Annotation of imach/src/imach.c, revision 1.201
1.201 ! brouard 1: /* $Id: imach.c,v 1.200 2015/09/09 16:53:55 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.201 ! brouard 4: Revision 1.200 2015/09/09 16:53:55 brouard
! 5: Summary: Big bug thanks to Flavia
! 6:
! 7: Even model=1+age+V2. did not work anymore
! 8:
1.200 brouard 9: Revision 1.199 2015/09/07 14:09:23 brouard
10: Summary: 0.98q6 changing default small png format for graph to vectorized svg.
11:
1.199 brouard 12: Revision 1.198 2015/09/03 07:14:39 brouard
13: Summary: 0.98q5 Flavia
14:
1.198 brouard 15: Revision 1.197 2015/09/01 18:24:39 brouard
16: *** empty log message ***
17:
1.197 brouard 18: Revision 1.196 2015/08/18 23:17:52 brouard
19: Summary: 0.98q5
20:
1.196 brouard 21: Revision 1.195 2015/08/18 16:28:39 brouard
22: Summary: Adding a hack for testing purpose
23:
24: After reading the title, ftol and model lines, if the comment line has
25: a q, starting with #q, the answer at the end of the run is quit. It
26: permits to run test files in batch with ctest. The former workaround was
27: $ echo q | imach foo.imach
28:
1.195 brouard 29: Revision 1.194 2015/08/18 13:32:00 brouard
30: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
31:
1.194 brouard 32: Revision 1.193 2015/08/04 07:17:42 brouard
33: Summary: 0.98q4
34:
1.193 brouard 35: Revision 1.192 2015/07/16 16:49:02 brouard
36: Summary: Fixing some outputs
37:
1.192 brouard 38: Revision 1.191 2015/07/14 10:00:33 brouard
39: Summary: Some fixes
40:
1.191 brouard 41: Revision 1.190 2015/05/05 08:51:13 brouard
42: Summary: Adding digits in output parameters (7 digits instead of 6)
43:
44: Fix 1+age+.
45:
1.190 brouard 46: Revision 1.189 2015/04/30 14:45:16 brouard
47: Summary: 0.98q2
48:
1.189 brouard 49: Revision 1.188 2015/04/30 08:27:53 brouard
50: *** empty log message ***
51:
1.188 brouard 52: Revision 1.187 2015/04/29 09:11:15 brouard
53: *** empty log message ***
54:
1.187 brouard 55: Revision 1.186 2015/04/23 12:01:52 brouard
56: Summary: V1*age is working now, version 0.98q1
57:
58: Some codes had been disabled in order to simplify and Vn*age was
59: working in the optimization phase, ie, giving correct MLE parameters,
60: but, as usual, outputs were not correct and program core dumped.
61:
1.186 brouard 62: Revision 1.185 2015/03/11 13:26:42 brouard
63: Summary: Inclusion of compile and links command line for Intel Compiler
64:
1.185 brouard 65: Revision 1.184 2015/03/11 11:52:39 brouard
66: Summary: Back from Windows 8. Intel Compiler
67:
1.184 brouard 68: Revision 1.183 2015/03/10 20:34:32 brouard
69: Summary: 0.98q0, trying with directest, mnbrak fixed
70:
71: We use directest instead of original Powell test; probably no
72: incidence on the results, but better justifications;
73: We fixed Numerical Recipes mnbrak routine which was wrong and gave
74: wrong results.
75:
1.183 brouard 76: Revision 1.182 2015/02/12 08:19:57 brouard
77: Summary: Trying to keep directest which seems simpler and more general
78: Author: Nicolas Brouard
79:
1.182 brouard 80: Revision 1.181 2015/02/11 23:22:24 brouard
81: Summary: Comments on Powell added
82:
83: Author:
84:
1.181 brouard 85: Revision 1.180 2015/02/11 17:33:45 brouard
86: Summary: Finishing move from main to function (hpijx and prevalence_limit)
87:
1.180 brouard 88: Revision 1.179 2015/01/04 09:57:06 brouard
89: Summary: back to OS/X
90:
1.179 brouard 91: Revision 1.178 2015/01/04 09:35:48 brouard
92: *** empty log message ***
93:
1.178 brouard 94: Revision 1.177 2015/01/03 18:40:56 brouard
95: Summary: Still testing ilc32 on OSX
96:
1.177 brouard 97: Revision 1.176 2015/01/03 16:45:04 brouard
98: *** empty log message ***
99:
1.176 brouard 100: Revision 1.175 2015/01/03 16:33:42 brouard
101: *** empty log message ***
102:
1.175 brouard 103: Revision 1.174 2015/01/03 16:15:49 brouard
104: Summary: Still in cross-compilation
105:
1.174 brouard 106: Revision 1.173 2015/01/03 12:06:26 brouard
107: Summary: trying to detect cross-compilation
108:
1.173 brouard 109: Revision 1.172 2014/12/27 12:07:47 brouard
110: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
111:
1.172 brouard 112: Revision 1.171 2014/12/23 13:26:59 brouard
113: Summary: Back from Visual C
114:
115: Still problem with utsname.h on Windows
116:
1.171 brouard 117: Revision 1.170 2014/12/23 11:17:12 brouard
118: Summary: Cleaning some \%% back to %%
119:
120: The escape was mandatory for a specific compiler (which one?), but too many warnings.
121:
1.170 brouard 122: Revision 1.169 2014/12/22 23:08:31 brouard
123: Summary: 0.98p
124:
125: Outputs some informations on compiler used, OS etc. Testing on different platforms.
126:
1.169 brouard 127: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 128: Summary: update
1.169 brouard 129:
1.168 brouard 130: Revision 1.167 2014/12/22 13:50:56 brouard
131: Summary: Testing uname and compiler version and if compiled 32 or 64
132:
133: Testing on Linux 64
134:
1.167 brouard 135: Revision 1.166 2014/12/22 11:40:47 brouard
136: *** empty log message ***
137:
1.166 brouard 138: Revision 1.165 2014/12/16 11:20:36 brouard
139: Summary: After compiling on Visual C
140:
141: * imach.c (Module): Merging 1.61 to 1.162
142:
1.165 brouard 143: Revision 1.164 2014/12/16 10:52:11 brouard
144: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
145:
146: * imach.c (Module): Merging 1.61 to 1.162
147:
1.164 brouard 148: Revision 1.163 2014/12/16 10:30:11 brouard
149: * imach.c (Module): Merging 1.61 to 1.162
150:
1.163 brouard 151: Revision 1.162 2014/09/25 11:43:39 brouard
152: Summary: temporary backup 0.99!
153:
1.162 brouard 154: Revision 1.1 2014/09/16 11:06:58 brouard
155: Summary: With some code (wrong) for nlopt
156:
157: Author:
158:
159: Revision 1.161 2014/09/15 20:41:41 brouard
160: Summary: Problem with macro SQR on Intel compiler
161:
1.161 brouard 162: Revision 1.160 2014/09/02 09:24:05 brouard
163: *** empty log message ***
164:
1.160 brouard 165: Revision 1.159 2014/09/01 10:34:10 brouard
166: Summary: WIN32
167: Author: Brouard
168:
1.159 brouard 169: Revision 1.158 2014/08/27 17:11:51 brouard
170: *** empty log message ***
171:
1.158 brouard 172: Revision 1.157 2014/08/27 16:26:55 brouard
173: Summary: Preparing windows Visual studio version
174: Author: Brouard
175:
176: In order to compile on Visual studio, time.h is now correct and time_t
177: and tm struct should be used. difftime should be used but sometimes I
178: just make the differences in raw time format (time(&now).
179: Trying to suppress #ifdef LINUX
180: Add xdg-open for __linux in order to open default browser.
181:
1.157 brouard 182: Revision 1.156 2014/08/25 20:10:10 brouard
183: *** empty log message ***
184:
1.156 brouard 185: Revision 1.155 2014/08/25 18:32:34 brouard
186: Summary: New compile, minor changes
187: Author: Brouard
188:
1.155 brouard 189: Revision 1.154 2014/06/20 17:32:08 brouard
190: Summary: Outputs now all graphs of convergence to period prevalence
191:
1.154 brouard 192: Revision 1.153 2014/06/20 16:45:46 brouard
193: Summary: If 3 live state, convergence to period prevalence on same graph
194: Author: Brouard
195:
1.153 brouard 196: Revision 1.152 2014/06/18 17:54:09 brouard
197: Summary: open browser, use gnuplot on same dir than imach if not found in the path
198:
1.152 brouard 199: Revision 1.151 2014/06/18 16:43:30 brouard
200: *** empty log message ***
201:
1.151 brouard 202: Revision 1.150 2014/06/18 16:42:35 brouard
203: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
204: Author: brouard
205:
1.150 brouard 206: Revision 1.149 2014/06/18 15:51:14 brouard
207: Summary: Some fixes in parameter files errors
208: Author: Nicolas Brouard
209:
1.149 brouard 210: Revision 1.148 2014/06/17 17:38:48 brouard
211: Summary: Nothing new
212: Author: Brouard
213:
214: Just a new packaging for OS/X version 0.98nS
215:
1.148 brouard 216: Revision 1.147 2014/06/16 10:33:11 brouard
217: *** empty log message ***
218:
1.147 brouard 219: Revision 1.146 2014/06/16 10:20:28 brouard
220: Summary: Merge
221: Author: Brouard
222:
223: Merge, before building revised version.
224:
1.146 brouard 225: Revision 1.145 2014/06/10 21:23:15 brouard
226: Summary: Debugging with valgrind
227: Author: Nicolas Brouard
228:
229: Lot of changes in order to output the results with some covariates
230: After the Edimburgh REVES conference 2014, it seems mandatory to
231: improve the code.
232: No more memory valgrind error but a lot has to be done in order to
233: continue the work of splitting the code into subroutines.
234: Also, decodemodel has been improved. Tricode is still not
235: optimal. nbcode should be improved. Documentation has been added in
236: the source code.
237:
1.144 brouard 238: Revision 1.143 2014/01/26 09:45:38 brouard
239: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
240:
241: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
242: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
243:
1.143 brouard 244: Revision 1.142 2014/01/26 03:57:36 brouard
245: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
246:
247: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
248:
1.142 brouard 249: Revision 1.141 2014/01/26 02:42:01 brouard
250: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
251:
1.141 brouard 252: Revision 1.140 2011/09/02 10:37:54 brouard
253: Summary: times.h is ok with mingw32 now.
254:
1.140 brouard 255: Revision 1.139 2010/06/14 07:50:17 brouard
256: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
257: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
258:
1.139 brouard 259: Revision 1.138 2010/04/30 18:19:40 brouard
260: *** empty log message ***
261:
1.138 brouard 262: Revision 1.137 2010/04/29 18:11:38 brouard
263: (Module): Checking covariates for more complex models
264: than V1+V2. A lot of change to be done. Unstable.
265:
1.137 brouard 266: Revision 1.136 2010/04/26 20:30:53 brouard
267: (Module): merging some libgsl code. Fixing computation
268: of likelione (using inter/intrapolation if mle = 0) in order to
269: get same likelihood as if mle=1.
270: Some cleaning of code and comments added.
271:
1.136 brouard 272: Revision 1.135 2009/10/29 15:33:14 brouard
273: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
274:
1.135 brouard 275: Revision 1.134 2009/10/29 13:18:53 brouard
276: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
277:
1.134 brouard 278: Revision 1.133 2009/07/06 10:21:25 brouard
279: just nforces
280:
1.133 brouard 281: Revision 1.132 2009/07/06 08:22:05 brouard
282: Many tings
283:
1.132 brouard 284: Revision 1.131 2009/06/20 16:22:47 brouard
285: Some dimensions resccaled
286:
1.131 brouard 287: Revision 1.130 2009/05/26 06:44:34 brouard
288: (Module): Max Covariate is now set to 20 instead of 8. A
289: lot of cleaning with variables initialized to 0. Trying to make
290: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
291:
1.130 brouard 292: Revision 1.129 2007/08/31 13:49:27 lievre
293: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
294:
1.129 lievre 295: Revision 1.128 2006/06/30 13:02:05 brouard
296: (Module): Clarifications on computing e.j
297:
1.128 brouard 298: Revision 1.127 2006/04/28 18:11:50 brouard
299: (Module): Yes the sum of survivors was wrong since
300: imach-114 because nhstepm was no more computed in the age
301: loop. Now we define nhstepma in the age loop.
302: (Module): In order to speed up (in case of numerous covariates) we
303: compute health expectancies (without variances) in a first step
304: and then all the health expectancies with variances or standard
305: deviation (needs data from the Hessian matrices) which slows the
306: computation.
307: In the future we should be able to stop the program is only health
308: expectancies and graph are needed without standard deviations.
309:
1.127 brouard 310: Revision 1.126 2006/04/28 17:23:28 brouard
311: (Module): Yes the sum of survivors was wrong since
312: imach-114 because nhstepm was no more computed in the age
313: loop. Now we define nhstepma in the age loop.
314: Version 0.98h
315:
1.126 brouard 316: Revision 1.125 2006/04/04 15:20:31 lievre
317: Errors in calculation of health expectancies. Age was not initialized.
318: Forecasting file added.
319:
320: Revision 1.124 2006/03/22 17:13:53 lievre
321: Parameters are printed with %lf instead of %f (more numbers after the comma).
322: The log-likelihood is printed in the log file
323:
324: Revision 1.123 2006/03/20 10:52:43 brouard
325: * imach.c (Module): <title> changed, corresponds to .htm file
326: name. <head> headers where missing.
327:
328: * imach.c (Module): Weights can have a decimal point as for
329: English (a comma might work with a correct LC_NUMERIC environment,
330: otherwise the weight is truncated).
331: Modification of warning when the covariates values are not 0 or
332: 1.
333: Version 0.98g
334:
335: Revision 1.122 2006/03/20 09:45:41 brouard
336: (Module): Weights can have a decimal point as for
337: English (a comma might work with a correct LC_NUMERIC environment,
338: otherwise the weight is truncated).
339: Modification of warning when the covariates values are not 0 or
340: 1.
341: Version 0.98g
342:
343: Revision 1.121 2006/03/16 17:45:01 lievre
344: * imach.c (Module): Comments concerning covariates added
345:
346: * imach.c (Module): refinements in the computation of lli if
347: status=-2 in order to have more reliable computation if stepm is
348: not 1 month. Version 0.98f
349:
350: Revision 1.120 2006/03/16 15:10:38 lievre
351: (Module): refinements in the computation of lli if
352: status=-2 in order to have more reliable computation if stepm is
353: not 1 month. Version 0.98f
354:
355: Revision 1.119 2006/03/15 17:42:26 brouard
356: (Module): Bug if status = -2, the loglikelihood was
357: computed as likelihood omitting the logarithm. Version O.98e
358:
359: Revision 1.118 2006/03/14 18:20:07 brouard
360: (Module): varevsij Comments added explaining the second
361: table of variances if popbased=1 .
362: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
363: (Module): Function pstamp added
364: (Module): Version 0.98d
365:
366: Revision 1.117 2006/03/14 17:16:22 brouard
367: (Module): varevsij Comments added explaining the second
368: table of variances if popbased=1 .
369: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
370: (Module): Function pstamp added
371: (Module): Version 0.98d
372:
373: Revision 1.116 2006/03/06 10:29:27 brouard
374: (Module): Variance-covariance wrong links and
375: varian-covariance of ej. is needed (Saito).
376:
377: Revision 1.115 2006/02/27 12:17:45 brouard
378: (Module): One freematrix added in mlikeli! 0.98c
379:
380: Revision 1.114 2006/02/26 12:57:58 brouard
381: (Module): Some improvements in processing parameter
382: filename with strsep.
383:
384: Revision 1.113 2006/02/24 14:20:24 brouard
385: (Module): Memory leaks checks with valgrind and:
386: datafile was not closed, some imatrix were not freed and on matrix
387: allocation too.
388:
389: Revision 1.112 2006/01/30 09:55:26 brouard
390: (Module): Back to gnuplot.exe instead of wgnuplot.exe
391:
392: Revision 1.111 2006/01/25 20:38:18 brouard
393: (Module): Lots of cleaning and bugs added (Gompertz)
394: (Module): Comments can be added in data file. Missing date values
395: can be a simple dot '.'.
396:
397: Revision 1.110 2006/01/25 00:51:50 brouard
398: (Module): Lots of cleaning and bugs added (Gompertz)
399:
400: Revision 1.109 2006/01/24 19:37:15 brouard
401: (Module): Comments (lines starting with a #) are allowed in data.
402:
403: Revision 1.108 2006/01/19 18:05:42 lievre
404: Gnuplot problem appeared...
405: To be fixed
406:
407: Revision 1.107 2006/01/19 16:20:37 brouard
408: Test existence of gnuplot in imach path
409:
410: Revision 1.106 2006/01/19 13:24:36 brouard
411: Some cleaning and links added in html output
412:
413: Revision 1.105 2006/01/05 20:23:19 lievre
414: *** empty log message ***
415:
416: Revision 1.104 2005/09/30 16:11:43 lievre
417: (Module): sump fixed, loop imx fixed, and simplifications.
418: (Module): If the status is missing at the last wave but we know
419: that the person is alive, then we can code his/her status as -2
420: (instead of missing=-1 in earlier versions) and his/her
421: contributions to the likelihood is 1 - Prob of dying from last
422: health status (= 1-p13= p11+p12 in the easiest case of somebody in
423: the healthy state at last known wave). Version is 0.98
424:
425: Revision 1.103 2005/09/30 15:54:49 lievre
426: (Module): sump fixed, loop imx fixed, and simplifications.
427:
428: Revision 1.102 2004/09/15 17:31:30 brouard
429: Add the possibility to read data file including tab characters.
430:
431: Revision 1.101 2004/09/15 10:38:38 brouard
432: Fix on curr_time
433:
434: Revision 1.100 2004/07/12 18:29:06 brouard
435: Add version for Mac OS X. Just define UNIX in Makefile
436:
437: Revision 1.99 2004/06/05 08:57:40 brouard
438: *** empty log message ***
439:
440: Revision 1.98 2004/05/16 15:05:56 brouard
441: New version 0.97 . First attempt to estimate force of mortality
442: directly from the data i.e. without the need of knowing the health
443: state at each age, but using a Gompertz model: log u =a + b*age .
444: This is the basic analysis of mortality and should be done before any
445: other analysis, in order to test if the mortality estimated from the
446: cross-longitudinal survey is different from the mortality estimated
447: from other sources like vital statistic data.
448:
449: The same imach parameter file can be used but the option for mle should be -3.
450:
1.133 brouard 451: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 452: former routines in order to include the new code within the former code.
453:
454: The output is very simple: only an estimate of the intercept and of
455: the slope with 95% confident intervals.
456:
457: Current limitations:
458: A) Even if you enter covariates, i.e. with the
459: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
460: B) There is no computation of Life Expectancy nor Life Table.
461:
462: Revision 1.97 2004/02/20 13:25:42 lievre
463: Version 0.96d. Population forecasting command line is (temporarily)
464: suppressed.
465:
466: Revision 1.96 2003/07/15 15:38:55 brouard
467: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
468: rewritten within the same printf. Workaround: many printfs.
469:
470: Revision 1.95 2003/07/08 07:54:34 brouard
471: * imach.c (Repository):
472: (Repository): Using imachwizard code to output a more meaningful covariance
473: matrix (cov(a12,c31) instead of numbers.
474:
475: Revision 1.94 2003/06/27 13:00:02 brouard
476: Just cleaning
477:
478: Revision 1.93 2003/06/25 16:33:55 brouard
479: (Module): On windows (cygwin) function asctime_r doesn't
480: exist so I changed back to asctime which exists.
481: (Module): Version 0.96b
482:
483: Revision 1.92 2003/06/25 16:30:45 brouard
484: (Module): On windows (cygwin) function asctime_r doesn't
485: exist so I changed back to asctime which exists.
486:
487: Revision 1.91 2003/06/25 15:30:29 brouard
488: * imach.c (Repository): Duplicated warning errors corrected.
489: (Repository): Elapsed time after each iteration is now output. It
490: helps to forecast when convergence will be reached. Elapsed time
491: is stamped in powell. We created a new html file for the graphs
492: concerning matrix of covariance. It has extension -cov.htm.
493:
494: Revision 1.90 2003/06/24 12:34:15 brouard
495: (Module): Some bugs corrected for windows. Also, when
496: mle=-1 a template is output in file "or"mypar.txt with the design
497: of the covariance matrix to be input.
498:
499: Revision 1.89 2003/06/24 12:30:52 brouard
500: (Module): Some bugs corrected for windows. Also, when
501: mle=-1 a template is output in file "or"mypar.txt with the design
502: of the covariance matrix to be input.
503:
504: Revision 1.88 2003/06/23 17:54:56 brouard
505: * 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.
506:
507: Revision 1.87 2003/06/18 12:26:01 brouard
508: Version 0.96
509:
510: Revision 1.86 2003/06/17 20:04:08 brouard
511: (Module): Change position of html and gnuplot routines and added
512: routine fileappend.
513:
514: Revision 1.85 2003/06/17 13:12:43 brouard
515: * imach.c (Repository): Check when date of death was earlier that
516: current date of interview. It may happen when the death was just
517: prior to the death. In this case, dh was negative and likelihood
518: was wrong (infinity). We still send an "Error" but patch by
519: assuming that the date of death was just one stepm after the
520: interview.
521: (Repository): Because some people have very long ID (first column)
522: we changed int to long in num[] and we added a new lvector for
523: memory allocation. But we also truncated to 8 characters (left
524: truncation)
525: (Repository): No more line truncation errors.
526:
527: Revision 1.84 2003/06/13 21:44:43 brouard
528: * imach.c (Repository): Replace "freqsummary" at a correct
529: place. It differs from routine "prevalence" which may be called
530: many times. Probs is memory consuming and must be used with
531: parcimony.
532: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
533:
534: Revision 1.83 2003/06/10 13:39:11 lievre
535: *** empty log message ***
536:
537: Revision 1.82 2003/06/05 15:57:20 brouard
538: Add log in imach.c and fullversion number is now printed.
539:
540: */
541: /*
542: Interpolated Markov Chain
543:
544: Short summary of the programme:
545:
546: This program computes Healthy Life Expectancies from
547: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
548: first survey ("cross") where individuals from different ages are
549: interviewed on their health status or degree of disability (in the
550: case of a health survey which is our main interest) -2- at least a
551: second wave of interviews ("longitudinal") which measure each change
552: (if any) in individual health status. Health expectancies are
553: computed from the time spent in each health state according to a
554: model. More health states you consider, more time is necessary to reach the
555: Maximum Likelihood of the parameters involved in the model. The
556: simplest model is the multinomial logistic model where pij is the
557: probability to be observed in state j at the second wave
558: conditional to be observed in state i at the first wave. Therefore
559: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
560: 'age' is age and 'sex' is a covariate. If you want to have a more
561: complex model than "constant and age", you should modify the program
562: where the markup *Covariates have to be included here again* invites
563: you to do it. More covariates you add, slower the
564: convergence.
565:
566: The advantage of this computer programme, compared to a simple
567: multinomial logistic model, is clear when the delay between waves is not
568: identical for each individual. Also, if a individual missed an
569: intermediate interview, the information is lost, but taken into
570: account using an interpolation or extrapolation.
571:
572: hPijx is the probability to be observed in state i at age x+h
573: conditional to the observed state i at age x. The delay 'h' can be
574: split into an exact number (nh*stepm) of unobserved intermediate
575: states. This elementary transition (by month, quarter,
576: semester or year) is modelled as a multinomial logistic. The hPx
577: matrix is simply the matrix product of nh*stepm elementary matrices
578: and the contribution of each individual to the likelihood is simply
579: hPijx.
580:
581: Also this programme outputs the covariance matrix of the parameters but also
582: of the life expectancies. It also computes the period (stable) prevalence.
583:
1.133 brouard 584: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
585: Institut national d'études démographiques, Paris.
1.126 brouard 586: This software have been partly granted by Euro-REVES, a concerted action
587: from the European Union.
588: It is copyrighted identically to a GNU software product, ie programme and
589: software can be distributed freely for non commercial use. Latest version
590: can be accessed at http://euroreves.ined.fr/imach .
591:
592: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
593: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
594:
595: **********************************************************************/
596: /*
597: main
598: read parameterfile
599: read datafile
600: concatwav
601: freqsummary
602: if (mle >= 1)
603: mlikeli
604: print results files
605: if mle==1
606: computes hessian
607: read end of parameter file: agemin, agemax, bage, fage, estepm
608: begin-prev-date,...
609: open gnuplot file
610: open html file
1.145 brouard 611: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
612: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
613: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
614: freexexit2 possible for memory heap.
615:
616: h Pij x | pij_nom ficrestpij
617: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
618: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
619: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
620:
621: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
622: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
623: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
624: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
625: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
626:
1.126 brouard 627: forecasting if prevfcast==1 prevforecast call prevalence()
628: health expectancies
629: Variance-covariance of DFLE
630: prevalence()
631: movingaverage()
632: varevsij()
633: if popbased==1 varevsij(,popbased)
634: total life expectancies
635: Variance of period (stable) prevalence
636: end
637: */
638:
1.187 brouard 639: /* #define DEBUG */
640: /* #define DEBUGBRENT */
1.165 brouard 641: #define POWELL /* Instead of NLOPT */
1.192 brouard 642: #define POWELLF1F3 /* Skip test */
1.186 brouard 643: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
644: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 645:
646: #include <math.h>
647: #include <stdio.h>
648: #include <stdlib.h>
649: #include <string.h>
1.159 brouard 650:
651: #ifdef _WIN32
652: #include <io.h>
1.172 brouard 653: #include <windows.h>
654: #include <tchar.h>
1.159 brouard 655: #else
1.126 brouard 656: #include <unistd.h>
1.159 brouard 657: #endif
1.126 brouard 658:
659: #include <limits.h>
660: #include <sys/types.h>
1.171 brouard 661:
662: #if defined(__GNUC__)
663: #include <sys/utsname.h> /* Doesn't work on Windows */
664: #endif
665:
1.126 brouard 666: #include <sys/stat.h>
667: #include <errno.h>
1.159 brouard 668: /* extern int errno; */
1.126 brouard 669:
1.157 brouard 670: /* #ifdef LINUX */
671: /* #include <time.h> */
672: /* #include "timeval.h" */
673: /* #else */
674: /* #include <sys/time.h> */
675: /* #endif */
676:
1.126 brouard 677: #include <time.h>
678:
1.136 brouard 679: #ifdef GSL
680: #include <gsl/gsl_errno.h>
681: #include <gsl/gsl_multimin.h>
682: #endif
683:
1.167 brouard 684:
1.162 brouard 685: #ifdef NLOPT
686: #include <nlopt.h>
687: typedef struct {
688: double (* function)(double [] );
689: } myfunc_data ;
690: #endif
691:
1.126 brouard 692: /* #include <libintl.h> */
693: /* #define _(String) gettext (String) */
694:
1.141 brouard 695: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 696:
697: #define GNUPLOTPROGRAM "gnuplot"
698: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
699: #define FILENAMELENGTH 132
700:
701: #define GLOCK_ERROR_NOPATH -1 /* empty path */
702: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
703:
1.144 brouard 704: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
705: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 706:
707: #define NINTERVMAX 8
1.144 brouard 708: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
709: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
710: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.197 brouard 711: #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.126 brouard 712: #define MAXN 20000
1.144 brouard 713: #define YEARM 12. /**< Number of months per year */
1.126 brouard 714: #define AGESUP 130
715: #define AGEBASE 40
1.194 brouard 716: #define AGEOVERFLOW 1.e20
1.164 brouard 717: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 718: #ifdef _WIN32
719: #define DIRSEPARATOR '\\'
720: #define CHARSEPARATOR "\\"
721: #define ODIRSEPARATOR '/'
722: #else
1.126 brouard 723: #define DIRSEPARATOR '/'
724: #define CHARSEPARATOR "/"
725: #define ODIRSEPARATOR '\\'
726: #endif
727:
1.201 ! brouard 728: /* $Id: imach.c,v 1.200 2015/09/09 16:53:55 brouard Exp $ */
1.126 brouard 729: /* $State: Exp $ */
1.196 brouard 730: #include "version.h"
731: char version[]=__IMACH_VERSION__;
1.197 brouard 732: 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";
1.201 ! brouard 733: char fullversion[]="$Revision: 1.200 $ $Date: 2015/09/09 16:53:55 $";
1.126 brouard 734: char strstart[80];
735: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 736: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 737: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 738: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
739: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
740: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
741: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
742: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
743: int cptcovprodnoage=0; /**< Number of covariate products without age */
744: int cptcoveff=0; /* Total number of covariates to vary for printing results */
745: int cptcov=0; /* Working variable */
1.126 brouard 746: int npar=NPARMAX;
747: int nlstate=2; /* Number of live states */
748: int ndeath=1; /* Number of dead states */
1.130 brouard 749: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.126 brouard 750: int popbased=0;
751:
752: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 753: int maxwav=0; /* Maxim number of waves */
754: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
755: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
756: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 757: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 758: int mle=1, weightopt=0;
1.126 brouard 759: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
760: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
761: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
762: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 763: int countcallfunc=0; /* Count the number of calls to func */
1.130 brouard 764: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 765: double **matprod2(); /* test */
1.126 brouard 766: double **oldm, **newm, **savm; /* Working pointers to matrices */
767: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.136 brouard 768: /*FILE *fic ; */ /* Used in readdata only */
769: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.126 brouard 770: FILE *ficlog, *ficrespow;
1.130 brouard 771: int globpr=0; /* Global variable for printing or not */
1.126 brouard 772: double fretone; /* Only one call to likelihood */
1.130 brouard 773: long ipmx=0; /* Number of contributions */
1.126 brouard 774: double sw; /* Sum of weights */
775: char filerespow[FILENAMELENGTH];
776: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
777: FILE *ficresilk;
778: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
779: FILE *ficresprobmorprev;
780: FILE *fichtm, *fichtmcov; /* Html File */
781: FILE *ficreseij;
782: char filerese[FILENAMELENGTH];
783: FILE *ficresstdeij;
784: char fileresstde[FILENAMELENGTH];
785: FILE *ficrescveij;
786: char filerescve[FILENAMELENGTH];
787: FILE *ficresvij;
788: char fileresv[FILENAMELENGTH];
789: FILE *ficresvpl;
790: char fileresvpl[FILENAMELENGTH];
791: char title[MAXLINE];
792: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
793: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
794: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
795: char command[FILENAMELENGTH];
796: int outcmd=0;
797:
798: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.201 ! brouard 799: char fileresu[FILENAMELENGTH]; /* Without r in front */
1.126 brouard 800: char filelog[FILENAMELENGTH]; /* Log file */
801: char filerest[FILENAMELENGTH];
802: char fileregp[FILENAMELENGTH];
803: char popfile[FILENAMELENGTH];
804:
805: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
806:
1.157 brouard 807: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
808: /* struct timezone tzp; */
809: /* extern int gettimeofday(); */
810: struct tm tml, *gmtime(), *localtime();
811:
812: extern time_t time();
813:
814: struct tm start_time, end_time, curr_time, last_time, forecast_time;
815: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
816: struct tm tm;
817:
1.126 brouard 818: char strcurr[80], strfor[80];
819:
820: char *endptr;
821: long lval;
822: double dval;
823:
824: #define NR_END 1
825: #define FREE_ARG char*
826: #define FTOL 1.0e-10
827:
828: #define NRANSI
829: #define ITMAX 200
830:
831: #define TOL 2.0e-4
832:
833: #define CGOLD 0.3819660
834: #define ZEPS 1.0e-10
835: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
836:
837: #define GOLD 1.618034
838: #define GLIMIT 100.0
839: #define TINY 1.0e-20
840:
841: static double maxarg1,maxarg2;
842: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
843: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
844:
845: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
846: #define rint(a) floor(a+0.5)
1.166 brouard 847: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 848: #define mytinydouble 1.0e-16
1.166 brouard 849: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
850: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
851: /* static double dsqrarg; */
852: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 853: static double sqrarg;
854: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
855: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
856: int agegomp= AGEGOMP;
857:
858: int imx;
859: int stepm=1;
860: /* Stepm, step in month: minimum step interpolation*/
861:
862: int estepm;
863: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
864:
865: int m,nb;
866: long *num;
1.197 brouard 867: int firstpass=0, lastpass=4,*cod, *cens;
1.192 brouard 868: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
869: covariate for which somebody answered excluding
870: undefined. Usually 2: 0 and 1. */
871: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
872: covariate for which somebody answered including
873: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 874: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
875: double **pmmij, ***probs;
876: double *ageexmed,*agecens;
877: double dateintmean=0;
878:
879: double *weight;
880: int **s; /* Status */
1.141 brouard 881: double *agedc;
1.145 brouard 882: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 883: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 884: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.141 brouard 885: double idx;
886: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.197 brouard 887: int *Tage;
1.145 brouard 888: int *Ndum; /** Freq of modality (tricode */
1.200 brouard 889: /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
1.141 brouard 890: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.126 brouard 891: double *lsurv, *lpop, *tpop;
892:
1.143 brouard 893: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
894: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 895:
896: /**************** split *************************/
897: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
898: {
899: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
900: the name of the file (name), its extension only (ext) and its first part of the name (finame)
901: */
902: char *ss; /* pointer */
1.186 brouard 903: int l1=0, l2=0; /* length counters */
1.126 brouard 904:
905: l1 = strlen(path ); /* length of path */
906: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
907: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
908: if ( ss == NULL ) { /* no directory, so determine current directory */
909: strcpy( name, path ); /* we got the fullname name because no directory */
910: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
911: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
912: /* get current working directory */
913: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 914: #ifdef WIN32
915: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
916: #else
917: if (getcwd(dirc, FILENAME_MAX) == NULL) {
918: #endif
1.126 brouard 919: return( GLOCK_ERROR_GETCWD );
920: }
921: /* got dirc from getcwd*/
922: printf(" DIRC = %s \n",dirc);
923: } else { /* strip direcotry from path */
924: ss++; /* after this, the filename */
925: l2 = strlen( ss ); /* length of filename */
926: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
927: strcpy( name, ss ); /* save file name */
928: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 929: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 930: printf(" DIRC2 = %s \n",dirc);
931: }
932: /* We add a separator at the end of dirc if not exists */
933: l1 = strlen( dirc ); /* length of directory */
934: if( dirc[l1-1] != DIRSEPARATOR ){
935: dirc[l1] = DIRSEPARATOR;
936: dirc[l1+1] = 0;
937: printf(" DIRC3 = %s \n",dirc);
938: }
939: ss = strrchr( name, '.' ); /* find last / */
940: if (ss >0){
941: ss++;
942: strcpy(ext,ss); /* save extension */
943: l1= strlen( name);
944: l2= strlen(ss)+1;
945: strncpy( finame, name, l1-l2);
946: finame[l1-l2]= 0;
947: }
948:
949: return( 0 ); /* we're done */
950: }
951:
952:
953: /******************************************/
954:
955: void replace_back_to_slash(char *s, char*t)
956: {
957: int i;
958: int lg=0;
959: i=0;
960: lg=strlen(t);
961: for(i=0; i<= lg; i++) {
962: (s[i] = t[i]);
963: if (t[i]== '\\') s[i]='/';
964: }
965: }
966:
1.132 brouard 967: char *trimbb(char *out, char *in)
1.137 brouard 968: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 969: char *s;
970: s=out;
971: while (*in != '\0'){
1.137 brouard 972: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 973: in++;
974: }
975: *out++ = *in++;
976: }
977: *out='\0';
978: return s;
979: }
980:
1.187 brouard 981: /* char *substrchaine(char *out, char *in, char *chain) */
982: /* { */
983: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
984: /* char *s, *t; */
985: /* t=in;s=out; */
986: /* while ((*in != *chain) && (*in != '\0')){ */
987: /* *out++ = *in++; */
988: /* } */
989:
990: /* /\* *in matches *chain *\/ */
991: /* while ((*in++ == *chain++) && (*in != '\0')){ */
992: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
993: /* } */
994: /* in--; chain--; */
995: /* while ( (*in != '\0')){ */
996: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
997: /* *out++ = *in++; */
998: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
999: /* } */
1000: /* *out='\0'; */
1001: /* out=s; */
1002: /* return out; */
1003: /* } */
1004: char *substrchaine(char *out, char *in, char *chain)
1005: {
1006: /* Substract chain 'chain' from 'in', return and output 'out' */
1007: /* in="V1+V1*age+age*age+V2", chain="age*age" */
1008:
1009: char *strloc;
1010:
1011: strcpy (out, in);
1012: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
1013: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
1014: if(strloc != NULL){
1015: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
1016: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
1017: /* strcpy (strloc, strloc +strlen(chain));*/
1018: }
1019: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
1020: return out;
1021: }
1022:
1023:
1.145 brouard 1024: char *cutl(char *blocc, char *alocc, char *in, char occ)
1025: {
1.187 brouard 1026: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 1027: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 1028: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 1029: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1030: */
1.160 brouard 1031: char *s, *t;
1.145 brouard 1032: t=in;s=in;
1033: while ((*in != occ) && (*in != '\0')){
1034: *alocc++ = *in++;
1035: }
1036: if( *in == occ){
1037: *(alocc)='\0';
1038: s=++in;
1039: }
1040:
1041: if (s == t) {/* occ not found */
1042: *(alocc-(in-s))='\0';
1043: in=s;
1044: }
1045: while ( *in != '\0'){
1046: *blocc++ = *in++;
1047: }
1048:
1049: *blocc='\0';
1050: return t;
1051: }
1.137 brouard 1052: char *cutv(char *blocc, char *alocc, char *in, char occ)
1053: {
1.187 brouard 1054: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1055: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1056: gives blocc="abcdef2ghi" and alocc="j".
