1: /* $Id: imach.c,v 1.185 2015/03/11 13:26:42 brouard Exp $
2: $State: Exp $
3: $Log: imach.c,v $
4: Revision 1.185 2015/03/11 13:26:42 brouard
5: Summary: Inclusion of compile and links command line for Intel Compiler
6:
7: Revision 1.184 2015/03/11 11:52:39 brouard
8: Summary: Back from Windows 8. Intel Compiler
9:
10: Revision 1.183 2015/03/10 20:34:32 brouard
11: Summary: 0.98q0, trying with directest, mnbrak fixed
12:
13: We use directest instead of original Powell test; probably no
14: incidence on the results, but better justifications;
15: We fixed Numerical Recipes mnbrak routine which was wrong and gave
16: wrong results.
17:
18: Revision 1.182 2015/02/12 08:19:57 brouard
19: Summary: Trying to keep directest which seems simpler and more general
20: Author: Nicolas Brouard
21:
22: Revision 1.181 2015/02/11 23:22:24 brouard
23: Summary: Comments on Powell added
24:
25: Author:
26:
27: Revision 1.180 2015/02/11 17:33:45 brouard
28: Summary: Finishing move from main to function (hpijx and prevalence_limit)
29:
30: Revision 1.179 2015/01/04 09:57:06 brouard
31: Summary: back to OS/X
32:
33: Revision 1.178 2015/01/04 09:35:48 brouard
34: *** empty log message ***
35:
36: Revision 1.177 2015/01/03 18:40:56 brouard
37: Summary: Still testing ilc32 on OSX
38:
39: Revision 1.176 2015/01/03 16:45:04 brouard
40: *** empty log message ***
41:
42: Revision 1.175 2015/01/03 16:33:42 brouard
43: *** empty log message ***
44:
45: Revision 1.174 2015/01/03 16:15:49 brouard
46: Summary: Still in cross-compilation
47:
48: Revision 1.173 2015/01/03 12:06:26 brouard
49: Summary: trying to detect cross-compilation
50:
51: Revision 1.172 2014/12/27 12:07:47 brouard
52: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
53:
54: Revision 1.171 2014/12/23 13:26:59 brouard
55: Summary: Back from Visual C
56:
57: Still problem with utsname.h on Windows
58:
59: Revision 1.170 2014/12/23 11:17:12 brouard
60: Summary: Cleaning some \%% back to %%
61:
62: The escape was mandatory for a specific compiler (which one?), but too many warnings.
63:
64: Revision 1.169 2014/12/22 23:08:31 brouard
65: Summary: 0.98p
66:
67: Outputs some informations on compiler used, OS etc. Testing on different platforms.
68:
69: Revision 1.168 2014/12/22 15:17:42 brouard
70: Summary: update
71:
72: Revision 1.167 2014/12/22 13:50:56 brouard
73: Summary: Testing uname and compiler version and if compiled 32 or 64
74:
75: Testing on Linux 64
76:
77: Revision 1.166 2014/12/22 11:40:47 brouard
78: *** empty log message ***
79:
80: Revision 1.165 2014/12/16 11:20:36 brouard
81: Summary: After compiling on Visual C
82:
83: * imach.c (Module): Merging 1.61 to 1.162
84:
85: Revision 1.164 2014/12/16 10:52:11 brouard
86: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
87:
88: * imach.c (Module): Merging 1.61 to 1.162
89:
90: Revision 1.163 2014/12/16 10:30:11 brouard
91: * imach.c (Module): Merging 1.61 to 1.162
92:
93: Revision 1.162 2014/09/25 11:43:39 brouard
94: Summary: temporary backup 0.99!
95:
96: Revision 1.1 2014/09/16 11:06:58 brouard
97: Summary: With some code (wrong) for nlopt
98:
99: Author:
100:
101: Revision 1.161 2014/09/15 20:41:41 brouard
102: Summary: Problem with macro SQR on Intel compiler
103:
104: Revision 1.160 2014/09/02 09:24:05 brouard
105: *** empty log message ***
106:
107: Revision 1.159 2014/09/01 10:34:10 brouard
108: Summary: WIN32
109: Author: Brouard
110:
111: Revision 1.158 2014/08/27 17:11:51 brouard
112: *** empty log message ***
113:
114: Revision 1.157 2014/08/27 16:26:55 brouard
115: Summary: Preparing windows Visual studio version
116: Author: Brouard
117:
118: In order to compile on Visual studio, time.h is now correct and time_t
119: and tm struct should be used. difftime should be used but sometimes I
120: just make the differences in raw time format (time(&now).
121: Trying to suppress #ifdef LINUX
122: Add xdg-open for __linux in order to open default browser.
123:
124: Revision 1.156 2014/08/25 20:10:10 brouard
125: *** empty log message ***
126:
127: Revision 1.155 2014/08/25 18:32:34 brouard
128: Summary: New compile, minor changes
129: Author: Brouard
130:
131: Revision 1.154 2014/06/20 17:32:08 brouard
132: Summary: Outputs now all graphs of convergence to period prevalence
133:
134: Revision 1.153 2014/06/20 16:45:46 brouard
135: Summary: If 3 live state, convergence to period prevalence on same graph
136: Author: Brouard
137:
138: Revision 1.152 2014/06/18 17:54:09 brouard
139: Summary: open browser, use gnuplot on same dir than imach if not found in the path
140:
141: Revision 1.151 2014/06/18 16:43:30 brouard
142: *** empty log message ***
143:
144: Revision 1.150 2014/06/18 16:42:35 brouard
145: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
146: Author: brouard
147:
148: Revision 1.149 2014/06/18 15:51:14 brouard
149: Summary: Some fixes in parameter files errors
150: Author: Nicolas Brouard
151:
152: Revision 1.148 2014/06/17 17:38:48 brouard
153: Summary: Nothing new
154: Author: Brouard
155:
156: Just a new packaging for OS/X version 0.98nS
157:
158: Revision 1.147 2014/06/16 10:33:11 brouard
159: *** empty log message ***
160:
161: Revision 1.146 2014/06/16 10:20:28 brouard
162: Summary: Merge
163: Author: Brouard
164:
165: Merge, before building revised version.
166:
167: Revision 1.145 2014/06/10 21:23:15 brouard
168: Summary: Debugging with valgrind
169: Author: Nicolas Brouard
170:
171: Lot of changes in order to output the results with some covariates
172: After the Edimburgh REVES conference 2014, it seems mandatory to
173: improve the code.
174: No more memory valgrind error but a lot has to be done in order to
175: continue the work of splitting the code into subroutines.
176: Also, decodemodel has been improved. Tricode is still not
177: optimal. nbcode should be improved. Documentation has been added in
178: the source code.
179:
180: Revision 1.143 2014/01/26 09:45:38 brouard
181: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
182:
183: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
184: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
185:
186: Revision 1.142 2014/01/26 03:57:36 brouard
187: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
188:
189: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
190:
191: Revision 1.141 2014/01/26 02:42:01 brouard
192: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
193:
194: Revision 1.140 2011/09/02 10:37:54 brouard
195: Summary: times.h is ok with mingw32 now.
196:
197: Revision 1.139 2010/06/14 07:50:17 brouard
198: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
199: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
200:
201: Revision 1.138 2010/04/30 18:19:40 brouard
202: *** empty log message ***
203:
204: Revision 1.137 2010/04/29 18:11:38 brouard
205: (Module): Checking covariates for more complex models
206: than V1+V2. A lot of change to be done. Unstable.
207:
208: Revision 1.136 2010/04/26 20:30:53 brouard
209: (Module): merging some libgsl code. Fixing computation
210: of likelione (using inter/intrapolation if mle = 0) in order to
211: get same likelihood as if mle=1.
212: Some cleaning of code and comments added.
213:
214: Revision 1.135 2009/10/29 15:33:14 brouard
215: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
216:
217: Revision 1.134 2009/10/29 13:18:53 brouard
218: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
219:
220: Revision 1.133 2009/07/06 10:21:25 brouard
221: just nforces
222:
223: Revision 1.132 2009/07/06 08:22:05 brouard
224: Many tings
225:
226: Revision 1.131 2009/06/20 16:22:47 brouard
227: Some dimensions resccaled
228:
229: Revision 1.130 2009/05/26 06:44:34 brouard
230: (Module): Max Covariate is now set to 20 instead of 8. A
231: lot of cleaning with variables initialized to 0. Trying to make
232: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
233:
234: Revision 1.129 2007/08/31 13:49:27 lievre
235: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
236:
237: Revision 1.128 2006/06/30 13:02:05 brouard
238: (Module): Clarifications on computing e.j
239:
240: Revision 1.127 2006/04/28 18:11:50 brouard
241: (Module): Yes the sum of survivors was wrong since
242: imach-114 because nhstepm was no more computed in the age
243: loop. Now we define nhstepma in the age loop.
244: (Module): In order to speed up (in case of numerous covariates) we
245: compute health expectancies (without variances) in a first step
246: and then all the health expectancies with variances or standard
247: deviation (needs data from the Hessian matrices) which slows the
248: computation.
249: In the future we should be able to stop the program is only health
250: expectancies and graph are needed without standard deviations.
251:
252: Revision 1.126 2006/04/28 17:23:28 brouard
253: (Module): Yes the sum of survivors was wrong since
254: imach-114 because nhstepm was no more computed in the age
255: loop. Now we define nhstepma in the age loop.
256: Version 0.98h
257:
258: Revision 1.125 2006/04/04 15:20:31 lievre
259: Errors in calculation of health expectancies. Age was not initialized.
260: Forecasting file added.
261:
262: Revision 1.124 2006/03/22 17:13:53 lievre
263: Parameters are printed with %lf instead of %f (more numbers after the comma).
264: The log-likelihood is printed in the log file
265:
266: Revision 1.123 2006/03/20 10:52:43 brouard
267: * imach.c (Module): <title> changed, corresponds to .htm file
268: name. <head> headers where missing.
269:
270: * imach.c (Module): Weights can have a decimal point as for
271: English (a comma might work with a correct LC_NUMERIC environment,
272: otherwise the weight is truncated).
273: Modification of warning when the covariates values are not 0 or
274: 1.
275: Version 0.98g
276:
277: Revision 1.122 2006/03/20 09:45:41 brouard
278: (Module): Weights can have a decimal point as for
279: English (a comma might work with a correct LC_NUMERIC environment,
280: otherwise the weight is truncated).
281: Modification of warning when the covariates values are not 0 or
282: 1.
283: Version 0.98g
284:
285: Revision 1.121 2006/03/16 17:45:01 lievre
286: * imach.c (Module): Comments concerning covariates added
287:
288: * imach.c (Module): refinements in the computation of lli if
289: status=-2 in order to have more reliable computation if stepm is
290: not 1 month. Version 0.98f
291:
292: Revision 1.120 2006/03/16 15:10:38 lievre
293: (Module): refinements in the computation of lli if
294: status=-2 in order to have more reliable computation if stepm is
295: not 1 month. Version 0.98f
296:
297: Revision 1.119 2006/03/15 17:42:26 brouard
298: (Module): Bug if status = -2, the loglikelihood was
299: computed as likelihood omitting the logarithm. Version O.98e
300:
301: Revision 1.118 2006/03/14 18:20:07 brouard
302: (Module): varevsij Comments added explaining the second
303: table of variances if popbased=1 .
304: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
305: (Module): Function pstamp added
306: (Module): Version 0.98d
307:
308: Revision 1.117 2006/03/14 17:16:22 brouard
309: (Module): varevsij Comments added explaining the second
310: table of variances if popbased=1 .
311: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
312: (Module): Function pstamp added
313: (Module): Version 0.98d
314:
315: Revision 1.116 2006/03/06 10:29:27 brouard
316: (Module): Variance-covariance wrong links and
317: varian-covariance of ej. is needed (Saito).
318:
319: Revision 1.115 2006/02/27 12:17:45 brouard
320: (Module): One freematrix added in mlikeli! 0.98c
321:
322: Revision 1.114 2006/02/26 12:57:58 brouard
323: (Module): Some improvements in processing parameter
324: filename with strsep.
325:
326: Revision 1.113 2006/02/24 14:20:24 brouard
327: (Module): Memory leaks checks with valgrind and:
328: datafile was not closed, some imatrix were not freed and on matrix
329: allocation too.
330:
331: Revision 1.112 2006/01/30 09:55:26 brouard
332: (Module): Back to gnuplot.exe instead of wgnuplot.exe
333:
334: Revision 1.111 2006/01/25 20:38:18 brouard
335: (Module): Lots of cleaning and bugs added (Gompertz)
336: (Module): Comments can be added in data file. Missing date values
337: can be a simple dot '.'.
338:
339: Revision 1.110 2006/01/25 00:51:50 brouard
340: (Module): Lots of cleaning and bugs added (Gompertz)
341:
342: Revision 1.109 2006/01/24 19:37:15 brouard
343: (Module): Comments (lines starting with a #) are allowed in data.
344:
345: Revision 1.108 2006/01/19 18:05:42 lievre
346: Gnuplot problem appeared...
347: To be fixed
348:
349: Revision 1.107 2006/01/19 16:20:37 brouard
350: Test existence of gnuplot in imach path
351:
352: Revision 1.106 2006/01/19 13:24:36 brouard
353: Some cleaning and links added in html output
354:
355: Revision 1.105 2006/01/05 20:23:19 lievre
356: *** empty log message ***
357:
358: Revision 1.104 2005/09/30 16:11:43 lievre
359: (Module): sump fixed, loop imx fixed, and simplifications.
360: (Module): If the status is missing at the last wave but we know
361: that the person is alive, then we can code his/her status as -2
362: (instead of missing=-1 in earlier versions) and his/her
363: contributions to the likelihood is 1 - Prob of dying from last
364: health status (= 1-p13= p11+p12 in the easiest case of somebody in
365: the healthy state at last known wave). Version is 0.98
366:
367: Revision 1.103 2005/09/30 15:54:49 lievre
368: (Module): sump fixed, loop imx fixed, and simplifications.
369:
370: Revision 1.102 2004/09/15 17:31:30 brouard
371: Add the possibility to read data file including tab characters.
372:
373: Revision 1.101 2004/09/15 10:38:38 brouard
374: Fix on curr_time
375:
376: Revision 1.100 2004/07/12 18:29:06 brouard
377: Add version for Mac OS X. Just define UNIX in Makefile
378:
379: Revision 1.99 2004/06/05 08:57:40 brouard
380: *** empty log message ***
381:
382: Revision 1.98 2004/05/16 15:05:56 brouard
383: New version 0.97 . First attempt to estimate force of mortality
384: directly from the data i.e. without the need of knowing the health
385: state at each age, but using a Gompertz model: log u =a + b*age .
386: This is the basic analysis of mortality and should be done before any
387: other analysis, in order to test if the mortality estimated from the
388: cross-longitudinal survey is different from the mortality estimated
389: from other sources like vital statistic data.
390:
391: The same imach parameter file can be used but the option for mle should be -3.
392:
393: Agnès, who wrote this part of the code, tried to keep most of the
394: former routines in order to include the new code within the former code.
395:
396: The output is very simple: only an estimate of the intercept and of
397: the slope with 95% confident intervals.
398:
399: Current limitations:
400: A) Even if you enter covariates, i.e. with the
401: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
402: B) There is no computation of Life Expectancy nor Life Table.
403:
404: Revision 1.97 2004/02/20 13:25:42 lievre
405: Version 0.96d. Population forecasting command line is (temporarily)
406: suppressed.
407:
408: Revision 1.96 2003/07/15 15:38:55 brouard
409: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
410: rewritten within the same printf. Workaround: many printfs.
411:
412: Revision 1.95 2003/07/08 07:54:34 brouard
413: * imach.c (Repository):
414: (Repository): Using imachwizard code to output a more meaningful covariance
415: matrix (cov(a12,c31) instead of numbers.
416:
417: Revision 1.94 2003/06/27 13:00:02 brouard
418: Just cleaning
419:
420: Revision 1.93 2003/06/25 16:33:55 brouard
421: (Module): On windows (cygwin) function asctime_r doesn't
422: exist so I changed back to asctime which exists.
423: (Module): Version 0.96b
424:
425: Revision 1.92 2003/06/25 16:30:45 brouard
426: (Module): On windows (cygwin) function asctime_r doesn't
427: exist so I changed back to asctime which exists.
428:
429: Revision 1.91 2003/06/25 15:30:29 brouard
430: * imach.c (Repository): Duplicated warning errors corrected.
431: (Repository): Elapsed time after each iteration is now output. It
432: helps to forecast when convergence will be reached. Elapsed time
433: is stamped in powell. We created a new html file for the graphs
434: concerning matrix of covariance. It has extension -cov.htm.
435:
436: Revision 1.90 2003/06/24 12:34:15 brouard
437: (Module): Some bugs corrected for windows. Also, when
438: mle=-1 a template is output in file "or"mypar.txt with the design
439: of the covariance matrix to be input.
440:
441: Revision 1.89 2003/06/24 12:30:52 brouard
442: (Module): Some bugs corrected for windows. Also, when
443: mle=-1 a template is output in file "or"mypar.txt with the design
444: of the covariance matrix to be input.
445:
446: Revision 1.88 2003/06/23 17:54:56 brouard
447: * 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.
448:
449: Revision 1.87 2003/06/18 12:26:01 brouard
450: Version 0.96
451:
452: Revision 1.86 2003/06/17 20:04:08 brouard
453: (Module): Change position of html and gnuplot routines and added
454: routine fileappend.
455:
456: Revision 1.85 2003/06/17 13:12:43 brouard
457: * imach.c (Repository): Check when date of death was earlier that
458: current date of interview. It may happen when the death was just
459: prior to the death. In this case, dh was negative and likelihood
460: was wrong (infinity). We still send an "Error" but patch by
461: assuming that the date of death was just one stepm after the
462: interview.
463: (Repository): Because some people have very long ID (first column)
464: we changed int to long in num[] and we added a new lvector for
465: memory allocation. But we also truncated to 8 characters (left
466: truncation)
467: (Repository): No more line truncation errors.
468:
469: Revision 1.84 2003/06/13 21:44:43 brouard
470: * imach.c (Repository): Replace "freqsummary" at a correct
471: place. It differs from routine "prevalence" which may be called
472: many times. Probs is memory consuming and must be used with
473: parcimony.
474: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
475:
476: Revision 1.83 2003/06/10 13:39:11 lievre
477: *** empty log message ***
478:
479: Revision 1.82 2003/06/05 15:57:20 brouard
480: Add log in imach.c and fullversion number is now printed.
481:
482: */
483: /*
484: Interpolated Markov Chain
485:
486: Short summary of the programme:
487:
488: This program computes Healthy Life Expectancies from
489: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
490: first survey ("cross") where individuals from different ages are
491: interviewed on their health status or degree of disability (in the
492: case of a health survey which is our main interest) -2- at least a
493: second wave of interviews ("longitudinal") which measure each change
494: (if any) in individual health status. Health expectancies are
495: computed from the time spent in each health state according to a
496: model. More health states you consider, more time is necessary to reach the
497: Maximum Likelihood of the parameters involved in the model. The
498: simplest model is the multinomial logistic model where pij is the
499: probability to be observed in state j at the second wave
500: conditional to be observed in state i at the first wave. Therefore
501: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
502: 'age' is age and 'sex' is a covariate. If you want to have a more
503: complex model than "constant and age", you should modify the program
504: where the markup *Covariates have to be included here again* invites
505: you to do it. More covariates you add, slower the
506: convergence.
