Annotation of imach/src/imach.c, revision 1.202
1.202 ! brouard 1: /* $Id: imach.c,v 1.201 2015/09/15 17:34:58 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.202 ! brouard 4: Revision 1.201 2015/09/15 17:34:58 brouard
! 5: Summary: 0.98r0
! 6:
! 7: - Some new graphs like suvival functions
! 8: - Some bugs fixed like model=1+age+V2.
! 9:
1.201 brouard 10: Revision 1.200 2015/09/09 16:53:55 brouard
11: Summary: Big bug thanks to Flavia
12:
13: Even model=1+age+V2. did not work anymore
14:
1.200 brouard 15: Revision 1.199 2015/09/07 14:09:23 brouard
16: Summary: 0.98q6 changing default small png format for graph to vectorized svg.
17:
1.199 brouard 18: Revision 1.198 2015/09/03 07:14:39 brouard
19: Summary: 0.98q5 Flavia
20:
1.198 brouard 21: Revision 1.197 2015/09/01 18:24:39 brouard
22: *** empty log message ***
23:
1.197 brouard 24: Revision 1.196 2015/08/18 23:17:52 brouard
25: Summary: 0.98q5
26:
1.196 brouard 27: Revision 1.195 2015/08/18 16:28:39 brouard
28: Summary: Adding a hack for testing purpose
29:
30: After reading the title, ftol and model lines, if the comment line has
31: a q, starting with #q, the answer at the end of the run is quit. It
32: permits to run test files in batch with ctest. The former workaround was
33: $ echo q | imach foo.imach
34:
1.195 brouard 35: Revision 1.194 2015/08/18 13:32:00 brouard
36: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
37:
1.194 brouard 38: Revision 1.193 2015/08/04 07:17:42 brouard
39: Summary: 0.98q4
40:
1.193 brouard 41: Revision 1.192 2015/07/16 16:49:02 brouard
42: Summary: Fixing some outputs
43:
1.192 brouard 44: Revision 1.191 2015/07/14 10:00:33 brouard
45: Summary: Some fixes
46:
1.191 brouard 47: Revision 1.190 2015/05/05 08:51:13 brouard
48: Summary: Adding digits in output parameters (7 digits instead of 6)
49:
50: Fix 1+age+.
51:
1.190 brouard 52: Revision 1.189 2015/04/30 14:45:16 brouard
53: Summary: 0.98q2
54:
1.189 brouard 55: Revision 1.188 2015/04/30 08:27:53 brouard
56: *** empty log message ***
57:
1.188 brouard 58: Revision 1.187 2015/04/29 09:11:15 brouard
59: *** empty log message ***
60:
1.187 brouard 61: Revision 1.186 2015/04/23 12:01:52 brouard
62: Summary: V1*age is working now, version 0.98q1
63:
64: Some codes had been disabled in order to simplify and Vn*age was
65: working in the optimization phase, ie, giving correct MLE parameters,
66: but, as usual, outputs were not correct and program core dumped.
67:
1.186 brouard 68: Revision 1.185 2015/03/11 13:26:42 brouard
69: Summary: Inclusion of compile and links command line for Intel Compiler
70:
1.185 brouard 71: Revision 1.184 2015/03/11 11:52:39 brouard
72: Summary: Back from Windows 8. Intel Compiler
73:
1.184 brouard 74: Revision 1.183 2015/03/10 20:34:32 brouard
75: Summary: 0.98q0, trying with directest, mnbrak fixed
76:
77: We use directest instead of original Powell test; probably no
78: incidence on the results, but better justifications;
79: We fixed Numerical Recipes mnbrak routine which was wrong and gave
80: wrong results.
81:
1.183 brouard 82: Revision 1.182 2015/02/12 08:19:57 brouard
83: Summary: Trying to keep directest which seems simpler and more general
84: Author: Nicolas Brouard
85:
1.182 brouard 86: Revision 1.181 2015/02/11 23:22:24 brouard
87: Summary: Comments on Powell added
88:
89: Author:
90:
1.181 brouard 91: Revision 1.180 2015/02/11 17:33:45 brouard
92: Summary: Finishing move from main to function (hpijx and prevalence_limit)
93:
1.180 brouard 94: Revision 1.179 2015/01/04 09:57:06 brouard
95: Summary: back to OS/X
96:
1.179 brouard 97: Revision 1.178 2015/01/04 09:35:48 brouard
98: *** empty log message ***
99:
1.178 brouard 100: Revision 1.177 2015/01/03 18:40:56 brouard
101: Summary: Still testing ilc32 on OSX
102:
1.177 brouard 103: Revision 1.176 2015/01/03 16:45:04 brouard
104: *** empty log message ***
105:
1.176 brouard 106: Revision 1.175 2015/01/03 16:33:42 brouard
107: *** empty log message ***
108:
1.175 brouard 109: Revision 1.174 2015/01/03 16:15:49 brouard
110: Summary: Still in cross-compilation
111:
1.174 brouard 112: Revision 1.173 2015/01/03 12:06:26 brouard
113: Summary: trying to detect cross-compilation
114:
1.173 brouard 115: Revision 1.172 2014/12/27 12:07:47 brouard
116: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
117:
1.172 brouard 118: Revision 1.171 2014/12/23 13:26:59 brouard
119: Summary: Back from Visual C
120:
121: Still problem with utsname.h on Windows
122:
1.171 brouard 123: Revision 1.170 2014/12/23 11:17:12 brouard
124: Summary: Cleaning some \%% back to %%
125:
126: The escape was mandatory for a specific compiler (which one?), but too many warnings.
127:
1.170 brouard 128: Revision 1.169 2014/12/22 23:08:31 brouard
129: Summary: 0.98p
130:
131: Outputs some informations on compiler used, OS etc. Testing on different platforms.
132:
1.169 brouard 133: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 134: Summary: update
1.169 brouard 135:
1.168 brouard 136: Revision 1.167 2014/12/22 13:50:56 brouard
137: Summary: Testing uname and compiler version and if compiled 32 or 64
138:
139: Testing on Linux 64
140:
1.167 brouard 141: Revision 1.166 2014/12/22 11:40:47 brouard
142: *** empty log message ***
143:
1.166 brouard 144: Revision 1.165 2014/12/16 11:20:36 brouard
145: Summary: After compiling on Visual C
146:
147: * imach.c (Module): Merging 1.61 to 1.162
148:
1.165 brouard 149: Revision 1.164 2014/12/16 10:52:11 brouard
150: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
151:
152: * imach.c (Module): Merging 1.61 to 1.162
153:
1.164 brouard 154: Revision 1.163 2014/12/16 10:30:11 brouard
155: * imach.c (Module): Merging 1.61 to 1.162
156:
1.163 brouard 157: Revision 1.162 2014/09/25 11:43:39 brouard
158: Summary: temporary backup 0.99!
159:
1.162 brouard 160: Revision 1.1 2014/09/16 11:06:58 brouard
161: Summary: With some code (wrong) for nlopt
162:
163: Author:
164:
165: Revision 1.161 2014/09/15 20:41:41 brouard
166: Summary: Problem with macro SQR on Intel compiler
167:
1.161 brouard 168: Revision 1.160 2014/09/02 09:24:05 brouard
169: *** empty log message ***
170:
1.160 brouard 171: Revision 1.159 2014/09/01 10:34:10 brouard
172: Summary: WIN32
173: Author: Brouard
174:
1.159 brouard 175: Revision 1.158 2014/08/27 17:11:51 brouard
176: *** empty log message ***
177:
1.158 brouard 178: Revision 1.157 2014/08/27 16:26:55 brouard
179: Summary: Preparing windows Visual studio version
180: Author: Brouard
181:
182: In order to compile on Visual studio, time.h is now correct and time_t
183: and tm struct should be used. difftime should be used but sometimes I
184: just make the differences in raw time format (time(&now).
185: Trying to suppress #ifdef LINUX
186: Add xdg-open for __linux in order to open default browser.
187:
1.157 brouard 188: Revision 1.156 2014/08/25 20:10:10 brouard
189: *** empty log message ***
190:
1.156 brouard 191: Revision 1.155 2014/08/25 18:32:34 brouard
192: Summary: New compile, minor changes
193: Author: Brouard
194:
1.155 brouard 195: Revision 1.154 2014/06/20 17:32:08 brouard
196: Summary: Outputs now all graphs of convergence to period prevalence
197:
1.154 brouard 198: Revision 1.153 2014/06/20 16:45:46 brouard
199: Summary: If 3 live state, convergence to period prevalence on same graph
200: Author: Brouard
201:
1.153 brouard 202: Revision 1.152 2014/06/18 17:54:09 brouard
203: Summary: open browser, use gnuplot on same dir than imach if not found in the path
204:
1.152 brouard 205: Revision 1.151 2014/06/18 16:43:30 brouard
206: *** empty log message ***
207:
1.151 brouard 208: Revision 1.150 2014/06/18 16:42:35 brouard
209: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
210: Author: brouard
211:
1.150 brouard 212: Revision 1.149 2014/06/18 15:51:14 brouard
213: Summary: Some fixes in parameter files errors
214: Author: Nicolas Brouard
215:
1.149 brouard 216: Revision 1.148 2014/06/17 17:38:48 brouard
217: Summary: Nothing new
218: Author: Brouard
219:
220: Just a new packaging for OS/X version 0.98nS
221:
1.148 brouard 222: Revision 1.147 2014/06/16 10:33:11 brouard
223: *** empty log message ***
224:
1.147 brouard 225: Revision 1.146 2014/06/16 10:20:28 brouard
226: Summary: Merge
227: Author: Brouard
228:
229: Merge, before building revised version.
230:
1.146 brouard 231: Revision 1.145 2014/06/10 21:23:15 brouard
232: Summary: Debugging with valgrind
233: Author: Nicolas Brouard
234:
235: Lot of changes in order to output the results with some covariates
236: After the Edimburgh REVES conference 2014, it seems mandatory to
237: improve the code.
238: No more memory valgrind error but a lot has to be done in order to
239: continue the work of splitting the code into subroutines.
240: Also, decodemodel has been improved. Tricode is still not
241: optimal. nbcode should be improved. Documentation has been added in
242: the source code.
243:
1.144 brouard 244: Revision 1.143 2014/01/26 09:45:38 brouard
245: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
246:
247: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
248: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
249:
1.143 brouard 250: Revision 1.142 2014/01/26 03:57:36 brouard
251: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
252:
253: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
254:
1.142 brouard 255: Revision 1.141 2014/01/26 02:42:01 brouard
256: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
257:
1.141 brouard 258: Revision 1.140 2011/09/02 10:37:54 brouard
259: Summary: times.h is ok with mingw32 now.
260:
1.140 brouard 261: Revision 1.139 2010/06/14 07:50:17 brouard
262: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
263: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
264:
1.139 brouard 265: Revision 1.138 2010/04/30 18:19:40 brouard
266: *** empty log message ***
267:
1.138 brouard 268: Revision 1.137 2010/04/29 18:11:38 brouard
269: (Module): Checking covariates for more complex models
270: than V1+V2. A lot of change to be done. Unstable.
271:
1.137 brouard 272: Revision 1.136 2010/04/26 20:30:53 brouard
273: (Module): merging some libgsl code. Fixing computation
274: of likelione (using inter/intrapolation if mle = 0) in order to
275: get same likelihood as if mle=1.
276: Some cleaning of code and comments added.
277:
1.136 brouard 278: Revision 1.135 2009/10/29 15:33:14 brouard
279: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
280:
1.135 brouard 281: Revision 1.134 2009/10/29 13:18:53 brouard
282: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
283:
1.134 brouard 284: Revision 1.133 2009/07/06 10:21:25 brouard
285: just nforces
286:
1.133 brouard 287: Revision 1.132 2009/07/06 08:22:05 brouard
288: Many tings
289:
1.132 brouard 290: Revision 1.131 2009/06/20 16:22:47 brouard
291: Some dimensions resccaled
292:
1.131 brouard 293: Revision 1.130 2009/05/26 06:44:34 brouard
294: (Module): Max Covariate is now set to 20 instead of 8. A
295: lot of cleaning with variables initialized to 0. Trying to make
296: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
297:
1.130 brouard 298: Revision 1.129 2007/08/31 13:49:27 lievre
299: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
300:
1.129 lievre 301: Revision 1.128 2006/06/30 13:02:05 brouard
302: (Module): Clarifications on computing e.j
303:
1.128 brouard 304: Revision 1.127 2006/04/28 18:11:50 brouard
305: (Module): Yes the sum of survivors was wrong since
306: imach-114 because nhstepm was no more computed in the age
307: loop. Now we define nhstepma in the age loop.
308: (Module): In order to speed up (in case of numerous covariates) we
309: compute health expectancies (without variances) in a first step
310: and then all the health expectancies with variances or standard
311: deviation (needs data from the Hessian matrices) which slows the
312: computation.
313: In the future we should be able to stop the program is only health
314: expectancies and graph are needed without standard deviations.
315:
1.127 brouard 316: Revision 1.126 2006/04/28 17:23:28 brouard
317: (Module): Yes the sum of survivors was wrong since
318: imach-114 because nhstepm was no more computed in the age
319: loop. Now we define nhstepma in the age loop.
320: Version 0.98h
321:
1.126 brouard 322: Revision 1.125 2006/04/04 15:20:31 lievre
323: Errors in calculation of health expectancies. Age was not initialized.
324: Forecasting file added.
325:
326: Revision 1.124 2006/03/22 17:13:53 lievre
327: Parameters are printed with %lf instead of %f (more numbers after the comma).
328: The log-likelihood is printed in the log file
329:
330: Revision 1.123 2006/03/20 10:52:43 brouard
331: * imach.c (Module): <title> changed, corresponds to .htm file
332: name. <head> headers where missing.
333:
334: * imach.c (Module): Weights can have a decimal point as for
335: English (a comma might work with a correct LC_NUMERIC environment,
336: otherwise the weight is truncated).
337: Modification of warning when the covariates values are not 0 or
338: 1.
339: Version 0.98g
340:
341: Revision 1.122 2006/03/20 09:45:41 brouard
342: (Module): Weights can have a decimal point as for
343: English (a comma might work with a correct LC_NUMERIC environment,
344: otherwise the weight is truncated).
345: Modification of warning when the covariates values are not 0 or
346: 1.
347: Version 0.98g
348:
349: Revision 1.121 2006/03/16 17:45:01 lievre
350: * imach.c (Module): Comments concerning covariates added
351:
352: * imach.c (Module): refinements in the computation of lli if
353: status=-2 in order to have more reliable computation if stepm is
354: not 1 month. Version 0.98f
355:
356: Revision 1.120 2006/03/16 15:10:38 lievre
357: (Module): refinements in the computation of lli if
358: status=-2 in order to have more reliable computation if stepm is
359: not 1 month. Version 0.98f
360:
361: Revision 1.119 2006/03/15 17:42:26 brouard
362: (Module): Bug if status = -2, the loglikelihood was
363: computed as likelihood omitting the logarithm. Version O.98e
364:
365: Revision 1.118 2006/03/14 18:20:07 brouard
366: (Module): varevsij Comments added explaining the second
367: table of variances if popbased=1 .
368: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
369: (Module): Function pstamp added
370: (Module): Version 0.98d
371:
372: Revision 1.117 2006/03/14 17:16:22 brouard
373: (Module): varevsij Comments added explaining the second
374: table of variances if popbased=1 .
375: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
376: (Module): Function pstamp added
377: (Module): Version 0.98d
378:
379: Revision 1.116 2006/03/06 10:29:27 brouard
380: (Module): Variance-covariance wrong links and
381: varian-covariance of ej. is needed (Saito).
382:
383: Revision 1.115 2006/02/27 12:17:45 brouard
384: (Module): One freematrix added in mlikeli! 0.98c
385:
386: Revision 1.114 2006/02/26 12:57:58 brouard
387: (Module): Some improvements in processing parameter
388: filename with strsep.
389:
390: Revision 1.113 2006/02/24 14:20:24 brouard
391: (Module): Memory leaks checks with valgrind and:
392: datafile was not closed, some imatrix were not freed and on matrix
393: allocation too.
394:
395: Revision 1.112 2006/01/30 09:55:26 brouard
396: (Module): Back to gnuplot.exe instead of wgnuplot.exe
397:
398: Revision 1.111 2006/01/25 20:38:18 brouard
399: (Module): Lots of cleaning and bugs added (Gompertz)
400: (Module): Comments can be added in data file. Missing date values
401: can be a simple dot '.'.
402:
403: Revision 1.110 2006/01/25 00:51:50 brouard
404: (Module): Lots of cleaning and bugs added (Gompertz)
405:
406: Revision 1.109 2006/01/24 19:37:15 brouard
407: (Module): Comments (lines starting with a #) are allowed in data.
408:
409: Revision 1.108 2006/01/19 18:05:42 lievre
410: Gnuplot problem appeared...
411: To be fixed
412:
413: Revision 1.107 2006/01/19 16:20:37 brouard
414: Test existence of gnuplot in imach path
415:
416: Revision 1.106 2006/01/19 13:24:36 brouard
417: Some cleaning and links added in html output
418:
419: Revision 1.105 2006/01/05 20:23:19 lievre
420: *** empty log message ***
421:
422: Revision 1.104 2005/09/30 16:11:43 lievre
423: (Module): sump fixed, loop imx fixed, and simplifications.
424: (Module): If the status is missing at the last wave but we know
425: that the person is alive, then we can code his/her status as -2
426: (instead of missing=-1 in earlier versions) and his/her
427: contributions to the likelihood is 1 - Prob of dying from last
428: health status (= 1-p13= p11+p12 in the easiest case of somebody in
429: the healthy state at last known wave). Version is 0.98
430:
431: Revision 1.103 2005/09/30 15:54:49 lievre
432: (Module): sump fixed, loop imx fixed, and simplifications.
433:
434: Revision 1.102 2004/09/15 17:31:30 brouard
435: Add the possibility to read data file including tab characters.
436:
437: Revision 1.101 2004/09/15 10:38:38 brouard
438: Fix on curr_time
439:
440: Revision 1.100 2004/07/12 18:29:06 brouard
441: Add version for Mac OS X. Just define UNIX in Makefile
442:
443: Revision 1.99 2004/06/05 08:57:40 brouard
444: *** empty log message ***
445:
446: Revision 1.98 2004/05/16 15:05:56 brouard
447: New version 0.97 . First attempt to estimate force of mortality
448: directly from the data i.e. without the need of knowing the health
449: state at each age, but using a Gompertz model: log u =a + b*age .
450: This is the basic analysis of mortality and should be done before any
451: other analysis, in order to test if the mortality estimated from the
452: cross-longitudinal survey is different from the mortality estimated
453: from other sources like vital statistic data.
454:
455: The same imach parameter file can be used but the option for mle should be -3.
456:
1.133 brouard 457: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 458: former routines in order to include the new code within the former code.
459:
460: The output is very simple: only an estimate of the intercept and of
461: the slope with 95% confident intervals.
462:
463: Current limitations:
464: A) Even if you enter covariates, i.e. with the
465: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
466: B) There is no computation of Life Expectancy nor Life Table.
467:
468: Revision 1.97 2004/02/20 13:25:42 lievre
469: Version 0.96d. Population forecasting command line is (temporarily)
470: suppressed.
471:
472: Revision 1.96 2003/07/15 15:38:55 brouard
473: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
474: rewritten within the same printf. Workaround: many printfs.
475:
476: Revision 1.95 2003/07/08 07:54:34 brouard
477: * imach.c (Repository):
478: (Repository): Using imachwizard code to output a more meaningful covariance
479: matrix (cov(a12,c31) instead of numbers.
480:
481: Revision 1.94 2003/06/27 13:00:02 brouard
482: Just cleaning
483:
484: Revision 1.93 2003/06/25 16:33:55 brouard
485: (Module): On windows (cygwin) function asctime_r doesn't
486: exist so I changed back to asctime which exists.
487: (Module): Version 0.96b
488:
489: Revision 1.92 2003/06/25 16:30:45 brouard
490: (Module): On windows (cygwin) function asctime_r doesn't
491: exist so I changed back to asctime which exists.
492:
493: Revision 1.91 2003/06/25 15:30:29 brouard
494: * imach.c (Repository): Duplicated warning errors corrected.
495: (Repository): Elapsed time after each iteration is now output. It
496: helps to forecast when convergence will be reached. Elapsed time
497: is stamped in powell. We created a new html file for the graphs
498: concerning matrix of covariance. It has extension -cov.htm.
499:
500: Revision 1.90 2003/06/24 12:34:15 brouard
501: (Module): Some bugs corrected for windows. Also, when
502: mle=-1 a template is output in file "or"mypar.txt with the design
503: of the covariance matrix to be input.
504:
505: Revision 1.89 2003/06/24 12:30:52 brouard
506: (Module): Some bugs corrected for windows. Also, when
507: mle=-1 a template is output in file "or"mypar.txt with the design
508: of the covariance matrix to be input.
509:
510: Revision 1.88 2003/06/23 17:54:56 brouard
511: * 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.
512:
513: Revision 1.87 2003/06/18 12:26:01 brouard
514: Version 0.96
515:
516: Revision 1.86 2003/06/17 20:04:08 brouard
517: (Module): Change position of html and gnuplot routines and added
518: routine fileappend.
519:
520: Revision 1.85 2003/06/17 13:12:43 brouard
521: * imach.c (Repository): Check when date of death was earlier that
522: current date of interview. It may happen when the death was just
523: prior to the death. In this case, dh was negative and likelihood
524: was wrong (infinity). We still send an "Error" but patch by
525: assuming that the date of death was just one stepm after the
526: interview.
527: (Repository): Because some people have very long ID (first column)
528: we changed int to long in num[] and we added a new lvector for
529: memory allocation. But we also truncated to 8 characters (left
530: truncation)
531: (Repository): No more line truncation errors.
532:
533: Revision 1.84 2003/06/13 21:44:43 brouard
534: * imach.c (Repository): Replace "freqsummary" at a correct
535: place. It differs from routine "prevalence" which may be called
536: many times. Probs is memory consuming and must be used with
537: parcimony.
538: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
539:
540: Revision 1.83 2003/06/10 13:39:11 lievre
541: *** empty log message ***
542:
543: Revision 1.82 2003/06/05 15:57:20 brouard
544: Add log in imach.c and fullversion number is now printed.
545:
546: */
547: /*
548: Interpolated Markov Chain
549:
550: Short summary of the programme:
551:
552: This program computes Healthy Life Expectancies from
553: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
554: first survey ("cross") where individuals from different ages are
555: interviewed on their health status or degree of disability (in the
556: case of a health survey which is our main interest) -2- at least a
557: second wave of interviews ("longitudinal") which measure each change
558: (if any) in individual health status. Health expectancies are
559: computed from the time spent in each health state according to a
560: model. More health states you consider, more time is necessary to reach the
561: Maximum Likelihood of the parameters involved in the model. The
562: simplest model is the multinomial logistic model where pij is the
563: probability to be observed in state j at the second wave
564: conditional to be observed in state i at the first wave. Therefore
565: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
566: 'age' is age and 'sex' is a covariate. If you want to have a more
567: complex model than "constant and age", you should modify the program
568: where the markup *Covariates have to be included here again* invites
569: you to do it. More covariates you add, slower the
570: convergence.
571:
572: The advantage of this computer programme, compared to a simple
573: multinomial logistic model, is clear when the delay between waves is not
574: identical for each individual. Also, if a individual missed an
575: intermediate interview, the information is lost, but taken into
576: account using an interpolation or extrapolation.
577:
578: hPijx is the probability to be observed in state i at age x+h
579: conditional to the observed state i at age x. The delay 'h' can be
580: split into an exact number (nh*stepm) of unobserved intermediate
581: states. This elementary transition (by month, quarter,
582: semester or year) is modelled as a multinomial logistic. The hPx
583: matrix is simply the matrix product of nh*stepm elementary matrices
584: and the contribution of each individual to the likelihood is simply
585: hPijx.
586:
587: Also this programme outputs the covariance matrix of the parameters but also
588: of the life expectancies. It also computes the period (stable) prevalence.
589:
1.133 brouard 590: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
591: Institut national d'études démographiques, Paris.
1.126 brouard 592: This software have been partly granted by Euro-REVES, a concerted action
593: from the European Union.
594: It is copyrighted identically to a GNU software product, ie programme and
595: software can be distributed freely for non commercial use. Latest version
596: can be accessed at http://euroreves.ined.fr/imach .
597:
598: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
599: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
600:
601: **********************************************************************/
602: /*
603: main
604: read parameterfile
605: read datafile
606: concatwav
607: freqsummary
608: if (mle >= 1)
609: mlikeli
610: print results files
611: if mle==1
612: computes hessian
613: read end of parameter file: agemin, agemax, bage, fage, estepm
614: begin-prev-date,...
615: open gnuplot file
616: open html file
1.145 brouard 617: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
618: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
619: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
620: freexexit2 possible for memory heap.
621:
622: h Pij x | pij_nom ficrestpij
623: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
624: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
625: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
626:
627: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
628: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
629: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
630: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
631: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
632:
1.126 brouard 633: forecasting if prevfcast==1 prevforecast call prevalence()
634: health expectancies
635: Variance-covariance of DFLE
636: prevalence()
637: movingaverage()
638: varevsij()
639: if popbased==1 varevsij(,popbased)
640: total life expectancies
641: Variance of period (stable) prevalence
642: end
643: */
644:
1.187 brouard 645: /* #define DEBUG */
646: /* #define DEBUGBRENT */
1.202 ! brouard 647: #define DEBUGLINMIN
1.165 brouard 648: #define POWELL /* Instead of NLOPT */
1.192 brouard 649: #define POWELLF1F3 /* Skip test */
1.186 brouard 650: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
651: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 652:
653: #include <math.h>
654: #include <stdio.h>
655: #include <stdlib.h>
656: #include <string.h>
1.159 brouard 657:
658: #ifdef _WIN32
659: #include <io.h>
1.172 brouard 660: #include <windows.h>
661: #include <tchar.h>
1.159 brouard 662: #else
1.126 brouard 663: #include <unistd.h>
1.159 brouard 664: #endif
1.126 brouard 665:
666: #include <limits.h>
667: #include <sys/types.h>
1.171 brouard 668:
669: #if defined(__GNUC__)
670: #include <sys/utsname.h> /* Doesn't work on Windows */
671: #endif
672:
1.126 brouard 673: #include <sys/stat.h>
674: #include <errno.h>
1.159 brouard 675: /* extern int errno; */
1.126 brouard 676:
1.157 brouard 677: /* #ifdef LINUX */
678: /* #include <time.h> */
679: /* #include "timeval.h" */
680: /* #else */
681: /* #include <sys/time.h> */
682: /* #endif */
683:
1.126 brouard 684: #include <time.h>
685:
1.136 brouard 686: #ifdef GSL
687: #include <gsl/gsl_errno.h>
688: #include <gsl/gsl_multimin.h>
689: #endif
690:
1.167 brouard 691:
1.162 brouard 692: #ifdef NLOPT
693: #include <nlopt.h>
694: typedef struct {
695: double (* function)(double [] );
696: } myfunc_data ;
697: #endif
698:
1.126 brouard 699: /* #include <libintl.h> */
700: /* #define _(String) gettext (String) */
701:
1.141 brouard 702: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 703:
704: #define GNUPLOTPROGRAM "gnuplot"
705: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
706: #define FILENAMELENGTH 132
707:
708: #define GLOCK_ERROR_NOPATH -1 /* empty path */
709: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
710:
1.144 brouard 711: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
712: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 713:
714: #define NINTERVMAX 8
1.144 brouard 715: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
716: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
717: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.197 brouard 718: #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.126 brouard 719: #define MAXN 20000
1.144 brouard 720: #define YEARM 12. /**< Number of months per year */
1.126 brouard 721: #define AGESUP 130
722: #define AGEBASE 40
1.194 brouard 723: #define AGEOVERFLOW 1.e20
1.164 brouard 724: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 725: #ifdef _WIN32
726: #define DIRSEPARATOR '\\'
727: #define CHARSEPARATOR "\\"
728: #define ODIRSEPARATOR '/'
729: #else
1.126 brouard 730: #define DIRSEPARATOR '/'
731: #define CHARSEPARATOR "/"
732: #define ODIRSEPARATOR '\\'
733: #endif
734:
1.202 ! brouard 735: /* $Id: imach.c,v 1.201 2015/09/15 17:34:58 brouard Exp $ */
1.126 brouard 736: /* $State: Exp $ */
1.196 brouard 737: #include "version.h"
738: char version[]=__IMACH_VERSION__;
1.197 brouard 739: char copyright[]="September 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
1.202 ! brouard 740: char fullversion[]="$Revision: 1.201 $ $Date: 2015/09/15 17:34:58 $";
1.126 brouard 741: char strstart[80];
742: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 743: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 744: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 745: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
746: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
747: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
748: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
749: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
750: int cptcovprodnoage=0; /**< Number of covariate products without age */
751: int cptcoveff=0; /* Total number of covariates to vary for printing results */
752: int cptcov=0; /* Working variable */
1.126 brouard 753: int npar=NPARMAX;
754: int nlstate=2; /* Number of live states */
755: int ndeath=1; /* Number of dead states */
1.130 brouard 756: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.126 brouard 757: int popbased=0;
758:
759: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 760: int maxwav=0; /* Maxim number of waves */
761: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
762: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
763: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 764: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 765: int mle=1, weightopt=0;
1.126 brouard 766: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
767: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
768: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
769: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 770: int countcallfunc=0; /* Count the number of calls to func */
1.130 brouard 771: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 772: double **matprod2(); /* test */
1.126 brouard 773: double **oldm, **newm, **savm; /* Working pointers to matrices */
774: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.136 brouard 775: /*FILE *fic ; */ /* Used in readdata only */
776: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.126 brouard 777: FILE *ficlog, *ficrespow;
1.130 brouard 778: int globpr=0; /* Global variable for printing or not */
1.126 brouard 779: double fretone; /* Only one call to likelihood */
1.130 brouard 780: long ipmx=0; /* Number of contributions */
1.126 brouard 781: double sw; /* Sum of weights */
782: char filerespow[FILENAMELENGTH];
783: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
784: FILE *ficresilk;
785: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
786: FILE *ficresprobmorprev;
787: FILE *fichtm, *fichtmcov; /* Html File */
788: FILE *ficreseij;
789: char filerese[FILENAMELENGTH];
790: FILE *ficresstdeij;
791: char fileresstde[FILENAMELENGTH];
792: FILE *ficrescveij;
793: char filerescve[FILENAMELENGTH];
794: FILE *ficresvij;
795: char fileresv[FILENAMELENGTH];
796: FILE *ficresvpl;
797: char fileresvpl[FILENAMELENGTH];
798: char title[MAXLINE];
799: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
800: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
801: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
802: char command[FILENAMELENGTH];
803: int outcmd=0;
804:
805: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.202 ! brouard 806: char fileresu[FILENAMELENGTH]; /* fileres without r in front */
1.126 brouard 807: char filelog[FILENAMELENGTH]; /* Log file */
808: char filerest[FILENAMELENGTH];
809: char fileregp[FILENAMELENGTH];
810: char popfile[FILENAMELENGTH];
811:
812: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
813:
1.157 brouard 814: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
815: /* struct timezone tzp; */
816: /* extern int gettimeofday(); */
817: struct tm tml, *gmtime(), *localtime();
818:
819: extern time_t time();
820:
821: struct tm start_time, end_time, curr_time, last_time, forecast_time;
822: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
823: struct tm tm;
824:
1.126 brouard 825: char strcurr[80], strfor[80];
826:
827: char *endptr;
828: long lval;
829: double dval;
830:
831: #define NR_END 1
832: #define FREE_ARG char*
833: #define FTOL 1.0e-10
834:
835: #define NRANSI
836: #define ITMAX 200
837:
838: #define TOL 2.0e-4
839:
840: #define CGOLD 0.3819660
841: #define ZEPS 1.0e-10
842: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
843:
844: #define GOLD 1.618034
845: #define GLIMIT 100.0
846: #define TINY 1.0e-20
847:
848: static double maxarg1,maxarg2;
849: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
850: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
851:
852: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
853: #define rint(a) floor(a+0.5)
1.166 brouard 854: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 855: #define mytinydouble 1.0e-16
1.166 brouard 856: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
857: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
858: /* static double dsqrarg; */
859: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 860: static double sqrarg;
861: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
862: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
863: int agegomp= AGEGOMP;
864:
865: int imx;
866: int stepm=1;
867: /* Stepm, step in month: minimum step interpolation*/
868:
869: int estepm;
870: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
871:
872: int m,nb;
873: long *num;
1.197 brouard 874: int firstpass=0, lastpass=4,*cod, *cens;
1.192 brouard 875: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
876: covariate for which somebody answered excluding
877: undefined. Usually 2: 0 and 1. */
878: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
879: covariate for which somebody answered including
880: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 881: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
882: double **pmmij, ***probs;
883: double *ageexmed,*agecens;
884: double dateintmean=0;
885:
886: double *weight;
887: int **s; /* Status */
1.141 brouard 888: double *agedc;
1.145 brouard 889: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 890: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 891: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.141 brouard 892: double idx;
893: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.197 brouard 894: int *Tage;
1.145 brouard 895: int *Ndum; /** Freq of modality (tricode */
1.200 brouard 896: /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
1.141 brouard 897: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.126 brouard 898: double *lsurv, *lpop, *tpop;
899:
1.143 brouard 900: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
901: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 902:
903: /**************** split *************************/
904: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
905: {
906: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
907: the name of the file (name), its extension only (ext) and its first part of the name (finame)
908: */
909: char *ss; /* pointer */
1.186 brouard 910: int l1=0, l2=0; /* length counters */
1.126 brouard 911:
912: l1 = strlen(path ); /* length of path */
913: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
914: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
915: if ( ss == NULL ) { /* no directory, so determine current directory */
916: strcpy( name, path ); /* we got the fullname name because no directory */
917: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
918: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
919: /* get current working directory */
920: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 921: #ifdef WIN32
922: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
923: #else
924: if (getcwd(dirc, FILENAME_MAX) == NULL) {
925: #endif
1.126 brouard 926: return( GLOCK_ERROR_GETCWD );
927: }
928: /* got dirc from getcwd*/
929: printf(" DIRC = %s \n",dirc);
930: } else { /* strip direcotry from path */
931: ss++; /* after this, the filename */
932: l2 = strlen( ss ); /* length of filename */
933: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
934: strcpy( name, ss ); /* save file name */
935: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 936: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 937: printf(" DIRC2 = %s \n",dirc);
938: }
939: /* We add a separator at the end of dirc if not exists */
940: l1 = strlen( dirc ); /* length of directory */
941: if( dirc[l1-1] != DIRSEPARATOR ){
942: dirc[l1] = DIRSEPARATOR;
943: dirc[l1+1] = 0;
944: printf(" DIRC3 = %s \n",dirc);
945: }
946: ss = strrchr( name, '.' ); /* find last / */
947: if (ss >0){
948: ss++;
949: strcpy(ext,ss); /* save extension */
950: l1= strlen( name);
951: l2= strlen(ss)+1;
952: strncpy( finame, name, l1-l2);
953: finame[l1-l2]= 0;
954: }
955:
956: return( 0 ); /* we're done */
957: }
958:
959:
960: /******************************************/
961:
962: void replace_back_to_slash(char *s, char*t)
963: {
964: int i;
965: int lg=0;
966: i=0;
967: lg=strlen(t);
968: for(i=0; i<= lg; i++) {
969: (s[i] = t[i]);
970: if (t[i]== '\\') s[i]='/';
971: }
972: }
973:
1.132 brouard 974: char *trimbb(char *out, char *in)
1.137 brouard 975: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 976: char *s;
977: s=out;
978: while (*in != '\0'){
1.137 brouard 979: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 980: in++;
981: }
982: *out++ = *in++;
983: }
984: *out='\0';
985: return s;
986: }
987:
1.187 brouard 988: /* char *substrchaine(char *out, char *in, char *chain) */
989: /* { */
990: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
991: /* char *s, *t; */
992: /* t=in;s=out; */
993: /* while ((*in != *chain) && (*in != '\0')){ */
994: /* *out++ = *in++; */
995: /* } */
996:
997: /* /\* *in matches *chain *\/ */
998: /* while ((*in++ == *chain++) && (*in != '\0')){ */
999: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1000: /* } */
1001: /* in--; chain--; */
1002: /* while ( (*in != '\0')){ */
1003: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1004: /* *out++ = *in++; */
1005: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1006: /* } */
1007: /* *out='\0'; */
1008: /* out=s; */
1009: /* return out; */
1010: /* } */
1011: char *substrchaine(char *out, char *in, char *chain)
1012: {
1013: /* Substract chain 'chain' from 'in', return and output 'out' */
1014: /* in="V1+V1*age+age*age+V2", chain="age*age" */
1015:
1016: char *strloc;
1017:
1018: strcpy (out, in);
1019: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
1020: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
1021: if(strloc != NULL){
1022: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
1023: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
1024: /* strcpy (strloc, strloc +strlen(chain));*/
1025: }
1026: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
1027: return out;
1028: }
1029:
1030:
1.145 brouard 1031: char *cutl(char *blocc, char *alocc, char *in, char occ)
1032: {
1.187 brouard 1033: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 1034: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 1035: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 1036: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1037: */
1.160 brouard 1038: char *s, *t;
1.145 brouard 1039: t=in;s=in;
1040: while ((*in != occ) && (*in != '\0')){
1041: *alocc++ = *in++;
1042: }
1043: if( *in == occ){
1044: *(alocc)='\0';
1045: s=++in;
1046: }
1047:
1048: if (s == t) {/* occ not found */
1049: *(alocc-(in-s))='\0';
1050: in=s;
1051: }
1052: while ( *in != '\0'){
1053: *blocc++ = *in++;
1054: }
1055:
1056: *blocc='\0';
1057: return t;
1058: }
1.137 brouard 1059: char *cutv(char *blocc, char *alocc, char *in, char occ)
1060: {
1.187 brouard 1061: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1062: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1063: gives blocc="abcdef2ghi" and alocc="j".