1057: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1058: */
1059: char *s, *t;
1060: t=in;s=in;
1061: while (*in != '\0'){
1062: while( *in == occ){
1063: *blocc++ = *in++;
1064: s=in;
1065: }
1066: *blocc++ = *in++;
1067: }
1068: if (s == t) /* occ not found */
1069: *(blocc-(in-s))='\0';
1070: else
1071: *(blocc-(in-s)-1)='\0';
1072: in=s;
1073: while ( *in != '\0'){
1074: *alocc++ = *in++;
1075: }
1076:
1077: *alocc='\0';
1078: return s;
1079: }
1080:
1.126 brouard 1081: int nbocc(char *s, char occ)
1082: {
1083: int i,j=0;
1084: int lg=20;
1085: i=0;
1086: lg=strlen(s);
1087: for(i=0; i<= lg; i++) {
1088: if (s[i] == occ ) j++;
1089: }
1090: return j;
1091: }
1092:
1.137 brouard 1093: /* void cutv(char *u,char *v, char*t, char occ) */
1094: /* { */
1095: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1096: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1097: /* gives u="abcdef2ghi" and v="j" *\/ */
1098: /* int i,lg,j,p=0; */
1099: /* i=0; */
1100: /* lg=strlen(t); */
1101: /* for(j=0; j<=lg-1; j++) { */
1102: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1103: /* } */
1.126 brouard 1104:
1.137 brouard 1105: /* for(j=0; j<p; j++) { */
1106: /* (u[j] = t[j]); */
1107: /* } */
1108: /* u[p]='\0'; */
1.126 brouard 1109:
1.137 brouard 1110: /* for(j=0; j<= lg; j++) { */
1111: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1112: /* } */
1113: /* } */
1.126 brouard 1114:
1.160 brouard 1115: #ifdef _WIN32
1116: char * strsep(char **pp, const char *delim)
1117: {
1118: char *p, *q;
1119:
1120: if ((p = *pp) == NULL)
1121: return 0;
1122: if ((q = strpbrk (p, delim)) != NULL)
1123: {
1124: *pp = q + 1;
1125: *q = '\0';
1126: }
1127: else
1128: *pp = 0;
1129: return p;
1130: }
1131: #endif
1132:
1.126 brouard 1133: /********************** nrerror ********************/
1134:
1135: void nrerror(char error_text[])
1136: {
1137: fprintf(stderr,"ERREUR ...\n");
1138: fprintf(stderr,"%s\n",error_text);
1139: exit(EXIT_FAILURE);
1140: }
1141: /*********************** vector *******************/
1142: double *vector(int nl, int nh)
1143: {
1144: double *v;
1145: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1146: if (!v) nrerror("allocation failure in vector");
1147: return v-nl+NR_END;
1148: }
1149:
1150: /************************ free vector ******************/
1151: void free_vector(double*v, int nl, int nh)
1152: {
1153: free((FREE_ARG)(v+nl-NR_END));
1154: }
1155:
1156: /************************ivector *******************************/
1157: int *ivector(long nl,long nh)
1158: {
1159: int *v;
1160: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1161: if (!v) nrerror("allocation failure in ivector");
1162: return v-nl+NR_END;
1163: }
1164:
1165: /******************free ivector **************************/
1166: void free_ivector(int *v, long nl, long nh)
1167: {
1168: free((FREE_ARG)(v+nl-NR_END));
1169: }
1170:
1171: /************************lvector *******************************/
1172: long *lvector(long nl,long nh)
1173: {
1174: long *v;
1175: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1176: if (!v) nrerror("allocation failure in ivector");
1177: return v-nl+NR_END;
1178: }
1179:
1180: /******************free lvector **************************/
1181: void free_lvector(long *v, long nl, long nh)
1182: {
1183: free((FREE_ARG)(v+nl-NR_END));
1184: }
1185:
1186: /******************* imatrix *******************************/
1187: int **imatrix(long nrl, long nrh, long ncl, long nch)
1188: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1189: {
1190: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1191: int **m;
1192:
1193: /* allocate pointers to rows */
1194: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1195: if (!m) nrerror("allocation failure 1 in matrix()");
1196: m += NR_END;
1197: m -= nrl;
1198:
1199:
1200: /* allocate rows and set pointers to them */
1201: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1202: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1203: m[nrl] += NR_END;
1204: m[nrl] -= ncl;
1205:
1206: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1207:
1208: /* return pointer to array of pointers to rows */
1209: return m;
1210: }
1211:
1212: /****************** free_imatrix *************************/
1213: void free_imatrix(m,nrl,nrh,ncl,nch)
1214: int **m;
1215: long nch,ncl,nrh,nrl;
1216: /* free an int matrix allocated by imatrix() */
1217: {
1218: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1219: free((FREE_ARG) (m+nrl-NR_END));
1220: }
1221:
1222: /******************* matrix *******************************/
1223: double **matrix(long nrl, long nrh, long ncl, long nch)
1224: {
1225: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1226: double **m;
1227:
1228: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1229: if (!m) nrerror("allocation failure 1 in matrix()");
1230: m += NR_END;
1231: m -= nrl;
1232:
1233: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1234: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1235: m[nrl] += NR_END;
1236: m[nrl] -= ncl;
1237:
1238: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1239: return m;
1.145 brouard 1240: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1241: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1242: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1243: */
1244: }
1245:
1246: /*************************free matrix ************************/
1247: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1248: {
1249: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1250: free((FREE_ARG)(m+nrl-NR_END));
1251: }
1252:
1253: /******************* ma3x *******************************/
1254: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1255: {
1256: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1257: double ***m;
1258:
1259: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1260: if (!m) nrerror("allocation failure 1 in matrix()");
1261: m += NR_END;
1262: m -= nrl;
1263:
1264: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1265: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1266: m[nrl] += NR_END;
1267: m[nrl] -= ncl;
1268:
1269: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1270:
1271: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1272: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1273: m[nrl][ncl] += NR_END;
1274: m[nrl][ncl] -= nll;
1275: for (j=ncl+1; j<=nch; j++)
1276: m[nrl][j]=m[nrl][j-1]+nlay;
1277:
1278: for (i=nrl+1; i<=nrh; i++) {
1279: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1280: for (j=ncl+1; j<=nch; j++)
1281: m[i][j]=m[i][j-1]+nlay;
1282: }
1283: return m;
1284: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1285: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1286: */
1287: }
1288:
1289: /*************************free ma3x ************************/
1290: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1291: {
1292: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1293: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1294: free((FREE_ARG)(m+nrl-NR_END));
1295: }
1296:
1297: /*************** function subdirf ***********/
1298: char *subdirf(char fileres[])
1299: {
1300: /* Caution optionfilefiname is hidden */
1301: strcpy(tmpout,optionfilefiname);
1302: strcat(tmpout,"/"); /* Add to the right */
1303: strcat(tmpout,fileres);
1304: return tmpout;
1305: }
1306:
1307: /*************** function subdirf2 ***********/
1308: char *subdirf2(char fileres[], char *preop)
1309: {
1310:
1311: /* Caution optionfilefiname is hidden */
1312: strcpy(tmpout,optionfilefiname);
1313: strcat(tmpout,"/");
1314: strcat(tmpout,preop);
1315: strcat(tmpout,fileres);
1316: return tmpout;
1317: }
1318:
1319: /*************** function subdirf3 ***********/
1320: char *subdirf3(char fileres[], char *preop, char *preop2)
1321: {
1322:
1323: /* Caution optionfilefiname is hidden */
1324: strcpy(tmpout,optionfilefiname);
1325: strcat(tmpout,"/");
1326: strcat(tmpout,preop);
1327: strcat(tmpout,preop2);
1328: strcat(tmpout,fileres);
1329: return tmpout;
1330: }
1331:
1.162 brouard 1332: char *asc_diff_time(long time_sec, char ascdiff[])
1333: {
1334: long sec_left, days, hours, minutes;
1335: days = (time_sec) / (60*60*24);
1336: sec_left = (time_sec) % (60*60*24);
1337: hours = (sec_left) / (60*60) ;
1338: sec_left = (sec_left) %(60*60);
1339: minutes = (sec_left) /60;
1340: sec_left = (sec_left) % (60);
1341: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1342: return ascdiff;
1343: }
1344:
1.126 brouard 1345: /***************** f1dim *************************/
1346: extern int ncom;
1347: extern double *pcom,*xicom;
1348: extern double (*nrfunc)(double []);
1349:
1350: double f1dim(double x)
1351: {
1352: int j;
1353: double f;
1354: double *xt;
1355:
1356: xt=vector(1,ncom);
1357: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1358: f=(*nrfunc)(xt);
1359: free_vector(xt,1,ncom);
1360: return f;
1361: }
1362:
1363: /*****************brent *************************/
1364: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1365: {
1366: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1367: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1368: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1369: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1370: * returned function value.
1371: */
1.126 brouard 1372: int iter;
1373: double a,b,d,etemp;
1.159 brouard 1374: double fu=0,fv,fw,fx;
1.164 brouard 1375: double ftemp=0.;
1.126 brouard 1376: double p,q,r,tol1,tol2,u,v,w,x,xm;
1377: double e=0.0;
1378:
1379: a=(ax < cx ? ax : cx);
1380: b=(ax > cx ? ax : cx);
1381: x=w=v=bx;
1382: fw=fv=fx=(*f)(x);
1383: for (iter=1;iter<=ITMAX;iter++) {
1384: xm=0.5*(a+b);
1385: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1386: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1387: printf(".");fflush(stdout);
1388: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1389: #ifdef DEBUGBRENT
1.126 brouard 1390: 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);
1391: 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);
1392: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1393: #endif
1394: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1395: *xmin=x;
1396: return fx;
1397: }
1398: ftemp=fu;
1399: if (fabs(e) > tol1) {
1400: r=(x-w)*(fx-fv);
1401: q=(x-v)*(fx-fw);
1402: p=(x-v)*q-(x-w)*r;
1403: q=2.0*(q-r);
1404: if (q > 0.0) p = -p;
1405: q=fabs(q);
1406: etemp=e;
1407: e=d;
1408: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1409: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1410: else {
1411: d=p/q;
1412: u=x+d;
1413: if (u-a < tol2 || b-u < tol2)
1414: d=SIGN(tol1,xm-x);
1415: }
1416: } else {
1417: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1418: }
1419: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1420: fu=(*f)(u);
1421: if (fu <= fx) {
1422: if (u >= x) a=x; else b=x;
1423: SHFT(v,w,x,u)
1.183 brouard 1424: SHFT(fv,fw,fx,fu)
1425: } else {
1426: if (u < x) a=u; else b=u;
1427: if (fu <= fw || w == x) {
1428: v=w;
1429: w=u;
1430: fv=fw;
1431: fw=fu;
1432: } else if (fu <= fv || v == x || v == w) {
1433: v=u;
1434: fv=fu;
1435: }
1436: }
1.126 brouard 1437: }
1438: nrerror("Too many iterations in brent");
1439: *xmin=x;
1440: return fx;
1441: }
1442:
1443: /****************** mnbrak ***********************/
1444:
1445: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1446: double (*func)(double))
1.183 brouard 1447: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1448: the downhill direction (defined by the function as evaluated at the initial points) and returns
1449: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1450: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1451: */
1.126 brouard 1452: double ulim,u,r,q, dum;
1453: double fu;
1.187 brouard 1454:
1455: double scale=10.;
1456: int iterscale=0;
1457:
1458: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1459: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1460:
1461:
1462: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1463: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1464: /* *bx = *ax - (*ax - *bx)/scale; */
1465: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1466: /* } */
1467:
1.126 brouard 1468: if (*fb > *fa) {
1469: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1470: SHFT(dum,*fb,*fa,dum)
1471: }
1.126 brouard 1472: *cx=(*bx)+GOLD*(*bx-*ax);
1473: *fc=(*func)(*cx);
1.183 brouard 1474: #ifdef DEBUG
1475: printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1476: fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1477: #endif
1478: while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
1.126 brouard 1479: r=(*bx-*ax)*(*fb-*fc);
1480: q=(*bx-*cx)*(*fb-*fa);
1481: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 1482: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1483: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1484: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 1485: fu=(*func)(u);
1.163 brouard 1486: #ifdef DEBUG
1487: /* f(x)=A(x-u)**2+f(u) */
1488: double A, fparabu;
1489: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1490: fparabu= *fa - A*(*ax-u)*(*ax-u);
1491: 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);
1492: 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 1493: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1494: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1495: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1496: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 1497: #endif
1.184 brouard 1498: #ifdef MNBRAKORIGINAL
1.183 brouard 1499: #else
1.191 brouard 1500: /* if (fu > *fc) { */
1501: /* #ifdef DEBUG */
1502: /* printf("mnbrak4 fu > fc \n"); */
1503: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
1504: /* #endif */
1505: /* /\* 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 *\\/ *\/ */
1506: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
1507: /* dum=u; /\* Shifting c and u *\/ */
1508: /* u = *cx; */
1509: /* *cx = dum; */
1510: /* dum = fu; */
1511: /* fu = *fc; */
1512: /* *fc =dum; */
1513: /* } else { /\* end *\/ */
1514: /* #ifdef DEBUG */
1515: /* printf("mnbrak3 fu < fc \n"); */
1516: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
1517: /* #endif */
1518: /* dum=u; /\* Shifting c and u *\/ */
1519: /* u = *cx; */
1520: /* *cx = dum; */
1521: /* dum = fu; */
1522: /* fu = *fc; */
1523: /* *fc =dum; */
1524: /* } */
1.183 brouard 1525: #ifdef DEBUG
1.191 brouard 1526: printf("mnbrak34 fu < or >= fc \n");
1527: fprintf(ficlog, "mnbrak34 fu < fc\n");
1.183 brouard 1528: #endif
1.191 brouard 1529: dum=u; /* Shifting c and u */
1530: u = *cx;
1531: *cx = dum;
1532: dum = fu;
1533: fu = *fc;
1534: *fc =dum;
1.183 brouard 1535: #endif
1.162 brouard 1536: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 1537: #ifdef DEBUG
1538: printf("mnbrak2 u after c but before ulim\n");
1539: fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
1540: #endif
1.126 brouard 1541: fu=(*func)(u);
1542: if (fu < *fc) {
1.183 brouard 1543: #ifdef DEBUG
1544: printf("mnbrak2 u after c but before ulim AND fu < fc\n");
1545: fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
1546: #endif
1.126 brouard 1547: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1.183 brouard 1548: SHFT(*fb,*fc,fu,(*func)(u))
1549: }
1.162 brouard 1550: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 1551: #ifdef DEBUG
1552: printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1553: fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1554: #endif
1.126 brouard 1555: u=ulim;
1556: fu=(*func)(u);
1.183 brouard 1557: } else { /* u could be left to b (if r > q parabola has a maximum) */
1558: #ifdef DEBUG
1559: printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1560: fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1561: #endif
1.126 brouard 1562: u=(*cx)+GOLD*(*cx-*bx);
1563: fu=(*func)(u);
1.183 brouard 1564: } /* end tests */
1.126 brouard 1565: SHFT(*ax,*bx,*cx,u)
1.183 brouard 1566: SHFT(*fa,*fb,*fc,fu)
1567: #ifdef DEBUG
1568: 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);
1569: 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);
1570: #endif
1571: } /* 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 1572: }
1573:
1574: /*************** linmin ************************/
1.162 brouard 1575: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1576: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1577: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1578: the value of func at the returned location p . This is actually all accomplished by calling the
1579: routines mnbrak and brent .*/
1.126 brouard 1580: int ncom;
1581: double *pcom,*xicom;
1582: double (*nrfunc)(double []);
1583:
1584: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1585: {
1586: double brent(double ax, double bx, double cx,
1587: double (*f)(double), double tol, double *xmin);
1588: double f1dim(double x);
1589: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1590: double *fc, double (*func)(double));
1591: int j;
1592: double xx,xmin,bx,ax;
1593: double fx,fb,fa;
1.187 brouard 1594:
1595: double scale=10., axs, xxs, xxss; /* Scale added for infinity */
1.126 brouard 1596:
1597: ncom=n;
1598: pcom=vector(1,n);
1599: xicom=vector(1,n);
1600: nrfunc=func;
1601: for (j=1;j<=n;j++) {
1602: pcom[j]=p[j];
1603: xicom[j]=xi[j];
1604: }
1.187 brouard 1605:
1.192 brouard 1606: /* axs=0.0; */
1607: /* xxss=1; /\* 1 and using scale *\/ */
1.187 brouard 1608: xxs=1;
1.192 brouard 1609: /* do{ */
1.187 brouard 1610: ax=0.;
1611: xx= xxs;
1612: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
1613: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
1614: /* 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)) */
1615: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
1616: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
1617: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
1618: /* 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 1619: /* if (fx != fx){ */
1620: /* xxs=xxs/scale; /\* Trying a smaller xx, closer to initial ax=0 *\/ */
1621: /* 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); */
1622: /* } */
1623: /* }while(fx != fx); */
1.187 brouard 1624:
1.191 brouard 1625: #ifdef DEBUGLINMIN
1626: 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);
1627: #endif
1.187 brouard 1628: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
1629: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
1630: /* fmin = f(p[j] + xmin * xi[j]) */
1631: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
1632: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 1633: #ifdef DEBUG
1634: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1635: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1636: #endif
1.191 brouard 1637: #ifdef DEBUGLINMIN
1638: printf("linmin end ");
1639: #endif
1.126 brouard 1640: for (j=1;j<=n;j++) {
1.188 brouard 1641: /* printf(" before xi[%d]=%12.8f", j,xi[j]); */
1.187 brouard 1642: xi[j] *= xmin; /* xi rescaled by xmin: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
1.189 brouard 1643: /* if(xxs <1.0) */
1644: /* 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 1645: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 1646: }
1.189 brouard 1647: /* printf("\n"); */
1.191 brouard 1648: #ifdef DEBUGLINMIN
1649: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1650: for (j=1;j<=n;j++) {
1651: printf(" xi[%d]= %12.7f p[%d]= %12.7f",j,xi[j],j,p[j]);
1652: if(j % ncovmodel == 0)
1653: printf("\n");
1654: }
1655: #endif
1.126 brouard 1656: free_vector(xicom,1,n);
1657: free_vector(pcom,1,n);
1658: }
1659:
1660:
1661: /*************** powell ************************/
1.162 brouard 1662: /*
1663: Minimization of a function func of n variables. Input consists of an initial starting point
1664: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1665: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1666: such that failure to decrease by more than this amount on one iteration signals doneness. On
1667: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1668: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1669: */
1.126 brouard 1670: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1671: double (*func)(double []))
1672: {
1673: void linmin(double p[], double xi[], int n, double *fret,
1674: double (*func)(double []));
1675: int i,ibig,j;
1676: double del,t,*pt,*ptt,*xit;
1.181 brouard 1677: double directest;
1.126 brouard 1678: double fp,fptt;
1679: double *xits;
1680: int niterf, itmp;
1681:
1682: pt=vector(1,n);
1683: ptt=vector(1,n);
1684: xit=vector(1,n);
1685: xits=vector(1,n);
1686: *fret=(*func)(p);
1687: for (j=1;j<=n;j++) pt[j]=p[j];
1.157 brouard 1688: rcurr_time = time(NULL);
1.126 brouard 1689: for (*iter=1;;++(*iter)) {
1.187 brouard 1690: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 1691: ibig=0;
1692: del=0.0;
1.157 brouard 1693: rlast_time=rcurr_time;
1694: /* (void) gettimeofday(&curr_time,&tzp); */
1695: rcurr_time = time(NULL);
1696: curr_time = *localtime(&rcurr_time);
1697: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1698: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1699: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 1700: for (i=1;i<=n;i++) {
1.126 brouard 1701: printf(" %d %.12f",i, p[i]);
1702: fprintf(ficlog," %d %.12lf",i, p[i]);
1703: fprintf(ficrespow," %.12lf", p[i]);
1704: }
1705: printf("\n");
1706: fprintf(ficlog,"\n");
1707: fprintf(ficrespow,"\n");fflush(ficrespow);
1708: if(*iter <=3){
1.157 brouard 1709: tml = *localtime(&rcurr_time);
1710: strcpy(strcurr,asctime(&tml));
1711: rforecast_time=rcurr_time;
1.126 brouard 1712: itmp = strlen(strcurr);
1713: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1714: strcurr[itmp-1]='\0';
1.162 brouard 1715: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 1716: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 1717: for(niterf=10;niterf<=30;niterf+=10){
1.157 brouard 1718: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1719: forecast_time = *localtime(&rforecast_time);
1720: strcpy(strfor,asctime(&forecast_time));
1.126 brouard 1721: itmp = strlen(strfor);
1722: if(strfor[itmp-1]=='\n')
1723: strfor[itmp-1]='\0';
1.157 brouard 1724: 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);
1725: 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 1726: }
1727: }
1.187 brouard 1728: for (i=1;i<=n;i++) { /* For each direction i */
1729: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 1730: fptt=(*fret);
1731: #ifdef DEBUG
1.164 brouard 1732: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1733: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 1734: #endif
1.187 brouard 1735: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 1736: fprintf(ficlog,"%d",i);fflush(ficlog);
1.188 brouard 1737: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1738: /* Outputs are fret(new point p) p is updated and xit rescaled */
1739: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1740: /* because that direction will be replaced unless the gain del is small */
1741: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
1742: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
1743: /* with the new direction. */
1.126 brouard 1744: del=fabs(fptt-(*fret));
1745: ibig=i;
1746: }
1747: #ifdef DEBUG
1748: printf("%d %.12e",i,(*fret));
1749: fprintf(ficlog,"%d %.12e",i,(*fret));
1750: for (j=1;j<=n;j++) {
1751: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1752: printf(" x(%d)=%.12e",j,xit[j]);
1753: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1754: }
1755: for(j=1;j<=n;j++) {
1.162 brouard 1756: printf(" p(%d)=%.12e",j,p[j]);
1757: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 1758: }
1759: printf("\n");
1760: fprintf(ficlog,"\n");
1761: #endif
1.187 brouard 1762: } /* end loop on each direction i */
1763: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 1764: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 1765: /* New value of last point Pn is not computed, P(n-1) */
1.182 brouard 1766: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1.188 brouard 1767: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
1768: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
1769: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
1770: /* decreased of more than 3.84 */
1771: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
1772: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
1773: /* By adding 10 parameters more the gain should be 18.31 */
1774:
1775: /* Starting the program with initial values given by a former maximization will simply change */
1776: /* the scales of the directions and the directions, because the are reset to canonical directions */
1777: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
1778: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 1779: #ifdef DEBUG
1780: int k[2],l;
1781: k[0]=1;
1782: k[1]=-1;
1783: printf("Max: %.12e",(*func)(p));
1784: fprintf(ficlog,"Max: %.12e",(*func)(p));
1785: for (j=1;j<=n;j++) {
1786: printf(" %.12e",p[j]);
1787: fprintf(ficlog," %.12e",p[j]);
1788: }
1789: printf("\n");
1790: fprintf(ficlog,"\n");
1791: for(l=0;l<=1;l++) {
1792: for (j=1;j<=n;j++) {
1793: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1794: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1795: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1796: }
1797: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1798: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1799: }
1800: #endif
1801:
1802:
1803: free_vector(xit,1,n);
1804: free_vector(xits,1,n);
1805: free_vector(ptt,1,n);
1806: free_vector(pt,1,n);
1807: return;
1.192 brouard 1808: } /* enough precision */
1.126 brouard 1809: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1.181 brouard 1810: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 1811: ptt[j]=2.0*p[j]-pt[j];
1812: xit[j]=p[j]-pt[j];
1813: pt[j]=p[j];
1814: }
1.181 brouard 1815: fptt=(*func)(ptt); /* f_3 */
1.192 brouard 1816: #ifdef POWELLF1F3
1817: #else
1.161 brouard 1818: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 1819: #endif
1.162 brouard 1820: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 1821: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 1822: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1823: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1824: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.181 brouard 1825: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
1.161 brouard 1826: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.183 brouard 1827: #ifdef NRCORIGINAL
1828: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
1829: #else
1830: 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 1831: t= t- del*SQR(fp-fptt);
1.183 brouard 1832: #endif
1.182 brouard 1833: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
1.161 brouard 1834: #ifdef DEBUG
1.181 brouard 1835: 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);
1836: 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 1837: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1838: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1839: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1840: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1841: 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);
1842: 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);
1843: #endif
1.183 brouard 1844: #ifdef POWELLORIGINAL
1845: if (t < 0.0) { /* Then we use it for new direction */
1846: #else
1.182 brouard 1847: if (directest*t < 0.0) { /* Contradiction between both tests */
1.192 brouard 1848: printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
1849: printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1850: fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
1851: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1852: }
1.181 brouard 1853: if (directest < 0.0) { /* Then we use it for new direction */
1854: #endif
1.191 brouard 1855: #ifdef DEBUGLINMIN
1856: printf("Before linmin in direction P%d-P0\n",n);
1857: for (j=1;j<=n;j++) {
1858: printf("Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1859: if(j % ncovmodel == 0)
1860: printf("\n");
1861: }
1862: #endif
1.187 brouard 1863: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.191 brouard 1864: #ifdef DEBUGLINMIN
1865: for (j=1;j<=n;j++) {
1866: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1867: if(j % ncovmodel == 0)
1868: printf("\n");
1869: }
1870: #endif
1.126 brouard 1871: for (j=1;j<=n;j++) {
1.181 brouard 1872: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
1873: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
1.126 brouard 1874: }
1.181 brouard 1875: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1876: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1.161 brouard 1877:
1.126 brouard 1878: #ifdef DEBUG
1.164 brouard 1879: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1880: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1.126 brouard 1881: for(j=1;j<=n;j++){
1882: printf(" %.12e",xit[j]);
1883: fprintf(ficlog," %.12e",xit[j]);
1884: }
1885: printf("\n");
1886: fprintf(ficlog,"\n");
1887: #endif
1.192 brouard 1888: } /* end of t or directest negative */
1889: #ifdef POWELLF1F3
1890: #else
1.162 brouard 1891: } /* end if (fptt < fp) */
1.192 brouard 1892: #endif
1893: } /* loop iteration */
1.126 brouard 1894: }
1895:
1896: /**** Prevalence limit (stable or period prevalence) ****************/
1897:
1898: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1899: {
1900: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1901: matrix by transitions matrix until convergence is reached */
1.169 brouard 1902:
1.126 brouard 1903: int i, ii,j,k;
1904: double min, max, maxmin, maxmax,sumnew=0.;
1.145 brouard 1905: /* double **matprod2(); */ /* test */
1.131 brouard 1906: double **out, cov[NCOVMAX+1], **pmij();
1.126 brouard 1907: double **newm;
1908: double agefin, delaymax=50 ; /* Max number of years to converge */
1.169 brouard 1909:
1.126 brouard 1910: for (ii=1;ii<=nlstate+ndeath;ii++)
1911: for (j=1;j<=nlstate+ndeath;j++){
1912: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1913: }
1.169 brouard 1914:
1915: cov[1]=1.;
1916:
1917: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.126 brouard 1918: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1919: newm=savm;
1920: /* Covariates have to be included here again */
1.138 brouard 1921: cov[2]=agefin;
1.187 brouard 1922: if(nagesqr==1)
1923: cov[3]= agefin*agefin;;
1.138 brouard 1924: for (k=1; k<=cptcovn;k++) {
1.200 brouard 1925: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1926: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
1.198 brouard 1927: /* 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 1928: }
1.186 brouard 1929: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 1930: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
1931: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
1.186 brouard 1932: for (k=1; k<=cptcovprod;k++) /* Useless */
1.200 brouard 1933: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
1934: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
1.138 brouard 1935:
1936: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1937: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1938: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 1939: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1940: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.142 brouard 1941: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 1942:
1.126 brouard 1943: savm=oldm;
1944: oldm=newm;
1945: maxmax=0.;
1946: for(j=1;j<=nlstate;j++){
1947: min=1.;
1948: max=0.;
1949: for(i=1; i<=nlstate; i++) {
1950: sumnew=0;
1951: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1952: prlim[i][j]= newm[i][j]/(1-sumnew);
1.145 brouard 1953: /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
1.126 brouard 1954: max=FMAX(max,prlim[i][j]);
1955: min=FMIN(min,prlim[i][j]);
1956: }
1957: maxmin=max-min;
1958: maxmax=FMAX(maxmax,maxmin);
1.169 brouard 1959: } /* j loop */
1.126 brouard 1960: if(maxmax < ftolpl){
1961: return prlim;
1962: }
1.169 brouard 1963: } /* age loop */
1964: return prlim; /* should not reach here */
1.126 brouard 1965: }
1966:
1967: /*************** transition probabilities ***************/
1968:
1969: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1970: {
1.138 brouard 1971: /* According to parameters values stored in x and the covariate's values stored in cov,
1972: computes the probability to be observed in state j being in state i by appying the
1973: model to the ncovmodel covariates (including constant and age).