507:
508: The advantage of this computer programme, compared to a simple
509: multinomial logistic model, is clear when the delay between waves is not
510: identical for each individual. Also, if a individual missed an
511: intermediate interview, the information is lost, but taken into
512: account using an interpolation or extrapolation.
513:
514: hPijx is the probability to be observed in state i at age x+h
515: conditional to the observed state i at age x. The delay 'h' can be
516: split into an exact number (nh*stepm) of unobserved intermediate
517: states. This elementary transition (by month, quarter,
518: semester or year) is modelled as a multinomial logistic. The hPx
519: matrix is simply the matrix product of nh*stepm elementary matrices
520: and the contribution of each individual to the likelihood is simply
521: hPijx.
522:
523: Also this programme outputs the covariance matrix of the parameters but also
524: of the life expectancies. It also computes the period (stable) prevalence.
525:
526: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
527: Institut national d'études démographiques, Paris.
528: This software have been partly granted by Euro-REVES, a concerted action
529: from the European Union.
530: It is copyrighted identically to a GNU software product, ie programme and
531: software can be distributed freely for non commercial use. Latest version
532: can be accessed at http://euroreves.ined.fr/imach .
533:
534: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
535: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
536:
537: **********************************************************************/
538: /*
539: main
540: read parameterfile
541: read datafile
542: concatwav
543: freqsummary
544: if (mle >= 1)
545: mlikeli
546: print results files
547: if mle==1
548: computes hessian
549: read end of parameter file: agemin, agemax, bage, fage, estepm
550: begin-prev-date,...
551: open gnuplot file
552: open html file
553: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
554: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
555: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
556: freexexit2 possible for memory heap.
557:
558: h Pij x | pij_nom ficrestpij
559: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
560: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
561: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
562:
563: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
564: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
565: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
566: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
567: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
568:
569: forecasting if prevfcast==1 prevforecast call prevalence()
570: health expectancies
571: Variance-covariance of DFLE
572: prevalence()
573: movingaverage()
574: varevsij()
575: if popbased==1 varevsij(,popbased)
576: total life expectancies
577: Variance of period (stable) prevalence
578: end
579: */
580:
581: #define POWELL /* Instead of NLOPT */
582: /* #define POWELLORIGINAL */ /* Don't use Directest to decide new direction but original Powell test */
583: /* #define MNBRAKORIGINAL */ /* Don't use mnbrak fix */
584:
585: #include <math.h>
586: #include <stdio.h>
587: #include <stdlib.h>
588: #include <string.h>
589:
590: #ifdef _WIN32
591: #include <io.h>
592: #include <windows.h>
593: #include <tchar.h>
594: #else
595: #include <unistd.h>
596: #endif
597:
598: #include <limits.h>
599: #include <sys/types.h>
600:
601: #if defined(__GNUC__)
602: #include <sys/utsname.h> /* Doesn't work on Windows */
603: #endif
604:
605: #include <sys/stat.h>
606: #include <errno.h>
607: /* extern int errno; */
608:
609: /* #ifdef LINUX */
610: /* #include <time.h> */
611: /* #include "timeval.h" */
612: /* #else */
613: /* #include <sys/time.h> */
614: /* #endif */
615:
616: #include <time.h>
617:
618: #ifdef GSL
619: #include <gsl/gsl_errno.h>
620: #include <gsl/gsl_multimin.h>
621: #endif
622:
623:
624: #ifdef NLOPT
625: #include <nlopt.h>
626: typedef struct {
627: double (* function)(double [] );
628: } myfunc_data ;
629: #endif
630:
631: /* #include <libintl.h> */
632: /* #define _(String) gettext (String) */
633:
634: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
635:
636: #define GNUPLOTPROGRAM "gnuplot"
637: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
638: #define FILENAMELENGTH 132
639:
640: #define GLOCK_ERROR_NOPATH -1 /* empty path */
641: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
642:
643: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
644: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
645:
646: #define NINTERVMAX 8
647: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
648: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
649: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
650: #define codtabm(h,k) 1 & (h-1) >> (k-1) ;
651: #define MAXN 20000
652: #define YEARM 12. /**< Number of months per year */
653: #define AGESUP 130
654: #define AGEBASE 40
655: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
656: #ifdef _WIN32
657: #define DIRSEPARATOR '\\'
658: #define CHARSEPARATOR "\\"
659: #define ODIRSEPARATOR '/'
660: #else
661: #define DIRSEPARATOR '/'
662: #define CHARSEPARATOR "/"
663: #define ODIRSEPARATOR '\\'
664: #endif
665:
666: /* $Id: imach.c,v 1.185 2015/03/11 13:26:42 brouard Exp $ */
667: /* $State: Exp $ */
668:
669: char version[]="Imach version 0.98q0, March 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
670: char fullversion[]="$Revision: 1.185 $ $Date: 2015/03/11 13:26:42 $";
671: char strstart[80];
672: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
673: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
674: int nvar=0, nforce=0; /* Number of variables, number of forces */
675: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
676: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
677: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
678: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
679: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
680: int cptcovprodnoage=0; /**< Number of covariate products without age */
681: int cptcoveff=0; /* Total number of covariates to vary for printing results */
682: int cptcov=0; /* Working variable */
683: int npar=NPARMAX;
684: int nlstate=2; /* Number of live states */
685: int ndeath=1; /* Number of dead states */
686: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
687: int popbased=0;
688:
689: int *wav; /* Number of waves for this individuual 0 is possible */
690: int maxwav=0; /* Maxim number of waves */
691: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
692: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
693: int gipmx=0, gsw=0; /* Global variables on the number of contributions
694: to the likelihood and the sum of weights (done by funcone)*/
695: int mle=1, weightopt=0;
696: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
697: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
698: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
699: * wave mi and wave mi+1 is not an exact multiple of stepm. */
700: int countcallfunc=0; /* Count the number of calls to func */
701: double jmean=1; /* Mean space between 2 waves */
702: double **matprod2(); /* test */
703: double **oldm, **newm, **savm; /* Working pointers to matrices */
704: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
705: /*FILE *fic ; */ /* Used in readdata only */
706: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
707: FILE *ficlog, *ficrespow;
708: int globpr=0; /* Global variable for printing or not */
709: double fretone; /* Only one call to likelihood */
710: long ipmx=0; /* Number of contributions */
711: double sw; /* Sum of weights */
712: char filerespow[FILENAMELENGTH];
713: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
714: FILE *ficresilk;
715: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
716: FILE *ficresprobmorprev;
717: FILE *fichtm, *fichtmcov; /* Html File */
718: FILE *ficreseij;
719: char filerese[FILENAMELENGTH];
720: FILE *ficresstdeij;
721: char fileresstde[FILENAMELENGTH];
722: FILE *ficrescveij;
723: char filerescve[FILENAMELENGTH];
724: FILE *ficresvij;
725: char fileresv[FILENAMELENGTH];
726: FILE *ficresvpl;
727: char fileresvpl[FILENAMELENGTH];
728: char title[MAXLINE];
729: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
730: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
731: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
732: char command[FILENAMELENGTH];
733: int outcmd=0;
734:
735: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
736:
737: char filelog[FILENAMELENGTH]; /* Log file */
738: char filerest[FILENAMELENGTH];
739: char fileregp[FILENAMELENGTH];
740: char popfile[FILENAMELENGTH];
741:
742: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
743:
744: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
745: /* struct timezone tzp; */
746: /* extern int gettimeofday(); */
747: struct tm tml, *gmtime(), *localtime();
748:
749: extern time_t time();
750:
751: struct tm start_time, end_time, curr_time, last_time, forecast_time;
752: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
753: struct tm tm;
754:
755: char strcurr[80], strfor[80];
756:
757: char *endptr;
758: long lval;
759: double dval;
760:
761: #define NR_END 1
762: #define FREE_ARG char*
763: #define FTOL 1.0e-10
764:
765: #define NRANSI
766: #define ITMAX 200
767:
768: #define TOL 2.0e-4
769:
770: #define CGOLD 0.3819660
771: #define ZEPS 1.0e-10
772: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
773:
774: #define GOLD 1.618034
775: #define GLIMIT 100.0
776: #define TINY 1.0e-20
777:
778: static double maxarg1,maxarg2;
779: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
780: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
781:
782: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
783: #define rint(a) floor(a+0.5)
784: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
785: #define mytinydouble 1.0e-16
786: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
787: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
788: /* static double dsqrarg; */
789: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
790: static double sqrarg;
791: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
792: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
793: int agegomp= AGEGOMP;
794:
795: int imx;
796: int stepm=1;
797: /* Stepm, step in month: minimum step interpolation*/
798:
799: int estepm;
800: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
801:
802: int m,nb;
803: long *num;
804: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
805: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
806: double **pmmij, ***probs;
807: double *ageexmed,*agecens;
808: double dateintmean=0;
809:
810: double *weight;
811: int **s; /* Status */
812: double *agedc;
813: double **covar; /**< covar[j,i], value of jth covariate for individual i,
814: * covar=matrix(0,NCOVMAX,1,n);
815: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
816: double idx;
817: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
818: int *Ndum; /** Freq of modality (tricode */
819: int **codtab; /**< codtab=imatrix(1,100,1,10); */
820: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
821: double *lsurv, *lpop, *tpop;
822:
823: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
824: double ftolhess; /**< Tolerance for computing hessian */
825:
826: /**************** split *************************/
827: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
828: {
829: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
830: the name of the file (name), its extension only (ext) and its first part of the name (finame)
831: */
832: char *ss; /* pointer */
833: int l1, l2; /* length counters */
834:
835: l1 = strlen(path ); /* length of path */
836: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
837: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
838: if ( ss == NULL ) { /* no directory, so determine current directory */
839: strcpy( name, path ); /* we got the fullname name because no directory */
840: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
841: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
842: /* get current working directory */
843: /* extern char* getcwd ( char *buf , int len);*/
844: #ifdef WIN32
845: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
846: #else
847: if (getcwd(dirc, FILENAME_MAX) == NULL) {
848: #endif
849: return( GLOCK_ERROR_GETCWD );
850: }
851: /* got dirc from getcwd*/
852: printf(" DIRC = %s \n",dirc);
853: } else { /* strip direcotry from path */
854: ss++; /* after this, the filename */
855: l2 = strlen( ss ); /* length of filename */
856: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
857: strcpy( name, ss ); /* save file name */
858: strncpy( dirc, path, l1 - l2 ); /* now the directory */
859: dirc[l1-l2] = 0; /* add zero */
860: printf(" DIRC2 = %s \n",dirc);
861: }
862: /* We add a separator at the end of dirc if not exists */
863: l1 = strlen( dirc ); /* length of directory */
864: if( dirc[l1-1] != DIRSEPARATOR ){
865: dirc[l1] = DIRSEPARATOR;
866: dirc[l1+1] = 0;
867: printf(" DIRC3 = %s \n",dirc);
868: }
869: ss = strrchr( name, '.' ); /* find last / */
870: if (ss >0){
871: ss++;
872: strcpy(ext,ss); /* save extension */
873: l1= strlen( name);
874: l2= strlen(ss)+1;
875: strncpy( finame, name, l1-l2);
876: finame[l1-l2]= 0;
877: }
878:
879: return( 0 ); /* we're done */
880: }
881:
882:
883: /******************************************/
884:
885: void replace_back_to_slash(char *s, char*t)
886: {
887: int i;
888: int lg=0;
889: i=0;
890: lg=strlen(t);
891: for(i=0; i<= lg; i++) {
892: (s[i] = t[i]);
893: if (t[i]== '\\') s[i]='/';
894: }
895: }
896:
897: char *trimbb(char *out, char *in)
898: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
899: char *s;
900: s=out;
901: while (*in != '\0'){
902: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
903: in++;
904: }
905: *out++ = *in++;
906: }
907: *out='\0';
908: return s;
909: }
910:
911: char *cutl(char *blocc, char *alocc, char *in, char occ)
912: {
913: /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ'
914: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
915: gives blocc="abcdef2ghi" and alocc="j".
916: If occ is not found blocc is null and alocc is equal to in. Returns blocc
917: */
918: char *s, *t;
919: t=in;s=in;
920: while ((*in != occ) && (*in != '\0')){
921: *alocc++ = *in++;
922: }
923: if( *in == occ){
924: *(alocc)='\0';
925: s=++in;
926: }
927:
928: if (s == t) {/* occ not found */
929: *(alocc-(in-s))='\0';
930: in=s;
931: }
932: while ( *in != '\0'){
933: *blocc++ = *in++;
934: }
935:
936: *blocc='\0';
937: return t;
938: }
939: char *cutv(char *blocc, char *alocc, char *in, char occ)
940: {
941: /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
942: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
943: gives blocc="abcdef2ghi" and alocc="j".
944: If occ is not found blocc is null and alocc is equal to in. Returns alocc
945: */
946: char *s, *t;
947: t=in;s=in;
948: while (*in != '\0'){
949: while( *in == occ){
950: *blocc++ = *in++;
951: s=in;
952: }
953: *blocc++ = *in++;
954: }
955: if (s == t) /* occ not found */
956: *(blocc-(in-s))='\0';
957: else
958: *(blocc-(in-s)-1)='\0';
959: in=s;
960: while ( *in != '\0'){
961: *alocc++ = *in++;
962: }
963:
964: *alocc='\0';
965: return s;
966: }
967:
968: int nbocc(char *s, char occ)
969: {
970: int i,j=0;
971: int lg=20;
972: i=0;
973: lg=strlen(s);
974: for(i=0; i<= lg; i++) {
975: if (s[i] == occ ) j++;
976: }
977: return j;
978: }
979:
980: /* void cutv(char *u,char *v, char*t, char occ) */
981: /* { */
982: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
983: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
984: /* gives u="abcdef2ghi" and v="j" *\/ */
985: /* int i,lg,j,p=0; */
986: /* i=0; */
987: /* lg=strlen(t); */
988: /* for(j=0; j<=lg-1; j++) { */
989: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
990: /* } */
991:
992: /* for(j=0; j<p; j++) { */
993: /* (u[j] = t[j]); */
994: /* } */
995: /* u[p]='\0'; */
996:
997: /* for(j=0; j<= lg; j++) { */
998: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
999: /* } */
1000: /* } */
1001:
1002: #ifdef _WIN32
1003: char * strsep(char **pp, const char *delim)
1004: {
1005: char *p, *q;
1006:
1007: if ((p = *pp) == NULL)
1008: return 0;
1009: if ((q = strpbrk (p, delim)) != NULL)
1010: {
1011: *pp = q + 1;
1012: *q = '\0';
1013: }
1014: else
1015: *pp = 0;
1016: return p;
1017: }
1018: #endif
1019:
1020: /********************** nrerror ********************/
1021:
1022: void nrerror(char error_text[])
1023: {
1024: fprintf(stderr,"ERREUR ...\n");
1025: fprintf(stderr,"%s\n",error_text);
1026: exit(EXIT_FAILURE);
1027: }
1028: /*********************** vector *******************/
1029: double *vector(int nl, int nh)
1030: {
1031: double *v;
1032: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1033: if (!v) nrerror("allocation failure in vector");
1034: return v-nl+NR_END;
1035: }
1036:
1037: /************************ free vector ******************/
1038: void free_vector(double*v, int nl, int nh)
1039: {
1040: free((FREE_ARG)(v+nl-NR_END));
1041: }
1042:
1043: /************************ivector *******************************/
1044: int *ivector(long nl,long nh)
1045: {
1046: int *v;
1047: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1048: if (!v) nrerror("allocation failure in ivector");
1049: return v-nl+NR_END;
1050: }
1051:
1052: /******************free ivector **************************/
1053: void free_ivector(int *v, long nl, long nh)
1054: {
1055: free((FREE_ARG)(v+nl-NR_END));
1056: }
1057:
1058: /************************lvector *******************************/
1059: long *lvector(long nl,long nh)
1060: {
1061: long *v;
1062: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1063: if (!v) nrerror("allocation failure in ivector");
1064: return v-nl+NR_END;
1065: }
1066:
1067: /******************free lvector **************************/
1068: void free_lvector(long *v, long nl, long nh)
1069: {
1070: free((FREE_ARG)(v+nl-NR_END));
1071: }
1072:
1073: /******************* imatrix *******************************/
1074: int **imatrix(long nrl, long nrh, long ncl, long nch)
1075: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1076: {
1077: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1078: int **m;
1079:
1080: /* allocate pointers to rows */
1081: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1082: if (!m) nrerror("allocation failure 1 in matrix()");
1083: m += NR_END;
1084: m -= nrl;
1085:
1086:
1087: /* allocate rows and set pointers to them */
1088: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1089: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1090: m[nrl] += NR_END;
1091: m[nrl] -= ncl;
1092:
1093: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1094:
1095: /* return pointer to array of pointers to rows */
1096: return m;
1097: }
1098:
1099: /****************** free_imatrix *************************/
1100: void free_imatrix(m,nrl,nrh,ncl,nch)
1101: int **m;
1102: long nch,ncl,nrh,nrl;
1103: /* free an int matrix allocated by imatrix() */
1104: {
1105: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1106: free((FREE_ARG) (m+nrl-NR_END));
1107: }
1108:
1109: /******************* matrix *******************************/
1110: double **matrix(long nrl, long nrh, long ncl, long nch)
1111: {
1112: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1113: double **m;
1114:
1115: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1116: if (!m) nrerror("allocation failure 1 in matrix()");
1117: m += NR_END;
1118: m -= nrl;
1119:
1120: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1121: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1122: m[nrl] += NR_END;
1123: m[nrl] -= ncl;
1124:
1125: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1126: return m;
1127: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1128: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1129: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1130: */
1131: }
1132:
1133: /*************************free matrix ************************/
1134: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1135: {
1136: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1137: free((FREE_ARG)(m+nrl-NR_END));
1138: }
1139:
1140: /******************* ma3x *******************************/
1141: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1142: {
1143: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1144: double ***m;
1145:
1146: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1147: if (!m) nrerror("allocation failure 1 in matrix()");
1148: m += NR_END;
1149: m -= nrl;
1150:
1151: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1152: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1153: m[nrl] += NR_END;
1154: m[nrl] -= ncl;
1155:
1156: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1157:
1158: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1159: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1160: m[nrl][ncl] += NR_END;
1161: m[nrl][ncl] -= nll;
1162: for (j=ncl+1; j<=nch; j++)
1163: m[nrl][j]=m[nrl][j-1]+nlay;
1164:
1165: for (i=nrl+1; i<=nrh; i++) {
1166: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1167: for (j=ncl+1; j<=nch; j++)
1168: m[i][j]=m[i][j-1]+nlay;
1169: }
1170: return m;
1171: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1172: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1173: */
1174: }
1175:
1176: /*************************free ma3x ************************/
1177: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1178: {
1179: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1180: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1181: free((FREE_ARG)(m+nrl-NR_END));
1182: }
1183:
1184: /*************** function subdirf ***********/
1185: char *subdirf(char fileres[])
1186: {
1187: /* Caution optionfilefiname is hidden */
1188: strcpy(tmpout,optionfilefiname);
1189: strcat(tmpout,"/"); /* Add to the right */
1190: strcat(tmpout,fileres);
1191: return tmpout;
1192: }
1193:
1194: /*************** function subdirf2 ***********/
1195: char *subdirf2(char fileres[], char *preop)
1196: {
1197:
1198: /* Caution optionfilefiname is hidden */
1199: strcpy(tmpout,optionfilefiname);
1200: strcat(tmpout,"/");
1201: strcat(tmpout,preop);
1202: strcat(tmpout,fileres);
1203: return tmpout;
1204: }
1205:
1206: /*************** function subdirf3 ***********/
1207: char *subdirf3(char fileres[], char *preop, char *preop2)
1208: {
1209:
1210: /* Caution optionfilefiname is hidden */
1211: strcpy(tmpout,optionfilefiname);
1212: strcat(tmpout,"/");
1213: strcat(tmpout,preop);
1214: strcat(tmpout,preop2);
1215: strcat(tmpout,fileres);
1216: return tmpout;
1217: }
1218:
1219: char *asc_diff_time(long time_sec, char ascdiff[])
1220: {
1221: long sec_left, days, hours, minutes;
1222: days = (time_sec) / (60*60*24);
1223: sec_left = (time_sec) % (60*60*24);
1224: hours = (sec_left) / (60*60) ;
1225: sec_left = (sec_left) %(60*60);
1226: minutes = (sec_left) /60;
1227: sec_left = (sec_left) % (60);
1228: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1229: return ascdiff;
1230: }
1231:
1232: /***************** f1dim *************************/
1233: extern int ncom;
1234: extern double *pcom,*xicom;
1235: extern double (*nrfunc)(double []);
1236:
1237: double f1dim(double x)
1238: {
1239: int j;
1240: double f;
1241: double *xt;
1242:
1243: xt=vector(1,ncom);
1244: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1245: f=(*nrfunc)(xt);
1246: free_vector(xt,1,ncom);
1247: return f;
1248: }
1249:
1250: /*****************brent *************************/
1251: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1252: {
1253: int iter;
1254: double a,b,d,etemp;
1255: double fu=0,fv,fw,fx;
1256: double ftemp=0.;
1257: double p,q,r,tol1,tol2,u,v,w,x,xm;
1258: double e=0.0;
1259:
1260: a=(ax < cx ? ax : cx);
1261: b=(ax > cx ? ax : cx);
1262: x=w=v=bx;
1263: fw=fv=fx=(*f)(x);
1264: for (iter=1;iter<=ITMAX;iter++) {
1265: xm=0.5*(a+b);
1266: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1267: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1268: printf(".");fflush(stdout);
1269: fprintf(ficlog,".");fflush(ficlog);
1270: #ifdef DEBUGBRENT
1271: 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);
1272: 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);
1273: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1274: #endif
1275: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1276: *xmin=x;
1277: return fx;
1278: }
1279: ftemp=fu;
1280: if (fabs(e) > tol1) {
1281: r=(x-w)*(fx-fv);
1282: q=(x-v)*(fx-fw);
1283: p=(x-v)*q-(x-w)*r;
1284: q=2.0*(q-r);
1285: if (q > 0.0) p = -p;
1286: q=fabs(q);
1287: etemp=e;
1288: e=d;
1289: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1290: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1291: else {
1292: d=p/q;
1293: u=x+d;
1294: if (u-a < tol2 || b-u < tol2)
1295: d=SIGN(tol1,xm-x);
1296: }
1297: } else {
1298: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1299: }
1300: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1301: fu=(*f)(u);
1302: if (fu <= fx) {
1303: if (u >= x) a=x; else b=x;
1304: SHFT(v,w,x,u)
1305: SHFT(fv,fw,fx,fu)
1306: } else {
1307: if (u < x) a=u; else b=u;
1308: if (fu <= fw || w == x) {
1309: v=w;
1310: w=u;
1311: fv=fw;
1312: fw=fu;
1313: } else if (fu <= fv || v == x || v == w) {
1314: v=u;
1315: fv=fu;
1316: }
1317: }
1318: }
1319: nrerror("Too many iterations in brent");
1320: *xmin=x;
1321: return fx;
1322: }
1323:
1324: /****************** mnbrak ***********************/
1325:
1326: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1327: double (*func)(double))
1328: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1329: the downhill direction (defined by the function as evaluated at the initial points) and returns
1330: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1331: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1332: */
1333: double ulim,u,r,q, dum;
1334: double fu;
1335:
1336: *fa=(*func)(*ax);
1337: *fb=(*func)(*bx);
1338: if (*fb > *fa) {
1339: SHFT(dum,*ax,*bx,dum)
1340: SHFT(dum,*fb,*fa,dum)
1341: }
1342: *cx=(*bx)+GOLD*(*bx-*ax);
1343: *fc=(*func)(*cx);
1344: #ifdef DEBUG
1345: printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1346: fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1347: #endif
1348: while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
1349: r=(*bx-*ax)*(*fb-*fc);
1350: q=(*bx-*cx)*(*fb-*fa);
1351: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1352: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1353: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1354: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1355: fu=(*func)(u);
1356: #ifdef DEBUG
1357: /* f(x)=A(x-u)**2+f(u) */
1358: double A, fparabu;
1359: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1360: fparabu= *fa - A*(*ax-u)*(*ax-u);
1361: 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);
1362: 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);
1363: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1364: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1365: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1366: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1367: #endif
1368: #ifdef MNBRAKORIGINAL
1369: #else
1370: if (fu > *fc) {
1371: #ifdef DEBUG
1372: printf("mnbrak4 fu > fc \n");
1373: fprintf(ficlog, "mnbrak4 fu > fc\n");
1374: #endif
1375: /* 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 *\/ */
1376: /* SHFT(*fa,*fc,fu,*fc) /\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\/ */
1377: dum=u; /* Shifting c and u */
1378: u = *cx;
1379: *cx = dum;
1380: dum = fu;
1381: fu = *fc;
1382: *fc =dum;
1383: } else { /* end */
1384: #ifdef DEBUG
1385: printf("mnbrak3 fu < fc \n");
1386: fprintf(ficlog, "mnbrak3 fu < fc\n");
1387: #endif
1388: dum=u; /* Shifting c and u */
1389: u = *cx;
1390: *cx = dum;
1391: dum = fu;
1392: fu = *fc;
1393: *fc =dum;
1394: }
1395: #endif
1396: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1397: #ifdef DEBUG
1398: printf("mnbrak2 u after c but before ulim\n");
1399: fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
1400: #endif
1401: fu=(*func)(u);
1402: if (fu < *fc) {
1403: #ifdef DEBUG
1404: printf("mnbrak2 u after c but before ulim AND fu < fc\n");
1405: fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
1406: #endif
1407: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1408: SHFT(*fb,*fc,fu,(*func)(u))
1409: }
1410: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1411: #ifdef DEBUG
1412: printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1413: fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1414: #endif
1415: u=ulim;
1416: fu=(*func)(u);
1417: } else { /* u could be left to b (if r > q parabola has a maximum) */
1418: #ifdef DEBUG
1419: printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1420: fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1421: #endif
1422: u=(*cx)+GOLD*(*cx-*bx);
1423: fu=(*func)(u);
1424: } /* end tests */
1425: SHFT(*ax,*bx,*cx,u)
1426: SHFT(*fa,*fb,*fc,fu)
1427: #ifdef DEBUG
1428: 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);
1429: 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);
1430: #endif
1431: } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
1432: }
1433:
1434: /*************** linmin ************************/
1435: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1436: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1437: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1438: the value of func at the returned location p . This is actually all accomplished by calling the
1439: routines mnbrak and brent .*/
1440: int ncom;
1441: double *pcom,*xicom;
1442: double (*nrfunc)(double []);
1443:
1444: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1445: {
1446: double brent(double ax, double bx, double cx,
1447: double (*f)(double), double tol, double *xmin);
1448: double f1dim(double x);
1449: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1450: double *fc, double (*func)(double));
1451: int j;
1452: double xx,xmin,bx,ax;
1453: double fx,fb,fa;
1454:
1455: ncom=n;
1456: pcom=vector(1,n);
1457: xicom=vector(1,n);
1458: nrfunc=func;
1459: for (j=1;j<=n;j++) {
1460: pcom[j]=p[j];
1461: xicom[j]=xi[j];
1462: }
1463: ax=0.0;
1464: xx=1.0;
1465: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
1466: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
1467: #ifdef DEBUG
1468: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1469: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1470: #endif
1471: for (j=1;j<=n;j++) {
1472: xi[j] *= xmin;
1473: p[j] += xi[j];
1474: }
1475: free_vector(xicom,1,n);
1476: free_vector(pcom,1,n);
1477: }
1478:
1479:
1480: /*************** powell ************************/
1481: /*
1482: Minimization of a function func of n variables. Input consists of an initial starting point
1483: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1484: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1485: such that failure to decrease by more than this amount on one iteration signals doneness. On
1486: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1487: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1488: */
1489: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1490: double (*func)(double []))
1491: {
1492: void linmin(double p[], double xi[], int n, double *fret,
1493: double (*func)(double []));
1494: int i,ibig,j;
1495: double del,t,*pt,*ptt,*xit;
1496: double directest;
1497: double fp,fptt;
1498: double *xits;
1499: int niterf, itmp;
1500:
1501: pt=vector(1,n);
1502: ptt=vector(1,n);
1503: xit=vector(1,n);
1504: xits=vector(1,n);
1505: *fret=(*func)(p);
1506: for (j=1;j<=n;j++) pt[j]=p[j];
1507: rcurr_time = time(NULL);
1508: for (*iter=1;;++(*iter)) {
1509: fp=(*fret);
1510: ibig=0;
1511: del=0.0;
1512: rlast_time=rcurr_time;
1513: /* (void) gettimeofday(&curr_time,&tzp); */
1514: rcurr_time = time(NULL);
1515: curr_time = *localtime(&rcurr_time);
1516: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1517: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1518: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1519: for (i=1;i<=n;i++) {
1520: printf(" %d %.12f",i, p[i]);
1521: fprintf(ficlog," %d %.12lf",i, p[i]);
1522: fprintf(ficrespow," %.12lf", p[i]);
1523: }
1524: printf("\n");
1525: fprintf(ficlog,"\n");
1526: fprintf(ficrespow,"\n");fflush(ficrespow);
1527: if(*iter <=3){
1528: tml = *localtime(&rcurr_time);
1529: strcpy(strcurr,asctime(&tml));
1530: rforecast_time=rcurr_time;
1531: itmp = strlen(strcurr);
1532: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1533: strcurr[itmp-1]='\0';
1534: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1535: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1536: for(niterf=10;niterf<=30;niterf+=10){
1537: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1538: forecast_time = *localtime(&rforecast_time);
1539: strcpy(strfor,asctime(&forecast_time));
1540: itmp = strlen(strfor);
1541: if(strfor[itmp-1]=='\n')
1542: strfor[itmp-1]='\0';
1543: 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);
1544: 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);
1545: }
1546: }
1547: for (i=1;i<=n;i++) {
1548: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1549: fptt=(*fret);
1550: #ifdef DEBUG
1551: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1552: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1553: #endif
1554: printf("%d",i);fflush(stdout);
1555: fprintf(ficlog,"%d",i);fflush(ficlog);
1556: linmin(p,xit,n,fret,func); /* xit[n] has been loaded for direction i */
1557: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions
1558: because that direction will be replaced unless the gain del is small
1559: in comparison with the 'probable' gain, mu^2, with the last average direction.
1560: Unless the n directions are conjugate some gain in the determinant may be obtained
1561: with the new direction.
1562: */
1563: del=fabs(fptt-(*fret));
1564: ibig=i;
1565: }
1566: #ifdef DEBUG
1567: printf("%d %.12e",i,(*fret));
1568: fprintf(ficlog,"%d %.12e",i,(*fret));
1569: for (j=1;j<=n;j++) {
1570: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1571: printf(" x(%d)=%.12e",j,xit[j]);
1572: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1573: }
1574: for(j=1;j<=n;j++) {
1575: printf(" p(%d)=%.12e",j,p[j]);
1576: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1577: }
1578: printf("\n");
1579: fprintf(ficlog,"\n");
1580: #endif
1581: } /* end i */
1582: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1583: #ifdef DEBUG
1584: int k[2],l;
1585: k[0]=1;
1586: k[1]=-1;
1587: printf("Max: %.12e",(*func)(p));
1588: fprintf(ficlog,"Max: %.12e",(*func)(p));
1589: for (j=1;j<=n;j++) {
1590: printf(" %.12e",p[j]);
1591: fprintf(ficlog," %.12e",p[j]);
1592: }
1593: printf("\n");
1594: fprintf(ficlog,"\n");
1595: for(l=0;l<=1;l++) {
1596: for (j=1;j<=n;j++) {
1597: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1598: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1599: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1600: }
1601: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1602: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1603: }
1604: #endif
1605:
1606:
1607: free_vector(xit,1,n);
1608: free_vector(xits,1,n);
1609: free_vector(ptt,1,n);
1610: free_vector(pt,1,n);
1611: return;
1612: }
1613: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1614: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1615: ptt[j]=2.0*p[j]-pt[j];
1616: xit[j]=p[j]-pt[j];
1617: pt[j]=p[j];
1618: }
1619: fptt=(*func)(ptt); /* f_3 */
1620: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1621: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1622: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1623: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1624: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1625: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1626: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
1627: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1628: #ifdef NRCORIGINAL
1629: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
1630: #else
1631: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
1632: t= t- del*SQR(fp-fptt);
1633: #endif
1634: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
1635: #ifdef DEBUG
1636: 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);
1637: 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);
1638: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1639: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1640: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1641: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1642: 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);
1643: 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);
1644: #endif
1645: #ifdef POWELLORIGINAL
1646: if (t < 0.0) { /* Then we use it for new direction */
1647: #else
1648: if (directest*t < 0.0) { /* Contradiction between both tests */
1649: printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
1650: printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1651: fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
1652: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1653: }
1654: if (directest < 0.0) { /* Then we use it for new direction */
1655: #endif
1656: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction.*/
1657: for (j=1;j<=n;j++) {
1658: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
1659: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
1660: }
1661: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1662: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1663:
1664: #ifdef DEBUG
1665: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1666: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1667: for(j=1;j<=n;j++){
1668: printf(" %.12e",xit[j]);
1669: fprintf(ficlog," %.12e",xit[j]);
1670: }
1671: printf("\n");
1672: fprintf(ficlog,"\n");
1673: #endif
1674: } /* end of t negative */
1675: } /* end if (fptt < fp) */
1676: }
1677: }
1678:
1679: /**** Prevalence limit (stable or period prevalence) ****************/
1680:
1681: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1682: {
1683: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1684: matrix by transitions matrix until convergence is reached */
1685:
1686: int i, ii,j,k;
1687: double min, max, maxmin, maxmax,sumnew=0.;
1688: /* double **matprod2(); */ /* test */
1689: double **out, cov[NCOVMAX+1], **pmij();
1690: double **newm;
1691: double agefin, delaymax=50 ; /* Max number of years to converge */
1692:
1693: for (ii=1;ii<=nlstate+ndeath;ii++)
1694: for (j=1;j<=nlstate+ndeath;j++){
1695: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1696: }
1697:
1698: cov[1]=1.;
1699:
1700: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1701: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1702: newm=savm;
1703: /* Covariates have to be included here again */
1704: cov[2]=agefin;
1705:
1706: for (k=1; k<=cptcovn;k++) {
1707: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1708: /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
1709: }
1710: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1711: /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
1712: /* cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
1713:
1714: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1715: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1716: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1717: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1718: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1719: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1720:
1721: savm=oldm;
1722: oldm=newm;
1723: maxmax=0.;
1724: for(j=1;j<=nlstate;j++){
1725: min=1.;
1726: max=0.;
1727: for(i=1; i<=nlstate; i++) {
1728: sumnew=0;
1729: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1730: prlim[i][j]= newm[i][j]/(1-sumnew);
1731: /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
1732: max=FMAX(max,prlim[i][j]);
1733: min=FMIN(min,prlim[i][j]);
1734: }
1735: maxmin=max-min;
1736: maxmax=FMAX(maxmax,maxmin);
1737: } /* j loop */
1738: if(maxmax < ftolpl){
1739: return prlim;
1740: }
1741: } /* age loop */
1742: return prlim; /* should not reach here */
1743: }
1744:
1745: /*************** transition probabilities ***************/
1746:
1747: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1748: {
1749: /* According to parameters values stored in x and the covariate's values stored in cov,
1750: computes the probability to be observed in state j being in state i by appying the
1751: model to the ncovmodel covariates (including constant and age).
1752: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1753: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1754: ncth covariate in the global vector x is given by the formula:
1755: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1756: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1757: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1758: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1759: Outputs ps[i][j] the probability to be observed in j being in j according to
1760: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1761: */
1762: double s1, lnpijopii;
1763: /*double t34;*/
1764: int i,j, nc, ii, jj;
1765:
1766: for(i=1; i<= nlstate; i++){
1767: for(j=1; j<i;j++){
1768: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1769: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1770: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1771: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1772: }
1773: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1774: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1775: }
1776: for(j=i+1; j<=nlstate+ndeath;j++){
1777: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1778: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
1779: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
1780: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1781: }
1782: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1783: }
1784: }
1785:
1786: for(i=1; i<= nlstate; i++){
1787: s1=0;
1788: for(j=1; j<i; j++){
1789: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1790: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1791: }
1792: for(j=i+1; j<=nlstate+ndeath; j++){
1793: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1794: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1795: }
1796: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1797: ps[i][i]=1./(s1+1.);
1798: /* Computing other pijs */
1799: for(j=1; j<i; j++)
1800: ps[i][j]= exp(ps[i][j])*ps[i][i];
1801: for(j=i+1; j<=nlstate+ndeath; j++)
1802: ps[i][j]= exp(ps[i][j])*ps[i][i];
1803: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1804: } /* end i */
1805:
1806: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1807: for(jj=1; jj<= nlstate+ndeath; jj++){
1808: ps[ii][jj]=0;
1809: ps[ii][ii]=1;
1810: }
1811: }
1812:
1813:
1814: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1815: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1816: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
1817: /* } */
1818: /* printf("\n "); */
1819: /* } */
1820: /* printf("\n ");printf("%lf ",cov[2]);*/
1821: /*
1822: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1823: goto end;*/
1824: return ps;
1825: }
1826:
1827: /**************** Product of 2 matrices ******************/
1828:
1829: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1830: {
1831: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1832: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1833: /* in, b, out are matrice of pointers which should have been initialized
1834: before: only the contents of out is modified. The function returns
1835: a pointer to pointers identical to out */
1836: int i, j, k;
1837: for(i=nrl; i<= nrh; i++)
1838: for(k=ncolol; k<=ncoloh; k++){
1839: out[i][k]=0.;
1840: for(j=ncl; j<=nch; j++)
1841: out[i][k] +=in[i][j]*b[j][k];
1842: }
1843: return out;
1844: }
1845:
1846:
1847: /************* Higher Matrix Product ***************/
1848:
1849: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1850: {
1851: /* Computes the transition matrix starting at age 'age' over
1852: 'nhstepm*hstepm*stepm' months (i.e. until
1853: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1854: nhstepm*hstepm matrices.
