Annotation of imach/src/imach.c, revision 1.214
1.214 ! brouard 1: /* $Id: imach.c,v 1.213 2015/12/11 18:22:17 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.214 ! brouard 4: Revision 1.213 2015/12/11 18:22:17 brouard
! 5: Summary: 0.98r4
! 6:
1.213 brouard 7: Revision 1.212 2015/11/21 12:47:24 brouard
8: Summary: minor typo
9:
1.212 brouard 10: Revision 1.211 2015/11/21 12:41:11 brouard
11: Summary: 0.98r3 with some graph of projected cross-sectional
12:
13: Author: Nicolas Brouard
14:
1.211 brouard 15: Revision 1.210 2015/11/18 17:41:20 brouard
16: Summary: Start working on projected prevalences
17:
1.210 brouard 18: Revision 1.209 2015/11/17 22:12:03 brouard
19: Summary: Adding ftolpl parameter
20: Author: N Brouard
21:
22: We had difficulties to get smoothed confidence intervals. It was due
23: to the period prevalence which wasn't computed accurately. The inner
24: parameter ftolpl is now an outer parameter of the .imach parameter
25: file after estepm. If ftolpl is small 1.e-4 and estepm too,
26: computation are long.
27:
1.209 brouard 28: Revision 1.208 2015/11/17 14:31:57 brouard
29: Summary: temporary
30:
1.208 brouard 31: Revision 1.207 2015/10/27 17:36:57 brouard
32: *** empty log message ***
33:
1.207 brouard 34: Revision 1.206 2015/10/24 07:14:11 brouard
35: *** empty log message ***
36:
1.206 brouard 37: Revision 1.205 2015/10/23 15:50:53 brouard
38: Summary: 0.98r3 some clarification for graphs on likelihood contributions
39:
1.205 brouard 40: Revision 1.204 2015/10/01 16:20:26 brouard
41: Summary: Some new graphs of contribution to likelihood
42:
1.204 brouard 43: Revision 1.203 2015/09/30 17:45:14 brouard
44: Summary: looking at better estimation of the hessian
45:
46: Also a better criteria for convergence to the period prevalence And
47: therefore adding the number of years needed to converge. (The
48: prevalence in any alive state shold sum to one
49:
1.203 brouard 50: Revision 1.202 2015/09/22 19:45:16 brouard
51: Summary: Adding some overall graph on contribution to likelihood. Might change
52:
1.202 brouard 53: Revision 1.201 2015/09/15 17:34:58 brouard
54: Summary: 0.98r0
55:
56: - Some new graphs like suvival functions
57: - Some bugs fixed like model=1+age+V2.
58:
1.201 brouard 59: Revision 1.200 2015/09/09 16:53:55 brouard
60: Summary: Big bug thanks to Flavia
61:
62: Even model=1+age+V2. did not work anymore
63:
1.200 brouard 64: Revision 1.199 2015/09/07 14:09:23 brouard
65: Summary: 0.98q6 changing default small png format for graph to vectorized svg.
66:
1.199 brouard 67: Revision 1.198 2015/09/03 07:14:39 brouard
68: Summary: 0.98q5 Flavia
69:
1.198 brouard 70: Revision 1.197 2015/09/01 18:24:39 brouard
71: *** empty log message ***
72:
1.197 brouard 73: Revision 1.196 2015/08/18 23:17:52 brouard
74: Summary: 0.98q5
75:
1.196 brouard 76: Revision 1.195 2015/08/18 16:28:39 brouard
77: Summary: Adding a hack for testing purpose
78:
79: After reading the title, ftol and model lines, if the comment line has
80: a q, starting with #q, the answer at the end of the run is quit. It
81: permits to run test files in batch with ctest. The former workaround was
82: $ echo q | imach foo.imach
83:
1.195 brouard 84: Revision 1.194 2015/08/18 13:32:00 brouard
85: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
86:
1.194 brouard 87: Revision 1.193 2015/08/04 07:17:42 brouard
88: Summary: 0.98q4
89:
1.193 brouard 90: Revision 1.192 2015/07/16 16:49:02 brouard
91: Summary: Fixing some outputs
92:
1.192 brouard 93: Revision 1.191 2015/07/14 10:00:33 brouard
94: Summary: Some fixes
95:
1.191 brouard 96: Revision 1.190 2015/05/05 08:51:13 brouard
97: Summary: Adding digits in output parameters (7 digits instead of 6)
98:
99: Fix 1+age+.
100:
1.190 brouard 101: Revision 1.189 2015/04/30 14:45:16 brouard
102: Summary: 0.98q2
103:
1.189 brouard 104: Revision 1.188 2015/04/30 08:27:53 brouard
105: *** empty log message ***
106:
1.188 brouard 107: Revision 1.187 2015/04/29 09:11:15 brouard
108: *** empty log message ***
109:
1.187 brouard 110: Revision 1.186 2015/04/23 12:01:52 brouard
111: Summary: V1*age is working now, version 0.98q1
112:
113: Some codes had been disabled in order to simplify and Vn*age was
114: working in the optimization phase, ie, giving correct MLE parameters,
115: but, as usual, outputs were not correct and program core dumped.
116:
1.186 brouard 117: Revision 1.185 2015/03/11 13:26:42 brouard
118: Summary: Inclusion of compile and links command line for Intel Compiler
119:
1.185 brouard 120: Revision 1.184 2015/03/11 11:52:39 brouard
121: Summary: Back from Windows 8. Intel Compiler
122:
1.184 brouard 123: Revision 1.183 2015/03/10 20:34:32 brouard
124: Summary: 0.98q0, trying with directest, mnbrak fixed
125:
126: We use directest instead of original Powell test; probably no
127: incidence on the results, but better justifications;
128: We fixed Numerical Recipes mnbrak routine which was wrong and gave
129: wrong results.
130:
1.183 brouard 131: Revision 1.182 2015/02/12 08:19:57 brouard
132: Summary: Trying to keep directest which seems simpler and more general
133: Author: Nicolas Brouard
134:
1.182 brouard 135: Revision 1.181 2015/02/11 23:22:24 brouard
136: Summary: Comments on Powell added
137:
138: Author:
139:
1.181 brouard 140: Revision 1.180 2015/02/11 17:33:45 brouard
141: Summary: Finishing move from main to function (hpijx and prevalence_limit)
142:
1.180 brouard 143: Revision 1.179 2015/01/04 09:57:06 brouard
144: Summary: back to OS/X
145:
1.179 brouard 146: Revision 1.178 2015/01/04 09:35:48 brouard
147: *** empty log message ***
148:
1.178 brouard 149: Revision 1.177 2015/01/03 18:40:56 brouard
150: Summary: Still testing ilc32 on OSX
151:
1.177 brouard 152: Revision 1.176 2015/01/03 16:45:04 brouard
153: *** empty log message ***
154:
1.176 brouard 155: Revision 1.175 2015/01/03 16:33:42 brouard
156: *** empty log message ***
157:
1.175 brouard 158: Revision 1.174 2015/01/03 16:15:49 brouard
159: Summary: Still in cross-compilation
160:
1.174 brouard 161: Revision 1.173 2015/01/03 12:06:26 brouard
162: Summary: trying to detect cross-compilation
163:
1.173 brouard 164: Revision 1.172 2014/12/27 12:07:47 brouard
165: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
166:
1.172 brouard 167: Revision 1.171 2014/12/23 13:26:59 brouard
168: Summary: Back from Visual C
169:
170: Still problem with utsname.h on Windows
171:
1.171 brouard 172: Revision 1.170 2014/12/23 11:17:12 brouard
173: Summary: Cleaning some \%% back to %%
174:
175: The escape was mandatory for a specific compiler (which one?), but too many warnings.
176:
1.170 brouard 177: Revision 1.169 2014/12/22 23:08:31 brouard
178: Summary: 0.98p
179:
180: Outputs some informations on compiler used, OS etc. Testing on different platforms.
181:
1.169 brouard 182: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 183: Summary: update
1.169 brouard 184:
1.168 brouard 185: Revision 1.167 2014/12/22 13:50:56 brouard
186: Summary: Testing uname and compiler version and if compiled 32 or 64
187:
188: Testing on Linux 64
189:
1.167 brouard 190: Revision 1.166 2014/12/22 11:40:47 brouard
191: *** empty log message ***
192:
1.166 brouard 193: Revision 1.165 2014/12/16 11:20:36 brouard
194: Summary: After compiling on Visual C
195:
196: * imach.c (Module): Merging 1.61 to 1.162
197:
1.165 brouard 198: Revision 1.164 2014/12/16 10:52:11 brouard
199: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
200:
201: * imach.c (Module): Merging 1.61 to 1.162
202:
1.164 brouard 203: Revision 1.163 2014/12/16 10:30:11 brouard
204: * imach.c (Module): Merging 1.61 to 1.162
205:
1.163 brouard 206: Revision 1.162 2014/09/25 11:43:39 brouard
207: Summary: temporary backup 0.99!
208:
1.162 brouard 209: Revision 1.1 2014/09/16 11:06:58 brouard
210: Summary: With some code (wrong) for nlopt
211:
212: Author:
213:
214: Revision 1.161 2014/09/15 20:41:41 brouard
215: Summary: Problem with macro SQR on Intel compiler
216:
1.161 brouard 217: Revision 1.160 2014/09/02 09:24:05 brouard
218: *** empty log message ***
219:
1.160 brouard 220: Revision 1.159 2014/09/01 10:34:10 brouard
221: Summary: WIN32
222: Author: Brouard
223:
1.159 brouard 224: Revision 1.158 2014/08/27 17:11:51 brouard
225: *** empty log message ***
226:
1.158 brouard 227: Revision 1.157 2014/08/27 16:26:55 brouard
228: Summary: Preparing windows Visual studio version
229: Author: Brouard
230:
231: In order to compile on Visual studio, time.h is now correct and time_t
232: and tm struct should be used. difftime should be used but sometimes I
233: just make the differences in raw time format (time(&now).
234: Trying to suppress #ifdef LINUX
235: Add xdg-open for __linux in order to open default browser.
236:
1.157 brouard 237: Revision 1.156 2014/08/25 20:10:10 brouard
238: *** empty log message ***
239:
1.156 brouard 240: Revision 1.155 2014/08/25 18:32:34 brouard
241: Summary: New compile, minor changes
242: Author: Brouard
243:
1.155 brouard 244: Revision 1.154 2014/06/20 17:32:08 brouard
245: Summary: Outputs now all graphs of convergence to period prevalence
246:
1.154 brouard 247: Revision 1.153 2014/06/20 16:45:46 brouard
248: Summary: If 3 live state, convergence to period prevalence on same graph
249: Author: Brouard
250:
1.153 brouard 251: Revision 1.152 2014/06/18 17:54:09 brouard
252: Summary: open browser, use gnuplot on same dir than imach if not found in the path
253:
1.152 brouard 254: Revision 1.151 2014/06/18 16:43:30 brouard
255: *** empty log message ***
256:
1.151 brouard 257: Revision 1.150 2014/06/18 16:42:35 brouard
258: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
259: Author: brouard
260:
1.150 brouard 261: Revision 1.149 2014/06/18 15:51:14 brouard
262: Summary: Some fixes in parameter files errors
263: Author: Nicolas Brouard
264:
1.149 brouard 265: Revision 1.148 2014/06/17 17:38:48 brouard
266: Summary: Nothing new
267: Author: Brouard
268:
269: Just a new packaging for OS/X version 0.98nS
270:
1.148 brouard 271: Revision 1.147 2014/06/16 10:33:11 brouard
272: *** empty log message ***
273:
1.147 brouard 274: Revision 1.146 2014/06/16 10:20:28 brouard
275: Summary: Merge
276: Author: Brouard
277:
278: Merge, before building revised version.
279:
1.146 brouard 280: Revision 1.145 2014/06/10 21:23:15 brouard
281: Summary: Debugging with valgrind
282: Author: Nicolas Brouard
283:
284: Lot of changes in order to output the results with some covariates
285: After the Edimburgh REVES conference 2014, it seems mandatory to
286: improve the code.
287: No more memory valgrind error but a lot has to be done in order to
288: continue the work of splitting the code into subroutines.
289: Also, decodemodel has been improved. Tricode is still not
290: optimal. nbcode should be improved. Documentation has been added in
291: the source code.
292:
1.144 brouard 293: Revision 1.143 2014/01/26 09:45:38 brouard
294: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
295:
296: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
297: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
298:
1.143 brouard 299: Revision 1.142 2014/01/26 03:57:36 brouard
300: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
301:
302: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
303:
1.142 brouard 304: Revision 1.141 2014/01/26 02:42:01 brouard
305: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
306:
1.141 brouard 307: Revision 1.140 2011/09/02 10:37:54 brouard
308: Summary: times.h is ok with mingw32 now.
309:
1.140 brouard 310: Revision 1.139 2010/06/14 07:50:17 brouard
311: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
312: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
313:
1.139 brouard 314: Revision 1.138 2010/04/30 18:19:40 brouard
315: *** empty log message ***
316:
1.138 brouard 317: Revision 1.137 2010/04/29 18:11:38 brouard
318: (Module): Checking covariates for more complex models
319: than V1+V2. A lot of change to be done. Unstable.
320:
1.137 brouard 321: Revision 1.136 2010/04/26 20:30:53 brouard
322: (Module): merging some libgsl code. Fixing computation
323: of likelione (using inter/intrapolation if mle = 0) in order to
324: get same likelihood as if mle=1.
325: Some cleaning of code and comments added.
326:
1.136 brouard 327: Revision 1.135 2009/10/29 15:33:14 brouard
328: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
329:
1.135 brouard 330: Revision 1.134 2009/10/29 13:18:53 brouard
331: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
332:
1.134 brouard 333: Revision 1.133 2009/07/06 10:21:25 brouard
334: just nforces
335:
1.133 brouard 336: Revision 1.132 2009/07/06 08:22:05 brouard
337: Many tings
338:
1.132 brouard 339: Revision 1.131 2009/06/20 16:22:47 brouard
340: Some dimensions resccaled
341:
1.131 brouard 342: Revision 1.130 2009/05/26 06:44:34 brouard
343: (Module): Max Covariate is now set to 20 instead of 8. A
344: lot of cleaning with variables initialized to 0. Trying to make
345: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
346:
1.130 brouard 347: Revision 1.129 2007/08/31 13:49:27 lievre
348: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
349:
1.129 lievre 350: Revision 1.128 2006/06/30 13:02:05 brouard
351: (Module): Clarifications on computing e.j
352:
1.128 brouard 353: Revision 1.127 2006/04/28 18:11:50 brouard
354: (Module): Yes the sum of survivors was wrong since
355: imach-114 because nhstepm was no more computed in the age
356: loop. Now we define nhstepma in the age loop.
357: (Module): In order to speed up (in case of numerous covariates) we
358: compute health expectancies (without variances) in a first step
359: and then all the health expectancies with variances or standard
360: deviation (needs data from the Hessian matrices) which slows the
361: computation.
362: In the future we should be able to stop the program is only health
363: expectancies and graph are needed without standard deviations.
364:
1.127 brouard 365: Revision 1.126 2006/04/28 17:23:28 brouard
366: (Module): Yes the sum of survivors was wrong since
367: imach-114 because nhstepm was no more computed in the age
368: loop. Now we define nhstepma in the age loop.
369: Version 0.98h
370:
1.126 brouard 371: Revision 1.125 2006/04/04 15:20:31 lievre
372: Errors in calculation of health expectancies. Age was not initialized.
373: Forecasting file added.
374:
375: Revision 1.124 2006/03/22 17:13:53 lievre
376: Parameters are printed with %lf instead of %f (more numbers after the comma).
377: The log-likelihood is printed in the log file
378:
379: Revision 1.123 2006/03/20 10:52:43 brouard
380: * imach.c (Module): <title> changed, corresponds to .htm file
381: name. <head> headers where missing.
382:
383: * imach.c (Module): Weights can have a decimal point as for
384: English (a comma might work with a correct LC_NUMERIC environment,
385: otherwise the weight is truncated).
386: Modification of warning when the covariates values are not 0 or
387: 1.
388: Version 0.98g
389:
390: Revision 1.122 2006/03/20 09:45:41 brouard
391: (Module): Weights can have a decimal point as for
392: English (a comma might work with a correct LC_NUMERIC environment,
393: otherwise the weight is truncated).
394: Modification of warning when the covariates values are not 0 or
395: 1.
396: Version 0.98g
397:
398: Revision 1.121 2006/03/16 17:45:01 lievre
399: * imach.c (Module): Comments concerning covariates added
400:
401: * imach.c (Module): refinements in the computation of lli if
402: status=-2 in order to have more reliable computation if stepm is
403: not 1 month. Version 0.98f
404:
405: Revision 1.120 2006/03/16 15:10:38 lievre
406: (Module): refinements in the computation of lli if
407: status=-2 in order to have more reliable computation if stepm is
408: not 1 month. Version 0.98f
409:
410: Revision 1.119 2006/03/15 17:42:26 brouard
411: (Module): Bug if status = -2, the loglikelihood was
412: computed as likelihood omitting the logarithm. Version O.98e
413:
414: Revision 1.118 2006/03/14 18:20:07 brouard
415: (Module): varevsij Comments added explaining the second
416: table of variances if popbased=1 .
417: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
418: (Module): Function pstamp added
419: (Module): Version 0.98d
420:
421: Revision 1.117 2006/03/14 17:16:22 brouard
422: (Module): varevsij Comments added explaining the second
423: table of variances if popbased=1 .
424: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
425: (Module): Function pstamp added
426: (Module): Version 0.98d
427:
428: Revision 1.116 2006/03/06 10:29:27 brouard
429: (Module): Variance-covariance wrong links and
430: varian-covariance of ej. is needed (Saito).
431:
432: Revision 1.115 2006/02/27 12:17:45 brouard
433: (Module): One freematrix added in mlikeli! 0.98c
434:
435: Revision 1.114 2006/02/26 12:57:58 brouard
436: (Module): Some improvements in processing parameter
437: filename with strsep.
438:
439: Revision 1.113 2006/02/24 14:20:24 brouard
440: (Module): Memory leaks checks with valgrind and:
441: datafile was not closed, some imatrix were not freed and on matrix
442: allocation too.
443:
444: Revision 1.112 2006/01/30 09:55:26 brouard
445: (Module): Back to gnuplot.exe instead of wgnuplot.exe
446:
447: Revision 1.111 2006/01/25 20:38:18 brouard
448: (Module): Lots of cleaning and bugs added (Gompertz)
449: (Module): Comments can be added in data file. Missing date values
450: can be a simple dot '.'.
451:
452: Revision 1.110 2006/01/25 00:51:50 brouard
453: (Module): Lots of cleaning and bugs added (Gompertz)
454:
455: Revision 1.109 2006/01/24 19:37:15 brouard
456: (Module): Comments (lines starting with a #) are allowed in data.
457:
458: Revision 1.108 2006/01/19 18:05:42 lievre
459: Gnuplot problem appeared...
460: To be fixed
461:
462: Revision 1.107 2006/01/19 16:20:37 brouard
463: Test existence of gnuplot in imach path
464:
465: Revision 1.106 2006/01/19 13:24:36 brouard
466: Some cleaning and links added in html output
467:
468: Revision 1.105 2006/01/05 20:23:19 lievre
469: *** empty log message ***
470:
471: Revision 1.104 2005/09/30 16:11:43 lievre
472: (Module): sump fixed, loop imx fixed, and simplifications.
473: (Module): If the status is missing at the last wave but we know
474: that the person is alive, then we can code his/her status as -2
475: (instead of missing=-1 in earlier versions) and his/her
476: contributions to the likelihood is 1 - Prob of dying from last
477: health status (= 1-p13= p11+p12 in the easiest case of somebody in
478: the healthy state at last known wave). Version is 0.98
479:
480: Revision 1.103 2005/09/30 15:54:49 lievre
481: (Module): sump fixed, loop imx fixed, and simplifications.
482:
483: Revision 1.102 2004/09/15 17:31:30 brouard
484: Add the possibility to read data file including tab characters.
485:
486: Revision 1.101 2004/09/15 10:38:38 brouard
487: Fix on curr_time
488:
489: Revision 1.100 2004/07/12 18:29:06 brouard
490: Add version for Mac OS X. Just define UNIX in Makefile
491:
492: Revision 1.99 2004/06/05 08:57:40 brouard
493: *** empty log message ***
494:
495: Revision 1.98 2004/05/16 15:05:56 brouard
496: New version 0.97 . First attempt to estimate force of mortality
497: directly from the data i.e. without the need of knowing the health
498: state at each age, but using a Gompertz model: log u =a + b*age .
499: This is the basic analysis of mortality and should be done before any
500: other analysis, in order to test if the mortality estimated from the
501: cross-longitudinal survey is different from the mortality estimated
502: from other sources like vital statistic data.
503:
504: The same imach parameter file can be used but the option for mle should be -3.
505:
1.133 brouard 506: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 507: former routines in order to include the new code within the former code.
508:
509: The output is very simple: only an estimate of the intercept and of
510: the slope with 95% confident intervals.
511:
512: Current limitations:
513: A) Even if you enter covariates, i.e. with the
514: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
515: B) There is no computation of Life Expectancy nor Life Table.
516:
517: Revision 1.97 2004/02/20 13:25:42 lievre
518: Version 0.96d. Population forecasting command line is (temporarily)
519: suppressed.
520:
521: Revision 1.96 2003/07/15 15:38:55 brouard
522: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
523: rewritten within the same printf. Workaround: many printfs.
524:
525: Revision 1.95 2003/07/08 07:54:34 brouard
526: * imach.c (Repository):
527: (Repository): Using imachwizard code to output a more meaningful covariance
528: matrix (cov(a12,c31) instead of numbers.
529:
530: Revision 1.94 2003/06/27 13:00:02 brouard
531: Just cleaning
532:
533: Revision 1.93 2003/06/25 16:33:55 brouard
534: (Module): On windows (cygwin) function asctime_r doesn't
535: exist so I changed back to asctime which exists.
536: (Module): Version 0.96b
537:
538: Revision 1.92 2003/06/25 16:30:45 brouard
539: (Module): On windows (cygwin) function asctime_r doesn't
540: exist so I changed back to asctime which exists.
541:
542: Revision 1.91 2003/06/25 15:30:29 brouard
543: * imach.c (Repository): Duplicated warning errors corrected.
544: (Repository): Elapsed time after each iteration is now output. It
545: helps to forecast when convergence will be reached. Elapsed time
546: is stamped in powell. We created a new html file for the graphs
547: concerning matrix of covariance. It has extension -cov.htm.
548:
549: Revision 1.90 2003/06/24 12:34:15 brouard
550: (Module): Some bugs corrected for windows. Also, when
551: mle=-1 a template is output in file "or"mypar.txt with the design
552: of the covariance matrix to be input.
553:
554: Revision 1.89 2003/06/24 12:30:52 brouard
555: (Module): Some bugs corrected for windows. Also, when
556: mle=-1 a template is output in file "or"mypar.txt with the design
557: of the covariance matrix to be input.
558:
559: Revision 1.88 2003/06/23 17:54:56 brouard
560: * 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.
561:
562: Revision 1.87 2003/06/18 12:26:01 brouard
563: Version 0.96
564:
565: Revision 1.86 2003/06/17 20:04:08 brouard
566: (Module): Change position of html and gnuplot routines and added
567: routine fileappend.
568:
569: Revision 1.85 2003/06/17 13:12:43 brouard
570: * imach.c (Repository): Check when date of death was earlier that
571: current date of interview. It may happen when the death was just
572: prior to the death. In this case, dh was negative and likelihood
573: was wrong (infinity). We still send an "Error" but patch by
574: assuming that the date of death was just one stepm after the
575: interview.
576: (Repository): Because some people have very long ID (first column)
577: we changed int to long in num[] and we added a new lvector for
578: memory allocation. But we also truncated to 8 characters (left
579: truncation)
580: (Repository): No more line truncation errors.
581:
582: Revision 1.84 2003/06/13 21:44:43 brouard
583: * imach.c (Repository): Replace "freqsummary" at a correct
584: place. It differs from routine "prevalence" which may be called
585: many times. Probs is memory consuming and must be used with
586: parcimony.
587: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
588:
589: Revision 1.83 2003/06/10 13:39:11 lievre
590: *** empty log message ***
591:
592: Revision 1.82 2003/06/05 15:57:20 brouard
593: Add log in imach.c and fullversion number is now printed.
594:
595: */
596: /*
597: Interpolated Markov Chain
598:
599: Short summary of the programme:
600:
601: This program computes Healthy Life Expectancies from
602: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
603: first survey ("cross") where individuals from different ages are
604: interviewed on their health status or degree of disability (in the
605: case of a health survey which is our main interest) -2- at least a
606: second wave of interviews ("longitudinal") which measure each change
607: (if any) in individual health status. Health expectancies are
608: computed from the time spent in each health state according to a
609: model. More health states you consider, more time is necessary to reach the
610: Maximum Likelihood of the parameters involved in the model. The
611: simplest model is the multinomial logistic model where pij is the
612: probability to be observed in state j at the second wave
613: conditional to be observed in state i at the first wave. Therefore
614: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
615: 'age' is age and 'sex' is a covariate. If you want to have a more
616: complex model than "constant and age", you should modify the program
617: where the markup *Covariates have to be included here again* invites
618: you to do it. More covariates you add, slower the
619: convergence.
620:
621: The advantage of this computer programme, compared to a simple
622: multinomial logistic model, is clear when the delay between waves is not
623: identical for each individual. Also, if a individual missed an
624: intermediate interview, the information is lost, but taken into
625: account using an interpolation or extrapolation.
626:
627: hPijx is the probability to be observed in state i at age x+h
628: conditional to the observed state i at age x. The delay 'h' can be
629: split into an exact number (nh*stepm) of unobserved intermediate
630: states. This elementary transition (by month, quarter,
631: semester or year) is modelled as a multinomial logistic. The hPx
632: matrix is simply the matrix product of nh*stepm elementary matrices
633: and the contribution of each individual to the likelihood is simply
634: hPijx.
635:
636: Also this programme outputs the covariance matrix of the parameters but also
637: of the life expectancies. It also computes the period (stable) prevalence.
638:
1.133 brouard 639: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
640: Institut national d'études démographiques, Paris.
1.126 brouard 641: This software have been partly granted by Euro-REVES, a concerted action
642: from the European Union.
643: It is copyrighted identically to a GNU software product, ie programme and
644: software can be distributed freely for non commercial use. Latest version
645: can be accessed at http://euroreves.ined.fr/imach .
646:
647: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
648: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
649:
650: **********************************************************************/
651: /*
652: main
653: read parameterfile
654: read datafile
655: concatwav
656: freqsummary
657: if (mle >= 1)
658: mlikeli
659: print results files
660: if mle==1
661: computes hessian
662: read end of parameter file: agemin, agemax, bage, fage, estepm
663: begin-prev-date,...
664: open gnuplot file
665: open html file
1.145 brouard 666: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
667: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
668: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
669: freexexit2 possible for memory heap.
670:
671: h Pij x | pij_nom ficrestpij
672: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
673: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
674: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
675:
676: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
677: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
678: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
679: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
680: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
681:
1.126 brouard 682: forecasting if prevfcast==1 prevforecast call prevalence()
683: health expectancies
684: Variance-covariance of DFLE
685: prevalence()
686: movingaverage()
687: varevsij()
688: if popbased==1 varevsij(,popbased)
689: total life expectancies
690: Variance of period (stable) prevalence
691: end
692: */
693:
1.187 brouard 694: /* #define DEBUG */
695: /* #define DEBUGBRENT */
1.203 brouard 696: /* #define DEBUGLINMIN */
697: /* #define DEBUGHESS */
698: #define DEBUGHESSIJ
699: /* #define LINMINORIGINAL /\* Don't use loop on scale in linmin (accepting nan)*\/ */
1.165 brouard 700: #define POWELL /* Instead of NLOPT */
1.192 brouard 701: #define POWELLF1F3 /* Skip test */
1.186 brouard 702: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
703: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 704:
705: #include <math.h>
706: #include <stdio.h>
707: #include <stdlib.h>
708: #include <string.h>
1.159 brouard 709:
710: #ifdef _WIN32
711: #include <io.h>
1.172 brouard 712: #include <windows.h>
713: #include <tchar.h>
1.159 brouard 714: #else
1.126 brouard 715: #include <unistd.h>
1.159 brouard 716: #endif
1.126 brouard 717:
718: #include <limits.h>
719: #include <sys/types.h>
1.171 brouard 720:
721: #if defined(__GNUC__)
722: #include <sys/utsname.h> /* Doesn't work on Windows */
723: #endif
724:
1.126 brouard 725: #include <sys/stat.h>
726: #include <errno.h>
1.159 brouard 727: /* extern int errno; */
1.126 brouard 728:
1.157 brouard 729: /* #ifdef LINUX */
730: /* #include <time.h> */
731: /* #include "timeval.h" */
732: /* #else */
733: /* #include <sys/time.h> */
734: /* #endif */
735:
1.126 brouard 736: #include <time.h>
737:
1.136 brouard 738: #ifdef GSL
739: #include <gsl/gsl_errno.h>
740: #include <gsl/gsl_multimin.h>
741: #endif
742:
1.167 brouard 743:
1.162 brouard 744: #ifdef NLOPT
745: #include <nlopt.h>
746: typedef struct {
747: double (* function)(double [] );
748: } myfunc_data ;
749: #endif
750:
1.126 brouard 751: /* #include <libintl.h> */
752: /* #define _(String) gettext (String) */
753:
1.141 brouard 754: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 755:
756: #define GNUPLOTPROGRAM "gnuplot"
757: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
758: #define FILENAMELENGTH 132
759:
760: #define GLOCK_ERROR_NOPATH -1 /* empty path */
761: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
762:
1.144 brouard 763: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
764: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 765:
766: #define NINTERVMAX 8
1.144 brouard 767: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
768: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
769: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.197 brouard 770: #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.211 brouard 771: /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
772: #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
1.126 brouard 773: #define MAXN 20000
1.144 brouard 774: #define YEARM 12. /**< Number of months per year */
1.126 brouard 775: #define AGESUP 130
776: #define AGEBASE 40
1.194 brouard 777: #define AGEOVERFLOW 1.e20
1.164 brouard 778: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 779: #ifdef _WIN32
780: #define DIRSEPARATOR '\\'
781: #define CHARSEPARATOR "\\"
782: #define ODIRSEPARATOR '/'
783: #else
1.126 brouard 784: #define DIRSEPARATOR '/'
785: #define CHARSEPARATOR "/"
786: #define ODIRSEPARATOR '\\'
787: #endif
788:
1.214 ! brouard 789: /* $Id: imach.c,v 1.213 2015/12/11 18:22:17 brouard Exp $ */
1.126 brouard 790: /* $State: Exp $ */
1.196 brouard 791: #include "version.h"
792: char version[]=__IMACH_VERSION__;
1.204 brouard 793: 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";
1.214 ! brouard 794: char fullversion[]="$Revision: 1.213 $ $Date: 2015/12/11 18:22:17 $";
1.126 brouard 795: char strstart[80];
796: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 797: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 798: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 799: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
800: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
801: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
802: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
803: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
804: int cptcovprodnoage=0; /**< Number of covariate products without age */
805: int cptcoveff=0; /* Total number of covariates to vary for printing results */
806: int cptcov=0; /* Working variable */
1.126 brouard 807: int npar=NPARMAX;
808: int nlstate=2; /* Number of live states */
809: int ndeath=1; /* Number of dead states */
1.130 brouard 810: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.126 brouard 811: int popbased=0;
812:
813: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 814: int maxwav=0; /* Maxim number of waves */
815: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
816: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
817: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 818: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 819: int mle=1, weightopt=0;
1.126 brouard 820: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
821: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
822: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
823: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 824: int countcallfunc=0; /* Count the number of calls to func */
1.130 brouard 825: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 826: double **matprod2(); /* test */
1.126 brouard 827: double **oldm, **newm, **savm; /* Working pointers to matrices */
828: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.136 brouard 829: /*FILE *fic ; */ /* Used in readdata only */
1.214 ! brouard 830: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.126 brouard 831: FILE *ficlog, *ficrespow;
1.130 brouard 832: int globpr=0; /* Global variable for printing or not */
1.126 brouard 833: double fretone; /* Only one call to likelihood */
1.130 brouard 834: long ipmx=0; /* Number of contributions */
1.126 brouard 835: double sw; /* Sum of weights */
836: char filerespow[FILENAMELENGTH];
837: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
838: FILE *ficresilk;
839: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
840: FILE *ficresprobmorprev;
841: FILE *fichtm, *fichtmcov; /* Html File */
842: FILE *ficreseij;
843: char filerese[FILENAMELENGTH];
844: FILE *ficresstdeij;
845: char fileresstde[FILENAMELENGTH];
846: FILE *ficrescveij;
847: char filerescve[FILENAMELENGTH];
848: FILE *ficresvij;
849: char fileresv[FILENAMELENGTH];
850: FILE *ficresvpl;
851: char fileresvpl[FILENAMELENGTH];
852: char title[MAXLINE];
853: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
854: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
855: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
856: char command[FILENAMELENGTH];
857: int outcmd=0;
858:
859: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.202 brouard 860: char fileresu[FILENAMELENGTH]; /* fileres without r in front */
1.126 brouard 861: char filelog[FILENAMELENGTH]; /* Log file */
862: char filerest[FILENAMELENGTH];
863: char fileregp[FILENAMELENGTH];
864: char popfile[FILENAMELENGTH];
865:
866: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
867:
1.157 brouard 868: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
869: /* struct timezone tzp; */
870: /* extern int gettimeofday(); */
871: struct tm tml, *gmtime(), *localtime();
872:
873: extern time_t time();
874:
875: struct tm start_time, end_time, curr_time, last_time, forecast_time;
876: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
877: struct tm tm;
878:
1.126 brouard 879: char strcurr[80], strfor[80];
880:
881: char *endptr;
882: long lval;
883: double dval;
884:
885: #define NR_END 1
886: #define FREE_ARG char*
887: #define FTOL 1.0e-10
888:
889: #define NRANSI
890: #define ITMAX 200
891:
892: #define TOL 2.0e-4
893:
894: #define CGOLD 0.3819660
895: #define ZEPS 1.0e-10
896: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
897:
898: #define GOLD 1.618034
899: #define GLIMIT 100.0
900: #define TINY 1.0e-20
901:
902: static double maxarg1,maxarg2;
903: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
904: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
905:
906: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
907: #define rint(a) floor(a+0.5)
1.166 brouard 908: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 909: #define mytinydouble 1.0e-16
1.166 brouard 910: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
911: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
912: /* static double dsqrarg; */
913: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 914: static double sqrarg;
915: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
916: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
917: int agegomp= AGEGOMP;
918:
919: int imx;
920: int stepm=1;
921: /* Stepm, step in month: minimum step interpolation*/
922:
923: int estepm;
924: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
925:
926: int m,nb;
927: long *num;
1.197 brouard 928: int firstpass=0, lastpass=4,*cod, *cens;
1.192 brouard 929: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
930: covariate for which somebody answered excluding
931: undefined. Usually 2: 0 and 1. */
932: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
933: covariate for which somebody answered including
934: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 935: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
936: double **pmmij, ***probs;
937: double *ageexmed,*agecens;
938: double dateintmean=0;
939:
940: double *weight;
941: int **s; /* Status */
1.141 brouard 942: double *agedc;
1.145 brouard 943: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 944: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 945: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.141 brouard 946: double idx;
947: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.197 brouard 948: int *Tage;
1.145 brouard 949: int *Ndum; /** Freq of modality (tricode */
1.200 brouard 950: /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
1.141 brouard 951: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.126 brouard 952: double *lsurv, *lpop, *tpop;
953:
1.143 brouard 954: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
955: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 956:
957: /**************** split *************************/
958: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
959: {
960: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
961: the name of the file (name), its extension only (ext) and its first part of the name (finame)
962: */
963: char *ss; /* pointer */
1.186 brouard 964: int l1=0, l2=0; /* length counters */
1.126 brouard 965:
966: l1 = strlen(path ); /* length of path */
967: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
968: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
969: if ( ss == NULL ) { /* no directory, so determine current directory */
970: strcpy( name, path ); /* we got the fullname name because no directory */
971: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
972: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
973: /* get current working directory */
974: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 975: #ifdef WIN32
976: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
977: #else
978: if (getcwd(dirc, FILENAME_MAX) == NULL) {
979: #endif
1.126 brouard 980: return( GLOCK_ERROR_GETCWD );
981: }
982: /* got dirc from getcwd*/
983: printf(" DIRC = %s \n",dirc);
1.205 brouard 984: } else { /* strip directory from path */
1.126 brouard 985: ss++; /* after this, the filename */
986: l2 = strlen( ss ); /* length of filename */
987: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
988: strcpy( name, ss ); /* save file name */
989: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 990: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 991: printf(" DIRC2 = %s \n",dirc);
992: }
993: /* We add a separator at the end of dirc if not exists */
994: l1 = strlen( dirc ); /* length of directory */
995: if( dirc[l1-1] != DIRSEPARATOR ){
996: dirc[l1] = DIRSEPARATOR;
997: dirc[l1+1] = 0;
998: printf(" DIRC3 = %s \n",dirc);
999: }
1000: ss = strrchr( name, '.' ); /* find last / */
1001: if (ss >0){
1002: ss++;
1003: strcpy(ext,ss); /* save extension */
1004: l1= strlen( name);
1005: l2= strlen(ss)+1;
1006: strncpy( finame, name, l1-l2);
1007: finame[l1-l2]= 0;
1008: }
1009:
1010: return( 0 ); /* we're done */
1011: }
1012:
1013:
1014: /******************************************/
1015:
1016: void replace_back_to_slash(char *s, char*t)
1017: {
1018: int i;
1019: int lg=0;
1020: i=0;
1021: lg=strlen(t);
1022: for(i=0; i<= lg; i++) {
1023: (s[i] = t[i]);
1024: if (t[i]== '\\') s[i]='/';
1025: }
1026: }
1027:
1.132 brouard 1028: char *trimbb(char *out, char *in)
1.137 brouard 1029: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 1030: char *s;
1031: s=out;
1032: while (*in != '\0'){
1.137 brouard 1033: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 1034: in++;
1035: }
1036: *out++ = *in++;
1037: }
1038: *out='\0';
1039: return s;
1040: }
1041:
1.187 brouard 1042: /* char *substrchaine(char *out, char *in, char *chain) */
1043: /* { */
1044: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
1045: /* char *s, *t; */
1046: /* t=in;s=out; */
1047: /* while ((*in != *chain) && (*in != '\0')){ */
1048: /* *out++ = *in++; */
1049: /* } */
1050:
1051: /* /\* *in matches *chain *\/ */
1052: /* while ((*in++ == *chain++) && (*in != '\0')){ */
1053: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1054: /* } */
1055: /* in--; chain--; */
1056: /* while ( (*in != '\0')){ */
1057: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1058: /* *out++ = *in++; */
1059: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1060: /* } */
1061: /* *out='\0'; */
1062: /* out=s; */
1063: /* return out; */
1064: /* } */
1065: char *substrchaine(char *out, char *in, char *chain)
1066: {
1067: /* Substract chain 'chain' from 'in', return and output 'out' */
1068: /* in="V1+V1*age+age*age+V2", chain="age*age" */
1069:
1070: char *strloc;
1071:
1072: strcpy (out, in);
1073: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
1074: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
1075: if(strloc != NULL){
1076: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
1077: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
1078: /* strcpy (strloc, strloc +strlen(chain));*/
1079: }
1080: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
1081: return out;
1082: }
1083:
1084:
1.145 brouard 1085: char *cutl(char *blocc, char *alocc, char *in, char occ)
1086: {
1.187 brouard 1087: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 1088: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 1089: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 1090: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1091: */
1.160 brouard 1092: char *s, *t;
1.145 brouard 1093: t=in;s=in;
1094: while ((*in != occ) && (*in != '\0')){
1095: *alocc++ = *in++;
1096: }
1097: if( *in == occ){
1098: *(alocc)='\0';
1099: s=++in;
1100: }
1101:
1102: if (s == t) {/* occ not found */
1103: *(alocc-(in-s))='\0';
1104: in=s;
1105: }
1106: while ( *in != '\0'){
1107: *blocc++ = *in++;
1108: }
1109:
1110: *blocc='\0';
1111: return t;
1112: }
1.137 brouard 1113: char *cutv(char *blocc, char *alocc, char *in, char occ)
1114: {
1.187 brouard 1115: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1116: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1117: gives blocc="abcdef2ghi" and alocc="j".