1974: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1975: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1976: ncth covariate in the global vector x is given by the formula:
1977: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1978: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1979: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1980: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1981: Outputs ps[i][j] the probability to be observed in j being in j according to
1982: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1983: */
1984: double s1, lnpijopii;
1.126 brouard 1985: /*double t34;*/
1.164 brouard 1986: int i,j, nc, ii, jj;
1.126 brouard 1987:
1988: for(i=1; i<= nlstate; i++){
1989: for(j=1; j<i;j++){
1.138 brouard 1990: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1991: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1992: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1993: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 1994: }
1.138 brouard 1995: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1996: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 1997: }
1998: for(j=i+1; j<=nlstate+ndeath;j++){
1.138 brouard 1999: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2000: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2001: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2002: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1.126 brouard 2003: }
1.138 brouard 2004: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1.126 brouard 2005: }
2006: }
2007:
2008: for(i=1; i<= nlstate; i++){
2009: s1=0;
1.131 brouard 2010: for(j=1; j<i; j++){
1.138 brouard 2011: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 2012: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2013: }
2014: for(j=i+1; j<=nlstate+ndeath; j++){
1.138 brouard 2015: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 2016: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2017: }
1.138 brouard 2018: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1.126 brouard 2019: ps[i][i]=1./(s1+1.);
1.138 brouard 2020: /* Computing other pijs */
1.126 brouard 2021: for(j=1; j<i; j++)
2022: ps[i][j]= exp(ps[i][j])*ps[i][i];
2023: for(j=i+1; j<=nlstate+ndeath; j++)
2024: ps[i][j]= exp(ps[i][j])*ps[i][i];
2025: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2026: } /* end i */
2027:
2028: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2029: for(jj=1; jj<= nlstate+ndeath; jj++){
2030: ps[ii][jj]=0;
2031: ps[ii][ii]=1;
2032: }
2033: }
2034:
1.145 brouard 2035:
2036: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2037: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2038: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2039: /* } */
2040: /* printf("\n "); */
2041: /* } */
2042: /* printf("\n ");printf("%lf ",cov[2]);*/
2043: /*
1.126 brouard 2044: for(i=1; i<= npar; i++) printf("%f ",x[i]);
2045: goto end;*/
2046: return ps;
2047: }
2048:
2049: /**************** Product of 2 matrices ******************/
2050:
1.145 brouard 2051: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 2052: {
2053: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
2054: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
2055: /* in, b, out are matrice of pointers which should have been initialized
2056: before: only the contents of out is modified. The function returns
2057: a pointer to pointers identical to out */
1.145 brouard 2058: int i, j, k;
1.126 brouard 2059: for(i=nrl; i<= nrh; i++)
1.145 brouard 2060: for(k=ncolol; k<=ncoloh; k++){
2061: out[i][k]=0.;
2062: for(j=ncl; j<=nch; j++)
2063: out[i][k] +=in[i][j]*b[j][k];
2064: }
1.126 brouard 2065: return out;
2066: }
2067:
2068:
2069: /************* Higher Matrix Product ***************/
2070:
2071: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
2072: {
2073: /* Computes the transition matrix starting at age 'age' over
2074: 'nhstepm*hstepm*stepm' months (i.e. until
2075: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2076: nhstepm*hstepm matrices.
2077: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2078: (typically every 2 years instead of every month which is too big
2079: for the memory).
2080: Model is determined by parameters x and covariates have to be
2081: included manually here.
2082:
2083: */
2084:
2085: int i, j, d, h, k;
1.131 brouard 2086: double **out, cov[NCOVMAX+1];
1.126 brouard 2087: double **newm;
1.187 brouard 2088: double agexact;
1.126 brouard 2089:
2090: /* Hstepm could be zero and should return the unit matrix */
2091: for (i=1;i<=nlstate+ndeath;i++)
2092: for (j=1;j<=nlstate+ndeath;j++){
2093: oldm[i][j]=(i==j ? 1.0 : 0.0);
2094: po[i][j][0]=(i==j ? 1.0 : 0.0);
2095: }
2096: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2097: for(h=1; h <=nhstepm; h++){
2098: for(d=1; d <=hstepm; d++){
2099: newm=savm;
2100: /* Covariates have to be included here again */
2101: cov[1]=1.;
1.187 brouard 2102: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
2103: cov[2]=agexact;
2104: if(nagesqr==1)
2105: cov[3]= agexact*agexact;
1.131 brouard 2106: for (k=1; k<=cptcovn;k++)
1.200 brouard 2107: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2108: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.186 brouard 2109: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
2110: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 2111: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2112: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
1.145 brouard 2113: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.200 brouard 2114: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
2115: /* 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 2116:
2117:
2118: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2119: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
2120: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
2121: pmij(pmmij,cov,ncovmodel,x,nlstate));
2122: savm=oldm;
2123: oldm=newm;
2124: }
2125: for(i=1; i<=nlstate+ndeath; i++)
2126: for(j=1;j<=nlstate+ndeath;j++) {
2127: po[i][j][h]=newm[i][j];
1.128 brouard 2128: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 2129: }
1.128 brouard 2130: /*printf("h=%d ",h);*/
1.126 brouard 2131: } /* end h */
1.128 brouard 2132: /* printf("\n H=%d \n",h); */
1.126 brouard 2133: return po;
2134: }
2135:
1.162 brouard 2136: #ifdef NLOPT
2137: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
2138: double fret;
2139: double *xt;
2140: int j;
2141: myfunc_data *d2 = (myfunc_data *) pd;
2142: /* xt = (p1-1); */
2143: xt=vector(1,n);
2144: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
2145:
2146: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
2147: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
2148: printf("Function = %.12lf ",fret);
2149: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
2150: printf("\n");
2151: free_vector(xt,1,n);
2152: return fret;
2153: }
2154: #endif
1.126 brouard 2155:
2156: /*************** log-likelihood *************/
2157: double func( double *x)
2158: {
2159: int i, ii, j, k, mi, d, kk;
1.131 brouard 2160: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2161: double **out;
2162: double sw; /* Sum of weights */
2163: double lli; /* Individual log likelihood */
2164: int s1, s2;
2165: double bbh, survp;
2166: long ipmx;
1.187 brouard 2167: double agexact;
1.126 brouard 2168: /*extern weight */
2169: /* We are differentiating ll according to initial status */
2170: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2171: /*for(i=1;i<imx;i++)
2172: printf(" %d\n",s[4][i]);
2173: */
1.162 brouard 2174:
2175: ++countcallfunc;
2176:
1.126 brouard 2177: cov[1]=1.;
2178:
2179: for(k=1; k<=nlstate; k++) ll[k]=0.;
2180:
2181: if(mle==1){
2182: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.138 brouard 2183: /* Computes the values of the ncovmodel covariates of the model
2184: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
2185: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
2186: to be observed in j being in i according to the model.
2187: */
1.145 brouard 2188: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1.187 brouard 2189: cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.145 brouard 2190: }
1.137 brouard 2191: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1.138 brouard 2192: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1.137 brouard 2193: has been calculated etc */
1.126 brouard 2194: for(mi=1; mi<= wav[i]-1; mi++){
2195: for (ii=1;ii<=nlstate+ndeath;ii++)
2196: for (j=1;j<=nlstate+ndeath;j++){
2197: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2198: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2199: }
2200: for(d=0; d<dh[mi][i]; d++){
2201: newm=savm;
1.187 brouard 2202: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2203: cov[2]=agexact;
2204: if(nagesqr==1)
2205: cov[3]= agexact*agexact;
1.126 brouard 2206: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2207: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
1.126 brouard 2208: }
2209: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2210: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2211: savm=oldm;
2212: oldm=newm;
2213: } /* end mult */
2214:
2215: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
2216: /* But now since version 0.9 we anticipate for bias at large stepm.
2217: * If stepm is larger than one month (smallest stepm) and if the exact delay
2218: * (in months) between two waves is not a multiple of stepm, we rounded to
2219: * the nearest (and in case of equal distance, to the lowest) interval but now
2220: * we keep into memory the bias bh[mi][i] and also the previous matrix product
2221: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
2222: * probability in order to take into account the bias as a fraction of the way
2223: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
2224: * -stepm/2 to stepm/2 .
2225: * For stepm=1 the results are the same as for previous versions of Imach.
2226: * For stepm > 1 the results are less biased than in previous versions.
2227: */
2228: s1=s[mw[mi][i]][i];
2229: s2=s[mw[mi+1][i]][i];
2230: bbh=(double)bh[mi][i]/(double)stepm;
2231: /* bias bh is positive if real duration
2232: * is higher than the multiple of stepm and negative otherwise.
2233: */
2234: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
2235: if( s2 > nlstate){
2236: /* i.e. if s2 is a death state and if the date of death is known
2237: then the contribution to the likelihood is the probability to
2238: die between last step unit time and current step unit time,
2239: which is also equal to probability to die before dh
2240: minus probability to die before dh-stepm .
2241: In version up to 0.92 likelihood was computed
2242: as if date of death was unknown. Death was treated as any other
2243: health state: the date of the interview describes the actual state
2244: and not the date of a change in health state. The former idea was
2245: to consider that at each interview the state was recorded
2246: (healthy, disable or death) and IMaCh was corrected; but when we
2247: introduced the exact date of death then we should have modified
2248: the contribution of an exact death to the likelihood. This new
2249: contribution is smaller and very dependent of the step unit
2250: stepm. It is no more the probability to die between last interview
2251: and month of death but the probability to survive from last
2252: interview up to one month before death multiplied by the
2253: probability to die within a month. Thanks to Chris
2254: Jackson for correcting this bug. Former versions increased
2255: mortality artificially. The bad side is that we add another loop
2256: which slows down the processing. The difference can be up to 10%
2257: lower mortality.
2258: */
1.183 brouard 2259: /* If, at the beginning of the maximization mostly, the
2260: cumulative probability or probability to be dead is
2261: constant (ie = 1) over time d, the difference is equal to
2262: 0. out[s1][3] = savm[s1][3]: probability, being at state
2263: s1 at precedent wave, to be dead a month before current
2264: wave is equal to probability, being at state s1 at
2265: precedent wave, to be dead at mont of the current
2266: wave. Then the observed probability (that this person died)
2267: is null according to current estimated parameter. In fact,
2268: it should be very low but not zero otherwise the log go to
2269: infinity.
2270: */
2271: /* #ifdef INFINITYORIGINAL */
2272: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2273: /* #else */
2274: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
2275: /* lli=log(mytinydouble); */
2276: /* else */
2277: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2278: /* #endif */
2279: lli=log(out[s1][s2] - savm[s1][s2]);
1.126 brouard 2280:
2281: } else if (s2==-2) {
2282: for (j=1,survp=0. ; j<=nlstate; j++)
2283: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2284: /*survp += out[s1][j]; */
2285: lli= log(survp);
2286: }
2287:
2288: else if (s2==-4) {
2289: for (j=3,survp=0. ; j<=nlstate; j++)
2290: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2291: lli= log(survp);
2292: }
2293:
2294: else if (s2==-5) {
2295: for (j=1,survp=0. ; j<=2; j++)
2296: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2297: lli= log(survp);
2298: }
2299:
2300: else{
2301: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2302: /* 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 */
2303: }
2304: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
2305: /*if(lli ==000.0)*/
2306: /*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); */
2307: ipmx +=1;
2308: sw += weight[i];
2309: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.183 brouard 2310: /* if (lli < log(mytinydouble)){ */
2311: /* 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); */
2312: /* 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]); */
2313: /* } */
1.126 brouard 2314: } /* end of wave */
2315: } /* end of individual */
2316: } else if(mle==2){
2317: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2318: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2319: for(mi=1; mi<= wav[i]-1; mi++){
2320: for (ii=1;ii<=nlstate+ndeath;ii++)
2321: for (j=1;j<=nlstate+ndeath;j++){
2322: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2323: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2324: }
2325: for(d=0; d<=dh[mi][i]; d++){
2326: newm=savm;
1.187 brouard 2327: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2328: cov[2]=agexact;
2329: if(nagesqr==1)
2330: cov[3]= agexact*agexact;
1.126 brouard 2331: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2332: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2333: }
2334: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2335: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2336: savm=oldm;
2337: oldm=newm;
2338: } /* end mult */
2339:
2340: s1=s[mw[mi][i]][i];
2341: s2=s[mw[mi+1][i]][i];
2342: bbh=(double)bh[mi][i]/(double)stepm;
2343: 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 */
2344: ipmx +=1;
2345: sw += weight[i];
2346: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2347: } /* end of wave */
2348: } /* end of individual */
2349: } else if(mle==3){ /* exponential inter-extrapolation */
2350: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2351: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2352: for(mi=1; mi<= wav[i]-1; mi++){
2353: for (ii=1;ii<=nlstate+ndeath;ii++)
2354: for (j=1;j<=nlstate+ndeath;j++){
2355: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2356: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2357: }
2358: for(d=0; d<dh[mi][i]; d++){
2359: newm=savm;
1.187 brouard 2360: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2361: cov[2]=agexact;
2362: if(nagesqr==1)
2363: cov[3]= agexact*agexact;
1.126 brouard 2364: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2365: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2366: }
2367: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2368: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2369: savm=oldm;
2370: oldm=newm;
2371: } /* end mult */
2372:
2373: s1=s[mw[mi][i]][i];
2374: s2=s[mw[mi+1][i]][i];
2375: bbh=(double)bh[mi][i]/(double)stepm;
2376: 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 */
2377: ipmx +=1;
2378: sw += weight[i];
2379: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2380: } /* end of wave */
2381: } /* end of individual */
2382: }else if (mle==4){ /* ml=4 no inter-extrapolation */
2383: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2384: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2385: for(mi=1; mi<= wav[i]-1; mi++){
2386: for (ii=1;ii<=nlstate+ndeath;ii++)
2387: for (j=1;j<=nlstate+ndeath;j++){
2388: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2389: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2390: }
2391: for(d=0; d<dh[mi][i]; d++){
2392: newm=savm;
1.187 brouard 2393: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2394: cov[2]=agexact;
2395: if(nagesqr==1)
2396: cov[3]= agexact*agexact;
1.126 brouard 2397: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2398: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2399: }
2400:
2401: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2402: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2403: savm=oldm;
2404: oldm=newm;
2405: } /* end mult */
2406:
2407: s1=s[mw[mi][i]][i];
2408: s2=s[mw[mi+1][i]][i];
2409: if( s2 > nlstate){
2410: lli=log(out[s1][s2] - savm[s1][s2]);
2411: }else{
2412: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2413: }
2414: ipmx +=1;
2415: sw += weight[i];
2416: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2417: /* 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]); */
2418: } /* end of wave */
2419: } /* end of individual */
2420: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
2421: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2422: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2423: for(mi=1; mi<= wav[i]-1; mi++){
2424: for (ii=1;ii<=nlstate+ndeath;ii++)
2425: for (j=1;j<=nlstate+ndeath;j++){
2426: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2427: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2428: }
2429: for(d=0; d<dh[mi][i]; d++){
2430: newm=savm;
1.187 brouard 2431: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2432: cov[2]=agexact;
2433: if(nagesqr==1)
2434: cov[3]= agexact*agexact;
1.126 brouard 2435: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2436: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2437: }
2438:
2439: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2440: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2441: savm=oldm;
2442: oldm=newm;
2443: } /* end mult */
2444:
2445: s1=s[mw[mi][i]][i];
2446: s2=s[mw[mi+1][i]][i];
2447: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2448: ipmx +=1;
2449: sw += weight[i];
2450: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2451: /*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]);*/
2452: } /* end of wave */
2453: } /* end of individual */
2454: } /* End of if */
2455: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2456: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2457: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2458: return -l;
2459: }
2460:
2461: /*************** log-likelihood *************/
2462: double funcone( double *x)
2463: {
2464: /* Same as likeli but slower because of a lot of printf and if */
2465: int i, ii, j, k, mi, d, kk;
1.131 brouard 2466: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2467: double **out;
2468: double lli; /* Individual log likelihood */
2469: double llt;
2470: int s1, s2;
2471: double bbh, survp;
1.187 brouard 2472: double agexact;
1.126 brouard 2473: /*extern weight */
2474: /* We are differentiating ll according to initial status */
2475: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2476: /*for(i=1;i<imx;i++)
2477: printf(" %d\n",s[4][i]);
2478: */
2479: cov[1]=1.;
2480:
2481: for(k=1; k<=nlstate; k++) ll[k]=0.;
2482:
2483: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2484: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2485: for(mi=1; mi<= wav[i]-1; mi++){
2486: for (ii=1;ii<=nlstate+ndeath;ii++)
2487: for (j=1;j<=nlstate+ndeath;j++){
2488: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2489: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2490: }
2491: for(d=0; d<dh[mi][i]; d++){
2492: newm=savm;
1.187 brouard 2493: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2494: cov[2]=agexact;
2495: if(nagesqr==1)
2496: cov[3]= agexact*agexact;
1.126 brouard 2497: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2498: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2499: }
1.187 brouard 2500:
1.145 brouard 2501: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.126 brouard 2502: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2503: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1.145 brouard 2504: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2505: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
1.126 brouard 2506: savm=oldm;
2507: oldm=newm;
2508: } /* end mult */
2509:
2510: s1=s[mw[mi][i]][i];
2511: s2=s[mw[mi+1][i]][i];
2512: bbh=(double)bh[mi][i]/(double)stepm;
2513: /* bias is positive if real duration
2514: * is higher than the multiple of stepm and negative otherwise.
2515: */
2516: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2517: lli=log(out[s1][s2] - savm[s1][s2]);
2518: } else if (s2==-2) {
2519: for (j=1,survp=0. ; j<=nlstate; j++)
2520: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2521: lli= log(survp);
2522: }else if (mle==1){
2523: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2524: } else if(mle==2){
2525: 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 */
2526: } else if(mle==3){ /* exponential inter-extrapolation */
2527: 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 */
2528: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2529: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 2530: } else{ /* mle=0 back to 1 */
2531: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2532: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 2533: } /* End of if */
2534: ipmx +=1;
2535: sw += weight[i];
2536: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 2537: /*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 2538: if(globpr){
1.141 brouard 2539: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
1.126 brouard 2540: %11.6f %11.6f %11.6f ", \
2541: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
2542: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2543: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2544: llt +=ll[k]*gipmx/gsw;
2545: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2546: }
2547: fprintf(ficresilk," %10.6f\n", -llt);
2548: }
2549: } /* end of wave */
2550: } /* end of individual */
2551: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2552: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2553: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2554: if(globpr==0){ /* First time we count the contributions and weights */
2555: gipmx=ipmx;
2556: gsw=sw;
2557: }
2558: return -l;
2559: }
2560:
2561:
2562: /*************** function likelione ***********/
2563: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2564: {
2565: /* This routine should help understanding what is done with
2566: the selection of individuals/waves and
2567: to check the exact contribution to the likelihood.
2568: Plotting could be done.
2569: */
2570: int k;
2571:
2572: if(*globpri !=0){ /* Just counts and sums, no printings */
1.201 ! brouard 2573: strcpy(fileresilk,"ILK_");
1.126 brouard 2574: strcat(fileresilk,fileres);
2575: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2576: printf("Problem with resultfile: %s\n", fileresilk);
2577: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2578: }
2579: 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");
2580: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
2581: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2582: for(k=1; k<=nlstate; k++)
2583: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2584: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2585: }
2586:
2587: *fretone=(*funcone)(p);
2588: if(*globpri !=0){
2589: fclose(ficresilk);
1.201 ! brouard 2590: fprintf(fichtm,"\n<br>File of contributions to the likelihood (if mle=1): <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1.126 brouard 2591: fflush(fichtm);
2592: }
2593: return;
2594: }
2595:
2596:
2597: /*********** Maximum Likelihood Estimation ***************/
2598:
2599: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2600: {
1.165 brouard 2601: int i,j, iter=0;
1.126 brouard 2602: double **xi;
2603: double fret;
2604: double fretone; /* Only one call to likelihood */
2605: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 2606:
2607: #ifdef NLOPT
2608: int creturn;
2609: nlopt_opt opt;
2610: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2611: double *lb;
2612: double minf; /* the minimum objective value, upon return */
2613: double * p1; /* Shifted parameters from 0 instead of 1 */
2614: myfunc_data dinst, *d = &dinst;
2615: #endif
2616:
2617:
1.126 brouard 2618: xi=matrix(1,npar,1,npar);
2619: for (i=1;i<=npar;i++)
2620: for (j=1;j<=npar;j++)
2621: xi[i][j]=(i==j ? 1.0 : 0.0);
2622: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.201 ! brouard 2623: strcpy(filerespow,"POW_");
1.126 brouard 2624: strcat(filerespow,fileres);
2625: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2626: printf("Problem with resultfile: %s\n", filerespow);
2627: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2628: }
2629: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2630: for (i=1;i<=nlstate;i++)
2631: for(j=1;j<=nlstate+ndeath;j++)
2632: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2633: fprintf(ficrespow,"\n");
1.162 brouard 2634: #ifdef POWELL
1.126 brouard 2635: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 2636: #endif
1.126 brouard 2637:
1.162 brouard 2638: #ifdef NLOPT
2639: #ifdef NEWUOA
2640: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2641: #else
2642: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2643: #endif
2644: lb=vector(0,npar-1);
2645: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2646: nlopt_set_lower_bounds(opt, lb);
2647: nlopt_set_initial_step1(opt, 0.1);
2648:
2649: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2650: d->function = func;
2651: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2652: nlopt_set_min_objective(opt, myfunc, d);
2653: nlopt_set_xtol_rel(opt, ftol);
2654: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2655: printf("nlopt failed! %d\n",creturn);
2656: }
2657: else {
2658: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2659: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2660: iter=1; /* not equal */
2661: }
2662: nlopt_destroy(opt);
2663: #endif
1.126 brouard 2664: free_matrix(xi,1,npar,1,npar);
2665: fclose(ficrespow);
1.180 brouard 2666: printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2667: fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2668: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 2669:
2670: }
2671:
2672: /**** Computes Hessian and covariance matrix ***/
2673: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
2674: {
2675: double **a,**y,*x,pd;
2676: double **hess;
1.164 brouard 2677: int i, j;
1.126 brouard 2678: int *indx;
2679:
2680: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
2681: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
2682: void lubksb(double **a, int npar, int *indx, double b[]) ;
2683: void ludcmp(double **a, int npar, int *indx, double *d) ;
2684: double gompertz(double p[]);
2685: hess=matrix(1,npar,1,npar);
2686:
2687: printf("\nCalculation of the hessian matrix. Wait...\n");
2688: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2689: for (i=1;i<=npar;i++){
2690: printf("%d",i);fflush(stdout);
2691: fprintf(ficlog,"%d",i);fflush(ficlog);
2692:
2693: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2694:
2695: /* printf(" %f ",p[i]);
2696: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2697: }
2698:
2699: for (i=1;i<=npar;i++) {
2700: for (j=1;j<=npar;j++) {
2701: if (j>i) {
2702: printf(".%d%d",i,j);fflush(stdout);
2703: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
2704: hess[i][j]=hessij(p,delti,i,j,func,npar);
2705:
2706: hess[j][i]=hess[i][j];
2707: /*printf(" %lf ",hess[i][j]);*/
2708: }
2709: }
2710: }
2711: printf("\n");
2712: fprintf(ficlog,"\n");
2713:
2714: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2715: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2716:
2717: a=matrix(1,npar,1,npar);
2718: y=matrix(1,npar,1,npar);
2719: x=vector(1,npar);
2720: indx=ivector(1,npar);
2721: for (i=1;i<=npar;i++)
2722: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2723: ludcmp(a,npar,indx,&pd);
2724:
2725: for (j=1;j<=npar;j++) {
2726: for (i=1;i<=npar;i++) x[i]=0;
2727: x[j]=1;
2728: lubksb(a,npar,indx,x);
2729: for (i=1;i<=npar;i++){
2730: matcov[i][j]=x[i];
2731: }
2732: }
2733:
2734: printf("\n#Hessian matrix#\n");
2735: fprintf(ficlog,"\n#Hessian matrix#\n");
2736: for (i=1;i<=npar;i++) {
2737: for (j=1;j<=npar;j++) {
2738: printf("%.3e ",hess[i][j]);
2739: fprintf(ficlog,"%.3e ",hess[i][j]);
2740: }
2741: printf("\n");
2742: fprintf(ficlog,"\n");
2743: }
2744:
2745: /* Recompute Inverse */
2746: for (i=1;i<=npar;i++)
2747: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
2748: ludcmp(a,npar,indx,&pd);
2749:
2750: /* printf("\n#Hessian matrix recomputed#\n");
2751:
2752: for (j=1;j<=npar;j++) {
2753: for (i=1;i<=npar;i++) x[i]=0;
2754: x[j]=1;
2755: lubksb(a,npar,indx,x);
2756: for (i=1;i<=npar;i++){
2757: y[i][j]=x[i];
2758: printf("%.3e ",y[i][j]);
2759: fprintf(ficlog,"%.3e ",y[i][j]);
2760: }
2761: printf("\n");
2762: fprintf(ficlog,"\n");
2763: }
2764: */
2765:
2766: free_matrix(a,1,npar,1,npar);
2767: free_matrix(y,1,npar,1,npar);
2768: free_vector(x,1,npar);
2769: free_ivector(indx,1,npar);
2770: free_matrix(hess,1,npar,1,npar);
2771:
2772:
2773: }
2774:
2775: /*************** hessian matrix ****************/
2776: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2777: {
2778: int i;
2779: int l=1, lmax=20;
2780: double k1,k2;
1.132 brouard 2781: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 2782: double res;
2783: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2784: double fx;
2785: int k=0,kmax=10;
2786: double l1;
2787:
2788: fx=func(x);
2789: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 2790: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 2791: l1=pow(10,l);
2792: delts=delt;
2793: for(k=1 ; k <kmax; k=k+1){
2794: delt = delta*(l1*k);
2795: p2[theta]=x[theta] +delt;
1.145 brouard 2796: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 2797: p2[theta]=x[theta]-delt;
2798: k2=func(p2)-fx;
2799: /*res= (k1-2.0*fx+k2)/delt/delt; */
2800: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2801:
1.132 brouard 2802: #ifdef DEBUGHESS
1.126 brouard 2803: 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);
2804: 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);
2805: #endif
2806: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2807: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2808: k=kmax;
2809: }
2810: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 2811: k=kmax; l=lmax*10;
1.126 brouard 2812: }
2813: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2814: delts=delt;
2815: }
2816: }
2817: }
2818: delti[theta]=delts;
2819: return res;
2820:
2821: }
2822:
2823: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2824: {
2825: int i;
1.164 brouard 2826: int l=1, lmax=20;
1.126 brouard 2827: double k1,k2,k3,k4,res,fx;
1.132 brouard 2828: double p2[MAXPARM+1];
1.126 brouard 2829: int k;
2830:
2831: fx=func(x);
2832: for (k=1; k<=2; k++) {
2833: for (i=1;i<=npar;i++) p2[i]=x[i];
2834: p2[thetai]=x[thetai]+delti[thetai]/k;
2835: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2836: k1=func(p2)-fx;
2837:
2838: p2[thetai]=x[thetai]+delti[thetai]/k;
2839: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2840: k2=func(p2)-fx;
2841:
2842: p2[thetai]=x[thetai]-delti[thetai]/k;
2843: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2844: k3=func(p2)-fx;
2845:
2846: p2[thetai]=x[thetai]-delti[thetai]/k;
2847: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2848: k4=func(p2)-fx;
2849: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2850: #ifdef DEBUG
2851: 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);
2852: 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);
2853: #endif
2854: }
2855: return res;
2856: }
2857:
2858: /************** Inverse of matrix **************/
2859: void ludcmp(double **a, int n, int *indx, double *d)
2860: {
2861: int i,imax,j,k;
2862: double big,dum,sum,temp;
2863: double *vv;
2864:
2865: vv=vector(1,n);
2866: *d=1.0;
2867: for (i=1;i<=n;i++) {
2868: big=0.0;
2869: for (j=1;j<=n;j++)
2870: if ((temp=fabs(a[i][j])) > big) big=temp;
2871: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2872: vv[i]=1.0/big;
2873: }
2874: for (j=1;j<=n;j++) {
2875: for (i=1;i<j;i++) {
2876: sum=a[i][j];
2877: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2878: a[i][j]=sum;
2879: }
2880: big=0.0;
2881: for (i=j;i<=n;i++) {
2882: sum=a[i][j];
2883: for (k=1;k<j;k++)
2884: sum -= a[i][k]*a[k][j];
2885: a[i][j]=sum;
2886: if ( (dum=vv[i]*fabs(sum)) >= big) {
2887: big=dum;
2888: imax=i;
2889: }
2890: }
2891: if (j != imax) {
2892: for (k=1;k<=n;k++) {
2893: dum=a[imax][k];
2894: a[imax][k]=a[j][k];
2895: a[j][k]=dum;
2896: }
2897: *d = -(*d);
2898: vv[imax]=vv[j];
2899: }
2900: indx[j]=imax;
2901: if (a[j][j] == 0.0) a[j][j]=TINY;
2902: if (j != n) {
2903: dum=1.0/(a[j][j]);
2904: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2905: }
2906: }
2907: free_vector(vv,1,n); /* Doesn't work */
2908: ;
2909: }
2910:
2911: void lubksb(double **a, int n, int *indx, double b[])
2912: {
2913: int i,ii=0,ip,j;
2914: double sum;
2915:
2916: for (i=1;i<=n;i++) {
2917: ip=indx[i];
2918: sum=b[ip];
2919: b[ip]=b[i];
2920: if (ii)
2921: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2922: else if (sum) ii=i;
2923: b[i]=sum;
2924: }
2925: for (i=n;i>=1;i--) {
2926: sum=b[i];
2927: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2928: b[i]=sum/a[i][i];
2929: }
2930: }
2931:
2932: void pstamp(FILE *fichier)
2933: {
1.196 brouard 2934: fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126 brouard 2935: }
2936:
2937: /************ Frequencies ********************/
2938: 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[])
2939: { /* Some frequencies */
2940:
1.164 brouard 2941: int i, m, jk, j1, bool, z1,j;
1.126 brouard 2942: int first;
2943: double ***freq; /* Frequencies */
2944: double *pp, **prop;
2945: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2946: char fileresp[FILENAMELENGTH];
2947:
2948: pp=vector(1,nlstate);
2949: prop=matrix(1,nlstate,iagemin,iagemax+3);
1.201 ! brouard 2950: strcpy(fileresp,"P_");
! 2951: strcat(fileresp,fileresu);
1.126 brouard 2952: if((ficresp=fopen(fileresp,"w"))==NULL) {
2953: printf("Problem with prevalence resultfile: %s\n", fileresp);
2954: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2955: exit(0);
2956: }
2957: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2958: j1=0;
2959:
2960: j=cptcoveff;
2961: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2962:
2963: first=1;
2964:
1.169 brouard 2965: /* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */
2966: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
2967: /* j1++; */
1.145 brouard 2968: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
1.126 brouard 2969: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2970: scanf("%d", i);*/
2971: for (i=-5; i<=nlstate+ndeath; i++)
2972: for (jk=-5; jk<=nlstate+ndeath; jk++)
2973: for(m=iagemin; m <= iagemax+3; m++)
2974: freq[i][jk][m]=0;
1.143 brouard 2975:
2976: for (i=1; i<=nlstate; i++)
2977: for(m=iagemin; m <= iagemax+3; m++)
2978: prop[i][m]=0;
1.126 brouard 2979:
2980: dateintsum=0;
2981: k2cpt=0;
2982: for (i=1; i<=imx; i++) {
2983: bool=1;
1.144 brouard 2984: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
2985: for (z1=1; z1<=cptcoveff; z1++)
1.198 brouard 2986: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
1.145 brouard 2987: /* Tests if the value of each of the covariates of i is equal to filter j1 */
1.144 brouard 2988: bool=0;
1.198 brouard 2989: /* 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",
2990: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
2991: j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
2992: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
1.144 brouard 2993: }
1.126 brouard 2994: }
1.144 brouard 2995:
1.126 brouard 2996: if (bool==1){
2997: for(m=firstpass; m<=lastpass; m++){
2998: k2=anint[m][i]+(mint[m][i]/12.);
2999: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
3000: if(agev[m][i]==0) agev[m][i]=iagemax+1;
3001: if(agev[m][i]==1) agev[m][i]=iagemax+2;
3002: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
3003: if (m<lastpass) {
3004: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
3005: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
3006: }
3007:
3008: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
3009: dateintsum=dateintsum+k2;
3010: k2cpt++;
3011: }
3012: /*}*/
3013: }
3014: }
1.145 brouard 3015: } /* end i */
1.126 brouard 3016:
3017: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
3018: pstamp(ficresp);
3019: if (cptcovn>0) {
3020: fprintf(ficresp, "\n#********** Variable ");
1.198 brouard 3021: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 3022: fprintf(ficresp, "**********\n#");
1.143 brouard 3023: fprintf(ficlog, "\n#********** Variable ");
1.198 brouard 3024: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.143 brouard 3025: fprintf(ficlog, "**********\n#");
1.126 brouard 3026: }
3027: for(i=1; i<=nlstate;i++)
3028: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
3029: fprintf(ficresp, "\n");
3030:
3031: for(i=iagemin; i <= iagemax+3; i++){
3032: if(i==iagemax+3){
3033: fprintf(ficlog,"Total");
3034: }else{
3035: if(first==1){
3036: first=0;
3037: printf("See log file for details...\n");
3038: }
3039: fprintf(ficlog,"Age %d", i);
3040: }
3041: for(jk=1; jk <=nlstate ; jk++){
3042: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
3043: pp[jk] += freq[jk][m][i];
3044: }
3045: for(jk=1; jk <=nlstate ; jk++){
3046: for(m=-1, pos=0; m <=0 ; m++)
3047: pos += freq[jk][m][i];
3048: if(pp[jk]>=1.e-10){
3049: if(first==1){
1.132 brouard 3050: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1.126 brouard 3051: }
3052: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
3053: }else{
3054: if(first==1)
3055: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3056: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3057: }
3058: }
3059:
3060: for(jk=1; jk <=nlstate ; jk++){
3061: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
3062: pp[jk] += freq[jk][m][i];
3063: }
3064: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
3065: pos += pp[jk];
3066: posprop += prop[jk][i];
3067: }
3068: for(jk=1; jk <=nlstate ; jk++){
3069: if(pos>=1.e-5){
3070: if(first==1)
3071: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3072: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3073: }else{
3074: if(first==1)
3075: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3076: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3077: }
3078: if( i <= iagemax){
3079: if(pos>=1.e-5){
3080: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
3081: /*probs[i][jk][j1]= pp[jk]/pos;*/
3082: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
3083: }
3084: else
3085: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
3086: }
3087: }
3088:
3089: for(jk=-1; jk <=nlstate+ndeath; jk++)
3090: for(m=-1; m <=nlstate+ndeath; m++)
3091: if(freq[jk][m][i] !=0 ) {
3092: if(first==1)
3093: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
3094: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
3095: }
3096: if(i <= iagemax)
3097: fprintf(ficresp,"\n");
3098: if(first==1)
3099: printf("Others in log...\n");
3100: fprintf(ficlog,"\n");
3101: }
1.145 brouard 3102: /*}*/
1.126 brouard 3103: }
3104: dateintmean=dateintsum/k2cpt;
3105:
3106: fclose(ficresp);
3107: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
3108: free_vector(pp,1,nlstate);
3109: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
3110: /* End of Freq */
3111: }
3112:
3113: /************ Prevalence ********************/
3114: 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)
3115: {
3116: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
3117: in each health status at the date of interview (if between dateprev1 and dateprev2).