1064: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1065: */
1066: char *s, *t;
1067: t=in;s=in;
1068: while (*in != '\0'){
1069: while( *in == occ){
1070: *blocc++ = *in++;
1071: s=in;
1072: }
1073: *blocc++ = *in++;
1074: }
1075: if (s == t) /* occ not found */
1076: *(blocc-(in-s))='\0';
1077: else
1078: *(blocc-(in-s)-1)='\0';
1079: in=s;
1080: while ( *in != '\0'){
1081: *alocc++ = *in++;
1082: }
1083:
1084: *alocc='\0';
1085: return s;
1086: }
1087:
1.126 brouard 1088: int nbocc(char *s, char occ)
1089: {
1090: int i,j=0;
1091: int lg=20;
1092: i=0;
1093: lg=strlen(s);
1094: for(i=0; i<= lg; i++) {
1095: if (s[i] == occ ) j++;
1096: }
1097: return j;
1098: }
1099:
1.137 brouard 1100: /* void cutv(char *u,char *v, char*t, char occ) */
1101: /* { */
1102: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1103: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1104: /* gives u="abcdef2ghi" and v="j" *\/ */
1105: /* int i,lg,j,p=0; */
1106: /* i=0; */
1107: /* lg=strlen(t); */
1108: /* for(j=0; j<=lg-1; j++) { */
1109: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1110: /* } */
1.126 brouard 1111:
1.137 brouard 1112: /* for(j=0; j<p; j++) { */
1113: /* (u[j] = t[j]); */
1114: /* } */
1115: /* u[p]='\0'; */
1.126 brouard 1116:
1.137 brouard 1117: /* for(j=0; j<= lg; j++) { */
1118: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1119: /* } */
1120: /* } */
1.126 brouard 1121:
1.160 brouard 1122: #ifdef _WIN32
1123: char * strsep(char **pp, const char *delim)
1124: {
1125: char *p, *q;
1126:
1127: if ((p = *pp) == NULL)
1128: return 0;
1129: if ((q = strpbrk (p, delim)) != NULL)
1130: {
1131: *pp = q + 1;
1132: *q = '\0';
1133: }
1134: else
1135: *pp = 0;
1136: return p;
1137: }
1138: #endif
1139:
1.126 brouard 1140: /********************** nrerror ********************/
1141:
1142: void nrerror(char error_text[])
1143: {
1144: fprintf(stderr,"ERREUR ...\n");
1145: fprintf(stderr,"%s\n",error_text);
1146: exit(EXIT_FAILURE);
1147: }
1148: /*********************** vector *******************/
1149: double *vector(int nl, int nh)
1150: {
1151: double *v;
1152: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1153: if (!v) nrerror("allocation failure in vector");
1154: return v-nl+NR_END;
1155: }
1156:
1157: /************************ free vector ******************/
1158: void free_vector(double*v, int nl, int nh)
1159: {
1160: free((FREE_ARG)(v+nl-NR_END));
1161: }
1162:
1163: /************************ivector *******************************/
1164: int *ivector(long nl,long nh)
1165: {
1166: int *v;
1167: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1168: if (!v) nrerror("allocation failure in ivector");
1169: return v-nl+NR_END;
1170: }
1171:
1172: /******************free ivector **************************/
1173: void free_ivector(int *v, long nl, long nh)
1174: {
1175: free((FREE_ARG)(v+nl-NR_END));
1176: }
1177:
1178: /************************lvector *******************************/
1179: long *lvector(long nl,long nh)
1180: {
1181: long *v;
1182: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1183: if (!v) nrerror("allocation failure in ivector");
1184: return v-nl+NR_END;
1185: }
1186:
1187: /******************free lvector **************************/
1188: void free_lvector(long *v, long nl, long nh)
1189: {
1190: free((FREE_ARG)(v+nl-NR_END));
1191: }
1192:
1193: /******************* imatrix *******************************/
1194: int **imatrix(long nrl, long nrh, long ncl, long nch)
1195: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1196: {
1197: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1198: int **m;
1199:
1200: /* allocate pointers to rows */
1201: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1202: if (!m) nrerror("allocation failure 1 in matrix()");
1203: m += NR_END;
1204: m -= nrl;
1205:
1206:
1207: /* allocate rows and set pointers to them */
1208: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1209: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1210: m[nrl] += NR_END;
1211: m[nrl] -= ncl;
1212:
1213: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1214:
1215: /* return pointer to array of pointers to rows */
1216: return m;
1217: }
1218:
1219: /****************** free_imatrix *************************/
1220: void free_imatrix(m,nrl,nrh,ncl,nch)
1221: int **m;
1222: long nch,ncl,nrh,nrl;
1223: /* free an int matrix allocated by imatrix() */
1224: {
1225: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1226: free((FREE_ARG) (m+nrl-NR_END));
1227: }
1228:
1229: /******************* matrix *******************************/
1230: double **matrix(long nrl, long nrh, long ncl, long nch)
1231: {
1232: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1233: double **m;
1234:
1235: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1236: if (!m) nrerror("allocation failure 1 in matrix()");
1237: m += NR_END;
1238: m -= nrl;
1239:
1240: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1241: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1242: m[nrl] += NR_END;
1243: m[nrl] -= ncl;
1244:
1245: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1246: return m;
1.145 brouard 1247: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1248: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1249: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1250: */
1251: }
1252:
1253: /*************************free matrix ************************/
1254: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1255: {
1256: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1257: free((FREE_ARG)(m+nrl-NR_END));
1258: }
1259:
1260: /******************* ma3x *******************************/
1261: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1262: {
1263: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1264: double ***m;
1265:
1266: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1267: if (!m) nrerror("allocation failure 1 in matrix()");
1268: m += NR_END;
1269: m -= nrl;
1270:
1271: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1272: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1273: m[nrl] += NR_END;
1274: m[nrl] -= ncl;
1275:
1276: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1277:
1278: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1279: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1280: m[nrl][ncl] += NR_END;
1281: m[nrl][ncl] -= nll;
1282: for (j=ncl+1; j<=nch; j++)
1283: m[nrl][j]=m[nrl][j-1]+nlay;
1284:
1285: for (i=nrl+1; i<=nrh; i++) {
1286: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1287: for (j=ncl+1; j<=nch; j++)
1288: m[i][j]=m[i][j-1]+nlay;
1289: }
1290: return m;
1291: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1292: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1293: */
1294: }
1295:
1296: /*************************free ma3x ************************/
1297: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1298: {
1299: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1300: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1301: free((FREE_ARG)(m+nrl-NR_END));
1302: }
1303:
1304: /*************** function subdirf ***********/
1305: char *subdirf(char fileres[])
1306: {
1307: /* Caution optionfilefiname is hidden */
1308: strcpy(tmpout,optionfilefiname);
1309: strcat(tmpout,"/"); /* Add to the right */
1310: strcat(tmpout,fileres);
1311: return tmpout;
1312: }
1313:
1314: /*************** function subdirf2 ***********/
1315: char *subdirf2(char fileres[], char *preop)
1316: {
1317:
1318: /* Caution optionfilefiname is hidden */
1319: strcpy(tmpout,optionfilefiname);
1320: strcat(tmpout,"/");
1321: strcat(tmpout,preop);
1322: strcat(tmpout,fileres);
1323: return tmpout;
1324: }
1325:
1326: /*************** function subdirf3 ***********/
1327: char *subdirf3(char fileres[], char *preop, char *preop2)
1328: {
1329:
1330: /* Caution optionfilefiname is hidden */
1331: strcpy(tmpout,optionfilefiname);
1332: strcat(tmpout,"/");
1333: strcat(tmpout,preop);
1334: strcat(tmpout,preop2);
1335: strcat(tmpout,fileres);
1336: return tmpout;
1337: }
1338:
1.162 brouard 1339: char *asc_diff_time(long time_sec, char ascdiff[])
1340: {
1341: long sec_left, days, hours, minutes;
1342: days = (time_sec) / (60*60*24);
1343: sec_left = (time_sec) % (60*60*24);
1344: hours = (sec_left) / (60*60) ;
1345: sec_left = (sec_left) %(60*60);
1346: minutes = (sec_left) /60;
1347: sec_left = (sec_left) % (60);
1348: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1349: return ascdiff;
1350: }
1351:
1.126 brouard 1352: /***************** f1dim *************************/
1353: extern int ncom;
1354: extern double *pcom,*xicom;
1355: extern double (*nrfunc)(double []);
1356:
1357: double f1dim(double x)
1358: {
1359: int j;
1360: double f;
1361: double *xt;
1362:
1363: xt=vector(1,ncom);
1364: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1365: f=(*nrfunc)(xt);
1366: free_vector(xt,1,ncom);
1367: return f;
1368: }
1369:
1370: /*****************brent *************************/
1371: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1372: {
1373: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1374: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1375: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1376: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1377: * returned function value.
1378: */
1.126 brouard 1379: int iter;
1380: double a,b,d,etemp;
1.159 brouard 1381: double fu=0,fv,fw,fx;
1.164 brouard 1382: double ftemp=0.;
1.126 brouard 1383: double p,q,r,tol1,tol2,u,v,w,x,xm;
1384: double e=0.0;
1385:
1386: a=(ax < cx ? ax : cx);
1387: b=(ax > cx ? ax : cx);
1388: x=w=v=bx;
1389: fw=fv=fx=(*f)(x);
1390: for (iter=1;iter<=ITMAX;iter++) {
1391: xm=0.5*(a+b);
1392: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1393: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1394: printf(".");fflush(stdout);
1395: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1396: #ifdef DEBUGBRENT
1.126 brouard 1397: 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);
1398: 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);
1399: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1400: #endif
1401: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1402: *xmin=x;
1403: return fx;
1404: }
1405: ftemp=fu;
1406: if (fabs(e) > tol1) {
1407: r=(x-w)*(fx-fv);
1408: q=(x-v)*(fx-fw);
1409: p=(x-v)*q-(x-w)*r;
1410: q=2.0*(q-r);
1411: if (q > 0.0) p = -p;
1412: q=fabs(q);
1413: etemp=e;
1414: e=d;
1415: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1416: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1417: else {
1418: d=p/q;
1419: u=x+d;
1420: if (u-a < tol2 || b-u < tol2)
1421: d=SIGN(tol1,xm-x);
1422: }
1423: } else {
1424: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1425: }
1426: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1427: fu=(*f)(u);
1428: if (fu <= fx) {
1429: if (u >= x) a=x; else b=x;
1430: SHFT(v,w,x,u)
1.183 brouard 1431: SHFT(fv,fw,fx,fu)
1432: } else {
1433: if (u < x) a=u; else b=u;
1434: if (fu <= fw || w == x) {
1435: v=w;
1436: w=u;
1437: fv=fw;
1438: fw=fu;
1439: } else if (fu <= fv || v == x || v == w) {
1440: v=u;
1441: fv=fu;
1442: }
1443: }
1.126 brouard 1444: }
1445: nrerror("Too many iterations in brent");
1446: *xmin=x;
1447: return fx;
1448: }
1449:
1450: /****************** mnbrak ***********************/
1451:
1452: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1453: double (*func)(double))
1.183 brouard 1454: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1455: the downhill direction (defined by the function as evaluated at the initial points) and returns
1456: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1457: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1458: */
1.126 brouard 1459: double ulim,u,r,q, dum;
1460: double fu;
1.187 brouard 1461:
1462: double scale=10.;
1463: int iterscale=0;
1464:
1465: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1466: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1467:
1468:
1469: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1470: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1471: /* *bx = *ax - (*ax - *bx)/scale; */
1472: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1473: /* } */
1474:
1.126 brouard 1475: if (*fb > *fa) {
1476: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1477: SHFT(dum,*fb,*fa,dum)
1478: }
1.126 brouard 1479: *cx=(*bx)+GOLD*(*bx-*ax);
1480: *fc=(*func)(*cx);
1.183 brouard 1481: #ifdef DEBUG
1482: printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1483: fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1484: #endif
1485: while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
1.126 brouard 1486: r=(*bx-*ax)*(*fb-*fc);
1487: q=(*bx-*cx)*(*fb-*fa);
1488: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 1489: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1490: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1491: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 1492: fu=(*func)(u);
1.163 brouard 1493: #ifdef DEBUG
1494: /* f(x)=A(x-u)**2+f(u) */
1495: double A, fparabu;
1496: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1497: fparabu= *fa - A*(*ax-u)*(*ax-u);
1498: 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);
1499: 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 1500: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1501: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1502: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1503: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 1504: #endif
1.184 brouard 1505: #ifdef MNBRAKORIGINAL
1.183 brouard 1506: #else
1.191 brouard 1507: /* if (fu > *fc) { */
1508: /* #ifdef DEBUG */
1509: /* printf("mnbrak4 fu > fc \n"); */
1510: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
1511: /* #endif */
1512: /* /\* 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 *\\/ *\/ */
1513: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
1514: /* dum=u; /\* Shifting c and u *\/ */
1515: /* u = *cx; */
1516: /* *cx = dum; */
1517: /* dum = fu; */
1518: /* fu = *fc; */
1519: /* *fc =dum; */
1520: /* } else { /\* end *\/ */
1521: /* #ifdef DEBUG */
1522: /* printf("mnbrak3 fu < fc \n"); */
1523: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
1524: /* #endif */
1525: /* dum=u; /\* Shifting c and u *\/ */
1526: /* u = *cx; */
1527: /* *cx = dum; */
1528: /* dum = fu; */
1529: /* fu = *fc; */
1530: /* *fc =dum; */
1531: /* } */
1.183 brouard 1532: #ifdef DEBUG
1.191 brouard 1533: printf("mnbrak34 fu < or >= fc \n");
1534: fprintf(ficlog, "mnbrak34 fu < fc\n");
1.183 brouard 1535: #endif
1.191 brouard 1536: dum=u; /* Shifting c and u */
1537: u = *cx;
1538: *cx = dum;
1539: dum = fu;
1540: fu = *fc;
1541: *fc =dum;
1.183 brouard 1542: #endif
1.162 brouard 1543: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 1544: #ifdef DEBUG
1545: printf("mnbrak2 u after c but before ulim\n");
1546: fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
1547: #endif
1.126 brouard 1548: fu=(*func)(u);
1549: if (fu < *fc) {
1.183 brouard 1550: #ifdef DEBUG
1551: printf("mnbrak2 u after c but before ulim AND fu < fc\n");
1552: fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
1553: #endif
1.126 brouard 1554: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1.183 brouard 1555: SHFT(*fb,*fc,fu,(*func)(u))
1556: }
1.162 brouard 1557: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 1558: #ifdef DEBUG
1559: printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1560: fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1561: #endif
1.126 brouard 1562: u=ulim;
1563: fu=(*func)(u);
1.183 brouard 1564: } else { /* u could be left to b (if r > q parabola has a maximum) */
1565: #ifdef DEBUG
1566: printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1567: fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1568: #endif
1.126 brouard 1569: u=(*cx)+GOLD*(*cx-*bx);
1570: fu=(*func)(u);
1.183 brouard 1571: } /* end tests */
1.126 brouard 1572: SHFT(*ax,*bx,*cx,u)
1.183 brouard 1573: SHFT(*fa,*fb,*fc,fu)
1574: #ifdef DEBUG
1575: 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);
1576: 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);
1577: #endif
1578: } /* 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 1579: }
1580:
1581: /*************** linmin ************************/
1.162 brouard 1582: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1583: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1584: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1585: the value of func at the returned location p . This is actually all accomplished by calling the
1586: routines mnbrak and brent .*/
1.126 brouard 1587: int ncom;
1588: double *pcom,*xicom;
1589: double (*nrfunc)(double []);
1590:
1591: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1592: {
1593: double brent(double ax, double bx, double cx,
1594: double (*f)(double), double tol, double *xmin);
1595: double f1dim(double x);
1596: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1597: double *fc, double (*func)(double));
1598: int j;
1599: double xx,xmin,bx,ax;
1600: double fx,fb,fa;
1.187 brouard 1601:
1602: double scale=10., axs, xxs, xxss; /* Scale added for infinity */
1.126 brouard 1603:
1604: ncom=n;
1605: pcom=vector(1,n);
1606: xicom=vector(1,n);
1607: nrfunc=func;
1608: for (j=1;j<=n;j++) {
1609: pcom[j]=p[j];
1.202 ! brouard 1610: xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
1.126 brouard 1611: }
1.187 brouard 1612:
1.192 brouard 1613: /* axs=0.0; */
1614: /* xxss=1; /\* 1 and using scale *\/ */
1.187 brouard 1615: xxs=1;
1.192 brouard 1616: /* do{ */
1.187 brouard 1617: ax=0.;
1618: xx= xxs;
1619: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
1620: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
1621: /* 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)) */
1622: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
1623: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
1624: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
1625: /* 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]]*/
1.192 brouard 1626: /* if (fx != fx){ */
1627: /* xxs=xxs/scale; /\* Trying a smaller xx, closer to initial ax=0 *\/ */
1628: /* 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); */
1629: /* } */
1630: /* }while(fx != fx); */
1.187 brouard 1631:
1.191 brouard 1632: #ifdef DEBUGLINMIN
1633: 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 1634: 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 1635: #endif
1.187 brouard 1636: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
1637: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
1638: /* fmin = f(p[j] + xmin * xi[j]) */
1639: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
1640: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 1641: #ifdef DEBUG
1642: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1643: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1644: #endif
1.191 brouard 1645: #ifdef DEBUGLINMIN
1646: printf("linmin end ");
1.202 ! brouard 1647: fprintf(ficlog,"linmin end ");
1.191 brouard 1648: #endif
1.126 brouard 1649: for (j=1;j<=n;j++) {
1.188 brouard 1650: /* printf(" before xi[%d]=%12.8f", j,xi[j]); */
1.187 brouard 1651: xi[j] *= xmin; /* xi rescaled by xmin: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
1.189 brouard 1652: /* if(xxs <1.0) */
1653: /* 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 ); */
1.187 brouard 1654: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 1655: }
1.189 brouard 1656: /* printf("\n"); */
1.191 brouard 1657: #ifdef DEBUGLINMIN
1658: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.202 ! brouard 1659: 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 1660: for (j=1;j<=n;j++) {
1.202 ! brouard 1661: printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
! 1662: fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
! 1663: if(j % ncovmodel == 0){
1.191 brouard 1664: printf("\n");
1.202 ! brouard 1665: fprintf(ficlog,"\n");
! 1666: }
1.191 brouard 1667: }
1668: #endif
1.126 brouard 1669: free_vector(xicom,1,n);
1670: free_vector(pcom,1,n);
1671: }
1672:
1673:
1674: /*************** powell ************************/
1.162 brouard 1675: /*
1676: Minimization of a function func of n variables. Input consists of an initial starting point
1677: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1678: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1679: such that failure to decrease by more than this amount on one iteration signals doneness. On
1680: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1681: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1682: */
1.126 brouard 1683: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1684: double (*func)(double []))
1685: {
1686: void linmin(double p[], double xi[], int n, double *fret,
1687: double (*func)(double []));
1688: int i,ibig,j;
1689: double del,t,*pt,*ptt,*xit;
1.181 brouard 1690: double directest;
1.126 brouard 1691: double fp,fptt;
1692: double *xits;
1693: int niterf, itmp;
1694:
1695: pt=vector(1,n);
1696: ptt=vector(1,n);
1697: xit=vector(1,n);
1698: xits=vector(1,n);
1699: *fret=(*func)(p);
1700: for (j=1;j<=n;j++) pt[j]=p[j];
1.202 ! brouard 1701: rcurr_time = time(NULL);
1.126 brouard 1702: for (*iter=1;;++(*iter)) {
1.187 brouard 1703: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 1704: ibig=0;
1705: del=0.0;
1.157 brouard 1706: rlast_time=rcurr_time;
1707: /* (void) gettimeofday(&curr_time,&tzp); */
1708: rcurr_time = time(NULL);
1709: curr_time = *localtime(&rcurr_time);
1710: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1711: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1712: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 1713: for (i=1;i<=n;i++) {
1.126 brouard 1714: printf(" %d %.12f",i, p[i]);
1715: fprintf(ficlog," %d %.12lf",i, p[i]);
1716: fprintf(ficrespow," %.12lf", p[i]);
1717: }
1718: printf("\n");
1719: fprintf(ficlog,"\n");
1720: fprintf(ficrespow,"\n");fflush(ficrespow);
1721: if(*iter <=3){
1.157 brouard 1722: tml = *localtime(&rcurr_time);
1723: strcpy(strcurr,asctime(&tml));
1724: rforecast_time=rcurr_time;
1.126 brouard 1725: itmp = strlen(strcurr);
1726: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1727: strcurr[itmp-1]='\0';
1.162 brouard 1728: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 1729: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 1730: for(niterf=10;niterf<=30;niterf+=10){
1.157 brouard 1731: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1732: forecast_time = *localtime(&rforecast_time);
1733: strcpy(strfor,asctime(&forecast_time));
1.126 brouard 1734: itmp = strlen(strfor);
1735: if(strfor[itmp-1]=='\n')
1736: strfor[itmp-1]='\0';
1.157 brouard 1737: 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);
1738: 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 1739: }
1740: }
1.187 brouard 1741: for (i=1;i<=n;i++) { /* For each direction i */
1742: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 1743: fptt=(*fret);
1744: #ifdef DEBUG
1.164 brouard 1745: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1746: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 1747: #endif
1.187 brouard 1748: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 1749: fprintf(ficlog,"%d",i);fflush(ficlog);
1.188 brouard 1750: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1751: /* Outputs are fret(new point p) p is updated and xit rescaled */
1752: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1753: /* because that direction will be replaced unless the gain del is small */
1754: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
1755: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
1756: /* with the new direction. */
1.126 brouard 1757: del=fabs(fptt-(*fret));
1758: ibig=i;
1759: }
1760: #ifdef DEBUG
1761: printf("%d %.12e",i,(*fret));
1762: fprintf(ficlog,"%d %.12e",i,(*fret));
1763: for (j=1;j<=n;j++) {
1764: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1765: printf(" x(%d)=%.12e",j,xit[j]);
1766: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1767: }
1768: for(j=1;j<=n;j++) {
1.162 brouard 1769: printf(" p(%d)=%.12e",j,p[j]);
1770: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 1771: }
1772: printf("\n");
1773: fprintf(ficlog,"\n");
1774: #endif
1.187 brouard 1775: } /* end loop on each direction i */
1776: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 1777: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 1778: /* New value of last point Pn is not computed, P(n-1) */
1.182 brouard 1779: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1.188 brouard 1780: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
1781: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
1782: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
1783: /* decreased of more than 3.84 */
1784: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
1785: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
1786: /* By adding 10 parameters more the gain should be 18.31 */
1787:
1788: /* Starting the program with initial values given by a former maximization will simply change */
1789: /* the scales of the directions and the directions, because the are reset to canonical directions */
1790: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
1791: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 1792: #ifdef DEBUG
1793: int k[2],l;
1794: k[0]=1;
1795: k[1]=-1;
1796: printf("Max: %.12e",(*func)(p));
1797: fprintf(ficlog,"Max: %.12e",(*func)(p));
1798: for (j=1;j<=n;j++) {
1799: printf(" %.12e",p[j]);
1800: fprintf(ficlog," %.12e",p[j]);
1801: }
1802: printf("\n");
1803: fprintf(ficlog,"\n");
1804: for(l=0;l<=1;l++) {
1805: for (j=1;j<=n;j++) {
1806: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1807: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1808: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1809: }
1810: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1811: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1812: }
1813: #endif
1814:
1815:
1816: free_vector(xit,1,n);
1817: free_vector(xits,1,n);
1818: free_vector(ptt,1,n);
1819: free_vector(pt,1,n);
1820: return;
1.192 brouard 1821: } /* enough precision */
1.126 brouard 1822: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1.181 brouard 1823: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 1824: ptt[j]=2.0*p[j]-pt[j];
1825: xit[j]=p[j]-pt[j];
1826: pt[j]=p[j];
1827: }
1.181 brouard 1828: fptt=(*func)(ptt); /* f_3 */
1.192 brouard 1829: #ifdef POWELLF1F3
1830: #else
1.161 brouard 1831: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 1832: #endif
1.162 brouard 1833: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 1834: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 1835: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1836: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1837: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.181 brouard 1838: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
1.161 brouard 1839: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.183 brouard 1840: #ifdef NRCORIGINAL
1841: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
1842: #else
1843: 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 1844: t= t- del*SQR(fp-fptt);
1.183 brouard 1845: #endif
1.202 ! brouard 1846: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
1.161 brouard 1847: #ifdef DEBUG
1.181 brouard 1848: 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);
1849: 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 1850: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1851: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1852: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1853: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1854: 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);
1855: 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);
1856: #endif
1.183 brouard 1857: #ifdef POWELLORIGINAL
1858: if (t < 0.0) { /* Then we use it for new direction */
1859: #else
1.182 brouard 1860: if (directest*t < 0.0) { /* Contradiction between both tests */
1.202 ! brouard 1861: 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 1862: 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 1863: 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 1864: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1865: }
1.181 brouard 1866: if (directest < 0.0) { /* Then we use it for new direction */
1867: #endif
1.191 brouard 1868: #ifdef DEBUGLINMIN
1869: printf("Before linmin in direction P%d-P0\n",n);
1870: for (j=1;j<=n;j++) {
1.202 ! brouard 1871: printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
! 1872: fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
! 1873: if(j % ncovmodel == 0){
1.191 brouard 1874: printf("\n");
1.202 ! brouard 1875: fprintf(ficlog,"\n");
! 1876: }
1.191 brouard 1877: }
1878: #endif
1.187 brouard 1879: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.191 brouard 1880: #ifdef DEBUGLINMIN
1881: for (j=1;j<=n;j++) {
1882: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1.202 ! brouard 1883: fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
! 1884: if(j % ncovmodel == 0){
1.191 brouard 1885: printf("\n");
1.202 ! brouard 1886: fprintf(ficlog,"\n");
! 1887: }
1.191 brouard 1888: }
1889: #endif
1.126 brouard 1890: for (j=1;j<=n;j++) {
1.181 brouard 1891: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
1892: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
1.126 brouard 1893: }
1.181 brouard 1894: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1895: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1.161 brouard 1896:
1.126 brouard 1897: #ifdef DEBUG
1.164 brouard 1898: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1899: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1.126 brouard 1900: for(j=1;j<=n;j++){
1901: printf(" %.12e",xit[j]);
1902: fprintf(ficlog," %.12e",xit[j]);
1903: }
1904: printf("\n");
1905: fprintf(ficlog,"\n");
1906: #endif
1.192 brouard 1907: } /* end of t or directest negative */
1908: #ifdef POWELLF1F3
1909: #else
1.162 brouard 1910: } /* end if (fptt < fp) */
1.192 brouard 1911: #endif
1912: } /* loop iteration */
1.126 brouard 1913: }
1914:
1915: /**** Prevalence limit (stable or period prevalence) ****************/
1916:
1917: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1918: {
1919: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1920: matrix by transitions matrix until convergence is reached */
1.169 brouard 1921:
1.126 brouard 1922: int i, ii,j,k;
1923: double min, max, maxmin, maxmax,sumnew=0.;
1.145 brouard 1924: /* double **matprod2(); */ /* test */
1.131 brouard 1925: double **out, cov[NCOVMAX+1], **pmij();
1.126 brouard 1926: double **newm;
1.202 ! brouard 1927: double agefin, delaymax=100 ; /* Max number of years to converge */
! 1928: long int ncvyear=0, ncvloop=0;
1.169 brouard 1929:
1.126 brouard 1930: for (ii=1;ii<=nlstate+ndeath;ii++)
1931: for (j=1;j<=nlstate+ndeath;j++){
1932: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1933: }
1.169 brouard 1934:
1935: cov[1]=1.;
1936:
1937: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.202 ! brouard 1938: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.126 brouard 1939: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1.202 ! brouard 1940: ncvloop++;
1.126 brouard 1941: newm=savm;
1942: /* Covariates have to be included here again */
1.138 brouard 1943: cov[2]=agefin;
1.187 brouard 1944: if(nagesqr==1)
1945: cov[3]= agefin*agefin;;
1.138 brouard 1946: for (k=1; k<=cptcovn;k++) {
1.200 brouard 1947: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1948: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
1.198 brouard 1949: /* 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 1950: }
1.186 brouard 1951: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 1952: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
1953: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
1.186 brouard 1954: for (k=1; k<=cptcovprod;k++) /* Useless */
1.200 brouard 1955: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
1956: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
1.138 brouard 1957:
1958: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1959: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1960: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 1961: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1962: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.142 brouard 1963: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 1964:
1.126 brouard 1965: savm=oldm;
1966: oldm=newm;
1967: maxmax=0.;
1968: for(j=1;j<=nlstate;j++){
1969: min=1.;
1970: max=0.;
1971: for(i=1; i<=nlstate; i++) {
1972: sumnew=0;
1973: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1974: prlim[i][j]= newm[i][j]/(1-sumnew);
1975: max=FMAX(max,prlim[i][j]);
1976: min=FMIN(min,prlim[i][j]);
1.202 ! brouard 1977: /* printf(" age= %d prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d max=%f min=%f\n", (int)age, i, j, i, j, prlim[i][j],(int)agefin, max, min); */
1.126 brouard 1978: }
1979: maxmin=max-min;
1980: maxmax=FMAX(maxmax,maxmin);
1.169 brouard 1981: } /* j loop */
1.126 brouard 1982: if(maxmax < ftolpl){
1.202 ! brouard 1983: /* printf("maxmax=%lf maxmin=%lf ncvloop=%ld, ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age-(int)agefin); */
1.126 brouard 1984: return prlim;
1985: }
1.169 brouard 1986: } /* age loop */
1.202 ! brouard 1987: printf("Warning: the stable prevalence did not converge with the required precision ftolpl=6*10^5*ftol=%g. \n\
! 1988: Earliest age to start was %d-%d=%d, ncvloop=%ld, ncvyear=%d\n\
! 1989: Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin);
1.169 brouard 1990: return prlim; /* should not reach here */
1.126 brouard 1991: }
1992:
1993: /*************** transition probabilities ***************/
1994:
1995: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1996: {
1.138 brouard 1997: /* According to parameters values stored in x and the covariate's values stored in cov,
1998: computes the probability to be observed in state j being in state i by appying the
1999: model to the ncovmodel covariates (including constant and age).