1118: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1119: */
1120: char *s, *t;
1121: t=in;s=in;
1122: while (*in != '\0'){
1123: while( *in == occ){
1124: *blocc++ = *in++;
1125: s=in;
1126: }
1127: *blocc++ = *in++;
1128: }
1129: if (s == t) /* occ not found */
1130: *(blocc-(in-s))='\0';
1131: else
1132: *(blocc-(in-s)-1)='\0';
1133: in=s;
1134: while ( *in != '\0'){
1135: *alocc++ = *in++;
1136: }
1137:
1138: *alocc='\0';
1139: return s;
1140: }
1141:
1.126 brouard 1142: int nbocc(char *s, char occ)
1143: {
1144: int i,j=0;
1145: int lg=20;
1146: i=0;
1147: lg=strlen(s);
1148: for(i=0; i<= lg; i++) {
1149: if (s[i] == occ ) j++;
1150: }
1151: return j;
1152: }
1153:
1.137 brouard 1154: /* void cutv(char *u,char *v, char*t, char occ) */
1155: /* { */
1156: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1157: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1158: /* gives u="abcdef2ghi" and v="j" *\/ */
1159: /* int i,lg,j,p=0; */
1160: /* i=0; */
1161: /* lg=strlen(t); */
1162: /* for(j=0; j<=lg-1; j++) { */
1163: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1164: /* } */
1.126 brouard 1165:
1.137 brouard 1166: /* for(j=0; j<p; j++) { */
1167: /* (u[j] = t[j]); */
1168: /* } */
1169: /* u[p]='\0'; */
1.126 brouard 1170:
1.137 brouard 1171: /* for(j=0; j<= lg; j++) { */
1172: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1173: /* } */
1174: /* } */
1.126 brouard 1175:
1.160 brouard 1176: #ifdef _WIN32
1177: char * strsep(char **pp, const char *delim)
1178: {
1179: char *p, *q;
1180:
1181: if ((p = *pp) == NULL)
1182: return 0;
1183: if ((q = strpbrk (p, delim)) != NULL)
1184: {
1185: *pp = q + 1;
1186: *q = '\0';
1187: }
1188: else
1189: *pp = 0;
1190: return p;
1191: }
1192: #endif
1193:
1.126 brouard 1194: /********************** nrerror ********************/
1195:
1196: void nrerror(char error_text[])
1197: {
1198: fprintf(stderr,"ERREUR ...\n");
1199: fprintf(stderr,"%s\n",error_text);
1200: exit(EXIT_FAILURE);
1201: }
1202: /*********************** vector *******************/
1203: double *vector(int nl, int nh)
1204: {
1205: double *v;
1206: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1207: if (!v) nrerror("allocation failure in vector");
1208: return v-nl+NR_END;
1209: }
1210:
1211: /************************ free vector ******************/
1212: void free_vector(double*v, int nl, int nh)
1213: {
1214: free((FREE_ARG)(v+nl-NR_END));
1215: }
1216:
1217: /************************ivector *******************************/
1218: int *ivector(long nl,long nh)
1219: {
1220: int *v;
1221: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1222: if (!v) nrerror("allocation failure in ivector");
1223: return v-nl+NR_END;
1224: }
1225:
1226: /******************free ivector **************************/
1227: void free_ivector(int *v, long nl, long nh)
1228: {
1229: free((FREE_ARG)(v+nl-NR_END));
1230: }
1231:
1232: /************************lvector *******************************/
1233: long *lvector(long nl,long nh)
1234: {
1235: long *v;
1236: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1237: if (!v) nrerror("allocation failure in ivector");
1238: return v-nl+NR_END;
1239: }
1240:
1241: /******************free lvector **************************/
1242: void free_lvector(long *v, long nl, long nh)
1243: {
1244: free((FREE_ARG)(v+nl-NR_END));
1245: }
1246:
1247: /******************* imatrix *******************************/
1248: int **imatrix(long nrl, long nrh, long ncl, long nch)
1249: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1250: {
1251: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1252: int **m;
1253:
1254: /* allocate pointers to rows */
1255: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1256: if (!m) nrerror("allocation failure 1 in matrix()");
1257: m += NR_END;
1258: m -= nrl;
1259:
1260:
1261: /* allocate rows and set pointers to them */
1262: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1263: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1264: m[nrl] += NR_END;
1265: m[nrl] -= ncl;
1266:
1267: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1268:
1269: /* return pointer to array of pointers to rows */
1270: return m;
1271: }
1272:
1273: /****************** free_imatrix *************************/
1274: void free_imatrix(m,nrl,nrh,ncl,nch)
1275: int **m;
1276: long nch,ncl,nrh,nrl;
1277: /* free an int matrix allocated by imatrix() */
1278: {
1279: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1280: free((FREE_ARG) (m+nrl-NR_END));
1281: }
1282:
1283: /******************* matrix *******************************/
1284: double **matrix(long nrl, long nrh, long ncl, long nch)
1285: {
1286: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1287: double **m;
1288:
1289: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1290: if (!m) nrerror("allocation failure 1 in matrix()");
1291: m += NR_END;
1292: m -= nrl;
1293:
1294: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1295: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1296: m[nrl] += NR_END;
1297: m[nrl] -= ncl;
1298:
1299: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1300: return m;
1.145 brouard 1301: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1302: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1303: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1304: */
1305: }
1306:
1307: /*************************free matrix ************************/
1308: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1309: {
1310: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1311: free((FREE_ARG)(m+nrl-NR_END));
1312: }
1313:
1314: /******************* ma3x *******************************/
1315: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1316: {
1317: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1318: double ***m;
1319:
1320: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1321: if (!m) nrerror("allocation failure 1 in matrix()");
1322: m += NR_END;
1323: m -= nrl;
1324:
1325: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1326: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1327: m[nrl] += NR_END;
1328: m[nrl] -= ncl;
1329:
1330: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1331:
1332: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1333: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1334: m[nrl][ncl] += NR_END;
1335: m[nrl][ncl] -= nll;
1336: for (j=ncl+1; j<=nch; j++)
1337: m[nrl][j]=m[nrl][j-1]+nlay;
1338:
1339: for (i=nrl+1; i<=nrh; i++) {
1340: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1341: for (j=ncl+1; j<=nch; j++)
1342: m[i][j]=m[i][j-1]+nlay;
1343: }
1344: return m;
1345: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1346: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1347: */
1348: }
1349:
1350: /*************************free ma3x ************************/
1351: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1352: {
1353: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1354: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1355: free((FREE_ARG)(m+nrl-NR_END));
1356: }
1357:
1358: /*************** function subdirf ***********/
1359: char *subdirf(char fileres[])
1360: {
1361: /* Caution optionfilefiname is hidden */
1362: strcpy(tmpout,optionfilefiname);
1363: strcat(tmpout,"/"); /* Add to the right */
1364: strcat(tmpout,fileres);
1365: return tmpout;
1366: }
1367:
1368: /*************** function subdirf2 ***********/
1369: char *subdirf2(char fileres[], char *preop)
1370: {
1371:
1372: /* Caution optionfilefiname is hidden */
1373: strcpy(tmpout,optionfilefiname);
1374: strcat(tmpout,"/");
1375: strcat(tmpout,preop);
1376: strcat(tmpout,fileres);
1377: return tmpout;
1378: }
1379:
1380: /*************** function subdirf3 ***********/
1381: char *subdirf3(char fileres[], char *preop, char *preop2)
1382: {
1383:
1384: /* Caution optionfilefiname is hidden */
1385: strcpy(tmpout,optionfilefiname);
1386: strcat(tmpout,"/");
1387: strcat(tmpout,preop);
1388: strcat(tmpout,preop2);
1389: strcat(tmpout,fileres);
1390: return tmpout;
1391: }
1.213 brouard 1392:
1393: /*************** function subdirfext ***********/
1394: char *subdirfext(char fileres[], char *preop, char *postop)
1395: {
1396:
1397: strcpy(tmpout,preop);
1398: strcat(tmpout,fileres);
1399: strcat(tmpout,postop);
1400: return tmpout;
1401: }
1.126 brouard 1402:
1.213 brouard 1403: /*************** function subdirfext3 ***********/
1404: char *subdirfext3(char fileres[], char *preop, char *postop)
1405: {
1406:
1407: /* Caution optionfilefiname is hidden */
1408: strcpy(tmpout,optionfilefiname);
1409: strcat(tmpout,"/");
1410: strcat(tmpout,preop);
1411: strcat(tmpout,fileres);
1412: strcat(tmpout,postop);
1413: return tmpout;
1414: }
1415:
1.162 brouard 1416: char *asc_diff_time(long time_sec, char ascdiff[])
1417: {
1418: long sec_left, days, hours, minutes;
1419: days = (time_sec) / (60*60*24);
1420: sec_left = (time_sec) % (60*60*24);
1421: hours = (sec_left) / (60*60) ;
1422: sec_left = (sec_left) %(60*60);
1423: minutes = (sec_left) /60;
1424: sec_left = (sec_left) % (60);
1425: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1426: return ascdiff;
1427: }
1428:
1.126 brouard 1429: /***************** f1dim *************************/
1430: extern int ncom;
1431: extern double *pcom,*xicom;
1432: extern double (*nrfunc)(double []);
1433:
1434: double f1dim(double x)
1435: {
1436: int j;
1437: double f;
1438: double *xt;
1439:
1440: xt=vector(1,ncom);
1441: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1442: f=(*nrfunc)(xt);
1443: free_vector(xt,1,ncom);
1444: return f;
1445: }
1446:
1447: /*****************brent *************************/
1448: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1449: {
1450: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1451: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1452: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1453: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1454: * returned function value.
1455: */
1.126 brouard 1456: int iter;
1457: double a,b,d,etemp;
1.159 brouard 1458: double fu=0,fv,fw,fx;
1.164 brouard 1459: double ftemp=0.;
1.126 brouard 1460: double p,q,r,tol1,tol2,u,v,w,x,xm;
1461: double e=0.0;
1462:
1463: a=(ax < cx ? ax : cx);
1464: b=(ax > cx ? ax : cx);
1465: x=w=v=bx;
1466: fw=fv=fx=(*f)(x);
1467: for (iter=1;iter<=ITMAX;iter++) {
1468: xm=0.5*(a+b);
1469: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1470: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1471: printf(".");fflush(stdout);
1472: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1473: #ifdef DEBUGBRENT
1.126 brouard 1474: 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);
1475: 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);
1476: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1477: #endif
1478: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1479: *xmin=x;
1480: return fx;
1481: }
1482: ftemp=fu;
1483: if (fabs(e) > tol1) {
1484: r=(x-w)*(fx-fv);
1485: q=(x-v)*(fx-fw);
1486: p=(x-v)*q-(x-w)*r;
1487: q=2.0*(q-r);
1488: if (q > 0.0) p = -p;
1489: q=fabs(q);
1490: etemp=e;
1491: e=d;
1492: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1493: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1494: else {
1495: d=p/q;
1496: u=x+d;
1497: if (u-a < tol2 || b-u < tol2)
1498: d=SIGN(tol1,xm-x);
1499: }
1500: } else {
1501: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1502: }
1503: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1504: fu=(*f)(u);
1505: if (fu <= fx) {
1506: if (u >= x) a=x; else b=x;
1507: SHFT(v,w,x,u)
1.183 brouard 1508: SHFT(fv,fw,fx,fu)
1509: } else {
1510: if (u < x) a=u; else b=u;
1511: if (fu <= fw || w == x) {
1512: v=w;
1513: w=u;
1514: fv=fw;
1515: fw=fu;
1516: } else if (fu <= fv || v == x || v == w) {
1517: v=u;
1518: fv=fu;
1519: }
1520: }
1.126 brouard 1521: }
1522: nrerror("Too many iterations in brent");
1523: *xmin=x;
1524: return fx;
1525: }
1526:
1527: /****************** mnbrak ***********************/
1528:
1529: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1530: double (*func)(double))
1.183 brouard 1531: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1532: the downhill direction (defined by the function as evaluated at the initial points) and returns
1533: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1534: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1535: */
1.126 brouard 1536: double ulim,u,r,q, dum;
1537: double fu;
1.187 brouard 1538:
1539: double scale=10.;
1540: int iterscale=0;
1541:
1542: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1543: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1544:
1545:
1546: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1547: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1548: /* *bx = *ax - (*ax - *bx)/scale; */
1549: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1550: /* } */
1551:
1.126 brouard 1552: if (*fb > *fa) {
1553: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1554: SHFT(dum,*fb,*fa,dum)
1555: }
1.126 brouard 1556: *cx=(*bx)+GOLD*(*bx-*ax);
1557: *fc=(*func)(*cx);
1.183 brouard 1558: #ifdef DEBUG
1559: printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1560: fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1561: #endif
1562: while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
1.126 brouard 1563: r=(*bx-*ax)*(*fb-*fc);
1564: q=(*bx-*cx)*(*fb-*fa);
1565: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 1566: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1567: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1568: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 1569: fu=(*func)(u);
1.163 brouard 1570: #ifdef DEBUG
1571: /* f(x)=A(x-u)**2+f(u) */
1572: double A, fparabu;
1573: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1574: fparabu= *fa - A*(*ax-u)*(*ax-u);
1575: 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);
1576: 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 1577: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1578: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1579: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1580: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 1581: #endif
1.184 brouard 1582: #ifdef MNBRAKORIGINAL
1.183 brouard 1583: #else
1.191 brouard 1584: /* if (fu > *fc) { */
1585: /* #ifdef DEBUG */
1586: /* printf("mnbrak4 fu > fc \n"); */
1587: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
1588: /* #endif */
1589: /* /\* 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 *\\/ *\/ */
1590: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
1591: /* dum=u; /\* Shifting c and u *\/ */
1592: /* u = *cx; */
1593: /* *cx = dum; */
1594: /* dum = fu; */
1595: /* fu = *fc; */
1596: /* *fc =dum; */
1597: /* } else { /\* end *\/ */
1598: /* #ifdef DEBUG */
1599: /* printf("mnbrak3 fu < fc \n"); */
1600: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
1601: /* #endif */
1602: /* dum=u; /\* Shifting c and u *\/ */
1603: /* u = *cx; */
1604: /* *cx = dum; */
1605: /* dum = fu; */
1606: /* fu = *fc; */
1607: /* *fc =dum; */
1608: /* } */
1.183 brouard 1609: #ifdef DEBUG
1.191 brouard 1610: printf("mnbrak34 fu < or >= fc \n");
1611: fprintf(ficlog, "mnbrak34 fu < fc\n");
1.183 brouard 1612: #endif
1.191 brouard 1613: dum=u; /* Shifting c and u */
1614: u = *cx;
1615: *cx = dum;
1616: dum = fu;
1617: fu = *fc;
1618: *fc =dum;
1.183 brouard 1619: #endif
1.162 brouard 1620: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 1621: #ifdef DEBUG
1622: printf("mnbrak2 u after c but before ulim\n");
1623: fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
1624: #endif
1.126 brouard 1625: fu=(*func)(u);
1626: if (fu < *fc) {
1.183 brouard 1627: #ifdef DEBUG
1628: printf("mnbrak2 u after c but before ulim AND fu < fc\n");
1629: fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
1630: #endif
1.126 brouard 1631: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1.183 brouard 1632: SHFT(*fb,*fc,fu,(*func)(u))
1633: }
1.162 brouard 1634: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 1635: #ifdef DEBUG
1636: printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1637: fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1638: #endif
1.126 brouard 1639: u=ulim;
1640: fu=(*func)(u);
1.183 brouard 1641: } else { /* u could be left to b (if r > q parabola has a maximum) */
1642: #ifdef DEBUG
1643: printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1644: fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1645: #endif
1.126 brouard 1646: u=(*cx)+GOLD*(*cx-*bx);
1647: fu=(*func)(u);
1.183 brouard 1648: } /* end tests */
1.126 brouard 1649: SHFT(*ax,*bx,*cx,u)
1.183 brouard 1650: SHFT(*fa,*fb,*fc,fu)
1651: #ifdef DEBUG
1652: 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);
1653: 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);
1654: #endif
1655: } /* 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 1656: }
1657:
1658: /*************** linmin ************************/
1.162 brouard 1659: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1660: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1661: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1662: the value of func at the returned location p . This is actually all accomplished by calling the
1663: routines mnbrak and brent .*/
1.126 brouard 1664: int ncom;
1665: double *pcom,*xicom;
1666: double (*nrfunc)(double []);
1667:
1668: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1669: {
1670: double brent(double ax, double bx, double cx,
1671: double (*f)(double), double tol, double *xmin);
1672: double f1dim(double x);
1673: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1674: double *fc, double (*func)(double));
1675: int j;
1676: double xx,xmin,bx,ax;
1677: double fx,fb,fa;
1.187 brouard 1678:
1.203 brouard 1679: #ifdef LINMINORIGINAL
1680: #else
1681: double scale=10., axs, xxs; /* Scale added for infinity */
1682: #endif
1683:
1.126 brouard 1684: ncom=n;
1685: pcom=vector(1,n);
1686: xicom=vector(1,n);
1687: nrfunc=func;
1688: for (j=1;j<=n;j++) {
1689: pcom[j]=p[j];
1.202 brouard 1690: xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
1.126 brouard 1691: }
1.187 brouard 1692:
1.203 brouard 1693: #ifdef LINMINORIGINAL
1694: xx=1.;
1695: #else
1696: axs=0.0;
1697: xxs=1.;
1698: do{
1699: xx= xxs;
1700: #endif
1.187 brouard 1701: ax=0.;
1702: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
1703: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
1704: /* 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)) */
1705: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
1706: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
1707: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
1708: /* 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 1709: #ifdef LINMINORIGINAL
1710: #else
1711: if (fx != fx){
1712: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
1713: printf("|");
1714: fprintf(ficlog,"|");
1715: #ifdef DEBUGLINMIN
1716: 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);
1717: #endif
1718: }
1719: }while(fx != fx);
1720: #endif
1721:
1.191 brouard 1722: #ifdef DEBUGLINMIN
1723: 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 1724: 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 1725: #endif
1.187 brouard 1726: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
1727: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
1728: /* fmin = f(p[j] + xmin * xi[j]) */
1729: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
1730: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 1731: #ifdef DEBUG
1732: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1733: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1734: #endif
1.191 brouard 1735: #ifdef DEBUGLINMIN
1736: printf("linmin end ");
1.202 brouard 1737: fprintf(ficlog,"linmin end ");
1.191 brouard 1738: #endif
1.126 brouard 1739: for (j=1;j<=n;j++) {
1.203 brouard 1740: #ifdef LINMINORIGINAL
1741: xi[j] *= xmin;
1742: #else
1743: #ifdef DEBUGLINMIN
1744: if(xxs <1.0)
1745: printf(" before xi[%d]=%12.8f", j,xi[j]);
1746: #endif
1747: 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) */
1748: #ifdef DEBUGLINMIN
1749: if(xxs <1.0)
1750: 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 );
1751: #endif
1752: #endif
1.187 brouard 1753: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 1754: }
1.191 brouard 1755: #ifdef DEBUGLINMIN
1.203 brouard 1756: printf("\n");
1.191 brouard 1757: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.202 brouard 1758: 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 1759: for (j=1;j<=n;j++) {
1.202 brouard 1760: printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1761: fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1762: if(j % ncovmodel == 0){
1.191 brouard 1763: printf("\n");
1.202 brouard 1764: fprintf(ficlog,"\n");
1765: }
1.191 brouard 1766: }
1.203 brouard 1767: #else
1.191 brouard 1768: #endif
1.126 brouard 1769: free_vector(xicom,1,n);
1770: free_vector(pcom,1,n);
1771: }
1772:
1773:
1774: /*************** powell ************************/
1.162 brouard 1775: /*
1776: Minimization of a function func of n variables. Input consists of an initial starting point
1777: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1778: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1779: such that failure to decrease by more than this amount on one iteration signals doneness. On
1780: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1781: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1782: */
1.126 brouard 1783: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1784: double (*func)(double []))
1785: {
1786: void linmin(double p[], double xi[], int n, double *fret,
1787: double (*func)(double []));
1788: int i,ibig,j;
1789: double del,t,*pt,*ptt,*xit;
1.181 brouard 1790: double directest;
1.126 brouard 1791: double fp,fptt;
1792: double *xits;
1793: int niterf, itmp;
1794:
1795: pt=vector(1,n);
1796: ptt=vector(1,n);
1797: xit=vector(1,n);
1798: xits=vector(1,n);
1799: *fret=(*func)(p);
1800: for (j=1;j<=n;j++) pt[j]=p[j];
1.202 brouard 1801: rcurr_time = time(NULL);
1.126 brouard 1802: for (*iter=1;;++(*iter)) {
1.187 brouard 1803: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 1804: ibig=0;
1805: del=0.0;
1.157 brouard 1806: rlast_time=rcurr_time;
1807: /* (void) gettimeofday(&curr_time,&tzp); */
1808: rcurr_time = time(NULL);
1809: curr_time = *localtime(&rcurr_time);
1810: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1811: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1812: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 1813: for (i=1;i<=n;i++) {
1.126 brouard 1814: printf(" %d %.12f",i, p[i]);
1815: fprintf(ficlog," %d %.12lf",i, p[i]);
1816: fprintf(ficrespow," %.12lf", p[i]);
1817: }
1818: printf("\n");
1819: fprintf(ficlog,"\n");
1820: fprintf(ficrespow,"\n");fflush(ficrespow);
1821: if(*iter <=3){
1.157 brouard 1822: tml = *localtime(&rcurr_time);
1823: strcpy(strcurr,asctime(&tml));
1824: rforecast_time=rcurr_time;
1.126 brouard 1825: itmp = strlen(strcurr);
1826: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1827: strcurr[itmp-1]='\0';
1.162 brouard 1828: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 1829: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 1830: for(niterf=10;niterf<=30;niterf+=10){
1.157 brouard 1831: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1832: forecast_time = *localtime(&rforecast_time);
1833: strcpy(strfor,asctime(&forecast_time));
1.126 brouard 1834: itmp = strlen(strfor);
1835: if(strfor[itmp-1]=='\n')
1836: strfor[itmp-1]='\0';
1.157 brouard 1837: 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);
1838: 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 1839: }
1840: }
1.187 brouard 1841: for (i=1;i<=n;i++) { /* For each direction i */
1842: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 1843: fptt=(*fret);
1844: #ifdef DEBUG
1.203 brouard 1845: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1846: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 1847: #endif
1.203 brouard 1848: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 1849: fprintf(ficlog,"%d",i);fflush(ficlog);
1.188 brouard 1850: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1851: /* Outputs are fret(new point p) p is updated and xit rescaled */
1852: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1853: /* because that direction will be replaced unless the gain del is small */
1854: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
1855: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
1856: /* with the new direction. */
1.126 brouard 1857: del=fabs(fptt-(*fret));
1858: ibig=i;
1859: }
1860: #ifdef DEBUG
1861: printf("%d %.12e",i,(*fret));
1862: fprintf(ficlog,"%d %.12e",i,(*fret));
1863: for (j=1;j<=n;j++) {
1864: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1865: printf(" x(%d)=%.12e",j,xit[j]);
1866: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1867: }
1868: for(j=1;j<=n;j++) {
1.162 brouard 1869: printf(" p(%d)=%.12e",j,p[j]);
1870: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 1871: }
1872: printf("\n");
1873: fprintf(ficlog,"\n");
1874: #endif
1.187 brouard 1875: } /* end loop on each direction i */
1876: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 1877: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 1878: /* New value of last point Pn is not computed, P(n-1) */
1.182 brouard 1879: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1.188 brouard 1880: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
1881: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
1882: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
1883: /* decreased of more than 3.84 */
1884: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
1885: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
1886: /* By adding 10 parameters more the gain should be 18.31 */
1887:
1888: /* Starting the program with initial values given by a former maximization will simply change */
1889: /* the scales of the directions and the directions, because the are reset to canonical directions */
1890: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
1891: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 1892: #ifdef DEBUG
1893: int k[2],l;
1894: k[0]=1;
1895: k[1]=-1;
1896: printf("Max: %.12e",(*func)(p));
1897: fprintf(ficlog,"Max: %.12e",(*func)(p));
1898: for (j=1;j<=n;j++) {
1899: printf(" %.12e",p[j]);
1900: fprintf(ficlog," %.12e",p[j]);
1901: }
1902: printf("\n");
1903: fprintf(ficlog,"\n");
1904: for(l=0;l<=1;l++) {
1905: for (j=1;j<=n;j++) {
1906: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1907: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1908: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1909: }
1910: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1911: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1912: }
1913: #endif
1914:
1915:
1916: free_vector(xit,1,n);
1917: free_vector(xits,1,n);
1918: free_vector(ptt,1,n);
1919: free_vector(pt,1,n);
1920: return;
1.192 brouard 1921: } /* enough precision */
1.126 brouard 1922: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1.181 brouard 1923: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 1924: ptt[j]=2.0*p[j]-pt[j];
1925: xit[j]=p[j]-pt[j];
1926: pt[j]=p[j];
1927: }
1.181 brouard 1928: fptt=(*func)(ptt); /* f_3 */
1.192 brouard 1929: #ifdef POWELLF1F3
1930: #else
1.161 brouard 1931: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 1932: #endif
1.162 brouard 1933: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 1934: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 1935: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1936: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1937: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.181 brouard 1938: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
1.161 brouard 1939: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.183 brouard 1940: #ifdef NRCORIGINAL
1941: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
1942: #else
1943: 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 1944: t= t- del*SQR(fp-fptt);
1.183 brouard 1945: #endif
1.202 brouard 1946: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
1.161 brouard 1947: #ifdef DEBUG
1.181 brouard 1948: 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);
1949: 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 1950: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1951: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1952: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1953: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1954: 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);
1955: 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);
1956: #endif
1.183 brouard 1957: #ifdef POWELLORIGINAL
1958: if (t < 0.0) { /* Then we use it for new direction */
1959: #else
1.182 brouard 1960: if (directest*t < 0.0) { /* Contradiction between both tests */
1.202 brouard 1961: 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 1962: 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 1963: 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 1964: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1965: }
1.181 brouard 1966: if (directest < 0.0) { /* Then we use it for new direction */
1967: #endif
1.191 brouard 1968: #ifdef DEBUGLINMIN
1969: printf("Before linmin in direction P%d-P0\n",n);
1970: for (j=1;j<=n;j++) {
1.202 brouard 1971: printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1972: fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1973: if(j % ncovmodel == 0){
1.191 brouard 1974: printf("\n");
1.202 brouard 1975: fprintf(ficlog,"\n");
1976: }
1.191 brouard 1977: }
1978: #endif
1.187 brouard 1979: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.191 brouard 1980: #ifdef DEBUGLINMIN
1981: for (j=1;j<=n;j++) {
1982: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1.202 brouard 1983: fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1984: if(j % ncovmodel == 0){
1.191 brouard 1985: printf("\n");
1.202 brouard 1986: fprintf(ficlog,"\n");
1987: }
1.191 brouard 1988: }
1989: #endif
1.126 brouard 1990: for (j=1;j<=n;j++) {
1.181 brouard 1991: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
1992: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
1.126 brouard 1993: }
1.181 brouard 1994: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1995: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1.161 brouard 1996:
1.126 brouard 1997: #ifdef DEBUG
1.164 brouard 1998: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1999: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1.126 brouard 2000: for(j=1;j<=n;j++){
2001: printf(" %.12e",xit[j]);
2002: fprintf(ficlog," %.12e",xit[j]);
2003: }
2004: printf("\n");
2005: fprintf(ficlog,"\n");
2006: #endif
1.192 brouard 2007: } /* end of t or directest negative */
2008: #ifdef POWELLF1F3
2009: #else
1.162 brouard 2010: } /* end if (fptt < fp) */
1.192 brouard 2011: #endif
2012: } /* loop iteration */
1.126 brouard 2013: }
2014:
2015: /**** Prevalence limit (stable or period prevalence) ****************/
2016:
1.203 brouard 2017: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij)
1.126 brouard 2018: {
2019: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1.203 brouard 2020: matrix by transitions matrix until convergence is reached with precision ftolpl */
1.206 brouard 2021: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
2022: /* Wx is row vector: population in state 1, population in state 2, population dead */
2023: /* or prevalence in state 1, prevalence in state 2, 0 */
2024: /* newm is the matrix after multiplications, its rows are identical at a factor */
2025: /* Initial matrix pimij */
2026: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2027: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2028: /* 0, 0 , 1} */
2029: /*
2030: * and after some iteration: */
2031: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2032: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2033: /* 0, 0 , 1} */
2034: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2035: /* {0.51571254859325999, 0.4842874514067399, */
2036: /* 0.51326036147820708, 0.48673963852179264} */
2037: /* If we start from prlim again, prlim tends to a constant matrix */
2038:
1.126 brouard 2039: int i, ii,j,k;
1.209 brouard 2040: double *min, *max, *meandiff, maxmax,sumnew=0.;
1.145 brouard 2041: /* double **matprod2(); */ /* test */
1.131 brouard 2042: double **out, cov[NCOVMAX+1], **pmij();
1.126 brouard 2043: double **newm;
1.209 brouard 2044: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
1.203 brouard 2045: int ncvloop=0;
1.169 brouard 2046:
1.209 brouard 2047: min=vector(1,nlstate);
2048: max=vector(1,nlstate);
2049: meandiff=vector(1,nlstate);
2050:
1.126 brouard 2051: for (ii=1;ii<=nlstate+ndeath;ii++)
2052: for (j=1;j<=nlstate+ndeath;j++){
2053: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2054: }
1.169 brouard 2055:
2056: cov[1]=1.;
2057:
2058: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.202 brouard 2059: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.126 brouard 2060: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1.202 brouard 2061: ncvloop++;
1.126 brouard 2062: newm=savm;
2063: /* Covariates have to be included here again */
1.138 brouard 2064: cov[2]=agefin;
1.187 brouard 2065: if(nagesqr==1)
2066: cov[3]= agefin*agefin;;
1.138 brouard 2067: for (k=1; k<=cptcovn;k++) {
1.200 brouard 2068: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
2069: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
1.198 brouard 2070: /* 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 2071: }
1.186 brouard 2072: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 2073: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
2074: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
1.186 brouard 2075: for (k=1; k<=cptcovprod;k++) /* Useless */
1.200 brouard 2076: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
2077: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
1.138 brouard 2078:
2079: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2080: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2081: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 2082: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2083: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.142 brouard 2084: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 2085:
1.126 brouard 2086: savm=oldm;
2087: oldm=newm;
1.209 brouard 2088:
2089: for(j=1; j<=nlstate; j++){
2090: max[j]=0.;
2091: min[j]=1.;
2092: }
2093: for(i=1;i<=nlstate;i++){
2094: sumnew=0;
2095: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
2096: for(j=1; j<=nlstate; j++){
2097: prlim[i][j]= newm[i][j]/(1-sumnew);
2098: max[j]=FMAX(max[j],prlim[i][j]);
2099: min[j]=FMIN(min[j],prlim[i][j]);
2100: }
2101: }
2102:
1.126 brouard 2103: maxmax=0.;
1.209 brouard 2104: for(j=1; j<=nlstate; j++){
2105: meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
2106: maxmax=FMAX(maxmax,meandiff[j]);
2107: /* 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 2108: } /* j loop */
1.203 brouard 2109: *ncvyear= (int)age- (int)agefin;
1.208 brouard 2110: /* 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 2111: if(maxmax < ftolpl){
1.209 brouard 2112: /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
2113: free_vector(min,1,nlstate);
2114: free_vector(max,1,nlstate);
2115: free_vector(meandiff,1,nlstate);
1.126 brouard 2116: return prlim;
2117: }
1.169 brouard 2118: } /* age loop */
1.208 brouard 2119: /* After some age loop it doesn't converge */
1.209 brouard 2120: 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 2121: 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 2122: /* 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); */
2123: free_vector(min,1,nlstate);
2124: free_vector(max,1,nlstate);
2125: free_vector(meandiff,1,nlstate);
1.208 brouard 2126:
1.169 brouard 2127: return prlim; /* should not reach here */
1.126 brouard 2128: }
2129:
2130: /*************** transition probabilities ***************/
2131:
2132: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
2133: {
1.138 brouard 2134: /* According to parameters values stored in x and the covariate's values stored in cov,
2135: computes the probability to be observed in state j being in state i by appying the
2136: model to the ncovmodel covariates (including constant and age).
2137: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2138: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2139: ncth covariate in the global vector x is given by the formula:
2140: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2141: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2142: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2143: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
2144: Outputs ps[i][j] the probability to be observed in j being in j according to
2145: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
2146: */
2147: double s1, lnpijopii;
1.126 brouard 2148: /*double t34;*/
1.164 brouard 2149: int i,j, nc, ii, jj;
1.126 brouard 2150:
2151: for(i=1; i<= nlstate; i++){
2152: for(j=1; j<i;j++){
1.138 brouard 2153: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2154: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2155: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2156: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 2157: }
1.138 brouard 2158: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2159: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 2160: }
2161: for(j=i+1; j<=nlstate+ndeath;j++){
1.138 brouard 2162: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2163: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2164: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2165: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1.126 brouard 2166: }
1.138 brouard 2167: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1.126 brouard 2168: }
2169: }
2170:
2171: for(i=1; i<= nlstate; i++){
2172: s1=0;
1.131 brouard 2173: for(j=1; j<i; j++){
1.138 brouard 2174: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 2175: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2176: }
2177: for(j=i+1; j<=nlstate+ndeath; j++){
1.138 brouard 2178: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 2179: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2180: }
1.138 brouard 2181: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1.126 brouard 2182: ps[i][i]=1./(s1+1.);
1.138 brouard 2183: /* Computing other pijs */
1.126 brouard 2184: for(j=1; j<i; j++)
2185: ps[i][j]= exp(ps[i][j])*ps[i][i];
2186: for(j=i+1; j<=nlstate+ndeath; j++)
2187: ps[i][j]= exp(ps[i][j])*ps[i][i];
2188: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2189: } /* end i */
2190:
2191: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2192: for(jj=1; jj<= nlstate+ndeath; jj++){
2193: ps[ii][jj]=0;
2194: ps[ii][ii]=1;
2195: }
2196: }
2197:
1.145 brouard 2198:
2199: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2200: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2201: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2202: /* } */
2203: /* printf("\n "); */
2204: /* } */
2205: /* printf("\n ");printf("%lf ",cov[2]);*/
2206: /*
1.126 brouard 2207: for(i=1; i<= npar; i++) printf("%f ",x[i]);
2208: goto end;*/
2209: return ps;
2210: }
2211:
2212: /**************** Product of 2 matrices ******************/
2213:
1.145 brouard 2214: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 2215: {
2216: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
2217: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
2218: /* in, b, out are matrice of pointers which should have been initialized
2219: before: only the contents of out is modified. The function returns
2220: a pointer to pointers identical to out */
1.145 brouard 2221: int i, j, k;
1.126 brouard 2222: for(i=nrl; i<= nrh; i++)
1.145 brouard 2223: for(k=ncolol; k<=ncoloh; k++){
2224: out[i][k]=0.;
2225: for(j=ncl; j<=nch; j++)
2226: out[i][k] +=in[i][j]*b[j][k];
2227: }
1.126 brouard 2228: return out;
2229: }
2230:
2231:
2232: /************* Higher Matrix Product ***************/
2233:
2234: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
2235: {
2236: /* Computes the transition matrix starting at age 'age' over
2237: 'nhstepm*hstepm*stepm' months (i.e. until
2238: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2239: nhstepm*hstepm matrices.