3118: We still use firstpass and lastpass as another selection.
3119: */
3120:
1.164 brouard 3121: int i, m, jk, j1, bool, z1,j;
3122:
3123: double **prop;
3124: double posprop;
1.126 brouard 3125: double y2; /* in fractional years */
3126: int iagemin, iagemax;
1.145 brouard 3127: int first; /** to stop verbosity which is redirected to log file */
1.126 brouard 3128:
3129: iagemin= (int) agemin;
3130: iagemax= (int) agemax;
3131: /*pp=vector(1,nlstate);*/
3132: prop=matrix(1,nlstate,iagemin,iagemax+3);
3133: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
3134: j1=0;
3135:
1.145 brouard 3136: /*j=cptcoveff;*/
1.126 brouard 3137: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3138:
1.145 brouard 3139: first=1;
3140: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
3141: /*for(i1=1; i1<=ncodemax[k1];i1++){
3142: j1++;*/
1.126 brouard 3143:
3144: for (i=1; i<=nlstate; i++)
3145: for(m=iagemin; m <= iagemax+3; m++)
3146: prop[i][m]=0.0;
3147:
3148: for (i=1; i<=imx; i++) { /* Each individual */
3149: bool=1;
3150: if (cptcovn>0) {
3151: for (z1=1; z1<=cptcoveff; z1++)
1.198 brouard 3152: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])
1.126 brouard 3153: bool=0;
3154: }
3155: if (bool==1) {
3156: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
3157: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
3158: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
3159: if(agev[m][i]==0) agev[m][i]=iagemax+1;
3160: if(agev[m][i]==1) agev[m][i]=iagemax+2;
3161: 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);
3162: if (s[m][i]>0 && s[m][i]<=nlstate) {
3163: /*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]]);*/
3164: prop[s[m][i]][(int)agev[m][i]] += weight[i];
3165: prop[s[m][i]][iagemax+3] += weight[i];
3166: }
3167: }
3168: } /* end selection of waves */
3169: }
3170: }
3171: for(i=iagemin; i <= iagemax+3; i++){
3172: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
3173: posprop += prop[jk][i];
3174: }
1.145 brouard 3175:
1.126 brouard 3176: for(jk=1; jk <=nlstate ; jk++){
3177: if( i <= iagemax){
3178: if(posprop>=1.e-5){
3179: probs[i][jk][j1]= prop[jk][i]/posprop;
1.145 brouard 3180: } else{
3181: if(first==1){
3182: first=0;
3183: 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]);
3184: }
3185: }
1.126 brouard 3186: }
3187: }/* end jk */
3188: }/* end i */
1.145 brouard 3189: /*} *//* end i1 */
3190: } /* end j1 */
1.126 brouard 3191:
3192: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
3193: /*free_vector(pp,1,nlstate);*/
3194: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
3195: } /* End of prevalence */
3196:
3197: /************* Waves Concatenation ***************/
3198:
3199: 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)
3200: {
3201: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
3202: Death is a valid wave (if date is known).
3203: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
3204: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3205: and mw[mi+1][i]. dh depends on stepm.
3206: */
3207:
3208: int i, mi, m;
3209: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
3210: double sum=0., jmean=0.;*/
3211: int first;
3212: int j, k=0,jk, ju, jl;
3213: double sum=0.;
3214: first=0;
1.164 brouard 3215: jmin=100000;
1.126 brouard 3216: jmax=-1;
3217: jmean=0.;
3218: for(i=1; i<=imx; i++){
3219: mi=0;
3220: m=firstpass;
3221: while(s[m][i] <= nlstate){
3222: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
3223: mw[++mi][i]=m;
3224: if(m >=lastpass)
3225: break;
3226: else
3227: m++;
3228: }/* end while */
3229: if (s[m][i] > nlstate){
3230: mi++; /* Death is another wave */
3231: /* if(mi==0) never been interviewed correctly before death */
3232: /* Only death is a correct wave */
3233: mw[mi][i]=m;
3234: }
3235:
3236: wav[i]=mi;
3237: if(mi==0){
3238: nbwarn++;
3239: if(first==0){
3240: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
3241: first=1;
3242: }
3243: if(first==1){
3244: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
3245: }
3246: } /* end mi==0 */
3247: } /* End individuals */
3248:
3249: for(i=1; i<=imx; i++){
3250: for(mi=1; mi<wav[i];mi++){
3251: if (stepm <=0)
3252: dh[mi][i]=1;
3253: else{
3254: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
3255: if (agedc[i] < 2*AGESUP) {
3256: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
3257: if(j==0) j=1; /* Survives at least one month after exam */
3258: else if(j<0){
3259: nberr++;
3260: 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]);
3261: j=1; /* Temporary Dangerous patch */
3262: 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);
3263: 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]);
3264: 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);
3265: }
3266: k=k+1;
3267: if (j >= jmax){
3268: jmax=j;
3269: ijmax=i;
3270: }
3271: if (j <= jmin){
3272: jmin=j;
3273: ijmin=i;
3274: }
3275: sum=sum+j;
3276: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
3277: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
3278: }
3279: }
3280: else{
3281: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
3282: /* 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]); */
3283:
3284: k=k+1;
3285: if (j >= jmax) {
3286: jmax=j;
3287: ijmax=i;
3288: }
3289: else if (j <= jmin){
3290: jmin=j;
3291: ijmin=i;
3292: }
3293: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
3294: /*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]);*/
3295: if(j<0){
3296: nberr++;
3297: 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]);
3298: 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]);
3299: }
3300: sum=sum+j;
3301: }
3302: jk= j/stepm;
3303: jl= j -jk*stepm;
3304: ju= j -(jk+1)*stepm;
3305: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
3306: if(jl==0){
3307: dh[mi][i]=jk;
3308: bh[mi][i]=0;
3309: }else{ /* We want a negative bias in order to only have interpolation ie
1.136 brouard 3310: * to avoid the price of an extra matrix product in likelihood */
1.126 brouard 3311: dh[mi][i]=jk+1;
3312: bh[mi][i]=ju;
3313: }
3314: }else{
3315: if(jl <= -ju){
3316: dh[mi][i]=jk;
3317: bh[mi][i]=jl; /* bias is positive if real duration
3318: * is higher than the multiple of stepm and negative otherwise.
3319: */
3320: }
3321: else{
3322: dh[mi][i]=jk+1;
3323: bh[mi][i]=ju;
3324: }
3325: if(dh[mi][i]==0){
3326: dh[mi][i]=1; /* At least one step */
3327: bh[mi][i]=ju; /* At least one step */
3328: /* 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);*/
3329: }
3330: } /* end if mle */
3331: }
3332: } /* end wave */
3333: }
3334: jmean=sum/k;
3335: 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 3336: 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 3337: }
3338:
3339: /*********** Tricode ****************************/
1.145 brouard 3340: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 3341: {
1.144 brouard 3342: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
3343: /* 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 3344: * Boring subroutine which should only output nbcode[Tvar[j]][k]
1.145 brouard 3345: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
1.169 brouard 3346: * nbcode[Tvar[j]][1]=
1.144 brouard 3347: */
1.130 brouard 3348:
1.145 brouard 3349: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 3350: int modmaxcovj=0; /* Modality max of covariates j */
1.145 brouard 3351: int cptcode=0; /* Modality max of covariates j */
3352: int modmincovj=0; /* Modality min of covariates j */
3353:
3354:
1.126 brouard 3355: cptcoveff=0;
3356:
1.144 brouard 3357: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 3358:
1.145 brouard 3359: /* Loop on covariates without age and products */
1.186 brouard 3360: for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
1.192 brouard 3361: for (k=-1; k < maxncov; k++) Ndum[k]=0;
1.186 brouard 3362: for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
1.136 brouard 3363: modality of this covariate Vj*/
1.145 brouard 3364: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
3365: * If product of Vn*Vm, still boolean *:
3366: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
3367: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
3368: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
1.136 brouard 3369: modality of the nth covariate of individual i. */
1.145 brouard 3370: if (ij > modmaxcovj)
3371: modmaxcovj=ij;
3372: else if (ij < modmincovj)
3373: modmincovj=ij;
3374: if ((ij < -1) && (ij > NCOVMAX)){
3375: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
3376: exit(1);
3377: }else
1.136 brouard 3378: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
1.145 brouard 3379: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
1.126 brouard 3380: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.136 brouard 3381: /* getting the maximum value of the modality of the covariate
3382: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
3383: female is 1, then modmaxcovj=1.*/
1.192 brouard 3384: } /* end for loop on individuals i */
1.145 brouard 3385: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
1.192 brouard 3386: 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 3387: cptcode=modmaxcovj;
1.137 brouard 3388: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
1.145 brouard 3389: /*for (i=0; i<=cptcode; i++) {*/
1.192 brouard 3390: for (k=modmincovj; k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
3391: printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
3392: fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
3393: if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
3394: if( k != -1){
3395: ncodemax[j]++; /* ncodemax[j]= Number of modalities of the j th
3396: covariate for which somebody answered excluding
3397: undefined. Usually 2: 0 and 1. */
3398: }
3399: ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
3400: covariate for which somebody answered including
3401: undefined. Usually 3: -1, 0 and 1. */
1.145 brouard 3402: }
3403: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
3404: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
1.131 brouard 3405: } /* Ndum[-1] number of undefined modalities */
1.126 brouard 3406:
1.136 brouard 3407: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
1.186 brouard 3408: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
3409: 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 3410: modmincovj=3; modmaxcovj = 7;
1.186 brouard 3411: There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
3412: which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
3413: defining two dummy variables: variables V1_1 and V1_2.
1.145 brouard 3414: nbcode[Tvar[j]][ij]=k;
3415: nbcode[Tvar[j]][1]=0;
3416: nbcode[Tvar[j]][2]=1;
3417: nbcode[Tvar[j]][3]=2;
1.197 brouard 3418: To be continued (not working yet).
1.145 brouard 3419: */
1.197 brouard 3420: ij=0; /* ij is similar to i but can jump over null modalities */
3421: 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*/
3422: if (Ndum[i] == 0) { /* If nobody responded to this modality k */
1.192 brouard 3423: break;
3424: }
3425: ij++;
1.197 brouard 3426: 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 3427: cptcode = ij; /* New max modality for covar j */
3428: } /* end of loop on modality i=-1 to 1 or more */
3429:
3430: /* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
3431: /* /\*recode from 0 *\/ */
3432: /* k is a modality. If we have model=V1+V1*sex */
3433: /* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
3434: /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
3435: /* } */
3436: /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
3437: /* if (ij > ncodemax[j]) { */
3438: /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
3439: /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
3440: /* break; */
3441: /* } */
3442: /* } /\* end of loop on modality k *\/ */
1.137 brouard 3443: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
3444:
1.145 brouard 3445: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.137 brouard 3446:
1.187 brouard 3447: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
1.145 brouard 3448: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
3449: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
1.187 brouard 3450: Ndum[ij]++; /* Might be supersed V1 + V1*age */
1.145 brouard 3451: }
1.126 brouard 3452:
1.192 brouard 3453: ij=0;
1.145 brouard 3454: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
3455: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
1.126 brouard 3456: if((Ndum[i]!=0) && (i<=ncovcol)){
1.192 brouard 3457: ij++;
1.145 brouard 3458: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
3459: Tvaraff[ij]=i; /*For printing (unclear) */
1.192 brouard 3460: }else{
3461: /* Tvaraff[ij]=0; */
3462: }
1.126 brouard 3463: }
1.192 brouard 3464: /* ij--; */
1.144 brouard 3465: cptcoveff=ij; /*Number of total covariates*/
1.145 brouard 3466:
1.126 brouard 3467: }
3468:
1.145 brouard 3469:
1.126 brouard 3470: /*********** Health Expectancies ****************/
3471:
1.127 brouard 3472: 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 3473:
3474: {
3475: /* Health expectancies, no variances */
1.164 brouard 3476: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 3477: int nhstepma, nstepma; /* Decreasing with age */
3478: double age, agelim, hf;
3479: double ***p3mat;
3480: double eip;
3481:
3482: pstamp(ficreseij);
3483: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3484: fprintf(ficreseij,"# Age");
3485: for(i=1; i<=nlstate;i++){
3486: for(j=1; j<=nlstate;j++){
3487: fprintf(ficreseij," e%1d%1d ",i,j);
3488: }
3489: fprintf(ficreseij," e%1d. ",i);
3490: }
3491: fprintf(ficreseij,"\n");
3492:
3493:
3494: if(estepm < stepm){
3495: printf ("Problem %d lower than %d\n",estepm, stepm);
3496: }
3497: else hstepm=estepm;
3498: /* We compute the life expectancy from trapezoids spaced every estepm months
3499: * This is mainly to measure the difference between two models: for example
3500: * if stepm=24 months pijx are given only every 2 years and by summing them
3501: * we are calculating an estimate of the Life Expectancy assuming a linear
3502: * progression in between and thus overestimating or underestimating according
3503: * to the curvature of the survival function. If, for the same date, we
3504: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3505: * to compare the new estimate of Life expectancy with the same linear
3506: * hypothesis. A more precise result, taking into account a more precise
3507: * curvature will be obtained if estepm is as small as stepm. */
3508:
3509: /* For example we decided to compute the life expectancy with the smallest unit */
3510: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3511: nhstepm is the number of hstepm from age to agelim
3512: nstepm is the number of stepm from age to agelin.
3513: Look at hpijx to understand the reason of that which relies in memory size
3514: and note for a fixed period like estepm months */
3515: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3516: survival function given by stepm (the optimization length). Unfortunately it
3517: means that if the survival funtion is printed only each two years of age and if
3518: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3519: results. So we changed our mind and took the option of the best precision.
3520: */
3521: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3522:
3523: agelim=AGESUP;
3524: /* If stepm=6 months */
3525: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3526: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3527:
3528: /* nhstepm age range expressed in number of stepm */
3529: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3530: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3531: /* if (stepm >= YEARM) hstepm=1;*/
3532: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3533: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3534:
3535: for (age=bage; age<=fage; age ++){
3536: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3537: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3538: /* if (stepm >= YEARM) hstepm=1;*/
3539: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3540:
3541: /* If stepm=6 months */
3542: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3543: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3544:
3545: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3546:
3547: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3548:
3549: printf("%d|",(int)age);fflush(stdout);
3550: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3551:
3552: /* Computing expectancies */
3553: for(i=1; i<=nlstate;i++)
3554: for(j=1; j<=nlstate;j++)
3555: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3556: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3557:
3558: /* 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]);*/
3559:
3560: }
3561:
3562: fprintf(ficreseij,"%3.0f",age );
3563: for(i=1; i<=nlstate;i++){
3564: eip=0;
3565: for(j=1; j<=nlstate;j++){
3566: eip +=eij[i][j][(int)age];
3567: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3568: }
3569: fprintf(ficreseij,"%9.4f", eip );
3570: }
3571: fprintf(ficreseij,"\n");
3572:
3573: }
3574: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3575: printf("\n");
3576: fprintf(ficlog,"\n");
3577:
3578: }
3579:
1.127 brouard 3580: 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 3581:
3582: {
3583: /* Covariances of health expectancies eij and of total life expectancies according
3584: to initial status i, ei. .
3585: */
3586: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3587: int nhstepma, nstepma; /* Decreasing with age */
3588: double age, agelim, hf;
3589: double ***p3matp, ***p3matm, ***varhe;
3590: double **dnewm,**doldm;
3591: double *xp, *xm;
3592: double **gp, **gm;
3593: double ***gradg, ***trgradg;
3594: int theta;
3595:
3596: double eip, vip;
3597:
3598: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
3599: xp=vector(1,npar);
3600: xm=vector(1,npar);
3601: dnewm=matrix(1,nlstate*nlstate,1,npar);
3602: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3603:
3604: pstamp(ficresstdeij);
3605: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3606: fprintf(ficresstdeij,"# Age");
3607: for(i=1; i<=nlstate;i++){
3608: for(j=1; j<=nlstate;j++)
3609: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3610: fprintf(ficresstdeij," e%1d. ",i);
3611: }
3612: fprintf(ficresstdeij,"\n");
3613:
3614: pstamp(ficrescveij);
3615: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3616: fprintf(ficrescveij,"# Age");
3617: for(i=1; i<=nlstate;i++)
3618: for(j=1; j<=nlstate;j++){
3619: cptj= (j-1)*nlstate+i;
3620: for(i2=1; i2<=nlstate;i2++)
3621: for(j2=1; j2<=nlstate;j2++){
3622: cptj2= (j2-1)*nlstate+i2;
3623: if(cptj2 <= cptj)
3624: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3625: }
3626: }
3627: fprintf(ficrescveij,"\n");
3628:
3629: if(estepm < stepm){
3630: printf ("Problem %d lower than %d\n",estepm, stepm);
3631: }
3632: else hstepm=estepm;
3633: /* We compute the life expectancy from trapezoids spaced every estepm months
3634: * This is mainly to measure the difference between two models: for example
3635: * if stepm=24 months pijx are given only every 2 years and by summing them
3636: * we are calculating an estimate of the Life Expectancy assuming a linear
3637: * progression in between and thus overestimating or underestimating according
3638: * to the curvature of the survival function. If, for the same date, we
3639: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3640: * to compare the new estimate of Life expectancy with the same linear
3641: * hypothesis. A more precise result, taking into account a more precise
3642: * curvature will be obtained if estepm is as small as stepm. */
3643:
3644: /* For example we decided to compute the life expectancy with the smallest unit */
3645: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3646: nhstepm is the number of hstepm from age to agelim
3647: nstepm is the number of stepm from age to agelin.
3648: Look at hpijx to understand the reason of that which relies in memory size
3649: and note for a fixed period like estepm months */
3650: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3651: survival function given by stepm (the optimization length). Unfortunately it
3652: means that if the survival funtion is printed only each two years of age and if
3653: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3654: results. So we changed our mind and took the option of the best precision.
3655: */
3656: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3657:
3658: /* If stepm=6 months */
3659: /* nhstepm age range expressed in number of stepm */
3660: agelim=AGESUP;
3661: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3662: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3663: /* if (stepm >= YEARM) hstepm=1;*/
3664: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3665:
3666: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3667: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3668: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3669: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3670: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3671: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3672:
3673: for (age=bage; age<=fage; age ++){
3674: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3675: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3676: /* if (stepm >= YEARM) hstepm=1;*/
3677: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3678:
3679: /* If stepm=6 months */
3680: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3681: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3682:
3683: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3684:
3685: /* Computing Variances of health expectancies */
3686: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3687: decrease memory allocation */
3688: for(theta=1; theta <=npar; theta++){
3689: for(i=1; i<=npar; i++){
3690: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3691: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3692: }
3693: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3694: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3695:
3696: for(j=1; j<= nlstate; j++){
3697: for(i=1; i<=nlstate; i++){
3698: for(h=0; h<=nhstepm-1; h++){
3699: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3700: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3701: }
3702: }
3703: }
3704:
3705: for(ij=1; ij<= nlstate*nlstate; ij++)
3706: for(h=0; h<=nhstepm-1; h++){
3707: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3708: }
3709: }/* End theta */
3710:
3711:
3712: for(h=0; h<=nhstepm-1; h++)
3713: for(j=1; j<=nlstate*nlstate;j++)
3714: for(theta=1; theta <=npar; theta++)
3715: trgradg[h][j][theta]=gradg[h][theta][j];
3716:
3717:
3718: for(ij=1;ij<=nlstate*nlstate;ij++)
3719: for(ji=1;ji<=nlstate*nlstate;ji++)
3720: varhe[ij][ji][(int)age] =0.;
3721:
3722: printf("%d|",(int)age);fflush(stdout);
3723: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3724: for(h=0;h<=nhstepm-1;h++){
3725: for(k=0;k<=nhstepm-1;k++){
3726: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3727: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3728: for(ij=1;ij<=nlstate*nlstate;ij++)
3729: for(ji=1;ji<=nlstate*nlstate;ji++)
3730: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3731: }
3732: }
3733:
3734: /* Computing expectancies */
3735: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3736: for(i=1; i<=nlstate;i++)
3737: for(j=1; j<=nlstate;j++)
3738: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3739: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3740:
3741: /* 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]);*/
3742:
3743: }
3744:
3745: fprintf(ficresstdeij,"%3.0f",age );
3746: for(i=1; i<=nlstate;i++){
3747: eip=0.;
3748: vip=0.;
3749: for(j=1; j<=nlstate;j++){
3750: eip += eij[i][j][(int)age];
3751: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3752: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3753: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3754: }
3755: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3756: }
3757: fprintf(ficresstdeij,"\n");
3758:
3759: fprintf(ficrescveij,"%3.0f",age );
3760: for(i=1; i<=nlstate;i++)
3761: for(j=1; j<=nlstate;j++){
3762: cptj= (j-1)*nlstate+i;
3763: for(i2=1; i2<=nlstate;i2++)
3764: for(j2=1; j2<=nlstate;j2++){
3765: cptj2= (j2-1)*nlstate+i2;
3766: if(cptj2 <= cptj)
3767: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3768: }
3769: }
3770: fprintf(ficrescveij,"\n");
3771:
3772: }
3773: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3774: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3775: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3776: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3777: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3778: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3779: printf("\n");
3780: fprintf(ficlog,"\n");
3781:
3782: free_vector(xm,1,npar);
3783: free_vector(xp,1,npar);
3784: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3785: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3786: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3787: }
3788:
3789: /************ Variance ******************/
3790: 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[])
3791: {
3792: /* Variance of health expectancies */
3793: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3794: /* double **newm;*/
1.169 brouard 3795: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
3796:
3797: int movingaverage();
1.126 brouard 3798: double **dnewm,**doldm;
3799: double **dnewmp,**doldmp;
3800: int i, j, nhstepm, hstepm, h, nstepm ;
1.164 brouard 3801: int k;
1.126 brouard 3802: double *xp;
3803: double **gp, **gm; /* for var eij */
3804: double ***gradg, ***trgradg; /*for var eij */
3805: double **gradgp, **trgradgp; /* for var p point j */
3806: double *gpp, *gmp; /* for var p point j */
3807: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3808: double ***p3mat;
3809: double age,agelim, hf;
3810: double ***mobaverage;
3811: int theta;
3812: char digit[4];
3813: char digitp[25];
3814:
3815: char fileresprobmorprev[FILENAMELENGTH];
3816:
3817: if(popbased==1){
3818: if(mobilav!=0)
1.201 ! brouard 3819: strcpy(digitp,"-POPULBASED-MOBILAV_");
! 3820: else strcpy(digitp,"-POPULBASED-NOMOBIL_");
1.126 brouard 3821: }
3822: else
1.201 ! brouard 3823: strcpy(digitp,"-STABLBASED_");
1.126 brouard 3824:
3825: if (mobilav!=0) {
3826: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3827: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3828: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3829: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3830: }
3831: }
3832:
1.201 ! brouard 3833: strcpy(fileresprobmorprev,"PRMORPREV-");
1.126 brouard 3834: sprintf(digit,"%-d",ij);
3835: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3836: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3837: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
3838: strcat(fileresprobmorprev,fileres);
3839: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3840: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3841: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3842: }
3843: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3844:
3845: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3846: pstamp(ficresprobmorprev);
3847: 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);
3848: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3849: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3850: fprintf(ficresprobmorprev," p.%-d SE",j);
3851: for(i=1; i<=nlstate;i++)
3852: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3853: }
3854: fprintf(ficresprobmorprev,"\n");
3855: fprintf(ficgp,"\n# Routine varevsij");
1.200 brouard 3856: fprintf(ficgp,"\nunset title \n");
3857: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
1.126 brouard 3858: 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");
3859: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3860: /* } */
3861: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3862: pstamp(ficresvij);
3863: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3864: if(popbased==1)
1.128 brouard 3865: 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 3866: else
3867: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3868: fprintf(ficresvij,"# Age");
3869: for(i=1; i<=nlstate;i++)
3870: for(j=1; j<=nlstate;j++)
3871: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3872: fprintf(ficresvij,"\n");
3873:
3874: xp=vector(1,npar);
3875: dnewm=matrix(1,nlstate,1,npar);
3876: doldm=matrix(1,nlstate,1,nlstate);
3877: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3878: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3879:
3880: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3881: gpp=vector(nlstate+1,nlstate+ndeath);
3882: gmp=vector(nlstate+1,nlstate+ndeath);
3883: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3884:
3885: if(estepm < stepm){
3886: printf ("Problem %d lower than %d\n",estepm, stepm);
3887: }
3888: else hstepm=estepm;
3889: /* For example we decided to compute the life expectancy with the smallest unit */
3890: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3891: nhstepm is the number of hstepm from age to agelim
3892: nstepm is the number of stepm from age to agelin.
1.128 brouard 3893: Look at function hpijx to understand why (it is linked to memory size questions) */
1.126 brouard 3894: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3895: survival function given by stepm (the optimization length). Unfortunately it
3896: means that if the survival funtion is printed every two years of age and if
3897: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3898: results. So we changed our mind and took the option of the best precision.
3899: */
3900: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3901: agelim = AGESUP;
3902: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3903: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3904: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3905: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3906: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3907: gp=matrix(0,nhstepm,1,nlstate);
3908: gm=matrix(0,nhstepm,1,nlstate);
3909:
3910:
3911: for(theta=1; theta <=npar; theta++){
3912: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3913: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3914: }
3915: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3916: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3917:
3918: if (popbased==1) {
3919: if(mobilav ==0){
3920: for(i=1; i<=nlstate;i++)
3921: prlim[i][i]=probs[(int)age][i][ij];
3922: }else{ /* mobilav */
3923: for(i=1; i<=nlstate;i++)
3924: prlim[i][i]=mobaverage[(int)age][i][ij];
3925: }
3926: }
3927:
3928: for(j=1; j<= nlstate; j++){
3929: for(h=0; h<=nhstepm; h++){
3930: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3931: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3932: }
3933: }
3934: /* This for computing probability of death (h=1 means
3935: computed over hstepm matrices product = hstepm*stepm months)
3936: as a weighted average of prlim.
3937: */
3938: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3939: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3940: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3941: }
3942: /* end probability of death */
3943:
3944: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3945: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3946: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3947: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3948:
3949: if (popbased==1) {
3950: if(mobilav ==0){
3951: for(i=1; i<=nlstate;i++)
3952: prlim[i][i]=probs[(int)age][i][ij];
3953: }else{ /* mobilav */
3954: for(i=1; i<=nlstate;i++)
3955: prlim[i][i]=mobaverage[(int)age][i][ij];
3956: }
3957: }
3958:
1.128 brouard 3959: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
1.126 brouard 3960: for(h=0; h<=nhstepm; h++){
3961: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3962: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3963: }
3964: }
3965: /* This for computing probability of death (h=1 means
3966: computed over hstepm matrices product = hstepm*stepm months)
3967: as a weighted average of prlim.
3968: */
3969: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3970: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3971: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3972: }
3973: /* end probability of death */
3974:
3975: for(j=1; j<= nlstate; j++) /* vareij */
3976: for(h=0; h<=nhstepm; h++){
3977: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3978: }
3979:
3980: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3981: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3982: }
3983:
3984: } /* End theta */
3985:
3986: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3987:
3988: for(h=0; h<=nhstepm; h++) /* veij */
3989: for(j=1; j<=nlstate;j++)
3990: for(theta=1; theta <=npar; theta++)
3991: trgradg[h][j][theta]=gradg[h][theta][j];
3992:
3993: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3994: for(theta=1; theta <=npar; theta++)
3995: trgradgp[j][theta]=gradgp[theta][j];
3996:
3997:
3998: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3999: for(i=1;i<=nlstate;i++)
4000: for(j=1;j<=nlstate;j++)
4001: vareij[i][j][(int)age] =0.;
4002:
4003: for(h=0;h<=nhstepm;h++){
4004: for(k=0;k<=nhstepm;k++){
4005: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
4006: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
4007: for(i=1;i<=nlstate;i++)
4008: for(j=1;j<=nlstate;j++)
4009: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
4010: }
4011: }
4012:
4013: /* pptj */
4014: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
4015: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
4016: for(j=nlstate+1;j<=nlstate+ndeath;j++)
4017: for(i=nlstate+1;i<=nlstate+ndeath;i++)
4018: varppt[j][i]=doldmp[j][i];
4019: /* end ppptj */
4020: /* x centered again */
4021: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
4022: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
4023:
4024: if (popbased==1) {
4025: if(mobilav ==0){
4026: for(i=1; i<=nlstate;i++)
4027: prlim[i][i]=probs[(int)age][i][ij];
4028: }else{ /* mobilav */
4029: for(i=1; i<=nlstate;i++)
4030: prlim[i][i]=mobaverage[(int)age][i][ij];
4031: }
4032: }
4033:
4034: /* This for computing probability of death (h=1 means
4035: computed over hstepm (estepm) matrices product = hstepm*stepm months)
4036: as a weighted average of prlim.