2000: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2001: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2002: ncth covariate in the global vector x is given by the formula:
2003: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2004: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2005: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2006: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
2007: Outputs ps[i][j] the probability to be observed in j being in j according to
2008: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
2009: */
2010: double s1, lnpijopii;
1.126 brouard 2011: /*double t34;*/
1.164 brouard 2012: int i,j, nc, ii, jj;
1.126 brouard 2013:
2014: for(i=1; i<= nlstate; i++){
2015: for(j=1; j<i;j++){
1.138 brouard 2016: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2017: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2018: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2019: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 2020: }
1.138 brouard 2021: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2022: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 2023: }
2024: for(j=i+1; j<=nlstate+ndeath;j++){
1.138 brouard 2025: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2026: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2027: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2028: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1.126 brouard 2029: }
1.138 brouard 2030: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1.126 brouard 2031: }
2032: }
2033:
2034: for(i=1; i<= nlstate; i++){
2035: s1=0;
1.131 brouard 2036: for(j=1; j<i; j++){
1.138 brouard 2037: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 2038: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2039: }
2040: for(j=i+1; j<=nlstate+ndeath; j++){
1.138 brouard 2041: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 2042: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2043: }
1.138 brouard 2044: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1.126 brouard 2045: ps[i][i]=1./(s1+1.);
1.138 brouard 2046: /* Computing other pijs */
1.126 brouard 2047: for(j=1; j<i; j++)
2048: ps[i][j]= exp(ps[i][j])*ps[i][i];
2049: for(j=i+1; j<=nlstate+ndeath; j++)
2050: ps[i][j]= exp(ps[i][j])*ps[i][i];
2051: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2052: } /* end i */
2053:
2054: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2055: for(jj=1; jj<= nlstate+ndeath; jj++){
2056: ps[ii][jj]=0;
2057: ps[ii][ii]=1;
2058: }
2059: }
2060:
1.145 brouard 2061:
2062: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2063: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2064: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2065: /* } */
2066: /* printf("\n "); */
2067: /* } */
2068: /* printf("\n ");printf("%lf ",cov[2]);*/
2069: /*
1.126 brouard 2070: for(i=1; i<= npar; i++) printf("%f ",x[i]);
2071: goto end;*/
2072: return ps;
2073: }
2074:
2075: /**************** Product of 2 matrices ******************/
2076:
1.145 brouard 2077: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 2078: {
2079: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
2080: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
2081: /* in, b, out are matrice of pointers which should have been initialized
2082: before: only the contents of out is modified. The function returns
2083: a pointer to pointers identical to out */
1.145 brouard 2084: int i, j, k;
1.126 brouard 2085: for(i=nrl; i<= nrh; i++)
1.145 brouard 2086: for(k=ncolol; k<=ncoloh; k++){
2087: out[i][k]=0.;
2088: for(j=ncl; j<=nch; j++)
2089: out[i][k] +=in[i][j]*b[j][k];
2090: }
1.126 brouard 2091: return out;
2092: }
2093:
2094:
2095: /************* Higher Matrix Product ***************/
2096:
2097: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
2098: {
2099: /* Computes the transition matrix starting at age 'age' over
2100: 'nhstepm*hstepm*stepm' months (i.e. until
2101: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2102: nhstepm*hstepm matrices.
2103: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2104: (typically every 2 years instead of every month which is too big
2105: for the memory).
2106: Model is determined by parameters x and covariates have to be
2107: included manually here.
2108:
2109: */
2110:
2111: int i, j, d, h, k;
1.131 brouard 2112: double **out, cov[NCOVMAX+1];
1.126 brouard 2113: double **newm;
1.187 brouard 2114: double agexact;
1.126 brouard 2115:
2116: /* Hstepm could be zero and should return the unit matrix */
2117: for (i=1;i<=nlstate+ndeath;i++)
2118: for (j=1;j<=nlstate+ndeath;j++){
2119: oldm[i][j]=(i==j ? 1.0 : 0.0);
2120: po[i][j][0]=(i==j ? 1.0 : 0.0);
2121: }
2122: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2123: for(h=1; h <=nhstepm; h++){
2124: for(d=1; d <=hstepm; d++){
2125: newm=savm;
2126: /* Covariates have to be included here again */
2127: cov[1]=1.;
1.187 brouard 2128: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
2129: cov[2]=agexact;
2130: if(nagesqr==1)
2131: cov[3]= agexact*agexact;
1.131 brouard 2132: for (k=1; k<=cptcovn;k++)
1.200 brouard 2133: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2134: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.186 brouard 2135: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
2136: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 2137: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2138: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
1.145 brouard 2139: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.200 brouard 2140: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
2141: /* 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 2142:
2143:
2144: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2145: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
2146: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
2147: pmij(pmmij,cov,ncovmodel,x,nlstate));
2148: savm=oldm;
2149: oldm=newm;
2150: }
2151: for(i=1; i<=nlstate+ndeath; i++)
2152: for(j=1;j<=nlstate+ndeath;j++) {
2153: po[i][j][h]=newm[i][j];
1.128 brouard 2154: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 2155: }
1.128 brouard 2156: /*printf("h=%d ",h);*/
1.126 brouard 2157: } /* end h */
1.128 brouard 2158: /* printf("\n H=%d \n",h); */
1.126 brouard 2159: return po;
2160: }
2161:
1.162 brouard 2162: #ifdef NLOPT
2163: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
2164: double fret;
2165: double *xt;
2166: int j;
2167: myfunc_data *d2 = (myfunc_data *) pd;
2168: /* xt = (p1-1); */
2169: xt=vector(1,n);
2170: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
2171:
2172: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
2173: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
2174: printf("Function = %.12lf ",fret);
2175: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
2176: printf("\n");
2177: free_vector(xt,1,n);
2178: return fret;
2179: }
2180: #endif
1.126 brouard 2181:
2182: /*************** log-likelihood *************/
2183: double func( double *x)
2184: {
2185: int i, ii, j, k, mi, d, kk;
1.131 brouard 2186: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2187: double **out;
2188: double sw; /* Sum of weights */
2189: double lli; /* Individual log likelihood */
2190: int s1, s2;
2191: double bbh, survp;
2192: long ipmx;
1.187 brouard 2193: double agexact;
1.126 brouard 2194: /*extern weight */
2195: /* We are differentiating ll according to initial status */
2196: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2197: /*for(i=1;i<imx;i++)
2198: printf(" %d\n",s[4][i]);
2199: */
1.162 brouard 2200:
2201: ++countcallfunc;
2202:
1.126 brouard 2203: cov[1]=1.;
2204:
2205: for(k=1; k<=nlstate; k++) ll[k]=0.;
2206:
2207: if(mle==1){
2208: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.138 brouard 2209: /* Computes the values of the ncovmodel covariates of the model
2210: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
2211: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
2212: to be observed in j being in i according to the model.
2213: */
1.145 brouard 2214: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1.187 brouard 2215: cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.145 brouard 2216: }
1.137 brouard 2217: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1.138 brouard 2218: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1.137 brouard 2219: has been calculated etc */
1.126 brouard 2220: for(mi=1; mi<= wav[i]-1; mi++){
2221: for (ii=1;ii<=nlstate+ndeath;ii++)
2222: for (j=1;j<=nlstate+ndeath;j++){
2223: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2224: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2225: }
2226: for(d=0; d<dh[mi][i]; d++){
2227: newm=savm;
1.187 brouard 2228: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2229: cov[2]=agexact;
2230: if(nagesqr==1)
2231: cov[3]= agexact*agexact;
1.126 brouard 2232: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2233: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
1.126 brouard 2234: }
2235: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2236: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2237: savm=oldm;
2238: oldm=newm;
2239: } /* end mult */
2240:
2241: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
2242: /* But now since version 0.9 we anticipate for bias at large stepm.
2243: * If stepm is larger than one month (smallest stepm) and if the exact delay
2244: * (in months) between two waves is not a multiple of stepm, we rounded to
2245: * the nearest (and in case of equal distance, to the lowest) interval but now
2246: * we keep into memory the bias bh[mi][i] and also the previous matrix product
2247: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
2248: * probability in order to take into account the bias as a fraction of the way
2249: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
2250: * -stepm/2 to stepm/2 .
2251: * For stepm=1 the results are the same as for previous versions of Imach.
2252: * For stepm > 1 the results are less biased than in previous versions.
2253: */
2254: s1=s[mw[mi][i]][i];
2255: s2=s[mw[mi+1][i]][i];
2256: bbh=(double)bh[mi][i]/(double)stepm;
2257: /* bias bh is positive if real duration
2258: * is higher than the multiple of stepm and negative otherwise.
2259: */
2260: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
2261: if( s2 > nlstate){
2262: /* i.e. if s2 is a death state and if the date of death is known
2263: then the contribution to the likelihood is the probability to
2264: die between last step unit time and current step unit time,
2265: which is also equal to probability to die before dh
2266: minus probability to die before dh-stepm .
2267: In version up to 0.92 likelihood was computed
2268: as if date of death was unknown. Death was treated as any other
2269: health state: the date of the interview describes the actual state
2270: and not the date of a change in health state. The former idea was
2271: to consider that at each interview the state was recorded
2272: (healthy, disable or death) and IMaCh was corrected; but when we
2273: introduced the exact date of death then we should have modified
2274: the contribution of an exact death to the likelihood. This new
2275: contribution is smaller and very dependent of the step unit
2276: stepm. It is no more the probability to die between last interview
2277: and month of death but the probability to survive from last
2278: interview up to one month before death multiplied by the
2279: probability to die within a month. Thanks to Chris
2280: Jackson for correcting this bug. Former versions increased
2281: mortality artificially. The bad side is that we add another loop
2282: which slows down the processing. The difference can be up to 10%
2283: lower mortality.
2284: */
1.183 brouard 2285: /* If, at the beginning of the maximization mostly, the
2286: cumulative probability or probability to be dead is
2287: constant (ie = 1) over time d, the difference is equal to
2288: 0. out[s1][3] = savm[s1][3]: probability, being at state
2289: s1 at precedent wave, to be dead a month before current
2290: wave is equal to probability, being at state s1 at
2291: precedent wave, to be dead at mont of the current
2292: wave. Then the observed probability (that this person died)
2293: is null according to current estimated parameter. In fact,
2294: it should be very low but not zero otherwise the log go to
2295: infinity.
2296: */
2297: /* #ifdef INFINITYORIGINAL */
2298: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2299: /* #else */
2300: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
2301: /* lli=log(mytinydouble); */
2302: /* else */
2303: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2304: /* #endif */
2305: lli=log(out[s1][s2] - savm[s1][s2]);
1.126 brouard 2306:
2307: } else if (s2==-2) {
2308: for (j=1,survp=0. ; j<=nlstate; j++)
2309: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2310: /*survp += out[s1][j]; */
2311: lli= log(survp);
2312: }
2313:
2314: else if (s2==-4) {
2315: for (j=3,survp=0. ; j<=nlstate; j++)
2316: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2317: lli= log(survp);
2318: }
2319:
2320: else if (s2==-5) {
2321: for (j=1,survp=0. ; j<=2; j++)
2322: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2323: lli= log(survp);
2324: }
2325:
2326: else{
2327: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2328: /* 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 */
2329: }
2330: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
2331: /*if(lli ==000.0)*/
2332: /*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); */
2333: ipmx +=1;
2334: sw += weight[i];
2335: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.183 brouard 2336: /* if (lli < log(mytinydouble)){ */
2337: /* 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); */
2338: /* 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]); */
2339: /* } */
1.126 brouard 2340: } /* end of wave */
2341: } /* end of individual */
2342: } else if(mle==2){
2343: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2344: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2345: for(mi=1; mi<= wav[i]-1; mi++){
2346: for (ii=1;ii<=nlstate+ndeath;ii++)
2347: for (j=1;j<=nlstate+ndeath;j++){
2348: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2349: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2350: }
2351: for(d=0; d<=dh[mi][i]; d++){
2352: newm=savm;
1.187 brouard 2353: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2354: cov[2]=agexact;
2355: if(nagesqr==1)
2356: cov[3]= agexact*agexact;
1.126 brouard 2357: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2358: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2359: }
2360: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2361: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2362: savm=oldm;
2363: oldm=newm;
2364: } /* end mult */
2365:
2366: s1=s[mw[mi][i]][i];
2367: s2=s[mw[mi+1][i]][i];
2368: bbh=(double)bh[mi][i]/(double)stepm;
2369: 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 */
2370: ipmx +=1;
2371: sw += weight[i];
2372: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2373: } /* end of wave */
2374: } /* end of individual */
2375: } else if(mle==3){ /* exponential inter-extrapolation */
2376: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2377: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2378: for(mi=1; mi<= wav[i]-1; mi++){
2379: for (ii=1;ii<=nlstate+ndeath;ii++)
2380: for (j=1;j<=nlstate+ndeath;j++){
2381: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2382: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2383: }
2384: for(d=0; d<dh[mi][i]; d++){
2385: newm=savm;
1.187 brouard 2386: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2387: cov[2]=agexact;
2388: if(nagesqr==1)
2389: cov[3]= agexact*agexact;
1.126 brouard 2390: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2391: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2392: }
2393: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2394: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2395: savm=oldm;
2396: oldm=newm;
2397: } /* end mult */
2398:
2399: s1=s[mw[mi][i]][i];
2400: s2=s[mw[mi+1][i]][i];
2401: bbh=(double)bh[mi][i]/(double)stepm;
2402: 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 */
2403: ipmx +=1;
2404: sw += weight[i];
2405: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2406: } /* end of wave */
2407: } /* end of individual */
2408: }else if (mle==4){ /* ml=4 no inter-extrapolation */
2409: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2410: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2411: for(mi=1; mi<= wav[i]-1; mi++){
2412: for (ii=1;ii<=nlstate+ndeath;ii++)
2413: for (j=1;j<=nlstate+ndeath;j++){
2414: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2415: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2416: }
2417: for(d=0; d<dh[mi][i]; d++){
2418: newm=savm;
1.187 brouard 2419: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2420: cov[2]=agexact;
2421: if(nagesqr==1)
2422: cov[3]= agexact*agexact;
1.126 brouard 2423: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2424: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2425: }
2426:
2427: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2428: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2429: savm=oldm;
2430: oldm=newm;
2431: } /* end mult */
2432:
2433: s1=s[mw[mi][i]][i];
2434: s2=s[mw[mi+1][i]][i];
2435: if( s2 > nlstate){
2436: lli=log(out[s1][s2] - savm[s1][s2]);
2437: }else{
2438: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2439: }
2440: ipmx +=1;
2441: sw += weight[i];
2442: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2443: /* 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]); */
2444: } /* end of wave */
2445: } /* end of individual */
2446: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
2447: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2448: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2449: for(mi=1; mi<= wav[i]-1; mi++){
2450: for (ii=1;ii<=nlstate+ndeath;ii++)
2451: for (j=1;j<=nlstate+ndeath;j++){
2452: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2453: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2454: }
2455: for(d=0; d<dh[mi][i]; d++){
2456: newm=savm;
1.187 brouard 2457: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2458: cov[2]=agexact;
2459: if(nagesqr==1)
2460: cov[3]= agexact*agexact;
1.126 brouard 2461: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2462: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2463: }
2464:
2465: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2466: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2467: savm=oldm;
2468: oldm=newm;
2469: } /* end mult */
2470:
2471: s1=s[mw[mi][i]][i];
2472: s2=s[mw[mi+1][i]][i];
2473: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2474: ipmx +=1;
2475: sw += weight[i];
2476: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2477: /*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]);*/
2478: } /* end of wave */
2479: } /* end of individual */
2480: } /* End of if */
2481: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2482: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2483: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2484: return -l;
2485: }
2486:
2487: /*************** log-likelihood *************/
2488: double funcone( double *x)
2489: {
2490: /* Same as likeli but slower because of a lot of printf and if */
2491: int i, ii, j, k, mi, d, kk;
1.131 brouard 2492: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2493: double **out;
2494: double lli; /* Individual log likelihood */
2495: double llt;
2496: int s1, s2;
2497: double bbh, survp;
1.187 brouard 2498: double agexact;
1.126 brouard 2499: /*extern weight */
2500: /* We are differentiating ll according to initial status */
2501: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2502: /*for(i=1;i<imx;i++)
2503: printf(" %d\n",s[4][i]);
2504: */
2505: cov[1]=1.;
2506:
2507: for(k=1; k<=nlstate; k++) ll[k]=0.;
2508:
2509: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2510: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2511: for(mi=1; mi<= wav[i]-1; mi++){
2512: for (ii=1;ii<=nlstate+ndeath;ii++)
2513: for (j=1;j<=nlstate+ndeath;j++){
2514: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2515: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2516: }
2517: for(d=0; d<dh[mi][i]; d++){
2518: newm=savm;
1.187 brouard 2519: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2520: cov[2]=agexact;
2521: if(nagesqr==1)
2522: cov[3]= agexact*agexact;
1.126 brouard 2523: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2524: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2525: }
1.187 brouard 2526:
1.145 brouard 2527: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.126 brouard 2528: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2529: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1.145 brouard 2530: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2531: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
1.126 brouard 2532: savm=oldm;
2533: oldm=newm;
2534: } /* end mult */
2535:
2536: s1=s[mw[mi][i]][i];
2537: s2=s[mw[mi+1][i]][i];
2538: bbh=(double)bh[mi][i]/(double)stepm;
2539: /* bias is positive if real duration
2540: * is higher than the multiple of stepm and negative otherwise.
2541: */
2542: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2543: lli=log(out[s1][s2] - savm[s1][s2]);
2544: } else if (s2==-2) {
2545: for (j=1,survp=0. ; j<=nlstate; j++)
2546: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2547: lli= log(survp);
2548: }else if (mle==1){
2549: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2550: } else if(mle==2){
2551: 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 */
2552: } else if(mle==3){ /* exponential inter-extrapolation */
2553: 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 */
2554: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2555: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 2556: } else{ /* mle=0 back to 1 */
2557: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2558: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 2559: } /* End of if */
2560: ipmx +=1;
2561: sw += weight[i];
2562: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 2563: /*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 2564: if(globpr){
1.202 ! brouard 2565: fprintf(ficresilk,"%9ld %6.1f %6d %2d %2d %2d %2d %3d %11.6f %8.4f\
1.126 brouard 2566: %11.6f %11.6f %11.6f ", \
1.202 ! brouard 2567: num[i], agexact, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1.126 brouard 2568: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2569: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2570: llt +=ll[k]*gipmx/gsw;
2571: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2572: }
2573: fprintf(ficresilk," %10.6f\n", -llt);
2574: }
2575: } /* end of wave */
2576: } /* end of individual */
2577: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2578: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2579: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2580: if(globpr==0){ /* First time we count the contributions and weights */
2581: gipmx=ipmx;
2582: gsw=sw;
2583: }
2584: return -l;
2585: }
2586:
2587:
2588: /*************** function likelione ***********/
2589: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2590: {
2591: /* This routine should help understanding what is done with
2592: the selection of individuals/waves and
2593: to check the exact contribution to the likelihood.
2594: Plotting could be done.
2595: */
2596: int k;
2597:
2598: if(*globpri !=0){ /* Just counts and sums, no printings */
1.201 brouard 2599: strcpy(fileresilk,"ILK_");
1.202 ! brouard 2600: strcat(fileresilk,fileresu);
1.126 brouard 2601: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2602: printf("Problem with resultfile: %s\n", fileresilk);
2603: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2604: }
2605: fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
1.202 ! brouard 2606: fprintf(ficresilk, "#num_i age i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1.126 brouard 2607: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2608: for(k=1; k<=nlstate; k++)
2609: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2610: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2611: }
2612:
2613: *fretone=(*funcone)(p);
2614: if(*globpri !=0){
2615: fclose(ficresilk);
1.202 ! brouard 2616: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle >= 1. You should at least run with mle >= 1 and starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
! 2617: fprintf(fichtm,"<br>- The first 3 individuals are drawn with lines. The function drawn is -2Log(L) in log scale: <a href=\"%s.png\">%s.png</a><br> \
! 2618: <img src=\"%s.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
! 2619: fflush(fichtm);
1.126 brouard 2620: }
2621: return;
2622: }
2623:
2624:
2625: /*********** Maximum Likelihood Estimation ***************/
2626:
2627: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2628: {
1.165 brouard 2629: int i,j, iter=0;
1.126 brouard 2630: double **xi;
2631: double fret;
2632: double fretone; /* Only one call to likelihood */
2633: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 2634:
2635: #ifdef NLOPT
2636: int creturn;
2637: nlopt_opt opt;
2638: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2639: double *lb;
2640: double minf; /* the minimum objective value, upon return */
2641: double * p1; /* Shifted parameters from 0 instead of 1 */
2642: myfunc_data dinst, *d = &dinst;
2643: #endif
2644:
2645:
1.126 brouard 2646: xi=matrix(1,npar,1,npar);
2647: for (i=1;i<=npar;i++)
2648: for (j=1;j<=npar;j++)
2649: xi[i][j]=(i==j ? 1.0 : 0.0);
2650: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.201 brouard 2651: strcpy(filerespow,"POW_");
1.126 brouard 2652: strcat(filerespow,fileres);
2653: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2654: printf("Problem with resultfile: %s\n", filerespow);
2655: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2656: }
2657: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2658: for (i=1;i<=nlstate;i++)
2659: for(j=1;j<=nlstate+ndeath;j++)
2660: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2661: fprintf(ficrespow,"\n");
1.162 brouard 2662: #ifdef POWELL
1.126 brouard 2663: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 2664: #endif
1.126 brouard 2665:
1.162 brouard 2666: #ifdef NLOPT
2667: #ifdef NEWUOA
2668: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2669: #else
2670: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2671: #endif
2672: lb=vector(0,npar-1);
2673: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2674: nlopt_set_lower_bounds(opt, lb);
2675: nlopt_set_initial_step1(opt, 0.1);
2676:
2677: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2678: d->function = func;
2679: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2680: nlopt_set_min_objective(opt, myfunc, d);
2681: nlopt_set_xtol_rel(opt, ftol);
2682: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2683: printf("nlopt failed! %d\n",creturn);
2684: }
2685: else {
2686: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2687: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2688: iter=1; /* not equal */
2689: }
2690: nlopt_destroy(opt);
2691: #endif
1.126 brouard 2692: free_matrix(xi,1,npar,1,npar);
2693: fclose(ficrespow);
1.180 brouard 2694: printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2695: fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2696: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 2697:
2698: }
2699:
2700: /**** Computes Hessian and covariance matrix ***/
2701: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
2702: {
2703: double **a,**y,*x,pd;
2704: double **hess;
1.164 brouard 2705: int i, j;
1.126 brouard 2706: int *indx;
2707:
2708: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
2709: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
2710: void lubksb(double **a, int npar, int *indx, double b[]) ;
2711: void ludcmp(double **a, int npar, int *indx, double *d) ;
2712: double gompertz(double p[]);
2713: hess=matrix(1,npar,1,npar);
2714:
2715: printf("\nCalculation of the hessian matrix. Wait...\n");
2716: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2717: for (i=1;i<=npar;i++){
2718: printf("%d",i);fflush(stdout);
2719: fprintf(ficlog,"%d",i);fflush(ficlog);
2720:
2721: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2722:
2723: /* printf(" %f ",p[i]);
2724: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2725: }
2726:
2727: for (i=1;i<=npar;i++) {
2728: for (j=1;j<=npar;j++) {
2729: if (j>i) {
2730: printf(".%d%d",i,j);fflush(stdout);
2731: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
2732: hess[i][j]=hessij(p,delti,i,j,func,npar);
2733:
2734: hess[j][i]=hess[i][j];
2735: /*printf(" %lf ",hess[i][j]);*/
2736: }
2737: }
2738: }
2739: printf("\n");
2740: fprintf(ficlog,"\n");
2741:
2742: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2743: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2744:
2745: a=matrix(1,npar,1,npar);
2746: y=matrix(1,npar,1,npar);
2747: x=vector(1,npar);
2748: indx=ivector(1,npar);
2749: for (i=1;i<=npar;i++)
2750: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2751: ludcmp(a,npar,indx,&pd);
2752:
2753: for (j=1;j<=npar;j++) {
2754: for (i=1;i<=npar;i++) x[i]=0;
2755: x[j]=1;
2756: lubksb(a,npar,indx,x);
2757: for (i=1;i<=npar;i++){
2758: matcov[i][j]=x[i];
2759: }
2760: }
2761:
2762: printf("\n#Hessian matrix#\n");
2763: fprintf(ficlog,"\n#Hessian matrix#\n");
2764: for (i=1;i<=npar;i++) {
2765: for (j=1;j<=npar;j++) {
2766: printf("%.3e ",hess[i][j]);
2767: fprintf(ficlog,"%.3e ",hess[i][j]);
2768: }
2769: printf("\n");
2770: fprintf(ficlog,"\n");
2771: }
2772:
2773: /* Recompute Inverse */
2774: for (i=1;i<=npar;i++)
2775: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
2776: ludcmp(a,npar,indx,&pd);
2777:
2778: /* printf("\n#Hessian matrix recomputed#\n");
2779:
2780: for (j=1;j<=npar;j++) {
2781: for (i=1;i<=npar;i++) x[i]=0;
2782: x[j]=1;
2783: lubksb(a,npar,indx,x);
2784: for (i=1;i<=npar;i++){
2785: y[i][j]=x[i];
2786: printf("%.3e ",y[i][j]);
2787: fprintf(ficlog,"%.3e ",y[i][j]);
2788: }
2789: printf("\n");
2790: fprintf(ficlog,"\n");
2791: }
2792: */
2793:
2794: free_matrix(a,1,npar,1,npar);
2795: free_matrix(y,1,npar,1,npar);
2796: free_vector(x,1,npar);
2797: free_ivector(indx,1,npar);
2798: free_matrix(hess,1,npar,1,npar);
2799:
2800:
2801: }
2802:
2803: /*************** hessian matrix ****************/
2804: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2805: {
2806: int i;
2807: int l=1, lmax=20;
2808: double k1,k2;
1.132 brouard 2809: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 2810: double res;
2811: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2812: double fx;
2813: int k=0,kmax=10;
2814: double l1;
2815:
2816: fx=func(x);
2817: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 2818: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 2819: l1=pow(10,l);
2820: delts=delt;
2821: for(k=1 ; k <kmax; k=k+1){
2822: delt = delta*(l1*k);
2823: p2[theta]=x[theta] +delt;
1.145 brouard 2824: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 2825: p2[theta]=x[theta]-delt;
2826: k2=func(p2)-fx;
2827: /*res= (k1-2.0*fx+k2)/delt/delt; */
2828: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2829:
1.132 brouard 2830: #ifdef DEBUGHESS
1.126 brouard 2831: 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);
2832: 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);
2833: #endif
2834: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2835: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2836: k=kmax;
2837: }
2838: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 2839: k=kmax; l=lmax*10;
1.126 brouard 2840: }
2841: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2842: delts=delt;
2843: }
2844: }
2845: }
2846: delti[theta]=delts;
2847: return res;
2848:
2849: }
2850:
2851: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2852: {
2853: int i;
1.164 brouard 2854: int l=1, lmax=20;
1.126 brouard 2855: double k1,k2,k3,k4,res,fx;
1.132 brouard 2856: double p2[MAXPARM+1];
1.126 brouard 2857: int k;
2858:
2859: fx=func(x);
2860: for (k=1; k<=2; k++) {
2861: for (i=1;i<=npar;i++) p2[i]=x[i];
2862: p2[thetai]=x[thetai]+delti[thetai]/k;
2863: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2864: k1=func(p2)-fx;
2865:
2866: p2[thetai]=x[thetai]+delti[thetai]/k;
2867: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2868: k2=func(p2)-fx;
2869:
2870: p2[thetai]=x[thetai]-delti[thetai]/k;
2871: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2872: k3=func(p2)-fx;
2873:
2874: p2[thetai]=x[thetai]-delti[thetai]/k;
2875: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2876: k4=func(p2)-fx;
2877: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2878: #ifdef DEBUG
2879: 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);
2880: 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);
2881: #endif
2882: }
2883: return res;
2884: }
2885:
2886: /************** Inverse of matrix **************/
2887: void ludcmp(double **a, int n, int *indx, double *d)
2888: {
2889: int i,imax,j,k;
2890: double big,dum,sum,temp;
2891: double *vv;
2892:
2893: vv=vector(1,n);
2894: *d=1.0;
2895: for (i=1;i<=n;i++) {
2896: big=0.0;
2897: for (j=1;j<=n;j++)
2898: if ((temp=fabs(a[i][j])) > big) big=temp;
2899: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2900: vv[i]=1.0/big;
2901: }
2902: for (j=1;j<=n;j++) {
2903: for (i=1;i<j;i++) {
2904: sum=a[i][j];
2905: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2906: a[i][j]=sum;
2907: }
2908: big=0.0;
2909: for (i=j;i<=n;i++) {
2910: sum=a[i][j];
2911: for (k=1;k<j;k++)
2912: sum -= a[i][k]*a[k][j];
2913: a[i][j]=sum;
2914: if ( (dum=vv[i]*fabs(sum)) >= big) {
2915: big=dum;
2916: imax=i;
2917: }
2918: }
2919: if (j != imax) {
2920: for (k=1;k<=n;k++) {
2921: dum=a[imax][k];
2922: a[imax][k]=a[j][k];
2923: a[j][k]=dum;
2924: }
2925: *d = -(*d);
2926: vv[imax]=vv[j];
2927: }
2928: indx[j]=imax;
2929: if (a[j][j] == 0.0) a[j][j]=TINY;
2930: if (j != n) {
2931: dum=1.0/(a[j][j]);
2932: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2933: }
2934: }
2935: free_vector(vv,1,n); /* Doesn't work */
2936: ;
2937: }
2938:
2939: void lubksb(double **a, int n, int *indx, double b[])
2940: {
2941: int i,ii=0,ip,j;
2942: double sum;
2943:
2944: for (i=1;i<=n;i++) {
2945: ip=indx[i];
2946: sum=b[ip];
2947: b[ip]=b[i];
2948: if (ii)
2949: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2950: else if (sum) ii=i;
2951: b[i]=sum;
2952: }
2953: for (i=n;i>=1;i--) {
2954: sum=b[i];
2955: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2956: b[i]=sum/a[i][i];
2957: }
2958: }
2959:
2960: void pstamp(FILE *fichier)
2961: {
1.196 brouard 2962: fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126 brouard 2963: }
2964:
2965: /************ Frequencies ********************/
2966: void freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
2967: { /* Some frequencies */
2968:
1.164 brouard 2969: int i, m, jk, j1, bool, z1,j;
1.126 brouard 2970: int first;
2971: double ***freq; /* Frequencies */
2972: double *pp, **prop;
2973: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2974: char fileresp[FILENAMELENGTH];
2975:
2976: pp=vector(1,nlstate);
2977: prop=matrix(1,nlstate,iagemin,iagemax+3);
1.201 brouard 2978: strcpy(fileresp,"P_");
2979: strcat(fileresp,fileresu);
1.126 brouard 2980: if((ficresp=fopen(fileresp,"w"))==NULL) {
2981: printf("Problem with prevalence resultfile: %s\n", fileresp);
2982: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2983: exit(0);
2984: }
2985: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2986: j1=0;
2987:
2988: j=cptcoveff;
2989: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2990:
2991: first=1;
2992:
1.169 brouard 2993: /* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */
2994: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
2995: /* j1++; */
1.145 brouard 2996: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
1.126 brouard 2997: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2998: scanf("%d", i);*/
2999: for (i=-5; i<=nlstate+ndeath; i++)
3000: for (jk=-5; jk<=nlstate+ndeath; jk++)
3001: for(m=iagemin; m <= iagemax+3; m++)
3002: freq[i][jk][m]=0;
1.143 brouard 3003:
3004: for (i=1; i<=nlstate; i++)
3005: for(m=iagemin; m <= iagemax+3; m++)
3006: prop[i][m]=0;
1.126 brouard 3007:
3008: dateintsum=0;
3009: k2cpt=0;
3010: for (i=1; i<=imx; i++) {
3011: bool=1;
1.144 brouard 3012: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
3013: for (z1=1; z1<=cptcoveff; z1++)
1.198 brouard 3014: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
1.145 brouard 3015: /* Tests if the value of each of the covariates of i is equal to filter j1 */
1.144 brouard 3016: bool=0;
1.198 brouard 3017: /* 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",
3018: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
3019: j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
3020: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
1.144 brouard 3021: }
1.126 brouard 3022: }
1.144 brouard 3023:
1.126 brouard 3024: if (bool==1){
3025: for(m=firstpass; m<=lastpass; m++){
3026: k2=anint[m][i]+(mint[m][i]/12.);
3027: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
3028: if(agev[m][i]==0) agev[m][i]=iagemax+1;
3029: if(agev[m][i]==1) agev[m][i]=iagemax+2;
3030: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
3031: if (m<lastpass) {
3032: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
3033: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
3034: }
3035:
3036: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
3037: dateintsum=dateintsum+k2;
3038: k2cpt++;
3039: }
3040: /*}*/
3041: }
3042: }
1.145 brouard 3043: } /* end i */
1.126 brouard 3044:
3045: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
3046: pstamp(ficresp);
3047: if (cptcovn>0) {
3048: fprintf(ficresp, "\n#********** Variable ");
1.198 brouard 3049: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 3050: fprintf(ficresp, "**********\n#");
1.143 brouard 3051: fprintf(ficlog, "\n#********** Variable ");
1.198 brouard 3052: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.143 brouard 3053: fprintf(ficlog, "**********\n#");
1.126 brouard 3054: }
3055: for(i=1; i<=nlstate;i++)
3056: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
3057: fprintf(ficresp, "\n");
3058:
3059: for(i=iagemin; i <= iagemax+3; i++){
3060: if(i==iagemax+3){
3061: fprintf(ficlog,"Total");
3062: }else{
3063: if(first==1){
3064: first=0;
3065: printf("See log file for details...\n");
3066: }
3067: fprintf(ficlog,"Age %d", i);
3068: }
3069: for(jk=1; jk <=nlstate ; jk++){
3070: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
3071: pp[jk] += freq[jk][m][i];
3072: }
3073: for(jk=1; jk <=nlstate ; jk++){
3074: for(m=-1, pos=0; m <=0 ; m++)
3075: pos += freq[jk][m][i];
3076: if(pp[jk]>=1.e-10){
3077: if(first==1){
1.132 brouard 3078: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1.126 brouard 3079: }
3080: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
3081: }else{
3082: if(first==1)
3083: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3084: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3085: }
3086: }
3087:
3088: for(jk=1; jk <=nlstate ; jk++){
3089: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
3090: pp[jk] += freq[jk][m][i];
3091: }
3092: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
3093: pos += pp[jk];
3094: posprop += prop[jk][i];
3095: }
3096: for(jk=1; jk <=nlstate ; jk++){
3097: if(pos>=1.e-5){
3098: if(first==1)
3099: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3100: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3101: }else{
3102: if(first==1)
3103: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3104: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3105: }
3106: if( i <= iagemax){
3107: if(pos>=1.e-5){
3108: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
3109: /*probs[i][jk][j1]= pp[jk]/pos;*/
3110: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
3111: }
3112: else
3113: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
3114: }
3115: }
3116:
3117: for(jk=-1; jk <=nlstate+ndeath; jk++)
3118: for(m=-1; m <=nlstate+ndeath; m++)
3119: if(freq[jk][m][i] !=0 ) {
3120: if(first==1)
3121: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
3122: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
3123: }
3124: if(i <= iagemax)
3125: fprintf(ficresp,"\n");
3126: if(first==1)
3127: printf("Others in log...\n");
3128: fprintf(ficlog,"\n");
3129: }
1.145 brouard 3130: /*}*/
1.126 brouard 3131: }
3132: dateintmean=dateintsum/k2cpt;
3133:
3134: fclose(ficresp);
3135: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
3136: free_vector(pp,1,nlstate);
3137: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
3138: /* End of Freq */
3139: }
3140:
3141: /************ Prevalence ********************/
3142: 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)
3143: {
3144: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
3145: in each health status at the date of interview (if between dateprev1 and dateprev2).