2240: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2241: (typically every 2 years instead of every month which is too big
2242: for the memory).
2243: Model is determined by parameters x and covariates have to be
2244: included manually here.
2245:
2246: */
2247:
2248: int i, j, d, h, k;
1.131 brouard 2249: double **out, cov[NCOVMAX+1];
1.126 brouard 2250: double **newm;
1.187 brouard 2251: double agexact;
1.214 ! brouard 2252: double agebegin, ageend;
1.126 brouard 2253:
2254: /* Hstepm could be zero and should return the unit matrix */
2255: for (i=1;i<=nlstate+ndeath;i++)
2256: for (j=1;j<=nlstate+ndeath;j++){
2257: oldm[i][j]=(i==j ? 1.0 : 0.0);
2258: po[i][j][0]=(i==j ? 1.0 : 0.0);
2259: }
2260: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2261: for(h=1; h <=nhstepm; h++){
2262: for(d=1; d <=hstepm; d++){
2263: newm=savm;
2264: /* Covariates have to be included here again */
2265: cov[1]=1.;
1.214 ! brouard 2266: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
1.187 brouard 2267: cov[2]=agexact;
2268: if(nagesqr==1)
2269: cov[3]= agexact*agexact;
1.131 brouard 2270: for (k=1; k<=cptcovn;k++)
1.200 brouard 2271: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2272: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.186 brouard 2273: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
2274: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 2275: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2276: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
1.145 brouard 2277: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.200 brouard 2278: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
2279: /* 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 2280:
2281:
2282: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2283: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
2284: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
2285: pmij(pmmij,cov,ncovmodel,x,nlstate));
2286: savm=oldm;
2287: oldm=newm;
2288: }
2289: for(i=1; i<=nlstate+ndeath; i++)
2290: for(j=1;j<=nlstate+ndeath;j++) {
2291: po[i][j][h]=newm[i][j];
1.128 brouard 2292: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 2293: }
1.128 brouard 2294: /*printf("h=%d ",h);*/
1.126 brouard 2295: } /* end h */
1.128 brouard 2296: /* printf("\n H=%d \n",h); */
1.126 brouard 2297: return po;
2298: }
2299:
1.162 brouard 2300: #ifdef NLOPT
2301: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
2302: double fret;
2303: double *xt;
2304: int j;
2305: myfunc_data *d2 = (myfunc_data *) pd;
2306: /* xt = (p1-1); */
2307: xt=vector(1,n);
2308: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
2309:
2310: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
2311: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
2312: printf("Function = %.12lf ",fret);
2313: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
2314: printf("\n");
2315: free_vector(xt,1,n);
2316: return fret;
2317: }
2318: #endif
1.126 brouard 2319:
2320: /*************** log-likelihood *************/
2321: double func( double *x)
2322: {
2323: int i, ii, j, k, mi, d, kk;
1.131 brouard 2324: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2325: double **out;
2326: double sw; /* Sum of weights */
2327: double lli; /* Individual log likelihood */
2328: int s1, s2;
2329: double bbh, survp;
2330: long ipmx;
1.187 brouard 2331: double agexact;
1.126 brouard 2332: /*extern weight */
2333: /* We are differentiating ll according to initial status */
2334: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2335: /*for(i=1;i<imx;i++)
2336: printf(" %d\n",s[4][i]);
2337: */
1.162 brouard 2338:
2339: ++countcallfunc;
2340:
1.126 brouard 2341: cov[1]=1.;
2342:
2343: for(k=1; k<=nlstate; k++) ll[k]=0.;
2344:
2345: if(mle==1){
2346: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.138 brouard 2347: /* Computes the values of the ncovmodel covariates of the model
2348: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
2349: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
2350: to be observed in j being in i according to the model.
2351: */
1.145 brouard 2352: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1.187 brouard 2353: cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.145 brouard 2354: }
1.137 brouard 2355: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1.138 brouard 2356: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1.137 brouard 2357: has been calculated etc */
1.126 brouard 2358: for(mi=1; mi<= wav[i]-1; mi++){
2359: for (ii=1;ii<=nlstate+ndeath;ii++)
2360: for (j=1;j<=nlstate+ndeath;j++){
2361: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2362: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2363: }
2364: for(d=0; d<dh[mi][i]; d++){
2365: newm=savm;
1.187 brouard 2366: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2367: cov[2]=agexact;
2368: if(nagesqr==1)
2369: cov[3]= agexact*agexact;
1.126 brouard 2370: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2371: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
1.126 brouard 2372: }
2373: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2374: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2375: savm=oldm;
2376: oldm=newm;
2377: } /* end mult */
2378:
2379: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
2380: /* But now since version 0.9 we anticipate for bias at large stepm.
2381: * If stepm is larger than one month (smallest stepm) and if the exact delay
2382: * (in months) between two waves is not a multiple of stepm, we rounded to
2383: * the nearest (and in case of equal distance, to the lowest) interval but now
2384: * we keep into memory the bias bh[mi][i] and also the previous matrix product
2385: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
2386: * probability in order to take into account the bias as a fraction of the way
2387: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
2388: * -stepm/2 to stepm/2 .
2389: * For stepm=1 the results are the same as for previous versions of Imach.
2390: * For stepm > 1 the results are less biased than in previous versions.
2391: */
2392: s1=s[mw[mi][i]][i];
2393: s2=s[mw[mi+1][i]][i];
2394: bbh=(double)bh[mi][i]/(double)stepm;
2395: /* bias bh is positive if real duration
2396: * is higher than the multiple of stepm and negative otherwise.
2397: */
2398: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
2399: if( s2 > nlstate){
2400: /* i.e. if s2 is a death state and if the date of death is known
2401: then the contribution to the likelihood is the probability to
2402: die between last step unit time and current step unit time,
2403: which is also equal to probability to die before dh
2404: minus probability to die before dh-stepm .
2405: In version up to 0.92 likelihood was computed
2406: as if date of death was unknown. Death was treated as any other
2407: health state: the date of the interview describes the actual state
2408: and not the date of a change in health state. The former idea was
2409: to consider that at each interview the state was recorded
2410: (healthy, disable or death) and IMaCh was corrected; but when we
2411: introduced the exact date of death then we should have modified
2412: the contribution of an exact death to the likelihood. This new
2413: contribution is smaller and very dependent of the step unit
2414: stepm. It is no more the probability to die between last interview
2415: and month of death but the probability to survive from last
2416: interview up to one month before death multiplied by the
2417: probability to die within a month. Thanks to Chris
2418: Jackson for correcting this bug. Former versions increased
2419: mortality artificially. The bad side is that we add another loop
2420: which slows down the processing. The difference can be up to 10%
2421: lower mortality.
2422: */
1.183 brouard 2423: /* If, at the beginning of the maximization mostly, the
2424: cumulative probability or probability to be dead is
2425: constant (ie = 1) over time d, the difference is equal to
2426: 0. out[s1][3] = savm[s1][3]: probability, being at state
2427: s1 at precedent wave, to be dead a month before current
2428: wave is equal to probability, being at state s1 at
2429: precedent wave, to be dead at mont of the current
2430: wave. Then the observed probability (that this person died)
2431: is null according to current estimated parameter. In fact,
2432: it should be very low but not zero otherwise the log go to
2433: infinity.
2434: */
2435: /* #ifdef INFINITYORIGINAL */
2436: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2437: /* #else */
2438: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
2439: /* lli=log(mytinydouble); */
2440: /* else */
2441: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2442: /* #endif */
2443: lli=log(out[s1][s2] - savm[s1][s2]);
1.126 brouard 2444:
2445: } else if (s2==-2) {
2446: for (j=1,survp=0. ; j<=nlstate; j++)
2447: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2448: /*survp += out[s1][j]; */
2449: lli= log(survp);
2450: }
2451:
2452: else if (s2==-4) {
2453: for (j=3,survp=0. ; j<=nlstate; j++)
2454: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2455: lli= log(survp);
2456: }
2457:
2458: else if (s2==-5) {
2459: for (j=1,survp=0. ; j<=2; j++)
2460: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2461: lli= log(survp);
2462: }
2463:
2464: else{
2465: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2466: /* 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 */
2467: }
2468: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
2469: /*if(lli ==000.0)*/
2470: /*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); */
2471: ipmx +=1;
2472: sw += weight[i];
2473: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.183 brouard 2474: /* if (lli < log(mytinydouble)){ */
2475: /* 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); */
2476: /* 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]); */
2477: /* } */
1.126 brouard 2478: } /* end of wave */
2479: } /* end of individual */
2480: } else if(mle==2){
2481: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2482: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2483: for(mi=1; mi<= wav[i]-1; mi++){
2484: for (ii=1;ii<=nlstate+ndeath;ii++)
2485: for (j=1;j<=nlstate+ndeath;j++){
2486: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2487: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2488: }
2489: for(d=0; d<=dh[mi][i]; d++){
2490: newm=savm;
1.187 brouard 2491: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2492: cov[2]=agexact;
2493: if(nagesqr==1)
2494: cov[3]= agexact*agexact;
1.126 brouard 2495: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2496: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2497: }
2498: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2499: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2500: savm=oldm;
2501: oldm=newm;
2502: } /* end mult */
2503:
2504: s1=s[mw[mi][i]][i];
2505: s2=s[mw[mi+1][i]][i];
2506: bbh=(double)bh[mi][i]/(double)stepm;
2507: 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 */
2508: ipmx +=1;
2509: sw += weight[i];
2510: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2511: } /* end of wave */
2512: } /* end of individual */
2513: } else if(mle==3){ /* exponential inter-extrapolation */
2514: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2515: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2516: for(mi=1; mi<= wav[i]-1; mi++){
2517: for (ii=1;ii<=nlstate+ndeath;ii++)
2518: for (j=1;j<=nlstate+ndeath;j++){
2519: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2520: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2521: }
2522: for(d=0; d<dh[mi][i]; d++){
2523: newm=savm;
1.187 brouard 2524: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2525: cov[2]=agexact;
2526: if(nagesqr==1)
2527: cov[3]= agexact*agexact;
1.126 brouard 2528: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2529: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2530: }
2531: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2532: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2533: savm=oldm;
2534: oldm=newm;
2535: } /* end mult */
2536:
2537: s1=s[mw[mi][i]][i];
2538: s2=s[mw[mi+1][i]][i];
2539: bbh=(double)bh[mi][i]/(double)stepm;
2540: 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 */
2541: ipmx +=1;
2542: sw += weight[i];
2543: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2544: } /* end of wave */
2545: } /* end of individual */
2546: }else if (mle==4){ /* ml=4 no inter-extrapolation */
2547: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2548: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2549: for(mi=1; mi<= wav[i]-1; mi++){
2550: for (ii=1;ii<=nlstate+ndeath;ii++)
2551: for (j=1;j<=nlstate+ndeath;j++){
2552: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2553: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2554: }
2555: for(d=0; d<dh[mi][i]; d++){
2556: newm=savm;
1.187 brouard 2557: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2558: cov[2]=agexact;
2559: if(nagesqr==1)
2560: cov[3]= agexact*agexact;
1.126 brouard 2561: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2562: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2563: }
2564:
2565: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2566: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2567: savm=oldm;
2568: oldm=newm;
2569: } /* end mult */
2570:
2571: s1=s[mw[mi][i]][i];
2572: s2=s[mw[mi+1][i]][i];
2573: if( s2 > nlstate){
2574: lli=log(out[s1][s2] - savm[s1][s2]);
2575: }else{
2576: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2577: }
2578: ipmx +=1;
2579: sw += weight[i];
2580: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2581: /* 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]); */
2582: } /* end of wave */
2583: } /* end of individual */
2584: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
2585: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2586: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2587: for(mi=1; mi<= wav[i]-1; mi++){
2588: for (ii=1;ii<=nlstate+ndeath;ii++)
2589: for (j=1;j<=nlstate+ndeath;j++){
2590: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2591: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2592: }
2593: for(d=0; d<dh[mi][i]; d++){
2594: newm=savm;
1.187 brouard 2595: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2596: cov[2]=agexact;
2597: if(nagesqr==1)
2598: cov[3]= agexact*agexact;
1.126 brouard 2599: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2600: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2601: }
2602:
2603: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2604: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2605: savm=oldm;
2606: oldm=newm;
2607: } /* end mult */
2608:
2609: s1=s[mw[mi][i]][i];
2610: s2=s[mw[mi+1][i]][i];
2611: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2612: ipmx +=1;
2613: sw += weight[i];
2614: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2615: /*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]);*/
2616: } /* end of wave */
2617: } /* end of individual */
2618: } /* End of if */
2619: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2620: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2621: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2622: return -l;
2623: }
2624:
2625: /*************** log-likelihood *************/
2626: double funcone( double *x)
2627: {
2628: /* Same as likeli but slower because of a lot of printf and if */
2629: int i, ii, j, k, mi, d, kk;
1.131 brouard 2630: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2631: double **out;
2632: double lli; /* Individual log likelihood */
2633: double llt;
2634: int s1, s2;
2635: double bbh, survp;
1.187 brouard 2636: double agexact;
1.214 ! brouard 2637: double agebegin, ageend;
1.126 brouard 2638: /*extern weight */
2639: /* We are differentiating ll according to initial status */
2640: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2641: /*for(i=1;i<imx;i++)
2642: printf(" %d\n",s[4][i]);
2643: */
2644: cov[1]=1.;
2645:
2646: for(k=1; k<=nlstate; k++) ll[k]=0.;
2647:
2648: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2649: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2650: for(mi=1; mi<= wav[i]-1; mi++){
2651: for (ii=1;ii<=nlstate+ndeath;ii++)
2652: for (j=1;j<=nlstate+ndeath;j++){
2653: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2654: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2655: }
1.214 ! brouard 2656:
! 2657: agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
! 2658: ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
! 2659: for(d=0; d<dh[mi][i]; d++){ /* Delay between two effective waves */
! 2660: /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
! 2661: and mw[mi+1][i]. dh depends on stepm.*/
1.126 brouard 2662: newm=savm;
1.187 brouard 2663: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2664: cov[2]=agexact;
2665: if(nagesqr==1)
2666: cov[3]= agexact*agexact;
1.126 brouard 2667: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2668: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2669: }
1.187 brouard 2670:
1.145 brouard 2671: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.126 brouard 2672: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2673: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1.145 brouard 2674: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2675: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
1.126 brouard 2676: savm=oldm;
2677: oldm=newm;
2678: } /* end mult */
2679:
2680: s1=s[mw[mi][i]][i];
2681: s2=s[mw[mi+1][i]][i];
2682: bbh=(double)bh[mi][i]/(double)stepm;
2683: /* bias is positive if real duration
2684: * is higher than the multiple of stepm and negative otherwise.
2685: */
2686: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2687: lli=log(out[s1][s2] - savm[s1][s2]);
2688: } else if (s2==-2) {
2689: for (j=1,survp=0. ; j<=nlstate; j++)
2690: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2691: lli= log(survp);
2692: }else if (mle==1){
2693: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2694: } else if(mle==2){
2695: 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 */
2696: } else if(mle==3){ /* exponential inter-extrapolation */
2697: 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 */
2698: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2699: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 2700: } else{ /* mle=0 back to 1 */
2701: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2702: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 2703: } /* End of if */
2704: ipmx +=1;
2705: sw += weight[i];
2706: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 2707: /*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 2708: if(globpr){
1.214 ! brouard 2709: fprintf(ficresilk,"%9ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %11.6f %8.4f %8.3f\
1.126 brouard 2710: %11.6f %11.6f %11.6f ", \
1.214 ! brouard 2711: num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
1.126 brouard 2712: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2713: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2714: llt +=ll[k]*gipmx/gsw;
2715: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2716: }
2717: fprintf(ficresilk," %10.6f\n", -llt);
2718: }
2719: } /* end of wave */
2720: } /* end of individual */
2721: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2722: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2723: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2724: if(globpr==0){ /* First time we count the contributions and weights */
2725: gipmx=ipmx;
2726: gsw=sw;
2727: }
2728: return -l;
2729: }
2730:
2731:
2732: /*************** function likelione ***********/
2733: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2734: {
2735: /* This routine should help understanding what is done with
2736: the selection of individuals/waves and
2737: to check the exact contribution to the likelihood.
2738: Plotting could be done.
2739: */
2740: int k;
2741:
2742: if(*globpri !=0){ /* Just counts and sums, no printings */
1.201 brouard 2743: strcpy(fileresilk,"ILK_");
1.202 brouard 2744: strcat(fileresilk,fileresu);
1.126 brouard 2745: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2746: printf("Problem with resultfile: %s\n", fileresilk);
2747: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2748: }
1.214 ! brouard 2749: fprintf(ficresilk, "#individual(line's_record) count ageb ageend 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");
! 2750: fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
1.126 brouard 2751: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2752: for(k=1; k<=nlstate; k++)
2753: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2754: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2755: }
2756:
2757: *fretone=(*funcone)(p);
2758: if(*globpri !=0){
2759: fclose(ficresilk);
1.205 brouard 2760: if (mle ==0)
2761: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
2762: else if(mle >=1)
2763: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
2764: 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 2765:
1.208 brouard 2766:
2767: for (k=1; k<= nlstate ; k++) {
1.211 brouard 2768: fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j. Dot's sizes are related to corresponding weight: <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \
1.208 brouard 2769: <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
2770: }
1.207 brouard 2771: 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 2772: <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 2773: fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
1.204 brouard 2774: <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 2775: fflush(fichtm);
1.205 brouard 2776: }
1.126 brouard 2777: return;
2778: }
2779:
2780:
2781: /*********** Maximum Likelihood Estimation ***************/
2782:
2783: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2784: {
1.165 brouard 2785: int i,j, iter=0;
1.126 brouard 2786: double **xi;
2787: double fret;
2788: double fretone; /* Only one call to likelihood */
2789: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 2790:
2791: #ifdef NLOPT
2792: int creturn;
2793: nlopt_opt opt;
2794: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2795: double *lb;
2796: double minf; /* the minimum objective value, upon return */
2797: double * p1; /* Shifted parameters from 0 instead of 1 */
2798: myfunc_data dinst, *d = &dinst;
2799: #endif
2800:
2801:
1.126 brouard 2802: xi=matrix(1,npar,1,npar);
2803: for (i=1;i<=npar;i++)
2804: for (j=1;j<=npar;j++)
2805: xi[i][j]=(i==j ? 1.0 : 0.0);
2806: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.201 brouard 2807: strcpy(filerespow,"POW_");
1.126 brouard 2808: strcat(filerespow,fileres);
2809: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2810: printf("Problem with resultfile: %s\n", filerespow);
2811: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2812: }
2813: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2814: for (i=1;i<=nlstate;i++)
2815: for(j=1;j<=nlstate+ndeath;j++)
2816: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2817: fprintf(ficrespow,"\n");
1.162 brouard 2818: #ifdef POWELL
1.126 brouard 2819: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 2820: #endif
1.126 brouard 2821:
1.162 brouard 2822: #ifdef NLOPT
2823: #ifdef NEWUOA
2824: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2825: #else
2826: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2827: #endif
2828: lb=vector(0,npar-1);
2829: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2830: nlopt_set_lower_bounds(opt, lb);
2831: nlopt_set_initial_step1(opt, 0.1);
2832:
2833: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2834: d->function = func;
2835: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2836: nlopt_set_min_objective(opt, myfunc, d);
2837: nlopt_set_xtol_rel(opt, ftol);
2838: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2839: printf("nlopt failed! %d\n",creturn);
2840: }
2841: else {
2842: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2843: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2844: iter=1; /* not equal */
2845: }
2846: nlopt_destroy(opt);
2847: #endif
1.126 brouard 2848: free_matrix(xi,1,npar,1,npar);
2849: fclose(ficrespow);
1.203 brouard 2850: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2851: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.180 brouard 2852: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 2853:
2854: }
2855:
2856: /**** Computes Hessian and covariance matrix ***/
1.203 brouard 2857: void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1.126 brouard 2858: {
2859: double **a,**y,*x,pd;
1.203 brouard 2860: /* double **hess; */
1.164 brouard 2861: int i, j;
1.126 brouard 2862: int *indx;
2863:
2864: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1.203 brouard 2865: double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
1.126 brouard 2866: void lubksb(double **a, int npar, int *indx, double b[]) ;
2867: void ludcmp(double **a, int npar, int *indx, double *d) ;
2868: double gompertz(double p[]);
1.203 brouard 2869: /* hess=matrix(1,npar,1,npar); */
1.126 brouard 2870:
2871: printf("\nCalculation of the hessian matrix. Wait...\n");
2872: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2873: for (i=1;i<=npar;i++){
1.203 brouard 2874: printf("%d-",i);fflush(stdout);
2875: fprintf(ficlog,"%d-",i);fflush(ficlog);
1.126 brouard 2876:
2877: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2878:
2879: /* printf(" %f ",p[i]);
2880: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2881: }
2882:
2883: for (i=1;i<=npar;i++) {
2884: for (j=1;j<=npar;j++) {
2885: if (j>i) {
1.203 brouard 2886: printf(".%d-%d",i,j);fflush(stdout);
2887: fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
2888: hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
1.126 brouard 2889:
2890: hess[j][i]=hess[i][j];
2891: /*printf(" %lf ",hess[i][j]);*/
2892: }
2893: }
2894: }
2895: printf("\n");
2896: fprintf(ficlog,"\n");
2897:
2898: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2899: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2900:
2901: a=matrix(1,npar,1,npar);
2902: y=matrix(1,npar,1,npar);
2903: x=vector(1,npar);
2904: indx=ivector(1,npar);
2905: for (i=1;i<=npar;i++)
2906: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2907: ludcmp(a,npar,indx,&pd);
2908:
2909: for (j=1;j<=npar;j++) {
2910: for (i=1;i<=npar;i++) x[i]=0;
2911: x[j]=1;
2912: lubksb(a,npar,indx,x);
2913: for (i=1;i<=npar;i++){
2914: matcov[i][j]=x[i];
2915: }
2916: }
2917:
2918: printf("\n#Hessian matrix#\n");
2919: fprintf(ficlog,"\n#Hessian matrix#\n");
2920: for (i=1;i<=npar;i++) {
2921: for (j=1;j<=npar;j++) {
1.203 brouard 2922: printf("%.6e ",hess[i][j]);
2923: fprintf(ficlog,"%.6e ",hess[i][j]);
1.126 brouard 2924: }
2925: printf("\n");
2926: fprintf(ficlog,"\n");
2927: }
2928:
1.203 brouard 2929: /* printf("\n#Covariance matrix#\n"); */
2930: /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
2931: /* for (i=1;i<=npar;i++) { */
2932: /* for (j=1;j<=npar;j++) { */
2933: /* printf("%.6e ",matcov[i][j]); */
2934: /* fprintf(ficlog,"%.6e ",matcov[i][j]); */
2935: /* } */
2936: /* printf("\n"); */
2937: /* fprintf(ficlog,"\n"); */
2938: /* } */
2939:
1.126 brouard 2940: /* Recompute Inverse */
1.203 brouard 2941: /* for (i=1;i<=npar;i++) */
2942: /* for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
2943: /* ludcmp(a,npar,indx,&pd); */
2944:
2945: /* printf("\n#Hessian matrix recomputed#\n"); */
2946:
2947: /* for (j=1;j<=npar;j++) { */
2948: /* for (i=1;i<=npar;i++) x[i]=0; */
2949: /* x[j]=1; */
2950: /* lubksb(a,npar,indx,x); */
2951: /* for (i=1;i<=npar;i++){ */
2952: /* y[i][j]=x[i]; */
2953: /* printf("%.3e ",y[i][j]); */
2954: /* fprintf(ficlog,"%.3e ",y[i][j]); */
2955: /* } */
2956: /* printf("\n"); */
2957: /* fprintf(ficlog,"\n"); */
2958: /* } */
2959:
2960: /* Verifying the inverse matrix */
2961: #ifdef DEBUGHESS
2962: y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
1.126 brouard 2963:
1.203 brouard 2964: printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
2965: fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
1.126 brouard 2966:
2967: for (j=1;j<=npar;j++) {
2968: for (i=1;i<=npar;i++){
1.203 brouard 2969: printf("%.2f ",y[i][j]);
2970: fprintf(ficlog,"%.2f ",y[i][j]);
1.126 brouard 2971: }
2972: printf("\n");
2973: fprintf(ficlog,"\n");
2974: }
1.203 brouard 2975: #endif
1.126 brouard 2976:
2977: free_matrix(a,1,npar,1,npar);
2978: free_matrix(y,1,npar,1,npar);
2979: free_vector(x,1,npar);
2980: free_ivector(indx,1,npar);
1.203 brouard 2981: /* free_matrix(hess,1,npar,1,npar); */
1.126 brouard 2982:
2983:
2984: }
2985:
2986: /*************** hessian matrix ****************/
2987: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.203 brouard 2988: { /* Around values of x, computes the function func and returns the scales delti and hessian */
1.126 brouard 2989: int i;
2990: int l=1, lmax=20;
1.203 brouard 2991: double k1,k2, res, fx;
1.132 brouard 2992: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 2993: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2994: int k=0,kmax=10;
2995: double l1;
2996:
2997: fx=func(x);
2998: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 2999: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 3000: l1=pow(10,l);
3001: delts=delt;
3002: for(k=1 ; k <kmax; k=k+1){
3003: delt = delta*(l1*k);
3004: p2[theta]=x[theta] +delt;
1.145 brouard 3005: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 3006: p2[theta]=x[theta]-delt;
3007: k2=func(p2)-fx;
3008: /*res= (k1-2.0*fx+k2)/delt/delt; */
1.203 brouard 3009: res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
1.126 brouard 3010:
1.203 brouard 3011: #ifdef DEBUGHESSII
1.126 brouard 3012: 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);
3013: 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);
3014: #endif
3015: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
3016: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
3017: k=kmax;
3018: }
3019: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 3020: k=kmax; l=lmax*10;
1.126 brouard 3021: }
3022: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
3023: delts=delt;
3024: }
1.203 brouard 3025: } /* End loop k */
1.126 brouard 3026: }
3027: delti[theta]=delts;
3028: return res;
3029:
3030: }
3031:
1.203 brouard 3032: double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.126 brouard 3033: {
3034: int i;
1.164 brouard 3035: int l=1, lmax=20;
1.126 brouard 3036: double k1,k2,k3,k4,res,fx;
1.132 brouard 3037: double p2[MAXPARM+1];
1.203 brouard 3038: int k, kmax=1;
3039: double v1, v2, cv12, lc1, lc2;
1.208 brouard 3040:
3041: int firstime=0;
1.203 brouard 3042:
1.126 brouard 3043: fx=func(x);
1.203 brouard 3044: for (k=1; k<=kmax; k=k+10) {
1.126 brouard 3045: for (i=1;i<=npar;i++) p2[i]=x[i];
1.203 brouard 3046: p2[thetai]=x[thetai]+delti[thetai]*k;
3047: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 3048: k1=func(p2)-fx;
3049:
1.203 brouard 3050: p2[thetai]=x[thetai]+delti[thetai]*k;
3051: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 3052: k2=func(p2)-fx;
3053:
1.203 brouard 3054: p2[thetai]=x[thetai]-delti[thetai]*k;
3055: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 3056: k3=func(p2)-fx;
3057:
1.203 brouard 3058: p2[thetai]=x[thetai]-delti[thetai]*k;
3059: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 3060: k4=func(p2)-fx;
1.203 brouard 3061: res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
3062: if(k1*k2*k3*k4 <0.){
1.208 brouard 3063: firstime=1;
1.203 brouard 3064: kmax=kmax+10;
1.208 brouard 3065: }
3066: if(kmax >=10 || firstime ==1){
1.203 brouard 3067: printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol);
3068: fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol);
3069: 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);
3070: 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);
3071: }
3072: #ifdef DEBUGHESSIJ
3073: v1=hess[thetai][thetai];
3074: v2=hess[thetaj][thetaj];
3075: cv12=res;
3076: /* Computing eigen value of Hessian matrix */
3077: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3078: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3079: if ((lc2 <0) || (lc1 <0) ){
3080: printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
3081: fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
3082: 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);
3083: 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);
3084: }
1.126 brouard 3085: #endif
3086: }
3087: return res;
3088: }
3089:
1.203 brouard 3090: /* Not done yet: Was supposed to fix if not exactly at the maximum */
3091: /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
3092: /* { */
3093: /* int i; */
3094: /* int l=1, lmax=20; */
3095: /* double k1,k2,k3,k4,res,fx; */
3096: /* double p2[MAXPARM+1]; */
3097: /* double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
3098: /* int k=0,kmax=10; */
3099: /* double l1; */
3100:
3101: /* fx=func(x); */
3102: /* for(l=0 ; l <=lmax; l++){ /\* Enlarging the zone around the Maximum *\/ */
3103: /* l1=pow(10,l); */
3104: /* delts=delt; */
3105: /* for(k=1 ; k <kmax; k=k+1){ */
3106: /* delt = delti*(l1*k); */
3107: /* for (i=1;i<=npar;i++) p2[i]=x[i]; */
3108: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3109: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3110: /* k1=func(p2)-fx; */
3111:
3112: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3113: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3114: /* k2=func(p2)-fx; */
3115:
3116: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3117: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3118: /* k3=func(p2)-fx; */
3119:
3120: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3121: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3122: /* k4=func(p2)-fx; */
3123: /* res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
3124: /* #ifdef DEBUGHESSIJ */
3125: /* 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); */
3126: /* 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); */
3127: /* #endif */
3128: /* if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
3129: /* k=kmax; */
3130: /* } */
3131: /* else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
3132: /* k=kmax; l=lmax*10; */
3133: /* } */
3134: /* else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ */
3135: /* delts=delt; */
3136: /* } */
3137: /* } /\* End loop k *\/ */
3138: /* } */
3139: /* delti[theta]=delts; */
3140: /* return res; */
3141: /* } */
3142:
3143:
1.126 brouard 3144: /************** Inverse of matrix **************/
3145: void ludcmp(double **a, int n, int *indx, double *d)
3146: {
3147: int i,imax,j,k;
3148: double big,dum,sum,temp;
3149: double *vv;
3150:
3151: vv=vector(1,n);
3152: *d=1.0;
3153: for (i=1;i<=n;i++) {
3154: big=0.0;
3155: for (j=1;j<=n;j++)
3156: if ((temp=fabs(a[i][j])) > big) big=temp;
3157: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
3158: vv[i]=1.0/big;
3159: }
3160: for (j=1;j<=n;j++) {
3161: for (i=1;i<j;i++) {
3162: sum=a[i][j];
3163: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
3164: a[i][j]=sum;
3165: }
3166: big=0.0;
3167: for (i=j;i<=n;i++) {
3168: sum=a[i][j];
3169: for (k=1;k<j;k++)
3170: sum -= a[i][k]*a[k][j];
3171: a[i][j]=sum;
3172: if ( (dum=vv[i]*fabs(sum)) >= big) {
3173: big=dum;
3174: imax=i;
3175: }
3176: }
3177: if (j != imax) {
3178: for (k=1;k<=n;k++) {
3179: dum=a[imax][k];
3180: a[imax][k]=a[j][k];
3181: a[j][k]=dum;
3182: }
3183: *d = -(*d);
3184: vv[imax]=vv[j];
3185: }
3186: indx[j]=imax;
3187: if (a[j][j] == 0.0) a[j][j]=TINY;
3188: if (j != n) {
3189: dum=1.0/(a[j][j]);
3190: for (i=j+1;i<=n;i++) a[i][j] *= dum;
3191: }
3192: }
3193: free_vector(vv,1,n); /* Doesn't work */
3194: ;
3195: }
3196:
3197: void lubksb(double **a, int n, int *indx, double b[])
3198: {
3199: int i,ii=0,ip,j;
3200: double sum;
3201:
3202: for (i=1;i<=n;i++) {
3203: ip=indx[i];
3204: sum=b[ip];
3205: b[ip]=b[i];
3206: if (ii)
3207: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
3208: else if (sum) ii=i;
3209: b[i]=sum;
3210: }
3211: for (i=n;i>=1;i--) {
3212: sum=b[i];
3213: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
3214: b[i]=sum/a[i][i];
3215: }
3216: }
3217:
3218: void pstamp(FILE *fichier)
3219: {
1.196 brouard 3220: fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126 brouard 3221: }
3222:
3223: /************ Frequencies ********************/
1.214 ! brouard 3224: void freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
! 3225: int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[],\
! 3226: int firstpass, int lastpass, int stepm, int weightopt, char model[])
1.126 brouard 3227: { /* Some frequencies */
3228:
1.164 brouard 3229: int i, m, jk, j1, bool, z1,j;
1.214 ! brouard 3230: int mi; /* Effective wave */
1.126 brouard 3231: int first;
3232: double ***freq; /* Frequencies */
3233: double *pp, **prop;
3234: double pos,posprop, k2, dateintsum=0,k2cpt=0;
1.214 ! brouard 3235: char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
! 3236: double agebegin, ageend;
! 3237:
1.126 brouard 3238: pp=vector(1,nlstate);
3239: prop=matrix(1,nlstate,iagemin,iagemax+3);
1.201 brouard 3240: strcpy(fileresp,"P_");
3241: strcat(fileresp,fileresu);
1.213 brouard 3242: /*strcat(fileresphtm,fileresu);*/
1.126 brouard 3243: if((ficresp=fopen(fileresp,"w"))==NULL) {
3244: printf("Problem with prevalence resultfile: %s\n", fileresp);
3245: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
3246: exit(0);
3247: }
1.214 ! brouard 3248:
1.213 brouard 3249: strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
3250: if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
3251: printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
3252: fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
3253: fflush(ficlog);
3254: exit(70);
3255: }
1.214 ! brouard 3256: else{
! 3257: fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
! 3258: <hr size=\"2\" color=\"#EC5E5E\"> \n\
! 3259: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
! 3260: fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
! 3261: }
! 3262: fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies and prevalence by age at begin of transition</h4>\n",fileresphtm, fileresphtm);
! 3263:
! 3264: strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
! 3265: if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
! 3266: printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
! 3267: fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
! 3268: fflush(ficlog);
! 3269: exit(70);
! 3270: }
! 3271: else{
! 3272: fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
! 3273: <hr size=\"2\" color=\"#EC5E5E\"> \n\
! 3274: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
! 3275: fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
! 3276: }
! 3277: fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies of all effective transitions by age at begin of transition </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr);
! 3278:
1.126 brouard 3279: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
3280: j1=0;
3281:
3282: j=cptcoveff;
3283: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3284:
3285: first=1;
3286:
1.214 ! brouard 3287: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){ /* Loop on covariates combination */
1.126 brouard 3288: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
3289: scanf("%d", i);*/
3290: for (i=-5; i<=nlstate+ndeath; i++)
3291: for (jk=-5; jk<=nlstate+ndeath; jk++)
3292: for(m=iagemin; m <= iagemax+3; m++)
3293: freq[i][jk][m]=0;
1.143 brouard 3294:
3295: for (i=1; i<=nlstate; i++)
3296: for(m=iagemin; m <= iagemax+3; m++)
3297: prop[i][m]=0;
1.126 brouard 3298:
3299: dateintsum=0;
3300: k2cpt=0;
1.214 ! brouard 3301: for (i=1; i<=imx; i++) { /* For each individual i */
1.126 brouard 3302: bool=1;
1.210 brouard 3303: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
1.144 brouard 3304: for (z1=1; z1<=cptcoveff; z1++)
1.198 brouard 3305: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
1.145 brouard 3306: /* Tests if the value of each of the covariates of i is equal to filter j1 */
1.144 brouard 3307: bool=0;
1.198 brouard 3308: /* 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",
3309: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
3310: j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
3311: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
1.144 brouard 3312: }
1.210 brouard 3313: } /* cptcovn > 0 */
1.214 ! brouard 3314:
1.126 brouard 3315: if (bool==1){
1.214 ! brouard 3316: /* for(m=firstpass; m<=lastpass; m++){ */
! 3317: for(mi=1; mi<wav[i];mi++){
! 3318: m=mw[mi][i];
! 3319: /* dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective (mi) waves m=mw[mi][i]
! 3320: and mw[mi+1][i]. dh depends on stepm. */
! 3321: agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
! 3322: ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /* Age at end of wave and transition */
! 3323: if(m >=firstpass && m <=lastpass){
! 3324: k2=anint[m][i]+(mint[m][i]/12.);
! 3325: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
! 3326: if(agev[m][i]==0) agev[m][i]=iagemax+1; /* All ages equal to 0 are in iagemax+1 */
! 3327: if(agev[m][i]==1) agev[m][i]=iagemax+2; /* All ages equal to 1 are in iagemax+2 */
! 3328: if (s[m][i]>0 && s[m][i]<=nlstate) /* If status at wave m is known and a live state */
! 3329: prop[s[m][i]][(int)agev[m][i]] += weight[i]; /* At age of beginning of transition, where status is known */
1.126 brouard 3330: if (m<lastpass) {
1.214 ! brouard 3331: /* if(s[m][i]==4 && s[m+1][i]==4) */
! 3332: /* printf(" num=%ld m=%d, i=%d s1=%d s2=%d agev at m=%d\n", num[i], m, i,s[m][i],s[m+1][i], (int)agev[m][i]); */
! 3333: if(s[m][i]==-1)
! 3334: printf(" num=%ld m=%d, i=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[i], m, i,s[m][i],s[m+1][i], (int)agev[m][i],agebegin, ageend, (int)((agebegin+ageend)/2.));
! 3335: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i]; /* At age of beginning of transition, where status is known */
! 3336: /* freq[s[m][i]][s[m+1][i]][(int)((agebegin+ageend)/2.)] += weight[i]; */
! 3337: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i]; /* Total is in iagemax+3 *//* At age of beginning of transition, where status is known */
1.126 brouard 3338: }
1.214 ! brouard 3339: }
! 3340: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3)) && (anint[m][i]!=9999) && (mint[m][i]!=99)) {
! 3341: dateintsum=dateintsum+k2;
! 3342: k2cpt++;
! 3343: /* printf("i=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",i, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
! 3344: }
! 3345: /*}*/
1.210 brouard 3346: } /* end m */
3347: } /* end bool */
3348: } /* end i = 1 to imx */
1.126 brouard 3349:
3350: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
3351: pstamp(ficresp);
3352: if (cptcovn>0) {
3353: fprintf(ficresp, "\n#********** Variable ");
1.214 ! brouard 3354: fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
! 3355: fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
1.213 brouard 3356: for (z1=1; z1<=cptcoveff; z1++){
3357: fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
3358: fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.214 ! brouard 3359: fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.213 brouard 3360: }
3361: fprintf(ficresp, "**********\n#");
1.214 ! brouard 3362: fprintf(ficresphtm, "**********</h3>\n");
! 3363: fprintf(ficresphtmfr, "**********</h3>\n");
1.143 brouard 3364: fprintf(ficlog, "\n#********** Variable ");
1.198 brouard 3365: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.214 ! brouard 3366: fprintf(ficlog, "**********\n");
1.126 brouard 3367: }
1.214 ! brouard 3368: fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
1.213 brouard 3369: for(i=1; i<=nlstate;i++) {
1.126 brouard 3370: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1.213 brouard 3371: fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
3372: }
1.126 brouard 3373: fprintf(ficresp, "\n");
1.213 brouard 3374: fprintf(ficresphtm, "\n");
1.126 brouard 3375:
1.214 ! brouard 3376: /* Header of frequency table by age */
! 3377: fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
! 3378: fprintf(ficresphtmfr,"<th>Age</th> ");
! 3379: for(jk=-1; jk <=nlstate+ndeath; jk++){
! 3380: for(m=-1; m <=nlstate+ndeath; m++){
! 3381: if(jk!=0 && m!=0)
! 3382: fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);
! 3383: }
! 3384: }
! 3385: fprintf(ficresphtmfr, "\n");
! 3386:
! 3387: /* For each age */
1.126 brouard 3388: for(i=iagemin; i <= iagemax+3; i++){
1.213 brouard 3389: fprintf(ficresphtm,"<tr>");
1.214 ! brouard 3390: if(i==iagemax+1){
! 3391: fprintf(ficlog,"1");
! 3392: fprintf(ficresphtmfr,"<tr><th>0</th> ");
! 3393: }else if(i==iagemax+2){
! 3394: fprintf(ficlog,"0");
! 3395: fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
! 3396: }else if(i==iagemax+3){
1.126 brouard 3397: fprintf(ficlog,"Total");
1.214 ! brouard 3398: fprintf(ficresphtmfr,"<tr><th>Total</th> ");
1.126 brouard 3399: }else{
3400: if(first==1){
3401: first=0;
3402: printf("See log file for details...\n");
3403: }
1.214 ! brouard 3404: fprintf(ficresphtmfr,"<tr><th>%d</th> ",i);
1.126 brouard 3405: fprintf(ficlog,"Age %d", i);
3406: }
3407: for(jk=1; jk <=nlstate ; jk++){
3408: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
3409: pp[jk] += freq[jk][m][i];
3410: }
3411: for(jk=1; jk <=nlstate ; jk++){
3412: for(m=-1, pos=0; m <=0 ; m++)
3413: pos += freq[jk][m][i];
3414: if(pp[jk]>=1.e-10){
3415: if(first==1){
1.132 brouard 3416: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1.126 brouard 3417: }
3418: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
3419: }else{
3420: if(first==1)
3421: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3422: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3423: }
3424: }
3425:
3426: for(jk=1; jk <=nlstate ; jk++){
3427: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
3428: pp[jk] += freq[jk][m][i];
3429: }
3430: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
3431: pos += pp[jk];
3432: posprop += prop[jk][i];
3433: }
3434: for(jk=1; jk <=nlstate ; jk++){
3435: if(pos>=1.e-5){
3436: if(first==1)
3437: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3438: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3439: }else{
3440: if(first==1)
3441: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3442: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3443: }
3444: if( i <= iagemax){
3445: if(pos>=1.e-5){
3446: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
1.213 brouard 3447: fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",i,prop[jk][i]/posprop, prop[jk][i],posprop);
1.126 brouard 3448: /*probs[i][jk][j1]= pp[jk]/pos;*/
3449: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
3450: }
1.213 brouard 3451: else{
1.126 brouard 3452: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
1.213 brouard 3453: fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",i, prop[jk][i],posprop);
3454: }
1.126 brouard 3455: }
3456: }
3457:
1.214 ! brouard 3458: for(jk=-1; jk <=nlstate+ndeath; jk++){
! 3459: for(m=-1; m <=nlstate+ndeath; m++){
! 3460: if(freq[jk][m][i] !=0 ) { /* minimizing output */
! 3461: if(first==1){
! 3462: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
! 3463: }
1.126 brouard 3464: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
3465: }
1.214 ! brouard 3466: if(jk!=0 && m!=0)
! 3467: fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][i]);
! 3468: }
! 3469: }
! 3470: fprintf(ficresphtmfr,"</tr>\n ");
1.213 brouard 3471: if(i <= iagemax){
1.126 brouard 3472: fprintf(ficresp,"\n");
1.213 brouard 3473: fprintf(ficresphtm,"</tr>\n");
3474: }
1.126 brouard 3475: if(first==1)
3476: printf("Others in log...\n");
3477: fprintf(ficlog,"\n");
1.210 brouard 3478: } /* end loop i */
1.213 brouard 3479: fprintf(ficresphtm,"</table>\n");
1.214 ! brouard 3480: fprintf(ficresphtmfr,"</table>\n");
1.145 brouard 3481: /*}*/
1.210 brouard 3482: } /* end j1 */
1.126 brouard 3483: dateintmean=dateintsum/k2cpt;
3484:
3485: fclose(ficresp);
1.213 brouard 3486: fclose(ficresphtm);
1.214 ! brouard 3487: fclose(ficresphtmfr);
1.126 brouard 3488: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
3489: free_vector(pp,1,nlstate);
3490: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
3491: /* End of Freq */
3492: }
3493:
3494: /************ Prevalence ********************/
3495: 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)
3496: {
3497: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
3498: in each health status at the date of interview (if between dateprev1 and dateprev2).