4037: */
4038: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4039: for(i=1,gmp[j]=0.;i<= nlstate; i++)
4040: gmp[j] += prlim[i][i]*p3mat[i][j][1];
4041: }
4042: /* end probability of death */
4043:
4044: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
4045: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
4046: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
4047: for(i=1; i<=nlstate;i++){
4048: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
4049: }
4050: }
4051: fprintf(ficresprobmorprev,"\n");
4052:
4053: fprintf(ficresvij,"%.0f ",age );
4054: for(i=1; i<=nlstate;i++)
4055: for(j=1; j<=nlstate;j++){
4056: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
4057: }
4058: fprintf(ficresvij,"\n");
4059: free_matrix(gp,0,nhstepm,1,nlstate);
4060: free_matrix(gm,0,nhstepm,1,nlstate);
4061: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
4062: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
4063: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4064: } /* End age */
4065: free_vector(gpp,nlstate+1,nlstate+ndeath);
4066: free_vector(gmp,nlstate+1,nlstate+ndeath);
4067: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
4068: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.199 brouard 4069: /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
4070: fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
1.126 brouard 4071: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
1.131 brouard 4072: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.201 ! brouard 4073: fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 4074: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
4075: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
4076: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.145 brouard 4077: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
1.170 brouard 4078: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
1.145 brouard 4079: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
1.126 brouard 4080: 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 4081: 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 4082: /* 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 4083: */
1.199 brouard 4084: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
1.201 ! brouard 4085: fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 4086:
4087: free_vector(xp,1,npar);
4088: free_matrix(doldm,1,nlstate,1,nlstate);
4089: free_matrix(dnewm,1,nlstate,1,npar);
4090: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4091: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
4092: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4093: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4094: fclose(ficresprobmorprev);
4095: fflush(ficgp);
4096: fflush(fichtm);
4097: } /* end varevsij */
4098:
4099: /************ Variance of prevlim ******************/
4100: 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[])
4101: {
4102: /* Variance of prevalence limit */
4103: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 4104:
1.126 brouard 4105: double **dnewm,**doldm;
4106: int i, j, nhstepm, hstepm;
4107: double *xp;
4108: double *gp, *gm;
4109: double **gradg, **trgradg;
4110: double age,agelim;
4111: int theta;
4112:
4113: pstamp(ficresvpl);
4114: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
4115: fprintf(ficresvpl,"# Age");
4116: for(i=1; i<=nlstate;i++)
4117: fprintf(ficresvpl," %1d-%1d",i,i);
4118: fprintf(ficresvpl,"\n");
4119:
4120: xp=vector(1,npar);
4121: dnewm=matrix(1,nlstate,1,npar);
4122: doldm=matrix(1,nlstate,1,nlstate);
4123:
4124: hstepm=1*YEARM; /* Every year of age */
4125: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
4126: agelim = AGESUP;
4127: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
4128: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4129: if (stepm >= YEARM) hstepm=1;
4130: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4131: gradg=matrix(1,npar,1,nlstate);
4132: gp=vector(1,nlstate);
4133: gm=vector(1,nlstate);
4134:
4135: for(theta=1; theta <=npar; theta++){
4136: for(i=1; i<=npar; i++){ /* Computes gradient */
4137: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4138: }
4139: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
4140: for(i=1;i<=nlstate;i++)
4141: gp[i] = prlim[i][i];
4142:
4143: for(i=1; i<=npar; i++) /* Computes gradient */
4144: xp[i] = x[i] - (i==theta ?delti[theta]:0);
4145: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
4146: for(i=1;i<=nlstate;i++)
4147: gm[i] = prlim[i][i];
4148:
4149: for(i=1;i<=nlstate;i++)
4150: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
4151: } /* End theta */
4152:
4153: trgradg =matrix(1,nlstate,1,npar);
4154:
4155: for(j=1; j<=nlstate;j++)
4156: for(theta=1; theta <=npar; theta++)
4157: trgradg[j][theta]=gradg[theta][j];
4158:
4159: for(i=1;i<=nlstate;i++)
4160: varpl[i][(int)age] =0.;
4161: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
4162: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
4163: for(i=1;i<=nlstate;i++)
4164: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
4165:
4166: fprintf(ficresvpl,"%.0f ",age );
4167: for(i=1; i<=nlstate;i++)
4168: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
4169: fprintf(ficresvpl,"\n");
4170: free_vector(gp,1,nlstate);
4171: free_vector(gm,1,nlstate);
4172: free_matrix(gradg,1,npar,1,nlstate);
4173: free_matrix(trgradg,1,nlstate,1,npar);
4174: } /* End age */
4175:
4176: free_vector(xp,1,npar);
4177: free_matrix(doldm,1,nlstate,1,npar);
4178: free_matrix(dnewm,1,nlstate,1,nlstate);
4179:
4180: }
4181:
4182: /************ Variance of one-step probabilities ******************/
4183: 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[])
4184: {
1.164 brouard 4185: int i, j=0, k1, l1, tj;
1.126 brouard 4186: int k2, l2, j1, z1;
1.164 brouard 4187: int k=0, l;
1.145 brouard 4188: int first=1, first1, first2;
1.126 brouard 4189: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
4190: double **dnewm,**doldm;
4191: double *xp;
4192: double *gp, *gm;
4193: double **gradg, **trgradg;
4194: double **mu;
1.164 brouard 4195: double age, cov[NCOVMAX+1];
1.126 brouard 4196: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
4197: int theta;
4198: char fileresprob[FILENAMELENGTH];
4199: char fileresprobcov[FILENAMELENGTH];
4200: char fileresprobcor[FILENAMELENGTH];
4201: double ***varpij;
4202:
1.201 ! brouard 4203: strcpy(fileresprob,"PROB_");
1.126 brouard 4204: strcat(fileresprob,fileres);
4205: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
4206: printf("Problem with resultfile: %s\n", fileresprob);
4207: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
4208: }
1.201 ! brouard 4209: strcpy(fileresprobcov,"PROBCOV_");
1.126 brouard 4210: strcat(fileresprobcov,fileres);
4211: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
4212: printf("Problem with resultfile: %s\n", fileresprobcov);
4213: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
4214: }
1.201 ! brouard 4215: strcpy(fileresprobcor,"PROBCOR_");
1.126 brouard 4216: strcat(fileresprobcor,fileres);
4217: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
4218: printf("Problem with resultfile: %s\n", fileresprobcor);
4219: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
4220: }
4221: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4222: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4223: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4224: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4225: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4226: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4227: pstamp(ficresprob);
4228: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
4229: fprintf(ficresprob,"# Age");
4230: pstamp(ficresprobcov);
4231: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
4232: fprintf(ficresprobcov,"# Age");
4233: pstamp(ficresprobcor);
4234: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
4235: fprintf(ficresprobcor,"# Age");
4236:
4237:
4238: for(i=1; i<=nlstate;i++)
4239: for(j=1; j<=(nlstate+ndeath);j++){
4240: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
4241: fprintf(ficresprobcov," p%1d-%1d ",i,j);
4242: fprintf(ficresprobcor," p%1d-%1d ",i,j);
4243: }
4244: /* fprintf(ficresprob,"\n");
4245: fprintf(ficresprobcov,"\n");
4246: fprintf(ficresprobcor,"\n");
4247: */
1.131 brouard 4248: xp=vector(1,npar);
1.126 brouard 4249: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4250: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4251: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
4252: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
4253: first=1;
4254: fprintf(ficgp,"\n# Routine varprob");
4255: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
4256: fprintf(fichtm,"\n");
4257:
1.200 brouard 4258: 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 4259: 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);
4260: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
1.126 brouard 4261: and drawn. It helps understanding how is the covariance between two incidences.\
4262: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
4263: 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. \
4264: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
4265: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
4266: standard deviations wide on each axis. <br>\
4267: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
4268: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
4269: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
4270:
4271: cov[1]=1;
1.145 brouard 4272: /* tj=cptcoveff; */
4273: tj = (int) pow(2,cptcoveff);
1.126 brouard 4274: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
4275: j1=0;
1.145 brouard 4276: for(j1=1; j1<=tj;j1++){
4277: /*for(i1=1; i1<=ncodemax[t];i1++){ */
4278: /*j1++;*/
1.126 brouard 4279: if (cptcovn>0) {
4280: fprintf(ficresprob, "\n#********** Variable ");
1.198 brouard 4281: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4282: fprintf(ficresprob, "**********\n#\n");
4283: fprintf(ficresprobcov, "\n#********** Variable ");
1.198 brouard 4284: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4285: fprintf(ficresprobcov, "**********\n#\n");
4286:
4287: fprintf(ficgp, "\n#********** Variable ");
1.198 brouard 4288: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4289: fprintf(ficgp, "**********\n#\n");
4290:
4291:
4292: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.198 brouard 4293: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4294: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
4295:
4296: fprintf(ficresprobcor, "\n#********** Variable ");
1.198 brouard 4297: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4298: fprintf(ficresprobcor, "**********\n#");
4299: }
4300:
1.145 brouard 4301: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
4302: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4303: gp=vector(1,(nlstate)*(nlstate+ndeath));
4304: gm=vector(1,(nlstate)*(nlstate+ndeath));
1.126 brouard 4305: for (age=bage; age<=fage; age ++){
4306: cov[2]=age;
1.187 brouard 4307: if(nagesqr==1)
4308: cov[3]= age*age;
1.126 brouard 4309: for (k=1; k<=cptcovn;k++) {
1.200 brouard 4310: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
4311: /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
1.145 brouard 4312: * 1 1 1 1 1
4313: * 2 2 1 1 1
4314: * 3 1 2 1 1
4315: */
4316: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
1.126 brouard 4317: }
1.186 brouard 4318: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 4319: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
1.126 brouard 4320: for (k=1; k<=cptcovprod;k++)
1.200 brouard 4321: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.126 brouard 4322:
4323:
4324: for(theta=1; theta <=npar; theta++){
4325: for(i=1; i<=npar; i++)
4326: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
4327:
4328: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4329:
4330: k=0;
4331: for(i=1; i<= (nlstate); i++){
4332: for(j=1; j<=(nlstate+ndeath);j++){
4333: k=k+1;
4334: gp[k]=pmmij[i][j];
4335: }
4336: }
4337:
4338: for(i=1; i<=npar; i++)
4339: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
4340:
4341: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4342: k=0;
4343: for(i=1; i<=(nlstate); i++){
4344: for(j=1; j<=(nlstate+ndeath);j++){
4345: k=k+1;
4346: gm[k]=pmmij[i][j];
4347: }
4348: }
4349:
4350: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
4351: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
4352: }
4353:
4354: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
4355: for(theta=1; theta <=npar; theta++)
4356: trgradg[j][theta]=gradg[theta][j];
4357:
4358: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
4359: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
4360:
4361: pmij(pmmij,cov,ncovmodel,x,nlstate);
4362:
4363: k=0;
4364: for(i=1; i<=(nlstate); i++){
4365: for(j=1; j<=(nlstate+ndeath);j++){
4366: k=k+1;
4367: mu[k][(int) age]=pmmij[i][j];
4368: }
4369: }
4370: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
4371: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
4372: varpij[i][j][(int)age] = doldm[i][j];
4373:
4374: /*printf("\n%d ",(int)age);
4375: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4376: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4377: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4378: }*/
4379:
4380: fprintf(ficresprob,"\n%d ",(int)age);
4381: fprintf(ficresprobcov,"\n%d ",(int)age);
4382: fprintf(ficresprobcor,"\n%d ",(int)age);
4383:
4384: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
4385: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
4386: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4387: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
4388: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
4389: }
4390: i=0;
4391: for (k=1; k<=(nlstate);k++){
4392: for (l=1; l<=(nlstate+ndeath);l++){
1.145 brouard 4393: i++;
1.126 brouard 4394: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
4395: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
4396: for (j=1; j<=i;j++){
1.145 brouard 4397: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
1.126 brouard 4398: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
4399: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
4400: }
4401: }
4402: }/* end of loop for state */
4403: } /* end of loop for age */
1.145 brouard 4404: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
4405: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
4406: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4407: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4408:
1.126 brouard 4409: /* Confidence intervalle of pij */
4410: /*
1.131 brouard 4411: fprintf(ficgp,"\nunset parametric;unset label");
1.126 brouard 4412: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
4413: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
4414: 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);
4415: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
4416: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
4417: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
4418: */
4419:
4420: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
1.145 brouard 4421: first1=1;first2=2;
1.126 brouard 4422: for (k2=1; k2<=(nlstate);k2++){
4423: for (l2=1; l2<=(nlstate+ndeath);l2++){
4424: if(l2==k2) continue;
4425: j=(k2-1)*(nlstate+ndeath)+l2;
4426: for (k1=1; k1<=(nlstate);k1++){
4427: for (l1=1; l1<=(nlstate+ndeath);l1++){
4428: if(l1==k1) continue;
4429: i=(k1-1)*(nlstate+ndeath)+l1;
4430: if(i<=j) continue;
4431: for (age=bage; age<=fage; age ++){
4432: if ((int)age %5==0){
4433: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
4434: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
4435: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
4436: mu1=mu[i][(int) age]/stepm*YEARM ;
4437: mu2=mu[j][(int) age]/stepm*YEARM;
4438: c12=cv12/sqrt(v1*v2);
4439: /* Computing eigen value of matrix of covariance */
4440: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4441: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
1.135 brouard 4442: if ((lc2 <0) || (lc1 <0) ){
1.145 brouard 4443: if(first2==1){
4444: first1=0;
4445: 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);
4446: }
4447: 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);
4448: /* lc1=fabs(lc1); */ /* If we want to have them positive */
4449: /* lc2=fabs(lc2); */
1.135 brouard 4450: }
4451:
1.126 brouard 4452: /* Eigen vectors */
4453: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
4454: /*v21=sqrt(1.-v11*v11); *//* error */
4455: v21=(lc1-v1)/cv12*v11;
4456: v12=-v21;
4457: v22=v11;
4458: tnalp=v21/v11;
4459: if(first1==1){
4460: first1=0;
4461: 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);
4462: }
4463: 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);
4464: /*printf(fignu*/
4465: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
4466: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
4467: if(first==1){
4468: first=0;
1.200 brouard 4469: fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
1.126 brouard 4470: fprintf(ficgp,"\nset parametric;unset label");
4471: 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 4472: fprintf(ficgp,"\nset ter svg size 640, 480");
1.126 brouard 4473: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.201 ! brouard 4474: :<a href=\"%s_%d%1d%1d-%1d%1d.svg\">\
! 4475: %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
! 4476: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,\
! 4477: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
! 4478: fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
1.126 brouard 4479: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
1.201 ! brouard 4480: fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
1.126 brouard 4481: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4482: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4483: 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",\
4484: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4485: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4486: }else{
4487: first=0;
4488: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4489: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4490: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4491: 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",\
4492: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4493: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4494: }/* if first */
4495: } /* age mod 5 */
4496: } /* end loop age */
1.201 ! brouard 4497: 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 4498: first=1;
4499: } /*l12 */
4500: } /* k12 */
4501: } /*l1 */
4502: }/* k1 */
1.169 brouard 4503: /* } */ /* loop covariates */
1.126 brouard 4504: }
4505: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4506: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4507: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4508: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4509: free_vector(xp,1,npar);
4510: fclose(ficresprob);
4511: fclose(ficresprobcov);
4512: fclose(ficresprobcor);
4513: fflush(ficgp);
4514: fflush(fichtmcov);
4515: }
4516:
4517:
4518: /******************* Printing html file ***********/
1.201 ! brouard 4519: void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 4520: int lastpass, int stepm, int weightopt, char model[],\
4521: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
4522: int popforecast, int estepm ,\
4523: double jprev1, double mprev1,double anprev1, \
4524: double jprev2, double mprev2,double anprev2){
4525: int jj1, k1, i1, cpt;
4526:
4527: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4528: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4529: </ul>");
4530: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
4531: - 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 4532: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
1.126 brouard 4533: fprintf(fichtm,"\
4534: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
1.201 ! brouard 4535: stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
1.126 brouard 4536: fprintf(fichtm,"\
4537: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.201 ! brouard 4538: subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
1.126 brouard 4539: fprintf(fichtm,"\
1.128 brouard 4540: - (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 4541: <a href=\"%s\">%s</a> <br>\n",
1.201 ! brouard 4542: estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
1.126 brouard 4543: fprintf(fichtm,"\
4544: - Population projections by age and states: \
1.201 ! brouard 4545: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
1.126 brouard 4546:
4547: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4548:
1.145 brouard 4549: m=pow(2,cptcoveff);
1.126 brouard 4550: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4551:
4552: jj1=0;
4553: for(k1=1; k1<=m;k1++){
1.192 brouard 4554: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
1.126 brouard 4555: jj1++;
4556: if (cptcovn > 0) {
4557: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.192 brouard 4558: for (cpt=1; cpt<=cptcoveff;cpt++){
1.198 brouard 4559: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
4560: printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
1.192 brouard 4561: }
1.126 brouard 4562: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4563: }
1.201 ! brouard 4564: /* aij, bij */
! 4565: 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> \
! 4566: <img src=\"%s_%d-1.svg\">",subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.126 brouard 4567: /* Pij */
1.201 ! brouard 4568: 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> \
! 4569: <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.126 brouard 4570: /* Quasi-incidences */
1.201 ! brouard 4571: fprintf(fichtm,"<br>\n- Iij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
! 4572: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too,\
! 4573: incidence (rates) are the limit when h tends to zero of the ratio of the probability hPij \
! 4574: divided by h: hPij/h : <a href=\"%s_%d-3.svg\">%s_%d-3.svg</a><br> \
! 4575: <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
! 4576: /* Survival functions (period) in state j */
! 4577: for(cpt=1; cpt<=nlstate;cpt++){
! 4578: 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> \
! 4579: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);
! 4580: }
! 4581: /* State specific survival functions (period) */
! 4582: for(cpt=1; cpt<=nlstate;cpt++){
! 4583: fprintf(fichtm,"<br>\n- Survival functions from state %d in any different live states and total.\
! 4584: Or probability to survive in various states (1 to %d) being in state %d at different ages.\
! 4585: <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);
! 4586: }
! 4587: /* Period (stable) prevalence in each health state */
! 4588: for(cpt=1; cpt<=nlstate;cpt++){
! 4589: 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> \
! 4590: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);
! 4591: }
1.126 brouard 4592: for(cpt=1; cpt<=nlstate;cpt++) {
1.201 ! brouard 4593: 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> \
! 4594: <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 4595: }
1.192 brouard 4596: /* } /\* end i1 *\/ */
1.126 brouard 4597: }/* End k1 */
4598: fprintf(fichtm,"</ul>");
4599:
4600: fprintf(fichtm,"\
4601: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 brouard 4602: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
1.197 brouard 4603: - 95%% confidence intervals and Wald tests of the estimated parameters are in the log file.<br> \
4604: But because parameters are usually highly correlated (a higher incidence of disability \
4605: and a higher incidence of recovery can give very close observed transition) it might \
4606: be very useful to look not only at linear confidence intervals estimated from the \
4607: variances but at the covariance matrix. And instead of looking at the estimated coefficients \
4608: (parameters) of the logistic regression, it might be more meaningful to visualize the \
4609: covariance matrix of the one-step probabilities. \
4610: See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
1.126 brouard 4611:
1.193 brouard 4612: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 ! brouard 4613: subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
1.126 brouard 4614: fprintf(fichtm,"\
4615: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 ! brouard 4616: subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
1.126 brouard 4617:
4618: fprintf(fichtm,"\
4619: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 ! brouard 4620: subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
1.126 brouard 4621: fprintf(fichtm,"\
4622: - 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): \
4623: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 ! brouard 4624: estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
1.126 brouard 4625: fprintf(fichtm,"\
4626: - (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): \
4627: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 ! brouard 4628: estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
1.126 brouard 4629: fprintf(fichtm,"\
1.128 brouard 4630: - 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 4631: estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
1.126 brouard 4632: fprintf(fichtm,"\
1.128 brouard 4633: - 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 4634: estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
1.126 brouard 4635: fprintf(fichtm,"\
4636: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
1.201 ! brouard 4637: subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
1.126 brouard 4638:
4639: /* if(popforecast==1) fprintf(fichtm,"\n */
4640: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4641: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4642: /* <br>",fileres,fileres,fileres,fileres); */
4643: /* else */
4644: /* 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); */
4645: fflush(fichtm);
4646: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4647:
1.145 brouard 4648: m=pow(2,cptcoveff);
1.126 brouard 4649: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4650:
4651: jj1=0;
4652: for(k1=1; k1<=m;k1++){
1.192 brouard 4653: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
1.126 brouard 4654: jj1++;
4655: if (cptcovn > 0) {
4656: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4657: for (cpt=1; cpt<=cptcoveff;cpt++)
1.198 brouard 4658: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
1.126 brouard 4659: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4660: }
4661: for(cpt=1; cpt<=nlstate;cpt++) {
4662: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
1.199 brouard 4663: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.svg <br>\
1.201 ! brouard 4664: <img src=\"%s_%d-%d.svg\">",cpt,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1);
1.126 brouard 4665: }
4666: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 4667: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4668: true period expectancies (those weighted with period prevalences are also\
4669: drawn in addition to the population based expectancies computed using\
1.201 ! brouard 4670: observed and cahotic prevalences: %s_%d.svg<br>\
! 4671: <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
1.192 brouard 4672: /* } /\* end i1 *\/ */
1.126 brouard 4673: }/* End k1 */
4674: fprintf(fichtm,"</ul>");
4675: fflush(fichtm);
4676: }
4677:
4678: /******************* Gnuplot file **************/
1.201 ! brouard 4679: void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 4680:
4681: char dirfileres[132],optfileres[132];
1.164 brouard 4682: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
1.130 brouard 4683: int ng=0;
1.201 ! brouard 4684: int vpopbased;
1.126 brouard 4685: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4686: /* printf("Problem with file %s",optionfilegnuplot); */
4687: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4688: /* } */
4689:
4690: /*#ifdef windows */
4691: fprintf(ficgp,"cd \"%s\" \n",pathc);
4692: /*#endif */
4693: m=pow(2,cptcoveff);
4694:
4695: strcpy(dirfileres,optionfilefiname);
4696: strcpy(optfileres,"vpl");
4697: /* 1eme*/
1.201 ! brouard 4698: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files\n");
1.126 brouard 4699: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.145 brouard 4700: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
1.201 ! brouard 4701: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
! 4702: fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
1.126 brouard 4703: fprintf(ficgp,"set xlabel \"Age\" \n\
4704: set ylabel \"Probability\" \n\
1.199 brouard 4705: set ter svg size 640, 480\n\
1.201 ! brouard 4706: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
1.126 brouard 4707:
4708: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4709: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4710: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4711: }
1.201 ! brouard 4712: 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 4713: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4714: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4715: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4716: }
1.201 ! brouard 4717: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
1.126 brouard 4718: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4719: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4720: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4721: }
1.201 ! brouard 4722: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
! 4723: fprintf(ficgp,"\nset out \n");
! 4724: } /* k1 */
! 4725: } /* cpt */
1.126 brouard 4726: /*2 eme*/
1.153 brouard 4727: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
1.126 brouard 4728: for (k1=1; k1<= m ; k1 ++) {
1.201 ! brouard 4729: fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
! 4730: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
! 4731: if(vpopbased==0)
! 4732: fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
! 4733: else
! 4734: fprintf(ficgp,"\nreplot ");
! 4735: for (i=1; i<= nlstate+1 ; i ++) {
! 4736: k=2*i;
! 4737: 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);
! 4738: for (j=1; j<= nlstate+1 ; j ++) {
! 4739: if (j==i) fprintf(ficgp," %%lf (%%lf)");
! 4740: else fprintf(ficgp," %%*lf (%%*lf)");
! 4741: }
! 4742: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
! 4743: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
! 4744: 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);
! 4745: for (j=1; j<= nlstate+1 ; j ++) {
! 4746: if (j==i) fprintf(ficgp," %%lf (%%lf)");
! 4747: else fprintf(ficgp," %%*lf (%%*lf)");
! 4748: }
! 4749: fprintf(ficgp,"\" t\"\" w l lt 0,");
! 4750: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
! 4751: for (j=1; j<= nlstate+1 ; j ++) {
! 4752: if (j==i) fprintf(ficgp," %%lf (%%lf)");
! 4753: else fprintf(ficgp," %%*lf (%%*lf)");
! 4754: }
! 4755: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
! 4756: else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
! 4757: } /* state */
! 4758: } /* vpopbased */
! 4759: fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
! 4760: } /* k1 */
1.126 brouard 4761: /*3eme*/
4762:
4763: for (k1=1; k1<= m ; k1 ++) {
4764: for (cpt=1; cpt<= nlstate ; cpt ++) {
4765: /* k=2+nlstate*(2*cpt-2); */
4766: k=2+(nlstate+1)*(cpt-1);
1.201 ! brouard 4767: fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
1.199 brouard 4768: fprintf(ficgp,"set ter svg size 640, 480\n\
1.201 ! brouard 4769: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
1.126 brouard 4770: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4771: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4772: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4773: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4774: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4775: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4776:
4777: */
4778: for (i=1; i< nlstate ; i ++) {
1.201 ! brouard 4779: 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 4780: /* 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);*/
4781:
4782: }
1.201 ! brouard 4783: 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 4784: }
4785: }
4786:
1.201 ! brouard 4787: /* Survival functions (period) from state i in state j by initial state i */
! 4788: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
! 4789: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
! 4790: k=3;
! 4791: fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'lij' files, cov=%d state=%d",k1, cpt);
! 4792: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
! 4793: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
! 4794: set ter svg size 640, 480\n\
! 4795: unset log y\n\
! 4796: plot [%.f:%.f] ", ageminpar, agemaxpar);
! 4797: for (i=1; i<= nlstate ; i ++){
! 4798: if(i==1)
! 4799: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
! 4800: else
! 4801: fprintf(ficgp,", '' ");
! 4802: l=(nlstate+ndeath)*(i-1)+1;
! 4803: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
! 4804: for (j=2; j<= nlstate+ndeath ; j ++)
! 4805: fprintf(ficgp,"+$%d",k+l+j-1);
! 4806: fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
! 4807: } /* nlstate */
! 4808: fprintf(ficgp,"\nset out\n");
! 4809: } /* end cpt state*/
! 4810: } /* end covariate */
! 4811:
! 4812: /* Survival functions (period) from state i in state j by final state j */
! 4813: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
! 4814: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
! 4815: k=3;
! 4816: 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);
! 4817: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
! 4818: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
! 4819: set ter svg size 640, 480\n\
! 4820: unset log y\n\
! 4821: plot [%.f:%.f] ", ageminpar, agemaxpar);
! 4822: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
! 4823: if(j==1)
! 4824: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
! 4825: else
! 4826: fprintf(ficgp,", '' ");
! 4827: l=(nlstate+ndeath)*(cpt-1) +j;
! 4828: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
! 4829: /* for (i=2; i<= nlstate+ndeath ; i ++) */
! 4830: /* fprintf(ficgp,"+$%d",k+l+i-1); */
! 4831: fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
! 4832: } /* nlstate */
! 4833: fprintf(ficgp,", '' ");
! 4834: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
! 4835: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
! 4836: l=(nlstate+ndeath)*(cpt-1) +j;
! 4837: if(j < nlstate)
! 4838: fprintf(ficgp,"$%d +",k+l);
! 4839: else
! 4840: fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
! 4841: }
! 4842: fprintf(ficgp,"\nset out\n");
! 4843: } /* end cpt state*/
! 4844: } /* end covariate */
! 4845:
1.126 brouard 4846: /* CV preval stable (period) */
1.153 brouard 4847: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
4848: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.126 brouard 4849: k=3;
1.153 brouard 4850: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
1.201 ! brouard 4851: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
1.126 brouard 4852: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.199 brouard 4853: set ter svg size 640, 480\n\
1.126 brouard 4854: unset log y\n\
1.153 brouard 4855: plot [%.f:%.f] ", ageminpar, agemaxpar);
4856: for (i=1; i<= nlstate ; i ++){
4857: if(i==1)
1.201 ! brouard 4858: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
1.153 brouard 4859: else
4860: fprintf(ficgp,", '' ");
1.154 brouard 4861: l=(nlstate+ndeath)*(i-1)+1;
4862: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
1.201 ! brouard 4863: for (j=2; j<= nlstate ; j ++)
! 4864: fprintf(ficgp,"+$%d",k+l+j-1);
1.153 brouard 4865: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
4866: } /* nlstate */
1.201 ! brouard 4867: fprintf(ficgp,"\nset out\n");
1.153 brouard 4868: } /* end cpt state*/
4869: } /* end covariate */
1.201 ! brouard 4870:
1.126 brouard 4871: /* proba elementaires */
1.187 brouard 4872: fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
1.126 brouard 4873: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 4874: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 4875: for(k=1; k <=(nlstate+ndeath); k++){
4876: if (k != i) {
1.187 brouard 4877: fprintf(ficgp,"# current state %d\n",k);
1.126 brouard 4878: for(j=1; j <=ncovmodel; j++){
1.187 brouard 4879: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
1.126 brouard 4880: jk++;
4881: }
1.187 brouard 4882: fprintf(ficgp,"\n");
1.126 brouard 4883: }
4884: }
4885: }
1.187 brouard 4886: fprintf(ficgp,"##############\n#\n");
4887:
1.145 brouard 4888: /*goto avoid;*/
1.200 brouard 4889: fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");
1.187 brouard 4890: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
4891: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
4892: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
4893: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
4894: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
4895: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
4896: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
4897: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
4898: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
4899: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
4900: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
4901: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
4902: fprintf(ficgp,"#\n");
1.201 ! brouard 4903: for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
1.187 brouard 4904: fprintf(ficgp,"# ng=%d\n",ng);
4905: fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);
1.126 brouard 4906: for(jk=1; jk <=m; jk++) {
1.187 brouard 4907: fprintf(ficgp,"# jk=%d\n",jk);
1.201 ! brouard 4908: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
! 4909: fprintf(ficgp,"\nset ter svg size 640, 480 ");
! 4910: if (ng==1){
! 4911: fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
! 4912: fprintf(ficgp,"\nunset log y");
! 4913: }else if (ng==2){
! 4914: fprintf(ficgp,"\nset ylabel \"Probability\"\n");
! 4915: fprintf(ficgp,"\nset log y");
! 4916: }else if (ng==3){
1.126 brouard 4917: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
1.201 ! brouard 4918: fprintf(ficgp,"\nset log y");
! 4919: }else
! 4920: fprintf(ficgp,"\nunset title ");
! 4921: fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar);
1.126 brouard 4922: i=1;
4923: for(k2=1; k2<=nlstate; k2++) {
4924: k3=i;
4925: for(k=1; k<=(nlstate+ndeath); k++) {
4926: if (k != k2){
1.201 ! brouard 4927: switch( ng) {
! 4928: case 1:
1.187 brouard 4929: if(nagesqr==0)
1.201 ! brouard 4930: fprintf(ficgp," p%d+p%d*x",i,i+1);
1.187 brouard 4931: else /* nagesqr =1 */
1.201 ! brouard 4932: fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
! 4933: break;
! 4934: case 2: /* ng=2 */
1.187 brouard 4935: if(nagesqr==0)
4936: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
4937: else /* nagesqr =1 */
1.201 ! brouard 4938: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
! 4939: break;
! 4940: case 3:
! 4941: if(nagesqr==0)
! 4942: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
! 4943: else /* nagesqr =1 */
! 4944: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
! 4945: break;
! 4946: }
1.141 brouard 4947: ij=1;/* To be checked else nbcode[0][0] wrong */
1.187 brouard 4948: for(j=3; j <=ncovmodel-nagesqr; j++) {
1.197 brouard 4949: /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
4950: if(ij <=cptcovage) { /* Bug valgrind */
4951: if((j-2)==Tage[ij]) { /* Bug valgrind */
1.200 brouard 4952: fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
4953: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
1.197 brouard 4954: ij++;
4955: }
1.186 brouard 4956: }
4957: else
1.198 brouard 4958: fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
1.126 brouard 4959: }
1.201 ! brouard 4960: if(ng != 1){
! 4961: fprintf(ficgp,")/(1");
1.126 brouard 4962:
1.201 ! brouard 4963: for(k1=1; k1 <=nlstate; k1++){
! 4964: if(nagesqr==0)
! 4965: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
! 4966: else /* nagesqr =1 */
! 4967: 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);
! 4968:
! 4969: ij=1;
! 4970: for(j=3; j <=ncovmodel-nagesqr; j++){
! 4971: if(ij <=cptcovage) { /* Bug valgrind */
! 4972: if((j-2)==Tage[ij]) { /* Bug valgrind */
! 4973: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
! 4974: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
! 4975: ij++;
! 4976: }
1.197 brouard 4977: }
1.201 ! brouard 4978: else
! 4979: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
1.186 brouard 4980: }
1.201 ! brouard 4981: fprintf(ficgp,")");
1.126 brouard 4982: }
4983: fprintf(ficgp,")");
1.201 ! brouard 4984: if(ng ==2)
! 4985: fprintf(ficgp," t \"p%d%d\" ", k2,k);
! 4986: else /* ng= 3 */
! 4987: fprintf(ficgp," t \"i%d%d\" ", k2,k);
! 4988: }else{ /* end ng <> 1 */
! 4989: fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
1.126 brouard 4990: }
4991: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
4992: i=i+ncovmodel;
4993: }
4994: } /* end k */
4995: } /* end k2 */
1.201 ! brouard 4996: fprintf(ficgp,"\n set out\n");
1.126 brouard 4997: } /* end jk */
4998: } /* end ng */
1.164 brouard 4999: /* avoid: */
1.126 brouard 5000: fflush(ficgp);
5001: } /* end gnuplot */
5002:
5003:
5004: /*************** Moving average **************/
5005: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
5006:
5007: int i, cpt, cptcod;
5008: int modcovmax =1;
5009: int mobilavrange, mob;
5010: double age;
5011:
5012: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
5013: a covariate has 2 modalities */
5014: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
5015:
5016: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
5017: if(mobilav==1) mobilavrange=5; /* default */
5018: else mobilavrange=mobilav;
5019: for (age=bage; age<=fage; age++)
5020: for (i=1; i<=nlstate;i++)
5021: for (cptcod=1;cptcod<=modcovmax;cptcod++)
5022: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
5023: /* We keep the original values on the extreme ages bage, fage and for
5024: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
5025: we use a 5 terms etc. until the borders are no more concerned.