1855: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1856: (typically every 2 years instead of every month which is too big
1857: for the memory).
1858: Model is determined by parameters x and covariates have to be
1859: included manually here.
1860:
1861: */
1862:
1863: int i, j, d, h, k;
1864: double **out, cov[NCOVMAX+1];
1865: double **newm;
1866:
1867: /* Hstepm could be zero and should return the unit matrix */
1868: for (i=1;i<=nlstate+ndeath;i++)
1869: for (j=1;j<=nlstate+ndeath;j++){
1870: oldm[i][j]=(i==j ? 1.0 : 0.0);
1871: po[i][j][0]=(i==j ? 1.0 : 0.0);
1872: }
1873: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1874: for(h=1; h <=nhstepm; h++){
1875: for(d=1; d <=hstepm; d++){
1876: newm=savm;
1877: /* Covariates have to be included here again */
1878: cov[1]=1.;
1879: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1880: for (k=1; k<=cptcovn;k++)
1881: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1882: for (k=1; k<=cptcovage;k++)
1883: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1884: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1885: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1886:
1887:
1888: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1889: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1890: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1891: pmij(pmmij,cov,ncovmodel,x,nlstate));
1892: savm=oldm;
1893: oldm=newm;
1894: }
1895: for(i=1; i<=nlstate+ndeath; i++)
1896: for(j=1;j<=nlstate+ndeath;j++) {
1897: po[i][j][h]=newm[i][j];
1898: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1899: }
1900: /*printf("h=%d ",h);*/
1901: } /* end h */
1902: /* printf("\n H=%d \n",h); */
1903: return po;
1904: }
1905:
1906: #ifdef NLOPT
1907: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
1908: double fret;
1909: double *xt;
1910: int j;
1911: myfunc_data *d2 = (myfunc_data *) pd;
1912: /* xt = (p1-1); */
1913: xt=vector(1,n);
1914: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
1915:
1916: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
1917: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
1918: printf("Function = %.12lf ",fret);
1919: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
1920: printf("\n");
1921: free_vector(xt,1,n);
1922: return fret;
1923: }
1924: #endif
1925:
1926: /*************** log-likelihood *************/
1927: double func( double *x)
1928: {
1929: int i, ii, j, k, mi, d, kk;
1930: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1931: double **out;
1932: double sw; /* Sum of weights */
1933: double lli; /* Individual log likelihood */
1934: int s1, s2;
1935: double bbh, survp;
1936: long ipmx;
1937: /*extern weight */
1938: /* We are differentiating ll according to initial status */
1939: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1940: /*for(i=1;i<imx;i++)
1941: printf(" %d\n",s[4][i]);
1942: */
1943:
1944: ++countcallfunc;
1945:
1946: cov[1]=1.;
1947:
1948: for(k=1; k<=nlstate; k++) ll[k]=0.;
1949:
1950: if(mle==1){
1951: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1952: /* Computes the values of the ncovmodel covariates of the model
1953: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
1954: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
1955: to be observed in j being in i according to the model.
1956: */
1957: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1958: cov[2+k]=covar[Tvar[k]][i];
1959: }
1960: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1961: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1962: has been calculated etc */
1963: for(mi=1; mi<= wav[i]-1; mi++){
1964: for (ii=1;ii<=nlstate+ndeath;ii++)
1965: for (j=1;j<=nlstate+ndeath;j++){
1966: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1967: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1968: }
1969: for(d=0; d<dh[mi][i]; d++){
1970: newm=savm;
1971: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1972: for (kk=1; kk<=cptcovage;kk++) {
1973: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
1974: }
1975: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1976: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1977: savm=oldm;
1978: oldm=newm;
1979: } /* end mult */
1980:
1981: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1982: /* But now since version 0.9 we anticipate for bias at large stepm.
1983: * If stepm is larger than one month (smallest stepm) and if the exact delay
1984: * (in months) between two waves is not a multiple of stepm, we rounded to
1985: * the nearest (and in case of equal distance, to the lowest) interval but now
1986: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1987: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1988: * probability in order to take into account the bias as a fraction of the way
1989: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1990: * -stepm/2 to stepm/2 .
1991: * For stepm=1 the results are the same as for previous versions of Imach.
1992: * For stepm > 1 the results are less biased than in previous versions.
1993: */
1994: s1=s[mw[mi][i]][i];
1995: s2=s[mw[mi+1][i]][i];
1996: bbh=(double)bh[mi][i]/(double)stepm;
1997: /* bias bh is positive if real duration
1998: * is higher than the multiple of stepm and negative otherwise.
1999: */
2000: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
2001: if( s2 > nlstate){
2002: /* i.e. if s2 is a death state and if the date of death is known
2003: then the contribution to the likelihood is the probability to
2004: die between last step unit time and current step unit time,
2005: which is also equal to probability to die before dh
2006: minus probability to die before dh-stepm .
2007: In version up to 0.92 likelihood was computed
2008: as if date of death was unknown. Death was treated as any other
2009: health state: the date of the interview describes the actual state
2010: and not the date of a change in health state. The former idea was
2011: to consider that at each interview the state was recorded
2012: (healthy, disable or death) and IMaCh was corrected; but when we
2013: introduced the exact date of death then we should have modified
2014: the contribution of an exact death to the likelihood. This new
2015: contribution is smaller and very dependent of the step unit
2016: stepm. It is no more the probability to die between last interview
2017: and month of death but the probability to survive from last
2018: interview up to one month before death multiplied by the
2019: probability to die within a month. Thanks to Chris
2020: Jackson for correcting this bug. Former versions increased
2021: mortality artificially. The bad side is that we add another loop
2022: which slows down the processing. The difference can be up to 10%
2023: lower mortality.
2024: */
2025: /* If, at the beginning of the maximization mostly, the
2026: cumulative probability or probability to be dead is
2027: constant (ie = 1) over time d, the difference is equal to
2028: 0. out[s1][3] = savm[s1][3]: probability, being at state
2029: s1 at precedent wave, to be dead a month before current
2030: wave is equal to probability, being at state s1 at
2031: precedent wave, to be dead at mont of the current
2032: wave. Then the observed probability (that this person died)
2033: is null according to current estimated parameter. In fact,
2034: it should be very low but not zero otherwise the log go to
2035: infinity.
2036: */
2037: /* #ifdef INFINITYORIGINAL */
2038: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2039: /* #else */
2040: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
2041: /* lli=log(mytinydouble); */
2042: /* else */
2043: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2044: /* #endif */
2045: lli=log(out[s1][s2] - savm[s1][s2]);
2046:
2047: } else if (s2==-2) {
2048: for (j=1,survp=0. ; j<=nlstate; j++)
2049: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2050: /*survp += out[s1][j]; */
2051: lli= log(survp);
2052: }
2053:
2054: else if (s2==-4) {
2055: for (j=3,survp=0. ; j<=nlstate; j++)
2056: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2057: lli= log(survp);
2058: }
2059:
2060: else if (s2==-5) {
2061: for (j=1,survp=0. ; j<=2; j++)
2062: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2063: lli= log(survp);
2064: }
2065:
2066: else{
2067: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2068: /* 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 */
2069: }
2070: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
2071: /*if(lli ==000.0)*/
2072: /*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); */
2073: ipmx +=1;
2074: sw += weight[i];
2075: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2076: /* if (lli < log(mytinydouble)){ */
2077: /* 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); */
2078: /* 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]); */
2079: /* } */
2080: } /* end of wave */
2081: } /* end of individual */
2082: } else if(mle==2){
2083: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2084: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2085: for(mi=1; mi<= wav[i]-1; mi++){
2086: for (ii=1;ii<=nlstate+ndeath;ii++)
2087: for (j=1;j<=nlstate+ndeath;j++){
2088: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2089: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2090: }
2091: for(d=0; d<=dh[mi][i]; d++){
2092: newm=savm;
2093: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2094: for (kk=1; kk<=cptcovage;kk++) {
2095: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2096: }
2097: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2098: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2099: savm=oldm;
2100: oldm=newm;
2101: } /* end mult */
2102:
2103: s1=s[mw[mi][i]][i];
2104: s2=s[mw[mi+1][i]][i];
2105: bbh=(double)bh[mi][i]/(double)stepm;
2106: 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 */
2107: ipmx +=1;
2108: sw += weight[i];
2109: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2110: } /* end of wave */
2111: } /* end of individual */
2112: } else if(mle==3){ /* exponential inter-extrapolation */
2113: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2114: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2115: for(mi=1; mi<= wav[i]-1; mi++){
2116: for (ii=1;ii<=nlstate+ndeath;ii++)
2117: for (j=1;j<=nlstate+ndeath;j++){
2118: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2119: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2120: }
2121: for(d=0; d<dh[mi][i]; d++){
2122: newm=savm;
2123: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2124: for (kk=1; kk<=cptcovage;kk++) {
2125: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2126: }
2127: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2128: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2129: savm=oldm;
2130: oldm=newm;
2131: } /* end mult */
2132:
2133: s1=s[mw[mi][i]][i];
2134: s2=s[mw[mi+1][i]][i];
2135: bbh=(double)bh[mi][i]/(double)stepm;
2136: 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 */
2137: ipmx +=1;
2138: sw += weight[i];
2139: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2140: } /* end of wave */
2141: } /* end of individual */
2142: }else if (mle==4){ /* ml=4 no inter-extrapolation */
2143: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2144: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2145: for(mi=1; mi<= wav[i]-1; mi++){
2146: for (ii=1;ii<=nlstate+ndeath;ii++)
2147: for (j=1;j<=nlstate+ndeath;j++){
2148: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2149: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2150: }
2151: for(d=0; d<dh[mi][i]; d++){
2152: newm=savm;
2153: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2154: for (kk=1; kk<=cptcovage;kk++) {
2155: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2156: }
2157:
2158: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2159: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2160: savm=oldm;
2161: oldm=newm;
2162: } /* end mult */
2163:
2164: s1=s[mw[mi][i]][i];
2165: s2=s[mw[mi+1][i]][i];
2166: if( s2 > nlstate){
2167: lli=log(out[s1][s2] - savm[s1][s2]);
2168: }else{
2169: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2170: }
2171: ipmx +=1;
2172: sw += weight[i];
2173: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2174: /* 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]); */
2175: } /* end of wave */
2176: } /* end of individual */
2177: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
2178: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2179: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2180: for(mi=1; mi<= wav[i]-1; mi++){
2181: for (ii=1;ii<=nlstate+ndeath;ii++)
2182: for (j=1;j<=nlstate+ndeath;j++){
2183: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2184: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2185: }
2186: for(d=0; d<dh[mi][i]; d++){
2187: newm=savm;
2188: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2189: for (kk=1; kk<=cptcovage;kk++) {
2190: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2191: }
2192:
2193: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2194: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2195: savm=oldm;
2196: oldm=newm;
2197: } /* end mult */
2198:
2199: s1=s[mw[mi][i]][i];
2200: s2=s[mw[mi+1][i]][i];
2201: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2202: ipmx +=1;
2203: sw += weight[i];
2204: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2205: /*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]);*/
2206: } /* end of wave */
2207: } /* end of individual */
2208: } /* End of if */
2209: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2210: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2211: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2212: return -l;
2213: }
2214:
2215: /*************** log-likelihood *************/
2216: double funcone( double *x)
2217: {
2218: /* Same as likeli but slower because of a lot of printf and if */
2219: int i, ii, j, k, mi, d, kk;
2220: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
2221: double **out;
2222: double lli; /* Individual log likelihood */
2223: double llt;
2224: int s1, s2;
2225: double bbh, survp;
2226: /*extern weight */
2227: /* We are differentiating ll according to initial status */
2228: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2229: /*for(i=1;i<imx;i++)
2230: printf(" %d\n",s[4][i]);
2231: */
2232: cov[1]=1.;
2233:
2234: for(k=1; k<=nlstate; k++) ll[k]=0.;
2235:
2236: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2237: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2238: for(mi=1; mi<= wav[i]-1; mi++){
2239: for (ii=1;ii<=nlstate+ndeath;ii++)
2240: for (j=1;j<=nlstate+ndeath;j++){
2241: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2242: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2243: }
2244: for(d=0; d<dh[mi][i]; d++){
2245: newm=savm;
2246: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2247: for (kk=1; kk<=cptcovage;kk++) {
2248: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2249: }
2250: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2251: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2252: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2253: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2254: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
2255: savm=oldm;
2256: oldm=newm;
2257: } /* end mult */
2258:
2259: s1=s[mw[mi][i]][i];
2260: s2=s[mw[mi+1][i]][i];
2261: bbh=(double)bh[mi][i]/(double)stepm;
2262: /* bias is positive if real duration
2263: * is higher than the multiple of stepm and negative otherwise.
2264: */
2265: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2266: lli=log(out[s1][s2] - savm[s1][s2]);
2267: } else if (s2==-2) {
2268: for (j=1,survp=0. ; j<=nlstate; j++)
2269: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2270: lli= log(survp);
2271: }else if (mle==1){
2272: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2273: } else if(mle==2){
2274: 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 */
2275: } else if(mle==3){ /* exponential inter-extrapolation */
2276: 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 */
2277: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2278: lli=log(out[s1][s2]); /* Original formula */
2279: } else{ /* mle=0 back to 1 */
2280: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2281: /*lli=log(out[s1][s2]); */ /* Original formula */
2282: } /* End of if */
2283: ipmx +=1;
2284: sw += weight[i];
2285: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2286: /*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]); */
2287: if(globpr){
2288: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
2289: %11.6f %11.6f %11.6f ", \
2290: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
2291: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2292: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2293: llt +=ll[k]*gipmx/gsw;
2294: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2295: }
2296: fprintf(ficresilk," %10.6f\n", -llt);
2297: }
2298: } /* end of wave */
2299: } /* end of individual */
2300: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2301: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2302: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2303: if(globpr==0){ /* First time we count the contributions and weights */
2304: gipmx=ipmx;
2305: gsw=sw;
2306: }
2307: return -l;
2308: }
2309:
2310:
2311: /*************** function likelione ***********/
2312: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2313: {
2314: /* This routine should help understanding what is done with
2315: the selection of individuals/waves and
2316: to check the exact contribution to the likelihood.
2317: Plotting could be done.