3499: We still use firstpass and lastpass as another selection.
3500: */
3501:
1.164 brouard 3502: int i, m, jk, j1, bool, z1,j;
1.214 ! brouard 3503: int mi; /* Effective wave */
! 3504: int iage;
! 3505: double agebegin, ageend;
1.164 brouard 3506:
3507: double **prop;
3508: double posprop;
1.126 brouard 3509: double y2; /* in fractional years */
3510: int iagemin, iagemax;
1.145 brouard 3511: int first; /** to stop verbosity which is redirected to log file */
1.126 brouard 3512:
3513: iagemin= (int) agemin;
3514: iagemax= (int) agemax;
3515: /*pp=vector(1,nlstate);*/
3516: prop=matrix(1,nlstate,iagemin,iagemax+3);
3517: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
3518: j1=0;
3519:
1.145 brouard 3520: /*j=cptcoveff;*/
1.126 brouard 3521: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3522:
1.145 brouard 3523: first=1;
3524: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
1.214 ! brouard 3525: for (i=1; i<=nlstate; i++)
! 3526: for(iage=iagemin; iage <= iagemax+3; iage++)
! 3527: prop[i][iage]=0.0;
! 3528:
! 3529: for (i=1; i<=imx; i++) { /* Each individual */
! 3530: bool=1;
! 3531: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
! 3532: for (z1=1; z1<=cptcoveff; z1++)
! 3533: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])
! 3534: bool=0;
! 3535: }
! 3536: if (bool==1) {
! 3537: /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
! 3538: for(mi=1; mi<wav[i];mi++){
! 3539: m=mw[mi][i];
! 3540: agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
! 3541: /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
! 3542: if(m >=firstpass && m <=lastpass){
1.126 brouard 3543: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
3544: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
3545: if(agev[m][i]==0) agev[m][i]=iagemax+1;
3546: if(agev[m][i]==1) agev[m][i]=iagemax+2;
3547: 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);
1.214 ! brouard 3548: if (s[m][i]>0 && s[m][i]<=nlstate) {
1.126 brouard 3549: /*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]]);*/
1.214 ! brouard 3550: prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
! 3551: prop[s[m][i]][iagemax+3] += weight[i];
! 3552: } /* end valid statuses */
! 3553: } /* end selection of dates */
1.126 brouard 3554: } /* end selection of waves */
1.214 ! brouard 3555: } /* end effective waves */
! 3556: } /* end bool */
! 3557: }
! 3558: for(i=iagemin; i <= iagemax+3; i++){
! 3559: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
! 3560: posprop += prop[jk][i];
! 3561: }
! 3562:
! 3563: for(jk=1; jk <=nlstate ; jk++){
! 3564: if( i <= iagemax){
! 3565: if(posprop>=1.e-5){
! 3566: probs[i][jk][j1]= prop[jk][i]/posprop;
! 3567: } else{
! 3568: if(first==1){
! 3569: first=0;
! 3570: 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]);
1.145 brouard 3571: }
1.214 ! brouard 3572: }
! 3573: }
! 3574: }/* end jk */
! 3575: }/* end i */
1.145 brouard 3576: /*} *//* end i1 */
3577: } /* end j1 */
1.126 brouard 3578:
3579: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
3580: /*free_vector(pp,1,nlstate);*/
3581: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
3582: } /* End of prevalence */
3583:
3584: /************* Waves Concatenation ***************/
3585:
3586: 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)
3587: {
3588: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
3589: Death is a valid wave (if date is known).
3590: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
3591: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3592: and mw[mi+1][i]. dh depends on stepm.
3593: */
3594:
3595: int i, mi, m;
3596: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
3597: double sum=0., jmean=0.;*/
1.214 ! brouard 3598: int first, firstwo;
1.126 brouard 3599: int j, k=0,jk, ju, jl;
3600: double sum=0.;
3601: first=0;
1.214 ! brouard 3602: firstwo=0;
1.164 brouard 3603: jmin=100000;
1.126 brouard 3604: jmax=-1;
3605: jmean=0.;
1.214 ! brouard 3606: for(i=1; i<=imx; i++){ /* For simple cases and if state is death */
1.126 brouard 3607: mi=0;
3608: m=firstpass;
1.214 ! brouard 3609: while(s[m][i] <= nlstate){ /* a live state */
1.126 brouard 3610: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
3611: mw[++mi][i]=m;
3612: if(m >=lastpass)
3613: break;
3614: else
3615: m++;
3616: }/* end while */
1.214 ! brouard 3617: if (s[m][i] > nlstate){ /* In a death state */
1.126 brouard 3618: mi++; /* Death is another wave */
3619: /* if(mi==0) never been interviewed correctly before death */
3620: /* Only death is a correct wave */
3621: mw[mi][i]=m;
1.214 ! brouard 3622: }else if (andc[i] != 9999) { /* A death occured after lastpass */
! 3623: m++;
! 3624: mi++;
! 3625: s[m][i]=nlstate+1; /* We are setting the status to the last of non live state */
! 3626: mw[mi][i]=m;
! 3627: nbwarn++;
! 3628: if(firstwo==0){
! 3629: printf("Warning! Death for individual %ld line=%d occurred after last wave %d. Since 0.98r4 we considered a status %d at wave %d\nOthers in log file only\n",num[i],i,lastpass,nlstate+1, m);
! 3630: fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred after last wave %d. Since 0.98r4 we considered a status %d at wave %d\n",num[i],i,lastpass,nlstate+1, m);
! 3631: firstwo=1;
! 3632: }
! 3633: if(firstwo==1){
! 3634: fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred after last wave %d. Since 0.98r4 we considered a status %d at wave %d\n",num[i],i,lastpass,nlstate+1, m);
! 3635: }
1.126 brouard 3636: }
3637: wav[i]=mi;
3638: if(mi==0){
3639: nbwarn++;
3640: if(first==0){
3641: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
3642: first=1;
3643: }
3644: if(first==1){
3645: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
3646: }
3647: } /* end mi==0 */
3648: } /* End individuals */
1.214 ! brouard 3649: /* wav and mw are no more changed */
1.126 brouard 3650:
1.214 ! brouard 3651:
1.126 brouard 3652: for(i=1; i<=imx; i++){
3653: for(mi=1; mi<wav[i];mi++){
3654: if (stepm <=0)
3655: dh[mi][i]=1;
3656: else{
3657: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
3658: if (agedc[i] < 2*AGESUP) {
3659: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
3660: if(j==0) j=1; /* Survives at least one month after exam */
3661: else if(j<0){
3662: nberr++;
3663: 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]);
3664: j=1; /* Temporary Dangerous patch */
3665: 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);
3666: 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]);
3667: 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);
3668: }
3669: k=k+1;
3670: if (j >= jmax){
3671: jmax=j;
3672: ijmax=i;
3673: }
3674: if (j <= jmin){
3675: jmin=j;
3676: ijmin=i;
3677: }
3678: sum=sum+j;
3679: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
3680: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
3681: }
3682: }
3683: else{
3684: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
3685: /* 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]); */
3686:
3687: k=k+1;
3688: if (j >= jmax) {
3689: jmax=j;
3690: ijmax=i;
3691: }
3692: else if (j <= jmin){
3693: jmin=j;
3694: ijmin=i;
3695: }
3696: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
3697: /*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]);*/
3698: if(j<0){
3699: nberr++;
3700: 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]);
3701: 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]);
3702: }
3703: sum=sum+j;
3704: }
3705: jk= j/stepm;
3706: jl= j -jk*stepm;
3707: ju= j -(jk+1)*stepm;
3708: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
3709: if(jl==0){
3710: dh[mi][i]=jk;
3711: bh[mi][i]=0;
3712: }else{ /* We want a negative bias in order to only have interpolation ie
1.136 brouard 3713: * to avoid the price of an extra matrix product in likelihood */
1.126 brouard 3714: dh[mi][i]=jk+1;
3715: bh[mi][i]=ju;
3716: }
3717: }else{
3718: if(jl <= -ju){
3719: dh[mi][i]=jk;
3720: bh[mi][i]=jl; /* bias is positive if real duration
3721: * is higher than the multiple of stepm and negative otherwise.
3722: */
3723: }
3724: else{
3725: dh[mi][i]=jk+1;
3726: bh[mi][i]=ju;
3727: }
3728: if(dh[mi][i]==0){
3729: dh[mi][i]=1; /* At least one step */
3730: bh[mi][i]=ju; /* At least one step */
3731: /* 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);*/
3732: }
3733: } /* end if mle */
3734: }
3735: } /* end wave */
3736: }
3737: jmean=sum/k;
3738: 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 3739: 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 3740: }
3741:
3742: /*********** Tricode ****************************/
1.145 brouard 3743: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 3744: {
1.144 brouard 3745: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
3746: /* 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 3747: * Boring subroutine which should only output nbcode[Tvar[j]][k]
1.145 brouard 3748: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
1.169 brouard 3749: * nbcode[Tvar[j]][1]=
1.144 brouard 3750: */
1.130 brouard 3751:
1.145 brouard 3752: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 3753: int modmaxcovj=0; /* Modality max of covariates j */
1.145 brouard 3754: int cptcode=0; /* Modality max of covariates j */
3755: int modmincovj=0; /* Modality min of covariates j */
3756:
3757:
1.126 brouard 3758: cptcoveff=0;
3759:
1.144 brouard 3760: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 3761:
1.145 brouard 3762: /* Loop on covariates without age and products */
1.186 brouard 3763: for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
1.192 brouard 3764: for (k=-1; k < maxncov; k++) Ndum[k]=0;
1.186 brouard 3765: for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
1.136 brouard 3766: modality of this covariate Vj*/
1.145 brouard 3767: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
3768: * If product of Vn*Vm, still boolean *:
3769: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
3770: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
3771: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
1.136 brouard 3772: modality of the nth covariate of individual i. */
1.145 brouard 3773: if (ij > modmaxcovj)
3774: modmaxcovj=ij;
3775: else if (ij < modmincovj)
3776: modmincovj=ij;
3777: if ((ij < -1) && (ij > NCOVMAX)){
3778: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
3779: exit(1);
3780: }else
1.136 brouard 3781: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
1.145 brouard 3782: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
1.126 brouard 3783: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.136 brouard 3784: /* getting the maximum value of the modality of the covariate
3785: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
3786: female is 1, then modmaxcovj=1.*/
1.192 brouard 3787: } /* end for loop on individuals i */
1.145 brouard 3788: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
1.192 brouard 3789: 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 3790: cptcode=modmaxcovj;
1.137 brouard 3791: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
1.145 brouard 3792: /*for (i=0; i<=cptcode; i++) {*/
1.192 brouard 3793: for (k=modmincovj; k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
3794: printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
3795: fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
3796: if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
3797: if( k != -1){
3798: ncodemax[j]++; /* ncodemax[j]= Number of modalities of the j th
3799: covariate for which somebody answered excluding
3800: undefined. Usually 2: 0 and 1. */
3801: }
3802: ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
3803: covariate for which somebody answered including
3804: undefined. Usually 3: -1, 0 and 1. */
1.145 brouard 3805: }
3806: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
3807: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
1.131 brouard 3808: } /* Ndum[-1] number of undefined modalities */
1.126 brouard 3809:
1.136 brouard 3810: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
1.186 brouard 3811: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
3812: 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 3813: modmincovj=3; modmaxcovj = 7;
1.186 brouard 3814: There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
3815: which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
3816: defining two dummy variables: variables V1_1 and V1_2.
1.145 brouard 3817: nbcode[Tvar[j]][ij]=k;
3818: nbcode[Tvar[j]][1]=0;
3819: nbcode[Tvar[j]][2]=1;
3820: nbcode[Tvar[j]][3]=2;
1.197 brouard 3821: To be continued (not working yet).
1.145 brouard 3822: */
1.197 brouard 3823: ij=0; /* ij is similar to i but can jump over null modalities */
3824: 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*/
3825: if (Ndum[i] == 0) { /* If nobody responded to this modality k */
1.192 brouard 3826: break;
3827: }
3828: ij++;
1.197 brouard 3829: 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 3830: cptcode = ij; /* New max modality for covar j */
3831: } /* end of loop on modality i=-1 to 1 or more */
3832:
3833: /* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
3834: /* /\*recode from 0 *\/ */
3835: /* k is a modality. If we have model=V1+V1*sex */
3836: /* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
3837: /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
3838: /* } */
3839: /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
3840: /* if (ij > ncodemax[j]) { */
3841: /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
3842: /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
3843: /* break; */
3844: /* } */
3845: /* } /\* end of loop on modality k *\/ */
1.137 brouard 3846: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
3847:
1.145 brouard 3848: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.137 brouard 3849:
1.187 brouard 3850: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
1.145 brouard 3851: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
3852: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
1.187 brouard 3853: Ndum[ij]++; /* Might be supersed V1 + V1*age */
1.145 brouard 3854: }
1.126 brouard 3855:
1.192 brouard 3856: ij=0;
1.145 brouard 3857: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
3858: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
1.126 brouard 3859: if((Ndum[i]!=0) && (i<=ncovcol)){
1.192 brouard 3860: ij++;
1.145 brouard 3861: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
3862: Tvaraff[ij]=i; /*For printing (unclear) */
1.192 brouard 3863: }else{
3864: /* Tvaraff[ij]=0; */
3865: }
1.126 brouard 3866: }
1.192 brouard 3867: /* ij--; */
1.144 brouard 3868: cptcoveff=ij; /*Number of total covariates*/
1.145 brouard 3869:
1.126 brouard 3870: }
3871:
1.145 brouard 3872:
1.126 brouard 3873: /*********** Health Expectancies ****************/
3874:
1.127 brouard 3875: 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 3876:
3877: {
3878: /* Health expectancies, no variances */
1.164 brouard 3879: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 3880: int nhstepma, nstepma; /* Decreasing with age */
3881: double age, agelim, hf;
3882: double ***p3mat;
3883: double eip;
3884:
3885: pstamp(ficreseij);
3886: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3887: fprintf(ficreseij,"# Age");
3888: for(i=1; i<=nlstate;i++){
3889: for(j=1; j<=nlstate;j++){
3890: fprintf(ficreseij," e%1d%1d ",i,j);
3891: }
3892: fprintf(ficreseij," e%1d. ",i);
3893: }
3894: fprintf(ficreseij,"\n");
3895:
3896:
3897: if(estepm < stepm){
3898: printf ("Problem %d lower than %d\n",estepm, stepm);
3899: }
3900: else hstepm=estepm;
3901: /* We compute the life expectancy from trapezoids spaced every estepm months
3902: * This is mainly to measure the difference between two models: for example
3903: * if stepm=24 months pijx are given only every 2 years and by summing them
3904: * we are calculating an estimate of the Life Expectancy assuming a linear
3905: * progression in between and thus overestimating or underestimating according
3906: * to the curvature of the survival function. If, for the same date, we
3907: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3908: * to compare the new estimate of Life expectancy with the same linear
3909: * hypothesis. A more precise result, taking into account a more precise
3910: * curvature will be obtained if estepm is as small as stepm. */
3911:
3912: /* For example we decided to compute the life expectancy with the smallest unit */
3913: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3914: nhstepm is the number of hstepm from age to agelim
3915: nstepm is the number of stepm from age to agelin.
3916: Look at hpijx to understand the reason of that which relies in memory size
3917: and note for a fixed period like estepm months */
3918: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3919: survival function given by stepm (the optimization length). Unfortunately it
3920: means that if the survival funtion is printed only each two years of age and if
3921: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3922: results. So we changed our mind and took the option of the best precision.
3923: */
3924: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3925:
3926: agelim=AGESUP;
3927: /* If stepm=6 months */
3928: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3929: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3930:
3931: /* nhstepm age range expressed in number of stepm */
3932: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3933: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3934: /* if (stepm >= YEARM) hstepm=1;*/
3935: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3936: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3937:
3938: for (age=bage; age<=fage; age ++){
3939: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3940: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3941: /* if (stepm >= YEARM) hstepm=1;*/
3942: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3943:
3944: /* If stepm=6 months */
3945: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3946: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3947:
3948: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3949:
3950: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3951:
3952: printf("%d|",(int)age);fflush(stdout);
3953: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3954:
3955: /* Computing expectancies */
3956: for(i=1; i<=nlstate;i++)
3957: for(j=1; j<=nlstate;j++)
3958: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3959: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3960:
3961: /* 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]);*/
3962:
3963: }
3964:
3965: fprintf(ficreseij,"%3.0f",age );
3966: for(i=1; i<=nlstate;i++){
3967: eip=0;
3968: for(j=1; j<=nlstate;j++){
3969: eip +=eij[i][j][(int)age];
3970: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3971: }
3972: fprintf(ficreseij,"%9.4f", eip );
3973: }
3974: fprintf(ficreseij,"\n");
3975:
3976: }
3977: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3978: printf("\n");
3979: fprintf(ficlog,"\n");
3980:
3981: }
3982:
1.127 brouard 3983: 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 3984:
3985: {
3986: /* Covariances of health expectancies eij and of total life expectancies according
3987: to initial status i, ei. .
3988: */
3989: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3990: int nhstepma, nstepma; /* Decreasing with age */
3991: double age, agelim, hf;
3992: double ***p3matp, ***p3matm, ***varhe;
3993: double **dnewm,**doldm;
3994: double *xp, *xm;
3995: double **gp, **gm;
3996: double ***gradg, ***trgradg;
3997: int theta;
3998:
3999: double eip, vip;
4000:
4001: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
4002: xp=vector(1,npar);
4003: xm=vector(1,npar);
4004: dnewm=matrix(1,nlstate*nlstate,1,npar);
4005: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
4006:
4007: pstamp(ficresstdeij);
4008: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
4009: fprintf(ficresstdeij,"# Age");
4010: for(i=1; i<=nlstate;i++){
4011: for(j=1; j<=nlstate;j++)
4012: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
4013: fprintf(ficresstdeij," e%1d. ",i);
4014: }
4015: fprintf(ficresstdeij,"\n");
4016:
4017: pstamp(ficrescveij);
4018: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
4019: fprintf(ficrescveij,"# Age");
4020: for(i=1; i<=nlstate;i++)
4021: for(j=1; j<=nlstate;j++){
4022: cptj= (j-1)*nlstate+i;
4023: for(i2=1; i2<=nlstate;i2++)
4024: for(j2=1; j2<=nlstate;j2++){
4025: cptj2= (j2-1)*nlstate+i2;
4026: if(cptj2 <= cptj)
4027: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
4028: }
4029: }
4030: fprintf(ficrescveij,"\n");
4031:
4032: if(estepm < stepm){
4033: printf ("Problem %d lower than %d\n",estepm, stepm);
4034: }
4035: else hstepm=estepm;
4036: /* We compute the life expectancy from trapezoids spaced every estepm months
4037: * This is mainly to measure the difference between two models: for example
4038: * if stepm=24 months pijx are given only every 2 years and by summing them
4039: * we are calculating an estimate of the Life Expectancy assuming a linear
4040: * progression in between and thus overestimating or underestimating according
4041: * to the curvature of the survival function. If, for the same date, we
4042: * estimate the model with stepm=1 month, we can keep estepm to 24 months
4043: * to compare the new estimate of Life expectancy with the same linear
4044: * hypothesis. A more precise result, taking into account a more precise
4045: * curvature will be obtained if estepm is as small as stepm. */
4046:
4047: /* For example we decided to compute the life expectancy with the smallest unit */
4048: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
4049: nhstepm is the number of hstepm from age to agelim
4050: nstepm is the number of stepm from age to agelin.
4051: Look at hpijx to understand the reason of that which relies in memory size
4052: and note for a fixed period like estepm months */
4053: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
4054: survival function given by stepm (the optimization length). Unfortunately it
4055: means that if the survival funtion is printed only each two years of age and if
4056: you sum them up and add 1 year (area under the trapezoids) you won't get the same
4057: results. So we changed our mind and took the option of the best precision.
4058: */
4059: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
4060:
4061: /* If stepm=6 months */
4062: /* nhstepm age range expressed in number of stepm */
4063: agelim=AGESUP;
4064: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
4065: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4066: /* if (stepm >= YEARM) hstepm=1;*/
4067: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
4068:
4069: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4070: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4071: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
4072: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
4073: gp=matrix(0,nhstepm,1,nlstate*nlstate);
4074: gm=matrix(0,nhstepm,1,nlstate*nlstate);
4075:
4076: for (age=bage; age<=fage; age ++){
4077: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
4078: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4079: /* if (stepm >= YEARM) hstepm=1;*/
4080: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
4081:
4082: /* If stepm=6 months */
4083: /* Computed by stepm unit matrices, product of hstepma matrices, stored
4084: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
4085:
4086: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
4087:
4088: /* Computing Variances of health expectancies */
4089: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
4090: decrease memory allocation */
4091: for(theta=1; theta <=npar; theta++){
4092: for(i=1; i<=npar; i++){
4093: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4094: xm[i] = x[i] - (i==theta ?delti[theta]:0);
4095: }
4096: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
4097: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
4098:
4099: for(j=1; j<= nlstate; j++){
4100: for(i=1; i<=nlstate; i++){
4101: for(h=0; h<=nhstepm-1; h++){
4102: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
4103: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
4104: }
4105: }
4106: }
4107:
4108: for(ij=1; ij<= nlstate*nlstate; ij++)
4109: for(h=0; h<=nhstepm-1; h++){
4110: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
4111: }
4112: }/* End theta */
4113:
4114:
4115: for(h=0; h<=nhstepm-1; h++)
4116: for(j=1; j<=nlstate*nlstate;j++)
4117: for(theta=1; theta <=npar; theta++)
4118: trgradg[h][j][theta]=gradg[h][theta][j];
4119:
4120:
4121: for(ij=1;ij<=nlstate*nlstate;ij++)
4122: for(ji=1;ji<=nlstate*nlstate;ji++)
4123: varhe[ij][ji][(int)age] =0.;
4124:
4125: printf("%d|",(int)age);fflush(stdout);
4126: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
4127: for(h=0;h<=nhstepm-1;h++){
4128: for(k=0;k<=nhstepm-1;k++){
4129: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
4130: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
4131: for(ij=1;ij<=nlstate*nlstate;ij++)
4132: for(ji=1;ji<=nlstate*nlstate;ji++)
4133: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
4134: }
4135: }
4136:
4137: /* Computing expectancies */
4138: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
4139: for(i=1; i<=nlstate;i++)
4140: for(j=1; j<=nlstate;j++)
4141: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
4142: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
4143:
4144: /* 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]);*/
4145:
4146: }
4147:
4148: fprintf(ficresstdeij,"%3.0f",age );
4149: for(i=1; i<=nlstate;i++){
4150: eip=0.;
4151: vip=0.;
4152: for(j=1; j<=nlstate;j++){
4153: eip += eij[i][j][(int)age];
4154: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
4155: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
4156: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
4157: }
4158: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
4159: }
4160: fprintf(ficresstdeij,"\n");
4161:
4162: fprintf(ficrescveij,"%3.0f",age );
4163: for(i=1; i<=nlstate;i++)
4164: for(j=1; j<=nlstate;j++){
4165: cptj= (j-1)*nlstate+i;
4166: for(i2=1; i2<=nlstate;i2++)
4167: for(j2=1; j2<=nlstate;j2++){
4168: cptj2= (j2-1)*nlstate+i2;
4169: if(cptj2 <= cptj)
4170: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
4171: }
4172: }
4173: fprintf(ficrescveij,"\n");
4174:
4175: }
4176: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
4177: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
4178: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
4179: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
4180: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4181: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4182: printf("\n");
4183: fprintf(ficlog,"\n");
4184:
4185: free_vector(xm,1,npar);
4186: free_vector(xp,1,npar);
4187: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
4188: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
4189: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
4190: }
4191:
4192: /************ Variance ******************/
1.209 brouard 4193: 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 4194: {
4195: /* Variance of health expectancies */
4196: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
4197: /* double **newm;*/
1.169 brouard 4198: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
4199:
4200: int movingaverage();
1.126 brouard 4201: double **dnewm,**doldm;
4202: double **dnewmp,**doldmp;
4203: int i, j, nhstepm, hstepm, h, nstepm ;
1.164 brouard 4204: int k;
1.126 brouard 4205: double *xp;
4206: double **gp, **gm; /* for var eij */
4207: double ***gradg, ***trgradg; /*for var eij */
4208: double **gradgp, **trgradgp; /* for var p point j */
4209: double *gpp, *gmp; /* for var p point j */
4210: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
4211: double ***p3mat;
4212: double age,agelim, hf;
4213: double ***mobaverage;
4214: int theta;
4215: char digit[4];
4216: char digitp[25];
4217:
4218: char fileresprobmorprev[FILENAMELENGTH];
4219:
4220: if(popbased==1){
4221: if(mobilav!=0)
1.201 brouard 4222: strcpy(digitp,"-POPULBASED-MOBILAV_");
4223: else strcpy(digitp,"-POPULBASED-NOMOBIL_");
1.126 brouard 4224: }
4225: else
1.201 brouard 4226: strcpy(digitp,"-STABLBASED_");
1.126 brouard 4227:
4228: if (mobilav!=0) {
4229: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4230: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
4231: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4232: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4233: }
4234: }
4235:
1.201 brouard 4236: strcpy(fileresprobmorprev,"PRMORPREV-");
1.126 brouard 4237: sprintf(digit,"%-d",ij);
4238: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
4239: strcat(fileresprobmorprev,digit); /* Tvar to be done */
4240: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
1.202 brouard 4241: strcat(fileresprobmorprev,fileresu);
1.126 brouard 4242: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
4243: printf("Problem with resultfile: %s\n", fileresprobmorprev);
4244: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
4245: }
4246: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
4247: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
4248: pstamp(ficresprobmorprev);
4249: 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);
4250: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
4251: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
4252: fprintf(ficresprobmorprev," p.%-d SE",j);
4253: for(i=1; i<=nlstate;i++)
4254: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
4255: }
4256: fprintf(ficresprobmorprev,"\n");
1.208 brouard 4257:
1.126 brouard 4258: fprintf(ficgp,"\n# Routine varevsij");
1.200 brouard 4259: fprintf(ficgp,"\nunset title \n");
4260: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
1.126 brouard 4261: 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");
4262: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
4263: /* } */
4264: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4265: pstamp(ficresvij);
4266: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
4267: if(popbased==1)
1.128 brouard 4268: 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 4269: else
4270: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
4271: fprintf(ficresvij,"# Age");
4272: for(i=1; i<=nlstate;i++)
4273: for(j=1; j<=nlstate;j++)
4274: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
4275: fprintf(ficresvij,"\n");
4276:
4277: xp=vector(1,npar);
4278: dnewm=matrix(1,nlstate,1,npar);
4279: doldm=matrix(1,nlstate,1,nlstate);
4280: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
4281: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4282:
4283: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
4284: gpp=vector(nlstate+1,nlstate+ndeath);
4285: gmp=vector(nlstate+1,nlstate+ndeath);
4286: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
4287:
4288: if(estepm < stepm){
4289: printf ("Problem %d lower than %d\n",estepm, stepm);
4290: }
4291: else hstepm=estepm;
4292: /* For example we decided to compute the life expectancy with the smallest unit */
4293: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
4294: nhstepm is the number of hstepm from age to agelim
1.208 brouard 4295: nstepm is the number of stepm from age to agelim.
1.209 brouard 4296: Look at function hpijx to understand why because of memory size limitations,
1.208 brouard 4297: we decided (b) to get a life expectancy respecting the most precise curvature of the
1.126 brouard 4298: survival function given by stepm (the optimization length). Unfortunately it
4299: means that if the survival funtion is printed every two years of age and if
4300: you sum them up and add 1 year (area under the trapezoids) you won't get the same
4301: results. So we changed our mind and took the option of the best precision.
4302: */
4303: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
4304: agelim = AGESUP;
4305: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
4306: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4307: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
4308: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4309: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
4310: gp=matrix(0,nhstepm,1,nlstate);
4311: gm=matrix(0,nhstepm,1,nlstate);
4312:
4313:
4314: for(theta=1; theta <=npar; theta++){
4315: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
4316: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4317: }
1.209 brouard 4318:
4319: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
1.126 brouard 4320:
4321: if (popbased==1) {
4322: if(mobilav ==0){
4323: for(i=1; i<=nlstate;i++)
4324: prlim[i][i]=probs[(int)age][i][ij];
4325: }else{ /* mobilav */
4326: for(i=1; i<=nlstate;i++)
4327: prlim[i][i]=mobaverage[(int)age][i][ij];
4328: }
4329: }
4330:
1.209 brouard 4331: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); /* Returns p3mat[i][j][h] for h=1 to nhstepm */
1.126 brouard 4332: for(j=1; j<= nlstate; j++){
4333: for(h=0; h<=nhstepm; h++){
4334: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
4335: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
4336: }
4337: }
1.209 brouard 4338: /* Next for computing probability of death (h=1 means
1.126 brouard 4339: computed over hstepm matrices product = hstepm*stepm months)
4340: as a weighted average of prlim.
4341: */
4342: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4343: for(i=1,gpp[j]=0.; i<= nlstate; i++)
4344: gpp[j] += prlim[i][i]*p3mat[i][j][1];
4345: }
4346: /* end probability of death */
4347:
4348: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
4349: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.209 brouard 4350:
4351: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij);
1.126 brouard 4352:
4353: if (popbased==1) {
4354: if(mobilav ==0){
4355: for(i=1; i<=nlstate;i++)
4356: prlim[i][i]=probs[(int)age][i][ij];
4357: }else{ /* mobilav */
4358: for(i=1; i<=nlstate;i++)
4359: prlim[i][i]=mobaverage[(int)age][i][ij];
4360: }
4361: }
4362:
1.209 brouard 4363: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
4364:
1.128 brouard 4365: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
1.126 brouard 4366: for(h=0; h<=nhstepm; h++){
4367: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
4368: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
4369: }
4370: }
4371: /* This for computing probability of death (h=1 means
4372: computed over hstepm matrices product = hstepm*stepm months)
4373: as a weighted average of prlim.