5026: */
5027: for (mob=3;mob <=mobilavrange;mob=mob+2){
5028: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
5029: for (i=1; i<=nlstate;i++){
5030: for (cptcod=1;cptcod<=modcovmax;cptcod++){
5031: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
5032: for (cpt=1;cpt<=(mob-1)/2;cpt++){
5033: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
5034: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
5035: }
5036: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
5037: }
5038: }
5039: }/* end age */
5040: }/* end mob */
5041: }else return -1;
5042: return 0;
5043: }/* End movingaverage */
5044:
5045:
5046: /************** Forecasting ******************/
1.169 brouard 5047: 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 5048: /* proj1, year, month, day of starting projection
5049: agemin, agemax range of age
5050: dateprev1 dateprev2 range of dates during which prevalence is computed
5051: anproj2 year of en of projection (same day and month as proj1).
5052: */
1.164 brouard 5053: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
1.126 brouard 5054: double agec; /* generic age */
5055: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
5056: double *popeffectif,*popcount;
5057: double ***p3mat;
5058: double ***mobaverage;
5059: char fileresf[FILENAMELENGTH];
5060:
5061: agelim=AGESUP;
5062: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5063:
1.201 ! brouard 5064: strcpy(fileresf,"F_");
! 5065: strcat(fileresf,fileresu);
1.126 brouard 5066: if((ficresf=fopen(fileresf,"w"))==NULL) {
5067: printf("Problem with forecast resultfile: %s\n", fileresf);
5068: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
5069: }
5070: printf("Computing forecasting: result on file '%s' \n", fileresf);
5071: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
5072:
5073: if (cptcoveff==0) ncodemax[cptcoveff]=1;
5074:
5075: if (mobilav!=0) {
5076: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5077: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
5078: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5079: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5080: }
5081: }
5082:
5083: stepsize=(int) (stepm+YEARM-1)/YEARM;
5084: if (stepm<=12) stepsize=1;
5085: if(estepm < stepm){
5086: printf ("Problem %d lower than %d\n",estepm, stepm);
5087: }
5088: else hstepm=estepm;
5089:
5090: hstepm=hstepm/stepm;
5091: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
5092: fractional in yp1 */
5093: anprojmean=yp;
5094: yp2=modf((yp1*12),&yp);
5095: mprojmean=yp;
5096: yp1=modf((yp2*30.5),&yp);
5097: jprojmean=yp;
5098: if(jprojmean==0) jprojmean=1;
5099: if(mprojmean==0) jprojmean=1;
5100:
5101: i1=cptcoveff;
5102: if (cptcovn < 1){i1=1;}
5103:
5104: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
5105:
5106: fprintf(ficresf,"#****** Routine prevforecast **\n");
5107:
5108: /* if (h==(int)(YEARM*yearp)){ */
5109: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
5110: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
5111: k=k+1;
5112: fprintf(ficresf,"\n#******");
5113: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 5114: 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 5115: }
5116: fprintf(ficresf,"******\n");
5117: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
5118: for(j=1; j<=nlstate+ndeath;j++){
5119: for(i=1; i<=nlstate;i++)
5120: fprintf(ficresf," p%d%d",i,j);
5121: fprintf(ficresf," p.%d",j);
5122: }
5123: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
5124: fprintf(ficresf,"\n");
5125: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
5126:
5127: for (agec=fage; agec>=(ageminpar-1); agec--){
5128: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
5129: nhstepm = nhstepm/hstepm;
5130: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5131: oldm=oldms;savm=savms;
5132: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
5133:
5134: for (h=0; h<=nhstepm; h++){
5135: if (h*hstepm/YEARM*stepm ==yearp) {
5136: fprintf(ficresf,"\n");
5137: for(j=1;j<=cptcoveff;j++)
1.198 brouard 5138: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 5139: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
5140: }
5141: for(j=1; j<=nlstate+ndeath;j++) {
5142: ppij=0.;
5143: for(i=1; i<=nlstate;i++) {
5144: if (mobilav==1)
5145: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
5146: else {
5147: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
5148: }
5149: if (h*hstepm/YEARM*stepm== yearp) {
5150: fprintf(ficresf," %.3f", p3mat[i][j][h]);
5151: }
5152: } /* end i */
5153: if (h*hstepm/YEARM*stepm==yearp) {
5154: fprintf(ficresf," %.3f", ppij);
5155: }
5156: }/* end j */
5157: } /* end h */
5158: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5159: } /* end agec */
5160: } /* end yearp */
5161: } /* end cptcod */
5162: } /* end cptcov */
5163:
5164: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5165:
5166: fclose(ficresf);
5167: }
5168:
5169: /************** Forecasting *****not tested NB*************/
1.169 brouard 5170: 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 5171:
5172: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
5173: int *popage;
5174: double calagedatem, agelim, kk1, kk2;
5175: double *popeffectif,*popcount;
5176: double ***p3mat,***tabpop,***tabpopprev;
5177: double ***mobaverage;
5178: char filerespop[FILENAMELENGTH];
5179:
5180: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5181: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5182: agelim=AGESUP;
5183: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
5184:
5185: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5186:
5187:
1.201 ! brouard 5188: strcpy(filerespop,"POP_");
! 5189: strcat(filerespop,fileresu);
1.126 brouard 5190: if((ficrespop=fopen(filerespop,"w"))==NULL) {
5191: printf("Problem with forecast resultfile: %s\n", filerespop);
5192: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
5193: }
5194: printf("Computing forecasting: result on file '%s' \n", filerespop);
5195: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
5196:
5197: if (cptcoveff==0) ncodemax[cptcoveff]=1;
5198:
5199: if (mobilav!=0) {
5200: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5201: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
5202: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5203: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5204: }
5205: }
5206:
5207: stepsize=(int) (stepm+YEARM-1)/YEARM;
5208: if (stepm<=12) stepsize=1;
5209:
5210: agelim=AGESUP;
5211:
5212: hstepm=1;
5213: hstepm=hstepm/stepm;
5214:
5215: if (popforecast==1) {
5216: if((ficpop=fopen(popfile,"r"))==NULL) {
5217: printf("Problem with population file : %s\n",popfile);exit(0);
5218: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
5219: }
5220: popage=ivector(0,AGESUP);
5221: popeffectif=vector(0,AGESUP);
5222: popcount=vector(0,AGESUP);
5223:
5224: i=1;
5225: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
5226:
5227: imx=i;
5228: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
5229: }
5230:
5231: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
5232: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
5233: k=k+1;
5234: fprintf(ficrespop,"\n#******");
5235: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 5236: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 5237: }
5238: fprintf(ficrespop,"******\n");
5239: fprintf(ficrespop,"# Age");
5240: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
5241: if (popforecast==1) fprintf(ficrespop," [Population]");
5242:
5243: for (cpt=0; cpt<=0;cpt++) {
5244: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5245:
5246: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5247: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5248: nhstepm = nhstepm/hstepm;
5249:
5250: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5251: oldm=oldms;savm=savms;
5252: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5253:
5254: for (h=0; h<=nhstepm; h++){
5255: if (h==(int) (calagedatem+YEARM*cpt)) {
5256: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5257: }
5258: for(j=1; j<=nlstate+ndeath;j++) {
5259: kk1=0.;kk2=0;
5260: for(i=1; i<=nlstate;i++) {
5261: if (mobilav==1)
5262: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
5263: else {
5264: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
5265: }
5266: }
5267: if (h==(int)(calagedatem+12*cpt)){
5268: tabpop[(int)(agedeb)][j][cptcod]=kk1;
5269: /*fprintf(ficrespop," %.3f", kk1);
5270: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
5271: }
5272: }
5273: for(i=1; i<=nlstate;i++){
5274: kk1=0.;
5275: for(j=1; j<=nlstate;j++){
5276: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
5277: }
5278: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
5279: }
5280:
5281: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
5282: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
5283: }
5284: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5285: }
5286: }
5287:
5288: /******/
5289:
5290: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
5291: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5292: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5293: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5294: nhstepm = nhstepm/hstepm;
5295:
5296: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5297: oldm=oldms;savm=savms;
5298: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5299: for (h=0; h<=nhstepm; h++){
5300: if (h==(int) (calagedatem+YEARM*cpt)) {
5301: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5302: }
5303: for(j=1; j<=nlstate+ndeath;j++) {
5304: kk1=0.;kk2=0;
5305: for(i=1; i<=nlstate;i++) {
5306: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
5307: }
5308: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
5309: }
5310: }
5311: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5312: }
5313: }
5314: }
5315: }
5316:
5317: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5318:
5319: if (popforecast==1) {
5320: free_ivector(popage,0,AGESUP);
5321: free_vector(popeffectif,0,AGESUP);
5322: free_vector(popcount,0,AGESUP);
5323: }
5324: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5325: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5326: fclose(ficrespop);
5327: } /* End of popforecast */
5328:
5329: int fileappend(FILE *fichier, char *optionfich)
5330: {
5331: if((fichier=fopen(optionfich,"a"))==NULL) {
5332: printf("Problem with file: %s\n", optionfich);
5333: fprintf(ficlog,"Problem with file: %s\n", optionfich);
5334: return (0);
5335: }
5336: fflush(fichier);
5337: return (1);
5338: }
5339:
5340:
5341: /**************** function prwizard **********************/
5342: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
5343: {
5344:
5345: /* Wizard to print covariance matrix template */
5346:
1.164 brouard 5347: char ca[32], cb[32];
5348: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 5349: int numlinepar;
5350:
5351: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5352: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5353: for(i=1; i <=nlstate; i++){
5354: jj=0;
5355: for(j=1; j <=nlstate+ndeath; j++){
5356: if(j==i) continue;
5357: jj++;
5358: /*ca[0]= k+'a'-1;ca[1]='\0';*/
5359: printf("%1d%1d",i,j);
5360: fprintf(ficparo,"%1d%1d",i,j);
5361: for(k=1; k<=ncovmodel;k++){
5362: /* printf(" %lf",param[i][j][k]); */
5363: /* fprintf(ficparo," %lf",param[i][j][k]); */
5364: printf(" 0.");
5365: fprintf(ficparo," 0.");
5366: }
5367: printf("\n");
5368: fprintf(ficparo,"\n");
5369: }
5370: }
5371: printf("# Scales (for hessian or gradient estimation)\n");
5372: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
5373: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
5374: for(i=1; i <=nlstate; i++){
5375: jj=0;
5376: for(j=1; j <=nlstate+ndeath; j++){
5377: if(j==i) continue;
5378: jj++;
5379: fprintf(ficparo,"%1d%1d",i,j);
5380: printf("%1d%1d",i,j);
5381: fflush(stdout);
5382: for(k=1; k<=ncovmodel;k++){
5383: /* printf(" %le",delti3[i][j][k]); */
5384: /* fprintf(ficparo," %le",delti3[i][j][k]); */
5385: printf(" 0.");
5386: fprintf(ficparo," 0.");
5387: }
5388: numlinepar++;
5389: printf("\n");
5390: fprintf(ficparo,"\n");
5391: }
5392: }
5393: printf("# Covariance matrix\n");
5394: /* # 121 Var(a12)\n\ */
5395: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5396: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5397: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5398: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5399: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5400: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5401: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5402: fflush(stdout);
5403: fprintf(ficparo,"# Covariance matrix\n");
5404: /* # 121 Var(a12)\n\ */
5405: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5406: /* # ...\n\ */
5407: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5408:
5409: for(itimes=1;itimes<=2;itimes++){
5410: jj=0;
5411: for(i=1; i <=nlstate; i++){
5412: for(j=1; j <=nlstate+ndeath; j++){
5413: if(j==i) continue;
5414: for(k=1; k<=ncovmodel;k++){
5415: jj++;
5416: ca[0]= k+'a'-1;ca[1]='\0';
5417: if(itimes==1){
5418: printf("#%1d%1d%d",i,j,k);
5419: fprintf(ficparo,"#%1d%1d%d",i,j,k);
5420: }else{
5421: printf("%1d%1d%d",i,j,k);
5422: fprintf(ficparo,"%1d%1d%d",i,j,k);
5423: /* printf(" %.5le",matcov[i][j]); */
5424: }
5425: ll=0;
5426: for(li=1;li <=nlstate; li++){
5427: for(lj=1;lj <=nlstate+ndeath; lj++){
5428: if(lj==li) continue;
5429: for(lk=1;lk<=ncovmodel;lk++){
5430: ll++;
5431: if(ll<=jj){
5432: cb[0]= lk +'a'-1;cb[1]='\0';
5433: if(ll<jj){
5434: if(itimes==1){
5435: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5436: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5437: }else{
5438: printf(" 0.");
5439: fprintf(ficparo," 0.");
5440: }
5441: }else{
5442: if(itimes==1){
5443: printf(" Var(%s%1d%1d)",ca,i,j);
5444: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
5445: }else{
5446: printf(" 0.");
5447: fprintf(ficparo," 0.");
5448: }
5449: }
5450: }
5451: } /* end lk */
5452: } /* end lj */
5453: } /* end li */
5454: printf("\n");
5455: fprintf(ficparo,"\n");
5456: numlinepar++;
5457: } /* end k*/
5458: } /*end j */
5459: } /* end i */
5460: } /* end itimes */
5461:
5462: } /* end of prwizard */
5463: /******************* Gompertz Likelihood ******************************/
5464: double gompertz(double x[])
5465: {
5466: double A,B,L=0.0,sump=0.,num=0.;
5467: int i,n=0; /* n is the size of the sample */
5468:
5469: for (i=0;i<=imx-1 ; i++) {
5470: sump=sump+weight[i];
5471: /* sump=sump+1;*/
5472: num=num+1;
5473: }
5474:
5475:
5476: /* for (i=0; i<=imx; i++)
5477: 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]);*/
5478:
5479: for (i=1;i<=imx ; i++)
5480: {
5481: if (cens[i] == 1 && wav[i]>1)
5482: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
5483:
5484: if (cens[i] == 0 && wav[i]>1)
5485: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
5486: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
5487:
5488: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5489: if (wav[i] > 1 ) { /* ??? */
5490: L=L+A*weight[i];
5491: /* 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]);*/
5492: }
5493: }
5494:
5495: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5496:
5497: return -2*L*num/sump;
5498: }
5499:
1.136 brouard 5500: #ifdef GSL
5501: /******************* Gompertz_f Likelihood ******************************/
5502: double gompertz_f(const gsl_vector *v, void *params)
5503: {
5504: double A,B,LL=0.0,sump=0.,num=0.;
5505: double *x= (double *) v->data;
5506: int i,n=0; /* n is the size of the sample */
5507:
5508: for (i=0;i<=imx-1 ; i++) {
5509: sump=sump+weight[i];
5510: /* sump=sump+1;*/
5511: num=num+1;
5512: }
5513:
5514:
5515: /* for (i=0; i<=imx; i++)
5516: 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]);*/
5517: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
5518: for (i=1;i<=imx ; i++)
5519: {
5520: if (cens[i] == 1 && wav[i]>1)
5521: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
5522:
5523: if (cens[i] == 0 && wav[i]>1)
5524: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
5525: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
5526:
5527: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5528: if (wav[i] > 1 ) { /* ??? */
5529: LL=LL+A*weight[i];
5530: /* 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]);*/
5531: }
5532: }
5533:
5534: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5535: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
5536:
5537: return -2*LL*num/sump;
5538: }
5539: #endif
5540:
1.126 brouard 5541: /******************* Printing html file ***********/
1.201 ! brouard 5542: void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 5543: int lastpass, int stepm, int weightopt, char model[],\
5544: int imx, double p[],double **matcov,double agemortsup){
5545: int i,k;
5546:
5547: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
5548: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
5549: for (i=1;i<=2;i++)
5550: 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 5551: fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
1.126 brouard 5552: fprintf(fichtm,"</ul>");
5553:
5554: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
5555:
5556: 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>");
5557:
5558: for (k=agegomp;k<(agemortsup-2);k++)
5559: 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]);
5560:
5561:
5562: fflush(fichtm);
5563: }
5564:
5565: /******************* Gnuplot file **************/
1.201 ! brouard 5566: void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 5567:
5568: char dirfileres[132],optfileres[132];
1.164 brouard 5569:
1.126 brouard 5570: int ng;
5571:
5572:
5573: /*#ifdef windows */
5574: fprintf(ficgp,"cd \"%s\" \n",pathc);
5575: /*#endif */
5576:
5577:
5578: strcpy(dirfileres,optionfilefiname);
5579: strcpy(optfileres,"vpl");
1.199 brouard 5580: fprintf(ficgp,"set out \"graphmort.svg\"\n ");
1.126 brouard 5581: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.199 brouard 5582: fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
1.145 brouard 5583: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 5584: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
5585:
5586: }
5587:
1.136 brouard 5588: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
5589: {
1.126 brouard 5590:
1.136 brouard 5591: /*-------- data file ----------*/
5592: FILE *fic;
5593: char dummy[]=" ";
1.164 brouard 5594: int i=0, j=0, n=0;
1.136 brouard 5595: int linei, month, year,iout;
5596: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 5597: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 5598: char *stratrunc;
5599: int lstra;
1.126 brouard 5600:
5601:
1.136 brouard 5602: if((fic=fopen(datafile,"r"))==NULL) {
1.195 brouard 5603: printf("Problem while opening datafile: %s\n", datafile);fflush(stdout);
5604: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);fflush(ficlog);return 1;
1.136 brouard 5605: }
1.126 brouard 5606:
1.136 brouard 5607: i=1;
5608: linei=0;
5609: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
5610: linei=linei+1;
5611: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
5612: if(line[j] == '\t')
5613: line[j] = ' ';
5614: }
5615: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
5616: ;
5617: };
5618: line[j+1]=0; /* Trims blanks at end of line */
5619: if(line[0]=='#'){
5620: fprintf(ficlog,"Comment line\n%s\n",line);
5621: printf("Comment line\n%s\n",line);
5622: continue;
5623: }
5624: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 5625: strcpy(line, linetmp);
1.136 brouard 5626:
1.126 brouard 5627:
1.136 brouard 5628: for (j=maxwav;j>=1;j--){
1.137 brouard 5629: cutv(stra, strb, line, ' ');
1.136 brouard 5630: if(strb[0]=='.') { /* Missing status */
5631: lval=-1;
5632: }else{
5633: errno=0;
5634: lval=strtol(strb,&endptr,10);
5635: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
5636: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5637: 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);
5638: 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 5639: return 1;
5640: }
5641: }
5642: s[j][i]=lval;
5643:
5644: strcpy(line,stra);
5645: cutv(stra, strb,line,' ');
1.169 brouard 5646: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5647: }
1.169 brouard 5648: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5649: month=99;
5650: year=9999;
5651: }else{
1.141 brouard 5652: 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);
5653: 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 5654: return 1;
5655: }
5656: anint[j][i]= (double) year;
5657: mint[j][i]= (double)month;
5658: strcpy(line,stra);
5659: } /* ENd Waves */
5660:
5661: cutv(stra, strb,line,' ');
1.169 brouard 5662: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5663: }
1.169 brouard 5664: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5665: month=99;
5666: year=9999;
5667: }else{
1.141 brouard 5668: 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);
5669: 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 5670: return 1;
5671: }
5672: andc[i]=(double) year;
5673: moisdc[i]=(double) month;
5674: strcpy(line,stra);
5675:
5676: cutv(stra, strb,line,' ');
1.169 brouard 5677: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5678: }
1.169 brouard 5679: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 5680: month=99;
5681: year=9999;
5682: }else{
1.141 brouard 5683: 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);
5684: 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 5685: return 1;
5686: }
5687: if (year==9999) {
1.141 brouard 5688: 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);
5689: 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 5690: return 1;
1.126 brouard 5691:
1.136 brouard 5692: }
5693: annais[i]=(double)(year);
5694: moisnais[i]=(double)(month);
5695: strcpy(line,stra);
5696:
5697: cutv(stra, strb,line,' ');
5698: errno=0;
5699: dval=strtod(strb,&endptr);
5700: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5701: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
5702: 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 5703: fflush(ficlog);
5704: return 1;
5705: }
5706: weight[i]=dval;
5707: strcpy(line,stra);
5708:
5709: for (j=ncovcol;j>=1;j--){
5710: cutv(stra, strb,line,' ');
5711: if(strb[0]=='.') { /* Missing status */
5712: lval=-1;
5713: }else{
5714: errno=0;
5715: lval=strtol(strb,&endptr,10);
5716: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5717: 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);
5718: 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 5719: return 1;
5720: }
5721: }
5722: if(lval <-1 || lval >1){
1.141 brouard 5723: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5724: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5725: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5726: For example, for multinomial values like 1, 2 and 3,\n \
5727: build V1=0 V2=0 for the reference value (1),\n \
5728: V1=1 V2=0 for (2) \n \
5729: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5730: output of IMaCh is often meaningless.\n \
5731: Exiting.\n",lval,linei, i,line,j);
1.141 brouard 5732: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5733: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5734: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5735: For example, for multinomial values like 1, 2 and 3,\n \
5736: build V1=0 V2=0 for the reference value (1),\n \
5737: V1=1 V2=0 for (2) \n \
5738: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5739: output of IMaCh is often meaningless.\n \
5740: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
5741: return 1;
5742: }
5743: covar[j][i]=(double)(lval);
5744: strcpy(line,stra);
5745: }
5746: lstra=strlen(stra);
5747:
5748: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
5749: stratrunc = &(stra[lstra-9]);
5750: num[i]=atol(stratrunc);
5751: }
5752: else
5753: num[i]=atol(stra);
5754: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
5755: 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;}*/
5756:
5757: i=i+1;
5758: } /* End loop reading data */
1.126 brouard 5759:
1.136 brouard 5760: *imax=i-1; /* Number of individuals */
5761: fclose(fic);
5762:
5763: return (0);
1.164 brouard 5764: /* endread: */
1.136 brouard 5765: printf("Exiting readdata: ");
5766: fclose(fic);
5767: return (1);
1.126 brouard 5768:
5769:
5770:
1.136 brouard 5771: }
1.145 brouard 5772: void removespace(char *str) {
5773: char *p1 = str, *p2 = str;
5774: do
5775: while (*p2 == ' ')
5776: p2++;
1.169 brouard 5777: while (*p1++ == *p2++);
1.145 brouard 5778: }
5779:
5780: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
1.187 brouard 5781: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
5782: * - nagesqr = 1 if age*age in the model, otherwise 0.
5783: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
5784: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
1.145 brouard 5785: * - cptcovage number of covariates with age*products =2
5786: * - cptcovs number of simple covariates
5787: * - 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
5788: * which is a new column after the 9 (ncovcol) variables.
5789: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
5790: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
5791: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
5792: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
5793: */
1.136 brouard 5794: {
1.145 brouard 5795: int i, j, k, ks;
1.164 brouard 5796: int j1, k1, k2;
1.136 brouard 5797: char modelsav[80];
1.145 brouard 5798: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 5799: char *strpt;
1.136 brouard 5800:
1.145 brouard 5801: /*removespace(model);*/
1.136 brouard 5802: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 5803: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 5804: if (strstr(model,"AGE") !=0){
1.192 brouard 5805: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
5806: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 5807: return 1;
5808: }
1.141 brouard 5809: if (strstr(model,"v") !=0){
5810: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
5811: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
5812: return 1;
5813: }
1.187 brouard 5814: strcpy(modelsav,model);
5815: if ((strpt=strstr(model,"age*age")) !=0){
5816: printf(" strpt=%s, model=%s\n",strpt, model);
5817: if(strpt != model){
5818: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 5819: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 5820: corresponding column of parameters.\n",model);
5821: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 5822: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 5823: corresponding column of parameters.\n",model); fflush(ficlog);
5824: return 1;
5825: }
5826:
5827: nagesqr=1;
5828: if (strstr(model,"+age*age") !=0)
5829: substrchaine(modelsav, model, "+age*age");
5830: else if (strstr(model,"age*age+") !=0)
5831: substrchaine(modelsav, model, "age*age+");
5832: else
5833: substrchaine(modelsav, model, "age*age");
5834: }else
5835: nagesqr=0;
5836: if (strlen(modelsav) >1){
5837: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
5838: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
5839: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2 */
5840: cptcovt= j+1; /* Number of total covariates in the model, not including
5841: * cst, age and age*age
5842: * V1+V1*age+ V3 + V3*V4+age*age=> 4*/
5843: /* including age products which are counted in cptcovage.
5844: * but the covariates which are products must be treated
5845: * separately: ncovn=4- 2=2 (V1+V3). */
5846: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
5847: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
5848:
5849:
5850: /* Design
5851: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
5852: * < ncovcol=8 >
5853: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
5854: * k= 1 2 3 4 5 6 7 8
5855: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
5856: * covar[k,i], value of kth covariate if not including age for individual i:
5857: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
5858: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
5859: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
5860: * Tage[++cptcovage]=k
5861: * if products, new covar are created after ncovcol with k1
5862: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
5863: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
5864: * 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
5865: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
5866: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
5867: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
5868: * < ncovcol=8 >
5869: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
5870: * k= 1 2 3 4 5 6 7 8 9 10 11 12
5871: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
5872: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5873: * p Tprod[1]@2={ 6, 5}
5874: *p Tvard[1][1]@4= {7, 8, 5, 6}
5875: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
5876: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
5877: *How to reorganize?