2318: */
2319: int k;
2320:
2321: if(*globpri !=0){ /* Just counts and sums, no printings */
2322: strcpy(fileresilk,"ilk");
2323: strcat(fileresilk,fileres);
2324: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2325: printf("Problem with resultfile: %s\n", fileresilk);
2326: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2327: }
2328: 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");
2329: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
2330: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2331: for(k=1; k<=nlstate; k++)
2332: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2333: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2334: }
2335:
2336: *fretone=(*funcone)(p);
2337: if(*globpri !=0){
2338: fclose(ficresilk);
2339: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
2340: fflush(fichtm);
2341: }
2342: return;
2343: }
2344:
2345:
2346: /*********** Maximum Likelihood Estimation ***************/
2347:
2348: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2349: {
2350: int i,j, iter=0;
2351: double **xi;
2352: double fret;
2353: double fretone; /* Only one call to likelihood */
2354: /* char filerespow[FILENAMELENGTH];*/
2355:
2356: #ifdef NLOPT
2357: int creturn;
2358: nlopt_opt opt;
2359: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2360: double *lb;
2361: double minf; /* the minimum objective value, upon return */
2362: double * p1; /* Shifted parameters from 0 instead of 1 */
2363: myfunc_data dinst, *d = &dinst;
2364: #endif
2365:
2366:
2367: xi=matrix(1,npar,1,npar);
2368: for (i=1;i<=npar;i++)
2369: for (j=1;j<=npar;j++)
2370: xi[i][j]=(i==j ? 1.0 : 0.0);
2371: printf("Powell\n"); fprintf(ficlog,"Powell\n");
2372: strcpy(filerespow,"pow");
2373: strcat(filerespow,fileres);
2374: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2375: printf("Problem with resultfile: %s\n", filerespow);
2376: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2377: }
2378: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2379: for (i=1;i<=nlstate;i++)
2380: for(j=1;j<=nlstate+ndeath;j++)
2381: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2382: fprintf(ficrespow,"\n");
2383: #ifdef POWELL
2384: powell(p,xi,npar,ftol,&iter,&fret,func);
2385: #endif
2386:
2387: #ifdef NLOPT
2388: #ifdef NEWUOA
2389: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2390: #else
2391: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2392: #endif
2393: lb=vector(0,npar-1);
2394: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2395: nlopt_set_lower_bounds(opt, lb);
2396: nlopt_set_initial_step1(opt, 0.1);
2397:
2398: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2399: d->function = func;
2400: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2401: nlopt_set_min_objective(opt, myfunc, d);
2402: nlopt_set_xtol_rel(opt, ftol);
2403: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2404: printf("nlopt failed! %d\n",creturn);
2405: }
2406: else {
2407: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2408: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2409: iter=1; /* not equal */
2410: }
2411: nlopt_destroy(opt);
2412: #endif
2413: free_matrix(xi,1,npar,1,npar);
2414: fclose(ficrespow);
2415: printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2416: fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2417: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2418:
2419: }
2420:
2421: /**** Computes Hessian and covariance matrix ***/
2422: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
2423: {
2424: double **a,**y,*x,pd;
2425: double **hess;
2426: int i, j;
2427: int *indx;
2428:
2429: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
2430: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
2431: void lubksb(double **a, int npar, int *indx, double b[]) ;
2432: void ludcmp(double **a, int npar, int *indx, double *d) ;
2433: double gompertz(double p[]);
2434: hess=matrix(1,npar,1,npar);
2435:
2436: printf("\nCalculation of the hessian matrix. Wait...\n");
2437: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2438: for (i=1;i<=npar;i++){
2439: printf("%d",i);fflush(stdout);
2440: fprintf(ficlog,"%d",i);fflush(ficlog);
2441:
2442: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2443:
2444: /* printf(" %f ",p[i]);
2445: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2446: }
2447:
2448: for (i=1;i<=npar;i++) {
2449: for (j=1;j<=npar;j++) {
2450: if (j>i) {
2451: printf(".%d%d",i,j);fflush(stdout);
2452: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
2453: hess[i][j]=hessij(p,delti,i,j,func,npar);
2454:
2455: hess[j][i]=hess[i][j];
2456: /*printf(" %lf ",hess[i][j]);*/
2457: }
2458: }
2459: }
2460: printf("\n");
2461: fprintf(ficlog,"\n");
2462:
2463: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2464: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2465:
2466: a=matrix(1,npar,1,npar);
2467: y=matrix(1,npar,1,npar);
2468: x=vector(1,npar);
2469: indx=ivector(1,npar);
2470: for (i=1;i<=npar;i++)
2471: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2472: ludcmp(a,npar,indx,&pd);
2473:
2474: for (j=1;j<=npar;j++) {
2475: for (i=1;i<=npar;i++) x[i]=0;
2476: x[j]=1;
2477: lubksb(a,npar,indx,x);
2478: for (i=1;i<=npar;i++){
2479: matcov[i][j]=x[i];
2480: }
2481: }
2482:
2483: printf("\n#Hessian matrix#\n");
2484: fprintf(ficlog,"\n#Hessian matrix#\n");
2485: for (i=1;i<=npar;i++) {
2486: for (j=1;j<=npar;j++) {
2487: printf("%.3e ",hess[i][j]);
2488: fprintf(ficlog,"%.3e ",hess[i][j]);
2489: }
2490: printf("\n");
2491: fprintf(ficlog,"\n");
2492: }
2493:
2494: /* Recompute Inverse */
2495: for (i=1;i<=npar;i++)
2496: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
2497: ludcmp(a,npar,indx,&pd);
2498:
2499: /* printf("\n#Hessian matrix recomputed#\n");
2500:
2501: for (j=1;j<=npar;j++) {
2502: for (i=1;i<=npar;i++) x[i]=0;
2503: x[j]=1;
2504: lubksb(a,npar,indx,x);
2505: for (i=1;i<=npar;i++){
2506: y[i][j]=x[i];
2507: printf("%.3e ",y[i][j]);
2508: fprintf(ficlog,"%.3e ",y[i][j]);
2509: }
2510: printf("\n");
2511: fprintf(ficlog,"\n");
2512: }
2513: */
2514:
2515: free_matrix(a,1,npar,1,npar);
2516: free_matrix(y,1,npar,1,npar);
2517: free_vector(x,1,npar);
2518: free_ivector(indx,1,npar);
2519: free_matrix(hess,1,npar,1,npar);
2520:
2521:
2522: }
2523:
2524: /*************** hessian matrix ****************/
2525: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2526: {
2527: int i;
2528: int l=1, lmax=20;
2529: double k1,k2;
2530: double p2[MAXPARM+1]; /* identical to x */
2531: double res;
2532: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2533: double fx;
2534: int k=0,kmax=10;
2535: double l1;
2536:
2537: fx=func(x);
2538: for (i=1;i<=npar;i++) p2[i]=x[i];
2539: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
2540: l1=pow(10,l);
2541: delts=delt;
2542: for(k=1 ; k <kmax; k=k+1){
2543: delt = delta*(l1*k);
2544: p2[theta]=x[theta] +delt;
2545: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
2546: p2[theta]=x[theta]-delt;
2547: k2=func(p2)-fx;
2548: /*res= (k1-2.0*fx+k2)/delt/delt; */
2549: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2550:
2551: #ifdef DEBUGHESS
2552: 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);
2553: 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);
2554: #endif
2555: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2556: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2557: k=kmax;
2558: }
2559: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
2560: k=kmax; l=lmax*10;
2561: }
2562: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2563: delts=delt;
2564: }
2565: }
2566: }
2567: delti[theta]=delts;
2568: return res;
2569:
2570: }
2571:
2572: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2573: {
2574: int i;
2575: int l=1, lmax=20;
2576: double k1,k2,k3,k4,res,fx;
2577: double p2[MAXPARM+1];
2578: int k;
2579:
2580: fx=func(x);
2581: for (k=1; k<=2; k++) {
2582: for (i=1;i<=npar;i++) p2[i]=x[i];
2583: p2[thetai]=x[thetai]+delti[thetai]/k;
2584: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2585: k1=func(p2)-fx;
2586:
2587: p2[thetai]=x[thetai]+delti[thetai]/k;
2588: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2589: k2=func(p2)-fx;
2590:
2591: p2[thetai]=x[thetai]-delti[thetai]/k;
2592: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2593: k3=func(p2)-fx;
2594:
2595: p2[thetai]=x[thetai]-delti[thetai]/k;
2596: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2597: k4=func(p2)-fx;
2598: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2599: #ifdef DEBUG
2600: 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);
2601: 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);
2602: #endif
2603: }
2604: return res;
2605: }
2606:
2607: /************** Inverse of matrix **************/
2608: void ludcmp(double **a, int n, int *indx, double *d)
2609: {
2610: int i,imax,j,k;
2611: double big,dum,sum,temp;
2612: double *vv;
2613:
2614: vv=vector(1,n);
2615: *d=1.0;
2616: for (i=1;i<=n;i++) {
2617: big=0.0;
2618: for (j=1;j<=n;j++)
2619: if ((temp=fabs(a[i][j])) > big) big=temp;
2620: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2621: vv[i]=1.0/big;
2622: }
2623: for (j=1;j<=n;j++) {
2624: for (i=1;i<j;i++) {
2625: sum=a[i][j];
2626: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2627: a[i][j]=sum;
2628: }
2629: big=0.0;
2630: for (i=j;i<=n;i++) {
2631: sum=a[i][j];
2632: for (k=1;k<j;k++)
2633: sum -= a[i][k]*a[k][j];
2634: a[i][j]=sum;
2635: if ( (dum=vv[i]*fabs(sum)) >= big) {
2636: big=dum;
2637: imax=i;
2638: }
2639: }
2640: if (j != imax) {
2641: for (k=1;k<=n;k++) {
2642: dum=a[imax][k];
2643: a[imax][k]=a[j][k];
2644: a[j][k]=dum;
2645: }
2646: *d = -(*d);
2647: vv[imax]=vv[j];
2648: }
2649: indx[j]=imax;
2650: if (a[j][j] == 0.0) a[j][j]=TINY;
2651: if (j != n) {
2652: dum=1.0/(a[j][j]);
2653: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2654: }
2655: }
2656: free_vector(vv,1,n); /* Doesn't work */
2657: ;
2658: }
2659:
2660: void lubksb(double **a, int n, int *indx, double b[])
2661: {
2662: int i,ii=0,ip,j;
2663: double sum;
2664:
2665: for (i=1;i<=n;i++) {
2666: ip=indx[i];
2667: sum=b[ip];
2668: b[ip]=b[i];
2669: if (ii)
2670: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2671: else if (sum) ii=i;
2672: b[i]=sum;
2673: }
2674: for (i=n;i>=1;i--) {
2675: sum=b[i];
2676: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2677: b[i]=sum/a[i][i];
2678: }
2679: }
2680:
2681: void pstamp(FILE *fichier)
2682: {
2683: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2684: }
2685:
2686: /************ Frequencies ********************/
2687: 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[])
2688: { /* Some frequencies */
2689:
2690: int i, m, jk, j1, bool, z1,j;
2691: int first;
2692: double ***freq; /* Frequencies */
2693: double *pp, **prop;
2694: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2695: char fileresp[FILENAMELENGTH];
2696:
2697: pp=vector(1,nlstate);
2698: prop=matrix(1,nlstate,iagemin,iagemax+3);
2699: strcpy(fileresp,"p");
2700: strcat(fileresp,fileres);
2701: if((ficresp=fopen(fileresp,"w"))==NULL) {
2702: printf("Problem with prevalence resultfile: %s\n", fileresp);
2703: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2704: exit(0);
2705: }
2706: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2707: j1=0;
2708:
2709: j=cptcoveff;
2710: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2711:
2712: first=1;
2713:
2714: /* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */
2715: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
2716: /* j1++; */
2717: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
2718: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2719: scanf("%d", i);*/
2720: for (i=-5; i<=nlstate+ndeath; i++)
2721: for (jk=-5; jk<=nlstate+ndeath; jk++)
2722: for(m=iagemin; m <= iagemax+3; m++)
2723: freq[i][jk][m]=0;
2724:
2725: for (i=1; i<=nlstate; i++)
2726: for(m=iagemin; m <= iagemax+3; m++)
2727: prop[i][m]=0;
2728:
2729: dateintsum=0;
2730: k2cpt=0;
2731: for (i=1; i<=imx; i++) {
2732: bool=1;
2733: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
2734: for (z1=1; z1<=cptcoveff; z1++)
2735: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
2736: /* Tests if the value of each of the covariates of i is equal to filter j1 */
2737: bool=0;
2738: /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n",
2739: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
2740: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
2741: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
2742: }
2743: }
2744:
2745: if (bool==1){
2746: for(m=firstpass; m<=lastpass; m++){
2747: k2=anint[m][i]+(mint[m][i]/12.);
2748: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2749: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2750: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2751: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2752: if (m<lastpass) {
2753: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2754: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2755: }
2756:
2757: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2758: dateintsum=dateintsum+k2;
2759: k2cpt++;
2760: }
2761: /*}*/
2762: }
2763: }
2764: } /* end i */
2765:
2766: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2767: pstamp(ficresp);
2768: if (cptcovn>0) {
2769: fprintf(ficresp, "\n#********** Variable ");
2770: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2771: fprintf(ficresp, "**********\n#");
2772: fprintf(ficlog, "\n#********** Variable ");
2773: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2774: fprintf(ficlog, "**********\n#");
2775: }
2776: for(i=1; i<=nlstate;i++)
2777: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2778: fprintf(ficresp, "\n");
2779:
2780: for(i=iagemin; i <= iagemax+3; i++){
2781: if(i==iagemax+3){
2782: fprintf(ficlog,"Total");
2783: }else{
2784: if(first==1){
2785: first=0;
2786: printf("See log file for details...\n");
2787: }
2788: fprintf(ficlog,"Age %d", i);
2789: }
2790: for(jk=1; jk <=nlstate ; jk++){
2791: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2792: pp[jk] += freq[jk][m][i];
2793: }
2794: for(jk=1; jk <=nlstate ; jk++){
2795: for(m=-1, pos=0; m <=0 ; m++)
2796: pos += freq[jk][m][i];
2797: if(pp[jk]>=1.e-10){
2798: if(first==1){
2799: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2800: }
2801: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2802: }else{
2803: if(first==1)
2804: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2805: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2806: }
2807: }
2808:
2809: for(jk=1; jk <=nlstate ; jk++){
2810: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2811: pp[jk] += freq[jk][m][i];
2812: }
2813: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2814: pos += pp[jk];
2815: posprop += prop[jk][i];
2816: }
2817: for(jk=1; jk <=nlstate ; jk++){
2818: if(pos>=1.e-5){
2819: if(first==1)
2820: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2821: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2822: }else{
2823: if(first==1)
2824: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2825: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2826: }
2827: if( i <= iagemax){
2828: if(pos>=1.e-5){
2829: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2830: /*probs[i][jk][j1]= pp[jk]/pos;*/
2831: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2832: }
2833: else
2834: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2835: }
2836: }
2837:
2838: for(jk=-1; jk <=nlstate+ndeath; jk++)
2839: for(m=-1; m <=nlstate+ndeath; m++)
2840: if(freq[jk][m][i] !=0 ) {
2841: if(first==1)
2842: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2843: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2844: }
2845: if(i <= iagemax)
2846: fprintf(ficresp,"\n");
2847: if(first==1)
2848: printf("Others in log...\n");
2849: fprintf(ficlog,"\n");
2850: }
2851: /*}*/
2852: }
2853: dateintmean=dateintsum/k2cpt;
2854:
2855: fclose(ficresp);
2856: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2857: free_vector(pp,1,nlstate);
2858: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2859: /* End of Freq */
2860: }
2861:
2862: /************ Prevalence ********************/
2863: 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)
2864: {
2865: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2866: in each health status at the date of interview (if between dateprev1 and dateprev2).
2867: We still use firstpass and lastpass as another selection.
2868: */
2869:
2870: int i, m, jk, j1, bool, z1,j;
2871:
2872: double **prop;
2873: double posprop;
2874: double y2; /* in fractional years */
2875: int iagemin, iagemax;
2876: int first; /** to stop verbosity which is redirected to log file */
2877:
2878: iagemin= (int) agemin;
2879: iagemax= (int) agemax;
2880: /*pp=vector(1,nlstate);*/
2881: prop=matrix(1,nlstate,iagemin,iagemax+3);
2882: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2883: j1=0;
2884:
2885: /*j=cptcoveff;*/
2886: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2887:
2888: first=1;
2889: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
2890: /*for(i1=1; i1<=ncodemax[k1];i1++){
2891: j1++;*/
2892:
2893: for (i=1; i<=nlstate; i++)
2894: for(m=iagemin; m <= iagemax+3; m++)
2895: prop[i][m]=0.0;
2896:
2897: for (i=1; i<=imx; i++) { /* Each individual */
2898: bool=1;
2899: if (cptcovn>0) {
2900: for (z1=1; z1<=cptcoveff; z1++)
2901: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2902: bool=0;
2903: }
2904: if (bool==1) {
2905: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2906: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2907: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2908: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2909: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2910: 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);
2911: if (s[m][i]>0 && s[m][i]<=nlstate) {
2912: /*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]]);*/
2913: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2914: prop[s[m][i]][iagemax+3] += weight[i];
2915: }
2916: }
2917: } /* end selection of waves */
2918: }
2919: }
2920: for(i=iagemin; i <= iagemax+3; i++){
2921: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2922: posprop += prop[jk][i];
2923: }
2924:
2925: for(jk=1; jk <=nlstate ; jk++){
2926: if( i <= iagemax){
2927: if(posprop>=1.e-5){
2928: probs[i][jk][j1]= prop[jk][i]/posprop;
2929: } else{
2930: if(first==1){
2931: first=0;
2932: 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]);
2933: }
2934: }
2935: }
2936: }/* end jk */
2937: }/* end i */
2938: /*} *//* end i1 */
2939: } /* end j1 */
2940:
2941: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2942: /*free_vector(pp,1,nlstate);*/
2943: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2944: } /* End of prevalence */
2945:
2946: /************* Waves Concatenation ***************/
2947:
2948: 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)
2949: {
2950: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2951: Death is a valid wave (if date is known).
2952: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2953: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2954: and mw[mi+1][i]. dh depends on stepm.
2955: */
2956:
2957: int i, mi, m;
2958: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2959: double sum=0., jmean=0.;*/
2960: int first;
2961: int j, k=0,jk, ju, jl;
2962: double sum=0.;
2963: first=0;
2964: jmin=100000;
2965: jmax=-1;
2966: jmean=0.;
2967: for(i=1; i<=imx; i++){
2968: mi=0;
2969: m=firstpass;
2970: while(s[m][i] <= nlstate){
2971: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2972: mw[++mi][i]=m;
2973: if(m >=lastpass)
2974: break;
2975: else
2976: m++;
2977: }/* end while */
2978: if (s[m][i] > nlstate){
2979: mi++; /* Death is another wave */
2980: /* if(mi==0) never been interviewed correctly before death */
2981: /* Only death is a correct wave */
2982: mw[mi][i]=m;
2983: }
2984:
2985: wav[i]=mi;
2986: if(mi==0){
2987: nbwarn++;
2988: if(first==0){
2989: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2990: first=1;
2991: }
2992: if(first==1){
2993: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2994: }
2995: } /* end mi==0 */
2996: } /* End individuals */
2997:
2998: for(i=1; i<=imx; i++){
2999: for(mi=1; mi<wav[i];mi++){
3000: if (stepm <=0)
3001: dh[mi][i]=1;
3002: else{
3003: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
3004: if (agedc[i] < 2*AGESUP) {
3005: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
3006: if(j==0) j=1; /* Survives at least one month after exam */
3007: else if(j<0){
3008: nberr++;
3009: 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]);
3010: j=1; /* Temporary Dangerous patch */
3011: 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);
3012: 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]);
3013: 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);
3014: }
3015: k=k+1;
3016: if (j >= jmax){
3017: jmax=j;
3018: ijmax=i;
3019: }
3020: if (j <= jmin){
3021: jmin=j;
3022: ijmin=i;
3023: }
3024: sum=sum+j;
3025: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
3026: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
3027: }
3028: }
3029: else{
3030: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
3031: /* 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]); */
3032:
3033: k=k+1;
3034: if (j >= jmax) {
3035: jmax=j;
3036: ijmax=i;
3037: }
3038: else if (j <= jmin){
3039: jmin=j;
3040: ijmin=i;
3041: }
3042: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
3043: /*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]);*/
3044: if(j<0){
3045: nberr++;
3046: 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]);
3047: 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]);
3048: }
3049: sum=sum+j;
3050: }
3051: jk= j/stepm;
3052: jl= j -jk*stepm;
3053: ju= j -(jk+1)*stepm;
3054: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
3055: if(jl==0){
3056: dh[mi][i]=jk;
3057: bh[mi][i]=0;
3058: }else{ /* We want a negative bias in order to only have interpolation ie
3059: * to avoid the price of an extra matrix product in likelihood */
3060: dh[mi][i]=jk+1;
3061: bh[mi][i]=ju;
3062: }
3063: }else{
3064: if(jl <= -ju){
3065: dh[mi][i]=jk;
3066: bh[mi][i]=jl; /* bias is positive if real duration
3067: * is higher than the multiple of stepm and negative otherwise.
3068: */
3069: }
3070: else{
3071: dh[mi][i]=jk+1;
3072: bh[mi][i]=ju;
3073: }
3074: if(dh[mi][i]==0){
3075: dh[mi][i]=1; /* At least one step */
3076: bh[mi][i]=ju; /* At least one step */
3077: /* 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);*/
3078: }
3079: } /* end if mle */
3080: }
3081: } /* end wave */
3082: }
3083: jmean=sum/k;
3084: 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);
3085: 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);
3086: }
3087:
3088: /*********** Tricode ****************************/
3089: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
3090: {
3091: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
3092: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
3093: * Boring subroutine which should only output nbcode[Tvar[j]][k]
3094: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
3095: * nbcode[Tvar[j]][1]=
3096: */
3097:
3098: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
3099: int modmaxcovj=0; /* Modality max of covariates j */
3100: int cptcode=0; /* Modality max of covariates j */
3101: int modmincovj=0; /* Modality min of covariates j */
3102:
3103:
3104: cptcoveff=0;
3105:
3106: for (k=-1; k < maxncov; k++) Ndum[k]=0;
3107: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
3108:
3109: /* Loop on covariates without age and products */
3110: for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
3111: for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the
3112: modality of this covariate Vj*/
3113: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
3114: * If product of Vn*Vm, still boolean *:
3115: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
3116: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
3117: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
3118: modality of the nth covariate of individual i. */
3119: if (ij > modmaxcovj)
3120: modmaxcovj=ij;
3121: else if (ij < modmincovj)
3122: modmincovj=ij;
3123: if ((ij < -1) && (ij > NCOVMAX)){
3124: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
3125: exit(1);
3126: }else
3127: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
3128: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
3129: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
3130: /* getting the maximum value of the modality of the covariate
3131: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
3132: female is 1, then modmaxcovj=1.*/
3133: }
3134: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
3135: cptcode=modmaxcovj;
3136: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
3137: /*for (i=0; i<=cptcode; i++) {*/
3138: for (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
3139: printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
3140: if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
3141: ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
3142: }
3143: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
3144: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
3145: } /* Ndum[-1] number of undefined modalities */
3146:
3147: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
3148: /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
3149: /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
3150: modmincovj=3; modmaxcovj = 7;
3151: There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
3152: which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy
3153: variables V1_1 and V1_2.
