------*/
8061: /* chdir(path); */
8062:
8063: free_ivector(wav,1,imx);
8064: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
8065: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
8066: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
8067: free_lvector(num,1,n);
8068: free_vector(agedc,1,n);
8069: /*free_matrix(covar,0,NCOVMAX,1,n);*/
8070: /*free_matrix(covar,1,NCOVMAX,1,n);*/
8071: fclose(ficparo);
8072: fclose(ficres);
8073:
8074:
1.186 brouard 8075: /* Other results (useful)*/
8076:
8077:
1.126 brouard 8078: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 8079: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
8080: prlim=matrix(1,nlstate,1,nlstate);
1.209 brouard 8081: prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, &ncvyear);
1.126 brouard 8082: fclose(ficrespl);
8083:
1.145 brouard 8084: #ifdef FREEEXIT2
8085: #include "freeexit2.h"
8086: #endif
8087:
1.126 brouard 8088: /*------------- h Pij x at various ages ------------*/
1.180 brouard 8089: /*#include "hpijx.h"*/
8090: hPijx(p, bage, fage);
1.145 brouard 8091: fclose(ficrespij);
1.126 brouard 8092:
1.145 brouard 8093: /*-------------- Variance of one-step probabilities---*/
8094: k=1;
1.126 brouard 8095: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
8096:
8097:
8098: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
8099: for(i=1;i<=AGESUP;i++)
8100: for(j=1;j<=NCOVMAX;j++)
8101: for(k=1;k<=NCOVMAX;k++)
8102: probs[i][j][k]=0.;
8103:
8104: /*---------- Forecasting ------------------*/
8105: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
8106: if(prevfcast==1){
8107: /* if(stepm ==1){*/
1.201 brouard 8108: prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.126 brouard 8109: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
8110: /* } */
8111: /* else{ */
8112: /* erreur=108; */
8113: /* 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); */
8114: /* 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); */
8115: /* } */
8116: }
1.186 brouard 8117:
8118: /* ------ Other prevalence ratios------------ */
1.126 brouard 8119:
1.127 brouard 8120: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
8121:
8122: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
8123: /* 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",\
8124: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
8125: */
1.126 brouard 8126:
1.127 brouard 8127: if (mobilav!=0) {
8128: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
8129: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
8130: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
8131: printf(" Error in movingaverage mobilav=%d\n",mobilav);
8132: }
1.126 brouard 8133: }
8134:
8135:
1.127 brouard 8136: /*---------- Health expectancies, no variances ------------*/
8137:
1.201 brouard 8138: strcpy(filerese,"E_");
8139: strcat(filerese,fileresu);
1.126 brouard 8140: if((ficreseij=fopen(filerese,"w"))==NULL) {
8141: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
8142: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
8143: }
1.208 brouard 8144: printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
8145: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
1.145 brouard 8146: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
8147: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
8148:
8149: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.127 brouard 8150: fprintf(ficreseij,"\n#****** ");
8151: for(j=1;j<=cptcoveff;j++) {
1.200 brouard 8152: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.127 brouard 8153: }
8154: fprintf(ficreseij,"******\n");
8155:
8156: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
8157: oldm=oldms;savm=savms;
8158: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
8159:
8160: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.145 brouard 8161: /*}*/
1.127 brouard 8162: }
8163: fclose(ficreseij);
1.208 brouard 8164: printf("done evsij\n");fflush(stdout);
8165: fprintf(ficlog,"done evsij\n");fflush(ficlog);
1.127 brouard 8166:
8167: /*---------- Health expectancies and variances ------------*/
8168:
8169:
1.201 brouard 8170: strcpy(filerest,"T_");
8171: strcat(filerest,fileresu);
1.127 brouard 8172: if((ficrest=fopen(filerest,"w"))==NULL) {
8173: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
8174: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
8175: }
1.208 brouard 8176: printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
8177: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
1.127 brouard 8178:
1.126 brouard 8179:
1.201 brouard 8180: strcpy(fileresstde,"STDE_");
8181: strcat(fileresstde,fileresu);
1.126 brouard 8182: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
8183: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
8184: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
8185: }
1.208 brouard 8186: printf(" Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
8187: fprintf(ficlog," Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
1.126 brouard 8188:
1.201 brouard 8189: strcpy(filerescve,"CVE_");
8190: strcat(filerescve,fileresu);
1.126 brouard 8191: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
8192: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
8193: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
8194: }
1.208 brouard 8195: printf(" Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
8196: fprintf(ficlog," Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
1.126 brouard 8197:
1.201 brouard 8198: strcpy(fileresv,"V_");
8199: strcat(fileresv,fileresu);
1.126 brouard 8200: if((ficresvij=fopen(fileresv,"w"))==NULL) {
8201: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
8202: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
8203: }