5878: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
5879: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5880: * {2, 1, 4, 8, 5, 6, 3, 7}
5881: * Struct []
5882: */
1.145 brouard 5883:
1.187 brouard 5884: /* This loop fills the array Tvar from the string 'model'.*/
5885: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
5886: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
5887: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
5888: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
5889: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
5890: /* k=1 Tvar[1]=2 (from V2) */
5891: /* k=5 Tvar[5] */
5892: /* for (k=1; k<=cptcovn;k++) { */
1.198 brouard 5893: /* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.187 brouard 5894: /* } */
1.198 brouard 5895: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
1.187 brouard 5896: /*
5897: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
5898: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
1.145 brouard 5899: Tvar[k]=0;
1.187 brouard 5900: cptcovage=0;
5901: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
5902: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5903: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
5904: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
5905: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5906: /*scanf("%d",i);*/
5907: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
5908: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
5909: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
5910: /* covar is not filled and then is empty */
5911: cptcovprod--;
5912: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
5913: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
5914: cptcovage++; /* Sums the number of covariates which include age as a product */
5915: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
5916: /*printf("stre=%s ", stre);*/
5917: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
5918: cptcovprod--;
5919: cutl(stre,strb,strc,'V');
5920: Tvar[k]=atoi(stre);
5921: cptcovage++;
5922: Tage[cptcovage]=k;
5923: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
5924: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
5925: cptcovn++;
5926: cptcovprodnoage++;k1++;
5927: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5928: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
5929: because this model-covariate is a construction we invent a new column
5930: ncovcol + k1
5931: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
5932: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
5933: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
5934: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
5935: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
5936: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
5937: k2=k2+2;
5938: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
5939: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
5940: for (i=1; i<=lastobs;i++){
5941: /* Computes the new covariate which is a product of
5942: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
5943: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
5944: }
5945: } /* End age is not in the model */
5946: } /* End if model includes a product */
5947: else { /* no more sum */
5948: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5949: /* scanf("%d",i);*/
5950: cutl(strd,strc,strb,'V');
5951: ks++; /**< Number of simple covariates */
1.145 brouard 5952: cptcovn++;
1.187 brouard 5953: Tvar[k]=atoi(strd);
5954: }
5955: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
5956: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5957: scanf("%d",i);*/
5958: } /* end of loop + on total covariates */
5959: } /* end if strlen(modelsave == 0) age*age might exist */
5960: } /* end if strlen(model == 0) */
1.136 brouard 5961:
5962: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5963: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5964:
5965: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5966: printf("cptcovprod=%d ", cptcovprod);
5967: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5968:
5969: scanf("%d ",i);*/
5970:
5971:
1.137 brouard 5972: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 5973: /*endread:*/
1.136 brouard 5974: printf("Exiting decodemodel: ");
5975: return (1);
5976: }
5977:
1.169 brouard 5978: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.136 brouard 5979: {
5980: int i, m;
5981:
5982: for (i=1; i<=imx; i++) {
5983: for(m=2; (m<= maxwav); m++) {
5984: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5985: anint[m][i]=9999;
5986: s[m][i]=-1;
5987: }
5988: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169 brouard 5989: *nberr = *nberr + 1;
5990: 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);
5991: 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 5992: s[m][i]=-1;
5993: }
5994: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 5995: (*nberr)++;
1.136 brouard 5996: 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]);
5997: 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]);
5998: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5999: }
6000: }
6001: }
6002:
6003: for (i=1; i<=imx; i++) {
6004: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
6005: for(m=firstpass; (m<= lastpass); m++){
6006: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
6007: if (s[m][i] >= nlstate+1) {
1.169 brouard 6008: if(agedc[i]>0){
6009: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 6010: agev[m][i]=agedc[i];
6011: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 6012: }else {
1.136 brouard 6013: if ((int)andc[i]!=9999){
6014: nbwarn++;
6015: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
6016: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
6017: agev[m][i]=-1;
6018: }
6019: }
1.169 brouard 6020: } /* agedc > 0 */
1.136 brouard 6021: }
6022: else if(s[m][i] !=9){ /* Standard case, age in fractional
6023: years but with the precision of a month */
6024: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
6025: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
6026: agev[m][i]=1;
6027: else if(agev[m][i] < *agemin){
6028: *agemin=agev[m][i];
6029: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
6030: }
6031: else if(agev[m][i] >*agemax){
6032: *agemax=agev[m][i];
1.156 brouard 6033: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 6034: }
6035: /*agev[m][i]=anint[m][i]-annais[i];*/
6036: /* agev[m][i] = age[i]+2*m;*/
6037: }
6038: else { /* =9 */
6039: agev[m][i]=1;
6040: s[m][i]=-1;
6041: }
6042: }
6043: else /*= 0 Unknown */
6044: agev[m][i]=1;
6045: }
6046:
6047: }
6048: for (i=1; i<=imx; i++) {
6049: for(m=firstpass; (m<=lastpass); m++){
6050: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 6051: (*nberr)++;
1.136 brouard 6052: 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);
6053: 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);
6054: return 1;
6055: }
6056: }
6057: }
6058:
6059: /*for (i=1; i<=imx; i++){
6060: for (m=firstpass; (m<lastpass); m++){
6061: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
6062: }
6063:
6064: }*/
6065:
6066:
1.139 brouard 6067: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
6068: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 6069:
6070: return (0);
1.164 brouard 6071: /* endread:*/
1.136 brouard 6072: printf("Exiting calandcheckages: ");
6073: return (1);
6074: }
6075:
1.172 brouard 6076: #if defined(_MSC_VER)
6077: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
6078: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
6079: //#include "stdafx.h"
6080: //#include <stdio.h>
6081: //#include <tchar.h>
6082: //#include <windows.h>
6083: //#include <iostream>
6084: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
6085:
6086: LPFN_ISWOW64PROCESS fnIsWow64Process;
6087:
6088: BOOL IsWow64()
6089: {
6090: BOOL bIsWow64 = FALSE;
6091:
6092: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
6093: // (HANDLE, PBOOL);
6094:
6095: //LPFN_ISWOW64PROCESS fnIsWow64Process;
6096:
6097: HMODULE module = GetModuleHandle(_T("kernel32"));
6098: const char funcName[] = "IsWow64Process";
6099: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
6100: GetProcAddress(module, funcName);
6101:
6102: if (NULL != fnIsWow64Process)
6103: {
6104: if (!fnIsWow64Process(GetCurrentProcess(),
6105: &bIsWow64))
6106: //throw std::exception("Unknown error");
6107: printf("Unknown error\n");
6108: }
6109: return bIsWow64 != FALSE;
6110: }
6111: #endif
1.177 brouard 6112:
1.191 brouard 6113: void syscompilerinfo(int logged)
1.167 brouard 6114: {
6115: /* #include "syscompilerinfo.h"*/
1.185 brouard 6116: /* command line Intel compiler 32bit windows, XP compatible:*/
6117: /* /GS /W3 /Gy
6118: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
6119: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
6120: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 6121: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
6122: */
6123: /* 64 bits */
1.185 brouard 6124: /*
6125: /GS /W3 /Gy
6126: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
6127: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
6128: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
6129: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
6130: /* Optimization are useless and O3 is slower than O2 */
6131: /*
6132: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
6133: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
6134: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
6135: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
6136: */
1.186 brouard 6137: /* Link is */ /* /OUT:"visual studio
1.185 brouard 6138: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
6139: /PDB:"visual studio
6140: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
6141: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
6142: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
6143: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
6144: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
6145: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
6146: uiAccess='false'"
6147: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
6148: /NOLOGO /TLBID:1
6149: */
1.177 brouard 6150: #if defined __INTEL_COMPILER
1.178 brouard 6151: #if defined(__GNUC__)
6152: struct utsname sysInfo; /* For Intel on Linux and OS/X */
6153: #endif
1.177 brouard 6154: #elif defined(__GNUC__)
1.179 brouard 6155: #ifndef __APPLE__
1.174 brouard 6156: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 6157: #endif
1.177 brouard 6158: struct utsname sysInfo;
1.178 brouard 6159: int cross = CROSS;
6160: if (cross){
6161: printf("Cross-");
1.191 brouard 6162: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 6163: }
1.174 brouard 6164: #endif
6165:
1.171 brouard 6166: #include <stdint.h>
1.178 brouard 6167:
1.191 brouard 6168: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 6169: #if defined(__clang__)
1.191 brouard 6170: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 6171: #endif
6172: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 6173: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 6174: #endif
6175: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 6176: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 6177: #endif
6178: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 6179: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 6180: #endif
6181: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 6182: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 6183: #endif
6184: #if defined(_MSC_VER)
1.191 brouard 6185: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 6186: #endif
6187: #if defined(__PGI)
1.191 brouard 6188: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 6189: #endif
6190: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 6191: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 6192: #endif
1.191 brouard 6193: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 6194:
1.167 brouard 6195: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
6196: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
6197: // Windows (x64 and x86)
1.191 brouard 6198: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 6199: #elif __unix__ // all unices, not all compilers
6200: // Unix
1.191 brouard 6201: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 6202: #elif __linux__
6203: // linux
1.191 brouard 6204: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 6205: #elif __APPLE__
1.174 brouard 6206: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 6207: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 6208: #endif
6209:
6210: /* __MINGW32__ */
6211: /* __CYGWIN__ */
6212: /* __MINGW64__ */
6213: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
6214: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
6215: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
6216: /* _WIN64 // Defined for applications for Win64. */
6217: /* _M_X64 // Defined for compilations that target x64 processors. */
6218: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 6219:
1.167 brouard 6220: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 6221: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 6222: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 6223: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 6224: #else
1.191 brouard 6225: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 6226: #endif
6227:
1.169 brouard 6228: #if defined(__GNUC__)
6229: # if defined(__GNUC_PATCHLEVEL__)
6230: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
6231: + __GNUC_MINOR__ * 100 \
6232: + __GNUC_PATCHLEVEL__)
6233: # else
6234: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
6235: + __GNUC_MINOR__ * 100)
6236: # endif
1.174 brouard 6237: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 6238: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 6239:
6240: if (uname(&sysInfo) != -1) {
6241: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 6242: 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 6243: }
6244: else
6245: perror("uname() error");
1.179 brouard 6246: //#ifndef __INTEL_COMPILER
6247: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 6248: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 6249: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 6250: #endif
1.169 brouard 6251: #endif
1.172 brouard 6252:
6253: // void main()
6254: // {
1.169 brouard 6255: #if defined(_MSC_VER)
1.174 brouard 6256: if (IsWow64()){
1.191 brouard 6257: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
6258: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 6259: }
6260: else{
1.191 brouard 6261: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
6262: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 6263: }
1.172 brouard 6264: // printf("\nPress Enter to continue...");
6265: // getchar();
6266: // }
6267:
1.169 brouard 6268: #endif
6269:
1.167 brouard 6270:
6271: }
1.136 brouard 6272:
1.180 brouard 6273: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){
6274: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6275: int i, j, k, i1 ;
6276: double ftolpl = 1.e-10;
6277: double age, agebase, agelim;
6278:
1.201 ! brouard 6279: strcpy(filerespl,"PL_");
! 6280: strcat(filerespl,fileresu);
1.180 brouard 6281: if((ficrespl=fopen(filerespl,"w"))==NULL) {
6282: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6283: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6284: }
6285: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6286: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6287: pstamp(ficrespl);
6288: fprintf(ficrespl,"# Period (stable) prevalence \n");
6289: fprintf(ficrespl,"#Age ");
6290: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
6291: fprintf(ficrespl,"\n");
6292:
6293: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
6294:
6295: agebase=ageminpar;
6296: agelim=agemaxpar;
6297:
6298: i1=pow(2,cptcoveff);
6299: if (cptcovn < 1){i1=1;}
6300:
6301: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6302: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
6303: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6304: k=k+1;
6305: /* to clean */
1.198 brouard 6306: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
1.200 brouard 6307: fprintf(ficrespl,"#******");
6308: printf("#******");
6309: fprintf(ficlog,"#******");
1.180 brouard 6310: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 6311: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
6312: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
6313: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.180 brouard 6314: }
6315: fprintf(ficrespl,"******\n");
6316: printf("******\n");
6317: fprintf(ficlog,"******\n");
6318:
6319: fprintf(ficrespl,"#Age ");
6320: for(j=1;j<=cptcoveff;j++) {
1.200 brouard 6321: fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.180 brouard 6322: }
6323: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
6324: fprintf(ficrespl,"\n");
6325:
6326: for (age=agebase; age<=agelim; age++){
6327: /* for (age=agebase; age<=agebase; age++){ */
6328: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6329: fprintf(ficrespl,"%.0f ",age );
6330: for(j=1;j<=cptcoveff;j++)
1.198 brouard 6331: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.180 brouard 6332: for(i=1; i<=nlstate;i++)
6333: fprintf(ficrespl," %.5f", prlim[i][i]);
6334: fprintf(ficrespl,"\n");
6335: } /* Age */
6336: /* was end of cptcod */
6337: } /* cptcov */
1.184 brouard 6338: return 0;
1.180 brouard 6339: }
6340:
6341: int hPijx(double *p, int bage, int fage){
6342: /*------------- h Pij x at various ages ------------*/
6343:
6344: int stepsize;
6345: int agelim;
6346: int hstepm;
6347: int nhstepm;
6348: int h, i, i1, j, k;
6349:
6350: double agedeb;
6351: double ***p3mat;
6352:
1.201 ! brouard 6353: strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu);
1.180 brouard 6354: if((ficrespij=fopen(filerespij,"w"))==NULL) {
6355: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
6356: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
6357: }
6358: printf("Computing pij: result on file '%s' \n", filerespij);
6359: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
6360:
6361: stepsize=(int) (stepm+YEARM-1)/YEARM;
6362: /*if (stepm<=24) stepsize=2;*/
6363:
6364: agelim=AGESUP;
6365: hstepm=stepsize*YEARM; /* Every year of age */
6366: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
6367:
6368: /* hstepm=1; aff par mois*/
6369: pstamp(ficrespij);
6370: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
6371: i1= pow(2,cptcoveff);
1.183 brouard 6372: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
6373: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
6374: /* k=k+1; */
6375: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6376: fprintf(ficrespij,"\n#****** ");
6377: for(j=1;j<=cptcoveff;j++)
1.198 brouard 6378: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.183 brouard 6379: fprintf(ficrespij,"******\n");
6380:
6381: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
6382: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6383: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6384:
6385: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 6386:
1.183 brouard 6387: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6388: oldm=oldms;savm=savms;
6389: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
6390: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
6391: for(i=1; i<=nlstate;i++)
6392: for(j=1; j<=nlstate+ndeath;j++)
6393: fprintf(ficrespij," %1d-%1d",i,j);
6394: fprintf(ficrespij,"\n");
6395: for (h=0; h<=nhstepm; h++){
6396: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
6397: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 6398: for(i=1; i<=nlstate;i++)
6399: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 6400: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 6401: fprintf(ficrespij,"\n");
6402: }
1.183 brouard 6403: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6404: fprintf(ficrespij,"\n");
6405: }
1.180 brouard 6406: /*}*/
6407: }
1.184 brouard 6408: return 0;
1.180 brouard 6409: }
6410:
6411:
1.136 brouard 6412: /***********************************************/
6413: /**************** Main Program *****************/
6414: /***********************************************/
6415:
6416: int main(int argc, char *argv[])
6417: {
6418: #ifdef GSL
6419: const gsl_multimin_fminimizer_type *T;
6420: size_t iteri = 0, it;
6421: int rval = GSL_CONTINUE;
6422: int status = GSL_SUCCESS;
6423: double ssval;
6424: #endif
6425: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 6426: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
6427:
6428: int jj, ll, li, lj, lk;
1.136 brouard 6429: int numlinepar=0; /* Current linenumber of parameter file */
1.197 brouard 6430: int num_filled;
1.136 brouard 6431: int itimes;
6432: int NDIM=2;
6433: int vpopbased=0;
6434:
1.164 brouard 6435: char ca[32], cb[32];
1.136 brouard 6436: /* FILE *fichtm; *//* Html File */
6437: /* FILE *ficgp;*/ /*Gnuplot File */
6438: struct stat info;
1.191 brouard 6439: double agedeb=0.;
1.194 brouard 6440:
6441: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.136 brouard 6442:
1.165 brouard 6443: double fret;
1.191 brouard 6444: double dum=0.; /* Dummy variable */
1.136 brouard 6445: double ***p3mat;
6446: double ***mobaverage;
1.164 brouard 6447:
6448: char line[MAXLINE];
1.197 brouard 6449: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
6450:
6451: char model[MAXLINE], modeltemp[MAXLINE];
1.136 brouard 6452: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 6453: char *tok, *val; /* pathtot */
1.136 brouard 6454: int firstobs=1, lastobs=10;
1.195 brouard 6455: int c, h , cpt, c2;
1.191 brouard 6456: int jl=0;
6457: int i1, j1, jk, stepsize=0;
1.194 brouard 6458: int count=0;
6459:
1.164 brouard 6460: int *tab;
1.136 brouard 6461: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
6462: int mobilav=0,popforecast=0;
1.191 brouard 6463: int hstepm=0, nhstepm=0;
1.136 brouard 6464: int agemortsup;
6465: float sumlpop=0.;
6466: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
6467: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
6468:
1.191 brouard 6469: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 6470: double ftolpl=FTOL;
6471: double **prlim;
6472: double ***param; /* Matrix of parameters */
6473: double *p;
6474: double **matcov; /* Matrix of covariance */
6475: double ***delti3; /* Scale */
6476: double *delti; /* Scale */
6477: double ***eij, ***vareij;
6478: double **varpl; /* Variances of prevalence limits by age */
6479: double *epj, vepp;
1.164 brouard 6480:
1.136 brouard 6481: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
6482: double **ximort;
1.145 brouard 6483: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 6484: int *dcwave;
6485:
1.164 brouard 6486: char z[1]="c";
1.136 brouard 6487:
6488: /*char *strt;*/
6489: char strtend[80];
1.126 brouard 6490:
1.164 brouard 6491:
1.126 brouard 6492: /* setlocale (LC_ALL, ""); */
6493: /* bindtextdomain (PACKAGE, LOCALEDIR); */
6494: /* textdomain (PACKAGE); */
6495: /* setlocale (LC_CTYPE, ""); */
6496: /* setlocale (LC_MESSAGES, ""); */
6497:
6498: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 6499: rstart_time = time(NULL);
6500: /* (void) gettimeofday(&start_time,&tzp);*/
6501: start_time = *localtime(&rstart_time);
1.126 brouard 6502: curr_time=start_time;
1.157 brouard 6503: /*tml = *localtime(&start_time.tm_sec);*/
6504: /* strcpy(strstart,asctime(&tml)); */
6505: strcpy(strstart,asctime(&start_time));
1.126 brouard 6506:
6507: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 6508: /* tp.tm_sec = tp.tm_sec +86400; */
6509: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 6510: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
6511: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
6512: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 6513: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 6514: /* strt=asctime(&tmg); */
6515: /* printf("Time(after) =%s",strstart); */
6516: /* (void) time (&time_value);
6517: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
6518: * tm = *localtime(&time_value);
6519: * strstart=asctime(&tm);
6520: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
6521: */
6522:
6523: nberr=0; /* Number of errors and warnings */
6524: nbwarn=0;
1.184 brouard 6525: #ifdef WIN32
6526: _getcwd(pathcd, size);
6527: #else
1.126 brouard 6528: getcwd(pathcd, size);
1.184 brouard 6529: #endif
1.191 brouard 6530: syscompilerinfo(0);
1.196 brouard 6531: printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126 brouard 6532: if(argc <=1){
6533: printf("\nEnter the parameter file name: ");
6534: fgets(pathr,FILENAMELENGTH,stdin);
6535: i=strlen(pathr);
6536: if(pathr[i-1]=='\n')
6537: pathr[i-1]='\0';
1.156 brouard 6538: i=strlen(pathr);
6539: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
6540: pathr[i-1]='\0';
1.126 brouard 6541: for (tok = pathr; tok != NULL; ){
6542: printf("Pathr |%s|\n",pathr);
6543: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
6544: printf("val= |%s| pathr=%s\n",val,pathr);
6545: strcpy (pathtot, val);
6546: if(pathr[0] == '\0') break; /* Dirty */
6547: }
6548: }
6549: else{
6550: strcpy(pathtot,argv[1]);
6551: }
6552: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
6553: /*cygwin_split_path(pathtot,path,optionfile);
6554: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
6555: /* cutv(path,optionfile,pathtot,'\\');*/
6556:
6557: /* Split argv[0], imach program to get pathimach */
6558: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
6559: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6560: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6561: /* strcpy(pathimach,argv[0]); */
6562: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
6563: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
6564: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 6565: #ifdef WIN32
6566: _chdir(path); /* Can be a relative path */
6567: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
6568: #else
1.126 brouard 6569: chdir(path); /* Can be a relative path */
1.184 brouard 6570: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
6571: #endif
6572: printf("Current directory %s!\n",pathcd);
1.126 brouard 6573: strcpy(command,"mkdir ");
6574: strcat(command,optionfilefiname);
6575: if((outcmd=system(command)) != 0){
1.169 brouard 6576: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 6577: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
6578: /* fclose(ficlog); */
6579: /* exit(1); */
6580: }
6581: /* if((imk=mkdir(optionfilefiname))<0){ */
6582: /* perror("mkdir"); */
6583: /* } */
6584:
6585: /*-------- arguments in the command line --------*/
6586:
1.186 brouard 6587: /* Main Log file */
1.126 brouard 6588: strcat(filelog, optionfilefiname);
6589: strcat(filelog,".log"); /* */
6590: if((ficlog=fopen(filelog,"w"))==NULL) {
6591: printf("Problem with logfile %s\n",filelog);
6592: goto end;
6593: }
6594: fprintf(ficlog,"Log filename:%s\n",filelog);
1.197 brouard 6595: fprintf(ficlog,"Version %s %s",version,fullversion);
1.126 brouard 6596: fprintf(ficlog,"\nEnter the parameter file name: \n");
6597: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
6598: path=%s \n\
6599: optionfile=%s\n\
6600: optionfilext=%s\n\
1.156 brouard 6601: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 6602:
1.197 brouard 6603: syscompilerinfo(1);
1.167 brouard 6604:
1.126 brouard 6605: printf("Local time (at start):%s",strstart);
6606: fprintf(ficlog,"Local time (at start): %s",strstart);
6607: fflush(ficlog);
6608: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 6609: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 6610:
6611: /* */
6612: strcpy(fileres,"r");
6613: strcat(fileres, optionfilefiname);
1.201 ! brouard 6614: strcat(fileresu, optionfilefiname); /* Without r in front */
1.126 brouard 6615: strcat(fileres,".txt"); /* Other files have txt extension */
1.201 ! brouard 6616: strcat(fileresu,".txt"); /* Other files have txt extension */
1.126 brouard 6617:
1.186 brouard 6618: /* Main ---------arguments file --------*/
1.126 brouard 6619:
6620: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 6621: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
6622: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 6623: fflush(ficlog);
1.149 brouard 6624: /* goto end; */
6625: exit(70);
1.126 brouard 6626: }
6627:
6628:
6629:
6630: strcpy(filereso,"o");
1.201 ! brouard 6631: strcat(filereso,fileresu);
1.126 brouard 6632: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
6633: printf("Problem with Output resultfile: %s\n", filereso);
6634: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
6635: fflush(ficlog);
6636: goto end;
6637: }
6638:
6639: /* Reads comments: lines beginning with '#' */
6640: numlinepar=0;
1.197 brouard 6641:
6642: /* First parameter line */
6643: while(fgets(line, MAXLINE, ficpar)) {
6644: /* If line starts with a # it is a comment */
6645: if (line[0] == '#') {
6646: numlinepar++;
6647: fputs(line,stdout);
6648: fputs(line,ficparo);
6649: fputs(line,ficlog);
6650: continue;
6651: }else
6652: break;
6653: }
6654: if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
6655: title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
6656: if (num_filled != 5) {
6657: printf("Should be 5 parameters\n");
6658: }
1.126 brouard 6659: numlinepar++;
1.197 brouard 6660: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
6661: }
6662: /* Second parameter line */
6663: while(fgets(line, MAXLINE, ficpar)) {
6664: /* If line starts with a # it is a comment */
6665: if (line[0] == '#') {
6666: numlinepar++;
6667: fputs(line,stdout);
6668: fputs(line,ficparo);
6669: fputs(line,ficlog);
6670: continue;
6671: }else
6672: break;
6673: }
6674: if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
6675: &ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
6676: if (num_filled != 8) {
6677: printf("Not 8\n");
6678: }
6679: 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 6680: }
6681:
1.197 brouard 6682: /* Third parameter line */
6683: while(fgets(line, MAXLINE, ficpar)) {
6684: /* If line starts with a # it is a comment */
6685: if (line[0] == '#') {
6686: numlinepar++;
6687: fputs(line,stdout);
6688: fputs(line,ficparo);
6689: fputs(line,ficlog);
6690: continue;
6691: }else
6692: break;
6693: }
1.201 ! brouard 6694: if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
! 6695: if (num_filled == 0)
! 6696: model[0]='\0';
! 6697: else if (num_filled != 1){
1.197 brouard 6698: printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
6699: fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
6700: model[0]='\0';
6701: goto end;
6702: }
6703: else{
6704: if (model[0]=='+'){
6705: for(i=1; i<=strlen(model);i++)
6706: modeltemp[i-1]=model[i];
1.201 ! brouard 6707: strcpy(model,modeltemp);
1.197 brouard 6708: }
6709: }
1.199 brouard 6710: /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
1.197 brouard 6711: }
6712: /* 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); */
6713: /* numlinepar=numlinepar+3; /\* In general *\/ */
6714: /* 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 6715: if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the model */
6716: model[strlen(model)-1]='\0';
1.197 brouard 6717: 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);
6718: 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 6719: fflush(ficlog);
1.190 brouard 6720: /* if(model[0]=='#'|| model[0]== '\0'){ */
6721: if(model[0]=='#'){
1.187 brouard 6722: printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
6723: 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
6724: 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \
6725: if(mle != -1){
6726: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
6727: exit(1);
6728: }
6729: }
1.126 brouard 6730: while((c=getc(ficpar))=='#' && c!= EOF){
6731: ungetc(c,ficpar);
6732: fgets(line, MAXLINE, ficpar);
6733: numlinepar++;
1.195 brouard 6734: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
6735: z[0]=line[1];
6736: }
6737: /* printf("****line [1] = %c \n",line[1]); */
1.141 brouard 6738: fputs(line, stdout);
6739: //puts(line);
1.126 brouard 6740: fputs(line,ficparo);
6741: fputs(line,ficlog);
6742: }
6743: ungetc(c,ficpar);
6744:
6745:
1.145 brouard 6746: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.136 brouard 6747: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
6748: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
6749: v1+v2*age+v2*v3 makes cptcovn = 3
6750: */
6751: if (strlen(model)>1)
1.187 brouard 6752: 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 6753: else
1.187 brouard 6754: ncovmodel=2; /* Constant and age */
1.133 brouard 6755: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
6756: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 6757: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
6758: 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);
6759: 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);
6760: fflush(stdout);
6761: fclose (ficlog);
6762: goto end;
6763: }
1.126 brouard 6764: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6765: delti=delti3[1][1];
6766: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
6767: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
6768: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 6769: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
6770: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 6771: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6772: fclose (ficparo);
6773: fclose (ficlog);
6774: goto end;
6775: exit(0);
6776: }
1.186 brouard 6777: else if(mle==-3) { /* Main Wizard */
1.126 brouard 6778: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 6779: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
6780: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 6781: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6782: matcov=matrix(1,npar,1,npar);
6783: }
6784: else{
1.145 brouard 6785: /* Read guessed parameters */
1.126 brouard 6786: /* Reads comments: lines beginning with '#' */
6787: while((c=getc(ficpar))=='#' && c!= EOF){
6788: ungetc(c,ficpar);
6789: fgets(line, MAXLINE, ficpar);
6790: numlinepar++;
1.141 brouard 6791: fputs(line,stdout);
1.126 brouard 6792: fputs(line,ficparo);
6793: fputs(line,ficlog);
6794: }
6795: ungetc(c,ficpar);
6796:
6797: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6798: for(i=1; i <=nlstate; i++){
6799: j=0;
6800: for(jj=1; jj <=nlstate+ndeath; jj++){
6801: if(jj==i) continue;
6802: j++;
6803: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.193 brouard 6804: if ((i1 != i) || (j1 != jj)){
1.126 brouard 6805: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
6806: It might be a problem of design; if ncovcol and the model are correct\n \
6807: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
6808: exit(1);
6809: }
6810: fprintf(ficparo,"%1d%1d",i1,j1);
6811: if(mle==1)
1.193 brouard 6812: printf("%1d%1d",i,jj);
6813: fprintf(ficlog,"%1d%1d",i,jj);
1.126 brouard 6814: for(k=1; k<=ncovmodel;k++){
6815: fscanf(ficpar," %lf",¶m[i][j][k]);
6816: if(mle==1){
6817: printf(" %lf",param[i][j][k]);
6818: fprintf(ficlog," %lf",param[i][j][k]);
6819: }
6820: else
6821: fprintf(ficlog," %lf",param[i][j][k]);
6822: fprintf(ficparo," %lf",param[i][j][k]);
6823: }
6824: fscanf(ficpar,"\n");
6825: numlinepar++;
6826: if(mle==1)
6827: printf("\n");
6828: fprintf(ficlog,"\n");
6829: fprintf(ficparo,"\n");
6830: }
6831: }
6832: fflush(ficlog);
6833:
1.145 brouard 6834: /* Reads scales values */
1.126 brouard 6835: p=param[1][1];
6836:
6837: /* Reads comments: lines beginning with '#' */
6838: while((c=getc(ficpar))=='#' && c!= EOF){
6839: ungetc(c,ficpar);
6840: fgets(line, MAXLINE, ficpar);
6841: numlinepar++;
1.141 brouard 6842: fputs(line,stdout);
1.126 brouard 6843: fputs(line,ficparo);
6844: fputs(line,ficlog);
6845: }
6846: ungetc(c,ficpar);
6847:
6848: for(i=1; i <=nlstate; i++){
6849: for(j=1; j <=nlstate+ndeath-1; j++){
6850: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.164 brouard 6851: if ( (i1-i) * (j1-j) != 0){
1.126 brouard 6852: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
6853: exit(1);
6854: }
6855: printf("%1d%1d",i,j);
6856: fprintf(ficparo,"%1d%1d",i1,j1);
6857: fprintf(ficlog,"%1d%1d",i1,j1);
6858: for(k=1; k<=ncovmodel;k++){
6859: fscanf(ficpar,"%le",&delti3[i][j][k]);
6860: printf(" %le",delti3[i][j][k]);
6861: fprintf(ficparo," %le",delti3[i][j][k]);
6862: fprintf(ficlog," %le",delti3[i][j][k]);
6863: }
6864: fscanf(ficpar,"\n");
6865: numlinepar++;
6866: printf("\n");
6867: fprintf(ficparo,"\n");
6868: fprintf(ficlog,"\n");
6869: }
6870: }
6871: fflush(ficlog);
6872:
1.145 brouard 6873: /* Reads covariance matrix */
1.126 brouard 6874: delti=delti3[1][1];
6875:
6876:
6877: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
6878:
6879: /* Reads comments: lines beginning with '#' */
6880: while((c=getc(ficpar))=='#' && c!= EOF){
6881: ungetc(c,ficpar);
6882: fgets(line, MAXLINE, ficpar);
6883: numlinepar++;
1.141 brouard 6884: fputs(line,stdout);
1.126 brouard 6885: fputs(line,ficparo);
6886: fputs(line,ficlog);
6887: }
6888: ungetc(c,ficpar);
6889:
6890: matcov=matrix(1,npar,1,npar);
1.131 brouard 6891: for(i=1; i <=npar; i++)
6892: for(j=1; j <=npar; j++) matcov[i][j]=0.;
6893:
1.194 brouard 6894: /* Scans npar lines */
1.126 brouard 6895: for(i=1; i <=npar; i++){
1.194 brouard 6896: count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk);
6897: if(count != 3){
6898: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
6899: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
6900: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
6901: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
6902: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
6903: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
6904: exit(1);
6905: }else
1.126 brouard 6906: if(mle==1)
1.194 brouard 6907: printf("%1d%1d%1d",i1,j1,jk);
6908: fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);
6909: fprintf(ficparo,"%1d%1d%1d",i1,j1,jk);
1.126 brouard 6910: for(j=1; j <=i; j++){
6911: fscanf(ficpar," %le",&matcov[i][j]);
6912: if(mle==1){
6913: printf(" %.5le",matcov[i][j]);
6914: }
6915: fprintf(ficlog," %.5le",matcov[i][j]);
6916: fprintf(ficparo," %.5le",matcov[i][j]);
6917: }
6918: fscanf(ficpar,"\n");
6919: numlinepar++;
6920: if(mle==1)
6921: printf("\n");
6922: fprintf(ficlog,"\n");
6923: fprintf(ficparo,"\n");
6924: }
1.194 brouard 6925: /* End of read covariance matrix npar lines */
1.126 brouard 6926: for(i=1; i <=npar; i++)
6927: for(j=i+1;j<=npar;j++)
6928: matcov[i][j]=matcov[j][i];
6929:
6930: if(mle==1)
6931: printf("\n");
6932: fprintf(ficlog,"\n");
6933:
6934: fflush(ficlog);
6935:
6936: /*-------- Rewriting parameter file ----------*/
6937: strcpy(rfileres,"r"); /* "Rparameterfile */
6938: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
6939: strcat(rfileres,"."); /* */
6940: strcat(rfileres,optionfilext); /* Other files have txt extension */
6941: if((ficres =fopen(rfileres,"w"))==NULL) {
1.201 ! brouard 6942: printf("Problem writing new parameter file: %s\n", rfileres);goto end;
! 6943: fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
1.126 brouard 6944: }
6945: fprintf(ficres,"#%s\n",version);
6946: } /* End of mle != -3 */
6947:
1.186 brouard 6948: /* Main data
6949: */
1.126 brouard 6950: n= lastobs;
6951: num=lvector(1,n);
6952: moisnais=vector(1,n);
6953: annais=vector(1,n);
6954: moisdc=vector(1,n);
6955: andc=vector(1,n);
6956: agedc=vector(1,n);
6957: cod=ivector(1,n);
6958: weight=vector(1,n);
6959: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
6960: mint=matrix(1,maxwav,1,n);
6961: anint=matrix(1,maxwav,1,n);
1.131 brouard 6962: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 6963: tab=ivector(1,NCOVMAX);
1.144 brouard 6964: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 6965: 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 6966:
1.136 brouard 6967: /* Reads data from file datafile */
6968: if (readdata(datafile, firstobs, lastobs, &imx)==1)
6969: goto end;
6970:
6971: /* Calculation of the number of parameters from char model */
1.137 brouard 6972: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
6973: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
6974: k=3 V4 Tvar[k=3]= 4 (from V4)
6975: k=2 V1 Tvar[k=2]= 1 (from V1)
6976: k=1 Tvar[1]=2 (from V2)
6977: */
6978: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
6979: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
6980: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
6981: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
6982: */
6983: /* For model-covariate k tells which data-covariate to use but