4374: */
4375: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4376: for(i=1,gmp[j]=0.; i<= nlstate; i++)
4377: gmp[j] += prlim[i][i]*p3mat[i][j][1];
4378: }
4379: /* end probability of death */
4380:
4381: for(j=1; j<= nlstate; j++) /* vareij */
4382: for(h=0; h<=nhstepm; h++){
4383: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
4384: }
4385:
4386: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
4387: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
4388: }
4389:
4390: } /* End theta */
4391:
4392: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
4393:
4394: for(h=0; h<=nhstepm; h++) /* veij */
4395: for(j=1; j<=nlstate;j++)
4396: for(theta=1; theta <=npar; theta++)
4397: trgradg[h][j][theta]=gradg[h][theta][j];
4398:
4399: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
4400: for(theta=1; theta <=npar; theta++)
4401: trgradgp[j][theta]=gradgp[theta][j];
4402:
4403:
4404: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
4405: for(i=1;i<=nlstate;i++)
4406: for(j=1;j<=nlstate;j++)
4407: vareij[i][j][(int)age] =0.;
4408:
4409: for(h=0;h<=nhstepm;h++){
4410: for(k=0;k<=nhstepm;k++){
4411: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
4412: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
4413: for(i=1;i<=nlstate;i++)
4414: for(j=1;j<=nlstate;j++)
4415: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
4416: }
4417: }
4418:
4419: /* pptj */
4420: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
4421: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
4422: for(j=nlstate+1;j<=nlstate+ndeath;j++)
4423: for(i=nlstate+1;i<=nlstate+ndeath;i++)
4424: varppt[j][i]=doldmp[j][i];
4425: /* end ppptj */
4426: /* x centered again */
1.209 brouard 4427:
4428: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij);
1.126 brouard 4429:
4430: if (popbased==1) {
4431: if(mobilav ==0){
4432: for(i=1; i<=nlstate;i++)
4433: prlim[i][i]=probs[(int)age][i][ij];
4434: }else{ /* mobilav */
4435: for(i=1; i<=nlstate;i++)
4436: prlim[i][i]=mobaverage[(int)age][i][ij];
4437: }
4438: }
4439:
4440: /* This for computing probability of death (h=1 means
4441: computed over hstepm (estepm) matrices product = hstepm*stepm months)
4442: as a weighted average of prlim.
4443: */
1.209 brouard 4444: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
1.126 brouard 4445: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4446: for(i=1,gmp[j]=0.;i<= nlstate; i++)
4447: gmp[j] += prlim[i][i]*p3mat[i][j][1];
4448: }
4449: /* end probability of death */
4450:
4451: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
4452: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
4453: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
4454: for(i=1; i<=nlstate;i++){
4455: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
4456: }
4457: }
4458: fprintf(ficresprobmorprev,"\n");
4459:
4460: fprintf(ficresvij,"%.0f ",age );
4461: for(i=1; i<=nlstate;i++)
4462: for(j=1; j<=nlstate;j++){
4463: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
4464: }
4465: fprintf(ficresvij,"\n");
4466: free_matrix(gp,0,nhstepm,1,nlstate);
4467: free_matrix(gm,0,nhstepm,1,nlstate);
4468: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
4469: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
4470: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4471: } /* End age */
4472: free_vector(gpp,nlstate+1,nlstate+ndeath);
4473: free_vector(gmp,nlstate+1,nlstate+ndeath);
4474: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
4475: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.199 brouard 4476: /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
4477: fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
1.126 brouard 4478: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
1.131 brouard 4479: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.201 brouard 4480: fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 4481: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
4482: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
4483: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.145 brouard 4484: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
1.170 brouard 4485: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
1.145 brouard 4486: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
1.126 brouard 4487: 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 4488: 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 4489: /* 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 4490: */
1.199 brouard 4491: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
1.201 brouard 4492: fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 4493:
4494: free_vector(xp,1,npar);
4495: free_matrix(doldm,1,nlstate,1,nlstate);
4496: free_matrix(dnewm,1,nlstate,1,npar);
4497: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4498: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
4499: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4500: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4501: fclose(ficresprobmorprev);
4502: fflush(ficgp);
4503: fflush(fichtm);
4504: } /* end varevsij */
4505:
4506: /************ Variance of prevlim ******************/
1.209 brouard 4507: 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 4508: {
1.205 brouard 4509: /* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
1.126 brouard 4510: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 4511:
1.126 brouard 4512: double **dnewm,**doldm;
4513: int i, j, nhstepm, hstepm;
4514: double *xp;
4515: double *gp, *gm;
4516: double **gradg, **trgradg;
1.208 brouard 4517: double **mgm, **mgp;
1.126 brouard 4518: double age,agelim;
4519: int theta;
4520:
4521: pstamp(ficresvpl);
4522: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
4523: fprintf(ficresvpl,"# Age");
4524: for(i=1; i<=nlstate;i++)
4525: fprintf(ficresvpl," %1d-%1d",i,i);
4526: fprintf(ficresvpl,"\n");
4527:
4528: xp=vector(1,npar);
4529: dnewm=matrix(1,nlstate,1,npar);
4530: doldm=matrix(1,nlstate,1,nlstate);
4531:
4532: hstepm=1*YEARM; /* Every year of age */
4533: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
4534: agelim = AGESUP;
4535: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
4536: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4537: if (stepm >= YEARM) hstepm=1;
4538: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4539: gradg=matrix(1,npar,1,nlstate);
1.208 brouard 4540: mgp=matrix(1,npar,1,nlstate);
4541: mgm=matrix(1,npar,1,nlstate);
1.126 brouard 4542: gp=vector(1,nlstate);
4543: gm=vector(1,nlstate);
4544:
4545: for(theta=1; theta <=npar; theta++){
4546: for(i=1; i<=npar; i++){ /* Computes gradient */
4547: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4548: }
1.209 brouard 4549: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
4550: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
4551: else
4552: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
1.208 brouard 4553: for(i=1;i<=nlstate;i++){
1.126 brouard 4554: gp[i] = prlim[i][i];
1.208 brouard 4555: mgp[theta][i] = prlim[i][i];
4556: }
1.126 brouard 4557: for(i=1; i<=npar; i++) /* Computes gradient */
4558: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.209 brouard 4559: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
4560: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
4561: else
4562: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
1.208 brouard 4563: for(i=1;i<=nlstate;i++){
1.126 brouard 4564: gm[i] = prlim[i][i];
1.208 brouard 4565: mgm[theta][i] = prlim[i][i];
4566: }
1.126 brouard 4567: for(i=1;i<=nlstate;i++)
4568: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1.209 brouard 4569: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
1.126 brouard 4570: } /* End theta */
4571:
4572: trgradg =matrix(1,nlstate,1,npar);
4573:
4574: for(j=1; j<=nlstate;j++)
4575: for(theta=1; theta <=npar; theta++)
4576: trgradg[j][theta]=gradg[theta][j];
1.209 brouard 4577: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
4578: /* printf("\nmgm mgp %d ",(int)age); */
4579: /* for(j=1; j<=nlstate;j++){ */
4580: /* printf(" %d ",j); */
4581: /* for(theta=1; theta <=npar; theta++) */
4582: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
4583: /* printf("\n "); */
4584: /* } */
4585: /* } */
4586: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
4587: /* printf("\n gradg %d ",(int)age); */
4588: /* for(j=1; j<=nlstate;j++){ */
4589: /* printf("%d ",j); */
4590: /* for(theta=1; theta <=npar; theta++) */
4591: /* printf("%d %lf ",theta,gradg[theta][j]); */
4592: /* printf("\n "); */
4593: /* } */
4594: /* } */
1.126 brouard 4595:
4596: for(i=1;i<=nlstate;i++)
4597: varpl[i][(int)age] =0.;
1.209 brouard 4598: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
1.205 brouard 4599: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
4600: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
4601: }else{
1.126 brouard 4602: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
4603: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 4604: }
1.126 brouard 4605: for(i=1;i<=nlstate;i++)
4606: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
4607:
4608: fprintf(ficresvpl,"%.0f ",age );
4609: for(i=1; i<=nlstate;i++)
4610: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
4611: fprintf(ficresvpl,"\n");
4612: free_vector(gp,1,nlstate);
4613: free_vector(gm,1,nlstate);
1.208 brouard 4614: free_matrix(mgm,1,npar,1,nlstate);
4615: free_matrix(mgp,1,npar,1,nlstate);
1.126 brouard 4616: free_matrix(gradg,1,npar,1,nlstate);
4617: free_matrix(trgradg,1,nlstate,1,npar);
4618: } /* End age */
4619:
4620: free_vector(xp,1,npar);
4621: free_matrix(doldm,1,nlstate,1,npar);
4622: free_matrix(dnewm,1,nlstate,1,nlstate);
4623:
4624: }
4625:
4626: /************ Variance of one-step probabilities ******************/
4627: 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[])
4628: {
1.164 brouard 4629: int i, j=0, k1, l1, tj;
1.126 brouard 4630: int k2, l2, j1, z1;
1.164 brouard 4631: int k=0, l;
1.145 brouard 4632: int first=1, first1, first2;
1.126 brouard 4633: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
4634: double **dnewm,**doldm;
4635: double *xp;
4636: double *gp, *gm;
4637: double **gradg, **trgradg;
4638: double **mu;
1.164 brouard 4639: double age, cov[NCOVMAX+1];
1.126 brouard 4640: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
4641: int theta;
4642: char fileresprob[FILENAMELENGTH];
4643: char fileresprobcov[FILENAMELENGTH];
4644: char fileresprobcor[FILENAMELENGTH];
4645: double ***varpij;
4646:
1.201 brouard 4647: strcpy(fileresprob,"PROB_");
1.126 brouard 4648: strcat(fileresprob,fileres);
4649: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
4650: printf("Problem with resultfile: %s\n", fileresprob);
4651: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
4652: }
1.201 brouard 4653: strcpy(fileresprobcov,"PROBCOV_");
1.202 brouard 4654: strcat(fileresprobcov,fileresu);
1.126 brouard 4655: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
4656: printf("Problem with resultfile: %s\n", fileresprobcov);
4657: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
4658: }
1.201 brouard 4659: strcpy(fileresprobcor,"PROBCOR_");
1.202 brouard 4660: strcat(fileresprobcor,fileresu);
1.126 brouard 4661: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
4662: printf("Problem with resultfile: %s\n", fileresprobcor);
4663: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
4664: }
4665: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4666: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4667: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4668: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4669: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4670: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4671: pstamp(ficresprob);
4672: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
4673: fprintf(ficresprob,"# Age");
4674: pstamp(ficresprobcov);
4675: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
4676: fprintf(ficresprobcov,"# Age");
4677: pstamp(ficresprobcor);
4678: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
4679: fprintf(ficresprobcor,"# Age");
4680:
4681:
4682: for(i=1; i<=nlstate;i++)
4683: for(j=1; j<=(nlstate+ndeath);j++){
4684: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
4685: fprintf(ficresprobcov," p%1d-%1d ",i,j);
4686: fprintf(ficresprobcor," p%1d-%1d ",i,j);
4687: }
4688: /* fprintf(ficresprob,"\n");
4689: fprintf(ficresprobcov,"\n");
4690: fprintf(ficresprobcor,"\n");
4691: */
1.131 brouard 4692: xp=vector(1,npar);
1.126 brouard 4693: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4694: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4695: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
4696: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
4697: first=1;
4698: fprintf(ficgp,"\n# Routine varprob");
4699: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
4700: fprintf(fichtm,"\n");
4701:
1.200 brouard 4702: 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 4703: 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);
4704: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
1.126 brouard 4705: and drawn. It helps understanding how is the covariance between two incidences.\
4706: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
4707: 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. \
4708: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
4709: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
4710: standard deviations wide on each axis. <br>\
4711: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
4712: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
4713: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
4714:
4715: cov[1]=1;
1.145 brouard 4716: /* tj=cptcoveff; */
4717: tj = (int) pow(2,cptcoveff);
1.126 brouard 4718: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
4719: j1=0;
1.145 brouard 4720: for(j1=1; j1<=tj;j1++){
4721: /*for(i1=1; i1<=ncodemax[t];i1++){ */
4722: /*j1++;*/
1.126 brouard 4723: if (cptcovn>0) {
4724: fprintf(ficresprob, "\n#********** Variable ");
1.198 brouard 4725: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4726: fprintf(ficresprob, "**********\n#\n");
4727: fprintf(ficresprobcov, "\n#********** Variable ");
1.198 brouard 4728: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4729: fprintf(ficresprobcov, "**********\n#\n");
4730:
4731: fprintf(ficgp, "\n#********** Variable ");
1.198 brouard 4732: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4733: fprintf(ficgp, "**********\n#\n");
4734:
4735:
4736: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.198 brouard 4737: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4738: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
4739:
4740: fprintf(ficresprobcor, "\n#********** Variable ");
1.198 brouard 4741: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4742: fprintf(ficresprobcor, "**********\n#");
4743: }
4744:
1.145 brouard 4745: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
4746: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4747: gp=vector(1,(nlstate)*(nlstate+ndeath));
4748: gm=vector(1,(nlstate)*(nlstate+ndeath));
1.126 brouard 4749: for (age=bage; age<=fage; age ++){
4750: cov[2]=age;
1.187 brouard 4751: if(nagesqr==1)
4752: cov[3]= age*age;
1.126 brouard 4753: for (k=1; k<=cptcovn;k++) {
1.200 brouard 4754: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
4755: /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
1.145 brouard 4756: * 1 1 1 1 1
4757: * 2 2 1 1 1
4758: * 3 1 2 1 1
4759: */
4760: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
1.126 brouard 4761: }
1.186 brouard 4762: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 4763: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
1.126 brouard 4764: for (k=1; k<=cptcovprod;k++)
1.200 brouard 4765: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.126 brouard 4766:
4767:
4768: for(theta=1; theta <=npar; theta++){
4769: for(i=1; i<=npar; i++)
4770: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
4771:
4772: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4773:
4774: k=0;
4775: for(i=1; i<= (nlstate); i++){
4776: for(j=1; j<=(nlstate+ndeath);j++){
4777: k=k+1;
4778: gp[k]=pmmij[i][j];
4779: }
4780: }
4781:
4782: for(i=1; i<=npar; i++)
4783: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
4784:
4785: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4786: k=0;
4787: for(i=1; i<=(nlstate); i++){
4788: for(j=1; j<=(nlstate+ndeath);j++){
4789: k=k+1;
4790: gm[k]=pmmij[i][j];
4791: }
4792: }
4793:
4794: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
4795: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
4796: }
4797:
4798: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
4799: for(theta=1; theta <=npar; theta++)
4800: trgradg[j][theta]=gradg[theta][j];
4801:
4802: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
4803: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
4804:
4805: pmij(pmmij,cov,ncovmodel,x,nlstate);
4806:
4807: k=0;
4808: for(i=1; i<=(nlstate); i++){
4809: for(j=1; j<=(nlstate+ndeath);j++){
4810: k=k+1;
4811: mu[k][(int) age]=pmmij[i][j];
4812: }
4813: }
4814: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
4815: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
4816: varpij[i][j][(int)age] = doldm[i][j];
4817:
4818: /*printf("\n%d ",(int)age);
4819: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4820: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4821: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4822: }*/
4823:
4824: fprintf(ficresprob,"\n%d ",(int)age);
4825: fprintf(ficresprobcov,"\n%d ",(int)age);
4826: fprintf(ficresprobcor,"\n%d ",(int)age);
4827:
4828: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
4829: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
4830: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4831: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
4832: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
4833: }
4834: i=0;
4835: for (k=1; k<=(nlstate);k++){
4836: for (l=1; l<=(nlstate+ndeath);l++){
1.145 brouard 4837: i++;
1.126 brouard 4838: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
4839: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
4840: for (j=1; j<=i;j++){
1.145 brouard 4841: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
1.126 brouard 4842: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
4843: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
4844: }
4845: }
4846: }/* end of loop for state */
4847: } /* end of loop for age */
1.145 brouard 4848: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
4849: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
4850: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4851: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4852:
1.126 brouard 4853: /* Confidence intervalle of pij */
4854: /*
1.131 brouard 4855: fprintf(ficgp,"\nunset parametric;unset label");
1.126 brouard 4856: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
4857: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
4858: 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);
4859: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
4860: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
4861: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
4862: */
4863:
4864: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
1.145 brouard 4865: first1=1;first2=2;
1.126 brouard 4866: for (k2=1; k2<=(nlstate);k2++){
4867: for (l2=1; l2<=(nlstate+ndeath);l2++){
4868: if(l2==k2) continue;
4869: j=(k2-1)*(nlstate+ndeath)+l2;
4870: for (k1=1; k1<=(nlstate);k1++){
4871: for (l1=1; l1<=(nlstate+ndeath);l1++){
4872: if(l1==k1) continue;
4873: i=(k1-1)*(nlstate+ndeath)+l1;
4874: if(i<=j) continue;
4875: for (age=bage; age<=fage; age ++){
4876: if ((int)age %5==0){
4877: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
4878: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
4879: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
4880: mu1=mu[i][(int) age]/stepm*YEARM ;
4881: mu2=mu[j][(int) age]/stepm*YEARM;
4882: c12=cv12/sqrt(v1*v2);
4883: /* Computing eigen value of matrix of covariance */
4884: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4885: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
1.135 brouard 4886: if ((lc2 <0) || (lc1 <0) ){
1.145 brouard 4887: if(first2==1){
4888: first1=0;
4889: 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);
4890: }
4891: 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);
4892: /* lc1=fabs(lc1); */ /* If we want to have them positive */
4893: /* lc2=fabs(lc2); */
1.135 brouard 4894: }
4895:
1.126 brouard 4896: /* Eigen vectors */
4897: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
4898: /*v21=sqrt(1.-v11*v11); *//* error */
4899: v21=(lc1-v1)/cv12*v11;
4900: v12=-v21;
4901: v22=v11;
4902: tnalp=v21/v11;
4903: if(first1==1){
4904: first1=0;
4905: 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);
4906: }
4907: 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);
4908: /*printf(fignu*/
4909: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
4910: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
4911: if(first==1){
4912: first=0;
1.200 brouard 4913: fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
1.126 brouard 4914: fprintf(ficgp,"\nset parametric;unset label");
4915: 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 4916: fprintf(ficgp,"\nset ter svg size 640, 480");
1.126 brouard 4917: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.201 brouard 4918: :<a href=\"%s_%d%1d%1d-%1d%1d.svg\">\
4919: %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
4920: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,\
4921: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
4922: fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
1.126 brouard 4923: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
1.201 brouard 4924: fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
1.126 brouard 4925: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4926: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4927: 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",\
4928: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4929: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4930: }else{
4931: first=0;
4932: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4933: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4934: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4935: 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",\
4936: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4937: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4938: }/* if first */
4939: } /* age mod 5 */
4940: } /* end loop age */
1.201 brouard 4941: 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 4942: first=1;
4943: } /*l12 */
4944: } /* k12 */
4945: } /*l1 */
4946: }/* k1 */
1.169 brouard 4947: /* } */ /* loop covariates */
1.126 brouard 4948: }
4949: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4950: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4951: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4952: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4953: free_vector(xp,1,npar);
4954: fclose(ficresprob);
4955: fclose(ficresprobcov);
4956: fclose(ficresprobcor);
4957: fflush(ficgp);
4958: fflush(fichtmcov);
4959: }
4960:
4961:
4962: /******************* Printing html file ***********/
1.201 brouard 4963: void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 4964: int lastpass, int stepm, int weightopt, char model[],\
4965: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
1.211 brouard 4966: int popforecast, int prevfcast, int estepm , \
1.213 brouard 4967: double jprev1, double mprev1,double anprev1, double dateprev1, \
4968: double jprev2, double mprev2,double anprev2, double dateprev2){
1.126 brouard 4969: int jj1, k1, i1, cpt;
4970:
4971: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4972: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4973: </ul>");
1.214 ! brouard 4974: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
! 4975: fprintf(fichtm,"<li>- Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file)<br/>\n",
! 4976: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
! 4977: fprintf(fichtm,"<li> - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file) ",
1.213 brouard 4978: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
4979: fprintf(fichtm,", <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
1.126 brouard 4980: fprintf(fichtm,"\
4981: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
1.201 brouard 4982: stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
1.126 brouard 4983: fprintf(fichtm,"\
4984: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4985: subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
1.126 brouard 4986: fprintf(fichtm,"\
1.211 brouard 4987: - (a) Life expectancies by health status at initial age, e<sub>i.</sub> (b) health expectancies by health status at initial age, e<sub>ij</sub> . 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 4988: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4989: estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
1.211 brouard 4990: if(prevfcast==1){
4991: fprintf(fichtm,"\
4992: - Prevalence projections by age and states: \
1.201 brouard 4993: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
1.211 brouard 4994: }
1.126 brouard 4995:
4996: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4997:
1.145 brouard 4998: m=pow(2,cptcoveff);
1.126 brouard 4999: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
5000:
5001: jj1=0;
5002: for(k1=1; k1<=m;k1++){
1.192 brouard 5003: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
1.126 brouard 5004: jj1++;
5005: if (cptcovn > 0) {
5006: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.192 brouard 5007: for (cpt=1; cpt<=cptcoveff;cpt++){
1.198 brouard 5008: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
5009: printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
1.192 brouard 5010: }
1.126 brouard 5011: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
5012: }
1.201 brouard 5013: /* aij, bij */
1.211 brouard 5014: fprintf(fichtm,"<br>- Logit model (yours is: 1+age+%s), 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> \
5015: <img src=\"%s_%d-1.svg\">",model,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.126 brouard 5016: /* Pij */
1.211 brouard 5017: fprintf(fichtm,"<br>\n- P<sub>ij</sub> 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 5018: <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.126 brouard 5019: /* Quasi-incidences */
1.211 brouard 5020: fprintf(fichtm,"<br>\n- I<sub>ij</sub> or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.201 brouard 5021: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too,\
1.211 brouard 5022: incidence (rates) are the limit when h tends to zero of the ratio of the probability <sub>h</sub>P<sub>ij</sub> \
5023: divided by h: <sub>h</sub>P<sub>ij</sub>/h : <a href=\"%s_%d-3.svg\">%s_%d-3.svg</a><br> \
1.201 brouard 5024: <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
5025: /* Survival functions (period) in state j */
5026: for(cpt=1; cpt<=nlstate;cpt++){
5027: 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> \
5028: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);
5029: }
5030: /* State specific survival functions (period) */
5031: for(cpt=1; cpt<=nlstate;cpt++){
1.208 brouard 5032: fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
1.201 brouard 5033: Or probability to survive in various states (1 to %d) being in state %d at different ages.\
5034: <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);
5035: }
5036: /* Period (stable) prevalence in each health state */
5037: for(cpt=1; cpt<=nlstate;cpt++){
5038: 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> \
5039: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);
5040: }
1.211 brouard 5041: if(prevfcast==1){
5042: /* Projection of prevalence up to period (stable) prevalence in each health state */
5043: for(cpt=1; cpt<=nlstate;cpt++){
1.214 ! brouard 5044: fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f) up 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> \
1.213 brouard 5045: <img src=\"%s_%d-%d.svg\">", dateprev1, dateprev2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1);
1.211 brouard 5046: }
5047: }
5048:
1.126 brouard 5049: for(cpt=1; cpt<=nlstate;cpt++) {
1.205 brouard 5050: 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 5051: <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 5052: }
1.192 brouard 5053: /* } /\* end i1 *\/ */
1.126 brouard 5054: }/* End k1 */
5055: fprintf(fichtm,"</ul>");
5056:
5057: fprintf(fichtm,"\
5058: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 brouard 5059: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
1.203 brouard 5060: - 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 5061: But because parameters are usually highly correlated (a higher incidence of disability \
5062: and a higher incidence of recovery can give very close observed transition) it might \
5063: be very useful to look not only at linear confidence intervals estimated from the \
5064: variances but at the covariance matrix. And instead of looking at the estimated coefficients \
5065: (parameters) of the logistic regression, it might be more meaningful to visualize the \
5066: covariance matrix of the one-step probabilities. \
5067: See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
1.126 brouard 5068:
1.193 brouard 5069: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 5070: subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
1.126 brouard 5071: fprintf(fichtm,"\
5072: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 5073: subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
1.126 brouard 5074:
5075: fprintf(fichtm,"\
5076: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 5077: subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
1.126 brouard 5078: fprintf(fichtm,"\
5079: - 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): \
5080: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 5081: estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
1.126 brouard 5082: fprintf(fichtm,"\
5083: - (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): \
5084: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 5085: estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
1.126 brouard 5086: fprintf(fichtm,"\
1.128 brouard 5087: - 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 5088: estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
1.126 brouard 5089: fprintf(fichtm,"\
1.128 brouard 5090: - 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 5091: estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
1.126 brouard 5092: fprintf(fichtm,"\
5093: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
1.201 brouard 5094: subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
1.126 brouard 5095:
5096: /* if(popforecast==1) fprintf(fichtm,"\n */
5097: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
5098: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
5099: /* <br>",fileres,fileres,fileres,fileres); */
5100: /* else */
5101: /* 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); */
5102: fflush(fichtm);
5103: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
5104:
1.145 brouard 5105: m=pow(2,cptcoveff);
1.126 brouard 5106: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
5107:
5108: jj1=0;
5109: for(k1=1; k1<=m;k1++){
1.192 brouard 5110: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
1.126 brouard 5111: jj1++;
5112: if (cptcovn > 0) {
5113: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
5114: for (cpt=1; cpt<=cptcoveff;cpt++)
1.198 brouard 5115: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
1.126 brouard 5116: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
5117: }
5118: for(cpt=1; cpt<=nlstate;cpt++) {
5119: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
1.205 brouard 5120: prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d%d.svg\"> %s_%d-%d.svg <br>\
5121: <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 5122: }
5123: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 5124: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
5125: true period expectancies (those weighted with period prevalences are also\
5126: drawn in addition to the population based expectancies computed using\
1.205 brouard 5127: observed and cahotic prevalences: <a href=\"%s_%d.svg\">%s_%d.svg<br>\
5128: <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
1.192 brouard 5129: /* } /\* end i1 *\/ */
1.126 brouard 5130: }/* End k1 */
5131: fprintf(fichtm,"</ul>");
5132: fflush(fichtm);
5133: }
5134:
5135: /******************* Gnuplot file **************/
1.211 brouard 5136: void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, char pathc[], double p[]){
1.126 brouard 5137:
5138: char dirfileres[132],optfileres[132];
1.164 brouard 5139: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
1.211 brouard 5140: int lv=0, vlv=0, kl=0;
1.130 brouard 5141: int ng=0;
1.201 brouard 5142: int vpopbased;
1.126 brouard 5143: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
5144: /* printf("Problem with file %s",optionfilegnuplot); */
5145: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
5146: /* } */
5147:
5148: /*#ifdef windows */
5149: fprintf(ficgp,"cd \"%s\" \n",pathc);
5150: /*#endif */
5151: m=pow(2,cptcoveff);
5152:
1.202 brouard 5153: /* Contribution to likelihood */
5154: /* Plot the probability implied in the likelihood */
5155: fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
5156: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
5157: /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
1.205 brouard 5158: fprintf(ficgp,"\nset ter pngcairo size 640, 480");
1.204 brouard 5159: /* nice for mle=4 plot by number of matrix products.
1.202 brouard 5160: replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
5161: /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */
5162: /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
1.204 brouard 5163: fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
1.214 ! brouard 5164: fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$13):6 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",subdirf(fileresilk));
1.204 brouard 5165: fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
1.214 ! brouard 5166: fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$13):5 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk));
1.204 brouard 5167: for (i=1; i<= nlstate ; i ++) {
5168: fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
1.205 brouard 5169: fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk));
1.214 ! brouard 5170: fprintf(ficgp," u 2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable \\\n",i,1,i,1);
1.204 brouard 5171: for (j=2; j<= nlstate+ndeath ; j ++) {
1.214 ! brouard 5172: fprintf(ficgp,",\\\n \"\" u 2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable ",i,j,i,j);
1.204 brouard 5173: }
5174: fprintf(ficgp,";\nset out; unset ylabel;\n");
5175: }
5176: /* 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 */
5177: /* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
5178: /* 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 5179: fprintf(ficgp,"\nset out;unset log\n");
1.202 brouard 5180: /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
5181:
1.126 brouard 5182: strcpy(dirfileres,optionfilefiname);
5183: strcpy(optfileres,"vpl");
5184: /* 1eme*/
1.211 brouard 5185: for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */
5186: for (k1=1; k1<= m ; k1 ++) { /* For each combination of covariate */
5187: /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
5188: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");
5189: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
5190: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
5191: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5192: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5193: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5194: vlv= nbcode[Tvaraff[lv]][lv];
5195: fprintf(ficgp," V%d=%d ",k,vlv);
5196: }
5197: fprintf(ficgp,"\n#\n");
5198:
1.201 brouard 5199: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
5200: fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
1.126 brouard 5201: fprintf(ficgp,"set xlabel \"Age\" \n\
5202: set ylabel \"Probability\" \n\
1.199 brouard 5203: set ter svg size 640, 480\n\
1.201 brouard 5204: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
1.126 brouard 5205:
5206: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 5207: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
5208: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 5209: }
1.201 brouard 5210: 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 5211: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 5212: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
5213: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 5214: }
1.201 brouard 5215: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
1.126 brouard 5216: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 5217: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
5218: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 5219: }
1.201 brouard 5220: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
5221: fprintf(ficgp,"\nset out \n");
5222: } /* k1 */
5223: } /* cpt */
1.126 brouard 5224: /*2 eme*/
5225: for (k1=1; k1<= m ; k1 ++) {
1.211 brouard 5226: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
5227: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
5228: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
5229: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5230: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5231: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5232: vlv= nbcode[Tvaraff[lv]][lv];
5233: fprintf(ficgp," V%d=%d ",k,vlv);
5234: }
5235: fprintf(ficgp,"\n#\n");
5236:
1.201 brouard 5237: fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
5238: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
5239: if(vpopbased==0)
5240: fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
5241: else
5242: fprintf(ficgp,"\nreplot ");
5243: for (i=1; i<= nlstate+1 ; i ++) {
5244: k=2*i;
5245: 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);
5246: for (j=1; j<= nlstate+1 ; j ++) {
5247: if (j==i) fprintf(ficgp," %%lf (%%lf)");
5248: else fprintf(ficgp," %%*lf (%%*lf)");
5249: }
5250: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
5251: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
5252: 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);
5253: for (j=1; j<= nlstate+1 ; j ++) {
5254: if (j==i) fprintf(ficgp," %%lf (%%lf)");
5255: else fprintf(ficgp," %%*lf (%%*lf)");
5256: }
5257: fprintf(ficgp,"\" t\"\" w l lt 0,");
5258: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
5259: for (j=1; j<= nlstate+1 ; j ++) {
5260: if (j==i) fprintf(ficgp," %%lf (%%lf)");
5261: else fprintf(ficgp," %%*lf (%%*lf)");
5262: }
5263: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
5264: else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
5265: } /* state */
5266: } /* vpopbased */
5267: fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
5268: } /* k1 */
1.211 brouard 5269:
5270:
1.126 brouard 5271: /*3eme*/
5272: for (k1=1; k1<= m ; k1 ++) {
5273: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.211 brouard 5274: fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files: cov=%d state=%d",k1, cpt);
5275: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
5276: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
5277: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5278: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5279: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5280: vlv= nbcode[Tvaraff[lv]][lv];
5281: fprintf(ficgp," V%d=%d ",k,vlv);
5282: }
5283: fprintf(ficgp,"\n#\n");
5284:
1.126 brouard 5285: /* k=2+nlstate*(2*cpt-2); */
5286: k=2+(nlstate+1)*(cpt-1);
1.201 brouard 5287: fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
1.199 brouard 5288: fprintf(ficgp,"set ter svg size 640, 480\n\
1.201 brouard 5289: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
1.126 brouard 5290: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
5291: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
5292: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
5293: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
5294: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
5295: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
5296:
5297: */
5298: for (i=1; i< nlstate ; i ++) {
1.201 brouard 5299: 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 5300: /* 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);*/
5301:
5302: }
1.201 brouard 5303: 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 5304: }
5305: }
5306:
1.201 brouard 5307: /* Survival functions (period) from state i in state j by initial state i */
5308: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
5309: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.211 brouard 5310: fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
5311: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
5312: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
5313: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5314: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5315: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5316: vlv= nbcode[Tvaraff[lv]][lv];
5317: fprintf(ficgp," V%d=%d ",k,vlv);
5318: }
5319: fprintf(ficgp,"\n#\n");
5320:
1.201 brouard 5321: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
5322: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
5323: set ter svg size 640, 480\n\
5324: unset log y\n\
5325: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 5326: k=3;
1.201 brouard 5327: for (i=1; i<= nlstate ; i ++){
5328: if(i==1)
5329: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
5330: else
5331: fprintf(ficgp,", '' ");
5332: l=(nlstate+ndeath)*(i-1)+1;
5333: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
5334: for (j=2; j<= nlstate+ndeath ; j ++)
5335: fprintf(ficgp,"+$%d",k+l+j-1);
5336: fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
5337: } /* nlstate */
5338: fprintf(ficgp,"\nset out\n");
5339: } /* end cpt state*/
5340: } /* end covariate */
5341:
5342: /* Survival functions (period) from state i in state j by final state j */
1.202 brouard 5343: for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
1.201 brouard 5344: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
5345: 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);
1.211 brouard 5346: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
5347: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
5348: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5349: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5350: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5351: vlv= nbcode[Tvaraff[lv]][lv];
5352: fprintf(ficgp," V%d=%d ",k,vlv);
5353: }
5354: fprintf(ficgp,"\n#\n");
5355:
1.201 brouard 5356: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
5357: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
5358: set ter svg size 640, 480\n\
5359: unset log y\n\
5360: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 5361: k=3;
1.201 brouard 5362: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
5363: if(j==1)
5364: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
5365: else
5366: fprintf(ficgp,", '' ");
5367: l=(nlstate+ndeath)*(cpt-1) +j;
5368: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
5369: /* for (i=2; i<= nlstate+ndeath ; i ++) */
5370: /* fprintf(ficgp,"+$%d",k+l+i-1); */
5371: fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
5372: } /* nlstate */
5373: fprintf(ficgp,", '' ");
5374: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
5375: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
5376: l=(nlstate+ndeath)*(cpt-1) +j;
5377: if(j < nlstate)
5378: fprintf(ficgp,"$%d +",k+l);
5379: else
5380: fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
5381: }
5382: fprintf(ficgp,"\nset out\n");
5383: } /* end cpt state*/
5384: } /* end covariate */
5385:
1.202 brouard 5386: /* CV preval stable (period) for each covariate */
1.211 brouard 5387: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
1.153 brouard 5388: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.211 brouard 5389: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
5390: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
5391: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
5392: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5393: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5394: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5395: vlv= nbcode[Tvaraff[lv]][lv];
5396: fprintf(ficgp," V%d=%d ",k,vlv);
5397: }
5398: fprintf(ficgp,"\n#\n");
5399:
1.201 brouard 5400: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
1.126 brouard 5401: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.199 brouard 5402: set ter svg size 640, 480\n\
1.126 brouard 5403: unset log y\n\
1.153 brouard 5404: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 5405: k=3; /* Offset */
1.153 brouard 5406: for (i=1; i<= nlstate ; i ++){
5407: if(i==1)
1.201 brouard 5408: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
1.153 brouard 5409: else
5410: fprintf(ficgp,", '' ");
1.154 brouard 5411: l=(nlstate+ndeath)*(i-1)+1;
5412: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
1.201 brouard 5413: for (j=2; j<= nlstate ; j ++)
5414: fprintf(ficgp,"+$%d",k+l+j-1);
1.153 brouard 5415: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
5416: } /* nlstate */
1.201 brouard 5417: fprintf(ficgp,"\nset out\n");
1.153 brouard 5418: } /* end cpt state*/
5419: } /* end covariate */
1.201 brouard 5420:
1.211 brouard 5421: if(prevfcast==1){
5422: /* Projection from cross-sectional to stable (period) for each covariate */
5423:
5424: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
5425: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
5426: fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
5427: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
5428: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
5429: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5430: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5431: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5432: vlv= nbcode[Tvaraff[lv]][lv];
5433: fprintf(ficgp," V%d=%d ",k,vlv);
5434: }
5435: fprintf(ficgp,"\n#\n");
5436:
5437: fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
5438: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);
5439: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
5440: set ter svg size 640, 480\n\
5441: unset log y\n\
5442: plot [%.f:%.f] ", ageminpar, agemaxpar);
5443: for (i=1; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
5444: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
5445: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
5446: /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
5447: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
5448: if(i==1){
5449: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
5450: }else{
5451: fprintf(ficgp,",\\\n '' ");
5452: }
5453: if(cptcoveff ==0){ /* No covariate */
5454: fprintf(ficgp," u 2:("); /* Age is in 2 */
5455: /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
5456: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
5457: if(i==nlstate+1)
5458: fprintf(ficgp," $%d/(1.-$%d)) t 'p.%d' with line ", \
5459: 2+(cpt-1)*(nlstate+1)+1+(i-1), 2+1+(i-1)+(nlstate+1)*nlstate,cpt );
5460: else
5461: fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \
5462: 2+(cpt-1)*(nlstate+1)+1+(i-1), 2+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
5463: }else{
5464: fprintf(ficgp,"u 6:(("); /* Age is in 6 */
5465: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
5466: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
5467: kl=0;
5468: for (k=1; k<=cptcoveff; k++){ /* For each covariate */
5469: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
5470: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5471: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5472: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5473: vlv= nbcode[Tvaraff[lv]][lv];
5474: kl++;
5475: /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
5476: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
5477: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
5478: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
5479: if(k==cptcoveff)
5480: if(i==nlstate+1)
5481: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ",kl, k,kl+1,nbcode[Tvaraff[lv]][lv], \
5482: 6+(cpt-1)*(nlstate+1)+1+(i-1), 6+1+(i-1)+(nlstate+1)*nlstate,cpt );
5483: else
5484: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ",kl, k,kl+1,nbcode[Tvaraff[lv]][lv], \
5485: 6+(cpt-1)*(nlstate+1)+1+(i-1), 6+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
5486: else{
5487: fprintf(ficgp,"$%d==%d && $%d==%d && ",kl, k,kl+1,nbcode[Tvaraff[lv]][lv]);
5488: kl++;
5489: }
5490: } /* end covariate */
5491: } /* end if covariate */
5492: } /* nlstate */
5493: fprintf(ficgp,"\nset out\n");
5494: } /* end cpt state*/
5495: } /* end covariate */
5496: } /* End if prevfcast */
5497:
5498:
1.126 brouard 5499: /* proba elementaires */
1.187 brouard 5500: fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
1.126 brouard 5501: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 5502: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 5503: for(k=1; k <=(nlstate+ndeath); k++){
5504: if (k != i) {
1.187 brouard 5505: fprintf(ficgp,"# current state %d\n",k);
1.126 brouard 5506: for(j=1; j <=ncovmodel; j++){
1.187 brouard 5507: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
1.126 brouard 5508: jk++;
5509: }
1.187 brouard 5510: fprintf(ficgp,"\n");
1.126 brouard 5511: }
5512: }
5513: }
1.187 brouard 5514: fprintf(ficgp,"##############\n#\n");
5515:
1.145 brouard 5516: /*goto avoid;*/
1.200 brouard 5517: fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");
1.187 brouard 5518: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
5519: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
5520: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
5521: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
5522: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
5523: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
5524: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
5525: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
5526: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
5527: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
5528: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
5529: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
5530: fprintf(ficgp,"#\n");
1.201 brouard 5531: for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
1.187 brouard 5532: fprintf(ficgp,"# ng=%d\n",ng);
5533: fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);
1.126 brouard 5534: for(jk=1; jk <=m; jk++) {
1.187 brouard 5535: fprintf(ficgp,"# jk=%d\n",jk);
1.201 brouard 5536: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
5537: fprintf(ficgp,"\nset ter svg size 640, 480 ");
5538: if (ng==1){
5539: fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
5540: fprintf(ficgp,"\nunset log y");
5541: }else if (ng==2){
5542: fprintf(ficgp,"\nset ylabel \"Probability\"\n");
5543: fprintf(ficgp,"\nset log y");
5544: }else if (ng==3){
1.126 brouard 5545: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
1.201 brouard 5546: fprintf(ficgp,"\nset log y");
5547: }else
5548: fprintf(ficgp,"\nunset title ");
5549: fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar);
1.126 brouard 5550: i=1;
5551: for(k2=1; k2<=nlstate; k2++) {
5552: k3=i;
5553: for(k=1; k<=(nlstate+ndeath); k++) {
5554: if (k != k2){
1.201 brouard 5555: switch( ng) {
5556: case 1:
1.187 brouard 5557: if(nagesqr==0)
1.201 brouard 5558: fprintf(ficgp," p%d+p%d*x",i,i+1);
1.187 brouard 5559: else /* nagesqr =1 */
1.201 brouard 5560: fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
5561: break;
5562: case 2: /* ng=2 */
1.187 brouard 5563: if(nagesqr==0)
5564: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
5565: else /* nagesqr =1 */
1.201 brouard 5566: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
5567: break;
5568: case 3:
5569: if(nagesqr==0)
5570: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
5571: else /* nagesqr =1 */
5572: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
5573: break;
5574: }
1.141 brouard 5575: ij=1;/* To be checked else nbcode[0][0] wrong */
1.187 brouard 5576: for(j=3; j <=ncovmodel-nagesqr; j++) {
1.197 brouard 5577: /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
5578: if(ij <=cptcovage) { /* Bug valgrind */
5579: if((j-2)==Tage[ij]) { /* Bug valgrind */
1.200 brouard 5580: fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
5581: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
1.197 brouard 5582: ij++;
5583: }
1.186 brouard 5584: }
5585: else
1.198 brouard 5586: fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
1.126 brouard 5587: }
1.201 brouard 5588: if(ng != 1){
5589: fprintf(ficgp,")/(1");
1.126 brouard 5590:
1.201 brouard 5591: for(k1=1; k1 <=nlstate; k1++){
5592: if(nagesqr==0)
5593: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
5594: else /* nagesqr =1 */
5595: 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);
5596:
5597: ij=1;
5598: for(j=3; j <=ncovmodel-nagesqr; j++){
5599: if(ij <=cptcovage) { /* Bug valgrind */
5600: if((j-2)==Tage[ij]) { /* Bug valgrind */
5601: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
5602: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
5603: ij++;
5604: }
1.197 brouard 5605: }
1.201 brouard 5606: else
5607: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
1.186 brouard 5608: }
1.201 brouard 5609: fprintf(ficgp,")");
1.126 brouard 5610: }
5611: fprintf(ficgp,")");
1.201 brouard 5612: if(ng ==2)
5613: fprintf(ficgp," t \"p%d%d\" ", k2,k);
5614: else /* ng= 3 */
5615: fprintf(ficgp," t \"i%d%d\" ", k2,k);
5616: }else{ /* end ng <> 1 */
5617: fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
1.126 brouard 5618: }
5619: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
5620: i=i+ncovmodel;
5621: }
5622: } /* end k */
5623: } /* end k2 */
1.201 brouard 5624: fprintf(ficgp,"\n set out\n");
1.126 brouard 5625: } /* end jk */
5626: } /* end ng */
1.164 brouard 5627: /* avoid: */
1.126 brouard 5628: fflush(ficgp);
5629: } /* end gnuplot */
5630:
5631:
5632: /*************** Moving average **************/
5633: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
5634:
5635: int i, cpt, cptcod;
5636: int modcovmax =1;
5637: int mobilavrange, mob;
5638: double age;
5639:
5640: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
5641: a covariate has 2 modalities */
5642: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
5643:
5644: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
5645: if(mobilav==1) mobilavrange=5; /* default */
5646: else mobilavrange=mobilav;
5647: for (age=bage; age<=fage; age++)
5648: for (i=1; i<=nlstate;i++)
5649: for (cptcod=1;cptcod<=modcovmax;cptcod++)
5650: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
5651: /* We keep the original values on the extreme ages bage, fage and for
5652: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
5653: we use a 5 terms etc. until the borders are no more concerned.