1.208 brouard 8204: printf(" Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(stdout);
8205: fprintf(ficlog," Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(ficlog);
1.126 brouard 8206:
1.145 brouard 8207: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
8208: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
8209:
8210: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.208 brouard 8211: fprintf(ficrest,"\n#****** ");
8212: for(j=1;j<=cptcoveff;j++)
8213: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8214: fprintf(ficrest,"******\n");
8215:
8216: fprintf(ficresstdeij,"\n#****** ");
8217: fprintf(ficrescveij,"\n#****** ");
8218: for(j=1;j<=cptcoveff;j++) {
8219: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8220: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8221: }
8222: fprintf(ficresstdeij,"******\n");
8223: fprintf(ficrescveij,"******\n");
8224:
8225: fprintf(ficresvij,"\n#****** ");
8226: for(j=1;j<=cptcoveff;j++)
8227: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8228: fprintf(ficresvij,"******\n");
8229:
8230: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
8231: oldm=oldms;savm=savms;
8232: printf(" cvevsij %d, ",k);
8233: fprintf(ficlog, " cvevsij %d, ",k);
8234: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
8235: printf(" end cvevsij \n ");
8236: fprintf(ficlog, " end cvevsij \n ");
8237:
8238: /*
8239: */
8240: /* goto endfree; */
8241:
8242: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
8243: pstamp(ficrest);
8244:
8245:
8246: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
8247: oldm=oldms;savm=savms; /* ZZ Segmentation fault */
8248: cptcod= 0; /* To be deleted */
8249: printf("varevsij %d \n",vpopbased);
8250: fprintf(ficlog, "varevsij %d \n",vpopbased);
1.209 brouard 8251: 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 */
1.208 brouard 8252: 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 ");
8253: if(vpopbased==1)
8254: 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);
8255: else
8256: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
8257: fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
8258: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
8259: fprintf(ficrest,"\n");
8260: /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
8261: epj=vector(1,nlstate+1);
8262: printf("Computing age specific period (stable) prevalences in each health state \n");
8263: fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
8264: for(age=bage; age <=fage ;age++){
1.209 brouard 8265: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k); /*ZZ Is it the correct prevalim */
1.208 brouard 8266: if (vpopbased==1) {
8267: if(mobilav ==0){
8268: for(i=1; i<=nlstate;i++)
8269: prlim[i][i]=probs[(int)age][i][k];
8270: }else{ /* mobilav */
8271: for(i=1; i<=nlstate;i++)
8272: prlim[i][i]=mobaverage[(int)age][i][k];
1.126 brouard 8273: }
1.208 brouard 8274: }
8275:
8276: fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
8277: /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
8278: /* printf(" age %4.0f ",age); */
8279: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
8280: for(i=1, epj[j]=0.;i <=nlstate;i++) {
8281: epj[j] += prlim[i][i]*eij[i][j][(int)age];
8282: /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
8283: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
1.126 brouard 8284: }
1.208 brouard 8285: epj[nlstate+1] +=epj[j];
8286: }
8287: /* printf(" age %4.0f \n",age); */
8288:
8289: for(i=1, vepp=0.;i <=nlstate;i++)
8290: for(j=1;j <=nlstate;j++)
8291: vepp += vareij[i][j][(int)age];
8292: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
8293: for(j=1;j <=nlstate;j++){
8294: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
1.126 brouard 8295: }
1.208 brouard 8296: fprintf(ficrest,"\n");
1.126 brouard 8297: }
1.208 brouard 8298: } /* End vpopbased */
8299: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
8300: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
8301: free_vector(epj,1,nlstate+1);
8302: printf("done \n");fflush(stdout);
8303: fprintf(ficlog,"done\n");fflush(ficlog);
8304:
1.145 brouard 8305: /*}*/
1.208 brouard 8306: } /* End k */
1.126 brouard 8307: free_vector(weight,1,n);
1.145 brouard 8308: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.126 brouard 8309: free_imatrix(s,1,maxwav+1,1,n);
8310: free_matrix(anint,1,maxwav,1,n);
8311: free_matrix(mint,1,maxwav,1,n);
8312: free_ivector(cod,1,n);
8313: free_ivector(tab,1,NCOVMAX);
8314: fclose(ficresstdeij);
8315: fclose(ficrescveij);
8316: fclose(ficresvij);
8317: fclose(ficrest);
1.208 brouard 8318: printf("done Health expectancies\n");fflush(stdout);
8319: fprintf(ficlog,"done Health expectancies\n");fflush(ficlog);
1.126 brouard 8320: fclose(ficpar);
8321:
8322: /*------- Variance of period (stable) prevalence------*/
8323:
1.201 brouard 8324: strcpy(fileresvpl,"VPL_");
8325: strcat(fileresvpl,fileresu);
1.126 brouard 8326: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
8327: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
8328: exit(0);
8329: }
1.208 brouard 8330: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
8331: fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
1.126 brouard 8332:
1.145 brouard 8333: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
8334: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
8335:
8336: for (k=1; k <= (int) pow(2,cptcoveff); k++){
8337: fprintf(ficresvpl,"\n#****** ");
1.126 brouard 8338: for(j=1;j<=cptcoveff;j++)
1.200 brouard 8339: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 8340: fprintf(ficresvpl,"******\n");
8341:
8342: varpl=matrix(1,nlstate,(int) bage, (int) fage);
8343: oldm=oldms;savm=savms;
1.209 brouard 8344: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart);