3146: We still use firstpass and lastpass as another selection.
3147: */
3148:
1.164 brouard 3149: int i, m, jk, j1, bool, z1,j;
3150:
3151: double **prop;
3152: double posprop;
1.126 brouard 3153: double y2; /* in fractional years */
3154: int iagemin, iagemax;
1.145 brouard 3155: int first; /** to stop verbosity which is redirected to log file */
1.126 brouard 3156:
3157: iagemin= (int) agemin;
3158: iagemax= (int) agemax;
3159: /*pp=vector(1,nlstate);*/
3160: prop=matrix(1,nlstate,iagemin,iagemax+3);
3161: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
3162: j1=0;
3163:
1.145 brouard 3164: /*j=cptcoveff;*/
1.126 brouard 3165: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3166:
1.145 brouard 3167: first=1;
3168: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
3169: /*for(i1=1; i1<=ncodemax[k1];i1++){
3170: j1++;*/
1.126 brouard 3171:
3172: for (i=1; i<=nlstate; i++)
3173: for(m=iagemin; m <= iagemax+3; m++)
3174: prop[i][m]=0.0;
3175:
3176: for (i=1; i<=imx; i++) { /* Each individual */
3177: bool=1;
3178: if (cptcovn>0) {
3179: for (z1=1; z1<=cptcoveff; z1++)
1.198 brouard 3180: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])
1.126 brouard 3181: bool=0;
3182: }
3183: if (bool==1) {
3184: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
3185: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
3186: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
3187: if(agev[m][i]==0) agev[m][i]=iagemax+1;
3188: if(agev[m][i]==1) agev[m][i]=iagemax+2;
3189: 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);
3190: if (s[m][i]>0 && s[m][i]<=nlstate) {
3191: /*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]]);*/
3192: prop[s[m][i]][(int)agev[m][i]] += weight[i];
3193: prop[s[m][i]][iagemax+3] += weight[i];
3194: }
3195: }
3196: } /* end selection of waves */
3197: }
3198: }
3199: for(i=iagemin; i <= iagemax+3; i++){
3200: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
3201: posprop += prop[jk][i];
3202: }
1.145 brouard 3203:
1.126 brouard 3204: for(jk=1; jk <=nlstate ; jk++){
3205: if( i <= iagemax){
3206: if(posprop>=1.e-5){
3207: probs[i][jk][j1]= prop[jk][i]/posprop;
1.145 brouard 3208: } else{
3209: if(first==1){
3210: first=0;
3211: 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]);
3212: }
3213: }
1.126 brouard 3214: }
3215: }/* end jk */
3216: }/* end i */
1.145 brouard 3217: /*} *//* end i1 */
3218: } /* end j1 */
1.126 brouard 3219:
3220: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
3221: /*free_vector(pp,1,nlstate);*/
3222: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
3223: } /* End of prevalence */
3224:
3225: /************* Waves Concatenation ***************/
3226:
3227: 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)
3228: {
3229: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
3230: Death is a valid wave (if date is known).
3231: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
3232: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3233: and mw[mi+1][i]. dh depends on stepm.
3234: */
3235:
3236: int i, mi, m;
3237: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
3238: double sum=0., jmean=0.;*/
3239: int first;
3240: int j, k=0,jk, ju, jl;
3241: double sum=0.;
3242: first=0;
1.164 brouard 3243: jmin=100000;
1.126 brouard 3244: jmax=-1;
3245: jmean=0.;
3246: for(i=1; i<=imx; i++){
3247: mi=0;
3248: m=firstpass;
3249: while(s[m][i] <= nlstate){
3250: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
3251: mw[++mi][i]=m;
3252: if(m >=lastpass)
3253: break;
3254: else
3255: m++;
3256: }/* end while */
3257: if (s[m][i] > nlstate){
3258: mi++; /* Death is another wave */
3259: /* if(mi==0) never been interviewed correctly before death */
3260: /* Only death is a correct wave */
3261: mw[mi][i]=m;
3262: }
3263:
3264: wav[i]=mi;
3265: if(mi==0){
3266: nbwarn++;
3267: if(first==0){
3268: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
3269: first=1;
3270: }
3271: if(first==1){
3272: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
3273: }
3274: } /* end mi==0 */
3275: } /* End individuals */
3276:
3277: for(i=1; i<=imx; i++){
3278: for(mi=1; mi<wav[i];mi++){
3279: if (stepm <=0)
3280: dh[mi][i]=1;
3281: else{
3282: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
3283: if (agedc[i] < 2*AGESUP) {
3284: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
3285: if(j==0) j=1; /* Survives at least one month after exam */
3286: else if(j<0){
3287: nberr++;
3288: 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]);
3289: j=1; /* Temporary Dangerous patch */
3290: 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);
3291: 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]);
3292: 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);
3293: }
3294: k=k+1;
3295: if (j >= jmax){
3296: jmax=j;
3297: ijmax=i;
3298: }
3299: if (j <= jmin){
3300: jmin=j;
3301: ijmin=i;
3302: }
3303: sum=sum+j;
3304: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
3305: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
3306: }
3307: }
3308: else{
3309: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
3310: /* 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]); */
3311:
3312: k=k+1;
3313: if (j >= jmax) {
3314: jmax=j;
3315: ijmax=i;
3316: }
3317: else if (j <= jmin){
3318: jmin=j;
3319: ijmin=i;
3320: }
3321: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
3322: /*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]);*/
3323: if(j<0){
3324: nberr++;
3325: 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]);
3326: 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]);
3327: }
3328: sum=sum+j;
3329: }
3330: jk= j/stepm;
3331: jl= j -jk*stepm;
3332: ju= j -(jk+1)*stepm;
3333: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
3334: if(jl==0){
3335: dh[mi][i]=jk;
3336: bh[mi][i]=0;
3337: }else{ /* We want a negative bias in order to only have interpolation ie
1.136 brouard 3338: * to avoid the price of an extra matrix product in likelihood */
1.126 brouard 3339: dh[mi][i]=jk+1;
3340: bh[mi][i]=ju;
3341: }
3342: }else{
3343: if(jl <= -ju){
3344: dh[mi][i]=jk;
3345: bh[mi][i]=jl; /* bias is positive if real duration
3346: * is higher than the multiple of stepm and negative otherwise.
3347: */
3348: }
3349: else{
3350: dh[mi][i]=jk+1;
3351: bh[mi][i]=ju;
3352: }
3353: if(dh[mi][i]==0){
3354: dh[mi][i]=1; /* At least one step */
3355: bh[mi][i]=ju; /* At least one step */
3356: /* 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);*/
3357: }
3358: } /* end if mle */
3359: }
3360: } /* end wave */
3361: }
3362: jmean=sum/k;
3363: 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 3364: 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 3365: }
3366:
3367: /*********** Tricode ****************************/
1.145 brouard 3368: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 3369: {
1.144 brouard 3370: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
3371: /* 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 3372: * Boring subroutine which should only output nbcode[Tvar[j]][k]
1.145 brouard 3373: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
1.169 brouard 3374: * nbcode[Tvar[j]][1]=
1.144 brouard 3375: */
1.130 brouard 3376:
1.145 brouard 3377: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 3378: int modmaxcovj=0; /* Modality max of covariates j */
1.145 brouard 3379: int cptcode=0; /* Modality max of covariates j */
3380: int modmincovj=0; /* Modality min of covariates j */
3381:
3382:
1.126 brouard 3383: cptcoveff=0;
3384:
1.144 brouard 3385: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 3386:
1.145 brouard 3387: /* Loop on covariates without age and products */
1.186 brouard 3388: for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
1.192 brouard 3389: for (k=-1; k < maxncov; k++) Ndum[k]=0;
1.186 brouard 3390: for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
1.136 brouard 3391: modality of this covariate Vj*/
1.145 brouard 3392: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
3393: * If product of Vn*Vm, still boolean *:
3394: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
3395: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
3396: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
1.136 brouard 3397: modality of the nth covariate of individual i. */
1.145 brouard 3398: if (ij > modmaxcovj)
3399: modmaxcovj=ij;
3400: else if (ij < modmincovj)
3401: modmincovj=ij;
3402: if ((ij < -1) && (ij > NCOVMAX)){
3403: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
3404: exit(1);
3405: }else
1.136 brouard 3406: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
1.145 brouard 3407: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
1.126 brouard 3408: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.136 brouard 3409: /* getting the maximum value of the modality of the covariate
3410: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
3411: female is 1, then modmaxcovj=1.*/
1.192 brouard 3412: } /* end for loop on individuals i */
1.145 brouard 3413: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
1.192 brouard 3414: 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 3415: cptcode=modmaxcovj;
1.137 brouard 3416: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
1.145 brouard 3417: /*for (i=0; i<=cptcode; i++) {*/
1.192 brouard 3418: for (k=modmincovj; k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
3419: printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
3420: fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
3421: if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
3422: if( k != -1){
3423: ncodemax[j]++; /* ncodemax[j]= Number of modalities of the j th
3424: covariate for which somebody answered excluding
3425: undefined. Usually 2: 0 and 1. */
3426: }
3427: ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
3428: covariate for which somebody answered including
3429: undefined. Usually 3: -1, 0 and 1. */
1.145 brouard 3430: }
3431: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
3432: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
1.131 brouard 3433: } /* Ndum[-1] number of undefined modalities */
1.126 brouard 3434:
1.136 brouard 3435: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
1.186 brouard 3436: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
3437: 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 3438: modmincovj=3; modmaxcovj = 7;
1.186 brouard 3439: There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
3440: which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
3441: defining two dummy variables: variables V1_1 and V1_2.
1.145 brouard 3442: nbcode[Tvar[j]][ij]=k;
3443: nbcode[Tvar[j]][1]=0;
3444: nbcode[Tvar[j]][2]=1;
3445: nbcode[Tvar[j]][3]=2;
1.197 brouard 3446: To be continued (not working yet).
1.145 brouard 3447: */
1.197 brouard 3448: ij=0; /* ij is similar to i but can jump over null modalities */
3449: 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*/
3450: if (Ndum[i] == 0) { /* If nobody responded to this modality k */
1.192 brouard 3451: break;
3452: }
3453: ij++;
1.197 brouard 3454: 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 3455: cptcode = ij; /* New max modality for covar j */
3456: } /* end of loop on modality i=-1 to 1 or more */
3457:
3458: /* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
3459: /* /\*recode from 0 *\/ */
3460: /* k is a modality. If we have model=V1+V1*sex */
3461: /* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
3462: /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
3463: /* } */
3464: /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
3465: /* if (ij > ncodemax[j]) { */
3466: /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
3467: /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
3468: /* break; */
3469: /* } */
3470: /* } /\* end of loop on modality k *\/ */
1.137 brouard 3471: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
3472:
1.145 brouard 3473: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.137 brouard 3474:
1.187 brouard 3475: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
1.145 brouard 3476: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
3477: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
1.187 brouard 3478: Ndum[ij]++; /* Might be supersed V1 + V1*age */
1.145 brouard 3479: }
1.126 brouard 3480:
1.192 brouard 3481: ij=0;
1.145 brouard 3482: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
3483: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
1.126 brouard 3484: if((Ndum[i]!=0) && (i<=ncovcol)){
1.192 brouard 3485: ij++;
1.145 brouard 3486: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
3487: Tvaraff[ij]=i; /*For printing (unclear) */
1.192 brouard 3488: }else{
3489: /* Tvaraff[ij]=0; */
3490: }
1.126 brouard 3491: }
1.192 brouard 3492: /* ij--; */
1.144 brouard 3493: cptcoveff=ij; /*Number of total covariates*/
1.145 brouard 3494:
1.126 brouard 3495: }
3496:
1.145 brouard 3497:
1.126 brouard 3498: /*********** Health Expectancies ****************/
3499:
1.127 brouard 3500: 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 3501:
3502: {
3503: /* Health expectancies, no variances */
1.164 brouard 3504: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 3505: int nhstepma, nstepma; /* Decreasing with age */
3506: double age, agelim, hf;
3507: double ***p3mat;
3508: double eip;
3509:
3510: pstamp(ficreseij);
3511: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3512: fprintf(ficreseij,"# Age");
3513: for(i=1; i<=nlstate;i++){
3514: for(j=1; j<=nlstate;j++){
3515: fprintf(ficreseij," e%1d%1d ",i,j);
3516: }
3517: fprintf(ficreseij," e%1d. ",i);
3518: }
3519: fprintf(ficreseij,"\n");
3520:
3521:
3522: if(estepm < stepm){
3523: printf ("Problem %d lower than %d\n",estepm, stepm);
3524: }
3525: else hstepm=estepm;
3526: /* We compute the life expectancy from trapezoids spaced every estepm months
3527: * This is mainly to measure the difference between two models: for example
3528: * if stepm=24 months pijx are given only every 2 years and by summing them
3529: * we are calculating an estimate of the Life Expectancy assuming a linear
3530: * progression in between and thus overestimating or underestimating according
3531: * to the curvature of the survival function. If, for the same date, we
3532: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3533: * to compare the new estimate of Life expectancy with the same linear
3534: * hypothesis. A more precise result, taking into account a more precise
3535: * curvature will be obtained if estepm is as small as stepm. */
3536:
3537: /* For example we decided to compute the life expectancy with the smallest unit */
3538: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3539: nhstepm is the number of hstepm from age to agelim
3540: nstepm is the number of stepm from age to agelin.
3541: Look at hpijx to understand the reason of that which relies in memory size
3542: and note for a fixed period like estepm months */
3543: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3544: survival function given by stepm (the optimization length). Unfortunately it
3545: means that if the survival funtion is printed only each two years of age and if
3546: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3547: results. So we changed our mind and took the option of the best precision.
3548: */
3549: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3550:
3551: agelim=AGESUP;
3552: /* If stepm=6 months */
3553: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3554: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3555:
3556: /* nhstepm age range expressed in number of stepm */
3557: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3558: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3559: /* if (stepm >= YEARM) hstepm=1;*/
3560: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3561: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3562:
3563: for (age=bage; age<=fage; age ++){
3564: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3565: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3566: /* if (stepm >= YEARM) hstepm=1;*/
3567: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3568:
3569: /* If stepm=6 months */
3570: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3571: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3572:
3573: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3574:
3575: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3576:
3577: printf("%d|",(int)age);fflush(stdout);
3578: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3579:
3580: /* Computing expectancies */
3581: for(i=1; i<=nlstate;i++)
3582: for(j=1; j<=nlstate;j++)
3583: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3584: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3585:
3586: /* 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]);*/
3587:
3588: }
3589:
3590: fprintf(ficreseij,"%3.0f",age );
3591: for(i=1; i<=nlstate;i++){
3592: eip=0;
3593: for(j=1; j<=nlstate;j++){
3594: eip +=eij[i][j][(int)age];
3595: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3596: }
3597: fprintf(ficreseij,"%9.4f", eip );
3598: }
3599: fprintf(ficreseij,"\n");
3600:
3601: }
3602: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3603: printf("\n");
3604: fprintf(ficlog,"\n");
3605:
3606: }
3607:
1.127 brouard 3608: 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 3609:
3610: {
3611: /* Covariances of health expectancies eij and of total life expectancies according
3612: to initial status i, ei. .
3613: */
3614: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3615: int nhstepma, nstepma; /* Decreasing with age */
3616: double age, agelim, hf;
3617: double ***p3matp, ***p3matm, ***varhe;
3618: double **dnewm,**doldm;
3619: double *xp, *xm;
3620: double **gp, **gm;
3621: double ***gradg, ***trgradg;
3622: int theta;
3623:
3624: double eip, vip;
3625:
3626: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
3627: xp=vector(1,npar);
3628: xm=vector(1,npar);
3629: dnewm=matrix(1,nlstate*nlstate,1,npar);
3630: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3631:
3632: pstamp(ficresstdeij);
3633: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3634: fprintf(ficresstdeij,"# Age");
3635: for(i=1; i<=nlstate;i++){
3636: for(j=1; j<=nlstate;j++)
3637: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3638: fprintf(ficresstdeij," e%1d. ",i);
3639: }
3640: fprintf(ficresstdeij,"\n");
3641:
3642: pstamp(ficrescveij);
3643: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3644: fprintf(ficrescveij,"# Age");
3645: for(i=1; i<=nlstate;i++)
3646: for(j=1; j<=nlstate;j++){
3647: cptj= (j-1)*nlstate+i;
3648: for(i2=1; i2<=nlstate;i2++)
3649: for(j2=1; j2<=nlstate;j2++){
3650: cptj2= (j2-1)*nlstate+i2;
3651: if(cptj2 <= cptj)
3652: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3653: }
3654: }
3655: fprintf(ficrescveij,"\n");
3656:
3657: if(estepm < stepm){
3658: printf ("Problem %d lower than %d\n",estepm, stepm);
3659: }
3660: else hstepm=estepm;
3661: /* We compute the life expectancy from trapezoids spaced every estepm months
3662: * This is mainly to measure the difference between two models: for example
3663: * if stepm=24 months pijx are given only every 2 years and by summing them
3664: * we are calculating an estimate of the Life Expectancy assuming a linear
3665: * progression in between and thus overestimating or underestimating according
3666: * to the curvature of the survival function. If, for the same date, we
3667: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3668: * to compare the new estimate of Life expectancy with the same linear
3669: * hypothesis. A more precise result, taking into account a more precise
3670: * curvature will be obtained if estepm is as small as stepm. */
3671:
3672: /* For example we decided to compute the life expectancy with the smallest unit */
3673: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3674: nhstepm is the number of hstepm from age to agelim
3675: nstepm is the number of stepm from age to agelin.
3676: Look at hpijx to understand the reason of that which relies in memory size
3677: and note for a fixed period like estepm months */
3678: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3679: survival function given by stepm (the optimization length). Unfortunately it
3680: means that if the survival funtion is printed only each two years of age and if
3681: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3682: results. So we changed our mind and took the option of the best precision.
3683: */
3684: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3685:
3686: /* If stepm=6 months */
3687: /* nhstepm age range expressed in number of stepm */
3688: agelim=AGESUP;
3689: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3690: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3691: /* if (stepm >= YEARM) hstepm=1;*/
3692: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3693:
3694: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3695: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3696: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3697: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3698: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3699: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3700:
3701: for (age=bage; age<=fage; age ++){
3702: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3703: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3704: /* if (stepm >= YEARM) hstepm=1;*/
3705: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3706:
3707: /* If stepm=6 months */
3708: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3709: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3710:
3711: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3712:
3713: /* Computing Variances of health expectancies */
3714: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3715: decrease memory allocation */
3716: for(theta=1; theta <=npar; theta++){
3717: for(i=1; i<=npar; i++){
3718: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3719: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3720: }
3721: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3722: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3723:
3724: for(j=1; j<= nlstate; j++){
3725: for(i=1; i<=nlstate; i++){
3726: for(h=0; h<=nhstepm-1; h++){
3727: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3728: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3729: }
3730: }
3731: }
3732:
3733: for(ij=1; ij<= nlstate*nlstate; ij++)
3734: for(h=0; h<=nhstepm-1; h++){
3735: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3736: }
3737: }/* End theta */
3738:
3739:
3740: for(h=0; h<=nhstepm-1; h++)
3741: for(j=1; j<=nlstate*nlstate;j++)
3742: for(theta=1; theta <=npar; theta++)
3743: trgradg[h][j][theta]=gradg[h][theta][j];
3744:
3745:
3746: for(ij=1;ij<=nlstate*nlstate;ij++)
3747: for(ji=1;ji<=nlstate*nlstate;ji++)
3748: varhe[ij][ji][(int)age] =0.;
3749:
3750: printf("%d|",(int)age);fflush(stdout);
3751: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3752: for(h=0;h<=nhstepm-1;h++){
3753: for(k=0;k<=nhstepm-1;k++){
3754: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3755: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3756: for(ij=1;ij<=nlstate*nlstate;ij++)
3757: for(ji=1;ji<=nlstate*nlstate;ji++)
3758: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3759: }
3760: }
3761:
3762: /* Computing expectancies */
3763: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3764: for(i=1; i<=nlstate;i++)
3765: for(j=1; j<=nlstate;j++)
3766: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3767: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3768:
3769: /* 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]);*/
3770:
3771: }
3772:
3773: fprintf(ficresstdeij,"%3.0f",age );
3774: for(i=1; i<=nlstate;i++){
3775: eip=0.;
3776: vip=0.;
3777: for(j=1; j<=nlstate;j++){
3778: eip += eij[i][j][(int)age];
3779: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3780: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3781: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3782: }
3783: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3784: }
3785: fprintf(ficresstdeij,"\n");
3786:
3787: fprintf(ficrescveij,"%3.0f",age );
3788: for(i=1; i<=nlstate;i++)
3789: for(j=1; j<=nlstate;j++){
3790: cptj= (j-1)*nlstate+i;
3791: for(i2=1; i2<=nlstate;i2++)
3792: for(j2=1; j2<=nlstate;j2++){
3793: cptj2= (j2-1)*nlstate+i2;
3794: if(cptj2 <= cptj)
3795: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3796: }
3797: }
3798: fprintf(ficrescveij,"\n");
3799:
3800: }
3801: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3802: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3803: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3804: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3805: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3806: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3807: printf("\n");
3808: fprintf(ficlog,"\n");
3809:
3810: free_vector(xm,1,npar);
3811: free_vector(xp,1,npar);
3812: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3813: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3814: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3815: }
3816:
3817: /************ Variance ******************/
3818: void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
3819: {
3820: /* Variance of health expectancies */
3821: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3822: /* double **newm;*/
1.169 brouard 3823: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
3824:
3825: int movingaverage();
1.126 brouard 3826: double **dnewm,**doldm;
3827: double **dnewmp,**doldmp;
3828: int i, j, nhstepm, hstepm, h, nstepm ;
1.164 brouard 3829: int k;
1.126 brouard 3830: double *xp;
3831: double **gp, **gm; /* for var eij */
3832: double ***gradg, ***trgradg; /*for var eij */
3833: double **gradgp, **trgradgp; /* for var p point j */
3834: double *gpp, *gmp; /* for var p point j */
3835: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3836: double ***p3mat;
3837: double age,agelim, hf;
3838: double ***mobaverage;
3839: int theta;
3840: char digit[4];
3841: char digitp[25];
3842:
3843: char fileresprobmorprev[FILENAMELENGTH];
3844:
3845: if(popbased==1){
3846: if(mobilav!=0)
1.201 brouard 3847: strcpy(digitp,"-POPULBASED-MOBILAV_");
3848: else strcpy(digitp,"-POPULBASED-NOMOBIL_");
1.126 brouard 3849: }
3850: else
1.201 brouard 3851: strcpy(digitp,"-STABLBASED_");
1.126 brouard 3852:
3853: if (mobilav!=0) {
3854: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3855: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3856: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3857: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3858: }
3859: }
3860:
1.201 brouard 3861: strcpy(fileresprobmorprev,"PRMORPREV-");
1.126 brouard 3862: sprintf(digit,"%-d",ij);
3863: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3864: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3865: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
1.202 ! brouard 3866: strcat(fileresprobmorprev,fileresu);
1.126 brouard 3867: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3868: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3869: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3870: }
3871: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3872:
3873: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3874: pstamp(ficresprobmorprev);
3875: 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);
3876: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3877: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3878: fprintf(ficresprobmorprev," p.%-d SE",j);
3879: for(i=1; i<=nlstate;i++)
3880: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3881: }
3882: fprintf(ficresprobmorprev,"\n");
3883: fprintf(ficgp,"\n# Routine varevsij");
1.200 brouard 3884: fprintf(ficgp,"\nunset title \n");
3885: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
1.126 brouard 3886: 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");
3887: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3888: /* } */
3889: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3890: pstamp(ficresvij);
3891: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3892: if(popbased==1)
1.128 brouard 3893: 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 3894: else
3895: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3896: fprintf(ficresvij,"# Age");
3897: for(i=1; i<=nlstate;i++)
3898: for(j=1; j<=nlstate;j++)
3899: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3900: fprintf(ficresvij,"\n");
3901:
3902: xp=vector(1,npar);
3903: dnewm=matrix(1,nlstate,1,npar);
3904: doldm=matrix(1,nlstate,1,nlstate);
3905: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3906: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3907:
3908: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3909: gpp=vector(nlstate+1,nlstate+ndeath);
3910: gmp=vector(nlstate+1,nlstate+ndeath);
3911: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3912:
3913: if(estepm < stepm){
3914: printf ("Problem %d lower than %d\n",estepm, stepm);
3915: }
3916: else hstepm=estepm;
3917: /* For example we decided to compute the life expectancy with the smallest unit */
3918: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3919: nhstepm is the number of hstepm from age to agelim
3920: nstepm is the number of stepm from age to agelin.
1.128 brouard 3921: Look at function hpijx to understand why (it is linked to memory size questions) */
1.126 brouard 3922: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3923: survival function given by stepm (the optimization length). Unfortunately it
3924: means that if the survival funtion is printed every two years of age and if
3925: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3926: results. So we changed our mind and took the option of the best precision.
3927: */
3928: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3929: agelim = AGESUP;
3930: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3931: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3932: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3933: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3934: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3935: gp=matrix(0,nhstepm,1,nlstate);
3936: gm=matrix(0,nhstepm,1,nlstate);
3937:
3938:
3939: for(theta=1; theta <=npar; theta++){
3940: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3941: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3942: }
3943: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3944: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3945:
3946: if (popbased==1) {
3947: if(mobilav ==0){
3948: for(i=1; i<=nlstate;i++)
3949: prlim[i][i]=probs[(int)age][i][ij];
3950: }else{ /* mobilav */
3951: for(i=1; i<=nlstate;i++)
3952: prlim[i][i]=mobaverage[(int)age][i][ij];
3953: }
3954: }
3955:
3956: for(j=1; j<= nlstate; j++){
3957: for(h=0; h<=nhstepm; h++){
3958: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3959: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3960: }
3961: }
3962: /* This for computing probability of death (h=1 means
3963: computed over hstepm matrices product = hstepm*stepm months)
3964: as a weighted average of prlim.
3965: */
3966: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3967: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3968: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3969: }
3970: /* end probability of death */
3971:
3972: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3973: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3974: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3975: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3976:
3977: if (popbased==1) {
3978: if(mobilav ==0){
3979: for(i=1; i<=nlstate;i++)
3980: prlim[i][i]=probs[(int)age][i][ij];
3981: }else{ /* mobilav */
3982: for(i=1; i<=nlstate;i++)
3983: prlim[i][i]=mobaverage[(int)age][i][ij];
3984: }
3985: }
3986:
1.128 brouard 3987: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
1.126 brouard 3988: for(h=0; h<=nhstepm; h++){
3989: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3990: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3991: }
3992: }
3993: /* This for computing probability of death (h=1 means
3994: computed over hstepm matrices product = hstepm*stepm months)
3995: as a weighted average of prlim.
3996: */
3997: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3998: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3999: gmp[j] += prlim[i][i]*p3mat[i][j][1];
4000: }
4001: /* end probability of death */
4002:
4003: for(j=1; j<= nlstate; j++) /* vareij */
4004: for(h=0; h<=nhstepm; h++){
4005: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
4006: }
4007:
4008: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
4009: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
4010: }
4011:
4012: } /* End theta */
4013:
4014: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
4015:
4016: for(h=0; h<=nhstepm; h++) /* veij */
4017: for(j=1; j<=nlstate;j++)
4018: for(theta=1; theta <=npar; theta++)
4019: trgradg[h][j][theta]=gradg[h][theta][j];
4020:
4021: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
4022: for(theta=1; theta <=npar; theta++)
4023: trgradgp[j][theta]=gradgp[theta][j];
4024:
4025:
4026: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
4027: for(i=1;i<=nlstate;i++)
4028: for(j=1;j<=nlstate;j++)
4029: vareij[i][j][(int)age] =0.;
4030:
4031: for(h=0;h<=nhstepm;h++){
4032: for(k=0;k<=nhstepm;k++){
4033: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
4034: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
4035: for(i=1;i<=nlstate;i++)
4036: for(j=1;j<=nlstate;j++)
4037: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
4038: }
4039: }
4040:
4041: /* pptj */
4042: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
4043: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
4044: for(j=nlstate+1;j<=nlstate+ndeath;j++)
4045: for(i=nlstate+1;i<=nlstate+ndeath;i++)
4046: varppt[j][i]=doldmp[j][i];
4047: /* end ppptj */
4048: /* x centered again */
4049: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
4050: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
4051:
4052: if (popbased==1) {
4053: if(mobilav ==0){
4054: for(i=1; i<=nlstate;i++)
4055: prlim[i][i]=probs[(int)age][i][ij];
4056: }else{ /* mobilav */
4057: for(i=1; i<=nlstate;i++)
4058: prlim[i][i]=mobaverage[(int)age][i][ij];
4059: }
4060: }
4061:
4062: /* This for computing probability of death (h=1 means
4063: computed over hstepm (estepm) matrices product = hstepm*stepm months)
4064: as a weighted average of prlim.