5654: */
5655: for (mob=3;mob <=mobilavrange;mob=mob+2){
5656: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
5657: for (i=1; i<=nlstate;i++){
5658: for (cptcod=1;cptcod<=modcovmax;cptcod++){
5659: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
5660: for (cpt=1;cpt<=(mob-1)/2;cpt++){
5661: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
5662: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
5663: }
5664: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
5665: }
5666: }
5667: }/* end age */
5668: }/* end mob */
5669: }else return -1;
5670: return 0;
5671: }/* End movingaverage */
5672:
5673:
5674: /************** Forecasting ******************/
1.169 brouard 5675: 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 5676: /* proj1, year, month, day of starting projection
5677: agemin, agemax range of age
5678: dateprev1 dateprev2 range of dates during which prevalence is computed
5679: anproj2 year of en of projection (same day and month as proj1).
5680: */
1.164 brouard 5681: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
1.126 brouard 5682: double agec; /* generic age */
5683: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
5684: double *popeffectif,*popcount;
5685: double ***p3mat;
5686: double ***mobaverage;
5687: char fileresf[FILENAMELENGTH];
5688:
5689: agelim=AGESUP;
1.211 brouard 5690: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
5691: in each health status at the date of interview (if between dateprev1 and dateprev2).
5692: We still use firstpass and lastpass as another selection.
5693: */
1.214 ! brouard 5694: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
! 5695: /* firstpass, lastpass, stepm, weightopt, model); */
1.126 brouard 5696: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5697:
1.201 brouard 5698: strcpy(fileresf,"F_");
5699: strcat(fileresf,fileresu);
1.126 brouard 5700: if((ficresf=fopen(fileresf,"w"))==NULL) {
5701: printf("Problem with forecast resultfile: %s\n", fileresf);
5702: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
5703: }
5704: printf("Computing forecasting: result on file '%s' \n", fileresf);
5705: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
5706:
5707: if (cptcoveff==0) ncodemax[cptcoveff]=1;
5708:
5709: if (mobilav!=0) {
5710: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5711: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
5712: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5713: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5714: }
5715: }
5716:
5717: stepsize=(int) (stepm+YEARM-1)/YEARM;
5718: if (stepm<=12) stepsize=1;
5719: if(estepm < stepm){
5720: printf ("Problem %d lower than %d\n",estepm, stepm);
5721: }
5722: else hstepm=estepm;
5723:
5724: hstepm=hstepm/stepm;
5725: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
5726: fractional in yp1 */
5727: anprojmean=yp;
5728: yp2=modf((yp1*12),&yp);
5729: mprojmean=yp;
5730: yp1=modf((yp2*30.5),&yp);
5731: jprojmean=yp;
5732: if(jprojmean==0) jprojmean=1;
5733: if(mprojmean==0) jprojmean=1;
5734:
5735: i1=cptcoveff;
5736: if (cptcovn < 1){i1=1;}
5737:
5738: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
5739:
5740: fprintf(ficresf,"#****** Routine prevforecast **\n");
5741:
5742: /* if (h==(int)(YEARM*yearp)){ */
5743: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
5744: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
5745: k=k+1;
1.211 brouard 5746: fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
1.126 brouard 5747: for(j=1;j<=cptcoveff;j++) {
1.211 brouard 5748: fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 5749: }
1.211 brouard 5750: fprintf(ficresf," yearproj age");
1.126 brouard 5751: for(j=1; j<=nlstate+ndeath;j++){
5752: for(i=1; i<=nlstate;i++)
5753: fprintf(ficresf," p%d%d",i,j);
5754: fprintf(ficresf," p.%d",j);
5755: }
5756: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
5757: fprintf(ficresf,"\n");
5758: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
5759:
5760: for (agec=fage; agec>=(ageminpar-1); agec--){
5761: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
5762: nhstepm = nhstepm/hstepm;
5763: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5764: oldm=oldms;savm=savms;
5765: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
5766:
5767: for (h=0; h<=nhstepm; h++){
5768: if (h*hstepm/YEARM*stepm ==yearp) {
5769: fprintf(ficresf,"\n");
5770: for(j=1;j<=cptcoveff;j++)
1.198 brouard 5771: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 5772: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
5773: }
5774: for(j=1; j<=nlstate+ndeath;j++) {
5775: ppij=0.;
5776: for(i=1; i<=nlstate;i++) {
5777: if (mobilav==1)
5778: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
5779: else {
5780: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
5781: }
5782: if (h*hstepm/YEARM*stepm== yearp) {
5783: fprintf(ficresf," %.3f", p3mat[i][j][h]);
5784: }
5785: } /* end i */
5786: if (h*hstepm/YEARM*stepm==yearp) {
5787: fprintf(ficresf," %.3f", ppij);
5788: }
5789: }/* end j */
5790: } /* end h */
5791: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5792: } /* end agec */
5793: } /* end yearp */
5794: } /* end cptcod */
5795: } /* end cptcov */
5796:
5797: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5798:
5799: fclose(ficresf);
5800: }
5801:
5802: /************** Forecasting *****not tested NB*************/
1.169 brouard 5803: 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 5804:
5805: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
5806: int *popage;
5807: double calagedatem, agelim, kk1, kk2;
5808: double *popeffectif,*popcount;
5809: double ***p3mat,***tabpop,***tabpopprev;
5810: double ***mobaverage;
5811: char filerespop[FILENAMELENGTH];
5812:
5813: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5814: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5815: agelim=AGESUP;
5816: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
5817:
5818: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5819:
5820:
1.201 brouard 5821: strcpy(filerespop,"POP_");
5822: strcat(filerespop,fileresu);
1.126 brouard 5823: if((ficrespop=fopen(filerespop,"w"))==NULL) {
5824: printf("Problem with forecast resultfile: %s\n", filerespop);
5825: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
5826: }
5827: printf("Computing forecasting: result on file '%s' \n", filerespop);
5828: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
5829:
5830: if (cptcoveff==0) ncodemax[cptcoveff]=1;
5831:
5832: if (mobilav!=0) {
5833: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5834: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
5835: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5836: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5837: }
5838: }
5839:
5840: stepsize=(int) (stepm+YEARM-1)/YEARM;
5841: if (stepm<=12) stepsize=1;
5842:
5843: agelim=AGESUP;
5844:
5845: hstepm=1;
5846: hstepm=hstepm/stepm;
5847:
5848: if (popforecast==1) {
5849: if((ficpop=fopen(popfile,"r"))==NULL) {
5850: printf("Problem with population file : %s\n",popfile);exit(0);
5851: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
5852: }
5853: popage=ivector(0,AGESUP);
5854: popeffectif=vector(0,AGESUP);
5855: popcount=vector(0,AGESUP);
5856:
5857: i=1;
5858: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
5859:
5860: imx=i;
5861: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
5862: }
5863:
5864: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
5865: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
5866: k=k+1;
5867: fprintf(ficrespop,"\n#******");
5868: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 5869: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 5870: }
5871: fprintf(ficrespop,"******\n");
5872: fprintf(ficrespop,"# Age");
5873: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
5874: if (popforecast==1) fprintf(ficrespop," [Population]");
5875:
5876: for (cpt=0; cpt<=0;cpt++) {
5877: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5878:
5879: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5880: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5881: nhstepm = nhstepm/hstepm;
5882:
5883: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5884: oldm=oldms;savm=savms;
5885: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5886:
5887: for (h=0; h<=nhstepm; h++){
5888: if (h==(int) (calagedatem+YEARM*cpt)) {
5889: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5890: }
5891: for(j=1; j<=nlstate+ndeath;j++) {
5892: kk1=0.;kk2=0;
5893: for(i=1; i<=nlstate;i++) {
5894: if (mobilav==1)
5895: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
5896: else {
5897: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
5898: }
5899: }
5900: if (h==(int)(calagedatem+12*cpt)){
5901: tabpop[(int)(agedeb)][j][cptcod]=kk1;
5902: /*fprintf(ficrespop," %.3f", kk1);
5903: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
5904: }
5905: }
5906: for(i=1; i<=nlstate;i++){
5907: kk1=0.;
5908: for(j=1; j<=nlstate;j++){
5909: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
5910: }
5911: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
5912: }
5913:
5914: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
5915: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
5916: }
5917: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5918: }
5919: }
5920:
5921: /******/
5922:
5923: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
5924: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5925: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5926: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5927: nhstepm = nhstepm/hstepm;
5928:
5929: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5930: oldm=oldms;savm=savms;
5931: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5932: for (h=0; h<=nhstepm; h++){
5933: if (h==(int) (calagedatem+YEARM*cpt)) {
5934: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5935: }
5936: for(j=1; j<=nlstate+ndeath;j++) {
5937: kk1=0.;kk2=0;
5938: for(i=1; i<=nlstate;i++) {
5939: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
5940: }
5941: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
5942: }
5943: }
5944: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5945: }
5946: }
5947: }
5948: }
5949:
5950: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5951:
5952: if (popforecast==1) {
5953: free_ivector(popage,0,AGESUP);
5954: free_vector(popeffectif,0,AGESUP);
5955: free_vector(popcount,0,AGESUP);
5956: }
5957: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5958: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5959: fclose(ficrespop);
5960: } /* End of popforecast */
5961:
5962: int fileappend(FILE *fichier, char *optionfich)
5963: {
5964: if((fichier=fopen(optionfich,"a"))==NULL) {
5965: printf("Problem with file: %s\n", optionfich);
5966: fprintf(ficlog,"Problem with file: %s\n", optionfich);
5967: return (0);
5968: }
5969: fflush(fichier);
5970: return (1);
5971: }
5972:
5973:
5974: /**************** function prwizard **********************/
5975: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
5976: {
5977:
5978: /* Wizard to print covariance matrix template */
5979:
1.164 brouard 5980: char ca[32], cb[32];
5981: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 5982: int numlinepar;
5983:
5984: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5985: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5986: for(i=1; i <=nlstate; i++){
5987: jj=0;
5988: for(j=1; j <=nlstate+ndeath; j++){
5989: if(j==i) continue;
5990: jj++;
5991: /*ca[0]= k+'a'-1;ca[1]='\0';*/
5992: printf("%1d%1d",i,j);
5993: fprintf(ficparo,"%1d%1d",i,j);
5994: for(k=1; k<=ncovmodel;k++){
5995: /* printf(" %lf",param[i][j][k]); */
5996: /* fprintf(ficparo," %lf",param[i][j][k]); */
5997: printf(" 0.");
5998: fprintf(ficparo," 0.");
5999: }
6000: printf("\n");
6001: fprintf(ficparo,"\n");
6002: }
6003: }
6004: printf("# Scales (for hessian or gradient estimation)\n");
6005: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
6006: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
6007: for(i=1; i <=nlstate; i++){
6008: jj=0;
6009: for(j=1; j <=nlstate+ndeath; j++){
6010: if(j==i) continue;
6011: jj++;
6012: fprintf(ficparo,"%1d%1d",i,j);
6013: printf("%1d%1d",i,j);
6014: fflush(stdout);
6015: for(k=1; k<=ncovmodel;k++){
6016: /* printf(" %le",delti3[i][j][k]); */
6017: /* fprintf(ficparo," %le",delti3[i][j][k]); */
6018: printf(" 0.");
6019: fprintf(ficparo," 0.");
6020: }
6021: numlinepar++;
6022: printf("\n");
6023: fprintf(ficparo,"\n");
6024: }
6025: }
6026: printf("# Covariance matrix\n");
6027: /* # 121 Var(a12)\n\ */
6028: /* # 122 Cov(b12,a12) Var(b12)\n\ */
6029: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
6030: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
6031: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
6032: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
6033: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
6034: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
6035: fflush(stdout);
6036: fprintf(ficparo,"# Covariance matrix\n");
6037: /* # 121 Var(a12)\n\ */
6038: /* # 122 Cov(b12,a12) Var(b12)\n\ */
6039: /* # ...\n\ */
6040: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
6041:
6042: for(itimes=1;itimes<=2;itimes++){
6043: jj=0;
6044: for(i=1; i <=nlstate; i++){
6045: for(j=1; j <=nlstate+ndeath; j++){
6046: if(j==i) continue;
6047: for(k=1; k<=ncovmodel;k++){
6048: jj++;
6049: ca[0]= k+'a'-1;ca[1]='\0';
6050: if(itimes==1){
6051: printf("#%1d%1d%d",i,j,k);
6052: fprintf(ficparo,"#%1d%1d%d",i,j,k);
6053: }else{
6054: printf("%1d%1d%d",i,j,k);
6055: fprintf(ficparo,"%1d%1d%d",i,j,k);
6056: /* printf(" %.5le",matcov[i][j]); */
6057: }
6058: ll=0;
6059: for(li=1;li <=nlstate; li++){
6060: for(lj=1;lj <=nlstate+ndeath; lj++){
6061: if(lj==li) continue;
6062: for(lk=1;lk<=ncovmodel;lk++){
6063: ll++;
6064: if(ll<=jj){
6065: cb[0]= lk +'a'-1;cb[1]='\0';
6066: if(ll<jj){
6067: if(itimes==1){
6068: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6069: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6070: }else{
6071: printf(" 0.");
6072: fprintf(ficparo," 0.");
6073: }
6074: }else{
6075: if(itimes==1){
6076: printf(" Var(%s%1d%1d)",ca,i,j);
6077: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
6078: }else{
6079: printf(" 0.");
6080: fprintf(ficparo," 0.");
6081: }
6082: }
6083: }
6084: } /* end lk */
6085: } /* end lj */
6086: } /* end li */
6087: printf("\n");
6088: fprintf(ficparo,"\n");
6089: numlinepar++;
6090: } /* end k*/
6091: } /*end j */
6092: } /* end i */
6093: } /* end itimes */
6094:
6095: } /* end of prwizard */
6096: /******************* Gompertz Likelihood ******************************/
6097: double gompertz(double x[])
6098: {
6099: double A,B,L=0.0,sump=0.,num=0.;
6100: int i,n=0; /* n is the size of the sample */
6101:
6102: for (i=0;i<=imx-1 ; i++) {
6103: sump=sump+weight[i];
6104: /* sump=sump+1;*/
6105: num=num+1;
6106: }
6107:
6108:
6109: /* for (i=0; i<=imx; i++)
6110: 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]);*/
6111:
6112: for (i=1;i<=imx ; i++)
6113: {
6114: if (cens[i] == 1 && wav[i]>1)
6115: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
6116:
6117: if (cens[i] == 0 && wav[i]>1)
6118: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
6119: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
6120:
6121: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
6122: if (wav[i] > 1 ) { /* ??? */
6123: L=L+A*weight[i];
6124: /* 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]);*/
6125: }
6126: }
6127:
6128: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
6129:
6130: return -2*L*num/sump;
6131: }
6132:
1.136 brouard 6133: #ifdef GSL
6134: /******************* Gompertz_f Likelihood ******************************/
6135: double gompertz_f(const gsl_vector *v, void *params)
6136: {
6137: double A,B,LL=0.0,sump=0.,num=0.;
6138: double *x= (double *) v->data;
6139: int i,n=0; /* n is the size of the sample */
6140:
6141: for (i=0;i<=imx-1 ; i++) {
6142: sump=sump+weight[i];
6143: /* sump=sump+1;*/
6144: num=num+1;
6145: }
6146:
6147:
6148: /* for (i=0; i<=imx; i++)
6149: 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]);*/
6150: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
6151: for (i=1;i<=imx ; i++)
6152: {
6153: if (cens[i] == 1 && wav[i]>1)
6154: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
6155:
6156: if (cens[i] == 0 && wav[i]>1)
6157: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
6158: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
6159:
6160: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
6161: if (wav[i] > 1 ) { /* ??? */
6162: LL=LL+A*weight[i];
6163: /* 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]);*/
6164: }
6165: }
6166:
6167: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
6168: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
6169:
6170: return -2*LL*num/sump;
6171: }
6172: #endif
6173:
1.126 brouard 6174: /******************* Printing html file ***********/
1.201 brouard 6175: void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 6176: int lastpass, int stepm, int weightopt, char model[],\
6177: int imx, double p[],double **matcov,double agemortsup){
6178: int i,k;
6179:
6180: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
6181: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
6182: for (i=1;i<=2;i++)
6183: 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 6184: fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
1.126 brouard 6185: fprintf(fichtm,"</ul>");
6186:
6187: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
6188:
6189: 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>");
6190:
6191: for (k=agegomp;k<(agemortsup-2);k++)
6192: 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]);
6193:
6194:
6195: fflush(fichtm);
6196: }
6197:
6198: /******************* Gnuplot file **************/
1.201 brouard 6199: void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 6200:
6201: char dirfileres[132],optfileres[132];
1.164 brouard 6202:
1.126 brouard 6203: int ng;
6204:
6205:
6206: /*#ifdef windows */
6207: fprintf(ficgp,"cd \"%s\" \n",pathc);
6208: /*#endif */
6209:
6210:
6211: strcpy(dirfileres,optionfilefiname);
6212: strcpy(optfileres,"vpl");
1.199 brouard 6213: fprintf(ficgp,"set out \"graphmort.svg\"\n ");
1.126 brouard 6214: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.199 brouard 6215: fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
1.145 brouard 6216: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 6217: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
6218:
6219: }
6220:
1.136 brouard 6221: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
6222: {
1.126 brouard 6223:
1.136 brouard 6224: /*-------- data file ----------*/
6225: FILE *fic;
6226: char dummy[]=" ";
1.164 brouard 6227: int i=0, j=0, n=0;
1.136 brouard 6228: int linei, month, year,iout;
6229: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 6230: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 6231: char *stratrunc;
6232: int lstra;
1.126 brouard 6233:
6234:
1.136 brouard 6235: if((fic=fopen(datafile,"r"))==NULL) {
1.195 brouard 6236: printf("Problem while opening datafile: %s\n", datafile);fflush(stdout);
6237: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);fflush(ficlog);return 1;
1.136 brouard 6238: }
1.126 brouard 6239:
1.136 brouard 6240: i=1;
6241: linei=0;
6242: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
6243: linei=linei+1;
6244: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
6245: if(line[j] == '\t')
6246: line[j] = ' ';
6247: }
6248: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
6249: ;
6250: };
6251: line[j+1]=0; /* Trims blanks at end of line */
6252: if(line[0]=='#'){
6253: fprintf(ficlog,"Comment line\n%s\n",line);
6254: printf("Comment line\n%s\n",line);
6255: continue;
6256: }
6257: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 6258: strcpy(line, linetmp);
1.136 brouard 6259:
1.126 brouard 6260:
1.136 brouard 6261: for (j=maxwav;j>=1;j--){
1.137 brouard 6262: cutv(stra, strb, line, ' ');
1.136 brouard 6263: if(strb[0]=='.') { /* Missing status */
6264: lval=-1;
6265: }else{
6266: errno=0;
6267: lval=strtol(strb,&endptr,10);
6268: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
6269: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 6270: 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);
6271: 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 6272: return 1;
6273: }
6274: }
6275: s[j][i]=lval;
6276:
6277: strcpy(line,stra);
6278: cutv(stra, strb,line,' ');
1.169 brouard 6279: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 6280: }
1.169 brouard 6281: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 6282: month=99;
6283: year=9999;
6284: }else{
1.141 brouard 6285: 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);
6286: 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 6287: return 1;
6288: }
6289: anint[j][i]= (double) year;
6290: mint[j][i]= (double)month;
6291: strcpy(line,stra);
6292: } /* ENd Waves */
6293:
6294: cutv(stra, strb,line,' ');
1.169 brouard 6295: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 6296: }
1.169 brouard 6297: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 6298: month=99;
6299: year=9999;
6300: }else{
1.141 brouard 6301: 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);
6302: 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 6303: return 1;
6304: }
6305: andc[i]=(double) year;
6306: moisdc[i]=(double) month;
6307: strcpy(line,stra);
6308:
6309: cutv(stra, strb,line,' ');
1.169 brouard 6310: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 6311: }
1.169 brouard 6312: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 6313: month=99;
6314: year=9999;
6315: }else{
1.141 brouard 6316: 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);
6317: 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 6318: return 1;
6319: }
6320: if (year==9999) {
1.141 brouard 6321: 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);
6322: 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 6323: return 1;
1.126 brouard 6324:
1.136 brouard 6325: }
6326: annais[i]=(double)(year);
6327: moisnais[i]=(double)(month);
6328: strcpy(line,stra);
6329:
6330: cutv(stra, strb,line,' ');
6331: errno=0;
6332: dval=strtod(strb,&endptr);
6333: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 6334: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
6335: 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 6336: fflush(ficlog);
6337: return 1;
6338: }
6339: weight[i]=dval;
6340: strcpy(line,stra);
6341:
6342: for (j=ncovcol;j>=1;j--){
6343: cutv(stra, strb,line,' ');
6344: if(strb[0]=='.') { /* Missing status */
6345: lval=-1;
6346: }else{
6347: errno=0;
6348: lval=strtol(strb,&endptr,10);
6349: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 6350: 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);
6351: 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 6352: return 1;
6353: }
6354: }
6355: if(lval <-1 || lval >1){
1.141 brouard 6356: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 6357: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
6358: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
6359: For example, for multinomial values like 1, 2 and 3,\n \
6360: build V1=0 V2=0 for the reference value (1),\n \
6361: V1=1 V2=0 for (2) \n \
6362: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
6363: output of IMaCh is often meaningless.\n \
6364: Exiting.\n",lval,linei, i,line,j);
1.141 brouard 6365: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 6366: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
6367: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
6368: For example, for multinomial values like 1, 2 and 3,\n \
6369: build V1=0 V2=0 for the reference value (1),\n \
6370: V1=1 V2=0 for (2) \n \
6371: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
6372: output of IMaCh is often meaningless.\n \
6373: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
6374: return 1;
6375: }
6376: covar[j][i]=(double)(lval);
6377: strcpy(line,stra);
6378: }
6379: lstra=strlen(stra);
6380:
6381: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
6382: stratrunc = &(stra[lstra-9]);
6383: num[i]=atol(stratrunc);
6384: }
6385: else
6386: num[i]=atol(stra);
6387: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
6388: 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;}*/
6389:
6390: i=i+1;
6391: } /* End loop reading data */
1.126 brouard 6392:
1.136 brouard 6393: *imax=i-1; /* Number of individuals */
6394: fclose(fic);
6395:
6396: return (0);
1.164 brouard 6397: /* endread: */
1.136 brouard 6398: printf("Exiting readdata: ");
6399: fclose(fic);
6400: return (1);
1.126 brouard 6401:
6402:
6403:
1.136 brouard 6404: }
1.145 brouard 6405: void removespace(char *str) {
6406: char *p1 = str, *p2 = str;
6407: do
6408: while (*p2 == ' ')
6409: p2++;
1.169 brouard 6410: while (*p1++ == *p2++);
1.145 brouard 6411: }
6412:
6413: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
1.187 brouard 6414: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
6415: * - nagesqr = 1 if age*age in the model, otherwise 0.
6416: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
6417: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
1.145 brouard 6418: * - cptcovage number of covariates with age*products =2
6419: * - cptcovs number of simple covariates
6420: * - 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
6421: * which is a new column after the 9 (ncovcol) variables.
6422: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
6423: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
6424: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
6425: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
6426: */
1.136 brouard 6427: {
1.145 brouard 6428: int i, j, k, ks;
1.164 brouard 6429: int j1, k1, k2;
1.136 brouard 6430: char modelsav[80];
1.145 brouard 6431: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 6432: char *strpt;
1.136 brouard 6433:
1.145 brouard 6434: /*removespace(model);*/
1.136 brouard 6435: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 6436: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 6437: if (strstr(model,"AGE") !=0){
1.192 brouard 6438: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
6439: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 6440: return 1;
6441: }
1.141 brouard 6442: if (strstr(model,"v") !=0){
6443: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
6444: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
6445: return 1;
6446: }
1.187 brouard 6447: strcpy(modelsav,model);
6448: if ((strpt=strstr(model,"age*age")) !=0){
6449: printf(" strpt=%s, model=%s\n",strpt, model);
6450: if(strpt != model){
6451: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 6452: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 6453: corresponding column of parameters.\n",model);
6454: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 6455: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 6456: corresponding column of parameters.\n",model); fflush(ficlog);
6457: return 1;
6458: }
6459:
6460: nagesqr=1;
6461: if (strstr(model,"+age*age") !=0)
6462: substrchaine(modelsav, model, "+age*age");
6463: else if (strstr(model,"age*age+") !=0)
6464: substrchaine(modelsav, model, "age*age+");
6465: else
6466: substrchaine(modelsav, model, "age*age");
6467: }else
6468: nagesqr=0;
6469: if (strlen(modelsav) >1){
6470: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
6471: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
6472: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2 */
6473: cptcovt= j+1; /* Number of total covariates in the model, not including
6474: * cst, age and age*age
6475: * V1+V1*age+ V3 + V3*V4+age*age=> 4*/
6476: /* including age products which are counted in cptcovage.
6477: * but the covariates which are products must be treated
6478: * separately: ncovn=4- 2=2 (V1+V3). */
6479: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
6480: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
6481:
6482:
6483: /* Design
6484: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
6485: * < ncovcol=8 >
6486: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
6487: * k= 1 2 3 4 5 6 7 8
6488: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
6489: * covar[k,i], value of kth covariate if not including age for individual i:
6490: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
6491: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
6492: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
6493: * Tage[++cptcovage]=k
6494: * if products, new covar are created after ncovcol with k1
6495: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
6496: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
6497: * 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
6498: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
6499: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
6500: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
6501: * < ncovcol=8 >
6502: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
6503: * k= 1 2 3 4 5 6 7 8 9 10 11 12
6504: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
6505: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
6506: * p Tprod[1]@2={ 6, 5}
6507: *p Tvard[1][1]@4= {7, 8, 5, 6}
6508: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
6509: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
6510: *How to reorganize?