3154: nbcode[Tvar[j]][ij]=k;
3155: nbcode[Tvar[j]][1]=0;
3156: nbcode[Tvar[j]][2]=1;
3157: nbcode[Tvar[j]][3]=2;
3158: */
3159: ij=1; /* ij is similar to i but can jumps over null modalities */
3160: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
3161: for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
3162: /*recode from 0 */
3163: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
3164: nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode.
3165: k is a modality. If we have model=V1+V1*sex
3166: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
3167: ij++;
3168: }
3169: if (ij > ncodemax[j]) break;
3170: } /* end of loop on */
3171: } /* end of loop on modality */
3172: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
3173:
3174: for (k=-1; k< maxncov; k++) Ndum[k]=0;
3175:
3176: for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
3177: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
3178: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
3179: Ndum[ij]++;
3180: }
3181:
3182: ij=1;
3183: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
3184: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
3185: if((Ndum[i]!=0) && (i<=ncovcol)){
3186: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
3187: Tvaraff[ij]=i; /*For printing (unclear) */
3188: ij++;
3189: }else
3190: Tvaraff[ij]=0;
3191: }
3192: ij--;
3193: cptcoveff=ij; /*Number of total covariates*/
3194:
3195: }
3196:
3197:
3198: /*********** Health Expectancies ****************/
3199:
3200: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
3201:
3202: {
3203: /* Health expectancies, no variances */
3204: int i, j, nhstepm, hstepm, h, nstepm;
3205: int nhstepma, nstepma; /* Decreasing with age */
3206: double age, agelim, hf;
3207: double ***p3mat;
3208: double eip;
3209:
3210: pstamp(ficreseij);
3211: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3212: fprintf(ficreseij,"# Age");
3213: for(i=1; i<=nlstate;i++){
3214: for(j=1; j<=nlstate;j++){
3215: fprintf(ficreseij," e%1d%1d ",i,j);
3216: }
3217: fprintf(ficreseij," e%1d. ",i);
3218: }
3219: fprintf(ficreseij,"\n");
3220:
3221:
3222: if(estepm < stepm){
3223: printf ("Problem %d lower than %d\n",estepm, stepm);
3224: }
3225: else hstepm=estepm;
3226: /* We compute the life expectancy from trapezoids spaced every estepm months
3227: * This is mainly to measure the difference between two models: for example
3228: * if stepm=24 months pijx are given only every 2 years and by summing them
3229: * we are calculating an estimate of the Life Expectancy assuming a linear
3230: * progression in between and thus overestimating or underestimating according
3231: * to the curvature of the survival function. If, for the same date, we
3232: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3233: * to compare the new estimate of Life expectancy with the same linear
3234: * hypothesis. A more precise result, taking into account a more precise
3235: * curvature will be obtained if estepm is as small as stepm. */
3236:
3237: /* For example we decided to compute the life expectancy with the smallest unit */
3238: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3239: nhstepm is the number of hstepm from age to agelim
3240: nstepm is the number of stepm from age to agelin.
3241: Look at hpijx to understand the reason of that which relies in memory size
3242: and note for a fixed period like estepm months */
3243: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3244: survival function given by stepm (the optimization length). Unfortunately it
3245: means that if the survival funtion is printed only each two years of age and if
3246: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3247: results. So we changed our mind and took the option of the best precision.
3248: */
3249: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3250:
3251: agelim=AGESUP;
3252: /* If stepm=6 months */
3253: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3254: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3255:
3256: /* nhstepm age range expressed in number of stepm */
3257: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3258: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3259: /* if (stepm >= YEARM) hstepm=1;*/
3260: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3261: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3262:
3263: for (age=bage; age<=fage; age ++){
3264: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3265: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3266: /* if (stepm >= YEARM) hstepm=1;*/
3267: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3268:
3269: /* If stepm=6 months */
3270: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3271: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3272:
3273: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3274:
3275: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3276:
3277: printf("%d|",(int)age);fflush(stdout);
3278: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3279:
3280: /* Computing expectancies */
3281: for(i=1; i<=nlstate;i++)
3282: for(j=1; j<=nlstate;j++)
3283: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3284: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3285:
3286: /* 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]);*/
3287:
3288: }
3289:
3290: fprintf(ficreseij,"%3.0f",age );
3291: for(i=1; i<=nlstate;i++){
3292: eip=0;
3293: for(j=1; j<=nlstate;j++){
3294: eip +=eij[i][j][(int)age];
3295: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3296: }
3297: fprintf(ficreseij,"%9.4f", eip );
3298: }
3299: fprintf(ficreseij,"\n");
3300:
3301: }
3302: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3303: printf("\n");
3304: fprintf(ficlog,"\n");
3305:
3306: }
3307:
3308: 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[] )
3309:
3310: {
3311: /* Covariances of health expectancies eij and of total life expectancies according
3312: to initial status i, ei. .
3313: */
3314: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3315: int nhstepma, nstepma; /* Decreasing with age */
3316: double age, agelim, hf;
3317: double ***p3matp, ***p3matm, ***varhe;
3318: double **dnewm,**doldm;
3319: double *xp, *xm;
3320: double **gp, **gm;
3321: double ***gradg, ***trgradg;
3322: int theta;
3323:
3324: double eip, vip;
3325:
3326: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
3327: xp=vector(1,npar);
3328: xm=vector(1,npar);
3329: dnewm=matrix(1,nlstate*nlstate,1,npar);
3330: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3331:
3332: pstamp(ficresstdeij);
3333: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3334: fprintf(ficresstdeij,"# Age");
3335: for(i=1; i<=nlstate;i++){
3336: for(j=1; j<=nlstate;j++)
3337: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3338: fprintf(ficresstdeij," e%1d. ",i);
3339: }
3340: fprintf(ficresstdeij,"\n");
3341:
3342: pstamp(ficrescveij);
3343: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3344: fprintf(ficrescveij,"# Age");
3345: for(i=1; i<=nlstate;i++)
3346: for(j=1; j<=nlstate;j++){
3347: cptj= (j-1)*nlstate+i;
3348: for(i2=1; i2<=nlstate;i2++)
3349: for(j2=1; j2<=nlstate;j2++){
3350: cptj2= (j2-1)*nlstate+i2;
3351: if(cptj2 <= cptj)
3352: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3353: }
3354: }
3355: fprintf(ficrescveij,"\n");
3356:
3357: if(estepm < stepm){
3358: printf ("Problem %d lower than %d\n",estepm, stepm);
3359: }
3360: else hstepm=estepm;
3361: /* We compute the life expectancy from trapezoids spaced every estepm months
3362: * This is mainly to measure the difference between two models: for example
3363: * if stepm=24 months pijx are given only every 2 years and by summing them
3364: * we are calculating an estimate of the Life Expectancy assuming a linear
3365: * progression in between and thus overestimating or underestimating according
3366: * to the curvature of the survival function. If, for the same date, we
3367: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3368: * to compare the new estimate of Life expectancy with the same linear
3369: * hypothesis. A more precise result, taking into account a more precise
3370: * curvature will be obtained if estepm is as small as stepm. */
3371:
3372: /* For example we decided to compute the life expectancy with the smallest unit */
3373: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3374: nhstepm is the number of hstepm from age to agelim
3375: nstepm is the number of stepm from age to agelin.
3376: Look at hpijx to understand the reason of that which relies in memory size
3377: and note for a fixed period like estepm months */
3378: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3379: survival function given by stepm (the optimization length). Unfortunately it
3380: means that if the survival funtion is printed only each two years of age and if
3381: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3382: results. So we changed our mind and took the option of the best precision.
3383: */
3384: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3385:
3386: /* If stepm=6 months */
3387: /* nhstepm age range expressed in number of stepm */
3388: agelim=AGESUP;
3389: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3390: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3391: /* if (stepm >= YEARM) hstepm=1;*/
3392: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3393:
3394: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3395: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3396: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3397: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3398: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3399: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3400:
3401: for (age=bage; age<=fage; age ++){
3402: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3403: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3404: /* if (stepm >= YEARM) hstepm=1;*/
3405: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3406:
3407: /* If stepm=6 months */
3408: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3409: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3410:
3411: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3412:
3413: /* Computing Variances of health expectancies */
3414: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3415: decrease memory allocation */
3416: for(theta=1; theta <=npar; theta++){
3417: for(i=1; i<=npar; i++){
3418: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3419: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3420: }
3421: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3422: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3423:
3424: for(j=1; j<= nlstate; j++){
3425: for(i=1; i<=nlstate; i++){
3426: for(h=0; h<=nhstepm-1; h++){
3427: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3428: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3429: }
3430: }
3431: }
3432:
3433: for(ij=1; ij<= nlstate*nlstate; ij++)
3434: for(h=0; h<=nhstepm-1; h++){
3435: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3436: }
3437: }/* End theta */
3438:
3439:
3440: for(h=0; h<=nhstepm-1; h++)
3441: for(j=1; j<=nlstate*nlstate;j++)
3442: for(theta=1; theta <=npar; theta++)
3443: trgradg[h][j][theta]=gradg[h][theta][j];
3444:
3445:
3446: for(ij=1;ij<=nlstate*nlstate;ij++)
3447: for(ji=1;ji<=nlstate*nlstate;ji++)
3448: varhe[ij][ji][(int)age] =0.;
3449:
3450: printf("%d|",(int)age);fflush(stdout);
3451: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3452: for(h=0;h<=nhstepm-1;h++){
3453: for(k=0;k<=nhstepm-1;k++){
3454: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3455: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3456: for(ij=1;ij<=nlstate*nlstate;ij++)
3457: for(ji=1;ji<=nlstate*nlstate;ji++)
3458: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3459: }
3460: }
3461:
3462: /* Computing expectancies */
3463: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3464: for(i=1; i<=nlstate;i++)
3465: for(j=1; j<=nlstate;j++)
3466: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3467: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3468:
3469: /* 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]);*/
3470:
3471: }
3472:
3473: fprintf(ficresstdeij,"%3.0f",age );
3474: for(i=1; i<=nlstate;i++){
3475: eip=0.;
3476: vip=0.;
3477: for(j=1; j<=nlstate;j++){
3478: eip += eij[i][j][(int)age];
3479: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3480: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3481: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3482: }
3483: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3484: }
3485: fprintf(ficresstdeij,"\n");
3486:
3487: fprintf(ficrescveij,"%3.0f",age );
3488: for(i=1; i<=nlstate;i++)
3489: for(j=1; j<=nlstate;j++){
3490: cptj= (j-1)*nlstate+i;
3491: for(i2=1; i2<=nlstate;i2++)
3492: for(j2=1; j2<=nlstate;j2++){
3493: cptj2= (j2-1)*nlstate+i2;
3494: if(cptj2 <= cptj)
3495: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3496: }
3497: }
3498: fprintf(ficrescveij,"\n");
3499:
3500: }
3501: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3502: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3503: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3504: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3505: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3506: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3507: printf("\n");
3508: fprintf(ficlog,"\n");
3509:
3510: free_vector(xm,1,npar);
3511: free_vector(xp,1,npar);
3512: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3513: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3514: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3515: }
3516:
3517: /************ Variance ******************/
3518: 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[])
3519: {
3520: /* Variance of health expectancies */
3521: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3522: /* double **newm;*/
3523: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
3524:
3525: int movingaverage();
3526: double **dnewm,**doldm;
3527: double **dnewmp,**doldmp;
3528: int i, j, nhstepm, hstepm, h, nstepm ;
3529: int k;
3530: double *xp;
3531: double **gp, **gm; /* for var eij */
3532: double ***gradg, ***trgradg; /*for var eij */
3533: double **gradgp, **trgradgp; /* for var p point j */
3534: double *gpp, *gmp; /* for var p point j */
3535: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3536: double ***p3mat;
3537: double age,agelim, hf;
3538: double ***mobaverage;
3539: int theta;
3540: char digit[4];
3541: char digitp[25];
3542:
3543: char fileresprobmorprev[FILENAMELENGTH];
3544:
3545: if(popbased==1){
3546: if(mobilav!=0)
3547: strcpy(digitp,"-populbased-mobilav-");
3548: else strcpy(digitp,"-populbased-nomobil-");
3549: }
3550: else
3551: strcpy(digitp,"-stablbased-");
3552:
3553: if (mobilav!=0) {
3554: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3555: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3556: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3557: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3558: }
3559: }
3560:
3561: strcpy(fileresprobmorprev,"prmorprev");
3562: sprintf(digit,"%-d",ij);
3563: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3564: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3565: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
3566: strcat(fileresprobmorprev,fileres);
3567: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3568: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3569: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3570: }
3571: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3572:
3573: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3574: pstamp(ficresprobmorprev);
3575: 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);
3576: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3577: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3578: fprintf(ficresprobmorprev," p.%-d SE",j);
3579: for(i=1; i<=nlstate;i++)
3580: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3581: }
3582: fprintf(ficresprobmorprev,"\n");
3583: fprintf(ficgp,"\n# Routine varevsij");
3584: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
3585: 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");
3586: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3587: /* } */
3588: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3589: pstamp(ficresvij);
3590: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3591: if(popbased==1)
3592: 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);
3593: else
3594: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3595: fprintf(ficresvij,"# Age");
3596: for(i=1; i<=nlstate;i++)
3597: for(j=1; j<=nlstate;j++)
3598: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3599: fprintf(ficresvij,"\n");
3600:
3601: xp=vector(1,npar);
3602: dnewm=matrix(1,nlstate,1,npar);
3603: doldm=matrix(1,nlstate,1,nlstate);
3604: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3605: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3606:
3607: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3608: gpp=vector(nlstate+1,nlstate+ndeath);
3609: gmp=vector(nlstate+1,nlstate+ndeath);
3610: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3611:
3612: if(estepm < stepm){
3613: printf ("Problem %d lower than %d\n",estepm, stepm);
3614: }
3615: else hstepm=estepm;
3616: /* For example we decided to compute the life expectancy with the smallest unit */
3617: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3618: nhstepm is the number of hstepm from age to agelim
3619: nstepm is the number of stepm from age to agelin.
3620: Look at function hpijx to understand why (it is linked to memory size questions) */
3621: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3622: survival function given by stepm (the optimization length). Unfortunately it
3623: means that if the survival funtion is printed every two years of age and if
3624: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3625: results. So we changed our mind and took the option of the best precision.
3626: */
3627: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3628: agelim = AGESUP;
3629: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3630: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3631: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3632: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3633: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3634: gp=matrix(0,nhstepm,1,nlstate);
3635: gm=matrix(0,nhstepm,1,nlstate);
3636:
3637:
3638: for(theta=1; theta <=npar; theta++){
3639: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3640: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3641: }
3642: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3643: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3644:
3645: if (popbased==1) {
3646: if(mobilav ==0){
3647: for(i=1; i<=nlstate;i++)
3648: prlim[i][i]=probs[(int)age][i][ij];
3649: }else{ /* mobilav */
3650: for(i=1; i<=nlstate;i++)
3651: prlim[i][i]=mobaverage[(int)age][i][ij];
3652: }
3653: }
3654:
3655: for(j=1; j<= nlstate; j++){
3656: for(h=0; h<=nhstepm; h++){
3657: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3658: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3659: }
3660: }
3661: /* This for computing probability of death (h=1 means
3662: computed over hstepm matrices product = hstepm*stepm months)
3663: as a weighted average of prlim.
3664: */
3665: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3666: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3667: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3668: }
3669: /* end probability of death */
3670:
3671: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3672: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3673: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3674: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3675:
3676: if (popbased==1) {
3677: if(mobilav ==0){
3678: for(i=1; i<=nlstate;i++)
3679: prlim[i][i]=probs[(int)age][i][ij];
3680: }else{ /* mobilav */
3681: for(i=1; i<=nlstate;i++)
3682: prlim[i][i]=mobaverage[(int)age][i][ij];
3683: }
3684: }
3685:
3686: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
3687: for(h=0; h<=nhstepm; h++){
3688: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3689: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3690: }
3691: }
3692: /* This for computing probability of death (h=1 means
3693: computed over hstepm matrices product = hstepm*stepm months)
3694: as a weighted average of prlim.
3695: */
3696: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3697: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3698: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3699: }
3700: /* end probability of death */
3701:
3702: for(j=1; j<= nlstate; j++) /* vareij */
3703: for(h=0; h<=nhstepm; h++){
3704: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3705: }
3706:
3707: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3708: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3709: }
3710:
3711: } /* End theta */
3712:
3713: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3714:
3715: for(h=0; h<=nhstepm; h++) /* veij */
3716: for(j=1; j<=nlstate;j++)
3717: for(theta=1; theta <=npar; theta++)
3718: trgradg[h][j][theta]=gradg[h][theta][j];
3719:
3720: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3721: for(theta=1; theta <=npar; theta++)
3722: trgradgp[j][theta]=gradgp[theta][j];
3723:
3724:
3725: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3726: for(i=1;i<=nlstate;i++)
3727: for(j=1;j<=nlstate;j++)
3728: vareij[i][j][(int)age] =0.;
3729:
3730: for(h=0;h<=nhstepm;h++){
3731: for(k=0;k<=nhstepm;k++){
3732: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3733: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3734: for(i=1;i<=nlstate;i++)
3735: for(j=1;j<=nlstate;j++)
3736: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3737: }
3738: }
3739:
3740: /* pptj */
3741: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3742: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3743: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3744: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3745: varppt[j][i]=doldmp[j][i];
3746: /* end ppptj */
3747: /* x centered again */
3748: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3749: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3750:
3751: if (popbased==1) {
3752: if(mobilav ==0){
3753: for(i=1; i<=nlstate;i++)
3754: prlim[i][i]=probs[(int)age][i][ij];
3755: }else{ /* mobilav */
3756: for(i=1; i<=nlstate;i++)
3757: prlim[i][i]=mobaverage[(int)age][i][ij];
3758: }
3759: }
3760:
3761: /* This for computing probability of death (h=1 means
3762: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3763: as a weighted average of prlim.