4065: */
4066: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4067: for(i=1,gmp[j]=0.;i<= nlstate; i++)
4068: gmp[j] += prlim[i][i]*p3mat[i][j][1];
4069: }
4070: /* end probability of death */
4071:
4072: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
4073: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
4074: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
4075: for(i=1; i<=nlstate;i++){
4076: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
4077: }
4078: }
4079: fprintf(ficresprobmorprev,"\n");
4080:
4081: fprintf(ficresvij,"%.0f ",age );
4082: for(i=1; i<=nlstate;i++)
4083: for(j=1; j<=nlstate;j++){
4084: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
4085: }
4086: fprintf(ficresvij,"\n");
4087: free_matrix(gp,0,nhstepm,1,nlstate);
4088: free_matrix(gm,0,nhstepm,1,nlstate);
4089: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
4090: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
4091: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4092: } /* End age */
4093: free_vector(gpp,nlstate+1,nlstate+ndeath);
4094: free_vector(gmp,nlstate+1,nlstate+ndeath);
4095: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
4096: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.199 brouard 4097: /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
4098: fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
1.126 brouard 4099: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
1.131 brouard 4100: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.201 brouard 4101: fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 4102: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
4103: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
4104: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.145 brouard 4105: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
1.170 brouard 4106: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
1.145 brouard 4107: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
1.126 brouard 4108: 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 4109: 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 4110: /* 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 4111: */
1.199 brouard 4112: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
1.201 brouard 4113: fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 4114:
4115: free_vector(xp,1,npar);
4116: free_matrix(doldm,1,nlstate,1,nlstate);
4117: free_matrix(dnewm,1,nlstate,1,npar);
4118: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4119: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
4120: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4121: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4122: fclose(ficresprobmorprev);
4123: fflush(ficgp);
4124: fflush(fichtm);
4125: } /* end varevsij */
4126:
4127: /************ Variance of prevlim ******************/
4128: void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
4129: {
4130: /* Variance of prevalence limit */
4131: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 4132:
1.126 brouard 4133: double **dnewm,**doldm;
4134: int i, j, nhstepm, hstepm;
4135: double *xp;
4136: double *gp, *gm;
4137: double **gradg, **trgradg;
4138: double age,agelim;
4139: int theta;
4140:
4141: pstamp(ficresvpl);
4142: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
4143: fprintf(ficresvpl,"# Age");
4144: for(i=1; i<=nlstate;i++)
4145: fprintf(ficresvpl," %1d-%1d",i,i);
4146: fprintf(ficresvpl,"\n");
4147:
4148: xp=vector(1,npar);
4149: dnewm=matrix(1,nlstate,1,npar);
4150: doldm=matrix(1,nlstate,1,nlstate);
4151:
4152: hstepm=1*YEARM; /* Every year of age */
4153: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
4154: agelim = AGESUP;
4155: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
4156: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4157: if (stepm >= YEARM) hstepm=1;
4158: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4159: gradg=matrix(1,npar,1,nlstate);
4160: gp=vector(1,nlstate);
4161: gm=vector(1,nlstate);
4162:
4163: for(theta=1; theta <=npar; theta++){
4164: for(i=1; i<=npar; i++){ /* Computes gradient */
4165: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4166: }
4167: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
4168: for(i=1;i<=nlstate;i++)
4169: gp[i] = prlim[i][i];
4170:
4171: for(i=1; i<=npar; i++) /* Computes gradient */
4172: xp[i] = x[i] - (i==theta ?delti[theta]:0);
4173: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
4174: for(i=1;i<=nlstate;i++)
4175: gm[i] = prlim[i][i];
4176:
4177: for(i=1;i<=nlstate;i++)
4178: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
4179: } /* End theta */
4180:
4181: trgradg =matrix(1,nlstate,1,npar);
4182:
4183: for(j=1; j<=nlstate;j++)
4184: for(theta=1; theta <=npar; theta++)
4185: trgradg[j][theta]=gradg[theta][j];
4186:
4187: for(i=1;i<=nlstate;i++)
4188: varpl[i][(int)age] =0.;
4189: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
4190: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
4191: for(i=1;i<=nlstate;i++)
4192: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
4193:
4194: fprintf(ficresvpl,"%.0f ",age );
4195: for(i=1; i<=nlstate;i++)
4196: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
4197: fprintf(ficresvpl,"\n");
4198: free_vector(gp,1,nlstate);
4199: free_vector(gm,1,nlstate);
4200: free_matrix(gradg,1,npar,1,nlstate);
4201: free_matrix(trgradg,1,nlstate,1,npar);
4202: } /* End age */
4203:
4204: free_vector(xp,1,npar);
4205: free_matrix(doldm,1,nlstate,1,npar);
4206: free_matrix(dnewm,1,nlstate,1,nlstate);
4207:
4208: }
4209:
4210: /************ Variance of one-step probabilities ******************/
4211: 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[])
4212: {
1.164 brouard 4213: int i, j=0, k1, l1, tj;
1.126 brouard 4214: int k2, l2, j1, z1;
1.164 brouard 4215: int k=0, l;
1.145 brouard 4216: int first=1, first1, first2;
1.126 brouard 4217: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
4218: double **dnewm,**doldm;
4219: double *xp;
4220: double *gp, *gm;
4221: double **gradg, **trgradg;
4222: double **mu;
1.164 brouard 4223: double age, cov[NCOVMAX+1];
1.126 brouard 4224: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
4225: int theta;
4226: char fileresprob[FILENAMELENGTH];
4227: char fileresprobcov[FILENAMELENGTH];
4228: char fileresprobcor[FILENAMELENGTH];
4229: double ***varpij;
4230:
1.201 brouard 4231: strcpy(fileresprob,"PROB_");
1.126 brouard 4232: strcat(fileresprob,fileres);
4233: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
4234: printf("Problem with resultfile: %s\n", fileresprob);
4235: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
4236: }
1.201 brouard 4237: strcpy(fileresprobcov,"PROBCOV_");
1.202 ! brouard 4238: strcat(fileresprobcov,fileresu);
1.126 brouard 4239: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
4240: printf("Problem with resultfile: %s\n", fileresprobcov);
4241: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
4242: }
1.201 brouard 4243: strcpy(fileresprobcor,"PROBCOR_");
1.202 ! brouard 4244: strcat(fileresprobcor,fileresu);
1.126 brouard 4245: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
4246: printf("Problem with resultfile: %s\n", fileresprobcor);
4247: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
4248: }
4249: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4250: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4251: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4252: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4253: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4254: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4255: pstamp(ficresprob);
4256: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
4257: fprintf(ficresprob,"# Age");
4258: pstamp(ficresprobcov);
4259: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
4260: fprintf(ficresprobcov,"# Age");
4261: pstamp(ficresprobcor);
4262: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
4263: fprintf(ficresprobcor,"# Age");
4264:
4265:
4266: for(i=1; i<=nlstate;i++)
4267: for(j=1; j<=(nlstate+ndeath);j++){
4268: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
4269: fprintf(ficresprobcov," p%1d-%1d ",i,j);
4270: fprintf(ficresprobcor," p%1d-%1d ",i,j);
4271: }
4272: /* fprintf(ficresprob,"\n");
4273: fprintf(ficresprobcov,"\n");
4274: fprintf(ficresprobcor,"\n");
4275: */
1.131 brouard 4276: xp=vector(1,npar);
1.126 brouard 4277: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4278: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4279: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
4280: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
4281: first=1;
4282: fprintf(ficgp,"\n# Routine varprob");
4283: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
4284: fprintf(fichtm,"\n");
4285:
1.200 brouard 4286: 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 4287: 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);
4288: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
1.126 brouard 4289: and drawn. It helps understanding how is the covariance between two incidences.\
4290: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
4291: 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. \
4292: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
4293: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
4294: standard deviations wide on each axis. <br>\
4295: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
4296: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
4297: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
4298:
4299: cov[1]=1;
1.145 brouard 4300: /* tj=cptcoveff; */
4301: tj = (int) pow(2,cptcoveff);
1.126 brouard 4302: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
4303: j1=0;
1.145 brouard 4304: for(j1=1; j1<=tj;j1++){
4305: /*for(i1=1; i1<=ncodemax[t];i1++){ */
4306: /*j1++;*/
1.126 brouard 4307: if (cptcovn>0) {
4308: fprintf(ficresprob, "\n#********** Variable ");
1.198 brouard 4309: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4310: fprintf(ficresprob, "**********\n#\n");
4311: fprintf(ficresprobcov, "\n#********** Variable ");
1.198 brouard 4312: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4313: fprintf(ficresprobcov, "**********\n#\n");
4314:
4315: fprintf(ficgp, "\n#********** Variable ");
1.198 brouard 4316: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4317: fprintf(ficgp, "**********\n#\n");
4318:
4319:
4320: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.198 brouard 4321: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4322: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
4323:
4324: fprintf(ficresprobcor, "\n#********** Variable ");
1.198 brouard 4325: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4326: fprintf(ficresprobcor, "**********\n#");
4327: }
4328:
1.145 brouard 4329: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
4330: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4331: gp=vector(1,(nlstate)*(nlstate+ndeath));
4332: gm=vector(1,(nlstate)*(nlstate+ndeath));
1.126 brouard 4333: for (age=bage; age<=fage; age ++){
4334: cov[2]=age;
1.187 brouard 4335: if(nagesqr==1)
4336: cov[3]= age*age;
1.126 brouard 4337: for (k=1; k<=cptcovn;k++) {
1.200 brouard 4338: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
4339: /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
1.145 brouard 4340: * 1 1 1 1 1
4341: * 2 2 1 1 1
4342: * 3 1 2 1 1
4343: */
4344: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
1.126 brouard 4345: }
1.186 brouard 4346: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 4347: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
1.126 brouard 4348: for (k=1; k<=cptcovprod;k++)
1.200 brouard 4349: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.126 brouard 4350:
4351:
4352: for(theta=1; theta <=npar; theta++){
4353: for(i=1; i<=npar; i++)
4354: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
4355:
4356: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4357:
4358: k=0;
4359: for(i=1; i<= (nlstate); i++){
4360: for(j=1; j<=(nlstate+ndeath);j++){
4361: k=k+1;
4362: gp[k]=pmmij[i][j];
4363: }
4364: }
4365:
4366: for(i=1; i<=npar; i++)
4367: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
4368:
4369: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4370: k=0;
4371: for(i=1; i<=(nlstate); i++){
4372: for(j=1; j<=(nlstate+ndeath);j++){
4373: k=k+1;
4374: gm[k]=pmmij[i][j];
4375: }
4376: }
4377:
4378: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
4379: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
4380: }
4381:
4382: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
4383: for(theta=1; theta <=npar; theta++)
4384: trgradg[j][theta]=gradg[theta][j];
4385:
4386: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
4387: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
4388:
4389: pmij(pmmij,cov,ncovmodel,x,nlstate);
4390:
4391: k=0;
4392: for(i=1; i<=(nlstate); i++){
4393: for(j=1; j<=(nlstate+ndeath);j++){
4394: k=k+1;
4395: mu[k][(int) age]=pmmij[i][j];
4396: }
4397: }
4398: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
4399: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
4400: varpij[i][j][(int)age] = doldm[i][j];
4401:
4402: /*printf("\n%d ",(int)age);
4403: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4404: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4405: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4406: }*/
4407:
4408: fprintf(ficresprob,"\n%d ",(int)age);
4409: fprintf(ficresprobcov,"\n%d ",(int)age);
4410: fprintf(ficresprobcor,"\n%d ",(int)age);
4411:
4412: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
4413: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
4414: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4415: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
4416: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
4417: }
4418: i=0;
4419: for (k=1; k<=(nlstate);k++){
4420: for (l=1; l<=(nlstate+ndeath);l++){
1.145 brouard 4421: i++;
1.126 brouard 4422: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
4423: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
4424: for (j=1; j<=i;j++){
1.145 brouard 4425: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
1.126 brouard 4426: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
4427: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
4428: }
4429: }
4430: }/* end of loop for state */
4431: } /* end of loop for age */
1.145 brouard 4432: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
4433: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
4434: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4435: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4436:
1.126 brouard 4437: /* Confidence intervalle of pij */
4438: /*
1.131 brouard 4439: fprintf(ficgp,"\nunset parametric;unset label");
1.126 brouard 4440: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
4441: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
4442: 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);
4443: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
4444: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
4445: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
4446: */
4447:
4448: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
1.145 brouard 4449: first1=1;first2=2;
1.126 brouard 4450: for (k2=1; k2<=(nlstate);k2++){
4451: for (l2=1; l2<=(nlstate+ndeath);l2++){
4452: if(l2==k2) continue;
4453: j=(k2-1)*(nlstate+ndeath)+l2;
4454: for (k1=1; k1<=(nlstate);k1++){
4455: for (l1=1; l1<=(nlstate+ndeath);l1++){
4456: if(l1==k1) continue;
4457: i=(k1-1)*(nlstate+ndeath)+l1;
4458: if(i<=j) continue;
4459: for (age=bage; age<=fage; age ++){
4460: if ((int)age %5==0){
4461: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
4462: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
4463: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
4464: mu1=mu[i][(int) age]/stepm*YEARM ;
4465: mu2=mu[j][(int) age]/stepm*YEARM;
4466: c12=cv12/sqrt(v1*v2);
4467: /* Computing eigen value of matrix of covariance */
4468: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4469: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
1.135 brouard 4470: if ((lc2 <0) || (lc1 <0) ){
1.145 brouard 4471: if(first2==1){
4472: first1=0;
4473: 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);
4474: }
4475: 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);
4476: /* lc1=fabs(lc1); */ /* If we want to have them positive */
4477: /* lc2=fabs(lc2); */
1.135 brouard 4478: }
4479:
1.126 brouard 4480: /* Eigen vectors */
4481: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
4482: /*v21=sqrt(1.-v11*v11); *//* error */
4483: v21=(lc1-v1)/cv12*v11;
4484: v12=-v21;
4485: v22=v11;
4486: tnalp=v21/v11;
4487: if(first1==1){
4488: first1=0;
4489: 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);
4490: }
4491: 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);
4492: /*printf(fignu*/
4493: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
4494: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
4495: if(first==1){
4496: first=0;
1.200 brouard 4497: fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
1.126 brouard 4498: fprintf(ficgp,"\nset parametric;unset label");
4499: 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 4500: fprintf(ficgp,"\nset ter svg size 640, 480");
1.126 brouard 4501: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.201 brouard 4502: :<a href=\"%s_%d%1d%1d-%1d%1d.svg\">\
4503: %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
4504: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,\
4505: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
4506: fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
1.126 brouard 4507: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
1.201 brouard 4508: fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
1.126 brouard 4509: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4510: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4511: 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",\
4512: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4513: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4514: }else{
4515: first=0;
4516: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4517: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4518: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4519: 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",\
4520: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4521: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4522: }/* if first */
4523: } /* age mod 5 */
4524: } /* end loop age */
1.201 brouard 4525: 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 4526: first=1;
4527: } /*l12 */
4528: } /* k12 */
4529: } /*l1 */
4530: }/* k1 */
1.169 brouard 4531: /* } */ /* loop covariates */
1.126 brouard 4532: }
4533: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4534: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4535: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4536: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4537: free_vector(xp,1,npar);
4538: fclose(ficresprob);
4539: fclose(ficresprobcov);
4540: fclose(ficresprobcor);
4541: fflush(ficgp);
4542: fflush(fichtmcov);
4543: }
4544:
4545:
4546: /******************* Printing html file ***********/
1.201 brouard 4547: void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 4548: int lastpass, int stepm, int weightopt, char model[],\
4549: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
4550: int popforecast, int estepm ,\
4551: double jprev1, double mprev1,double anprev1, \
4552: double jprev2, double mprev2,double anprev2){
4553: int jj1, k1, i1, cpt;
4554:
4555: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4556: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4557: </ul>");
4558: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
4559: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
1.201 brouard 4560: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
1.126 brouard 4561: fprintf(fichtm,"\
4562: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
1.201 brouard 4563: stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
1.126 brouard 4564: fprintf(fichtm,"\
4565: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4566: subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
1.126 brouard 4567: fprintf(fichtm,"\
1.128 brouard 4568: - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
1.126 brouard 4569: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4570: estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
1.126 brouard 4571: fprintf(fichtm,"\
4572: - Population projections by age and states: \
1.201 brouard 4573: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
1.126 brouard 4574:
4575: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4576:
1.145 brouard 4577: m=pow(2,cptcoveff);
1.126 brouard 4578: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4579:
4580: jj1=0;
4581: for(k1=1; k1<=m;k1++){
1.192 brouard 4582: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
1.126 brouard 4583: jj1++;
4584: if (cptcovn > 0) {
4585: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.192 brouard 4586: for (cpt=1; cpt<=cptcoveff;cpt++){
1.198 brouard 4587: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
4588: printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
1.192 brouard 4589: }
1.126 brouard 4590: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4591: }
1.201 brouard 4592: /* aij, bij */
4593: fprintf(fichtm,"<br>- Logit model, for example: logit(pij)=log(pij/pii)= aij+ bij age + V1 age + etc. as a function of age: <a href=\"%s_%d-1.svg\">%s_%d-1.svg</a><br> \
4594: <img src=\"%s_%d-1.svg\">",subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.126 brouard 4595: /* Pij */
1.202 ! brouard 4596: fprintf(fichtm,"<br>\n- Pij or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2.svg\">%s_%d-2.svg</a><br> \
1.201 brouard 4597: <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.126 brouard 4598: /* Quasi-incidences */
1.201 brouard 4599: fprintf(fichtm,"<br>\n- Iij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
4600: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too,\
4601: incidence (rates) are the limit when h tends to zero of the ratio of the probability hPij \
4602: divided by h: hPij/h : <a href=\"%s_%d-3.svg\">%s_%d-3.svg</a><br> \
4603: <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
4604: /* Survival functions (period) in state j */
4605: for(cpt=1; cpt<=nlstate;cpt++){
4606: 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> \
4607: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);
4608: }
4609: /* State specific survival functions (period) */
4610: for(cpt=1; cpt<=nlstate;cpt++){
4611: fprintf(fichtm,"<br>\n- Survival functions from state %d in any different live states and total.\
4612: Or probability to survive in various states (1 to %d) being in state %d at different ages.\
4613: <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);
4614: }
4615: /* Period (stable) prevalence in each health state */
4616: for(cpt=1; cpt<=nlstate;cpt++){
4617: 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> \
4618: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);
4619: }
1.126 brouard 4620: for(cpt=1; cpt<=nlstate;cpt++) {
1.201 brouard 4621: 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> \
4622: <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 4623: }
1.192 brouard 4624: /* } /\* end i1 *\/ */
1.126 brouard 4625: }/* End k1 */
4626: fprintf(fichtm,"</ul>");
4627:
4628: fprintf(fichtm,"\
4629: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 brouard 4630: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
1.197 brouard 4631: - 95%% confidence intervals and Wald tests of the estimated parameters are in the log file.<br> \
4632: But because parameters are usually highly correlated (a higher incidence of disability \
4633: and a higher incidence of recovery can give very close observed transition) it might \
4634: be very useful to look not only at linear confidence intervals estimated from the \
4635: variances but at the covariance matrix. And instead of looking at the estimated coefficients \
4636: (parameters) of the logistic regression, it might be more meaningful to visualize the \
4637: covariance matrix of the one-step probabilities. \
4638: See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
1.126 brouard 4639:
1.193 brouard 4640: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4641: subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
1.126 brouard 4642: fprintf(fichtm,"\
4643: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4644: subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
1.126 brouard 4645:
4646: fprintf(fichtm,"\
4647: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4648: subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
1.126 brouard 4649: fprintf(fichtm,"\
4650: - 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): \
4651: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 4652: estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
1.126 brouard 4653: fprintf(fichtm,"\
4654: - (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): \
4655: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 4656: estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
1.126 brouard 4657: fprintf(fichtm,"\
1.128 brouard 4658: - 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 4659: estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
1.126 brouard 4660: fprintf(fichtm,"\
1.128 brouard 4661: - 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 4662: estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
1.126 brouard 4663: fprintf(fichtm,"\
4664: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
1.201 brouard 4665: subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
1.126 brouard 4666:
4667: /* if(popforecast==1) fprintf(fichtm,"\n */
4668: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4669: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4670: /* <br>",fileres,fileres,fileres,fileres); */
4671: /* else */
4672: /* 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); */
4673: fflush(fichtm);
4674: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4675:
1.145 brouard 4676: m=pow(2,cptcoveff);
1.126 brouard 4677: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4678:
4679: jj1=0;
4680: for(k1=1; k1<=m;k1++){
1.192 brouard 4681: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
1.126 brouard 4682: jj1++;
4683: if (cptcovn > 0) {
4684: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4685: for (cpt=1; cpt<=cptcoveff;cpt++)
1.198 brouard 4686: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
1.126 brouard 4687: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4688: }
4689: for(cpt=1; cpt<=nlstate;cpt++) {
4690: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
1.199 brouard 4691: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.svg <br>\
1.201 brouard 4692: <img src=\"%s_%d-%d.svg\">",cpt,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1);
1.126 brouard 4693: }
4694: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 4695: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4696: true period expectancies (those weighted with period prevalences are also\
4697: drawn in addition to the population based expectancies computed using\
1.201 brouard 4698: observed and cahotic prevalences: %s_%d.svg<br>\
4699: <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
1.192 brouard 4700: /* } /\* end i1 *\/ */
1.126 brouard 4701: }/* End k1 */
4702: fprintf(fichtm,"</ul>");
4703: fflush(fichtm);
4704: }
4705:
4706: /******************* Gnuplot file **************/
1.201 brouard 4707: void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 4708:
4709: char dirfileres[132],optfileres[132];
1.164 brouard 4710: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
1.130 brouard 4711: int ng=0;
1.201 brouard 4712: int vpopbased;
1.126 brouard 4713: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4714: /* printf("Problem with file %s",optionfilegnuplot); */
4715: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4716: /* } */
4717:
4718: /*#ifdef windows */
4719: fprintf(ficgp,"cd \"%s\" \n",pathc);
4720: /*#endif */
4721: m=pow(2,cptcoveff);
4722:
1.202 ! brouard 4723: /* Contribution to likelihood */
! 4724: /* Plot the probability implied in the likelihood */
! 4725: fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
! 4726: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
! 4727: /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
! 4728: fprintf(ficgp,"\nset ter png size 640, 480");
! 4729: /* good for mle=4 plot by number of matrix products.
! 4730: replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
! 4731: /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */
! 4732: /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
! 4733: fprintf(ficgp,"\nset out \"%s.png\";",subdirf2(optionfilefiname,"ILK_"));
! 4734: fprintf(ficgp,"\nplot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk));
! 4735: fprintf(ficgp,"\nreplot \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk));
! 4736: fprintf(ficgp,"\nset out\n");
! 4737: /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
! 4738:
1.126 brouard 4739: strcpy(dirfileres,optionfilefiname);
4740: strcpy(optfileres,"vpl");
4741: /* 1eme*/
1.201 brouard 4742: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files\n");
1.126 brouard 4743: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.145 brouard 4744: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
1.201 brouard 4745: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
4746: fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
1.126 brouard 4747: fprintf(ficgp,"set xlabel \"Age\" \n\
4748: set ylabel \"Probability\" \n\
1.199 brouard 4749: set ter svg size 640, 480\n\
1.201 brouard 4750: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
1.126 brouard 4751:
4752: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4753: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4754: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4755: }
1.201 brouard 4756: 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 4757: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4758: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4759: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4760: }
1.201 brouard 4761: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
1.126 brouard 4762: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4763: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4764: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4765: }
1.201 brouard 4766: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
4767: fprintf(ficgp,"\nset out \n");
4768: } /* k1 */
4769: } /* cpt */
1.126 brouard 4770: /*2 eme*/
1.153 brouard 4771: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
1.126 brouard 4772: for (k1=1; k1<= m ; k1 ++) {
1.201 brouard 4773: fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
4774: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
4775: if(vpopbased==0)
4776: fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
4777: else
4778: fprintf(ficgp,"\nreplot ");
4779: for (i=1; i<= nlstate+1 ; i ++) {
4780: k=2*i;
4781: 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);
4782: for (j=1; j<= nlstate+1 ; j ++) {
4783: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4784: else fprintf(ficgp," %%*lf (%%*lf)");
4785: }
4786: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
4787: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
4788: 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);
4789: for (j=1; j<= nlstate+1 ; j ++) {
4790: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4791: else fprintf(ficgp," %%*lf (%%*lf)");
4792: }
4793: fprintf(ficgp,"\" t\"\" w l lt 0,");
4794: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
4795: for (j=1; j<= nlstate+1 ; j ++) {
4796: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4797: else fprintf(ficgp," %%*lf (%%*lf)");
4798: }
4799: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4800: else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
4801: } /* state */
4802: } /* vpopbased */
4803: fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
4804: } /* k1 */
1.126 brouard 4805: /*3eme*/
4806:
4807: for (k1=1; k1<= m ; k1 ++) {
4808: for (cpt=1; cpt<= nlstate ; cpt ++) {
4809: /* k=2+nlstate*(2*cpt-2); */
4810: k=2+(nlstate+1)*(cpt-1);
1.201 brouard 4811: fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
1.199 brouard 4812: fprintf(ficgp,"set ter svg size 640, 480\n\
1.201 brouard 4813: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
1.126 brouard 4814: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4815: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4816: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4817: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4818: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4819: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4820:
4821: */
4822: for (i=1; i< nlstate ; i ++) {
1.201 brouard 4823: 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 4824: /* 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);*/
4825:
4826: }
1.201 brouard 4827: 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 4828: }
4829: }
4830:
1.201 brouard 4831: /* Survival functions (period) from state i in state j by initial state i */
4832: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
4833: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
4834: k=3;
4835: fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'lij' files, cov=%d state=%d",k1, cpt);
4836: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
4837: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
4838: set ter svg size 640, 480\n\
4839: unset log y\n\
4840: plot [%.f:%.f] ", ageminpar, agemaxpar);
4841: for (i=1; i<= nlstate ; i ++){
4842: if(i==1)
4843: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
4844: else
4845: fprintf(ficgp,", '' ");
4846: l=(nlstate+ndeath)*(i-1)+1;
4847: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
4848: for (j=2; j<= nlstate+ndeath ; j ++)
4849: fprintf(ficgp,"+$%d",k+l+j-1);
4850: fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
4851: } /* nlstate */
4852: fprintf(ficgp,"\nset out\n");
4853: } /* end cpt state*/
4854: } /* end covariate */
4855:
4856: /* Survival functions (period) from state i in state j by final state j */
1.202 ! brouard 4857: for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
1.201 brouard 4858: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
4859: k=3;
4860: 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);
4861: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
4862: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
4863: set ter svg size 640, 480\n\
4864: unset log y\n\
4865: plot [%.f:%.f] ", ageminpar, agemaxpar);
4866: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
4867: if(j==1)
4868: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
4869: else
4870: fprintf(ficgp,", '' ");
4871: l=(nlstate+ndeath)*(cpt-1) +j;
4872: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
4873: /* for (i=2; i<= nlstate+ndeath ; i ++) */
4874: /* fprintf(ficgp,"+$%d",k+l+i-1); */
4875: fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
4876: } /* nlstate */
4877: fprintf(ficgp,", '' ");
4878: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
4879: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
4880: l=(nlstate+ndeath)*(cpt-1) +j;
4881: if(j < nlstate)
4882: fprintf(ficgp,"$%d +",k+l);
4883: else
4884: fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
4885: }
4886: fprintf(ficgp,"\nset out\n");
4887: } /* end cpt state*/
4888: } /* end covariate */
4889:
1.202 ! brouard 4890: /* CV preval stable (period) for each covariate */
! 4891: for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
1.153 brouard 4892: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.126 brouard 4893: k=3;
1.153 brouard 4894: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
1.201 brouard 4895: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
1.126 brouard 4896: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.199 brouard 4897: set ter svg size 640, 480\n\
1.126 brouard 4898: unset log y\n\
1.153 brouard 4899: plot [%.f:%.f] ", ageminpar, agemaxpar);
4900: for (i=1; i<= nlstate ; i ++){
4901: if(i==1)
1.201 brouard 4902: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
1.153 brouard 4903: else
4904: fprintf(ficgp,", '' ");
1.154 brouard 4905: l=(nlstate+ndeath)*(i-1)+1;
4906: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
1.201 brouard 4907: for (j=2; j<= nlstate ; j ++)
4908: fprintf(ficgp,"+$%d",k+l+j-1);
1.153 brouard 4909: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
4910: } /* nlstate */
1.201 brouard 4911: fprintf(ficgp,"\nset out\n");
1.153 brouard 4912: } /* end cpt state*/
4913: } /* end covariate */
1.201 brouard 4914:
1.126 brouard 4915: /* proba elementaires */
1.187 brouard 4916: fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
1.126 brouard 4917: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 4918: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 4919: for(k=1; k <=(nlstate+ndeath); k++){
4920: if (k != i) {
1.187 brouard 4921: fprintf(ficgp,"# current state %d\n",k);
1.126 brouard 4922: for(j=1; j <=ncovmodel; j++){
1.187 brouard 4923: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
1.126 brouard 4924: jk++;
4925: }
1.187 brouard 4926: fprintf(ficgp,"\n");
1.126 brouard 4927: }
4928: }
4929: }
1.187 brouard 4930: fprintf(ficgp,"##############\n#\n");
4931:
1.145 brouard 4932: /*goto avoid;*/
1.200 brouard 4933: fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");
1.187 brouard 4934: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
4935: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
4936: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
4937: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
4938: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
4939: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
4940: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
4941: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
4942: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
4943: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
4944: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
4945: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
4946: fprintf(ficgp,"#\n");
1.201 brouard 4947: for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
1.187 brouard 4948: fprintf(ficgp,"# ng=%d\n",ng);
4949: fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);
1.126 brouard 4950: for(jk=1; jk <=m; jk++) {
1.187 brouard 4951: fprintf(ficgp,"# jk=%d\n",jk);
1.201 brouard 4952: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
4953: fprintf(ficgp,"\nset ter svg size 640, 480 ");
4954: if (ng==1){
4955: fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
4956: fprintf(ficgp,"\nunset log y");
4957: }else if (ng==2){
4958: fprintf(ficgp,"\nset ylabel \"Probability\"\n");
4959: fprintf(ficgp,"\nset log y");
4960: }else if (ng==3){
1.126 brouard 4961: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
1.201 brouard 4962: fprintf(ficgp,"\nset log y");
4963: }else
4964: fprintf(ficgp,"\nunset title ");
4965: fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar);
1.126 brouard 4966: i=1;
4967: for(k2=1; k2<=nlstate; k2++) {
4968: k3=i;
4969: for(k=1; k<=(nlstate+ndeath); k++) {
4970: if (k != k2){
1.201 brouard 4971: switch( ng) {
4972: case 1:
1.187 brouard 4973: if(nagesqr==0)
1.201 brouard 4974: fprintf(ficgp," p%d+p%d*x",i,i+1);
1.187 brouard 4975: else /* nagesqr =1 */
1.201 brouard 4976: fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
4977: break;
4978: case 2: /* ng=2 */
1.187 brouard 4979: if(nagesqr==0)
4980: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
4981: else /* nagesqr =1 */
1.201 brouard 4982: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
4983: break;
4984: case 3:
4985: if(nagesqr==0)
4986: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
4987: else /* nagesqr =1 */
4988: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
4989: break;
4990: }
1.141 brouard 4991: ij=1;/* To be checked else nbcode[0][0] wrong */
1.187 brouard 4992: for(j=3; j <=ncovmodel-nagesqr; j++) {
1.197 brouard 4993: /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
4994: if(ij <=cptcovage) { /* Bug valgrind */
4995: if((j-2)==Tage[ij]) { /* Bug valgrind */
1.200 brouard 4996: fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
4997: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
1.197 brouard 4998: ij++;
4999: }
1.186 brouard 5000: }
5001: else
1.198 brouard 5002: fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
1.126 brouard 5003: }
1.201 brouard 5004: if(ng != 1){
5005: fprintf(ficgp,")/(1");
1.126 brouard 5006:
1.201 brouard 5007: for(k1=1; k1 <=nlstate; k1++){
5008: if(nagesqr==0)
5009: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
5010: else /* nagesqr =1 */
5011: 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);
5012:
5013: ij=1;
5014: for(j=3; j <=ncovmodel-nagesqr; j++){
5015: if(ij <=cptcovage) { /* Bug valgrind */
5016: if((j-2)==Tage[ij]) { /* Bug valgrind */
5017: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
5018: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
5019: ij++;
5020: }
1.197 brouard 5021: }
1.201 brouard 5022: else
5023: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
1.186 brouard 5024: }
1.201 brouard 5025: fprintf(ficgp,")");
1.126 brouard 5026: }
5027: fprintf(ficgp,")");
1.201 brouard 5028: if(ng ==2)
5029: fprintf(ficgp," t \"p%d%d\" ", k2,k);
5030: else /* ng= 3 */
5031: fprintf(ficgp," t \"i%d%d\" ", k2,k);
5032: }else{ /* end ng <> 1 */
5033: fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
1.126 brouard 5034: }
5035: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
5036: i=i+ncovmodel;
5037: }
5038: } /* end k */
5039: } /* end k2 */
1.201 brouard 5040: fprintf(ficgp,"\n set out\n");
1.126 brouard 5041: } /* end jk */
5042: } /* end ng */
1.164 brouard 5043: /* avoid: */
1.126 brouard 5044: fflush(ficgp);
5045: } /* end gnuplot */
5046:
5047:
5048: /*************** Moving average **************/
5049: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
5050:
5051: int i, cpt, cptcod;
5052: int modcovmax =1;
5053: int mobilavrange, mob;
5054: double age;
5055:
5056: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
5057: a covariate has 2 modalities */
5058: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
5059:
5060: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
5061: if(mobilav==1) mobilavrange=5; /* default */
5062: else mobilavrange=mobilav;
5063: for (age=bage; age<=fage; age++)
5064: for (i=1; i<=nlstate;i++)
5065: for (cptcod=1;cptcod<=modcovmax;cptcod++)
5066: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
5067: /* We keep the original values on the extreme ages bage, fage and for
5068: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
5069: we use a 5 terms etc. until the borders are no more concerned.