1.126 brouard 8345: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 8346: /*}*/
1.126 brouard 8347: }
8348:
8349: fclose(ficresvpl);
1.208 brouard 8350: printf("done variance-covariance of period prevalence\n");fflush(stdout);
8351: fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
1.126 brouard 8352:
8353: /*---------- End : free ----------------*/
8354: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
8355: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
8356: } /* mle==-3 arrives here for freeing */
1.164 brouard 8357: /* endfree:*/
1.141 brouard 8358: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.126 brouard 8359: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
8360: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
8361: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
8362: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
8363: free_matrix(covar,0,NCOVMAX,1,n);
8364: free_matrix(matcov,1,npar,1,npar);
1.203 brouard 8365: free_matrix(hess,1,npar,1,npar);
1.126 brouard 8366: /*free_vector(delti,1,npar);*/
8367: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
8368: free_matrix(agev,1,maxwav,1,imx);
8369: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
8370:
1.145 brouard 8371: free_ivector(ncodemax,1,NCOVMAX);
1.192 brouard 8372: free_ivector(ncodemaxwundef,1,NCOVMAX);
1.145 brouard 8373: free_ivector(Tvar,1,NCOVMAX);
8374: free_ivector(Tprod,1,NCOVMAX);
8375: free_ivector(Tvaraff,1,NCOVMAX);
8376: free_ivector(Tage,1,NCOVMAX);
1.126 brouard 8377:
8378: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
1.200 brouard 8379: /* free_imatrix(codtab,1,100,1,10); */
1.126 brouard 8380: fflush(fichtm);
8381: fflush(ficgp);
8382:
8383:
8384: if((nberr >0) || (nbwarn>0)){
8385: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
8386: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
8387: }else{
8388: printf("End of Imach\n");
8389: fprintf(ficlog,"End of Imach\n");
8390: }
8391: printf("See log file on %s\n",filelog);
8392: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 8393: /*(void) gettimeofday(&end_time,&tzp);*/
8394: rend_time = time(NULL);
8395: end_time = *localtime(&rend_time);
8396: /* tml = *localtime(&end_time.tm_sec); */
8397: strcpy(strtend,asctime(&end_time));
1.126 brouard 8398: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
8399: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 8400: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.126 brouard 8401:
1.157 brouard 8402: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
8403: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
8404: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 8405: /* printf("Total time was %d uSec.\n", total_usecs);*/
8406: /* if(fileappend(fichtm,optionfilehtm)){ */
8407: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
8408: fclose(fichtm);
8409: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
8410: fclose(fichtmcov);
8411: fclose(ficgp);
8412: fclose(ficlog);
8413: /*------ End -----------*/
8414:
8415:
8416: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 8417: #ifdef WIN32
8418: if (_chdir(pathcd) != 0)
8419: printf("Can't move to directory %s!\n",path);
8420: if(_getcwd(pathcd,MAXLINE) > 0)
8421: #else
1.126 brouard 8422: if(chdir(pathcd) != 0)
1.184 brouard 8423: printf("Can't move to directory %s!\n", path);
8424: if (getcwd(pathcd, MAXLINE) > 0)
8425: #endif
1.126 brouard 8426: printf("Current directory %s!\n",pathcd);
8427: /*strcat(plotcmd,CHARSEPARATOR);*/
8428: sprintf(plotcmd,"gnuplot");
1.157 brouard 8429: #ifdef _WIN32
1.126 brouard 8430: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
8431: #endif
8432: if(!stat(plotcmd,&info)){
1.158 brouard 8433: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 8434: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 8435: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 8436: }else
8437: strcpy(pplotcmd,plotcmd);
1.157 brouard 8438: #ifdef __unix
1.126 brouard 8439: strcpy(plotcmd,GNUPLOTPROGRAM);
8440: if(!stat(plotcmd,&info)){
1.158 brouard 8441: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 8442: }else
8443: strcpy(pplotcmd,plotcmd);
8444: #endif
8445: }else
8446: strcpy(pplotcmd,plotcmd);
8447:
8448: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 8449: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 8450:
8451: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 8452: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 8453: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 8454: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 8455: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 8456: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 8457: }
1.158 brouard 8458: printf(" Successful, please wait...");
1.126 brouard 8459: while (z[0] != 'q') {
8460: /* chdir(path); */
1.154 brouard 8461: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 8462: scanf("%s",z);
8463: /* if (z[0] == 'c') system("./imach"); */
8464: if (z[0] == 'e') {
1.158 brouard 8465: #ifdef __APPLE__
1.152 brouard 8466: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 8467: #elif __linux
8468: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 8469: #else
1.152 brouard 8470: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 8471: #endif
8472: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
8473: system(pplotcmd);
1.126 brouard 8474: }
8475: else if (z[0] == 'g') system(plotcmd);
8476: else if (z[0] == 'q') exit(0);
8477: }
8478: end:
8479: while (z[0] != 'q') {
1.195 brouard 8480: printf("\nType q for exiting: "); fflush(stdout);
1.126 brouard 8481: scanf("%s",z);
8482: }
8483: }
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