3764: */
3765: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3766: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3767: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3768: }
3769: /* end probability of death */
3770:
3771: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3772: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3773: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3774: for(i=1; i<=nlstate;i++){
3775: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3776: }
3777: }
3778: fprintf(ficresprobmorprev,"\n");
3779:
3780: fprintf(ficresvij,"%.0f ",age );
3781: for(i=1; i<=nlstate;i++)
3782: for(j=1; j<=nlstate;j++){
3783: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3784: }
3785: fprintf(ficresvij,"\n");
3786: free_matrix(gp,0,nhstepm,1,nlstate);
3787: free_matrix(gm,0,nhstepm,1,nlstate);
3788: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3789: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3790: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3791: } /* End age */
3792: free_vector(gpp,nlstate+1,nlstate+ndeath);
3793: free_vector(gmp,nlstate+1,nlstate+ndeath);
3794: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3795: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3796: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
3797: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
3798: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
3799: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3800: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3801: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
3802: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
3803: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
3804: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
3805: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3806: fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3807: /* 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.png\"> <br>\n", stepm,YEARM,digitp,digit);
3808: */
3809: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3810: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3811:
3812: free_vector(xp,1,npar);
3813: free_matrix(doldm,1,nlstate,1,nlstate);
3814: free_matrix(dnewm,1,nlstate,1,npar);
3815: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3816: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3817: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3818: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3819: fclose(ficresprobmorprev);
3820: fflush(ficgp);
3821: fflush(fichtm);
3822: } /* end varevsij */
3823:
3824: /************ Variance of prevlim ******************/
3825: 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[])
3826: {
3827: /* Variance of prevalence limit */
3828: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
3829:
3830: double **dnewm,**doldm;
3831: int i, j, nhstepm, hstepm;
3832: double *xp;
3833: double *gp, *gm;
3834: double **gradg, **trgradg;
3835: double age,agelim;
3836: int theta;
3837:
3838: pstamp(ficresvpl);
3839: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3840: fprintf(ficresvpl,"# Age");
3841: for(i=1; i<=nlstate;i++)
3842: fprintf(ficresvpl," %1d-%1d",i,i);
3843: fprintf(ficresvpl,"\n");
3844:
3845: xp=vector(1,npar);
3846: dnewm=matrix(1,nlstate,1,npar);
3847: doldm=matrix(1,nlstate,1,nlstate);
3848:
3849: hstepm=1*YEARM; /* Every year of age */
3850: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3851: agelim = AGESUP;
3852: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3853: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3854: if (stepm >= YEARM) hstepm=1;
3855: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3856: gradg=matrix(1,npar,1,nlstate);
3857: gp=vector(1,nlstate);
3858: gm=vector(1,nlstate);
3859:
3860: for(theta=1; theta <=npar; theta++){
3861: for(i=1; i<=npar; i++){ /* Computes gradient */
3862: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3863: }
3864: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3865: for(i=1;i<=nlstate;i++)
3866: gp[i] = prlim[i][i];
3867:
3868: for(i=1; i<=npar; i++) /* Computes gradient */
3869: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3870: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3871: for(i=1;i<=nlstate;i++)
3872: gm[i] = prlim[i][i];
3873:
3874: for(i=1;i<=nlstate;i++)
3875: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3876: } /* End theta */
3877:
3878: trgradg =matrix(1,nlstate,1,npar);
3879:
3880: for(j=1; j<=nlstate;j++)
3881: for(theta=1; theta <=npar; theta++)
3882: trgradg[j][theta]=gradg[theta][j];
3883:
3884: for(i=1;i<=nlstate;i++)
3885: varpl[i][(int)age] =0.;
3886: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3887: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3888: for(i=1;i<=nlstate;i++)
3889: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3890:
3891: fprintf(ficresvpl,"%.0f ",age );
3892: for(i=1; i<=nlstate;i++)
3893: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3894: fprintf(ficresvpl,"\n");
3895: free_vector(gp,1,nlstate);
3896: free_vector(gm,1,nlstate);
3897: free_matrix(gradg,1,npar,1,nlstate);
3898: free_matrix(trgradg,1,nlstate,1,npar);
3899: } /* End age */
3900:
3901: free_vector(xp,1,npar);
3902: free_matrix(doldm,1,nlstate,1,npar);
3903: free_matrix(dnewm,1,nlstate,1,nlstate);
3904:
3905: }
3906:
3907: /************ Variance of one-step probabilities ******************/
3908: 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[])
3909: {
3910: int i, j=0, k1, l1, tj;
3911: int k2, l2, j1, z1;
3912: int k=0, l;
3913: int first=1, first1, first2;
3914: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3915: double **dnewm,**doldm;
3916: double *xp;
3917: double *gp, *gm;
3918: double **gradg, **trgradg;
3919: double **mu;
3920: double age, cov[NCOVMAX+1];
3921: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3922: int theta;
3923: char fileresprob[FILENAMELENGTH];
3924: char fileresprobcov[FILENAMELENGTH];
3925: char fileresprobcor[FILENAMELENGTH];
3926: double ***varpij;
3927:
3928: strcpy(fileresprob,"prob");
3929: strcat(fileresprob,fileres);
3930: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3931: printf("Problem with resultfile: %s\n", fileresprob);
3932: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3933: }
3934: strcpy(fileresprobcov,"probcov");
3935: strcat(fileresprobcov,fileres);
3936: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3937: printf("Problem with resultfile: %s\n", fileresprobcov);
3938: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3939: }
3940: strcpy(fileresprobcor,"probcor");
3941: strcat(fileresprobcor,fileres);
3942: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3943: printf("Problem with resultfile: %s\n", fileresprobcor);
3944: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3945: }
3946: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3947: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3948: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3949: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3950: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3951: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3952: pstamp(ficresprob);
3953: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3954: fprintf(ficresprob,"# Age");
3955: pstamp(ficresprobcov);
3956: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3957: fprintf(ficresprobcov,"# Age");
3958: pstamp(ficresprobcor);
3959: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3960: fprintf(ficresprobcor,"# Age");
3961:
3962:
3963: for(i=1; i<=nlstate;i++)
3964: for(j=1; j<=(nlstate+ndeath);j++){
3965: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3966: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3967: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3968: }
3969: /* fprintf(ficresprob,"\n");
3970: fprintf(ficresprobcov,"\n");
3971: fprintf(ficresprobcor,"\n");
3972: */
3973: xp=vector(1,npar);
3974: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3975: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3976: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3977: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3978: first=1;
3979: fprintf(ficgp,"\n# Routine varprob");
3980: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3981: fprintf(fichtm,"\n");
3982:
3983: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3984: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3985: file %s<br>\n",optionfilehtmcov);
3986: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3987: and drawn. It helps understanding how is the covariance between two incidences.\
3988: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3989: 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. \
3990: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3991: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3992: standard deviations wide on each axis. <br>\
3993: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3994: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3995: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3996:
3997: cov[1]=1;
3998: /* tj=cptcoveff; */
3999: tj = (int) pow(2,cptcoveff);
4000: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
4001: j1=0;
4002: for(j1=1; j1<=tj;j1++){
4003: /*for(i1=1; i1<=ncodemax[t];i1++){ */
4004: /*j1++;*/
4005: if (cptcovn>0) {
4006: fprintf(ficresprob, "\n#********** Variable ");
4007: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4008: fprintf(ficresprob, "**********\n#\n");
4009: fprintf(ficresprobcov, "\n#********** Variable ");
4010: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4011: fprintf(ficresprobcov, "**********\n#\n");
4012:
4013: fprintf(ficgp, "\n#********** Variable ");
4014: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4015: fprintf(ficgp, "**********\n#\n");
4016:
4017:
4018: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
4019: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4020: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
4021:
4022: fprintf(ficresprobcor, "\n#********** Variable ");
4023: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4024: fprintf(ficresprobcor, "**********\n#");
4025: }
4026:
4027: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
4028: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4029: gp=vector(1,(nlstate)*(nlstate+ndeath));
4030: gm=vector(1,(nlstate)*(nlstate+ndeath));
4031: for (age=bage; age<=fage; age ++){
4032: cov[2]=age;
4033: for (k=1; k<=cptcovn;k++) {
4034: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
4035: * 1 1 1 1 1
4036: * 2 2 1 1 1
4037: * 3 1 2 1 1
4038: */
4039: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
4040: }
4041: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
4042: for (k=1; k<=cptcovprod;k++)
4043: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
4044:
4045:
4046: for(theta=1; theta <=npar; theta++){
4047: for(i=1; i<=npar; i++)
4048: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
4049:
4050: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4051:
4052: k=0;
4053: for(i=1; i<= (nlstate); i++){
4054: for(j=1; j<=(nlstate+ndeath);j++){
4055: k=k+1;
4056: gp[k]=pmmij[i][j];
4057: }
4058: }
4059:
4060: for(i=1; i<=npar; i++)
4061: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
4062:
4063: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4064: k=0;
4065: for(i=1; i<=(nlstate); i++){
4066: for(j=1; j<=(nlstate+ndeath);j++){
4067: k=k+1;
4068: gm[k]=pmmij[i][j];
4069: }
4070: }
4071:
4072: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
4073: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
4074: }
4075:
4076: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
4077: for(theta=1; theta <=npar; theta++)
4078: trgradg[j][theta]=gradg[theta][j];
4079:
4080: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
4081: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
4082:
4083: pmij(pmmij,cov,ncovmodel,x,nlstate);
4084:
4085: k=0;
4086: for(i=1; i<=(nlstate); i++){
4087: for(j=1; j<=(nlstate+ndeath);j++){
4088: k=k+1;
4089: mu[k][(int) age]=pmmij[i][j];
4090: }
4091: }
4092: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
4093: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
4094: varpij[i][j][(int)age] = doldm[i][j];
4095:
4096: /*printf("\n%d ",(int)age);
4097: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4098: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4099: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4100: }*/
4101:
4102: fprintf(ficresprob,"\n%d ",(int)age);
4103: fprintf(ficresprobcov,"\n%d ",(int)age);
4104: fprintf(ficresprobcor,"\n%d ",(int)age);
4105:
4106: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
4107: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
4108: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4109: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
4110: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
4111: }
4112: i=0;
4113: for (k=1; k<=(nlstate);k++){
4114: for (l=1; l<=(nlstate+ndeath);l++){
4115: i++;
4116: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
4117: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
4118: for (j=1; j<=i;j++){
4119: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
4120: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
4121: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
4122: }
4123: }
4124: }/* end of loop for state */
4125: } /* end of loop for age */
4126: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
4127: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
4128: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4129: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4130:
4131: /* Confidence intervalle of pij */
4132: /*
4133: fprintf(ficgp,"\nunset parametric;unset label");
4134: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
4135: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
4136: 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);
4137: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
4138: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
4139: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
4140: */
4141:
4142: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
4143: first1=1;first2=2;
4144: for (k2=1; k2<=(nlstate);k2++){
4145: for (l2=1; l2<=(nlstate+ndeath);l2++){
4146: if(l2==k2) continue;
4147: j=(k2-1)*(nlstate+ndeath)+l2;
4148: for (k1=1; k1<=(nlstate);k1++){
4149: for (l1=1; l1<=(nlstate+ndeath);l1++){
4150: if(l1==k1) continue;
4151: i=(k1-1)*(nlstate+ndeath)+l1;
4152: if(i<=j) continue;
4153: for (age=bage; age<=fage; age ++){
4154: if ((int)age %5==0){
4155: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
4156: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
4157: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
4158: mu1=mu[i][(int) age]/stepm*YEARM ;
4159: mu2=mu[j][(int) age]/stepm*YEARM;
4160: c12=cv12/sqrt(v1*v2);
4161: /* Computing eigen value of matrix of covariance */
4162: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4163: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4164: if ((lc2 <0) || (lc1 <0) ){
4165: if(first2==1){
4166: first1=0;
4167: 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);
4168: }
4169: 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);
4170: /* lc1=fabs(lc1); */ /* If we want to have them positive */
4171: /* lc2=fabs(lc2); */
4172: }
4173:
4174: /* Eigen vectors */
4175: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
4176: /*v21=sqrt(1.-v11*v11); *//* error */
4177: v21=(lc1-v1)/cv12*v11;
4178: v12=-v21;
4179: v22=v11;
4180: tnalp=v21/v11;
4181: if(first1==1){
4182: first1=0;
4183: 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);
4184: }
4185: 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);
4186: /*printf(fignu*/
4187: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
4188: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
4189: if(first==1){
4190: first=0;
4191: fprintf(ficgp,"\nset parametric;unset label");
4192: 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);
4193: fprintf(ficgp,"\nset ter png small size 320, 240");
4194: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
4195: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
4196: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
4197: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
4198: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4199: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4200: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
4201: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4202: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4203: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4204: 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",\
4205: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4206: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4207: }else{
4208: first=0;
4209: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4210: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4211: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4212: 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",\
4213: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4214: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4215: }/* if first */
4216: } /* age mod 5 */
4217: } /* end loop age */
4218: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4219: first=1;
4220: } /*l12 */
4221: } /* k12 */
4222: } /*l1 */
4223: }/* k1 */
4224: /* } */ /* loop covariates */
4225: }
4226: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4227: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4228: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4229: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4230: free_vector(xp,1,npar);
4231: fclose(ficresprob);
4232: fclose(ficresprobcov);
4233: fclose(ficresprobcor);
4234: fflush(ficgp);
4235: fflush(fichtmcov);
4236: }
4237:
4238:
4239: /******************* Printing html file ***********/
4240: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
4241: int lastpass, int stepm, int weightopt, char model[],\
4242: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
4243: int popforecast, int estepm ,\
4244: double jprev1, double mprev1,double anprev1, \
4245: double jprev2, double mprev2,double anprev2){
4246: int jj1, k1, i1, cpt;
4247:
4248: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4249: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4250: </ul>");
4251: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
4252: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
4253: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
4254: fprintf(fichtm,"\
4255: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
4256: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
4257: fprintf(fichtm,"\
4258: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
4259: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
4260: fprintf(fichtm,"\
4261: - (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): \
4262: <a href=\"%s\">%s</a> <br>\n",
4263: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
4264: fprintf(fichtm,"\
4265: - Population projections by age and states: \
4266: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
4267:
4268: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4269:
4270: m=pow(2,cptcoveff);
4271: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4272:
4273: jj1=0;
4274: for(k1=1; k1<=m;k1++){
4275: for(i1=1; i1<=ncodemax[k1];i1++){
4276: jj1++;
4277: if (cptcovn > 0) {
4278: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4279: for (cpt=1; cpt<=cptcoveff;cpt++)
4280: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4281: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4282: }
4283: /* Pij */
4284: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
4285: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
4286: /* Quasi-incidences */
4287: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
4288: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
4289: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
4290: /* Period (stable) prevalence in each health state */
4291: for(cpt=1; cpt<=nlstate;cpt++){
4292: fprintf(fichtm,"<br>- 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.png\">%s%d_%d.png</a><br> \
4293: <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
4294: }
4295: for(cpt=1; cpt<=nlstate;cpt++) {
4296: 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) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
4297: <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
4298: }
4299: } /* end i1 */
4300: }/* End k1 */
4301: fprintf(fichtm,"</ul>");
4302:
4303:
4304: fprintf(fichtm,"\
4305: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
4306: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
4307:
4308: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4309: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
4310: fprintf(fichtm,"\
4311: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4312: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
4313:
4314: fprintf(fichtm,"\
4315: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4316: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
4317: fprintf(fichtm,"\
4318: - 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): \
4319: <a href=\"%s\">%s</a> <br>\n</li>",
4320: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
4321: fprintf(fichtm,"\
4322: - (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): \
4323: <a href=\"%s\">%s</a> <br>\n</li>",
4324: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
4325: fprintf(fichtm,"\
4326: - 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",
4327: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
4328: fprintf(fichtm,"\
4329: - 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",
4330: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
4331: fprintf(fichtm,"\
4332: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
4333: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
4334:
4335: /* if(popforecast==1) fprintf(fichtm,"\n */
4336: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4337: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4338: /* <br>",fileres,fileres,fileres,fileres); */
4339: /* else */
4340: /* 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); */
4341: fflush(fichtm);
4342: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4343:
4344: m=pow(2,cptcoveff);
4345: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4346:
4347: jj1=0;
4348: for(k1=1; k1<=m;k1++){
4349: for(i1=1; i1<=ncodemax[k1];i1++){
4350: jj1++;
4351: if (cptcovn > 0) {
4352: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4353: for (cpt=1; cpt<=cptcoveff;cpt++)
4354: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4355: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4356: }
4357: for(cpt=1; cpt<=nlstate;cpt++) {
4358: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
4359: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
4360: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
4361: }
4362: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
4363: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4364: true period expectancies (those weighted with period prevalences are also\
4365: drawn in addition to the population based expectancies computed using\
4366: observed and cahotic prevalences: %s%d.png<br>\
4367: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
4368: } /* end i1 */
4369: }/* End k1 */
4370: fprintf(fichtm,"</ul>");
4371: fflush(fichtm);
4372: }
4373:
4374: /******************* Gnuplot file **************/
4375: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4376:
4377: char dirfileres[132],optfileres[132];
4378: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
4379: int ng=0;
4380: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4381: /* printf("Problem with file %s",optionfilegnuplot); */
4382: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4383: /* } */
4384:
4385: /*#ifdef windows */
4386: fprintf(ficgp,"cd \"%s\" \n",pathc);
4387: /*#endif */
4388: m=pow(2,cptcoveff);
4389:
4390: strcpy(dirfileres,optionfilefiname);
4391: strcpy(optfileres,"vpl");
4392: /* 1eme*/
4393: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
4394: for (cpt=1; cpt<= nlstate ; cpt ++) {
4395: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
4396: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
4397: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
4398: fprintf(ficgp,"set xlabel \"Age\" \n\
4399: set ylabel \"Probability\" \n\
4400: set ter png small size 320, 240\n\
4401: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
4402:
4403: for (i=1; i<= nlstate ; i ++) {
4404: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4405: else fprintf(ficgp," %%*lf (%%*lf)");
4406: }
4407: fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
4408: for (i=1; i<= nlstate ; i ++) {
4409: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4410: else fprintf(ficgp," %%*lf (%%*lf)");
4411: }
4412: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
4413: for (i=1; i<= nlstate ; i ++) {
4414: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4415: else fprintf(ficgp," %%*lf (%%*lf)");
4416: }
4417: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
4418: }
4419: }
4420: /*2 eme*/
4421: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
4422: for (k1=1; k1<= m ; k1 ++) {
4423: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
4424: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
4425:
4426: for (i=1; i<= nlstate+1 ; i ++) {
4427: k=2*i;
4428: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4429: for (j=1; j<= nlstate+1 ; j ++) {
4430: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4431: else fprintf(ficgp," %%*lf (%%*lf)");
4432: }
4433: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
4434: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
4435: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4436: for (j=1; j<= nlstate+1 ; j ++) {
4437: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4438: else fprintf(ficgp," %%*lf (%%*lf)");
4439: }
4440: fprintf(ficgp,"\" t\"\" w l lt 0,");
4441: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4442: for (j=1; j<= nlstate+1 ; j ++) {
4443: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4444: else fprintf(ficgp," %%*lf (%%*lf)");
4445: }
4446: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4447: else fprintf(ficgp,"\" t\"\" w l lt 0,");
4448: }
4449: }
4450:
4451: /*3eme*/
4452:
4453: for (k1=1; k1<= m ; k1 ++) {
4454: for (cpt=1; cpt<= nlstate ; cpt ++) {
4455: /* k=2+nlstate*(2*cpt-2); */
4456: k=2+(nlstate+1)*(cpt-1);
4457: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
4458: fprintf(ficgp,"set ter png small size 320, 240\n\
4459: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
4460: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4461: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4462: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4463: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4464: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4465: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4466:
4467: */
4468: for (i=1; i< nlstate ; i ++) {
4469: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
4470: /* 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);*/
4471:
4472: }
4473: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
4474: }
4475: }
4476:
4477: /* CV preval stable (period) */
4478: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
4479: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
4480: k=3;
4481: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
4482: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
4483: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
4484: set ter png small size 320, 240\n\
4485: unset log y\n\
4486: plot [%.f:%.f] ", ageminpar, agemaxpar);
4487: for (i=1; i<= nlstate ; i ++){
4488: if(i==1)
4489: fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
4490: else
4491: fprintf(ficgp,", '' ");
4492: l=(nlstate+ndeath)*(i-1)+1;
4493: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
4494: for (j=1; j<= (nlstate-1) ; j ++)
4495: fprintf(ficgp,"+$%d",k+l+j);
4496: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
4497: } /* nlstate */
4498: fprintf(ficgp,"\n");
4499: } /* end cpt state*/
4500: } /* end covariate */
4501:
4502: /* proba elementaires */
4503: for(i=1,jk=1; i <=nlstate; i++){
4504: for(k=1; k <=(nlstate+ndeath); k++){
4505: if (k != i) {
4506: for(j=1; j <=ncovmodel; j++){
4507: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
4508: jk++;
4509: fprintf(ficgp,"\n");
4510: }
4511: }
4512: }
4513: }
4514: /*goto avoid;*/
4515: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
4516: for(jk=1; jk <=m; jk++) {
4517: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
4518: if (ng==2)
4519: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
4520: else
4521: fprintf(ficgp,"\nset title \"Probability\"\n");
4522: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
4523: i=1;
4524: for(k2=1; k2<=nlstate; k2++) {
4525: k3=i;
4526: for(k=1; k<=(nlstate+ndeath); k++) {
4527: if (k != k2){
4528: if(ng==2)
4529: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
4530: else
4531: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
4532: ij=1;/* To be checked else nbcode[0][0] wrong */
4533: for(j=3; j <=ncovmodel; j++) {
4534: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
4535: /* /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
4536: /* ij++; */
4537: /* } */
4538: /* else */
4539: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4540: }
4541: fprintf(ficgp,")/(1");
4542:
4543: for(k1=1; k1 <=nlstate; k1++){
4544: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
4545: ij=1;
4546: for(j=3; j <=ncovmodel; j++){
4547: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
4548: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
4549: /* ij++; */
4550: /* } */
4551: /* else */
4552: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4553: }
4554: fprintf(ficgp,")");
4555: }
4556: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
4557: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
4558: i=i+ncovmodel;
4559: }
4560: } /* end k */
4561: } /* end k2 */
4562: } /* end jk */
4563: } /* end ng */
4564: /* avoid: */
4565: fflush(ficgp);
4566: } /* end gnuplot */
4567:
4568:
4569: /*************** Moving average **************/
4570: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
4571:
4572: int i, cpt, cptcod;
4573: int modcovmax =1;
4574: int mobilavrange, mob;
4575: double age;
4576:
4577: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
4578: a covariate has 2 modalities */
4579: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
4580:
4581: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
4582: if(mobilav==1) mobilavrange=5; /* default */
4583: else mobilavrange=mobilav;
4584: for (age=bage; age<=fage; age++)
4585: for (i=1; i<=nlstate;i++)
4586: for (cptcod=1;cptcod<=modcovmax;cptcod++)
4587: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
4588: /* We keep the original values on the extreme ages bage, fage and for
4589: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
4590: we use a 5 terms etc. until the borders are no more concerned.