5070: */
5071: for (mob=3;mob <=mobilavrange;mob=mob+2){
5072: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
5073: for (i=1; i<=nlstate;i++){
5074: for (cptcod=1;cptcod<=modcovmax;cptcod++){
5075: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
5076: for (cpt=1;cpt<=(mob-1)/2;cpt++){
5077: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
5078: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
5079: }
5080: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
5081: }
5082: }
5083: }/* end age */
5084: }/* end mob */
5085: }else return -1;
5086: return 0;
5087: }/* End movingaverage */
5088:
5089:
5090: /************** Forecasting ******************/
1.169 brouard 5091: 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 5092: /* proj1, year, month, day of starting projection
5093: agemin, agemax range of age
5094: dateprev1 dateprev2 range of dates during which prevalence is computed
5095: anproj2 year of en of projection (same day and month as proj1).
5096: */
1.164 brouard 5097: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
1.126 brouard 5098: double agec; /* generic age */
5099: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
5100: double *popeffectif,*popcount;
5101: double ***p3mat;
5102: double ***mobaverage;
5103: char fileresf[FILENAMELENGTH];
5104:
5105: agelim=AGESUP;
5106: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5107:
1.201 brouard 5108: strcpy(fileresf,"F_");
5109: strcat(fileresf,fileresu);
1.126 brouard 5110: if((ficresf=fopen(fileresf,"w"))==NULL) {
5111: printf("Problem with forecast resultfile: %s\n", fileresf);
5112: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
5113: }
5114: printf("Computing forecasting: result on file '%s' \n", fileresf);
5115: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
5116:
5117: if (cptcoveff==0) ncodemax[cptcoveff]=1;
5118:
5119: if (mobilav!=0) {
5120: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5121: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
5122: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5123: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5124: }
5125: }
5126:
5127: stepsize=(int) (stepm+YEARM-1)/YEARM;
5128: if (stepm<=12) stepsize=1;
5129: if(estepm < stepm){
5130: printf ("Problem %d lower than %d\n",estepm, stepm);
5131: }
5132: else hstepm=estepm;
5133:
5134: hstepm=hstepm/stepm;
5135: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
5136: fractional in yp1 */
5137: anprojmean=yp;
5138: yp2=modf((yp1*12),&yp);
5139: mprojmean=yp;
5140: yp1=modf((yp2*30.5),&yp);
5141: jprojmean=yp;
5142: if(jprojmean==0) jprojmean=1;
5143: if(mprojmean==0) jprojmean=1;
5144:
5145: i1=cptcoveff;
5146: if (cptcovn < 1){i1=1;}
5147:
5148: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
5149:
5150: fprintf(ficresf,"#****** Routine prevforecast **\n");
5151:
5152: /* if (h==(int)(YEARM*yearp)){ */
5153: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
5154: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
5155: k=k+1;
5156: fprintf(ficresf,"\n#******");
5157: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 5158: fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 5159: }
5160: fprintf(ficresf,"******\n");
5161: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
5162: for(j=1; j<=nlstate+ndeath;j++){
5163: for(i=1; i<=nlstate;i++)
5164: fprintf(ficresf," p%d%d",i,j);
5165: fprintf(ficresf," p.%d",j);
5166: }
5167: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
5168: fprintf(ficresf,"\n");
5169: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
5170:
5171: for (agec=fage; agec>=(ageminpar-1); agec--){
5172: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
5173: nhstepm = nhstepm/hstepm;
5174: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5175: oldm=oldms;savm=savms;
5176: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
5177:
5178: for (h=0; h<=nhstepm; h++){
5179: if (h*hstepm/YEARM*stepm ==yearp) {
5180: fprintf(ficresf,"\n");
5181: for(j=1;j<=cptcoveff;j++)
1.198 brouard 5182: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 5183: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
5184: }
5185: for(j=1; j<=nlstate+ndeath;j++) {
5186: ppij=0.;
5187: for(i=1; i<=nlstate;i++) {
5188: if (mobilav==1)
5189: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
5190: else {
5191: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
5192: }
5193: if (h*hstepm/YEARM*stepm== yearp) {
5194: fprintf(ficresf," %.3f", p3mat[i][j][h]);
5195: }
5196: } /* end i */
5197: if (h*hstepm/YEARM*stepm==yearp) {
5198: fprintf(ficresf," %.3f", ppij);
5199: }
5200: }/* end j */
5201: } /* end h */
5202: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5203: } /* end agec */
5204: } /* end yearp */
5205: } /* end cptcod */
5206: } /* end cptcov */
5207:
5208: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5209:
5210: fclose(ficresf);
5211: }
5212:
5213: /************** Forecasting *****not tested NB*************/
1.169 brouard 5214: 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 5215:
5216: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
5217: int *popage;
5218: double calagedatem, agelim, kk1, kk2;
5219: double *popeffectif,*popcount;
5220: double ***p3mat,***tabpop,***tabpopprev;
5221: double ***mobaverage;
5222: char filerespop[FILENAMELENGTH];
5223:
5224: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5225: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5226: agelim=AGESUP;
5227: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
5228:
5229: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5230:
5231:
1.201 brouard 5232: strcpy(filerespop,"POP_");
5233: strcat(filerespop,fileresu);
1.126 brouard 5234: if((ficrespop=fopen(filerespop,"w"))==NULL) {
5235: printf("Problem with forecast resultfile: %s\n", filerespop);
5236: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
5237: }
5238: printf("Computing forecasting: result on file '%s' \n", filerespop);
5239: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
5240:
5241: if (cptcoveff==0) ncodemax[cptcoveff]=1;
5242:
5243: if (mobilav!=0) {
5244: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5245: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
5246: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5247: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5248: }
5249: }
5250:
5251: stepsize=(int) (stepm+YEARM-1)/YEARM;
5252: if (stepm<=12) stepsize=1;
5253:
5254: agelim=AGESUP;
5255:
5256: hstepm=1;
5257: hstepm=hstepm/stepm;
5258:
5259: if (popforecast==1) {
5260: if((ficpop=fopen(popfile,"r"))==NULL) {
5261: printf("Problem with population file : %s\n",popfile);exit(0);
5262: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
5263: }
5264: popage=ivector(0,AGESUP);
5265: popeffectif=vector(0,AGESUP);
5266: popcount=vector(0,AGESUP);
5267:
5268: i=1;
5269: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
5270:
5271: imx=i;
5272: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
5273: }
5274:
5275: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
5276: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
5277: k=k+1;
5278: fprintf(ficrespop,"\n#******");
5279: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 5280: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 5281: }
5282: fprintf(ficrespop,"******\n");
5283: fprintf(ficrespop,"# Age");
5284: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
5285: if (popforecast==1) fprintf(ficrespop," [Population]");
5286:
5287: for (cpt=0; cpt<=0;cpt++) {
5288: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5289:
5290: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5291: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5292: nhstepm = nhstepm/hstepm;
5293:
5294: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5295: oldm=oldms;savm=savms;
5296: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5297:
5298: for (h=0; h<=nhstepm; h++){
5299: if (h==(int) (calagedatem+YEARM*cpt)) {
5300: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5301: }
5302: for(j=1; j<=nlstate+ndeath;j++) {
5303: kk1=0.;kk2=0;
5304: for(i=1; i<=nlstate;i++) {
5305: if (mobilav==1)
5306: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
5307: else {
5308: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
5309: }
5310: }
5311: if (h==(int)(calagedatem+12*cpt)){
5312: tabpop[(int)(agedeb)][j][cptcod]=kk1;
5313: /*fprintf(ficrespop," %.3f", kk1);
5314: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
5315: }
5316: }
5317: for(i=1; i<=nlstate;i++){
5318: kk1=0.;
5319: for(j=1; j<=nlstate;j++){
5320: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
5321: }
5322: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
5323: }
5324:
5325: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
5326: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
5327: }
5328: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5329: }
5330: }
5331:
5332: /******/
5333:
5334: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
5335: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5336: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5337: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5338: nhstepm = nhstepm/hstepm;
5339:
5340: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5341: oldm=oldms;savm=savms;
5342: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5343: for (h=0; h<=nhstepm; h++){
5344: if (h==(int) (calagedatem+YEARM*cpt)) {
5345: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5346: }
5347: for(j=1; j<=nlstate+ndeath;j++) {
5348: kk1=0.;kk2=0;
5349: for(i=1; i<=nlstate;i++) {
5350: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
5351: }
5352: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
5353: }
5354: }
5355: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5356: }
5357: }
5358: }
5359: }
5360:
5361: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5362:
5363: if (popforecast==1) {
5364: free_ivector(popage,0,AGESUP);
5365: free_vector(popeffectif,0,AGESUP);
5366: free_vector(popcount,0,AGESUP);
5367: }
5368: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5369: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5370: fclose(ficrespop);
5371: } /* End of popforecast */
5372:
5373: int fileappend(FILE *fichier, char *optionfich)
5374: {
5375: if((fichier=fopen(optionfich,"a"))==NULL) {
5376: printf("Problem with file: %s\n", optionfich);
5377: fprintf(ficlog,"Problem with file: %s\n", optionfich);
5378: return (0);
5379: }
5380: fflush(fichier);
5381: return (1);
5382: }
5383:
5384:
5385: /**************** function prwizard **********************/
5386: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
5387: {
5388:
5389: /* Wizard to print covariance matrix template */
5390:
1.164 brouard 5391: char ca[32], cb[32];
5392: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 5393: int numlinepar;
5394:
5395: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5396: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5397: for(i=1; i <=nlstate; i++){
5398: jj=0;
5399: for(j=1; j <=nlstate+ndeath; j++){
5400: if(j==i) continue;
5401: jj++;
5402: /*ca[0]= k+'a'-1;ca[1]='\0';*/
5403: printf("%1d%1d",i,j);
5404: fprintf(ficparo,"%1d%1d",i,j);
5405: for(k=1; k<=ncovmodel;k++){
5406: /* printf(" %lf",param[i][j][k]); */
5407: /* fprintf(ficparo," %lf",param[i][j][k]); */
5408: printf(" 0.");
5409: fprintf(ficparo," 0.");
5410: }
5411: printf("\n");
5412: fprintf(ficparo,"\n");
5413: }
5414: }
5415: printf("# Scales (for hessian or gradient estimation)\n");
5416: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
5417: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
5418: for(i=1; i <=nlstate; i++){
5419: jj=0;
5420: for(j=1; j <=nlstate+ndeath; j++){
5421: if(j==i) continue;
5422: jj++;
5423: fprintf(ficparo,"%1d%1d",i,j);
5424: printf("%1d%1d",i,j);
5425: fflush(stdout);
5426: for(k=1; k<=ncovmodel;k++){
5427: /* printf(" %le",delti3[i][j][k]); */
5428: /* fprintf(ficparo," %le",delti3[i][j][k]); */
5429: printf(" 0.");
5430: fprintf(ficparo," 0.");
5431: }
5432: numlinepar++;
5433: printf("\n");
5434: fprintf(ficparo,"\n");
5435: }
5436: }
5437: printf("# Covariance matrix\n");
5438: /* # 121 Var(a12)\n\ */
5439: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5440: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5441: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5442: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5443: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5444: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5445: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5446: fflush(stdout);
5447: fprintf(ficparo,"# Covariance matrix\n");
5448: /* # 121 Var(a12)\n\ */
5449: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5450: /* # ...\n\ */
5451: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5452:
5453: for(itimes=1;itimes<=2;itimes++){
5454: jj=0;
5455: for(i=1; i <=nlstate; i++){
5456: for(j=1; j <=nlstate+ndeath; j++){
5457: if(j==i) continue;
5458: for(k=1; k<=ncovmodel;k++){
5459: jj++;
5460: ca[0]= k+'a'-1;ca[1]='\0';
5461: if(itimes==1){
5462: printf("#%1d%1d%d",i,j,k);
5463: fprintf(ficparo,"#%1d%1d%d",i,j,k);
5464: }else{
5465: printf("%1d%1d%d",i,j,k);
5466: fprintf(ficparo,"%1d%1d%d",i,j,k);
5467: /* printf(" %.5le",matcov[i][j]); */
5468: }
5469: ll=0;
5470: for(li=1;li <=nlstate; li++){
5471: for(lj=1;lj <=nlstate+ndeath; lj++){
5472: if(lj==li) continue;
5473: for(lk=1;lk<=ncovmodel;lk++){
5474: ll++;
5475: if(ll<=jj){
5476: cb[0]= lk +'a'-1;cb[1]='\0';
5477: if(ll<jj){
5478: if(itimes==1){
5479: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5480: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5481: }else{
5482: printf(" 0.");
5483: fprintf(ficparo," 0.");
5484: }
5485: }else{
5486: if(itimes==1){
5487: printf(" Var(%s%1d%1d)",ca,i,j);
5488: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
5489: }else{
5490: printf(" 0.");
5491: fprintf(ficparo," 0.");
5492: }
5493: }
5494: }
5495: } /* end lk */
5496: } /* end lj */
5497: } /* end li */
5498: printf("\n");
5499: fprintf(ficparo,"\n");
5500: numlinepar++;
5501: } /* end k*/
5502: } /*end j */
5503: } /* end i */
5504: } /* end itimes */
5505:
5506: } /* end of prwizard */
5507: /******************* Gompertz Likelihood ******************************/
5508: double gompertz(double x[])
5509: {
5510: double A,B,L=0.0,sump=0.,num=0.;
5511: int i,n=0; /* n is the size of the sample */
5512:
5513: for (i=0;i<=imx-1 ; i++) {
5514: sump=sump+weight[i];
5515: /* sump=sump+1;*/
5516: num=num+1;
5517: }
5518:
5519:
5520: /* for (i=0; i<=imx; i++)
5521: 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]);*/
5522:
5523: for (i=1;i<=imx ; i++)
5524: {
5525: if (cens[i] == 1 && wav[i]>1)
5526: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
5527:
5528: if (cens[i] == 0 && wav[i]>1)
5529: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
5530: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
5531:
5532: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5533: if (wav[i] > 1 ) { /* ??? */
5534: L=L+A*weight[i];
5535: /* 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]);*/
5536: }
5537: }
5538:
5539: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5540:
5541: return -2*L*num/sump;
5542: }
5543:
1.136 brouard 5544: #ifdef GSL
5545: /******************* Gompertz_f Likelihood ******************************/
5546: double gompertz_f(const gsl_vector *v, void *params)
5547: {
5548: double A,B,LL=0.0,sump=0.,num=0.;
5549: double *x= (double *) v->data;
5550: int i,n=0; /* n is the size of the sample */
5551:
5552: for (i=0;i<=imx-1 ; i++) {
5553: sump=sump+weight[i];
5554: /* sump=sump+1;*/
5555: num=num+1;
5556: }
5557:
5558:
5559: /* for (i=0; i<=imx; i++)
5560: 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]);*/
5561: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
5562: for (i=1;i<=imx ; i++)
5563: {
5564: if (cens[i] == 1 && wav[i]>1)
5565: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
5566:
5567: if (cens[i] == 0 && wav[i]>1)
5568: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
5569: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
5570:
5571: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5572: if (wav[i] > 1 ) { /* ??? */
5573: LL=LL+A*weight[i];
5574: /* 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]);*/
5575: }
5576: }
5577:
5578: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5579: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
5580:
5581: return -2*LL*num/sump;
5582: }
5583: #endif
5584:
1.126 brouard 5585: /******************* Printing html file ***********/
1.201 brouard 5586: void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 5587: int lastpass, int stepm, int weightopt, char model[],\
5588: int imx, double p[],double **matcov,double agemortsup){
5589: int i,k;
5590:
5591: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
5592: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
5593: for (i=1;i<=2;i++)
5594: 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 5595: fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
1.126 brouard 5596: fprintf(fichtm,"</ul>");
5597:
5598: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
5599:
5600: 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>");
5601:
5602: for (k=agegomp;k<(agemortsup-2);k++)
5603: 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]);
5604:
5605:
5606: fflush(fichtm);
5607: }
5608:
5609: /******************* Gnuplot file **************/
1.201 brouard 5610: void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 5611:
5612: char dirfileres[132],optfileres[132];
1.164 brouard 5613:
1.126 brouard 5614: int ng;
5615:
5616:
5617: /*#ifdef windows */
5618: fprintf(ficgp,"cd \"%s\" \n",pathc);
5619: /*#endif */
5620:
5621:
5622: strcpy(dirfileres,optionfilefiname);
5623: strcpy(optfileres,"vpl");
1.199 brouard 5624: fprintf(ficgp,"set out \"graphmort.svg\"\n ");
1.126 brouard 5625: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.199 brouard 5626: fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
1.145 brouard 5627: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 5628: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
5629:
5630: }
5631:
1.136 brouard 5632: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
5633: {
1.126 brouard 5634:
1.136 brouard 5635: /*-------- data file ----------*/
5636: FILE *fic;
5637: char dummy[]=" ";
1.164 brouard 5638: int i=0, j=0, n=0;
1.136 brouard 5639: int linei, month, year,iout;
5640: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 5641: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 5642: char *stratrunc;
5643: int lstra;
1.126 brouard 5644:
5645:
1.136 brouard 5646: if((fic=fopen(datafile,"r"))==NULL) {
1.195 brouard 5647: printf("Problem while opening datafile: %s\n", datafile);fflush(stdout);
5648: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);fflush(ficlog);return 1;
1.136 brouard 5649: }
1.126 brouard 5650:
1.136 brouard 5651: i=1;
5652: linei=0;
5653: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
5654: linei=linei+1;
5655: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
5656: if(line[j] == '\t')
5657: line[j] = ' ';
5658: }
5659: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
5660: ;
5661: };
5662: line[j+1]=0; /* Trims blanks at end of line */
5663: if(line[0]=='#'){
5664: fprintf(ficlog,"Comment line\n%s\n",line);
5665: printf("Comment line\n%s\n",line);
5666: continue;
5667: }
5668: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 5669: strcpy(line, linetmp);
1.136 brouard 5670:
1.126 brouard 5671:
1.136 brouard 5672: for (j=maxwav;j>=1;j--){
1.137 brouard 5673: cutv(stra, strb, line, ' ');
1.136 brouard 5674: if(strb[0]=='.') { /* Missing status */
5675: lval=-1;
5676: }else{
5677: errno=0;
5678: lval=strtol(strb,&endptr,10);
5679: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
5680: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5681: 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);
5682: 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 5683: return 1;
5684: }
5685: }
5686: s[j][i]=lval;
5687:
5688: strcpy(line,stra);
5689: cutv(stra, strb,line,' ');
1.169 brouard 5690: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5691: }
1.169 brouard 5692: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5693: month=99;
5694: year=9999;
5695: }else{
1.141 brouard 5696: 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);
5697: 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 5698: return 1;
5699: }
5700: anint[j][i]= (double) year;
5701: mint[j][i]= (double)month;
5702: strcpy(line,stra);
5703: } /* ENd Waves */
5704:
5705: cutv(stra, strb,line,' ');
1.169 brouard 5706: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5707: }
1.169 brouard 5708: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5709: month=99;
5710: year=9999;
5711: }else{
1.141 brouard 5712: 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);
5713: 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 5714: return 1;
5715: }
5716: andc[i]=(double) year;
5717: moisdc[i]=(double) month;
5718: strcpy(line,stra);
5719:
5720: cutv(stra, strb,line,' ');
1.169 brouard 5721: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5722: }
1.169 brouard 5723: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 5724: month=99;
5725: year=9999;
5726: }else{
1.141 brouard 5727: 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);
5728: 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 5729: return 1;
5730: }
5731: if (year==9999) {
1.141 brouard 5732: 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);
5733: 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 5734: return 1;
1.126 brouard 5735:
1.136 brouard 5736: }
5737: annais[i]=(double)(year);
5738: moisnais[i]=(double)(month);
5739: strcpy(line,stra);
5740:
5741: cutv(stra, strb,line,' ');
5742: errno=0;
5743: dval=strtod(strb,&endptr);
5744: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5745: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
5746: 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 5747: fflush(ficlog);
5748: return 1;
5749: }
5750: weight[i]=dval;
5751: strcpy(line,stra);
5752:
5753: for (j=ncovcol;j>=1;j--){
5754: cutv(stra, strb,line,' ');
5755: if(strb[0]=='.') { /* Missing status */
5756: lval=-1;
5757: }else{
5758: errno=0;
5759: lval=strtol(strb,&endptr,10);
5760: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5761: 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);
5762: 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 5763: return 1;
5764: }
5765: }
5766: if(lval <-1 || lval >1){
1.141 brouard 5767: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5768: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5769: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5770: For example, for multinomial values like 1, 2 and 3,\n \
5771: build V1=0 V2=0 for the reference value (1),\n \
5772: V1=1 V2=0 for (2) \n \
5773: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5774: output of IMaCh is often meaningless.\n \
5775: Exiting.\n",lval,linei, i,line,j);
1.141 brouard 5776: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5777: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5778: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5779: For example, for multinomial values like 1, 2 and 3,\n \
5780: build V1=0 V2=0 for the reference value (1),\n \
5781: V1=1 V2=0 for (2) \n \
5782: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5783: output of IMaCh is often meaningless.\n \
5784: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
5785: return 1;
5786: }
5787: covar[j][i]=(double)(lval);
5788: strcpy(line,stra);
5789: }
5790: lstra=strlen(stra);
5791:
5792: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
5793: stratrunc = &(stra[lstra-9]);
5794: num[i]=atol(stratrunc);
5795: }
5796: else
5797: num[i]=atol(stra);
5798: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
5799: 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;}*/
5800:
5801: i=i+1;
5802: } /* End loop reading data */
1.126 brouard 5803:
1.136 brouard 5804: *imax=i-1; /* Number of individuals */
5805: fclose(fic);
5806:
5807: return (0);
1.164 brouard 5808: /* endread: */
1.136 brouard 5809: printf("Exiting readdata: ");
5810: fclose(fic);
5811: return (1);
1.126 brouard 5812:
5813:
5814:
1.136 brouard 5815: }
1.145 brouard 5816: void removespace(char *str) {
5817: char *p1 = str, *p2 = str;
5818: do
5819: while (*p2 == ' ')
5820: p2++;
1.169 brouard 5821: while (*p1++ == *p2++);
1.145 brouard 5822: }
5823:
5824: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
1.187 brouard 5825: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
5826: * - nagesqr = 1 if age*age in the model, otherwise 0.
5827: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
5828: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
1.145 brouard 5829: * - cptcovage number of covariates with age*products =2
5830: * - cptcovs number of simple covariates
5831: * - 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
5832: * which is a new column after the 9 (ncovcol) variables.
5833: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
5834: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
5835: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
5836: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
5837: */
1.136 brouard 5838: {
1.145 brouard 5839: int i, j, k, ks;
1.164 brouard 5840: int j1, k1, k2;
1.136 brouard 5841: char modelsav[80];
1.145 brouard 5842: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 5843: char *strpt;
1.136 brouard 5844:
1.145 brouard 5845: /*removespace(model);*/
1.136 brouard 5846: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 5847: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 5848: if (strstr(model,"AGE") !=0){
1.192 brouard 5849: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
5850: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 5851: return 1;
5852: }
1.141 brouard 5853: if (strstr(model,"v") !=0){
5854: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
5855: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
5856: return 1;
5857: }
1.187 brouard 5858: strcpy(modelsav,model);
5859: if ((strpt=strstr(model,"age*age")) !=0){
5860: printf(" strpt=%s, model=%s\n",strpt, model);
5861: if(strpt != model){
5862: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 5863: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 5864: corresponding column of parameters.\n",model);
5865: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 5866: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 5867: corresponding column of parameters.\n",model); fflush(ficlog);
5868: return 1;
5869: }
5870:
5871: nagesqr=1;
5872: if (strstr(model,"+age*age") !=0)
5873: substrchaine(modelsav, model, "+age*age");
5874: else if (strstr(model,"age*age+") !=0)
5875: substrchaine(modelsav, model, "age*age+");
5876: else
5877: substrchaine(modelsav, model, "age*age");
5878: }else
5879: nagesqr=0;
5880: if (strlen(modelsav) >1){
5881: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
5882: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
5883: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2 */
5884: cptcovt= j+1; /* Number of total covariates in the model, not including
5885: * cst, age and age*age
5886: * V1+V1*age+ V3 + V3*V4+age*age=> 4*/
5887: /* including age products which are counted in cptcovage.
5888: * but the covariates which are products must be treated
5889: * separately: ncovn=4- 2=2 (V1+V3). */
5890: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
5891: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
5892:
5893:
5894: /* Design
5895: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
5896: * < ncovcol=8 >
5897: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
5898: * k= 1 2 3 4 5 6 7 8
5899: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
5900: * covar[k,i], value of kth covariate if not including age for individual i:
5901: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
5902: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
5903: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
5904: * Tage[++cptcovage]=k
5905: * if products, new covar are created after ncovcol with k1
5906: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
5907: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
5908: * 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
5909: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
5910: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
5911: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
5912: * < ncovcol=8 >
5913: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
5914: * k= 1 2 3 4 5 6 7 8 9 10 11 12
5915: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
5916: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5917: * p Tprod[1]@2={ 6, 5}
5918: *p Tvard[1][1]@4= {7, 8, 5, 6}
5919: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
5920: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
5921: *How to reorganize?