6984: because this model-covariate is a construction we invent a new column
6985: ncovcol + k1
6986: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
6987: Tvar[3=V1*V4]=4+1 etc */
1.145 brouard 6988: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
1.137 brouard 6989: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
6990: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
6991: */
1.145 brouard 6992: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
6993: 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 6994: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
6995: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 6996: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 6997: 4 covariates (3 plus signs)
6998: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
6999: */
1.136 brouard 7000:
1.186 brouard 7001: /* Main decodemodel */
7002:
1.187 brouard 7003:
1.136 brouard 7004: if(decodemodel(model, lastobs) == 1)
7005: goto end;
7006:
1.137 brouard 7007: if((double)(lastobs-imx)/(double)imx > 1.10){
7008: nbwarn++;
7009: 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);
7010: 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);
7011: }
1.136 brouard 7012: /* if(mle==1){*/
1.137 brouard 7013: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
7014: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 7015: }
7016:
7017: /*-calculation of age at interview from date of interview and age at death -*/
7018: agev=matrix(1,maxwav,1,imx);
7019:
7020: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
7021: goto end;
7022:
1.126 brouard 7023:
1.136 brouard 7024: agegomp=(int)agemin;
7025: free_vector(moisnais,1,n);
7026: free_vector(annais,1,n);
1.126 brouard 7027: /* free_matrix(mint,1,maxwav,1,n);
7028: free_matrix(anint,1,maxwav,1,n);*/
7029: free_vector(moisdc,1,n);
7030: free_vector(andc,1,n);
1.145 brouard 7031: /* */
7032:
1.126 brouard 7033: wav=ivector(1,imx);
7034: dh=imatrix(1,lastpass-firstpass+1,1,imx);
7035: bh=imatrix(1,lastpass-firstpass+1,1,imx);
7036: mw=imatrix(1,lastpass-firstpass+1,1,imx);
7037:
7038: /* Concatenates waves */
7039: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 brouard 7040: /* */
7041:
1.126 brouard 7042: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
7043:
7044: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
7045: ncodemax[1]=1;
1.145 brouard 7046: Ndum =ivector(-1,NCOVMAX);
1.187 brouard 7047: if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */
1.145 brouard 7048: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.186 brouard 7049: /* Nbcode gives the value of the lth modality of jth covariate, in
7050: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
7051: /* 1 to ncodemax[j] is the maximum value of this jth covariate */
1.145 brouard 7052:
1.200 brouard 7053: /* codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
1.198 brouard 7054: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
1.186 brouard 7055: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.145 brouard 7056: h=0;
7057:
7058:
7059: /*if (cptcovn > 0) */
1.126 brouard 7060:
1.145 brouard 7061:
1.126 brouard 7062: m=pow(2,cptcoveff);
7063:
1.144 brouard 7064: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.186 brouard 7065: * For k=4 covariates, h goes from 1 to 2**k
7066: * codtabm(h,k)= 1 & (h-1) >> (k-1) ;
7067: * h\k 1 2 3 4
1.143 brouard 7068: *______________________________
7069: * 1 i=1 1 i=1 1 i=1 1 i=1 1
7070: * 2 2 1 1 1
7071: * 3 i=2 1 2 1 1
7072: * 4 2 2 1 1
7073: * 5 i=3 1 i=2 1 2 1
7074: * 6 2 1 2 1
7075: * 7 i=4 1 2 2 1
7076: * 8 2 2 2 1
1.197 brouard 7077: * 9 i=5 1 i=3 1 i=2 1 2
7078: * 10 2 1 1 2
7079: * 11 i=6 1 2 1 2
7080: * 12 2 2 1 2
7081: * 13 i=7 1 i=4 1 2 2
7082: * 14 2 1 2 2
7083: * 15 i=8 1 2 2 2
7084: * 16 2 2 2 2
1.143 brouard 7085: */
1.197 brouard 7086: for(h=1; h <=100 ;h++){
7087: /* printf("h=%2d ", h); */
1.200 brouard 7088: /* for(k=1; k <=10; k++){ */
1.197 brouard 7089: /* printf("k=%d %d ",k,codtabm(h,k)); */
1.200 brouard 7090: /* codtab[h][k]=codtabm(h,k); */
7091: /* } */
1.197 brouard 7092: /* printf("\n"); */
7093: }
7094: /* for(k=1;k<=cptcoveff; k++){ /\* scans any effective covariate *\/ */
7095: /* 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 *\/ */
7096: /* for(j=1; j <= ncodemax[k]; j++){ /\* For each modality of this covariate ncodemax=2*\/ */
7097: /* for(cpt=1; cpt <=pow(2,k-1); cpt++){ /\* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 *\/ */
7098: /* h++; */
7099: /* if (h>m) */
7100: /* h=1; */
7101: /* codtab[h][k]=j; */
7102: /* /\* codtab[12][3]=1; *\/ */
7103: /* /\*codtab[h][Tvar[k]]=j;*\/ */
7104: /* /\* 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]]); *\/ */
7105: /* } */
7106: /* } */
7107: /* } */
7108: /* } */
1.126 brouard 7109: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
7110: codtab[1][2]=1;codtab[2][2]=2; */
1.197 brouard 7111: /* for(i=1; i <=m ;i++){ */
7112: /* for(k=1; k <=cptcovn; k++){ */
7113: /* printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); */
7114: /* } */
7115: /* printf("\n"); */
7116: /* } */
7117: /* scanf("%d",i);*/
1.145 brouard 7118:
7119: free_ivector(Ndum,-1,NCOVMAX);
7120:
7121:
1.126 brouard 7122:
1.186 brouard 7123: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 7124: strcpy(optionfilegnuplot,optionfilefiname);
7125: if(mle==-3)
1.201 ! brouard 7126: strcat(optionfilegnuplot,"-MORT_");
1.126 brouard 7127: strcat(optionfilegnuplot,".gp");
7128:
7129: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
7130: printf("Problem with file %s",optionfilegnuplot);
7131: }
7132: else{
7133: fprintf(ficgp,"\n# %s\n", version);
7134: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 7135: //fprintf(ficgp,"set missing 'NaNq'\n");
7136: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 7137: }
7138: /* fclose(ficgp);*/
1.186 brouard 7139:
7140:
7141: /* Initialisation of --------- index.htm --------*/
1.126 brouard 7142:
7143: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
7144: if(mle==-3)
1.201 ! brouard 7145: strcat(optionfilehtm,"-MORT_");
1.126 brouard 7146: strcat(optionfilehtm,".htm");
7147: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 7148: printf("Problem with %s \n",optionfilehtm);
7149: exit(0);
1.126 brouard 7150: }
7151:
7152: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
7153: strcat(optionfilehtmcov,"-cov.htm");
7154: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
7155: printf("Problem with %s \n",optionfilehtmcov), exit(0);
7156: }
7157: else{
7158: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
7159: <hr size=\"2\" color=\"#EC5E5E\"> \n\
7160: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
7161: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
7162: }
7163:
7164: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
7165: <hr size=\"2\" color=\"#EC5E5E\"> \n\
7166: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
7167: \n\
7168: <hr size=\"2\" color=\"#EC5E5E\">\
7169: <ul><li><h4>Parameter files</h4>\n\
7170: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
7171: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
7172: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
7173: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
7174: - Date and time at start: %s</ul>\n",\
7175: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
7176: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
7177: fileres,fileres,\
7178: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
7179: fflush(fichtm);
7180:
7181: strcpy(pathr,path);
7182: strcat(pathr,optionfilefiname);
1.184 brouard 7183: #ifdef WIN32
7184: _chdir(optionfilefiname); /* Move to directory named optionfile */
7185: #else
1.126 brouard 7186: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 7187: #endif
7188:
1.126 brouard 7189:
7190: /* Calculates basic frequencies. Computes observed prevalence at single age
7191: and prints on file fileres'p'. */
7192: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
7193:
7194: fprintf(fichtm,"\n");
7195: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
7196: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
7197: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
7198: imx,agemin,agemax,jmin,jmax,jmean);
7199: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7200: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7201: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7202: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7203: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
7204:
7205:
7206: /* For Powell, parameters are in a vector p[] starting at p[1]
7207: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
7208: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
7209:
7210: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 7211: /* For mortality only */
1.126 brouard 7212: if (mle==-3){
1.136 brouard 7213: ximort=matrix(1,NDIM,1,NDIM);
1.186 brouard 7214: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 7215: cens=ivector(1,n);
7216: ageexmed=vector(1,n);
7217: agecens=vector(1,n);
7218: dcwave=ivector(1,n);
7219:
7220: for (i=1; i<=imx; i++){
7221: dcwave[i]=-1;
7222: for (m=firstpass; m<=lastpass; m++)
7223: if (s[m][i]>nlstate) {
7224: dcwave[i]=m;
7225: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
7226: break;
7227: }
7228: }
7229:
7230: for (i=1; i<=imx; i++) {
7231: if (wav[i]>0){
7232: ageexmed[i]=agev[mw[1][i]][i];
7233: j=wav[i];
7234: agecens[i]=1.;
7235:
7236: if (ageexmed[i]> 1 && wav[i] > 0){
7237: agecens[i]=agev[mw[j][i]][i];
7238: cens[i]= 1;
7239: }else if (ageexmed[i]< 1)
7240: cens[i]= -1;
7241: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
7242: cens[i]=0 ;
7243: }
7244: else cens[i]=-1;
7245: }
7246:
7247: for (i=1;i<=NDIM;i++) {
7248: for (j=1;j<=NDIM;j++)
7249: ximort[i][j]=(i == j ? 1.0 : 0.0);
7250: }
7251:
1.145 brouard 7252: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 7253: /*printf("%lf %lf", p[1], p[2]);*/
7254:
7255:
1.136 brouard 7256: #ifdef GSL
7257: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 7258: #else
1.126 brouard 7259: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 7260: #endif
1.201 ! brouard 7261: strcpy(filerespow,"POW-MORT_");
! 7262: strcat(filerespow,fileresu);
1.126 brouard 7263: if((ficrespow=fopen(filerespow,"w"))==NULL) {
7264: printf("Problem with resultfile: %s\n", filerespow);
7265: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
7266: }
1.136 brouard 7267: #ifdef GSL
7268: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 7269: #else
1.126 brouard 7270: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 7271: #endif
1.126 brouard 7272: /* for (i=1;i<=nlstate;i++)
7273: for(j=1;j<=nlstate+ndeath;j++)
7274: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
7275: */
7276: fprintf(ficrespow,"\n");
1.136 brouard 7277: #ifdef GSL
7278: /* gsl starts here */
7279: T = gsl_multimin_fminimizer_nmsimplex;
7280: gsl_multimin_fminimizer *sfm = NULL;
7281: gsl_vector *ss, *x;
7282: gsl_multimin_function minex_func;
7283:
7284: /* Initial vertex size vector */
7285: ss = gsl_vector_alloc (NDIM);
7286:
7287: if (ss == NULL){
7288: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
7289: }
7290: /* Set all step sizes to 1 */
7291: gsl_vector_set_all (ss, 0.001);
7292:
7293: /* Starting point */
1.126 brouard 7294:
1.136 brouard 7295: x = gsl_vector_alloc (NDIM);
7296:
7297: if (x == NULL){
7298: gsl_vector_free(ss);
7299: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
7300: }
7301:
7302: /* Initialize method and iterate */
7303: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 7304: /* gsl_vector_set(x, 0, 0.0268); */
7305: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 7306: gsl_vector_set(x, 0, p[1]);
7307: gsl_vector_set(x, 1, p[2]);
7308:
7309: minex_func.f = &gompertz_f;
7310: minex_func.n = NDIM;
7311: minex_func.params = (void *)&p; /* ??? */
7312:
7313: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
7314: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
7315:
7316: printf("Iterations beginning .....\n\n");
7317: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
7318:
7319: iteri=0;
7320: while (rval == GSL_CONTINUE){
7321: iteri++;
7322: status = gsl_multimin_fminimizer_iterate(sfm);
7323:
7324: if (status) printf("error: %s\n", gsl_strerror (status));
7325: fflush(0);
7326:
7327: if (status)
7328: break;
7329:
7330: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
7331: ssval = gsl_multimin_fminimizer_size (sfm);
7332:
7333: if (rval == GSL_SUCCESS)
7334: printf ("converged to a local maximum at\n");
7335:
7336: printf("%5d ", iteri);
7337: for (it = 0; it < NDIM; it++){
7338: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
7339: }
7340: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
7341: }
7342:
7343: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
7344:
7345: gsl_vector_free(x); /* initial values */
7346: gsl_vector_free(ss); /* inital step size */
7347: for (it=0; it<NDIM; it++){
7348: p[it+1]=gsl_vector_get(sfm->x,it);
7349: fprintf(ficrespow," %.12lf", p[it]);
7350: }
7351: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
7352: #endif
7353: #ifdef POWELL
7354: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
7355: #endif
1.126 brouard 7356: fclose(ficrespow);
7357:
7358: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
7359:
7360: for(i=1; i <=NDIM; i++)
7361: for(j=i+1;j<=NDIM;j++)
7362: matcov[i][j]=matcov[j][i];
7363:
7364: printf("\nCovariance matrix\n ");
7365: for(i=1; i <=NDIM; i++) {
7366: for(j=1;j<=NDIM;j++){
7367: printf("%f ",matcov[i][j]);
7368: }
7369: printf("\n ");
7370: }
7371:
7372: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 brouard 7373: for (i=1;i<=NDIM;i++) {
1.126 brouard 7374: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 brouard 7375: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
7376: }
1.126 brouard 7377: lsurv=vector(1,AGESUP);
7378: lpop=vector(1,AGESUP);
7379: tpop=vector(1,AGESUP);
7380: lsurv[agegomp]=100000;
7381:
7382: for (k=agegomp;k<=AGESUP;k++) {
7383: agemortsup=k;
7384: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
7385: }
7386:
7387: for (k=agegomp;k<agemortsup;k++)
7388: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
7389:
7390: for (k=agegomp;k<agemortsup;k++){
7391: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
7392: sumlpop=sumlpop+lpop[k];
7393: }
7394:
7395: tpop[agegomp]=sumlpop;
7396: for (k=agegomp;k<(agemortsup-3);k++){
7397: /* tpop[k+1]=2;*/
7398: tpop[k+1]=tpop[k]-lpop[k];
7399: }
7400:
7401:
7402: printf("\nAge lx qx dx Lx Tx e(x)\n");
7403: for (k=agegomp;k<(agemortsup-2);k++)
7404: 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]);
7405:
7406:
7407: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 7408: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
7409: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7410: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7411: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7412: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7413: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7414: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7415: }else
1.201 ! brouard 7416: printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
! 7417: printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
1.126 brouard 7418: stepm, weightopt,\
7419: model,imx,p,matcov,agemortsup);
7420:
7421: free_vector(lsurv,1,AGESUP);
7422: free_vector(lpop,1,AGESUP);
7423: free_vector(tpop,1,AGESUP);
1.136 brouard 7424: #ifdef GSL
7425: free_ivector(cens,1,n);
7426: free_vector(agecens,1,n);
7427: free_ivector(dcwave,1,n);
7428: free_matrix(ximort,1,NDIM,1,NDIM);
7429: #endif
1.186 brouard 7430: } /* Endof if mle==-3 mortality only */
7431: /* Standard maximisation */
1.126 brouard 7432: else{ /* For mle >=1 */
1.132 brouard 7433: globpr=0;/* debug */
1.186 brouard 7434: /* Computes likelihood for initial parameters */
1.132 brouard 7435: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 7436: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7437: for (k=1; k<=npar;k++)
7438: printf(" %d %8.5f",k,p[k]);
7439: printf("\n");
1.186 brouard 7440: globpr=1; /* again, to print the contributions */
1.126 brouard 7441: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
7442: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7443: for (k=1; k<=npar;k++)
7444: printf(" %d %8.5f",k,p[k]);
7445: printf("\n");
1.186 brouard 7446: if(mle>=1){ /* Could be 1 or 2, Real Maximisation */
1.126 brouard 7447: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
7448: }
7449:
7450: /*--------- results files --------------*/
1.192 brouard 7451: 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 7452:
7453:
7454: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7455: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7456: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7457: for(i=1,jk=1; i <=nlstate; i++){
7458: for(k=1; k <=(nlstate+ndeath); k++){
7459: if (k != i) {
7460: printf("%d%d ",i,k);
7461: fprintf(ficlog,"%d%d ",i,k);
7462: fprintf(ficres,"%1d%1d ",i,k);
7463: for(j=1; j <=ncovmodel; j++){
1.190 brouard 7464: printf("%12.7f ",p[jk]);
7465: fprintf(ficlog,"%12.7f ",p[jk]);
7466: fprintf(ficres,"%12.7f ",p[jk]);
1.126 brouard 7467: jk++;
7468: }
7469: printf("\n");
7470: fprintf(ficlog,"\n");
7471: fprintf(ficres,"\n");
7472: }
7473: }
7474: }
7475: if(mle!=0){
7476: /* Computing hessian and covariance matrix */
7477: ftolhess=ftol; /* Usually correct */
7478: hesscov(matcov, p, npar, delti, ftolhess, func);
7479: }
1.197 brouard 7480: 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");
7481: 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 7482: for(i=1,jk=1; i <=nlstate; i++){
7483: for(k=1; k <=(nlstate+ndeath); k++){
7484: if (k != i) {
7485: printf("%d%d ",i,k);
7486: fprintf(ficlog,"%d%d ",i,k);
7487: for(j=1; j <=ncovmodel; j++){
1.197 brouard 7488: 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]));
7489: 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 7490: jk++;
7491: }
7492: printf("\n");
7493: fprintf(ficlog,"\n");
7494: }
7495: }
7496: }
7497:
1.126 brouard 7498: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
7499: printf("# Scales (for hessian or gradient estimation)\n");
7500: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
7501: for(i=1,jk=1; i <=nlstate; i++){
7502: for(j=1; j <=nlstate+ndeath; j++){
7503: if (j!=i) {
7504: fprintf(ficres,"%1d%1d",i,j);
7505: printf("%1d%1d",i,j);
7506: fprintf(ficlog,"%1d%1d",i,j);
7507: for(k=1; k<=ncovmodel;k++){
7508: printf(" %.5e",delti[jk]);
7509: fprintf(ficlog," %.5e",delti[jk]);
7510: fprintf(ficres," %.5e",delti[jk]);
7511: jk++;
7512: }
7513: printf("\n");
7514: fprintf(ficlog,"\n");
7515: fprintf(ficres,"\n");
7516: }
7517: }
7518: }
7519:
7520: 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");
7521: if(mle>=1)
7522: 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");
7523: 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");
7524: /* # 121 Var(a12)\n\ */
7525: /* # 122 Cov(b12,a12) Var(b12)\n\ */
7526: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
7527: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
7528: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
7529: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
7530: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
7531: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
7532:
7533:
7534: /* Just to have a covariance matrix which will be more understandable
7535: even is we still don't want to manage dictionary of variables
7536: */
7537: for(itimes=1;itimes<=2;itimes++){
7538: jj=0;
7539: for(i=1; i <=nlstate; i++){
7540: for(j=1; j <=nlstate+ndeath; j++){
7541: if(j==i) continue;
7542: for(k=1; k<=ncovmodel;k++){
7543: jj++;
7544: ca[0]= k+'a'-1;ca[1]='\0';
7545: if(itimes==1){
7546: if(mle>=1)
7547: printf("#%1d%1d%d",i,j,k);
7548: fprintf(ficlog,"#%1d%1d%d",i,j,k);
7549: fprintf(ficres,"#%1d%1d%d",i,j,k);
7550: }else{
7551: if(mle>=1)
7552: printf("%1d%1d%d",i,j,k);
7553: fprintf(ficlog,"%1d%1d%d",i,j,k);
7554: fprintf(ficres,"%1d%1d%d",i,j,k);
7555: }
7556: ll=0;
7557: for(li=1;li <=nlstate; li++){
7558: for(lj=1;lj <=nlstate+ndeath; lj++){
7559: if(lj==li) continue;
7560: for(lk=1;lk<=ncovmodel;lk++){
7561: ll++;
7562: if(ll<=jj){
7563: cb[0]= lk +'a'-1;cb[1]='\0';
7564: if(ll<jj){
7565: if(itimes==1){
7566: if(mle>=1)
7567: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7568: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7569: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7570: }else{
7571: if(mle>=1)
7572: printf(" %.5e",matcov[jj][ll]);
7573: fprintf(ficlog," %.5e",matcov[jj][ll]);
7574: fprintf(ficres," %.5e",matcov[jj][ll]);
7575: }
7576: }else{
7577: if(itimes==1){
7578: if(mle>=1)
7579: printf(" Var(%s%1d%1d)",ca,i,j);
7580: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
7581: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
7582: }else{
7583: if(mle>=1)
7584: printf(" %.5e",matcov[jj][ll]);
7585: fprintf(ficlog," %.5e",matcov[jj][ll]);
7586: fprintf(ficres," %.5e",matcov[jj][ll]);
7587: }
7588: }
7589: }
7590: } /* end lk */
7591: } /* end lj */
7592: } /* end li */
7593: if(mle>=1)
7594: printf("\n");
7595: fprintf(ficlog,"\n");
7596: fprintf(ficres,"\n");
7597: numlinepar++;
7598: } /* end k*/
7599: } /*end j */
7600: } /* end i */
7601: } /* end itimes */
7602:
7603: fflush(ficlog);
7604: fflush(ficres);
7605:
7606: while((c=getc(ficpar))=='#' && c!= EOF){
7607: ungetc(c,ficpar);
7608: fgets(line, MAXLINE, ficpar);
1.141 brouard 7609: fputs(line,stdout);
1.126 brouard 7610: fputs(line,ficparo);
7611: }
7612: ungetc(c,ficpar);
7613:
7614: estepm=0;
7615: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
7616: if (estepm==0 || estepm < stepm) estepm=stepm;
7617: if (fage <= 2) {
7618: bage = ageminpar;
7619: fage = agemaxpar;
7620: }
7621:
7622: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
7623: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
7624: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
1.186 brouard 7625:
7626: /* Other stuffs, more or less useful */
1.126 brouard 7627: while((c=getc(ficpar))=='#' && c!= EOF){
7628: ungetc(c,ficpar);
7629: fgets(line, MAXLINE, ficpar);
1.141 brouard 7630: fputs(line,stdout);
1.126 brouard 7631: fputs(line,ficparo);
7632: }
7633: ungetc(c,ficpar);
7634:
7635: 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);
7636: 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);
7637: 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);
7638: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
7639: 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);
7640:
7641: while((c=getc(ficpar))=='#' && c!= EOF){
7642: ungetc(c,ficpar);
7643: fgets(line, MAXLINE, ficpar);
1.141 brouard 7644: fputs(line,stdout);
1.126 brouard 7645: fputs(line,ficparo);
7646: }
7647: ungetc(c,ficpar);
7648:
7649:
7650: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
7651: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
7652:
7653: fscanf(ficpar,"pop_based=%d\n",&popbased);
1.193 brouard 7654: fprintf(ficlog,"pop_based=%d\n",popbased);
1.126 brouard 7655: fprintf(ficparo,"pop_based=%d\n",popbased);
7656: fprintf(ficres,"pop_based=%d\n",popbased);
7657:
7658: while((c=getc(ficpar))=='#' && c!= EOF){
7659: ungetc(c,ficpar);
7660: fgets(line, MAXLINE, ficpar);
1.141 brouard 7661: fputs(line,stdout);
1.126 brouard 7662: fputs(line,ficparo);
7663: }
7664: ungetc(c,ficpar);
7665:
7666: 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);
7667: 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);
7668: 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);
7669: 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);
7670: 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);
7671: /* day and month of proj2 are not used but only year anproj2.*/
7672:
7673:
7674:
1.145 brouard 7675: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
7676: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 7677:
7678: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 7679: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
7680: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7681: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7682: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7683: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7684: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7685: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7686: }else
1.201 ! brouard 7687: printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.126 brouard 7688:
1.201 ! brouard 7689: printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt,\
1.126 brouard 7690: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
7691: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
7692:
7693: /*------------ free_vector -------------*/
7694: /* chdir(path); */
7695:
7696: free_ivector(wav,1,imx);
7697: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
7698: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
7699: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
7700: free_lvector(num,1,n);
7701: free_vector(agedc,1,n);
7702: /*free_matrix(covar,0,NCOVMAX,1,n);*/
7703: /*free_matrix(covar,1,NCOVMAX,1,n);*/
7704: fclose(ficparo);
7705: fclose(ficres);
7706:
7707:
1.186 brouard 7708: /* Other results (useful)*/
7709:
7710:
1.126 brouard 7711: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 7712: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
7713: prlim=matrix(1,nlstate,1,nlstate);
7714: prevalence_limit(p, prlim, ageminpar, agemaxpar);
1.126 brouard 7715: fclose(ficrespl);
7716:
1.145 brouard 7717: #ifdef FREEEXIT2
7718: #include "freeexit2.h"
7719: #endif
7720:
1.126 brouard 7721: /*------------- h Pij x at various ages ------------*/
1.180 brouard 7722: /*#include "hpijx.h"*/
7723: hPijx(p, bage, fage);
1.145 brouard 7724: fclose(ficrespij);
1.126 brouard 7725:
1.145 brouard 7726: /*-------------- Variance of one-step probabilities---*/
7727: k=1;
1.126 brouard 7728: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
7729:
7730:
7731: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7732: for(i=1;i<=AGESUP;i++)
7733: for(j=1;j<=NCOVMAX;j++)
7734: for(k=1;k<=NCOVMAX;k++)
7735: probs[i][j][k]=0.;
7736:
7737: /*---------- Forecasting ------------------*/
7738: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
7739: if(prevfcast==1){
7740: /* if(stepm ==1){*/
1.201 ! brouard 7741: prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.126 brouard 7742: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
7743: /* } */
7744: /* else{ */
7745: /* erreur=108; */
7746: /* 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); */
7747: /* 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); */
7748: /* } */
7749: }
1.186 brouard 7750:
7751: /* ------ Other prevalence ratios------------ */
1.126 brouard 7752:
1.127 brouard 7753: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
7754:
7755: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
7756: /* 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",\
7757: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
7758: */
1.126 brouard 7759:
1.127 brouard 7760: if (mobilav!=0) {
7761: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7762: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
7763: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
7764: printf(" Error in movingaverage mobilav=%d\n",mobilav);
7765: }
1.126 brouard 7766: }
7767:
7768:
1.127 brouard 7769: /*---------- Health expectancies, no variances ------------*/
7770:
1.201 ! brouard 7771: strcpy(filerese,"E_");
! 7772: strcat(filerese,fileresu);
1.126 brouard 7773: if((ficreseij=fopen(filerese,"w"))==NULL) {
7774: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
7775: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
7776: }
7777: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
7778: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.145 brouard 7779: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7780: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7781:
7782: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.127 brouard 7783: fprintf(ficreseij,"\n#****** ");
7784: for(j=1;j<=cptcoveff;j++) {
1.200 brouard 7785: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.127 brouard 7786: }
7787: fprintf(ficreseij,"******\n");
7788:
7789: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7790: oldm=oldms;savm=savms;
7791: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
7792:
7793: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.145 brouard 7794: /*}*/
1.127 brouard 7795: }
7796: fclose(ficreseij);
7797:
7798:
7799: /*---------- Health expectancies and variances ------------*/
7800:
7801:
1.201 ! brouard 7802: strcpy(filerest,"T_");
! 7803: strcat(filerest,fileresu);
1.127 brouard 7804: if((ficrest=fopen(filerest,"w"))==NULL) {
7805: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
7806: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
7807: }
7808: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
7809: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
7810:
1.126 brouard 7811:
1.201 ! brouard 7812: strcpy(fileresstde,"STDE_");
! 7813: strcat(fileresstde,fileresu);
1.126 brouard 7814: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
7815: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
7816: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
7817: }
7818: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
7819: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
7820:
1.201 ! brouard 7821: strcpy(filerescve,"CVE_");
! 7822: strcat(filerescve,fileresu);
1.126 brouard 7823: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
7824: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
7825: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
7826: }
7827: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
7828: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
7829:
1.201 ! brouard 7830: strcpy(fileresv,"V_");
! 7831: strcat(fileresv,fileresu);
1.126 brouard 7832: if((ficresvij=fopen(fileresv,"w"))==NULL) {
7833: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
7834: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
7835: }
7836: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
7837: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
7838:
1.145 brouard 7839: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7840: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7841:
7842: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7843: fprintf(ficrest,"\n#****** ");
1.126 brouard 7844: for(j=1;j<=cptcoveff;j++)
1.200 brouard 7845: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 7846: fprintf(ficrest,"******\n");
7847:
7848: fprintf(ficresstdeij,"\n#****** ");
7849: fprintf(ficrescveij,"\n#****** ");
7850: for(j=1;j<=cptcoveff;j++) {
1.200 brouard 7851: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
7852: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 7853: }
7854: fprintf(ficresstdeij,"******\n");
7855: fprintf(ficrescveij,"******\n");
7856:
7857: fprintf(ficresvij,"\n#****** ");
7858: for(j=1;j<=cptcoveff;j++)
1.200 brouard 7859: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 7860: fprintf(ficresvij,"******\n");
7861:
7862: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7863: oldm=oldms;savm=savms;
1.127 brouard 7864: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
1.145 brouard 7865: /*
7866: */
7867: /* goto endfree; */
1.126 brouard 7868:
7869: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7870: pstamp(ficrest);
1.145 brouard 7871:
7872:
1.128 brouard 7873: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.199 brouard 7874: oldm=oldms;savm=savms; /* ZZ Segmentation fault */
1.161 brouard 7875: cptcod= 0; /* To be deleted */
7876: 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 7877: 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 7878: if(vpopbased==1)
7879: 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);
7880: else
7881: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
1.201 ! brouard 7882: fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
1.128 brouard 7883: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
7884: fprintf(ficrest,"\n");
1.199 brouard 7885: /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
1.128 brouard 7886: epj=vector(1,nlstate+1);
7887: for(age=bage; age <=fage ;age++){
1.199 brouard 7888: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k); /*ZZ Is it the correct prevalim */
1.128 brouard 7889: if (vpopbased==1) {
7890: if(mobilav ==0){
7891: for(i=1; i<=nlstate;i++)
7892: prlim[i][i]=probs[(int)age][i][k];
7893: }else{ /* mobilav */
7894: for(i=1; i<=nlstate;i++)
7895: prlim[i][i]=mobaverage[(int)age][i][k];
7896: }
1.126 brouard 7897: }
7898:
1.201 ! brouard 7899: fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
1.199 brouard 7900: /* printf(" age %4.0f ",age); */
1.128 brouard 7901: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
7902: for(i=1, epj[j]=0.;i <=nlstate;i++) {
7903: epj[j] += prlim[i][i]*eij[i][j][(int)age];
1.199 brouard 7904: /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
7905: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
1.128 brouard 7906: }
7907: epj[nlstate+1] +=epj[j];
1.126 brouard 7908: }
1.199 brouard 7909: /* printf(" age %4.0f \n",age); */
1.126 brouard 7910:
1.128 brouard 7911: for(i=1, vepp=0.;i <=nlstate;i++)
7912: for(j=1;j <=nlstate;j++)
7913: vepp += vareij[i][j][(int)age];
7914: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
7915: for(j=1;j <=nlstate;j++){
7916: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
7917: }
7918: fprintf(ficrest,"\n");
1.126 brouard 7919: }
7920: }
7921: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
7922: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
7923: free_vector(epj,1,nlstate+1);
1.145 brouard 7924: /*}*/
1.126 brouard 7925: }
7926: free_vector(weight,1,n);
1.145 brouard 7927: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.126 brouard 7928: free_imatrix(s,1,maxwav+1,1,n);
7929: free_matrix(anint,1,maxwav,1,n);
7930: free_matrix(mint,1,maxwav,1,n);
7931: free_ivector(cod,1,n);
7932: free_ivector(tab,1,NCOVMAX);
7933: fclose(ficresstdeij);
7934: fclose(ficrescveij);
7935: fclose(ficresvij);
7936: fclose(ficrest);
7937: fclose(ficpar);
7938:
7939: /*------- Variance of period (stable) prevalence------*/
7940:
1.201 ! brouard 7941: strcpy(fileresvpl,"VPL_");
! 7942: strcat(fileresvpl,fileresu);
1.126 brouard 7943: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
7944: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
7945: exit(0);
7946: }
7947: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
7948:
1.145 brouard 7949: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7950: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7951:
7952: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7953: fprintf(ficresvpl,"\n#****** ");
1.126 brouard 7954: for(j=1;j<=cptcoveff;j++)
1.200 brouard 7955: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 7956: fprintf(ficresvpl,"******\n");
7957:
7958: varpl=matrix(1,nlstate,(int) bage, (int) fage);
7959: oldm=oldms;savm=savms;
7960: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
7961: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 7962: /*}*/
1.126 brouard 7963: }
7964:
7965: fclose(ficresvpl);
7966:
7967: /*---------- End : free ----------------*/
7968: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7969: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7970: } /* mle==-3 arrives here for freeing */
1.164 brouard 7971: /* endfree:*/
1.141 brouard 7972: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.126 brouard 7973: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
7974: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
7975: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
7976: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
7977: free_matrix(covar,0,NCOVMAX,1,n);
7978: free_matrix(matcov,1,npar,1,npar);
7979: /*free_vector(delti,1,npar);*/
7980: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7981: free_matrix(agev,1,maxwav,1,imx);
7982: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7983:
1.145 brouard 7984: free_ivector(ncodemax,1,NCOVMAX);
1.192 brouard 7985: free_ivector(ncodemaxwundef,1,NCOVMAX);
1.145 brouard 7986: free_ivector(Tvar,1,NCOVMAX);
7987: free_ivector(Tprod,1,NCOVMAX);
7988: free_ivector(Tvaraff,1,NCOVMAX);
7989: free_ivector(Tage,1,NCOVMAX);
1.126 brouard 7990:
7991: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
1.200 brouard 7992: /* free_imatrix(codtab,1,100,1,10); */
1.126 brouard 7993: fflush(fichtm);
7994: fflush(ficgp);
7995:
7996:
7997: if((nberr >0) || (nbwarn>0)){
7998: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
7999: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
8000: }else{
8001: printf("End of Imach\n");
8002: fprintf(ficlog,"End of Imach\n");
8003: }
8004: printf("See log file on %s\n",filelog);
8005: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 8006: /*(void) gettimeofday(&end_time,&tzp);*/
8007: rend_time = time(NULL);
8008: end_time = *localtime(&rend_time);
8009: /* tml = *localtime(&end_time.tm_sec); */
8010: strcpy(strtend,asctime(&end_time));
1.126 brouard 8011: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
8012: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 8013: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.126 brouard 8014:
1.157 brouard 8015: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
8016: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
8017: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 8018: /* printf("Total time was %d uSec.\n", total_usecs);*/
8019: /* if(fileappend(fichtm,optionfilehtm)){ */
8020: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
8021: fclose(fichtm);
8022: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
8023: fclose(fichtmcov);
8024: fclose(ficgp);
8025: fclose(ficlog);
8026: /*------ End -----------*/
8027:
8028:
8029: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 8030: #ifdef WIN32
8031: if (_chdir(pathcd) != 0)
8032: printf("Can't move to directory %s!\n",path);
8033: if(_getcwd(pathcd,MAXLINE) > 0)
8034: #else
1.126 brouard 8035: if(chdir(pathcd) != 0)
1.184 brouard 8036: printf("Can't move to directory %s!\n", path);
8037: if (getcwd(pathcd, MAXLINE) > 0)
8038: #endif
1.126 brouard 8039: printf("Current directory %s!\n",pathcd);
8040: /*strcat(plotcmd,CHARSEPARATOR);*/
8041: sprintf(plotcmd,"gnuplot");
1.157 brouard 8042: #ifdef _WIN32
1.126 brouard 8043: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
8044: #endif
8045: if(!stat(plotcmd,&info)){
1.158 brouard 8046: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 8047: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 8048: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 8049: }else
8050: strcpy(pplotcmd,plotcmd);
1.157 brouard 8051: #ifdef __unix
1.126 brouard 8052: strcpy(plotcmd,GNUPLOTPROGRAM);
8053: if(!stat(plotcmd,&info)){
1.158 brouard 8054: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 8055: }else
8056: strcpy(pplotcmd,plotcmd);
8057: #endif
8058: }else
8059: strcpy(pplotcmd,plotcmd);
8060:
8061: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 8062: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 8063:
8064: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 8065: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 8066: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 8067: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 8068: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 8069: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 8070: }
1.158 brouard 8071: printf(" Successful, please wait...");
1.126 brouard 8072: while (z[0] != 'q') {
8073: /* chdir(path); */
1.154 brouard 8074: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 8075: scanf("%s",z);
8076: /* if (z[0] == 'c') system("./imach"); */
8077: if (z[0] == 'e') {
1.158 brouard 8078: #ifdef __APPLE__
1.152 brouard 8079: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 8080: #elif __linux
8081: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 8082: #else
1.152 brouard 8083: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 8084: #endif
8085: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
8086: system(pplotcmd);
1.126 brouard 8087: }
8088: else if (z[0] == 'g') system(plotcmd);
8089: else if (z[0] == 'q') exit(0);
8090: }
8091: end:
8092: while (z[0] != 'q') {
1.195 brouard 8093: printf("\nType q for exiting: "); fflush(stdout);
1.126 brouard 8094: scanf("%s",z);
8095: }
8096: }
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