6511: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
6512: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
6513: * {2, 1, 4, 8, 5, 6, 3, 7}
6514: * Struct []
6515: */
1.145 brouard 6516:
1.187 brouard 6517: /* This loop fills the array Tvar from the string 'model'.*/
6518: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
6519: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
6520: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
6521: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
6522: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
6523: /* k=1 Tvar[1]=2 (from V2) */
6524: /* k=5 Tvar[5] */
6525: /* for (k=1; k<=cptcovn;k++) { */
1.198 brouard 6526: /* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.187 brouard 6527: /* } */
1.198 brouard 6528: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
1.187 brouard 6529: /*
6530: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
6531: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
1.145 brouard 6532: Tvar[k]=0;
1.187 brouard 6533: cptcovage=0;
6534: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
6535: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
6536: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
6537: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
6538: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
6539: /*scanf("%d",i);*/
6540: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
6541: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
6542: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
6543: /* covar is not filled and then is empty */
6544: cptcovprod--;
6545: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
6546: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
6547: cptcovage++; /* Sums the number of covariates which include age as a product */
6548: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
6549: /*printf("stre=%s ", stre);*/
6550: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
6551: cptcovprod--;
6552: cutl(stre,strb,strc,'V');
6553: Tvar[k]=atoi(stre);
6554: cptcovage++;
6555: Tage[cptcovage]=k;
6556: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
6557: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
6558: cptcovn++;
6559: cptcovprodnoage++;k1++;
6560: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
6561: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
6562: because this model-covariate is a construction we invent a new column
6563: ncovcol + k1
6564: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
6565: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
6566: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
6567: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
6568: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
6569: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
6570: k2=k2+2;
6571: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
6572: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
6573: for (i=1; i<=lastobs;i++){
6574: /* Computes the new covariate which is a product of
6575: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
6576: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
6577: }
6578: } /* End age is not in the model */
6579: } /* End if model includes a product */
6580: else { /* no more sum */
6581: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
6582: /* scanf("%d",i);*/
6583: cutl(strd,strc,strb,'V');
6584: ks++; /**< Number of simple covariates */
1.145 brouard 6585: cptcovn++;
1.187 brouard 6586: Tvar[k]=atoi(strd);
6587: }
6588: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
6589: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
6590: scanf("%d",i);*/
6591: } /* end of loop + on total covariates */
6592: } /* end if strlen(modelsave == 0) age*age might exist */
6593: } /* end if strlen(model == 0) */
1.136 brouard 6594:
6595: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
6596: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
6597:
6598: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
6599: printf("cptcovprod=%d ", cptcovprod);
6600: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
6601:
6602: scanf("%d ",i);*/
6603:
6604:
1.137 brouard 6605: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 6606: /*endread:*/
1.136 brouard 6607: printf("Exiting decodemodel: ");
6608: return (1);
6609: }
6610:
1.169 brouard 6611: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.136 brouard 6612: {
6613: int i, m;
6614:
6615: for (i=1; i<=imx; i++) {
6616: for(m=2; (m<= maxwav); m++) {
6617: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
6618: anint[m][i]=9999;
6619: s[m][i]=-1;
6620: }
6621: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169 brouard 6622: *nberr = *nberr + 1;
6623: 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);
6624: 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 6625: s[m][i]=-1;
6626: }
6627: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 6628: (*nberr)++;
1.136 brouard 6629: 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]);
6630: 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]);
6631: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
6632: }
6633: }
6634: }
6635:
6636: for (i=1; i<=imx; i++) {
6637: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
6638: for(m=firstpass; (m<= lastpass); m++){
1.214 ! brouard 6639: if(s[m][i] >0 || s[m][i]==-1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){ /* What if s[m][i]=-1 */
1.136 brouard 6640: if (s[m][i] >= nlstate+1) {
1.169 brouard 6641: if(agedc[i]>0){
6642: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 6643: agev[m][i]=agedc[i];
1.214 ! brouard 6644: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 6645: }else {
1.136 brouard 6646: if ((int)andc[i]!=9999){
6647: nbwarn++;
6648: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
6649: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
6650: agev[m][i]=-1;
6651: }
6652: }
1.169 brouard 6653: } /* agedc > 0 */
1.214 ! brouard 6654: } /* end if */
1.136 brouard 6655: else if(s[m][i] !=9){ /* Standard case, age in fractional
6656: years but with the precision of a month */
6657: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
6658: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
6659: agev[m][i]=1;
6660: else if(agev[m][i] < *agemin){
6661: *agemin=agev[m][i];
6662: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
6663: }
6664: else if(agev[m][i] >*agemax){
6665: *agemax=agev[m][i];
1.156 brouard 6666: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 6667: }
6668: /*agev[m][i]=anint[m][i]-annais[i];*/
6669: /* agev[m][i] = age[i]+2*m;*/
1.214 ! brouard 6670: } /* en if 9*/
1.136 brouard 6671: else { /* =9 */
1.214 ! brouard 6672: /* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */
1.136 brouard 6673: agev[m][i]=1;
6674: s[m][i]=-1;
6675: }
6676: }
1.214 ! brouard 6677: else if(s[m][i]==0) /*= 0 Unknown */
1.136 brouard 6678: agev[m][i]=1;
1.214 ! brouard 6679: else{
! 6680: printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
! 6681: fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
! 6682: agev[m][i]=0;
! 6683: }
! 6684: } /* End for lastpass */
! 6685: }
1.136 brouard 6686:
6687: for (i=1; i<=imx; i++) {
6688: for(m=firstpass; (m<=lastpass); m++){
6689: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 6690: (*nberr)++;
1.136 brouard 6691: 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);
6692: 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);
6693: return 1;
6694: }
6695: }
6696: }
6697:
6698: /*for (i=1; i<=imx; i++){
6699: for (m=firstpass; (m<lastpass); m++){
6700: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
6701: }
6702:
6703: }*/
6704:
6705:
1.139 brouard 6706: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
6707: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 6708:
6709: return (0);
1.164 brouard 6710: /* endread:*/
1.136 brouard 6711: printf("Exiting calandcheckages: ");
6712: return (1);
6713: }
6714:
1.172 brouard 6715: #if defined(_MSC_VER)
6716: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
6717: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
6718: //#include "stdafx.h"
6719: //#include <stdio.h>
6720: //#include <tchar.h>
6721: //#include <windows.h>
6722: //#include <iostream>
6723: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
6724:
6725: LPFN_ISWOW64PROCESS fnIsWow64Process;
6726:
6727: BOOL IsWow64()
6728: {
6729: BOOL bIsWow64 = FALSE;
6730:
6731: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
6732: // (HANDLE, PBOOL);
6733:
6734: //LPFN_ISWOW64PROCESS fnIsWow64Process;
6735:
6736: HMODULE module = GetModuleHandle(_T("kernel32"));
6737: const char funcName[] = "IsWow64Process";
6738: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
6739: GetProcAddress(module, funcName);
6740:
6741: if (NULL != fnIsWow64Process)
6742: {
6743: if (!fnIsWow64Process(GetCurrentProcess(),
6744: &bIsWow64))
6745: //throw std::exception("Unknown error");
6746: printf("Unknown error\n");
6747: }
6748: return bIsWow64 != FALSE;
6749: }
6750: #endif
1.177 brouard 6751:
1.191 brouard 6752: void syscompilerinfo(int logged)
1.167 brouard 6753: {
6754: /* #include "syscompilerinfo.h"*/
1.185 brouard 6755: /* command line Intel compiler 32bit windows, XP compatible:*/
6756: /* /GS /W3 /Gy
6757: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
6758: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
6759: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 6760: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
6761: */
6762: /* 64 bits */
1.185 brouard 6763: /*
6764: /GS /W3 /Gy
6765: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
6766: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
6767: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
6768: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
6769: /* Optimization are useless and O3 is slower than O2 */
6770: /*
6771: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
6772: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
6773: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
6774: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
6775: */
1.186 brouard 6776: /* Link is */ /* /OUT:"visual studio
1.185 brouard 6777: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
6778: /PDB:"visual studio
6779: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
6780: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
6781: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
6782: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
6783: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
6784: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
6785: uiAccess='false'"
6786: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
6787: /NOLOGO /TLBID:1
6788: */
1.177 brouard 6789: #if defined __INTEL_COMPILER
1.178 brouard 6790: #if defined(__GNUC__)
6791: struct utsname sysInfo; /* For Intel on Linux and OS/X */
6792: #endif
1.177 brouard 6793: #elif defined(__GNUC__)
1.179 brouard 6794: #ifndef __APPLE__
1.174 brouard 6795: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 6796: #endif
1.177 brouard 6797: struct utsname sysInfo;
1.178 brouard 6798: int cross = CROSS;
6799: if (cross){
6800: printf("Cross-");
1.191 brouard 6801: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 6802: }
1.174 brouard 6803: #endif
6804:
1.171 brouard 6805: #include <stdint.h>
1.178 brouard 6806:
1.191 brouard 6807: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 6808: #if defined(__clang__)
1.191 brouard 6809: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 6810: #endif
6811: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 6812: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 6813: #endif
6814: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 6815: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 6816: #endif
6817: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 6818: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 6819: #endif
6820: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 6821: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 6822: #endif
6823: #if defined(_MSC_VER)
1.191 brouard 6824: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 6825: #endif
6826: #if defined(__PGI)
1.191 brouard 6827: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 6828: #endif
6829: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 6830: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 6831: #endif
1.191 brouard 6832: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 6833:
1.167 brouard 6834: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
6835: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
6836: // Windows (x64 and x86)
1.191 brouard 6837: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 6838: #elif __unix__ // all unices, not all compilers
6839: // Unix
1.191 brouard 6840: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 6841: #elif __linux__
6842: // linux
1.191 brouard 6843: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 6844: #elif __APPLE__
1.174 brouard 6845: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 6846: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 6847: #endif
6848:
6849: /* __MINGW32__ */
6850: /* __CYGWIN__ */
6851: /* __MINGW64__ */
6852: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
6853: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
6854: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
6855: /* _WIN64 // Defined for applications for Win64. */
6856: /* _M_X64 // Defined for compilations that target x64 processors. */
6857: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 6858:
1.167 brouard 6859: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 6860: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 6861: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 6862: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 6863: #else
1.191 brouard 6864: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 6865: #endif
6866:
1.169 brouard 6867: #if defined(__GNUC__)
6868: # if defined(__GNUC_PATCHLEVEL__)
6869: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
6870: + __GNUC_MINOR__ * 100 \
6871: + __GNUC_PATCHLEVEL__)
6872: # else
6873: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
6874: + __GNUC_MINOR__ * 100)
6875: # endif
1.174 brouard 6876: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 6877: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 6878:
6879: if (uname(&sysInfo) != -1) {
6880: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 6881: 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 6882: }
6883: else
6884: perror("uname() error");
1.179 brouard 6885: //#ifndef __INTEL_COMPILER
6886: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 6887: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 6888: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 6889: #endif
1.169 brouard 6890: #endif
1.172 brouard 6891:
6892: // void main()
6893: // {
1.169 brouard 6894: #if defined(_MSC_VER)
1.174 brouard 6895: if (IsWow64()){
1.191 brouard 6896: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
6897: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 6898: }
6899: else{
1.191 brouard 6900: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
6901: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 6902: }
1.172 brouard 6903: // printf("\nPress Enter to continue...");
6904: // getchar();
6905: // }
6906:
1.169 brouard 6907: #endif
6908:
1.167 brouard 6909:
6910: }
1.136 brouard 6911:
1.209 brouard 6912: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
1.180 brouard 6913: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6914: int i, j, k, i1 ;
1.202 brouard 6915: /* double ftolpl = 1.e-10; */
1.180 brouard 6916: double age, agebase, agelim;
1.203 brouard 6917: double tot;
1.180 brouard 6918:
1.202 brouard 6919: strcpy(filerespl,"PL_");
6920: strcat(filerespl,fileresu);
6921: if((ficrespl=fopen(filerespl,"w"))==NULL) {
6922: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6923: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6924: }
6925: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6926: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6927: pstamp(ficrespl);
1.203 brouard 6928: fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.202 brouard 6929: fprintf(ficrespl,"#Age ");
6930: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
6931: fprintf(ficrespl,"\n");
1.180 brouard 6932:
6933: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
6934:
6935: agebase=ageminpar;
6936: agelim=agemaxpar;
6937:
6938: i1=pow(2,cptcoveff);
6939: if (cptcovn < 1){i1=1;}
6940:
6941: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6942: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
6943: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6944: k=k+1;
6945: /* to clean */
1.198 brouard 6946: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
1.200 brouard 6947: fprintf(ficrespl,"#******");
6948: printf("#******");
6949: fprintf(ficlog,"#******");
1.180 brouard 6950: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 6951: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
6952: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
6953: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.180 brouard 6954: }
6955: fprintf(ficrespl,"******\n");
6956: printf("******\n");
6957: fprintf(ficlog,"******\n");
6958:
6959: fprintf(ficrespl,"#Age ");
6960: for(j=1;j<=cptcoveff;j++) {
1.200 brouard 6961: fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.180 brouard 6962: }
1.203 brouard 6963: for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);
6964: fprintf(ficrespl,"Total Years_to_converge\n");
1.180 brouard 6965:
6966: for (age=agebase; age<=agelim; age++){
6967: /* for (age=agebase; age<=agebase; age++){ */
1.209 brouard 6968: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k);
1.180 brouard 6969: fprintf(ficrespl,"%.0f ",age );
6970: for(j=1;j<=cptcoveff;j++)
1.198 brouard 6971: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.203 brouard 6972: tot=0.;
6973: for(i=1; i<=nlstate;i++){
6974: tot += prlim[i][i];
1.180 brouard 6975: fprintf(ficrespl," %.5f", prlim[i][i]);
1.203 brouard 6976: }
1.209 brouard 6977: fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
1.180 brouard 6978: } /* Age */
6979: /* was end of cptcod */
6980: } /* cptcov */
1.184 brouard 6981: return 0;
1.180 brouard 6982: }
6983:
6984: int hPijx(double *p, int bage, int fage){
6985: /*------------- h Pij x at various ages ------------*/
6986:
6987: int stepsize;
6988: int agelim;
6989: int hstepm;
6990: int nhstepm;
6991: int h, i, i1, j, k;
6992:
6993: double agedeb;
6994: double ***p3mat;
6995:
1.201 brouard 6996: strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu);
1.180 brouard 6997: if((ficrespij=fopen(filerespij,"w"))==NULL) {
6998: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
6999: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
7000: }
7001: printf("Computing pij: result on file '%s' \n", filerespij);
7002: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
7003:
7004: stepsize=(int) (stepm+YEARM-1)/YEARM;
7005: /*if (stepm<=24) stepsize=2;*/
7006:
7007: agelim=AGESUP;
7008: hstepm=stepsize*YEARM; /* Every year of age */
7009: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
7010:
7011: /* hstepm=1; aff par mois*/
7012: pstamp(ficrespij);
7013: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
7014: i1= pow(2,cptcoveff);
1.183 brouard 7015: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
7016: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
7017: /* k=k+1; */
7018: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7019: fprintf(ficrespij,"\n#****** ");
7020: for(j=1;j<=cptcoveff;j++)
1.198 brouard 7021: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.183 brouard 7022: fprintf(ficrespij,"******\n");
7023:
7024: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
7025: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
7026: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
7027:
7028: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 7029:
1.183 brouard 7030: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
7031: oldm=oldms;savm=savms;
7032: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
7033: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
7034: for(i=1; i<=nlstate;i++)
7035: for(j=1; j<=nlstate+ndeath;j++)
7036: fprintf(ficrespij," %1d-%1d",i,j);
7037: fprintf(ficrespij,"\n");
7038: for (h=0; h<=nhstepm; h++){
7039: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
7040: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 7041: for(i=1; i<=nlstate;i++)
7042: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 7043: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 7044: fprintf(ficrespij,"\n");
7045: }
1.183 brouard 7046: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
7047: fprintf(ficrespij,"\n");
7048: }
1.180 brouard 7049: /*}*/
7050: }
1.184 brouard 7051: return 0;
1.180 brouard 7052: }
7053:
7054:
1.136 brouard 7055: /***********************************************/
7056: /**************** Main Program *****************/
7057: /***********************************************/
7058:
7059: int main(int argc, char *argv[])
7060: {
7061: #ifdef GSL
7062: const gsl_multimin_fminimizer_type *T;
7063: size_t iteri = 0, it;
7064: int rval = GSL_CONTINUE;
7065: int status = GSL_SUCCESS;
7066: double ssval;
7067: #endif
7068: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 7069: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
1.209 brouard 7070: int ncvyear=0; /* Number of years needed for the period prevalence to converge */
1.164 brouard 7071: int jj, ll, li, lj, lk;
1.136 brouard 7072: int numlinepar=0; /* Current linenumber of parameter file */
1.197 brouard 7073: int num_filled;
1.136 brouard 7074: int itimes;
7075: int NDIM=2;
7076: int vpopbased=0;
7077:
1.164 brouard 7078: char ca[32], cb[32];
1.136 brouard 7079: /* FILE *fichtm; *//* Html File */
7080: /* FILE *ficgp;*/ /*Gnuplot File */
7081: struct stat info;
1.191 brouard 7082: double agedeb=0.;
1.194 brouard 7083:
7084: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.136 brouard 7085:
1.165 brouard 7086: double fret;
1.191 brouard 7087: double dum=0.; /* Dummy variable */
1.136 brouard 7088: double ***p3mat;
7089: double ***mobaverage;
1.164 brouard 7090:
7091: char line[MAXLINE];
1.197 brouard 7092: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
7093:
7094: char model[MAXLINE], modeltemp[MAXLINE];
1.136 brouard 7095: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 7096: char *tok, *val; /* pathtot */
1.136 brouard 7097: int firstobs=1, lastobs=10;
1.195 brouard 7098: int c, h , cpt, c2;
1.191 brouard 7099: int jl=0;
7100: int i1, j1, jk, stepsize=0;
1.194 brouard 7101: int count=0;
7102:
1.164 brouard 7103: int *tab;
1.136 brouard 7104: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
7105: int mobilav=0,popforecast=0;
1.191 brouard 7106: int hstepm=0, nhstepm=0;
1.136 brouard 7107: int agemortsup;
7108: float sumlpop=0.;
7109: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
7110: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
7111:
1.191 brouard 7112: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 7113: double ftolpl=FTOL;
7114: double **prlim;
7115: double ***param; /* Matrix of parameters */
7116: double *p;
7117: double **matcov; /* Matrix of covariance */
1.203 brouard 7118: double **hess; /* Hessian matrix */
1.136 brouard 7119: double ***delti3; /* Scale */
7120: double *delti; /* Scale */
7121: double ***eij, ***vareij;
7122: double **varpl; /* Variances of prevalence limits by age */
7123: double *epj, vepp;
1.164 brouard 7124:
1.136 brouard 7125: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
7126: double **ximort;
1.145 brouard 7127: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 7128: int *dcwave;
7129:
1.164 brouard 7130: char z[1]="c";
1.136 brouard 7131:
7132: /*char *strt;*/
7133: char strtend[80];
1.126 brouard 7134:
1.164 brouard 7135:
1.126 brouard 7136: /* setlocale (LC_ALL, ""); */
7137: /* bindtextdomain (PACKAGE, LOCALEDIR); */
7138: /* textdomain (PACKAGE); */
7139: /* setlocale (LC_CTYPE, ""); */
7140: /* setlocale (LC_MESSAGES, ""); */
7141:
7142: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 7143: rstart_time = time(NULL);
7144: /* (void) gettimeofday(&start_time,&tzp);*/
7145: start_time = *localtime(&rstart_time);
1.126 brouard 7146: curr_time=start_time;
1.157 brouard 7147: /*tml = *localtime(&start_time.tm_sec);*/
7148: /* strcpy(strstart,asctime(&tml)); */
7149: strcpy(strstart,asctime(&start_time));
1.126 brouard 7150:
7151: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 7152: /* tp.tm_sec = tp.tm_sec +86400; */
7153: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 7154: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
7155: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
7156: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 7157: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 7158: /* strt=asctime(&tmg); */
7159: /* printf("Time(after) =%s",strstart); */
7160: /* (void) time (&time_value);
7161: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
7162: * tm = *localtime(&time_value);
7163: * strstart=asctime(&tm);
7164: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
7165: */
7166:
7167: nberr=0; /* Number of errors and warnings */
7168: nbwarn=0;
1.184 brouard 7169: #ifdef WIN32
7170: _getcwd(pathcd, size);
7171: #else
1.126 brouard 7172: getcwd(pathcd, size);
1.184 brouard 7173: #endif
1.191 brouard 7174: syscompilerinfo(0);
1.196 brouard 7175: printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126 brouard 7176: if(argc <=1){
7177: printf("\nEnter the parameter file name: ");
1.205 brouard 7178: if(!fgets(pathr,FILENAMELENGTH,stdin)){
7179: printf("ERROR Empty parameter file name\n");
7180: goto end;
7181: }
1.126 brouard 7182: i=strlen(pathr);
7183: if(pathr[i-1]=='\n')
7184: pathr[i-1]='\0';
1.156 brouard 7185: i=strlen(pathr);
1.205 brouard 7186: if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
1.156 brouard 7187: pathr[i-1]='\0';
1.205 brouard 7188: }
7189: i=strlen(pathr);
7190: if( i==0 ){
7191: printf("ERROR Empty parameter file name\n");
7192: goto end;
7193: }
7194: for (tok = pathr; tok != NULL; ){
1.126 brouard 7195: printf("Pathr |%s|\n",pathr);
7196: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
7197: printf("val= |%s| pathr=%s\n",val,pathr);
7198: strcpy (pathtot, val);
7199: if(pathr[0] == '\0') break; /* Dirty */
7200: }
7201: }
7202: else{
7203: strcpy(pathtot,argv[1]);
7204: }
7205: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
7206: /*cygwin_split_path(pathtot,path,optionfile);
7207: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
7208: /* cutv(path,optionfile,pathtot,'\\');*/
7209:
7210: /* Split argv[0], imach program to get pathimach */
7211: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
7212: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
7213: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
7214: /* strcpy(pathimach,argv[0]); */
7215: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
7216: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
7217: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 7218: #ifdef WIN32
7219: _chdir(path); /* Can be a relative path */
7220: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
7221: #else
1.126 brouard 7222: chdir(path); /* Can be a relative path */
1.184 brouard 7223: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
7224: #endif
7225: printf("Current directory %s!\n",pathcd);
1.126 brouard 7226: strcpy(command,"mkdir ");
7227: strcat(command,optionfilefiname);
7228: if((outcmd=system(command)) != 0){
1.169 brouard 7229: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 7230: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
7231: /* fclose(ficlog); */
7232: /* exit(1); */
7233: }
7234: /* if((imk=mkdir(optionfilefiname))<0){ */
7235: /* perror("mkdir"); */
7236: /* } */
7237:
7238: /*-------- arguments in the command line --------*/
7239:
1.186 brouard 7240: /* Main Log file */
1.126 brouard 7241: strcat(filelog, optionfilefiname);
7242: strcat(filelog,".log"); /* */
7243: if((ficlog=fopen(filelog,"w"))==NULL) {
7244: printf("Problem with logfile %s\n",filelog);
7245: goto end;
7246: }
7247: fprintf(ficlog,"Log filename:%s\n",filelog);
1.197 brouard 7248: fprintf(ficlog,"Version %s %s",version,fullversion);
1.126 brouard 7249: fprintf(ficlog,"\nEnter the parameter file name: \n");
7250: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
7251: path=%s \n\
7252: optionfile=%s\n\
7253: optionfilext=%s\n\
1.156 brouard 7254: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 7255:
1.197 brouard 7256: syscompilerinfo(1);
1.167 brouard 7257:
1.126 brouard 7258: printf("Local time (at start):%s",strstart);
7259: fprintf(ficlog,"Local time (at start): %s",strstart);
7260: fflush(ficlog);
7261: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 7262: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 7263:
7264: /* */
7265: strcpy(fileres,"r");
7266: strcat(fileres, optionfilefiname);
1.201 brouard 7267: strcat(fileresu, optionfilefiname); /* Without r in front */
1.126 brouard 7268: strcat(fileres,".txt"); /* Other files have txt extension */
1.201 brouard 7269: strcat(fileresu,".txt"); /* Other files have txt extension */
1.126 brouard 7270:
1.186 brouard 7271: /* Main ---------arguments file --------*/
1.126 brouard 7272:
7273: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 7274: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
7275: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 7276: fflush(ficlog);
1.149 brouard 7277: /* goto end; */
7278: exit(70);
1.126 brouard 7279: }
7280:
7281:
7282:
7283: strcpy(filereso,"o");
1.201 brouard 7284: strcat(filereso,fileresu);
1.126 brouard 7285: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
7286: printf("Problem with Output resultfile: %s\n", filereso);
7287: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
7288: fflush(ficlog);
7289: goto end;
7290: }
7291:
7292: /* Reads comments: lines beginning with '#' */
7293: numlinepar=0;
1.197 brouard 7294:
7295: /* First parameter line */
7296: while(fgets(line, MAXLINE, ficpar)) {
7297: /* If line starts with a # it is a comment */
7298: if (line[0] == '#') {
7299: numlinepar++;
7300: fputs(line,stdout);
7301: fputs(line,ficparo);
7302: fputs(line,ficlog);
7303: continue;
7304: }else
7305: break;
7306: }
7307: if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
7308: title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
7309: if (num_filled != 5) {
7310: printf("Should be 5 parameters\n");
7311: }
1.126 brouard 7312: numlinepar++;
1.197 brouard 7313: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
7314: }
7315: /* Second parameter line */
7316: while(fgets(line, MAXLINE, ficpar)) {
7317: /* If line starts with a # it is a comment */
7318: if (line[0] == '#') {
7319: numlinepar++;
7320: fputs(line,stdout);
7321: fputs(line,ficparo);
7322: fputs(line,ficlog);
7323: continue;
7324: }else
7325: break;
7326: }
7327: if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
7328: &ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
7329: if (num_filled != 8) {
1.209 brouard 7330: 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");
7331: printf("but line=%s\n",line);
1.197 brouard 7332: }
7333: 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 7334: }
1.203 brouard 7335: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
1.209 brouard 7336: /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
1.197 brouard 7337: /* Third parameter line */
7338: while(fgets(line, MAXLINE, ficpar)) {
7339: /* If line starts with a # it is a comment */
7340: if (line[0] == '#') {
7341: numlinepar++;
7342: fputs(line,stdout);
7343: fputs(line,ficparo);
7344: fputs(line,ficlog);
7345: continue;
7346: }else
7347: break;
7348: }
1.201 brouard 7349: if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
7350: if (num_filled == 0)
7351: model[0]='\0';
7352: else if (num_filled != 1){
1.197 brouard 7353: printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
7354: fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
7355: model[0]='\0';
7356: goto end;
7357: }
7358: else{
7359: if (model[0]=='+'){
7360: for(i=1; i<=strlen(model);i++)
7361: modeltemp[i-1]=model[i];
1.201 brouard 7362: strcpy(model,modeltemp);
1.197 brouard 7363: }
7364: }
1.199 brouard 7365: /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
1.203 brouard 7366: printf("model=1+age+%s\n",model);fflush(stdout);
1.197 brouard 7367: }
7368: /* 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); */
7369: /* numlinepar=numlinepar+3; /\* In general *\/ */
7370: /* 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 7371: 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);
7372: 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 7373: fflush(ficlog);
1.190 brouard 7374: /* if(model[0]=='#'|| model[0]== '\0'){ */
7375: if(model[0]=='#'){
1.187 brouard 7376: printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
7377: 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
7378: 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \
7379: if(mle != -1){
7380: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
7381: exit(1);
7382: }
7383: }
1.126 brouard 7384: while((c=getc(ficpar))=='#' && c!= EOF){
7385: ungetc(c,ficpar);
7386: fgets(line, MAXLINE, ficpar);
7387: numlinepar++;
1.195 brouard 7388: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
7389: z[0]=line[1];
7390: }
7391: /* printf("****line [1] = %c \n",line[1]); */
1.141 brouard 7392: fputs(line, stdout);
7393: //puts(line);
1.126 brouard 7394: fputs(line,ficparo);
7395: fputs(line,ficlog);
7396: }
7397: ungetc(c,ficpar);
7398:
7399:
1.145 brouard 7400: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.136 brouard 7401: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
7402: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
7403: v1+v2*age+v2*v3 makes cptcovn = 3
7404: */
7405: if (strlen(model)>1)
1.187 brouard 7406: 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 7407: else
1.187 brouard 7408: ncovmodel=2; /* Constant and age */
1.133 brouard 7409: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
7410: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 7411: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
7412: 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);
7413: 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);
7414: fflush(stdout);
7415: fclose (ficlog);
7416: goto end;
7417: }
1.126 brouard 7418: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
7419: delti=delti3[1][1];
7420: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
7421: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
7422: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 7423: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
7424: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 7425: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7426: fclose (ficparo);
7427: fclose (ficlog);
7428: goto end;
7429: exit(0);
7430: }
1.186 brouard 7431: else if(mle==-3) { /* Main Wizard */
1.126 brouard 7432: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 7433: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
7434: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 7435: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
7436: matcov=matrix(1,npar,1,npar);
1.203 brouard 7437: hess=matrix(1,npar,1,npar);
1.126 brouard 7438: }
7439: else{
1.145 brouard 7440: /* Read guessed parameters */
1.126 brouard 7441: /* Reads comments: lines beginning with '#' */
7442: while((c=getc(ficpar))=='#' && c!= EOF){
7443: ungetc(c,ficpar);
7444: fgets(line, MAXLINE, ficpar);
7445: numlinepar++;
1.141 brouard 7446: fputs(line,stdout);
1.126 brouard 7447: fputs(line,ficparo);
7448: fputs(line,ficlog);
7449: }
7450: ungetc(c,ficpar);
7451:
7452: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
7453: for(i=1; i <=nlstate; i++){
7454: j=0;
7455: for(jj=1; jj <=nlstate+ndeath; jj++){
7456: if(jj==i) continue;
7457: j++;
7458: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.193 brouard 7459: if ((i1 != i) || (j1 != jj)){
1.126 brouard 7460: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
7461: It might be a problem of design; if ncovcol and the model are correct\n \
7462: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
7463: exit(1);
7464: }
7465: fprintf(ficparo,"%1d%1d",i1,j1);
7466: if(mle==1)
1.193 brouard 7467: printf("%1d%1d",i,jj);
7468: fprintf(ficlog,"%1d%1d",i,jj);
1.126 brouard 7469: for(k=1; k<=ncovmodel;k++){
7470: fscanf(ficpar," %lf",¶m[i][j][k]);
7471: if(mle==1){
7472: printf(" %lf",param[i][j][k]);
7473: fprintf(ficlog," %lf",param[i][j][k]);
7474: }
7475: else
7476: fprintf(ficlog," %lf",param[i][j][k]);
7477: fprintf(ficparo," %lf",param[i][j][k]);
7478: }
7479: fscanf(ficpar,"\n");
7480: numlinepar++;
7481: if(mle==1)
7482: printf("\n");
7483: fprintf(ficlog,"\n");
7484: fprintf(ficparo,"\n");
7485: }
7486: }
7487: fflush(ficlog);
7488:
1.145 brouard 7489: /* Reads scales values */
1.126 brouard 7490: p=param[1][1];
7491:
7492: /* Reads comments: lines beginning with '#' */
7493: while((c=getc(ficpar))=='#' && c!= EOF){
7494: ungetc(c,ficpar);
7495: fgets(line, MAXLINE, ficpar);
7496: numlinepar++;
1.141 brouard 7497: fputs(line,stdout);
1.126 brouard 7498: fputs(line,ficparo);
7499: fputs(line,ficlog);
7500: }
7501: ungetc(c,ficpar);
7502:
7503: for(i=1; i <=nlstate; i++){
7504: for(j=1; j <=nlstate+ndeath-1; j++){
7505: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.164 brouard 7506: if ( (i1-i) * (j1-j) != 0){
1.126 brouard 7507: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
7508: exit(1);
7509: }
7510: printf("%1d%1d",i,j);
7511: fprintf(ficparo,"%1d%1d",i1,j1);
7512: fprintf(ficlog,"%1d%1d",i1,j1);
7513: for(k=1; k<=ncovmodel;k++){
7514: fscanf(ficpar,"%le",&delti3[i][j][k]);
7515: printf(" %le",delti3[i][j][k]);
7516: fprintf(ficparo," %le",delti3[i][j][k]);
7517: fprintf(ficlog," %le",delti3[i][j][k]);
7518: }
7519: fscanf(ficpar,"\n");
7520: numlinepar++;
7521: printf("\n");
7522: fprintf(ficparo,"\n");
7523: fprintf(ficlog,"\n");
7524: }
7525: }
7526: fflush(ficlog);
7527:
1.145 brouard 7528: /* Reads covariance matrix */
1.126 brouard 7529: delti=delti3[1][1];
7530:
7531:
7532: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
7533:
7534: /* Reads comments: lines beginning with '#' */
7535: while((c=getc(ficpar))=='#' && c!= EOF){
7536: ungetc(c,ficpar);
7537: fgets(line, MAXLINE, ficpar);
7538: numlinepar++;
1.141 brouard 7539: fputs(line,stdout);
1.126 brouard 7540: fputs(line,ficparo);
7541: fputs(line,ficlog);
7542: }
7543: ungetc(c,ficpar);
7544:
7545: matcov=matrix(1,npar,1,npar);
1.203 brouard 7546: hess=matrix(1,npar,1,npar);
1.131 brouard 7547: for(i=1; i <=npar; i++)
7548: for(j=1; j <=npar; j++) matcov[i][j]=0.;
7549:
1.194 brouard 7550: /* Scans npar lines */
1.126 brouard 7551: for(i=1; i <=npar; i++){
1.194 brouard 7552: count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk);
7553: if(count != 3){
7554: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
7555: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
7556: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
7557: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
7558: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
7559: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
7560: exit(1);
7561: }else
1.126 brouard 7562: if(mle==1)
1.194 brouard 7563: printf("%1d%1d%1d",i1,j1,jk);
7564: fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);
7565: fprintf(ficparo,"%1d%1d%1d",i1,j1,jk);
1.126 brouard 7566: for(j=1; j <=i; j++){
7567: fscanf(ficpar," %le",&matcov[i][j]);
7568: if(mle==1){
7569: printf(" %.5le",matcov[i][j]);
7570: }
7571: fprintf(ficlog," %.5le",matcov[i][j]);
7572: fprintf(ficparo," %.5le",matcov[i][j]);
7573: }
7574: fscanf(ficpar,"\n");
7575: numlinepar++;
7576: if(mle==1)
7577: printf("\n");
7578: fprintf(ficlog,"\n");
7579: fprintf(ficparo,"\n");
7580: }
1.194 brouard 7581: /* End of read covariance matrix npar lines */
1.126 brouard 7582: for(i=1; i <=npar; i++)
7583: for(j=i+1;j<=npar;j++)
7584: matcov[i][j]=matcov[j][i];
7585:
7586: if(mle==1)
7587: printf("\n");
7588: fprintf(ficlog,"\n");
7589:
7590: fflush(ficlog);
7591:
7592: /*-------- Rewriting parameter file ----------*/
7593: strcpy(rfileres,"r"); /* "Rparameterfile */
7594: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
7595: strcat(rfileres,"."); /* */
7596: strcat(rfileres,optionfilext); /* Other files have txt extension */
7597: if((ficres =fopen(rfileres,"w"))==NULL) {
1.201 brouard 7598: printf("Problem writing new parameter file: %s\n", rfileres);goto end;
7599: fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
1.126 brouard 7600: }
7601: fprintf(ficres,"#%s\n",version);
7602: } /* End of mle != -3 */
7603:
1.186 brouard 7604: /* Main data
7605: */
1.126 brouard 7606: n= lastobs;
7607: num=lvector(1,n);
7608: moisnais=vector(1,n);
7609: annais=vector(1,n);
7610: moisdc=vector(1,n);
7611: andc=vector(1,n);
7612: agedc=vector(1,n);
7613: cod=ivector(1,n);
7614: weight=vector(1,n);
7615: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
7616: mint=matrix(1,maxwav,1,n);
7617: anint=matrix(1,maxwav,1,n);
1.131 brouard 7618: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 7619: tab=ivector(1,NCOVMAX);
1.144 brouard 7620: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 7621: 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 7622:
1.136 brouard 7623: /* Reads data from file datafile */
7624: if (readdata(datafile, firstobs, lastobs, &imx)==1)
7625: goto end;
7626:
7627: /* Calculation of the number of parameters from char model */
1.137 brouard 7628: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
7629: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
7630: k=3 V4 Tvar[k=3]= 4 (from V4)
7631: k=2 V1 Tvar[k=2]= 1 (from V1)
7632: k=1 Tvar[1]=2 (from V2)
7633: */
7634: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
7635: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
7636: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
7637: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
7638: */
7639: /* For model-covariate k tells which data-covariate to use but
7640: because this model-covariate is a construction we invent a new column
7641: ncovcol + k1
7642: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
7643: Tvar[3=V1*V4]=4+1 etc */
1.145 brouard 7644: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
1.137 brouard 7645: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
7646: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
7647: */
1.145 brouard 7648: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
7649: 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 7650: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
7651: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 7652: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 7653: 4 covariates (3 plus signs)
7654: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
7655: */
1.136 brouard 7656:
1.186 brouard 7657: /* Main decodemodel */
7658:
1.187 brouard 7659:
1.136 brouard 7660: if(decodemodel(model, lastobs) == 1)
7661: goto end;
7662:
1.137 brouard 7663: if((double)(lastobs-imx)/(double)imx > 1.10){
7664: nbwarn++;
7665: 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);
7666: 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);
7667: }
1.136 brouard 7668: /* if(mle==1){*/
1.137 brouard 7669: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
7670: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 7671: }
7672:
7673: /*-calculation of age at interview from date of interview and age at death -*/
7674: agev=matrix(1,maxwav,1,imx);
7675:
7676: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
7677: goto end;
7678:
1.126 brouard 7679:
1.136 brouard 7680: agegomp=(int)agemin;
7681: free_vector(moisnais,1,n);
7682: free_vector(annais,1,n);
1.126 brouard 7683: /* free_matrix(mint,1,maxwav,1,n);
7684: free_matrix(anint,1,maxwav,1,n);*/
7685: free_vector(moisdc,1,n);
7686: free_vector(andc,1,n);
1.145 brouard 7687: /* */
7688:
1.126 brouard 7689: wav=ivector(1,imx);
1.214 ! brouard 7690: /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
! 7691: /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
! 7692: /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
! 7693: dh=imatrix(1,lastpass-firstpass+2,1,imx); /* We are adding a wave if status is unknown at last wave but death occurs after last wave.*/
! 7694: bh=imatrix(1,lastpass-firstpass+2,1,imx);
! 7695: mw=imatrix(1,lastpass-firstpass+2,1,imx);
1.126 brouard 7696:
7697: /* Concatenates waves */
1.214 ! brouard 7698: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
! 7699: Death is a valid wave (if date is known).
! 7700: mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i
! 7701: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
! 7702: and mw[mi+1][i]. dh depends on stepm.
! 7703: */
! 7704:
1.126 brouard 7705: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 brouard 7706: /* */
7707:
1.126 brouard 7708: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
7709:
7710: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
7711: ncodemax[1]=1;
1.145 brouard 7712: Ndum =ivector(-1,NCOVMAX);
1.187 brouard 7713: if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */
1.145 brouard 7714: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.211 brouard 7715: /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
1.186 brouard 7716: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
1.211 brouard 7717: /* 1 to ncodemax[j] which is the maximum value of this jth covariate */
1.145 brouard 7718:
1.200 brouard 7719: /* codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
1.198 brouard 7720: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
1.186 brouard 7721: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.211 brouard 7722: /* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j,
7723: * codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded
7724: * (currently 0 or 1) in the data.
7725: * In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of
7726: * corresponding modality (h,j).
7727: */
7728:
1.145 brouard 7729: h=0;
7730:
7731:
7732: /*if (cptcovn > 0) */
1.126 brouard 7733:
1.145 brouard 7734:
1.126 brouard 7735: m=pow(2,cptcoveff);
7736:
1.144 brouard 7737: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.211 brouard 7738: * For k=4 covariates, h goes from 1 to m=2**k
7739: * codtabm(h,k)= (1 & (h-1) >> (k-1)) + 1;
7740: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.186 brouard 7741: * h\k 1 2 3 4
1.143 brouard 7742: *______________________________
7743: * 1 i=1 1 i=1 1 i=1 1 i=1 1
7744: * 2 2 1 1 1
7745: * 3 i=2 1 2 1 1
7746: * 4 2 2 1 1
7747: * 5 i=3 1 i=2 1 2 1
7748: * 6 2 1 2 1
7749: * 7 i=4 1 2 2 1
7750: * 8 2 2 2 1
1.197 brouard 7751: * 9 i=5 1 i=3 1 i=2 1 2
7752: * 10 2 1 1 2
7753: * 11 i=6 1 2 1 2
7754: * 12 2 2 1 2
7755: * 13 i=7 1 i=4 1 2 2
7756: * 14 2 1 2 2
7757: * 15 i=8 1 2 2 2
7758: * 16 2 2 2 2
1.143 brouard 7759: */
1.212 brouard 7760: /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
1.211 brouard 7761: /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
7762: * and the value of each covariate?
7763: * V1=1, V2=1, V3=2, V4=1 ?
7764: * h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok.
7765: * h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st.
7766: * In order to get the real value in the data, we use nbcode
7767: * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
7768: * We are keeping this crazy system in order to be able (in the future?)
7769: * to have more than 2 values (0 or 1) for a covariate.
7770: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
7771: * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
7772: * bbbbbbbb
7773: * 76543210
7774: * h-1 00000101 (6-1=5)
7775: *(h-1)>>(k-1)= 00000001 >> (2-1) = 1 right shift
7776: * &
7777: * 1 00000001 (1)
7778: * 00000001 = 1 & ((h-1) >> (k-1))
7779: * +1= 00000010 =2
7780: *
7781: * h=14, k=3 => h'=h-1=13, k'=k-1=2
7782: * h' 1101 =2^3+2^2+0x2^1+2^0
7783: * >>k' 11
7784: * & 00000001
7785: * = 00000001
7786: * +1 = 00000010=2 = codtabm(14,3)
7787: * Reverse h=6 and m=16?