5922: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
5923: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5924: * {2, 1, 4, 8, 5, 6, 3, 7}
5925: * Struct []
5926: */
1.145 brouard 5927:
1.187 brouard 5928: /* This loop fills the array Tvar from the string 'model'.*/
5929: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
5930: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
5931: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
5932: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
5933: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
5934: /* k=1 Tvar[1]=2 (from V2) */
5935: /* k=5 Tvar[5] */
5936: /* for (k=1; k<=cptcovn;k++) { */
1.198 brouard 5937: /* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.187 brouard 5938: /* } */
1.198 brouard 5939: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
1.187 brouard 5940: /*
5941: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
5942: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
1.145 brouard 5943: Tvar[k]=0;
1.187 brouard 5944: cptcovage=0;
5945: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
5946: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5947: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
5948: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
5949: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5950: /*scanf("%d",i);*/
5951: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
5952: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
5953: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
5954: /* covar is not filled and then is empty */
5955: cptcovprod--;
5956: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
5957: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
5958: cptcovage++; /* Sums the number of covariates which include age as a product */
5959: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
5960: /*printf("stre=%s ", stre);*/
5961: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
5962: cptcovprod--;
5963: cutl(stre,strb,strc,'V');
5964: Tvar[k]=atoi(stre);
5965: cptcovage++;
5966: Tage[cptcovage]=k;
5967: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
5968: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
5969: cptcovn++;
5970: cptcovprodnoage++;k1++;
5971: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5972: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
5973: because this model-covariate is a construction we invent a new column
5974: ncovcol + k1
5975: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
5976: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
5977: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
5978: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
5979: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
5980: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
5981: k2=k2+2;
5982: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
5983: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
5984: for (i=1; i<=lastobs;i++){
5985: /* Computes the new covariate which is a product of
5986: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
5987: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
5988: }
5989: } /* End age is not in the model */
5990: } /* End if model includes a product */
5991: else { /* no more sum */
5992: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5993: /* scanf("%d",i);*/
5994: cutl(strd,strc,strb,'V');
5995: ks++; /**< Number of simple covariates */
1.145 brouard 5996: cptcovn++;
1.187 brouard 5997: Tvar[k]=atoi(strd);
5998: }
5999: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
6000: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
6001: scanf("%d",i);*/
6002: } /* end of loop + on total covariates */
6003: } /* end if strlen(modelsave == 0) age*age might exist */
6004: } /* end if strlen(model == 0) */
1.136 brouard 6005:
6006: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
6007: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
6008:
6009: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
6010: printf("cptcovprod=%d ", cptcovprod);
6011: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
6012:
6013: scanf("%d ",i);*/
6014:
6015:
1.137 brouard 6016: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 6017: /*endread:*/
1.136 brouard 6018: printf("Exiting decodemodel: ");
6019: return (1);
6020: }
6021:
1.169 brouard 6022: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.136 brouard 6023: {
6024: int i, m;
6025:
6026: for (i=1; i<=imx; i++) {
6027: for(m=2; (m<= maxwav); m++) {
6028: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
6029: anint[m][i]=9999;
6030: s[m][i]=-1;
6031: }
6032: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169 brouard 6033: *nberr = *nberr + 1;
6034: 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);
6035: 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 6036: s[m][i]=-1;
6037: }
6038: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 6039: (*nberr)++;
1.136 brouard 6040: 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]);
6041: 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]);
6042: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
6043: }
6044: }
6045: }
6046:
6047: for (i=1; i<=imx; i++) {
6048: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
6049: for(m=firstpass; (m<= lastpass); m++){
6050: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
6051: if (s[m][i] >= nlstate+1) {
1.169 brouard 6052: if(agedc[i]>0){
6053: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 6054: agev[m][i]=agedc[i];
6055: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 6056: }else {
1.136 brouard 6057: if ((int)andc[i]!=9999){
6058: nbwarn++;
6059: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
6060: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
6061: agev[m][i]=-1;
6062: }
6063: }
1.169 brouard 6064: } /* agedc > 0 */
1.136 brouard 6065: }
6066: else if(s[m][i] !=9){ /* Standard case, age in fractional
6067: years but with the precision of a month */
6068: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
6069: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
6070: agev[m][i]=1;
6071: else if(agev[m][i] < *agemin){
6072: *agemin=agev[m][i];
6073: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
6074: }
6075: else if(agev[m][i] >*agemax){
6076: *agemax=agev[m][i];
1.156 brouard 6077: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 6078: }
6079: /*agev[m][i]=anint[m][i]-annais[i];*/
6080: /* agev[m][i] = age[i]+2*m;*/
6081: }
6082: else { /* =9 */
6083: agev[m][i]=1;
6084: s[m][i]=-1;
6085: }
6086: }
6087: else /*= 0 Unknown */
6088: agev[m][i]=1;
6089: }
6090:
6091: }
6092: for (i=1; i<=imx; i++) {
6093: for(m=firstpass; (m<=lastpass); m++){
6094: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 6095: (*nberr)++;
1.136 brouard 6096: 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);
6097: 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);
6098: return 1;
6099: }
6100: }
6101: }
6102:
6103: /*for (i=1; i<=imx; i++){
6104: for (m=firstpass; (m<lastpass); m++){
6105: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
6106: }
6107:
6108: }*/
6109:
6110:
1.139 brouard 6111: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
6112: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 6113:
6114: return (0);
1.164 brouard 6115: /* endread:*/
1.136 brouard 6116: printf("Exiting calandcheckages: ");
6117: return (1);
6118: }
6119:
1.172 brouard 6120: #if defined(_MSC_VER)
6121: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
6122: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
6123: //#include "stdafx.h"
6124: //#include <stdio.h>
6125: //#include <tchar.h>
6126: //#include <windows.h>
6127: //#include <iostream>
6128: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
6129:
6130: LPFN_ISWOW64PROCESS fnIsWow64Process;
6131:
6132: BOOL IsWow64()
6133: {
6134: BOOL bIsWow64 = FALSE;
6135:
6136: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
6137: // (HANDLE, PBOOL);
6138:
6139: //LPFN_ISWOW64PROCESS fnIsWow64Process;
6140:
6141: HMODULE module = GetModuleHandle(_T("kernel32"));
6142: const char funcName[] = "IsWow64Process";
6143: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
6144: GetProcAddress(module, funcName);
6145:
6146: if (NULL != fnIsWow64Process)
6147: {
6148: if (!fnIsWow64Process(GetCurrentProcess(),
6149: &bIsWow64))
6150: //throw std::exception("Unknown error");
6151: printf("Unknown error\n");
6152: }
6153: return bIsWow64 != FALSE;
6154: }
6155: #endif
1.177 brouard 6156:
1.191 brouard 6157: void syscompilerinfo(int logged)
1.167 brouard 6158: {
6159: /* #include "syscompilerinfo.h"*/
1.185 brouard 6160: /* command line Intel compiler 32bit windows, XP compatible:*/
6161: /* /GS /W3 /Gy
6162: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
6163: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
6164: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 6165: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
6166: */
6167: /* 64 bits */
1.185 brouard 6168: /*
6169: /GS /W3 /Gy
6170: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
6171: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
6172: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
6173: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
6174: /* Optimization are useless and O3 is slower than O2 */
6175: /*
6176: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
6177: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
6178: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
6179: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
6180: */
1.186 brouard 6181: /* Link is */ /* /OUT:"visual studio
1.185 brouard 6182: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
6183: /PDB:"visual studio
6184: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
6185: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
6186: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
6187: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
6188: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
6189: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
6190: uiAccess='false'"
6191: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
6192: /NOLOGO /TLBID:1
6193: */
1.177 brouard 6194: #if defined __INTEL_COMPILER
1.178 brouard 6195: #if defined(__GNUC__)
6196: struct utsname sysInfo; /* For Intel on Linux and OS/X */
6197: #endif
1.177 brouard 6198: #elif defined(__GNUC__)
1.179 brouard 6199: #ifndef __APPLE__
1.174 brouard 6200: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 6201: #endif
1.177 brouard 6202: struct utsname sysInfo;
1.178 brouard 6203: int cross = CROSS;
6204: if (cross){
6205: printf("Cross-");
1.191 brouard 6206: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 6207: }
1.174 brouard 6208: #endif
6209:
1.171 brouard 6210: #include <stdint.h>
1.178 brouard 6211:
1.191 brouard 6212: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 6213: #if defined(__clang__)
1.191 brouard 6214: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 6215: #endif
6216: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 6217: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 6218: #endif
6219: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 6220: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 6221: #endif
6222: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 6223: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 6224: #endif
6225: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 6226: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 6227: #endif
6228: #if defined(_MSC_VER)
1.191 brouard 6229: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 6230: #endif
6231: #if defined(__PGI)
1.191 brouard 6232: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 6233: #endif
6234: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 6235: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 6236: #endif
1.191 brouard 6237: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 6238:
1.167 brouard 6239: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
6240: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
6241: // Windows (x64 and x86)
1.191 brouard 6242: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 6243: #elif __unix__ // all unices, not all compilers
6244: // Unix
1.191 brouard 6245: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 6246: #elif __linux__
6247: // linux
1.191 brouard 6248: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 6249: #elif __APPLE__
1.174 brouard 6250: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 6251: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 6252: #endif
6253:
6254: /* __MINGW32__ */
6255: /* __CYGWIN__ */
6256: /* __MINGW64__ */
6257: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
6258: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
6259: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
6260: /* _WIN64 // Defined for applications for Win64. */
6261: /* _M_X64 // Defined for compilations that target x64 processors. */
6262: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 6263:
1.167 brouard 6264: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 6265: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 6266: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 6267: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 6268: #else
1.191 brouard 6269: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 6270: #endif
6271:
1.169 brouard 6272: #if defined(__GNUC__)
6273: # if defined(__GNUC_PATCHLEVEL__)
6274: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
6275: + __GNUC_MINOR__ * 100 \
6276: + __GNUC_PATCHLEVEL__)
6277: # else
6278: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
6279: + __GNUC_MINOR__ * 100)
6280: # endif
1.174 brouard 6281: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 6282: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 6283:
6284: if (uname(&sysInfo) != -1) {
6285: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 6286: 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 6287: }
6288: else
6289: perror("uname() error");
1.179 brouard 6290: //#ifndef __INTEL_COMPILER
6291: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 6292: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 6293: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 6294: #endif
1.169 brouard 6295: #endif
1.172 brouard 6296:
6297: // void main()
6298: // {
1.169 brouard 6299: #if defined(_MSC_VER)
1.174 brouard 6300: if (IsWow64()){
1.191 brouard 6301: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
6302: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 6303: }
6304: else{
1.191 brouard 6305: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
6306: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 6307: }
1.172 brouard 6308: // printf("\nPress Enter to continue...");
6309: // getchar();
6310: // }
6311:
1.169 brouard 6312: #endif
6313:
1.167 brouard 6314:
6315: }
1.136 brouard 6316:
1.202 ! brouard 6317: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl){
1.180 brouard 6318: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6319: int i, j, k, i1 ;
1.202 ! brouard 6320: /* double ftolpl = 1.e-10; */
1.180 brouard 6321: double age, agebase, agelim;
6322:
1.202 ! brouard 6323: strcpy(filerespl,"PL_");
! 6324: strcat(filerespl,fileresu);
! 6325: if((ficrespl=fopen(filerespl,"w"))==NULL) {
! 6326: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
! 6327: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
! 6328: }
! 6329: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
! 6330: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
! 6331: pstamp(ficrespl);
! 6332: fprintf(ficrespl,"# Period (stable) prevalence \n");
! 6333: fprintf(ficrespl,"#Age ");
! 6334: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
! 6335: fprintf(ficrespl,"\n");
1.180 brouard 6336:
6337: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
6338:
6339: agebase=ageminpar;
6340: agelim=agemaxpar;
6341:
6342: i1=pow(2,cptcoveff);
6343: if (cptcovn < 1){i1=1;}
6344:
6345: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6346: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
6347: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6348: k=k+1;
6349: /* to clean */
1.198 brouard 6350: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
1.200 brouard 6351: fprintf(ficrespl,"#******");
6352: printf("#******");
6353: fprintf(ficlog,"#******");
1.180 brouard 6354: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 6355: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
6356: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
6357: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.180 brouard 6358: }
6359: fprintf(ficrespl,"******\n");
6360: printf("******\n");
6361: fprintf(ficlog,"******\n");
6362:
6363: fprintf(ficrespl,"#Age ");
6364: for(j=1;j<=cptcoveff;j++) {
1.200 brouard 6365: fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.180 brouard 6366: }
6367: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
6368: fprintf(ficrespl,"\n");
6369:
6370: for (age=agebase; age<=agelim; age++){
6371: /* for (age=agebase; age<=agebase; age++){ */
6372: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6373: fprintf(ficrespl,"%.0f ",age );
6374: for(j=1;j<=cptcoveff;j++)
1.198 brouard 6375: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.180 brouard 6376: for(i=1; i<=nlstate;i++)
6377: fprintf(ficrespl," %.5f", prlim[i][i]);
6378: fprintf(ficrespl,"\n");
6379: } /* Age */
6380: /* was end of cptcod */
6381: } /* cptcov */
1.184 brouard 6382: return 0;
1.180 brouard 6383: }
6384:
6385: int hPijx(double *p, int bage, int fage){
6386: /*------------- h Pij x at various ages ------------*/
6387:
6388: int stepsize;
6389: int agelim;
6390: int hstepm;
6391: int nhstepm;
6392: int h, i, i1, j, k;
6393:
6394: double agedeb;
6395: double ***p3mat;
6396:
1.201 brouard 6397: strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu);
1.180 brouard 6398: if((ficrespij=fopen(filerespij,"w"))==NULL) {
6399: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
6400: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
6401: }
6402: printf("Computing pij: result on file '%s' \n", filerespij);
6403: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
6404:
6405: stepsize=(int) (stepm+YEARM-1)/YEARM;
6406: /*if (stepm<=24) stepsize=2;*/
6407:
6408: agelim=AGESUP;
6409: hstepm=stepsize*YEARM; /* Every year of age */
6410: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
6411:
6412: /* hstepm=1; aff par mois*/
6413: pstamp(ficrespij);
6414: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
6415: i1= pow(2,cptcoveff);
1.183 brouard 6416: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
6417: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
6418: /* k=k+1; */
6419: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6420: fprintf(ficrespij,"\n#****** ");
6421: for(j=1;j<=cptcoveff;j++)
1.198 brouard 6422: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.183 brouard 6423: fprintf(ficrespij,"******\n");
6424:
6425: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
6426: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6427: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6428:
6429: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 6430:
1.183 brouard 6431: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6432: oldm=oldms;savm=savms;
6433: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
6434: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
6435: for(i=1; i<=nlstate;i++)
6436: for(j=1; j<=nlstate+ndeath;j++)
6437: fprintf(ficrespij," %1d-%1d",i,j);
6438: fprintf(ficrespij,"\n");
6439: for (h=0; h<=nhstepm; h++){
6440: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
6441: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 6442: for(i=1; i<=nlstate;i++)
6443: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 6444: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 6445: fprintf(ficrespij,"\n");
6446: }
1.183 brouard 6447: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6448: fprintf(ficrespij,"\n");
6449: }
1.180 brouard 6450: /*}*/
6451: }
1.184 brouard 6452: return 0;
1.180 brouard 6453: }
6454:
6455:
1.136 brouard 6456: /***********************************************/
6457: /**************** Main Program *****************/
6458: /***********************************************/
6459:
6460: int main(int argc, char *argv[])
6461: {
6462: #ifdef GSL
6463: const gsl_multimin_fminimizer_type *T;
6464: size_t iteri = 0, it;
6465: int rval = GSL_CONTINUE;
6466: int status = GSL_SUCCESS;
6467: double ssval;
6468: #endif
6469: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 6470: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
6471:
6472: int jj, ll, li, lj, lk;
1.136 brouard 6473: int numlinepar=0; /* Current linenumber of parameter file */
1.197 brouard 6474: int num_filled;
1.136 brouard 6475: int itimes;
6476: int NDIM=2;
6477: int vpopbased=0;
6478:
1.164 brouard 6479: char ca[32], cb[32];
1.136 brouard 6480: /* FILE *fichtm; *//* Html File */
6481: /* FILE *ficgp;*/ /*Gnuplot File */
6482: struct stat info;
1.191 brouard 6483: double agedeb=0.;
1.194 brouard 6484:
6485: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.136 brouard 6486:
1.165 brouard 6487: double fret;
1.191 brouard 6488: double dum=0.; /* Dummy variable */
1.136 brouard 6489: double ***p3mat;
6490: double ***mobaverage;
1.164 brouard 6491:
6492: char line[MAXLINE];
1.197 brouard 6493: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
6494:
6495: char model[MAXLINE], modeltemp[MAXLINE];
1.136 brouard 6496: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 6497: char *tok, *val; /* pathtot */
1.136 brouard 6498: int firstobs=1, lastobs=10;
1.195 brouard 6499: int c, h , cpt, c2;
1.191 brouard 6500: int jl=0;
6501: int i1, j1, jk, stepsize=0;
1.194 brouard 6502: int count=0;
6503:
1.164 brouard 6504: int *tab;
1.136 brouard 6505: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
6506: int mobilav=0,popforecast=0;
1.191 brouard 6507: int hstepm=0, nhstepm=0;
1.136 brouard 6508: int agemortsup;
6509: float sumlpop=0.;
6510: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
6511: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
6512:
1.191 brouard 6513: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 6514: double ftolpl=FTOL;
6515: double **prlim;
6516: double ***param; /* Matrix of parameters */
6517: double *p;
6518: double **matcov; /* Matrix of covariance */
6519: double ***delti3; /* Scale */
6520: double *delti; /* Scale */
6521: double ***eij, ***vareij;
6522: double **varpl; /* Variances of prevalence limits by age */
6523: double *epj, vepp;
1.164 brouard 6524:
1.136 brouard 6525: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
6526: double **ximort;
1.145 brouard 6527: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 6528: int *dcwave;
6529:
1.164 brouard 6530: char z[1]="c";
1.136 brouard 6531:
6532: /*char *strt;*/
6533: char strtend[80];
1.126 brouard 6534:
1.164 brouard 6535:
1.126 brouard 6536: /* setlocale (LC_ALL, ""); */
6537: /* bindtextdomain (PACKAGE, LOCALEDIR); */
6538: /* textdomain (PACKAGE); */
6539: /* setlocale (LC_CTYPE, ""); */
6540: /* setlocale (LC_MESSAGES, ""); */
6541:
6542: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 6543: rstart_time = time(NULL);
6544: /* (void) gettimeofday(&start_time,&tzp);*/
6545: start_time = *localtime(&rstart_time);
1.126 brouard 6546: curr_time=start_time;
1.157 brouard 6547: /*tml = *localtime(&start_time.tm_sec);*/
6548: /* strcpy(strstart,asctime(&tml)); */
6549: strcpy(strstart,asctime(&start_time));
1.126 brouard 6550:
6551: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 6552: /* tp.tm_sec = tp.tm_sec +86400; */
6553: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 6554: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
6555: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
6556: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 6557: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 6558: /* strt=asctime(&tmg); */
6559: /* printf("Time(after) =%s",strstart); */
6560: /* (void) time (&time_value);
6561: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
6562: * tm = *localtime(&time_value);
6563: * strstart=asctime(&tm);
6564: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
6565: */
6566:
6567: nberr=0; /* Number of errors and warnings */
6568: nbwarn=0;
1.184 brouard 6569: #ifdef WIN32
6570: _getcwd(pathcd, size);
6571: #else
1.126 brouard 6572: getcwd(pathcd, size);
1.184 brouard 6573: #endif
1.191 brouard 6574: syscompilerinfo(0);
1.196 brouard 6575: printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126 brouard 6576: if(argc <=1){
6577: printf("\nEnter the parameter file name: ");
6578: fgets(pathr,FILENAMELENGTH,stdin);
6579: i=strlen(pathr);
6580: if(pathr[i-1]=='\n')
6581: pathr[i-1]='\0';
1.156 brouard 6582: i=strlen(pathr);
6583: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
6584: pathr[i-1]='\0';
1.126 brouard 6585: for (tok = pathr; tok != NULL; ){
6586: printf("Pathr |%s|\n",pathr);
6587: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
6588: printf("val= |%s| pathr=%s\n",val,pathr);
6589: strcpy (pathtot, val);
6590: if(pathr[0] == '\0') break; /* Dirty */
6591: }
6592: }
6593: else{
6594: strcpy(pathtot,argv[1]);
6595: }
6596: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
6597: /*cygwin_split_path(pathtot,path,optionfile);
6598: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
6599: /* cutv(path,optionfile,pathtot,'\\');*/
6600:
6601: /* Split argv[0], imach program to get pathimach */
6602: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
6603: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6604: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6605: /* strcpy(pathimach,argv[0]); */
6606: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
6607: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
6608: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 6609: #ifdef WIN32
6610: _chdir(path); /* Can be a relative path */
6611: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
6612: #else
1.126 brouard 6613: chdir(path); /* Can be a relative path */
1.184 brouard 6614: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
6615: #endif
6616: printf("Current directory %s!\n",pathcd);
1.126 brouard 6617: strcpy(command,"mkdir ");
6618: strcat(command,optionfilefiname);
6619: if((outcmd=system(command)) != 0){
1.169 brouard 6620: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 6621: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
6622: /* fclose(ficlog); */
6623: /* exit(1); */
6624: }
6625: /* if((imk=mkdir(optionfilefiname))<0){ */
6626: /* perror("mkdir"); */
6627: /* } */
6628:
6629: /*-------- arguments in the command line --------*/
6630:
1.186 brouard 6631: /* Main Log file */
1.126 brouard 6632: strcat(filelog, optionfilefiname);
6633: strcat(filelog,".log"); /* */
6634: if((ficlog=fopen(filelog,"w"))==NULL) {
6635: printf("Problem with logfile %s\n",filelog);
6636: goto end;
6637: }
6638: fprintf(ficlog,"Log filename:%s\n",filelog);
1.197 brouard 6639: fprintf(ficlog,"Version %s %s",version,fullversion);
1.126 brouard 6640: fprintf(ficlog,"\nEnter the parameter file name: \n");
6641: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
6642: path=%s \n\
6643: optionfile=%s\n\
6644: optionfilext=%s\n\
1.156 brouard 6645: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 6646:
1.197 brouard 6647: syscompilerinfo(1);
1.167 brouard 6648:
1.126 brouard 6649: printf("Local time (at start):%s",strstart);
6650: fprintf(ficlog,"Local time (at start): %s",strstart);
6651: fflush(ficlog);
6652: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 6653: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 6654:
6655: /* */
6656: strcpy(fileres,"r");
6657: strcat(fileres, optionfilefiname);
1.201 brouard 6658: strcat(fileresu, optionfilefiname); /* Without r in front */
1.126 brouard 6659: strcat(fileres,".txt"); /* Other files have txt extension */
1.201 brouard 6660: strcat(fileresu,".txt"); /* Other files have txt extension */
1.126 brouard 6661:
1.186 brouard 6662: /* Main ---------arguments file --------*/
1.126 brouard 6663:
6664: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 6665: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
6666: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 6667: fflush(ficlog);
1.149 brouard 6668: /* goto end; */
6669: exit(70);
1.126 brouard 6670: }
6671:
6672:
6673:
6674: strcpy(filereso,"o");
1.201 brouard 6675: strcat(filereso,fileresu);
1.126 brouard 6676: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
6677: printf("Problem with Output resultfile: %s\n", filereso);
6678: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
6679: fflush(ficlog);
6680: goto end;
6681: }
6682:
6683: /* Reads comments: lines beginning with '#' */
6684: numlinepar=0;
1.197 brouard 6685:
6686: /* First parameter line */
6687: while(fgets(line, MAXLINE, ficpar)) {
6688: /* If line starts with a # it is a comment */
6689: if (line[0] == '#') {
6690: numlinepar++;
6691: fputs(line,stdout);
6692: fputs(line,ficparo);
6693: fputs(line,ficlog);
6694: continue;
6695: }else
6696: break;
6697: }
6698: if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
6699: title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
6700: if (num_filled != 5) {
6701: printf("Should be 5 parameters\n");
6702: }
1.126 brouard 6703: numlinepar++;
1.197 brouard 6704: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
6705: }
6706: /* Second parameter line */
6707: while(fgets(line, MAXLINE, ficpar)) {
6708: /* If line starts with a # it is a comment */
6709: if (line[0] == '#') {
6710: numlinepar++;
6711: fputs(line,stdout);
6712: fputs(line,ficparo);
6713: fputs(line,ficlog);
6714: continue;
6715: }else
6716: break;
6717: }
6718: if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
6719: &ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
6720: if (num_filled != 8) {
6721: printf("Not 8\n");
6722: }
6723: 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 6724: }
1.202 ! brouard 6725: ftolpl=6*ftol*1.e5; /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
1.197 brouard 6726: /* Third parameter line */
6727: while(fgets(line, MAXLINE, ficpar)) {
6728: /* If line starts with a # it is a comment */
6729: if (line[0] == '#') {
6730: numlinepar++;
6731: fputs(line,stdout);
6732: fputs(line,ficparo);
6733: fputs(line,ficlog);
6734: continue;
6735: }else
6736: break;
6737: }
1.201 brouard 6738: if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
6739: if (num_filled == 0)
6740: model[0]='\0';
6741: else if (num_filled != 1){
1.197 brouard 6742: printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
6743: fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
6744: model[0]='\0';
6745: goto end;
6746: }
6747: else{
6748: if (model[0]=='+'){
6749: for(i=1; i<=strlen(model);i++)
6750: modeltemp[i-1]=model[i];
1.201 brouard 6751: strcpy(model,modeltemp);
1.197 brouard 6752: }
6753: }
1.199 brouard 6754: /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
1.197 brouard 6755: }
6756: /* 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); */
6757: /* numlinepar=numlinepar+3; /\* In general *\/ */
6758: /* 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); */
1.187 brouard 6759: if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the model */
6760: model[strlen(model)-1]='\0';
1.197 brouard 6761: 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);
6762: 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 6763: fflush(ficlog);
1.190 brouard 6764: /* if(model[0]=='#'|| model[0]== '\0'){ */
6765: if(model[0]=='#'){
1.187 brouard 6766: printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
6767: 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
6768: 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \
6769: if(mle != -1){
6770: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
6771: exit(1);
6772: }
6773: }
1.126 brouard 6774: while((c=getc(ficpar))=='#' && c!= EOF){
6775: ungetc(c,ficpar);
6776: fgets(line, MAXLINE, ficpar);
6777: numlinepar++;
1.195 brouard 6778: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
6779: z[0]=line[1];
6780: }
6781: /* printf("****line [1] = %c \n",line[1]); */
1.141 brouard 6782: fputs(line, stdout);
6783: //puts(line);
1.126 brouard 6784: fputs(line,ficparo);
6785: fputs(line,ficlog);
6786: }
6787: ungetc(c,ficpar);
6788:
6789:
1.145 brouard 6790: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.136 brouard 6791: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
6792: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
6793: v1+v2*age+v2*v3 makes cptcovn = 3
6794: */
6795: if (strlen(model)>1)
1.187 brouard 6796: 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 6797: else
1.187 brouard 6798: ncovmodel=2; /* Constant and age */
1.133 brouard 6799: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
6800: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 6801: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
6802: 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);
6803: 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);
6804: fflush(stdout);
6805: fclose (ficlog);
6806: goto end;
6807: }
1.126 brouard 6808: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6809: delti=delti3[1][1];
6810: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
6811: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
6812: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 6813: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
6814: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 6815: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6816: fclose (ficparo);
6817: fclose (ficlog);
6818: goto end;
6819: exit(0);
6820: }
1.186 brouard 6821: else if(mle==-3) { /* Main Wizard */
1.126 brouard 6822: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 6823: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
6824: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 6825: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6826: matcov=matrix(1,npar,1,npar);
6827: }
6828: else{
1.145 brouard 6829: /* Read guessed parameters */
1.126 brouard 6830: /* Reads comments: lines beginning with '#' */
6831: while((c=getc(ficpar))=='#' && c!= EOF){
6832: ungetc(c,ficpar);
6833: fgets(line, MAXLINE, ficpar);
6834: numlinepar++;
1.141 brouard 6835: fputs(line,stdout);
1.126 brouard 6836: fputs(line,ficparo);
6837: fputs(line,ficlog);
6838: }
6839: ungetc(c,ficpar);
6840:
6841: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6842: for(i=1; i <=nlstate; i++){
6843: j=0;
6844: for(jj=1; jj <=nlstate+ndeath; jj++){
6845: if(jj==i) continue;
6846: j++;
6847: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.193 brouard 6848: if ((i1 != i) || (j1 != jj)){
1.126 brouard 6849: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
6850: It might be a problem of design; if ncovcol and the model are correct\n \
6851: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
6852: exit(1);
6853: }
6854: fprintf(ficparo,"%1d%1d",i1,j1);
6855: if(mle==1)
1.193 brouard 6856: printf("%1d%1d",i,jj);
6857: fprintf(ficlog,"%1d%1d",i,jj);
1.126 brouard 6858: for(k=1; k<=ncovmodel;k++){
6859: fscanf(ficpar," %lf",¶m[i][j][k]);
6860: if(mle==1){
6861: printf(" %lf",param[i][j][k]);
6862: fprintf(ficlog," %lf",param[i][j][k]);
6863: }
6864: else
6865: fprintf(ficlog," %lf",param[i][j][k]);
6866: fprintf(ficparo," %lf",param[i][j][k]);
6867: }
6868: fscanf(ficpar,"\n");
6869: numlinepar++;
6870: if(mle==1)
6871: printf("\n");
6872: fprintf(ficlog,"\n");
6873: fprintf(ficparo,"\n");
6874: }
6875: }
6876: fflush(ficlog);
6877:
1.145 brouard 6878: /* Reads scales values */
1.126 brouard 6879: p=param[1][1];
6880:
6881: /* Reads comments: lines beginning with '#' */
6882: while((c=getc(ficpar))=='#' && c!= EOF){
6883: ungetc(c,ficpar);
6884: fgets(line, MAXLINE, ficpar);
6885: numlinepar++;
1.141 brouard 6886: fputs(line,stdout);
1.126 brouard 6887: fputs(line,ficparo);
6888: fputs(line,ficlog);
6889: }
6890: ungetc(c,ficpar);
6891:
6892: for(i=1; i <=nlstate; i++){
6893: for(j=1; j <=nlstate+ndeath-1; j++){
6894: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.164 brouard 6895: if ( (i1-i) * (j1-j) != 0){
1.126 brouard 6896: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
6897: exit(1);
6898: }
6899: printf("%1d%1d",i,j);
6900: fprintf(ficparo,"%1d%1d",i1,j1);
6901: fprintf(ficlog,"%1d%1d",i1,j1);
6902: for(k=1; k<=ncovmodel;k++){
6903: fscanf(ficpar,"%le",&delti3[i][j][k]);
6904: printf(" %le",delti3[i][j][k]);
6905: fprintf(ficparo," %le",delti3[i][j][k]);
6906: fprintf(ficlog," %le",delti3[i][j][k]);
6907: }
6908: fscanf(ficpar,"\n");
6909: numlinepar++;
6910: printf("\n");
6911: fprintf(ficparo,"\n");
6912: fprintf(ficlog,"\n");
6913: }
6914: }
6915: fflush(ficlog);
6916:
1.145 brouard 6917: /* Reads covariance matrix */
1.126 brouard 6918: delti=delti3[1][1];
6919:
6920:
6921: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
6922:
6923: /* Reads comments: lines beginning with '#' */
6924: while((c=getc(ficpar))=='#' && c!= EOF){
6925: ungetc(c,ficpar);
6926: fgets(line, MAXLINE, ficpar);
6927: numlinepar++;
1.141 brouard 6928: fputs(line,stdout);
1.126 brouard 6929: fputs(line,ficparo);
6930: fputs(line,ficlog);
6931: }
6932: ungetc(c,ficpar);
6933:
6934: matcov=matrix(1,npar,1,npar);
1.131 brouard 6935: for(i=1; i <=npar; i++)
6936: for(j=1; j <=npar; j++) matcov[i][j]=0.;
6937:
1.194 brouard 6938: /* Scans npar lines */
1.126 brouard 6939: for(i=1; i <=npar; i++){
1.194 brouard 6940: count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk);
6941: if(count != 3){
6942: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
6943: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
6944: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
6945: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
6946: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
6947: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
6948: exit(1);
6949: }else
1.126 brouard 6950: if(mle==1)
1.194 brouard 6951: printf("%1d%1d%1d",i1,j1,jk);
6952: fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);
6953: fprintf(ficparo,"%1d%1d%1d",i1,j1,jk);
1.126 brouard 6954: for(j=1; j <=i; j++){
6955: fscanf(ficpar," %le",&matcov[i][j]);
6956: if(mle==1){
6957: printf(" %.5le",matcov[i][j]);
6958: }
6959: fprintf(ficlog," %.5le",matcov[i][j]);
6960: fprintf(ficparo," %.5le",matcov[i][j]);
6961: }
6962: fscanf(ficpar,"\n");
6963: numlinepar++;
6964: if(mle==1)
6965: printf("\n");
6966: fprintf(ficlog,"\n");
6967: fprintf(ficparo,"\n");
6968: }
1.194 brouard 6969: /* End of read covariance matrix npar lines */
1.126 brouard 6970: for(i=1; i <=npar; i++)
6971: for(j=i+1;j<=npar;j++)
6972: matcov[i][j]=matcov[j][i];
6973:
6974: if(mle==1)
6975: printf("\n");
6976: fprintf(ficlog,"\n");
6977:
6978: fflush(ficlog);
6979:
6980: /*-------- Rewriting parameter file ----------*/
6981: strcpy(rfileres,"r"); /* "Rparameterfile */
6982: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
6983: strcat(rfileres,"."); /* */
6984: strcat(rfileres,optionfilext); /* Other files have txt extension */
6985: if((ficres =fopen(rfileres,"w"))==NULL) {
1.201 brouard 6986: printf("Problem writing new parameter file: %s\n", rfileres);goto end;
6987: fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
1.126 brouard 6988: }
6989: fprintf(ficres,"#%s\n",version);
6990: } /* End of mle != -3 */
6991:
1.186 brouard 6992: /* Main data
6993: */
1.126 brouard 6994: n= lastobs;
6995: num=lvector(1,n);
6996: moisnais=vector(1,n);
6997: annais=vector(1,n);
6998: moisdc=vector(1,n);
6999: andc=vector(1,n);
7000: agedc=vector(1,n);
7001: cod=ivector(1,n);
7002: weight=vector(1,n);
7003: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
7004: mint=matrix(1,maxwav,1,n);
7005: anint=matrix(1,maxwav,1,n);
1.131 brouard 7006: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 7007: tab=ivector(1,NCOVMAX);
1.144 brouard 7008: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 7009: 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 7010:
1.136 brouard 7011: /* Reads data from file datafile */
7012: if (readdata(datafile, firstobs, lastobs, &imx)==1)
7013: goto end;
7014:
7015: /* Calculation of the number of parameters from char model */
1.137 brouard 7016: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
7017: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
7018: k=3 V4 Tvar[k=3]= 4 (from V4)
7019: k=2 V1 Tvar[k=2]= 1 (from V1)
7020: k=1 Tvar[1]=2 (from V2)
7021: */
7022: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
7023: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
7024: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
7025: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
7026: */