7788: * cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1.
7789: * for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff)
7790: * decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1
7791: * decodtabm(h,j,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (j-1)) & 1) +1 : -1)
7792: * V3=decodtabm(14,3,2**4)=2
7793: * h'=13 1101 =2^3+2^2+0x2^1+2^0
7794: *(h-1) >> (j-1) 0011 =13 >> 2
7795: * &1 000000001
7796: * = 000000001
7797: * +1= 000000010 =2
7798: * 2211
7799: * V1=1+1, V2=0+1, V3=1+1, V4=1+1
7800: * V3=2
7801: */
7802:
1.202 brouard 7803: /* /\* for(h=1; h <=100 ;h++){ *\/ */
7804: /* /\* printf("h=%2d ", h); *\/ */
7805: /* /\* for(k=1; k <=10; k++){ *\/ */
7806: /* /\* printf("k=%d %d ",k,codtabm(h,k)); *\/ */
7807: /* /\* codtab[h][k]=codtabm(h,k); *\/ */
7808: /* /\* } *\/ */
7809: /* /\* printf("\n"); *\/ */
7810: /* } */
1.197 brouard 7811: /* for(k=1;k<=cptcoveff; k++){ /\* scans any effective covariate *\/ */
7812: /* 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 *\/ */
7813: /* for(j=1; j <= ncodemax[k]; j++){ /\* For each modality of this covariate ncodemax=2*\/ */
7814: /* for(cpt=1; cpt <=pow(2,k-1); cpt++){ /\* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 *\/ */
7815: /* h++; */
7816: /* if (h>m) */
7817: /* h=1; */
7818: /* codtab[h][k]=j; */
7819: /* /\* codtab[12][3]=1; *\/ */
7820: /* /\*codtab[h][Tvar[k]]=j;*\/ */
7821: /* /\* 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]]); *\/ */
7822: /* } */
7823: /* } */
7824: /* } */
7825: /* } */
1.126 brouard 7826: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
7827: codtab[1][2]=1;codtab[2][2]=2; */
1.197 brouard 7828: /* for(i=1; i <=m ;i++){ */
7829: /* for(k=1; k <=cptcovn; k++){ */
7830: /* printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); */
7831: /* } */
7832: /* printf("\n"); */
7833: /* } */
7834: /* scanf("%d",i);*/
1.145 brouard 7835:
7836: free_ivector(Ndum,-1,NCOVMAX);
7837:
7838:
1.126 brouard 7839:
1.186 brouard 7840: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 7841: strcpy(optionfilegnuplot,optionfilefiname);
7842: if(mle==-3)
1.201 brouard 7843: strcat(optionfilegnuplot,"-MORT_");
1.126 brouard 7844: strcat(optionfilegnuplot,".gp");
7845:
7846: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
7847: printf("Problem with file %s",optionfilegnuplot);
7848: }
7849: else{
1.204 brouard 7850: fprintf(ficgp,"\n# IMaCh-%s\n", version);
1.126 brouard 7851: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 7852: //fprintf(ficgp,"set missing 'NaNq'\n");
7853: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 7854: }
7855: /* fclose(ficgp);*/
1.186 brouard 7856:
7857:
7858: /* Initialisation of --------- index.htm --------*/
1.126 brouard 7859:
7860: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
7861: if(mle==-3)
1.201 brouard 7862: strcat(optionfilehtm,"-MORT_");
1.126 brouard 7863: strcat(optionfilehtm,".htm");
7864: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 7865: printf("Problem with %s \n",optionfilehtm);
7866: exit(0);
1.126 brouard 7867: }
7868:
7869: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
7870: strcat(optionfilehtmcov,"-cov.htm");
7871: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
7872: printf("Problem with %s \n",optionfilehtmcov), exit(0);
7873: }
7874: else{
7875: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
7876: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 7877: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.126 brouard 7878: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
7879: }
7880:
1.213 brouard 7881: 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-2013-2016-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 2015-2018</a></font><br> \
1.204 brouard 7882: <hr size=\"2\" color=\"#EC5E5E\"> \n\
7883: <font size=\"2\">IMaCh-%s <br> %s</font> \
1.126 brouard 7884: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 7885: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
1.126 brouard 7886: \n\
7887: <hr size=\"2\" color=\"#EC5E5E\">\
7888: <ul><li><h4>Parameter files</h4>\n\
7889: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
7890: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
7891: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
7892: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
7893: - Date and time at start: %s</ul>\n",\
7894: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
7895: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
7896: fileres,fileres,\
7897: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
7898: fflush(fichtm);
7899:
7900: strcpy(pathr,path);
7901: strcat(pathr,optionfilefiname);
1.184 brouard 7902: #ifdef WIN32
7903: _chdir(optionfilefiname); /* Move to directory named optionfile */
7904: #else
1.126 brouard 7905: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 7906: #endif
7907:
1.126 brouard 7908:
7909: /* Calculates basic frequencies. Computes observed prevalence at single age
7910: and prints on file fileres'p'. */
1.214 ! brouard 7911: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\
! 7912: firstpass, lastpass, stepm, weightopt, model);
1.126 brouard 7913:
7914: fprintf(fichtm,"\n");
7915: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
7916: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
7917: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
7918: imx,agemin,agemax,jmin,jmax,jmean);
7919: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7920: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7921: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7922: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7923: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
7924:
7925:
7926: /* For Powell, parameters are in a vector p[] starting at p[1]
7927: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
7928: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
7929:
7930: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 7931: /* For mortality only */
1.126 brouard 7932: if (mle==-3){
1.136 brouard 7933: ximort=matrix(1,NDIM,1,NDIM);
1.186 brouard 7934: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 7935: cens=ivector(1,n);
7936: ageexmed=vector(1,n);
7937: agecens=vector(1,n);
7938: dcwave=ivector(1,n);
7939:
7940: for (i=1; i<=imx; i++){
7941: dcwave[i]=-1;
7942: for (m=firstpass; m<=lastpass; m++)
7943: if (s[m][i]>nlstate) {
7944: dcwave[i]=m;
7945: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
7946: break;
7947: }
7948: }
7949:
7950: for (i=1; i<=imx; i++) {
7951: if (wav[i]>0){
7952: ageexmed[i]=agev[mw[1][i]][i];
7953: j=wav[i];
7954: agecens[i]=1.;
7955:
7956: if (ageexmed[i]> 1 && wav[i] > 0){
7957: agecens[i]=agev[mw[j][i]][i];
7958: cens[i]= 1;
7959: }else if (ageexmed[i]< 1)
7960: cens[i]= -1;
7961: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
7962: cens[i]=0 ;
7963: }
7964: else cens[i]=-1;
7965: }
7966:
7967: for (i=1;i<=NDIM;i++) {
7968: for (j=1;j<=NDIM;j++)
7969: ximort[i][j]=(i == j ? 1.0 : 0.0);
7970: }
7971:
1.145 brouard 7972: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 7973: /*printf("%lf %lf", p[1], p[2]);*/
7974:
7975:
1.136 brouard 7976: #ifdef GSL
7977: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 7978: #else
1.126 brouard 7979: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 7980: #endif
1.201 brouard 7981: strcpy(filerespow,"POW-MORT_");
7982: strcat(filerespow,fileresu);
1.126 brouard 7983: if((ficrespow=fopen(filerespow,"w"))==NULL) {
7984: printf("Problem with resultfile: %s\n", filerespow);
7985: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
7986: }
1.136 brouard 7987: #ifdef GSL
7988: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 7989: #else
1.126 brouard 7990: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 7991: #endif
1.126 brouard 7992: /* for (i=1;i<=nlstate;i++)
7993: for(j=1;j<=nlstate+ndeath;j++)
7994: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
7995: */
7996: fprintf(ficrespow,"\n");
1.136 brouard 7997: #ifdef GSL
7998: /* gsl starts here */
7999: T = gsl_multimin_fminimizer_nmsimplex;
8000: gsl_multimin_fminimizer *sfm = NULL;
8001: gsl_vector *ss, *x;
8002: gsl_multimin_function minex_func;
8003:
8004: /* Initial vertex size vector */
8005: ss = gsl_vector_alloc (NDIM);
8006:
8007: if (ss == NULL){
8008: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
8009: }
8010: /* Set all step sizes to 1 */
8011: gsl_vector_set_all (ss, 0.001);
8012:
8013: /* Starting point */
1.126 brouard 8014:
1.136 brouard 8015: x = gsl_vector_alloc (NDIM);
8016:
8017: if (x == NULL){
8018: gsl_vector_free(ss);
8019: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
8020: }
8021:
8022: /* Initialize method and iterate */
8023: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 8024: /* gsl_vector_set(x, 0, 0.0268); */
8025: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 8026: gsl_vector_set(x, 0, p[1]);
8027: gsl_vector_set(x, 1, p[2]);
8028:
8029: minex_func.f = &gompertz_f;
8030: minex_func.n = NDIM;
8031: minex_func.params = (void *)&p; /* ??? */
8032:
8033: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
8034: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
8035:
8036: printf("Iterations beginning .....\n\n");
8037: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
8038:
8039: iteri=0;
8040: while (rval == GSL_CONTINUE){
8041: iteri++;
8042: status = gsl_multimin_fminimizer_iterate(sfm);
8043:
8044: if (status) printf("error: %s\n", gsl_strerror (status));
8045: fflush(0);
8046:
8047: if (status)
8048: break;
8049:
8050: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
8051: ssval = gsl_multimin_fminimizer_size (sfm);
8052:
8053: if (rval == GSL_SUCCESS)
8054: printf ("converged to a local maximum at\n");
8055:
8056: printf("%5d ", iteri);
8057: for (it = 0; it < NDIM; it++){
8058: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
8059: }
8060: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
8061: }
8062:
8063: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
8064:
8065: gsl_vector_free(x); /* initial values */
8066: gsl_vector_free(ss); /* inital step size */
8067: for (it=0; it<NDIM; it++){
8068: p[it+1]=gsl_vector_get(sfm->x,it);
8069: fprintf(ficrespow," %.12lf", p[it]);
8070: }
8071: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
8072: #endif
8073: #ifdef POWELL
8074: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
8075: #endif
1.126 brouard 8076: fclose(ficrespow);
8077:
1.203 brouard 8078: hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz);
1.126 brouard 8079:
8080: for(i=1; i <=NDIM; i++)
8081: for(j=i+1;j<=NDIM;j++)
8082: matcov[i][j]=matcov[j][i];
8083:
8084: printf("\nCovariance matrix\n ");
1.203 brouard 8085: fprintf(ficlog,"\nCovariance matrix\n ");
1.126 brouard 8086: for(i=1; i <=NDIM; i++) {
8087: for(j=1;j<=NDIM;j++){
8088: printf("%f ",matcov[i][j]);
1.203 brouard 8089: fprintf(ficlog,"%f ",matcov[i][j]);
1.126 brouard 8090: }
1.203 brouard 8091: printf("\n "); fprintf(ficlog,"\n ");
1.126 brouard 8092: }
8093:
8094: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 brouard 8095: for (i=1;i<=NDIM;i++) {
1.126 brouard 8096: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 brouard 8097: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
8098: }
1.126 brouard 8099: lsurv=vector(1,AGESUP);
8100: lpop=vector(1,AGESUP);
8101: tpop=vector(1,AGESUP);
8102: lsurv[agegomp]=100000;
8103:
8104: for (k=agegomp;k<=AGESUP;k++) {
8105: agemortsup=k;
8106: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
8107: }
8108:
8109: for (k=agegomp;k<agemortsup;k++)
8110: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
8111:
8112: for (k=agegomp;k<agemortsup;k++){
8113: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
8114: sumlpop=sumlpop+lpop[k];
8115: }
8116:
8117: tpop[agegomp]=sumlpop;
8118: for (k=agegomp;k<(agemortsup-3);k++){
8119: /* tpop[k+1]=2;*/
8120: tpop[k+1]=tpop[k]-lpop[k];
8121: }
8122:
8123:
8124: printf("\nAge lx qx dx Lx Tx e(x)\n");
8125: for (k=agegomp;k<(agemortsup-2);k++)
8126: 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]);
8127:
8128:
8129: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 8130: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
8131: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
8132: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
8133: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
8134: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
8135: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
8136: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
8137: }else
1.201 brouard 8138: printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
8139: printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
1.126 brouard 8140: stepm, weightopt,\
8141: model,imx,p,matcov,agemortsup);
8142:
8143: free_vector(lsurv,1,AGESUP);
8144: free_vector(lpop,1,AGESUP);
8145: free_vector(tpop,1,AGESUP);
1.136 brouard 8146: #ifdef GSL
8147: free_ivector(cens,1,n);
8148: free_vector(agecens,1,n);
8149: free_ivector(dcwave,1,n);
8150: free_matrix(ximort,1,NDIM,1,NDIM);
8151: #endif
1.186 brouard 8152: } /* Endof if mle==-3 mortality only */
1.205 brouard 8153: /* Standard */
8154: else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
8155: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
8156: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
1.132 brouard 8157: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 8158: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
8159: for (k=1; k<=npar;k++)
8160: printf(" %d %8.5f",k,p[k]);
8161: printf("\n");
1.205 brouard 8162: if(mle>=1){ /* Could be 1 or 2, Real Maximization */
8163: /* mlikeli uses func not funcone */
8164: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
8165: }
8166: if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
8167: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
8168: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
8169: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
8170: }
8171: globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
1.126 brouard 8172: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
8173: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
8174: for (k=1; k<=npar;k++)
8175: printf(" %d %8.5f",k,p[k]);
8176: printf("\n");
8177:
8178: /*--------- results files --------------*/
1.192 brouard 8179: 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 8180:
8181:
8182: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
8183: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
8184: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
8185: for(i=1,jk=1; i <=nlstate; i++){
8186: for(k=1; k <=(nlstate+ndeath); k++){
8187: if (k != i) {
8188: printf("%d%d ",i,k);
8189: fprintf(ficlog,"%d%d ",i,k);
8190: fprintf(ficres,"%1d%1d ",i,k);
8191: for(j=1; j <=ncovmodel; j++){
1.190 brouard 8192: printf("%12.7f ",p[jk]);
8193: fprintf(ficlog,"%12.7f ",p[jk]);
8194: fprintf(ficres,"%12.7f ",p[jk]);
1.126 brouard 8195: jk++;
8196: }
8197: printf("\n");
8198: fprintf(ficlog,"\n");
8199: fprintf(ficres,"\n");
8200: }
8201: }
8202: }
1.203 brouard 8203: if(mle != 0){
8204: /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
1.126 brouard 8205: ftolhess=ftol; /* Usually correct */
1.203 brouard 8206: hesscov(matcov, hess, p, npar, delti, ftolhess, func);
8207: 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");
8208: 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");
8209: for(i=1,jk=1; i <=nlstate; i++){
8210: for(k=1; k <=(nlstate+ndeath); k++){
8211: if (k != i) {
8212: printf("%d%d ",i,k);
8213: fprintf(ficlog,"%d%d ",i,k);
8214: for(j=1; j <=ncovmodel; j++){
8215: 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]));
8216: 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]));
8217: jk++;
8218: }
8219: printf("\n");
8220: fprintf(ficlog,"\n");
1.193 brouard 8221: }
8222: }
8223: }
1.203 brouard 8224: } /* end of hesscov and Wald tests */
1.193 brouard 8225:
1.203 brouard 8226: /* */
1.126 brouard 8227: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
8228: printf("# Scales (for hessian or gradient estimation)\n");
8229: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
8230: for(i=1,jk=1; i <=nlstate; i++){
8231: for(j=1; j <=nlstate+ndeath; j++){
8232: if (j!=i) {
8233: fprintf(ficres,"%1d%1d",i,j);
8234: printf("%1d%1d",i,j);
8235: fprintf(ficlog,"%1d%1d",i,j);
8236: for(k=1; k<=ncovmodel;k++){
8237: printf(" %.5e",delti[jk]);
8238: fprintf(ficlog," %.5e",delti[jk]);
8239: fprintf(ficres," %.5e",delti[jk]);
8240: jk++;
8241: }
8242: printf("\n");
8243: fprintf(ficlog,"\n");
8244: fprintf(ficres,"\n");
8245: }
8246: }
8247: }
8248:
8249: 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 8250: if(mle >= 1) /* To big for the screen */
1.126 brouard 8251: 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");
8252: 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");
8253: /* # 121 Var(a12)\n\ */
8254: /* # 122 Cov(b12,a12) Var(b12)\n\ */
8255: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
8256: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
8257: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
8258: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
8259: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
8260: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
8261:
8262:
8263: /* Just to have a covariance matrix which will be more understandable
8264: even is we still don't want to manage dictionary of variables
8265: */
8266: for(itimes=1;itimes<=2;itimes++){
8267: jj=0;
8268: for(i=1; i <=nlstate; i++){
8269: for(j=1; j <=nlstate+ndeath; j++){
8270: if(j==i) continue;
8271: for(k=1; k<=ncovmodel;k++){
8272: jj++;
8273: ca[0]= k+'a'-1;ca[1]='\0';
8274: if(itimes==1){
8275: if(mle>=1)
8276: printf("#%1d%1d%d",i,j,k);
8277: fprintf(ficlog,"#%1d%1d%d",i,j,k);
8278: fprintf(ficres,"#%1d%1d%d",i,j,k);
8279: }else{
8280: if(mle>=1)
8281: printf("%1d%1d%d",i,j,k);
8282: fprintf(ficlog,"%1d%1d%d",i,j,k);
8283: fprintf(ficres,"%1d%1d%d",i,j,k);
8284: }
8285: ll=0;
8286: for(li=1;li <=nlstate; li++){
8287: for(lj=1;lj <=nlstate+ndeath; lj++){
8288: if(lj==li) continue;
8289: for(lk=1;lk<=ncovmodel;lk++){
8290: ll++;
8291: if(ll<=jj){
8292: cb[0]= lk +'a'-1;cb[1]='\0';
8293: if(ll<jj){
8294: if(itimes==1){
8295: if(mle>=1)
8296: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
8297: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
8298: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
8299: }else{
8300: if(mle>=1)
8301: printf(" %.5e",matcov[jj][ll]);
8302: fprintf(ficlog," %.5e",matcov[jj][ll]);
8303: fprintf(ficres," %.5e",matcov[jj][ll]);
8304: }
8305: }else{
8306: if(itimes==1){
8307: if(mle>=1)
8308: printf(" Var(%s%1d%1d)",ca,i,j);
8309: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
8310: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
8311: }else{
8312: if(mle>=1)
1.203 brouard 8313: printf(" %.7e",matcov[jj][ll]);
8314: fprintf(ficlog," %.7e",matcov[jj][ll]);
8315: fprintf(ficres," %.7e",matcov[jj][ll]);
1.126 brouard 8316: }
8317: }
8318: }
8319: } /* end lk */
8320: } /* end lj */
8321: } /* end li */
8322: if(mle>=1)
8323: printf("\n");
8324: fprintf(ficlog,"\n");
8325: fprintf(ficres,"\n");
8326: numlinepar++;
8327: } /* end k*/
8328: } /*end j */
8329: } /* end i */
8330: } /* end itimes */
8331:
8332: fflush(ficlog);
8333: fflush(ficres);
1.209 brouard 8334: while(fgets(line, MAXLINE, ficpar)) {
8335: /* If line starts with a # it is a comment */
8336: if (line[0] == '#') {
8337: numlinepar++;
1.141 brouard 8338: fputs(line,stdout);
1.126 brouard 8339: fputs(line,ficparo);
1.209 brouard 8340: fputs(line,ficlog);
8341: continue;
8342: }else
8343: break;
8344: }
8345:
8346: /* while((c=getc(ficpar))=='#' && c!= EOF){ */
8347: /* ungetc(c,ficpar); */
8348: /* fgets(line, MAXLINE, ficpar); */
8349: /* fputs(line,stdout); */
8350: /* fputs(line,ficparo); */
8351: /* } */
8352: /* ungetc(c,ficpar); */
1.126 brouard 8353:
8354: estepm=0;
1.209 brouard 8355: 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){
8356:
8357: if (num_filled != 6) {
8358: printf("Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n");
8359: printf("but line=%s\n",line);
8360: goto end;
8361: }
8362: printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
8363: }
8364: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
8365: /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
8366:
8367: /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
1.126 brouard 8368: if (estepm==0 || estepm < stepm) estepm=stepm;
8369: if (fage <= 2) {
8370: bage = ageminpar;
8371: fage = agemaxpar;
8372: }
8373:
8374: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
1.211 brouard 8375: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
8376: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
1.186 brouard 8377:
8378: /* Other stuffs, more or less useful */
1.126 brouard 8379: while((c=getc(ficpar))=='#' && c!= EOF){
8380: ungetc(c,ficpar);
8381: fgets(line, MAXLINE, ficpar);
1.141 brouard 8382: fputs(line,stdout);
1.126 brouard 8383: fputs(line,ficparo);
8384: }
8385: ungetc(c,ficpar);
8386:
8387: 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);
8388: 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);
8389: 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);
8390: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
8391: 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);
8392:
8393: while((c=getc(ficpar))=='#' && c!= EOF){
8394: ungetc(c,ficpar);
8395: fgets(line, MAXLINE, ficpar);
1.141 brouard 8396: fputs(line,stdout);
1.126 brouard 8397: fputs(line,ficparo);
8398: }
8399: ungetc(c,ficpar);
8400:
8401:
8402: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
8403: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
8404:
8405: fscanf(ficpar,"pop_based=%d\n",&popbased);
1.193 brouard 8406: fprintf(ficlog,"pop_based=%d\n",popbased);
1.126 brouard 8407: fprintf(ficparo,"pop_based=%d\n",popbased);
8408: fprintf(ficres,"pop_based=%d\n",popbased);
8409:
8410: while((c=getc(ficpar))=='#' && c!= EOF){
8411: ungetc(c,ficpar);
8412: fgets(line, MAXLINE, ficpar);
1.141 brouard 8413: fputs(line,stdout);
1.126 brouard 8414: fputs(line,ficparo);
8415: }
8416: ungetc(c,ficpar);
8417:
8418: 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);
8419: 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);
8420: 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);
8421: 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);
8422: 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);
8423: /* day and month of proj2 are not used but only year anproj2.*/
8424:
8425:
8426:
1.145 brouard 8427: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
8428: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 8429:
8430: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 8431: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
8432: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
8433: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
8434: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
8435: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
8436: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
8437: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
8438: }else
1.211 brouard 8439: printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, pathc,p);
1.126 brouard 8440:
1.201 brouard 8441: printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt,\
1.211 brouard 8442: model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,estepm, \
1.213 brouard 8443: jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);
1.126 brouard 8444:
8445: /*------------ free_vector -------------*/
8446: /* chdir(path); */
8447:
8448: free_ivector(wav,1,imx);
1.214 ! brouard 8449: free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
! 8450: free_imatrix(bh,1,lastpass-firstpass+2,1,imx);
! 8451: free_imatrix(mw,1,lastpass-firstpass+2,1,imx);
1.126 brouard 8452: free_lvector(num,1,n);
8453: free_vector(agedc,1,n);
8454: /*free_matrix(covar,0,NCOVMAX,1,n);*/
8455: /*free_matrix(covar,1,NCOVMAX,1,n);*/
8456: fclose(ficparo);
8457: fclose(ficres);
8458:
8459:
1.186 brouard 8460: /* Other results (useful)*/
8461:
8462:
1.126 brouard 8463: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 8464: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
8465: prlim=matrix(1,nlstate,1,nlstate);
1.209 brouard 8466: prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, &ncvyear);
1.126 brouard 8467: fclose(ficrespl);
8468:
1.145 brouard 8469: #ifdef FREEEXIT2
8470: #include "freeexit2.h"
8471: #endif
8472:
1.126 brouard 8473: /*------------- h Pij x at various ages ------------*/
1.180 brouard 8474: /*#include "hpijx.h"*/
8475: hPijx(p, bage, fage);
1.145 brouard 8476: fclose(ficrespij);
1.126 brouard 8477:
1.145 brouard 8478: /*-------------- Variance of one-step probabilities---*/
8479: k=1;
1.126 brouard 8480: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
8481:
8482:
8483: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
8484: for(i=1;i<=AGESUP;i++)
8485: for(j=1;j<=NCOVMAX;j++)
8486: for(k=1;k<=NCOVMAX;k++)
8487: probs[i][j][k]=0.;
8488:
8489: /*---------- Forecasting ------------------*/
8490: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
8491: if(prevfcast==1){
8492: /* if(stepm ==1){*/
1.201 brouard 8493: prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.126 brouard 8494: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
8495: /* } */
8496: /* else{ */
8497: /* erreur=108; */
8498: /* 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); */
8499: /* 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); */
8500: /* } */
8501: }
1.186 brouard 8502:
8503: /* ------ Other prevalence ratios------------ */
1.126 brouard 8504:
1.127 brouard 8505: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
8506:
8507: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
8508: /* 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",\
8509: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
8510: */
1.126 brouard 8511:
1.127 brouard 8512: if (mobilav!=0) {
8513: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
8514: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
8515: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
8516: printf(" Error in movingaverage mobilav=%d\n",mobilav);
8517: }
1.126 brouard 8518: }
8519:
8520:
1.127 brouard 8521: /*---------- Health expectancies, no variances ------------*/
8522:
1.201 brouard 8523: strcpy(filerese,"E_");
8524: strcat(filerese,fileresu);
1.126 brouard 8525: if((ficreseij=fopen(filerese,"w"))==NULL) {
8526: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
8527: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
8528: }
1.208 brouard 8529: printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
8530: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
1.145 brouard 8531: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
8532: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
8533:
8534: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.127 brouard 8535: fprintf(ficreseij,"\n#****** ");
8536: for(j=1;j<=cptcoveff;j++) {
1.200 brouard 8537: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.127 brouard 8538: }
8539: fprintf(ficreseij,"******\n");
8540:
8541: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
8542: oldm=oldms;savm=savms;
8543: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
8544:
8545: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.145 brouard 8546: /*}*/
1.127 brouard 8547: }
8548: fclose(ficreseij);
1.208 brouard 8549: printf("done evsij\n");fflush(stdout);
8550: fprintf(ficlog,"done evsij\n");fflush(ficlog);
1.127 brouard 8551:
8552: /*---------- Health expectancies and variances ------------*/
8553:
8554:
1.201 brouard 8555: strcpy(filerest,"T_");
8556: strcat(filerest,fileresu);
1.127 brouard 8557: if((ficrest=fopen(filerest,"w"))==NULL) {
8558: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
8559: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
8560: }
1.208 brouard 8561: printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
8562: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
1.127 brouard 8563:
1.126 brouard 8564:
1.201 brouard 8565: strcpy(fileresstde,"STDE_");
8566: strcat(fileresstde,fileresu);
1.126 brouard 8567: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
8568: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
8569: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
8570: }
1.208 brouard 8571: printf(" Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
8572: fprintf(ficlog," Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
1.126 brouard 8573:
1.201 brouard 8574: strcpy(filerescve,"CVE_");
8575: strcat(filerescve,fileresu);
1.126 brouard 8576: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
8577: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
8578: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
8579: }
1.208 brouard 8580: printf(" Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
8581: fprintf(ficlog," Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
1.126 brouard 8582:
1.201 brouard 8583: strcpy(fileresv,"V_");
8584: strcat(fileresv,fileresu);
1.126 brouard 8585: if((ficresvij=fopen(fileresv,"w"))==NULL) {
8586: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
8587: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
8588: }
1.208 brouard 8589: printf(" Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(stdout);
8590: fprintf(ficlog," Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(ficlog);
1.126 brouard 8591:
1.145 brouard 8592: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
8593: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
8594:
8595: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.208 brouard 8596: fprintf(ficrest,"\n#****** ");
8597: for(j=1;j<=cptcoveff;j++)
8598: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8599: fprintf(ficrest,"******\n");
8600:
8601: fprintf(ficresstdeij,"\n#****** ");
8602: fprintf(ficrescveij,"\n#****** ");
8603: for(j=1;j<=cptcoveff;j++) {
8604: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8605: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8606: }
8607: fprintf(ficresstdeij,"******\n");
8608: fprintf(ficrescveij,"******\n");
8609:
8610: fprintf(ficresvij,"\n#****** ");
8611: for(j=1;j<=cptcoveff;j++)
8612: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8613: fprintf(ficresvij,"******\n");
8614:
8615: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
8616: oldm=oldms;savm=savms;
8617: printf(" cvevsij %d, ",k);
8618: fprintf(ficlog, " cvevsij %d, ",k);
8619: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
8620: printf(" end cvevsij \n ");
8621: fprintf(ficlog, " end cvevsij \n ");
8622:
8623: /*
8624: */
8625: /* goto endfree; */
8626:
8627: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
8628: pstamp(ficrest);
8629:
8630:
8631: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
8632: oldm=oldms;savm=savms; /* ZZ Segmentation fault */
8633: cptcod= 0; /* To be deleted */
8634: printf("varevsij %d \n",vpopbased);
8635: fprintf(ficlog, "varevsij %d \n",vpopbased);
1.209 brouard 8636: 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 8637: 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 ");
8638: if(vpopbased==1)
8639: 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);
8640: else
8641: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
8642: fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
8643: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
8644: fprintf(ficrest,"\n");
8645: /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
8646: epj=vector(1,nlstate+1);
8647: printf("Computing age specific period (stable) prevalences in each health state \n");
8648: fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
8649: for(age=bage; age <=fage ;age++){
1.209 brouard 8650: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k); /*ZZ Is it the correct prevalim */
1.208 brouard 8651: if (vpopbased==1) {
8652: if(mobilav ==0){
8653: for(i=1; i<=nlstate;i++)
8654: prlim[i][i]=probs[(int)age][i][k];
8655: }else{ /* mobilav */
8656: for(i=1; i<=nlstate;i++)
8657: prlim[i][i]=mobaverage[(int)age][i][k];
1.126 brouard 8658: }
1.208 brouard 8659: }
8660:
8661: fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
8662: /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
8663: /* printf(" age %4.0f ",age); */
8664: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
8665: for(i=1, epj[j]=0.;i <=nlstate;i++) {
8666: epj[j] += prlim[i][i]*eij[i][j][(int)age];
8667: /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
8668: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
1.126 brouard 8669: }
1.208 brouard 8670: epj[nlstate+1] +=epj[j];
8671: }
8672: /* printf(" age %4.0f \n",age); */
8673:
8674: for(i=1, vepp=0.;i <=nlstate;i++)
8675: for(j=1;j <=nlstate;j++)
8676: vepp += vareij[i][j][(int)age];
8677: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
8678: for(j=1;j <=nlstate;j++){
8679: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
1.126 brouard 8680: }
1.208 brouard 8681: fprintf(ficrest,"\n");
1.126 brouard 8682: }
1.208 brouard 8683: } /* End vpopbased */
8684: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
8685: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
8686: free_vector(epj,1,nlstate+1);
8687: printf("done \n");fflush(stdout);
8688: fprintf(ficlog,"done\n");fflush(ficlog);
8689:
1.145 brouard 8690: /*}*/
1.208 brouard 8691: } /* End k */
1.126 brouard 8692: free_vector(weight,1,n);
1.145 brouard 8693: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.126 brouard 8694: free_imatrix(s,1,maxwav+1,1,n);
8695: free_matrix(anint,1,maxwav,1,n);
8696: free_matrix(mint,1,maxwav,1,n);
8697: free_ivector(cod,1,n);
8698: free_ivector(tab,1,NCOVMAX);
8699: fclose(ficresstdeij);
8700: fclose(ficrescveij);
8701: fclose(ficresvij);
8702: fclose(ficrest);
1.208 brouard 8703: printf("done Health expectancies\n");fflush(stdout);
8704: fprintf(ficlog,"done Health expectancies\n");fflush(ficlog);
1.126 brouard 8705: fclose(ficpar);
8706:
8707: /*------- Variance of period (stable) prevalence------*/
8708:
1.201 brouard 8709: strcpy(fileresvpl,"VPL_");
8710: strcat(fileresvpl,fileresu);
1.126 brouard 8711: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
8712: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
8713: exit(0);
8714: }
1.208 brouard 8715: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
8716: fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
1.126 brouard 8717:
1.145 brouard 8718: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
8719: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
8720:
8721: for (k=1; k <= (int) pow(2,cptcoveff); k++){
8722: fprintf(ficresvpl,"\n#****** ");
1.126 brouard 8723: for(j=1;j<=cptcoveff;j++)
1.200 brouard 8724: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 8725: fprintf(ficresvpl,"******\n");
8726:
8727: varpl=matrix(1,nlstate,(int) bage, (int) fage);
8728: oldm=oldms;savm=savms;
1.209 brouard 8729: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart);
1.126 brouard 8730: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 8731: /*}*/
1.126 brouard 8732: }
8733:
8734: fclose(ficresvpl);
1.208 brouard 8735: printf("done variance-covariance of period prevalence\n");fflush(stdout);
8736: fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
1.126 brouard 8737:
8738: /*---------- End : free ----------------*/
8739: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
8740: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
8741: } /* mle==-3 arrives here for freeing */
1.164 brouard 8742: /* endfree:*/
1.141 brouard 8743: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.126 brouard 8744: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
8745: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
8746: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
8747: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
8748: free_matrix(covar,0,NCOVMAX,1,n);
8749: free_matrix(matcov,1,npar,1,npar);
1.203 brouard 8750: free_matrix(hess,1,npar,1,npar);
1.126 brouard 8751: /*free_vector(delti,1,npar);*/
8752: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
8753: free_matrix(agev,1,maxwav,1,imx);
8754: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
8755:
1.145 brouard 8756: free_ivector(ncodemax,1,NCOVMAX);
1.192 brouard 8757: free_ivector(ncodemaxwundef,1,NCOVMAX);
1.145 brouard 8758: free_ivector(Tvar,1,NCOVMAX);
8759: free_ivector(Tprod,1,NCOVMAX);
8760: free_ivector(Tvaraff,1,NCOVMAX);
8761: free_ivector(Tage,1,NCOVMAX);
1.126 brouard 8762:
8763: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
1.200 brouard 8764: /* free_imatrix(codtab,1,100,1,10); */
1.126 brouard 8765: fflush(fichtm);
8766: fflush(ficgp);
8767:
8768:
8769: if((nberr >0) || (nbwarn>0)){
8770: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
8771: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
8772: }else{
8773: printf("End of Imach\n");
8774: fprintf(ficlog,"End of Imach\n");
8775: }
8776: printf("See log file on %s\n",filelog);
8777: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 8778: /*(void) gettimeofday(&end_time,&tzp);*/
8779: rend_time = time(NULL);
8780: end_time = *localtime(&rend_time);
8781: /* tml = *localtime(&end_time.tm_sec); */
8782: strcpy(strtend,asctime(&end_time));
1.126 brouard 8783: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
8784: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 8785: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.126 brouard 8786:
1.157 brouard 8787: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
8788: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
8789: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 8790: /* printf("Total time was %d uSec.\n", total_usecs);*/
8791: /* if(fileappend(fichtm,optionfilehtm)){ */
8792: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
8793: fclose(fichtm);
8794: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
8795: fclose(fichtmcov);
8796: fclose(ficgp);
8797: fclose(ficlog);
8798: /*------ End -----------*/
8799:
8800:
8801: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 8802: #ifdef WIN32
8803: if (_chdir(pathcd) != 0)
8804: printf("Can't move to directory %s!\n",path);
8805: if(_getcwd(pathcd,MAXLINE) > 0)
8806: #else
1.126 brouard 8807: if(chdir(pathcd) != 0)
1.184 brouard 8808: printf("Can't move to directory %s!\n", path);
8809: if (getcwd(pathcd, MAXLINE) > 0)
8810: #endif
1.126 brouard 8811: printf("Current directory %s!\n",pathcd);
8812: /*strcat(plotcmd,CHARSEPARATOR);*/
8813: sprintf(plotcmd,"gnuplot");
1.157 brouard 8814: #ifdef _WIN32
1.126 brouard 8815: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
8816: #endif
8817: if(!stat(plotcmd,&info)){
1.158 brouard 8818: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 8819: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 8820: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 8821: }else
8822: strcpy(pplotcmd,plotcmd);
1.157 brouard 8823: #ifdef __unix
1.126 brouard 8824: strcpy(plotcmd,GNUPLOTPROGRAM);
8825: if(!stat(plotcmd,&info)){
1.158 brouard 8826: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 8827: }else
8828: strcpy(pplotcmd,plotcmd);
8829: #endif
8830: }else
8831: strcpy(pplotcmd,plotcmd);
8832:
8833: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 8834: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 8835:
8836: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 8837: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 8838: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 8839: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 8840: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 8841: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 8842: }
1.158 brouard 8843: printf(" Successful, please wait...");
1.126 brouard 8844: while (z[0] != 'q') {
8845: /* chdir(path); */
1.154 brouard 8846: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 8847: scanf("%s",z);
8848: /* if (z[0] == 'c') system("./imach"); */
8849: if (z[0] == 'e') {
1.158 brouard 8850: #ifdef __APPLE__
1.152 brouard 8851: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 8852: #elif __linux
8853: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 8854: #else
1.152 brouard 8855: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 8856: #endif
8857: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
8858: system(pplotcmd);
1.126 brouard 8859: }
8860: else if (z[0] == 'g') system(plotcmd);
8861: else if (z[0] == 'q') exit(0);
8862: }
8863: end:
8864: while (z[0] != 'q') {
1.195 brouard 8865: printf("\nType q for exiting: "); fflush(stdout);
1.126 brouard 8866: scanf("%s",z);
8867: }
8868: }
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