7027: /* For model-covariate k tells which data-covariate to use but
7028: because this model-covariate is a construction we invent a new column
7029: ncovcol + k1
7030: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
7031: Tvar[3=V1*V4]=4+1 etc */
1.145 brouard 7032: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
1.137 brouard 7033: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
7034: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
7035: */
1.145 brouard 7036: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
7037: 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 7038: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
7039: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 7040: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 7041: 4 covariates (3 plus signs)
7042: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
7043: */
1.136 brouard 7044:
1.186 brouard 7045: /* Main decodemodel */
7046:
1.187 brouard 7047:
1.136 brouard 7048: if(decodemodel(model, lastobs) == 1)
7049: goto end;
7050:
1.137 brouard 7051: if((double)(lastobs-imx)/(double)imx > 1.10){
7052: nbwarn++;
7053: 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);
7054: 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);
7055: }
1.136 brouard 7056: /* if(mle==1){*/
1.137 brouard 7057: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
7058: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 7059: }
7060:
7061: /*-calculation of age at interview from date of interview and age at death -*/
7062: agev=matrix(1,maxwav,1,imx);
7063:
7064: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
7065: goto end;
7066:
1.126 brouard 7067:
1.136 brouard 7068: agegomp=(int)agemin;
7069: free_vector(moisnais,1,n);
7070: free_vector(annais,1,n);
1.126 brouard 7071: /* free_matrix(mint,1,maxwav,1,n);
7072: free_matrix(anint,1,maxwav,1,n);*/
7073: free_vector(moisdc,1,n);
7074: free_vector(andc,1,n);
1.145 brouard 7075: /* */
7076:
1.126 brouard 7077: wav=ivector(1,imx);
7078: dh=imatrix(1,lastpass-firstpass+1,1,imx);
7079: bh=imatrix(1,lastpass-firstpass+1,1,imx);
7080: mw=imatrix(1,lastpass-firstpass+1,1,imx);
7081:
7082: /* Concatenates waves */
7083: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 brouard 7084: /* */
7085:
1.126 brouard 7086: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
7087:
7088: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
7089: ncodemax[1]=1;
1.145 brouard 7090: Ndum =ivector(-1,NCOVMAX);
1.187 brouard 7091: if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */
1.145 brouard 7092: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.186 brouard 7093: /* Nbcode gives the value of the lth modality of jth covariate, in
7094: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
7095: /* 1 to ncodemax[j] is the maximum value of this jth covariate */
1.145 brouard 7096:
1.200 brouard 7097: /* codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
1.198 brouard 7098: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
1.186 brouard 7099: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.145 brouard 7100: h=0;
7101:
7102:
7103: /*if (cptcovn > 0) */
1.126 brouard 7104:
1.145 brouard 7105:
1.126 brouard 7106: m=pow(2,cptcoveff);
7107:
1.144 brouard 7108: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.186 brouard 7109: * For k=4 covariates, h goes from 1 to 2**k
7110: * codtabm(h,k)= 1 & (h-1) >> (k-1) ;
7111: * h\k 1 2 3 4
1.143 brouard 7112: *______________________________
7113: * 1 i=1 1 i=1 1 i=1 1 i=1 1
7114: * 2 2 1 1 1
7115: * 3 i=2 1 2 1 1
7116: * 4 2 2 1 1
7117: * 5 i=3 1 i=2 1 2 1
7118: * 6 2 1 2 1
7119: * 7 i=4 1 2 2 1
7120: * 8 2 2 2 1
1.197 brouard 7121: * 9 i=5 1 i=3 1 i=2 1 2
7122: * 10 2 1 1 2
7123: * 11 i=6 1 2 1 2
7124: * 12 2 2 1 2
7125: * 13 i=7 1 i=4 1 2 2
7126: * 14 2 1 2 2
7127: * 15 i=8 1 2 2 2
7128: * 16 2 2 2 2
1.143 brouard 7129: */
1.202 ! brouard 7130: /* /\* for(h=1; h <=100 ;h++){ *\/ */
! 7131: /* /\* printf("h=%2d ", h); *\/ */
! 7132: /* /\* for(k=1; k <=10; k++){ *\/ */
! 7133: /* /\* printf("k=%d %d ",k,codtabm(h,k)); *\/ */
! 7134: /* /\* codtab[h][k]=codtabm(h,k); *\/ */
! 7135: /* /\* } *\/ */
! 7136: /* /\* printf("\n"); *\/ */
! 7137: /* } */
1.197 brouard 7138: /* for(k=1;k<=cptcoveff; k++){ /\* scans any effective covariate *\/ */
7139: /* 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 *\/ */
7140: /* for(j=1; j <= ncodemax[k]; j++){ /\* For each modality of this covariate ncodemax=2*\/ */
7141: /* for(cpt=1; cpt <=pow(2,k-1); cpt++){ /\* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 *\/ */
7142: /* h++; */
7143: /* if (h>m) */
7144: /* h=1; */
7145: /* codtab[h][k]=j; */
7146: /* /\* codtab[12][3]=1; *\/ */
7147: /* /\*codtab[h][Tvar[k]]=j;*\/ */
7148: /* /\* 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]]); *\/ */
7149: /* } */
7150: /* } */
7151: /* } */
7152: /* } */
1.126 brouard 7153: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
7154: codtab[1][2]=1;codtab[2][2]=2; */
1.197 brouard 7155: /* for(i=1; i <=m ;i++){ */
7156: /* for(k=1; k <=cptcovn; k++){ */
7157: /* printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); */
7158: /* } */
7159: /* printf("\n"); */
7160: /* } */
7161: /* scanf("%d",i);*/
1.145 brouard 7162:
7163: free_ivector(Ndum,-1,NCOVMAX);
7164:
7165:
1.126 brouard 7166:
1.186 brouard 7167: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 7168: strcpy(optionfilegnuplot,optionfilefiname);
7169: if(mle==-3)
1.201 brouard 7170: strcat(optionfilegnuplot,"-MORT_");
1.126 brouard 7171: strcat(optionfilegnuplot,".gp");
7172:
7173: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
7174: printf("Problem with file %s",optionfilegnuplot);
7175: }
7176: else{
7177: fprintf(ficgp,"\n# %s\n", version);
7178: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 7179: //fprintf(ficgp,"set missing 'NaNq'\n");
7180: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 7181: }
7182: /* fclose(ficgp);*/
1.186 brouard 7183:
7184:
7185: /* Initialisation of --------- index.htm --------*/
1.126 brouard 7186:
7187: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
7188: if(mle==-3)
1.201 brouard 7189: strcat(optionfilehtm,"-MORT_");
1.126 brouard 7190: strcat(optionfilehtm,".htm");
7191: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 7192: printf("Problem with %s \n",optionfilehtm);
7193: exit(0);
1.126 brouard 7194: }
7195:
7196: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
7197: strcat(optionfilehtmcov,"-cov.htm");
7198: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
7199: printf("Problem with %s \n",optionfilehtmcov), exit(0);
7200: }
7201: else{
7202: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
7203: <hr size=\"2\" color=\"#EC5E5E\"> \n\
7204: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
7205: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
7206: }
7207:
7208: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
7209: <hr size=\"2\" color=\"#EC5E5E\"> \n\
7210: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
7211: \n\
7212: <hr size=\"2\" color=\"#EC5E5E\">\
7213: <ul><li><h4>Parameter files</h4>\n\
7214: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
7215: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
7216: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
7217: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
7218: - Date and time at start: %s</ul>\n",\
7219: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
7220: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
7221: fileres,fileres,\
7222: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
7223: fflush(fichtm);
7224:
7225: strcpy(pathr,path);
7226: strcat(pathr,optionfilefiname);
1.184 brouard 7227: #ifdef WIN32
7228: _chdir(optionfilefiname); /* Move to directory named optionfile */
7229: #else
1.126 brouard 7230: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 7231: #endif
7232:
1.126 brouard 7233:
7234: /* Calculates basic frequencies. Computes observed prevalence at single age
7235: and prints on file fileres'p'. */
7236: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
7237:
7238: fprintf(fichtm,"\n");
7239: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
7240: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
7241: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
7242: imx,agemin,agemax,jmin,jmax,jmean);
7243: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7244: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7245: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7246: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7247: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
7248:
7249:
7250: /* For Powell, parameters are in a vector p[] starting at p[1]
7251: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
7252: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
7253:
7254: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 7255: /* For mortality only */
1.126 brouard 7256: if (mle==-3){
1.136 brouard 7257: ximort=matrix(1,NDIM,1,NDIM);
1.186 brouard 7258: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 7259: cens=ivector(1,n);
7260: ageexmed=vector(1,n);
7261: agecens=vector(1,n);
7262: dcwave=ivector(1,n);
7263:
7264: for (i=1; i<=imx; i++){
7265: dcwave[i]=-1;
7266: for (m=firstpass; m<=lastpass; m++)
7267: if (s[m][i]>nlstate) {
7268: dcwave[i]=m;
7269: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
7270: break;
7271: }
7272: }
7273:
7274: for (i=1; i<=imx; i++) {
7275: if (wav[i]>0){
7276: ageexmed[i]=agev[mw[1][i]][i];
7277: j=wav[i];
7278: agecens[i]=1.;
7279:
7280: if (ageexmed[i]> 1 && wav[i] > 0){
7281: agecens[i]=agev[mw[j][i]][i];
7282: cens[i]= 1;
7283: }else if (ageexmed[i]< 1)
7284: cens[i]= -1;
7285: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
7286: cens[i]=0 ;
7287: }
7288: else cens[i]=-1;
7289: }
7290:
7291: for (i=1;i<=NDIM;i++) {
7292: for (j=1;j<=NDIM;j++)
7293: ximort[i][j]=(i == j ? 1.0 : 0.0);
7294: }
7295:
1.145 brouard 7296: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 7297: /*printf("%lf %lf", p[1], p[2]);*/
7298:
7299:
1.136 brouard 7300: #ifdef GSL
7301: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 7302: #else
1.126 brouard 7303: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 7304: #endif
1.201 brouard 7305: strcpy(filerespow,"POW-MORT_");
7306: strcat(filerespow,fileresu);
1.126 brouard 7307: if((ficrespow=fopen(filerespow,"w"))==NULL) {
7308: printf("Problem with resultfile: %s\n", filerespow);
7309: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
7310: }
1.136 brouard 7311: #ifdef GSL
7312: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 7313: #else
1.126 brouard 7314: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 7315: #endif
1.126 brouard 7316: /* for (i=1;i<=nlstate;i++)
7317: for(j=1;j<=nlstate+ndeath;j++)
7318: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
7319: */
7320: fprintf(ficrespow,"\n");
1.136 brouard 7321: #ifdef GSL
7322: /* gsl starts here */
7323: T = gsl_multimin_fminimizer_nmsimplex;
7324: gsl_multimin_fminimizer *sfm = NULL;
7325: gsl_vector *ss, *x;
7326: gsl_multimin_function minex_func;
7327:
7328: /* Initial vertex size vector */
7329: ss = gsl_vector_alloc (NDIM);
7330:
7331: if (ss == NULL){
7332: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
7333: }
7334: /* Set all step sizes to 1 */
7335: gsl_vector_set_all (ss, 0.001);
7336:
7337: /* Starting point */
1.126 brouard 7338:
1.136 brouard 7339: x = gsl_vector_alloc (NDIM);
7340:
7341: if (x == NULL){
7342: gsl_vector_free(ss);
7343: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
7344: }
7345:
7346: /* Initialize method and iterate */
7347: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 7348: /* gsl_vector_set(x, 0, 0.0268); */
7349: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 7350: gsl_vector_set(x, 0, p[1]);
7351: gsl_vector_set(x, 1, p[2]);
7352:
7353: minex_func.f = &gompertz_f;
7354: minex_func.n = NDIM;
7355: minex_func.params = (void *)&p; /* ??? */
7356:
7357: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
7358: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
7359:
7360: printf("Iterations beginning .....\n\n");
7361: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
7362:
7363: iteri=0;
7364: while (rval == GSL_CONTINUE){
7365: iteri++;
7366: status = gsl_multimin_fminimizer_iterate(sfm);
7367:
7368: if (status) printf("error: %s\n", gsl_strerror (status));
7369: fflush(0);
7370:
7371: if (status)
7372: break;
7373:
7374: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
7375: ssval = gsl_multimin_fminimizer_size (sfm);
7376:
7377: if (rval == GSL_SUCCESS)
7378: printf ("converged to a local maximum at\n");
7379:
7380: printf("%5d ", iteri);
7381: for (it = 0; it < NDIM; it++){
7382: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
7383: }
7384: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
7385: }
7386:
7387: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
7388:
7389: gsl_vector_free(x); /* initial values */
7390: gsl_vector_free(ss); /* inital step size */
7391: for (it=0; it<NDIM; it++){
7392: p[it+1]=gsl_vector_get(sfm->x,it);
7393: fprintf(ficrespow," %.12lf", p[it]);
7394: }
7395: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
7396: #endif
7397: #ifdef POWELL
7398: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
7399: #endif
1.126 brouard 7400: fclose(ficrespow);
7401:
7402: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
7403:
7404: for(i=1; i <=NDIM; i++)
7405: for(j=i+1;j<=NDIM;j++)
7406: matcov[i][j]=matcov[j][i];
7407:
7408: printf("\nCovariance matrix\n ");
7409: for(i=1; i <=NDIM; i++) {
7410: for(j=1;j<=NDIM;j++){
7411: printf("%f ",matcov[i][j]);
7412: }
7413: printf("\n ");
7414: }
7415:
7416: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 brouard 7417: for (i=1;i<=NDIM;i++) {
1.126 brouard 7418: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 brouard 7419: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
7420: }
1.126 brouard 7421: lsurv=vector(1,AGESUP);
7422: lpop=vector(1,AGESUP);
7423: tpop=vector(1,AGESUP);
7424: lsurv[agegomp]=100000;
7425:
7426: for (k=agegomp;k<=AGESUP;k++) {
7427: agemortsup=k;
7428: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
7429: }
7430:
7431: for (k=agegomp;k<agemortsup;k++)
7432: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
7433:
7434: for (k=agegomp;k<agemortsup;k++){
7435: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
7436: sumlpop=sumlpop+lpop[k];
7437: }
7438:
7439: tpop[agegomp]=sumlpop;
7440: for (k=agegomp;k<(agemortsup-3);k++){
7441: /* tpop[k+1]=2;*/
7442: tpop[k+1]=tpop[k]-lpop[k];
7443: }
7444:
7445:
7446: printf("\nAge lx qx dx Lx Tx e(x)\n");
7447: for (k=agegomp;k<(agemortsup-2);k++)
7448: 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]);
7449:
7450:
7451: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 7452: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
7453: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7454: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7455: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7456: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7457: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7458: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7459: }else
1.201 brouard 7460: printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
7461: printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
1.126 brouard 7462: stepm, weightopt,\
7463: model,imx,p,matcov,agemortsup);
7464:
7465: free_vector(lsurv,1,AGESUP);
7466: free_vector(lpop,1,AGESUP);
7467: free_vector(tpop,1,AGESUP);
1.136 brouard 7468: #ifdef GSL
7469: free_ivector(cens,1,n);
7470: free_vector(agecens,1,n);
7471: free_ivector(dcwave,1,n);
7472: free_matrix(ximort,1,NDIM,1,NDIM);
7473: #endif
1.186 brouard 7474: } /* Endof if mle==-3 mortality only */
7475: /* Standard maximisation */
1.126 brouard 7476: else{ /* For mle >=1 */
1.132 brouard 7477: globpr=0;/* debug */
1.186 brouard 7478: /* Computes likelihood for initial parameters */
1.132 brouard 7479: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 7480: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7481: for (k=1; k<=npar;k++)
7482: printf(" %d %8.5f",k,p[k]);
7483: printf("\n");
1.186 brouard 7484: globpr=1; /* again, to print the contributions */
1.126 brouard 7485: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
7486: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7487: for (k=1; k<=npar;k++)
7488: printf(" %d %8.5f",k,p[k]);
7489: printf("\n");
1.186 brouard 7490: if(mle>=1){ /* Could be 1 or 2, Real Maximisation */
1.126 brouard 7491: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
7492: }
7493:
7494: /*--------- results files --------------*/
1.192 brouard 7495: 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 7496:
7497:
7498: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7499: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7500: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7501: for(i=1,jk=1; i <=nlstate; i++){
7502: for(k=1; k <=(nlstate+ndeath); k++){
7503: if (k != i) {
7504: printf("%d%d ",i,k);
7505: fprintf(ficlog,"%d%d ",i,k);
7506: fprintf(ficres,"%1d%1d ",i,k);
7507: for(j=1; j <=ncovmodel; j++){
1.190 brouard 7508: printf("%12.7f ",p[jk]);
7509: fprintf(ficlog,"%12.7f ",p[jk]);
7510: fprintf(ficres,"%12.7f ",p[jk]);
1.126 brouard 7511: jk++;
7512: }
7513: printf("\n");
7514: fprintf(ficlog,"\n");
7515: fprintf(ficres,"\n");
7516: }
7517: }
7518: }
7519: if(mle!=0){
7520: /* Computing hessian and covariance matrix */
7521: ftolhess=ftol; /* Usually correct */
7522: hesscov(matcov, p, npar, delti, ftolhess, func);
7523: }
1.197 brouard 7524: 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");
7525: 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");
1.193 brouard 7526: for(i=1,jk=1; i <=nlstate; i++){
7527: for(k=1; k <=(nlstate+ndeath); k++){
7528: if (k != i) {
7529: printf("%d%d ",i,k);
7530: fprintf(ficlog,"%d%d ",i,k);
7531: for(j=1; j <=ncovmodel; j++){
1.197 brouard 7532: 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]));
7533: 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]));
1.193 brouard 7534: jk++;
7535: }
7536: printf("\n");
7537: fprintf(ficlog,"\n");
7538: }
7539: }
7540: }
7541:
1.126 brouard 7542: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
7543: printf("# Scales (for hessian or gradient estimation)\n");
7544: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
7545: for(i=1,jk=1; i <=nlstate; i++){
7546: for(j=1; j <=nlstate+ndeath; j++){
7547: if (j!=i) {
7548: fprintf(ficres,"%1d%1d",i,j);
7549: printf("%1d%1d",i,j);
7550: fprintf(ficlog,"%1d%1d",i,j);
7551: for(k=1; k<=ncovmodel;k++){
7552: printf(" %.5e",delti[jk]);
7553: fprintf(ficlog," %.5e",delti[jk]);
7554: fprintf(ficres," %.5e",delti[jk]);
7555: jk++;
7556: }
7557: printf("\n");
7558: fprintf(ficlog,"\n");
7559: fprintf(ficres,"\n");
7560: }
7561: }
7562: }
7563:
7564: 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");
7565: if(mle>=1)
7566: 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");
7567: 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");
7568: /* # 121 Var(a12)\n\ */
7569: /* # 122 Cov(b12,a12) Var(b12)\n\ */
7570: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
7571: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
7572: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
7573: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
7574: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
7575: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
7576:
7577:
7578: /* Just to have a covariance matrix which will be more understandable
7579: even is we still don't want to manage dictionary of variables
7580: */
7581: for(itimes=1;itimes<=2;itimes++){
7582: jj=0;
7583: for(i=1; i <=nlstate; i++){
7584: for(j=1; j <=nlstate+ndeath; j++){
7585: if(j==i) continue;
7586: for(k=1; k<=ncovmodel;k++){
7587: jj++;
7588: ca[0]= k+'a'-1;ca[1]='\0';
7589: if(itimes==1){
7590: if(mle>=1)
7591: printf("#%1d%1d%d",i,j,k);
7592: fprintf(ficlog,"#%1d%1d%d",i,j,k);
7593: fprintf(ficres,"#%1d%1d%d",i,j,k);
7594: }else{
7595: if(mle>=1)
7596: printf("%1d%1d%d",i,j,k);
7597: fprintf(ficlog,"%1d%1d%d",i,j,k);
7598: fprintf(ficres,"%1d%1d%d",i,j,k);
7599: }
7600: ll=0;
7601: for(li=1;li <=nlstate; li++){
7602: for(lj=1;lj <=nlstate+ndeath; lj++){
7603: if(lj==li) continue;
7604: for(lk=1;lk<=ncovmodel;lk++){
7605: ll++;
7606: if(ll<=jj){
7607: cb[0]= lk +'a'-1;cb[1]='\0';
7608: if(ll<jj){
7609: if(itimes==1){
7610: if(mle>=1)
7611: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7612: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7613: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7614: }else{
7615: if(mle>=1)
7616: printf(" %.5e",matcov[jj][ll]);
7617: fprintf(ficlog," %.5e",matcov[jj][ll]);
7618: fprintf(ficres," %.5e",matcov[jj][ll]);
7619: }
7620: }else{
7621: if(itimes==1){
7622: if(mle>=1)
7623: printf(" Var(%s%1d%1d)",ca,i,j);
7624: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
7625: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
7626: }else{
7627: if(mle>=1)
7628: printf(" %.5e",matcov[jj][ll]);
7629: fprintf(ficlog," %.5e",matcov[jj][ll]);
7630: fprintf(ficres," %.5e",matcov[jj][ll]);
7631: }
7632: }
7633: }
7634: } /* end lk */
7635: } /* end lj */
7636: } /* end li */
7637: if(mle>=1)
7638: printf("\n");
7639: fprintf(ficlog,"\n");
7640: fprintf(ficres,"\n");
7641: numlinepar++;
7642: } /* end k*/
7643: } /*end j */
7644: } /* end i */
7645: } /* end itimes */
7646:
7647: fflush(ficlog);
7648: fflush(ficres);
7649:
7650: while((c=getc(ficpar))=='#' && c!= EOF){
7651: ungetc(c,ficpar);
7652: fgets(line, MAXLINE, ficpar);
1.141 brouard 7653: fputs(line,stdout);
1.126 brouard 7654: fputs(line,ficparo);
7655: }
7656: ungetc(c,ficpar);
7657:
7658: estepm=0;
7659: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
7660: if (estepm==0 || estepm < stepm) estepm=stepm;
7661: if (fage <= 2) {
7662: bage = ageminpar;
7663: fage = agemaxpar;
7664: }
7665:
7666: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
7667: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
7668: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
1.186 brouard 7669:
7670: /* Other stuffs, more or less useful */
1.126 brouard 7671: while((c=getc(ficpar))=='#' && c!= EOF){
7672: ungetc(c,ficpar);
7673: fgets(line, MAXLINE, ficpar);
1.141 brouard 7674: fputs(line,stdout);
1.126 brouard 7675: fputs(line,ficparo);
7676: }
7677: ungetc(c,ficpar);
7678:
7679: 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);
7680: 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);
7681: 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);
7682: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
7683: 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);
7684:
7685: while((c=getc(ficpar))=='#' && c!= EOF){
7686: ungetc(c,ficpar);
7687: fgets(line, MAXLINE, ficpar);
1.141 brouard 7688: fputs(line,stdout);
1.126 brouard 7689: fputs(line,ficparo);
7690: }
7691: ungetc(c,ficpar);
7692:
7693:
7694: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
7695: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
7696:
7697: fscanf(ficpar,"pop_based=%d\n",&popbased);
1.193 brouard 7698: fprintf(ficlog,"pop_based=%d\n",popbased);
1.126 brouard 7699: fprintf(ficparo,"pop_based=%d\n",popbased);
7700: fprintf(ficres,"pop_based=%d\n",popbased);
7701:
7702: while((c=getc(ficpar))=='#' && c!= EOF){
7703: ungetc(c,ficpar);
7704: fgets(line, MAXLINE, ficpar);
1.141 brouard 7705: fputs(line,stdout);
1.126 brouard 7706: fputs(line,ficparo);
7707: }
7708: ungetc(c,ficpar);
7709:
7710: 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);
7711: 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);
7712: 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);
7713: 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);
7714: 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);
7715: /* day and month of proj2 are not used but only year anproj2.*/
7716:
7717:
7718:
1.145 brouard 7719: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
7720: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 7721:
7722: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 7723: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
7724: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7725: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7726: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7727: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7728: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7729: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7730: }else
1.201 brouard 7731: printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.126 brouard 7732:
1.201 brouard 7733: printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt,\
1.126 brouard 7734: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
7735: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
7736:
7737: /*------------ free_vector -------------*/
7738: /* chdir(path); */
7739:
7740: free_ivector(wav,1,imx);
7741: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
7742: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
7743: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
7744: free_lvector(num,1,n);
7745: free_vector(agedc,1,n);
7746: /*free_matrix(covar,0,NCOVMAX,1,n);*/
7747: /*free_matrix(covar,1,NCOVMAX,1,n);*/
7748: fclose(ficparo);
7749: fclose(ficres);
7750:
7751:
1.186 brouard 7752: /* Other results (useful)*/
7753:
7754:
1.126 brouard 7755: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 7756: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
7757: prlim=matrix(1,nlstate,1,nlstate);
1.202 ! brouard 7758: prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl);
1.126 brouard 7759: fclose(ficrespl);
7760:
1.145 brouard 7761: #ifdef FREEEXIT2
7762: #include "freeexit2.h"
7763: #endif
7764:
1.126 brouard 7765: /*------------- h Pij x at various ages ------------*/
1.180 brouard 7766: /*#include "hpijx.h"*/
7767: hPijx(p, bage, fage);
1.145 brouard 7768: fclose(ficrespij);
1.126 brouard 7769:
1.145 brouard 7770: /*-------------- Variance of one-step probabilities---*/
7771: k=1;
1.126 brouard 7772: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
7773:
7774:
7775: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7776: for(i=1;i<=AGESUP;i++)
7777: for(j=1;j<=NCOVMAX;j++)
7778: for(k=1;k<=NCOVMAX;k++)
7779: probs[i][j][k]=0.;
7780:
7781: /*---------- Forecasting ------------------*/
7782: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
7783: if(prevfcast==1){
7784: /* if(stepm ==1){*/
1.201 brouard 7785: prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.126 brouard 7786: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
7787: /* } */
7788: /* else{ */
7789: /* erreur=108; */
7790: /* 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); */
7791: /* 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); */
7792: /* } */
7793: }
1.186 brouard 7794:
7795: /* ------ Other prevalence ratios------------ */
1.126 brouard 7796:
1.127 brouard 7797: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
7798:
7799: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
7800: /* 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",\
7801: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
7802: */
1.126 brouard 7803:
1.127 brouard 7804: if (mobilav!=0) {
7805: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7806: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
7807: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
7808: printf(" Error in movingaverage mobilav=%d\n",mobilav);
7809: }
1.126 brouard 7810: }
7811:
7812:
1.127 brouard 7813: /*---------- Health expectancies, no variances ------------*/
7814:
1.201 brouard 7815: strcpy(filerese,"E_");
7816: strcat(filerese,fileresu);
1.126 brouard 7817: if((ficreseij=fopen(filerese,"w"))==NULL) {
7818: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
7819: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
7820: }
7821: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
7822: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.145 brouard 7823: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7824: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7825:
7826: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.127 brouard 7827: fprintf(ficreseij,"\n#****** ");
7828: for(j=1;j<=cptcoveff;j++) {
1.200 brouard 7829: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.127 brouard 7830: }
7831: fprintf(ficreseij,"******\n");
7832:
7833: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7834: oldm=oldms;savm=savms;
7835: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
7836:
7837: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.145 brouard 7838: /*}*/
1.127 brouard 7839: }
7840: fclose(ficreseij);
7841:
7842:
7843: /*---------- Health expectancies and variances ------------*/
7844:
7845:
1.201 brouard 7846: strcpy(filerest,"T_");
7847: strcat(filerest,fileresu);
1.127 brouard 7848: if((ficrest=fopen(filerest,"w"))==NULL) {
7849: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
7850: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
7851: }
7852: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
7853: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
7854:
1.126 brouard 7855:
1.201 brouard 7856: strcpy(fileresstde,"STDE_");
7857: strcat(fileresstde,fileresu);
1.126 brouard 7858: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
7859: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
7860: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
7861: }
7862: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
7863: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
7864:
1.201 brouard 7865: strcpy(filerescve,"CVE_");
7866: strcat(filerescve,fileresu);
1.126 brouard 7867: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
7868: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
7869: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
7870: }
7871: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
7872: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
7873:
1.201 brouard 7874: strcpy(fileresv,"V_");
7875: strcat(fileresv,fileresu);
1.126 brouard 7876: if((ficresvij=fopen(fileresv,"w"))==NULL) {
7877: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
7878: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
7879: }
7880: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
7881: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
7882:
1.145 brouard 7883: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7884: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7885:
7886: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7887: fprintf(ficrest,"\n#****** ");
1.126 brouard 7888: for(j=1;j<=cptcoveff;j++)
1.200 brouard 7889: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 7890: fprintf(ficrest,"******\n");
7891:
7892: fprintf(ficresstdeij,"\n#****** ");
7893: fprintf(ficrescveij,"\n#****** ");
7894: for(j=1;j<=cptcoveff;j++) {
1.200 brouard 7895: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
7896: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 7897: }
7898: fprintf(ficresstdeij,"******\n");
7899: fprintf(ficrescveij,"******\n");
7900:
7901: fprintf(ficresvij,"\n#****** ");
7902: for(j=1;j<=cptcoveff;j++)
1.200 brouard 7903: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 7904: fprintf(ficresvij,"******\n");
7905:
7906: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7907: oldm=oldms;savm=savms;
1.127 brouard 7908: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
1.145 brouard 7909: /*
7910: */
7911: /* goto endfree; */
1.126 brouard 7912:
7913: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7914: pstamp(ficrest);
1.145 brouard 7915:
7916:
1.128 brouard 7917: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.199 brouard 7918: oldm=oldms;savm=savms; /* ZZ Segmentation fault */
1.161 brouard 7919: cptcod= 0; /* To be deleted */
7920: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
1.145 brouard 7921: fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# (weighted average of eij where weights are ");
1.128 brouard 7922: if(vpopbased==1)
7923: 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);
7924: else
7925: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
1.201 brouard 7926: fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
1.128 brouard 7927: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
7928: fprintf(ficrest,"\n");
1.199 brouard 7929: /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
1.128 brouard 7930: epj=vector(1,nlstate+1);
7931: for(age=bage; age <=fage ;age++){
1.199 brouard 7932: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k); /*ZZ Is it the correct prevalim */
1.128 brouard 7933: if (vpopbased==1) {
7934: if(mobilav ==0){
7935: for(i=1; i<=nlstate;i++)
7936: prlim[i][i]=probs[(int)age][i][k];
7937: }else{ /* mobilav */
7938: for(i=1; i<=nlstate;i++)
7939: prlim[i][i]=mobaverage[(int)age][i][k];
7940: }
1.126 brouard 7941: }
7942:
1.201 brouard 7943: fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
1.199 brouard 7944: /* printf(" age %4.0f ",age); */
1.128 brouard 7945: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
7946: for(i=1, epj[j]=0.;i <=nlstate;i++) {
7947: epj[j] += prlim[i][i]*eij[i][j][(int)age];
1.199 brouard 7948: /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
7949: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
1.128 brouard 7950: }
7951: epj[nlstate+1] +=epj[j];
1.126 brouard 7952: }
1.199 brouard 7953: /* printf(" age %4.0f \n",age); */
1.126 brouard 7954:
1.128 brouard 7955: for(i=1, vepp=0.;i <=nlstate;i++)
7956: for(j=1;j <=nlstate;j++)
7957: vepp += vareij[i][j][(int)age];
7958: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
7959: for(j=1;j <=nlstate;j++){
7960: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
7961: }
7962: fprintf(ficrest,"\n");
1.126 brouard 7963: }
7964: }
7965: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
7966: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
7967: free_vector(epj,1,nlstate+1);
1.145 brouard 7968: /*}*/
1.126 brouard 7969: }
7970: free_vector(weight,1,n);
1.145 brouard 7971: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.126 brouard 7972: free_imatrix(s,1,maxwav+1,1,n);
7973: free_matrix(anint,1,maxwav,1,n);
7974: free_matrix(mint,1,maxwav,1,n);
7975: free_ivector(cod,1,n);
7976: free_ivector(tab,1,NCOVMAX);
7977: fclose(ficresstdeij);
7978: fclose(ficrescveij);
7979: fclose(ficresvij);
7980: fclose(ficrest);
7981: fclose(ficpar);
7982:
7983: /*------- Variance of period (stable) prevalence------*/
7984:
1.201 brouard 7985: strcpy(fileresvpl,"VPL_");
7986: strcat(fileresvpl,fileresu);
1.126 brouard 7987: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
7988: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
7989: exit(0);
7990: }
7991: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
7992:
1.145 brouard 7993: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7994: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7995:
7996: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7997: fprintf(ficresvpl,"\n#****** ");
1.126 brouard 7998: for(j=1;j<=cptcoveff;j++)
1.200 brouard 7999: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 8000: fprintf(ficresvpl,"******\n");
8001:
8002: varpl=matrix(1,nlstate,(int) bage, (int) fage);
8003: oldm=oldms;savm=savms;
8004: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
8005: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 8006: /*}*/
1.126 brouard 8007: }
8008:
8009: fclose(ficresvpl);
8010:
8011: /*---------- End : free ----------------*/
8012: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
8013: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
8014: } /* mle==-3 arrives here for freeing */
1.164 brouard 8015: /* endfree:*/
1.141 brouard 8016: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.126 brouard 8017: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
8018: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
8019: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
8020: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
8021: free_matrix(covar,0,NCOVMAX,1,n);
8022: free_matrix(matcov,1,npar,1,npar);
8023: /*free_vector(delti,1,npar);*/
8024: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
8025: free_matrix(agev,1,maxwav,1,imx);
8026: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
8027:
1.145 brouard 8028: free_ivector(ncodemax,1,NCOVMAX);
1.192 brouard 8029: free_ivector(ncodemaxwundef,1,NCOVMAX);
1.145 brouard 8030: free_ivector(Tvar,1,NCOVMAX);
8031: free_ivector(Tprod,1,NCOVMAX);
8032: free_ivector(Tvaraff,1,NCOVMAX);
8033: free_ivector(Tage,1,NCOVMAX);
1.126 brouard 8034:
8035: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
1.200 brouard 8036: /* free_imatrix(codtab,1,100,1,10); */
1.126 brouard 8037: fflush(fichtm);
8038: fflush(ficgp);
8039:
8040:
8041: if((nberr >0) || (nbwarn>0)){
8042: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
8043: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
8044: }else{
8045: printf("End of Imach\n");
8046: fprintf(ficlog,"End of Imach\n");
8047: }
8048: printf("See log file on %s\n",filelog);
8049: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 8050: /*(void) gettimeofday(&end_time,&tzp);*/
8051: rend_time = time(NULL);
8052: end_time = *localtime(&rend_time);
8053: /* tml = *localtime(&end_time.tm_sec); */
8054: strcpy(strtend,asctime(&end_time));
1.126 brouard 8055: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
8056: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 8057: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.126 brouard 8058:
1.157 brouard 8059: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
8060: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
8061: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 8062: /* printf("Total time was %d uSec.\n", total_usecs);*/
8063: /* if(fileappend(fichtm,optionfilehtm)){ */
8064: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
8065: fclose(fichtm);
8066: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
8067: fclose(fichtmcov);
8068: fclose(ficgp);
8069: fclose(ficlog);
8070: /*------ End -----------*/
8071:
8072:
8073: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 8074: #ifdef WIN32
8075: if (_chdir(pathcd) != 0)
8076: printf("Can't move to directory %s!\n",path);
8077: if(_getcwd(pathcd,MAXLINE) > 0)
8078: #else
1.126 brouard 8079: if(chdir(pathcd) != 0)
1.184 brouard 8080: printf("Can't move to directory %s!\n", path);
8081: if (getcwd(pathcd, MAXLINE) > 0)
8082: #endif
1.126 brouard 8083: printf("Current directory %s!\n",pathcd);
8084: /*strcat(plotcmd,CHARSEPARATOR);*/
8085: sprintf(plotcmd,"gnuplot");
1.157 brouard 8086: #ifdef _WIN32
1.126 brouard 8087: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
8088: #endif
8089: if(!stat(plotcmd,&info)){
1.158 brouard 8090: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 8091: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 8092: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 8093: }else
8094: strcpy(pplotcmd,plotcmd);
1.157 brouard 8095: #ifdef __unix
1.126 brouard 8096: strcpy(plotcmd,GNUPLOTPROGRAM);
8097: if(!stat(plotcmd,&info)){
1.158 brouard 8098: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 8099: }else
8100: strcpy(pplotcmd,plotcmd);
8101: #endif
8102: }else
8103: strcpy(pplotcmd,plotcmd);
8104:
8105: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 8106: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 8107:
8108: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 8109: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 8110: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 8111: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 8112: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 8113: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 8114: }
1.158 brouard 8115: printf(" Successful, please wait...");
1.126 brouard 8116: while (z[0] != 'q') {
8117: /* chdir(path); */
1.154 brouard 8118: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 8119: scanf("%s",z);
8120: /* if (z[0] == 'c') system("./imach"); */
8121: if (z[0] == 'e') {
1.158 brouard 8122: #ifdef __APPLE__
1.152 brouard 8123: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 8124: #elif __linux
8125: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 8126: #else
1.152 brouard 8127: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 8128: #endif
8129: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
8130: system(pplotcmd);
1.126 brouard 8131: }
8132: else if (z[0] == 'g') system(plotcmd);
8133: else if (z[0] == 'q') exit(0);
8134: }
8135: end:
8136: while (z[0] != 'q') {
1.195 brouard 8137: printf("\nType q for exiting: "); fflush(stdout);
1.126 brouard 8138: scanf("%s",z);
8139: }
8140: }
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