4591: */
4592: for (mob=3;mob <=mobilavrange;mob=mob+2){
4593: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
4594: for (i=1; i<=nlstate;i++){
4595: for (cptcod=1;cptcod<=modcovmax;cptcod++){
4596: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
4597: for (cpt=1;cpt<=(mob-1)/2;cpt++){
4598: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
4599: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
4600: }
4601: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
4602: }
4603: }
4604: }/* end age */
4605: }/* end mob */
4606: }else return -1;
4607: return 0;
4608: }/* End movingaverage */
4609:
4610:
4611: /************** Forecasting ******************/
4612: 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){
4613: /* proj1, year, month, day of starting projection
4614: agemin, agemax range of age
4615: dateprev1 dateprev2 range of dates during which prevalence is computed
4616: anproj2 year of en of projection (same day and month as proj1).
4617: */
4618: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
4619: double agec; /* generic age */
4620: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
4621: double *popeffectif,*popcount;
4622: double ***p3mat;
4623: double ***mobaverage;
4624: char fileresf[FILENAMELENGTH];
4625:
4626: agelim=AGESUP;
4627: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4628:
4629: strcpy(fileresf,"f");
4630: strcat(fileresf,fileres);
4631: if((ficresf=fopen(fileresf,"w"))==NULL) {
4632: printf("Problem with forecast resultfile: %s\n", fileresf);
4633: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
4634: }
4635: printf("Computing forecasting: result on file '%s' \n", fileresf);
4636: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
4637:
4638: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4639:
4640: if (mobilav!=0) {
4641: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4642: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4643: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4644: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4645: }
4646: }
4647:
4648: stepsize=(int) (stepm+YEARM-1)/YEARM;
4649: if (stepm<=12) stepsize=1;
4650: if(estepm < stepm){
4651: printf ("Problem %d lower than %d\n",estepm, stepm);
4652: }
4653: else hstepm=estepm;
4654:
4655: hstepm=hstepm/stepm;
4656: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
4657: fractional in yp1 */
4658: anprojmean=yp;
4659: yp2=modf((yp1*12),&yp);
4660: mprojmean=yp;
4661: yp1=modf((yp2*30.5),&yp);
4662: jprojmean=yp;
4663: if(jprojmean==0) jprojmean=1;
4664: if(mprojmean==0) jprojmean=1;
4665:
4666: i1=cptcoveff;
4667: if (cptcovn < 1){i1=1;}
4668:
4669: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4670:
4671: fprintf(ficresf,"#****** Routine prevforecast **\n");
4672:
4673: /* if (h==(int)(YEARM*yearp)){ */
4674: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4675: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4676: k=k+1;
4677: fprintf(ficresf,"\n#******");
4678: for(j=1;j<=cptcoveff;j++) {
4679: fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4680: }
4681: fprintf(ficresf,"******\n");
4682: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4683: for(j=1; j<=nlstate+ndeath;j++){
4684: for(i=1; i<=nlstate;i++)
4685: fprintf(ficresf," p%d%d",i,j);
4686: fprintf(ficresf," p.%d",j);
4687: }
4688: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4689: fprintf(ficresf,"\n");
4690: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4691:
4692: for (agec=fage; agec>=(ageminpar-1); agec--){
4693: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4694: nhstepm = nhstepm/hstepm;
4695: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4696: oldm=oldms;savm=savms;
4697: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4698:
4699: for (h=0; h<=nhstepm; h++){
4700: if (h*hstepm/YEARM*stepm ==yearp) {
4701: fprintf(ficresf,"\n");
4702: for(j=1;j<=cptcoveff;j++)
4703: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4704: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4705: }
4706: for(j=1; j<=nlstate+ndeath;j++) {
4707: ppij=0.;
4708: for(i=1; i<=nlstate;i++) {
4709: if (mobilav==1)
4710: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4711: else {
4712: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4713: }
4714: if (h*hstepm/YEARM*stepm== yearp) {
4715: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4716: }
4717: } /* end i */
4718: if (h*hstepm/YEARM*stepm==yearp) {
4719: fprintf(ficresf," %.3f", ppij);
4720: }
4721: }/* end j */
4722: } /* end h */
4723: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4724: } /* end agec */
4725: } /* end yearp */
4726: } /* end cptcod */
4727: } /* end cptcov */
4728:
4729: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4730:
4731: fclose(ficresf);
4732: }
4733:
4734: /************** Forecasting *****not tested NB*************/
4735: 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){
4736:
4737: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4738: int *popage;
4739: double calagedatem, agelim, kk1, kk2;
4740: double *popeffectif,*popcount;
4741: double ***p3mat,***tabpop,***tabpopprev;
4742: double ***mobaverage;
4743: char filerespop[FILENAMELENGTH];
4744:
4745: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4746: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4747: agelim=AGESUP;
4748: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4749:
4750: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4751:
4752:
4753: strcpy(filerespop,"pop");
4754: strcat(filerespop,fileres);
4755: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4756: printf("Problem with forecast resultfile: %s\n", filerespop);
4757: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4758: }
4759: printf("Computing forecasting: result on file '%s' \n", filerespop);
4760: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4761:
4762: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4763:
4764: if (mobilav!=0) {
4765: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4766: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4767: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4768: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4769: }
4770: }
4771:
4772: stepsize=(int) (stepm+YEARM-1)/YEARM;
4773: if (stepm<=12) stepsize=1;
4774:
4775: agelim=AGESUP;
4776:
4777: hstepm=1;
4778: hstepm=hstepm/stepm;
4779:
4780: if (popforecast==1) {
4781: if((ficpop=fopen(popfile,"r"))==NULL) {
4782: printf("Problem with population file : %s\n",popfile);exit(0);
4783: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4784: }
4785: popage=ivector(0,AGESUP);
4786: popeffectif=vector(0,AGESUP);
4787: popcount=vector(0,AGESUP);
4788:
4789: i=1;
4790: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4791:
4792: imx=i;
4793: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4794: }
4795:
4796: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4797: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4798: k=k+1;
4799: fprintf(ficrespop,"\n#******");
4800: for(j=1;j<=cptcoveff;j++) {
4801: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4802: }
4803: fprintf(ficrespop,"******\n");
4804: fprintf(ficrespop,"# Age");
4805: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4806: if (popforecast==1) fprintf(ficrespop," [Population]");
4807:
4808: for (cpt=0; cpt<=0;cpt++) {
4809: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4810:
4811: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4812: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4813: nhstepm = nhstepm/hstepm;
4814:
4815: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4816: oldm=oldms;savm=savms;
4817: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4818:
4819: for (h=0; h<=nhstepm; h++){
4820: if (h==(int) (calagedatem+YEARM*cpt)) {
4821: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4822: }
4823: for(j=1; j<=nlstate+ndeath;j++) {
4824: kk1=0.;kk2=0;
4825: for(i=1; i<=nlstate;i++) {
4826: if (mobilav==1)
4827: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4828: else {
4829: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4830: }
4831: }
4832: if (h==(int)(calagedatem+12*cpt)){
4833: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4834: /*fprintf(ficrespop," %.3f", kk1);
4835: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4836: }
4837: }
4838: for(i=1; i<=nlstate;i++){
4839: kk1=0.;
4840: for(j=1; j<=nlstate;j++){
4841: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4842: }
4843: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
4844: }
4845:
4846: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
4847: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4848: }
4849: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4850: }
4851: }
4852:
4853: /******/
4854:
4855: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4856: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4857: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4858: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4859: nhstepm = nhstepm/hstepm;
4860:
4861: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4862: oldm=oldms;savm=savms;
4863: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4864: for (h=0; h<=nhstepm; h++){
4865: if (h==(int) (calagedatem+YEARM*cpt)) {
4866: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4867: }
4868: for(j=1; j<=nlstate+ndeath;j++) {
4869: kk1=0.;kk2=0;
4870: for(i=1; i<=nlstate;i++) {
4871: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4872: }
4873: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
4874: }
4875: }
4876: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4877: }
4878: }
4879: }
4880: }
4881:
4882: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4883:
4884: if (popforecast==1) {
4885: free_ivector(popage,0,AGESUP);
4886: free_vector(popeffectif,0,AGESUP);
4887: free_vector(popcount,0,AGESUP);
4888: }
4889: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4890: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4891: fclose(ficrespop);
4892: } /* End of popforecast */
4893:
4894: int fileappend(FILE *fichier, char *optionfich)
4895: {
4896: if((fichier=fopen(optionfich,"a"))==NULL) {
4897: printf("Problem with file: %s\n", optionfich);
4898: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4899: return (0);
4900: }
4901: fflush(fichier);
4902: return (1);
4903: }
4904:
4905:
4906: /**************** function prwizard **********************/
4907: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4908: {
4909:
4910: /* Wizard to print covariance matrix template */
4911:
4912: char ca[32], cb[32];
4913: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
4914: int numlinepar;
4915:
4916: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4917: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4918: for(i=1; i <=nlstate; i++){
4919: jj=0;
4920: for(j=1; j <=nlstate+ndeath; j++){
4921: if(j==i) continue;
4922: jj++;
4923: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4924: printf("%1d%1d",i,j);
4925: fprintf(ficparo,"%1d%1d",i,j);
4926: for(k=1; k<=ncovmodel;k++){
4927: /* printf(" %lf",param[i][j][k]); */
4928: /* fprintf(ficparo," %lf",param[i][j][k]); */
4929: printf(" 0.");
4930: fprintf(ficparo," 0.");
4931: }
4932: printf("\n");
4933: fprintf(ficparo,"\n");
4934: }
4935: }
4936: printf("# Scales (for hessian or gradient estimation)\n");
4937: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4938: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4939: for(i=1; i <=nlstate; i++){
4940: jj=0;
4941: for(j=1; j <=nlstate+ndeath; j++){
4942: if(j==i) continue;
4943: jj++;
4944: fprintf(ficparo,"%1d%1d",i,j);
4945: printf("%1d%1d",i,j);
4946: fflush(stdout);
4947: for(k=1; k<=ncovmodel;k++){
4948: /* printf(" %le",delti3[i][j][k]); */
4949: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4950: printf(" 0.");
4951: fprintf(ficparo," 0.");
4952: }
4953: numlinepar++;
4954: printf("\n");
4955: fprintf(ficparo,"\n");
4956: }
4957: }
4958: printf("# Covariance matrix\n");
4959: /* # 121 Var(a12)\n\ */
4960: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4961: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4962: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4963: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4964: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4965: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4966: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4967: fflush(stdout);
4968: fprintf(ficparo,"# Covariance matrix\n");
4969: /* # 121 Var(a12)\n\ */
4970: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4971: /* # ...\n\ */
4972: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4973:
4974: for(itimes=1;itimes<=2;itimes++){
4975: jj=0;
4976: for(i=1; i <=nlstate; i++){
4977: for(j=1; j <=nlstate+ndeath; j++){
4978: if(j==i) continue;
4979: for(k=1; k<=ncovmodel;k++){
4980: jj++;
4981: ca[0]= k+'a'-1;ca[1]='\0';
4982: if(itimes==1){
4983: printf("#%1d%1d%d",i,j,k);
4984: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4985: }else{
4986: printf("%1d%1d%d",i,j,k);
4987: fprintf(ficparo,"%1d%1d%d",i,j,k);
4988: /* printf(" %.5le",matcov[i][j]); */
4989: }
4990: ll=0;
4991: for(li=1;li <=nlstate; li++){
4992: for(lj=1;lj <=nlstate+ndeath; lj++){
4993: if(lj==li) continue;
4994: for(lk=1;lk<=ncovmodel;lk++){
4995: ll++;
4996: if(ll<=jj){
4997: cb[0]= lk +'a'-1;cb[1]='\0';
4998: if(ll<jj){
4999: if(itimes==1){
5000: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5001: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5002: }else{
5003: printf(" 0.");
5004: fprintf(ficparo," 0.");
5005: }
5006: }else{
5007: if(itimes==1){
5008: printf(" Var(%s%1d%1d)",ca,i,j);
5009: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
5010: }else{
5011: printf(" 0.");
5012: fprintf(ficparo," 0.");
5013: }
5014: }
5015: }
5016: } /* end lk */
5017: } /* end lj */
5018: } /* end li */
5019: printf("\n");
5020: fprintf(ficparo,"\n");
5021: numlinepar++;
5022: } /* end k*/
5023: } /*end j */
5024: } /* end i */
5025: } /* end itimes */
5026:
5027: } /* end of prwizard */
5028: /******************* Gompertz Likelihood ******************************/
5029: double gompertz(double x[])
5030: {
5031: double A,B,L=0.0,sump=0.,num=0.;
5032: int i,n=0; /* n is the size of the sample */
5033:
5034: for (i=0;i<=imx-1 ; i++) {
5035: sump=sump+weight[i];
5036: /* sump=sump+1;*/
5037: num=num+1;
5038: }
5039:
5040:
5041: /* for (i=0; i<=imx; i++)
5042: 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]);*/
5043:
5044: for (i=1;i<=imx ; i++)
5045: {
5046: if (cens[i] == 1 && wav[i]>1)
5047: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
5048:
5049: if (cens[i] == 0 && wav[i]>1)
5050: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
5051: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
5052:
5053: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5054: if (wav[i] > 1 ) { /* ??? */
5055: L=L+A*weight[i];
5056: /* 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]);*/
5057: }
5058: }
5059:
5060: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5061:
5062: return -2*L*num/sump;
5063: }
5064:
5065: #ifdef GSL
5066: /******************* Gompertz_f Likelihood ******************************/
5067: double gompertz_f(const gsl_vector *v, void *params)
5068: {
5069: double A,B,LL=0.0,sump=0.,num=0.;
5070: double *x= (double *) v->data;
5071: int i,n=0; /* n is the size of the sample */
5072:
5073: for (i=0;i<=imx-1 ; i++) {
5074: sump=sump+weight[i];
5075: /* sump=sump+1;*/
5076: num=num+1;
5077: }
5078:
5079:
5080: /* for (i=0; i<=imx; i++)
5081: 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]);*/
5082: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
5083: for (i=1;i<=imx ; i++)
5084: {
5085: if (cens[i] == 1 && wav[i]>1)
5086: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
5087:
5088: if (cens[i] == 0 && wav[i]>1)
5089: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
5090: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
5091:
5092: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5093: if (wav[i] > 1 ) { /* ??? */
5094: LL=LL+A*weight[i];
5095: /* 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]);*/
5096: }
5097: }
5098:
5099: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5100: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
5101:
5102: return -2*LL*num/sump;
5103: }
5104: #endif
5105:
5106: /******************* Printing html file ***********/
5107: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
5108: int lastpass, int stepm, int weightopt, char model[],\
5109: int imx, double p[],double **matcov,double agemortsup){
5110: int i,k;
5111:
5112: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
5113: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
5114: for (i=1;i<=2;i++)
5115: 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]));
5116: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
5117: fprintf(fichtm,"</ul>");
5118:
5119: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
5120:
5121: 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>");
5122:
5123: for (k=agegomp;k<(agemortsup-2);k++)
5124: 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]);
5125:
5126:
5127: fflush(fichtm);
5128: }
5129:
5130: /******************* Gnuplot file **************/
5131: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
5132:
5133: char dirfileres[132],optfileres[132];
5134:
5135: int ng;
5136:
5137:
5138: /*#ifdef windows */
5139: fprintf(ficgp,"cd \"%s\" \n",pathc);
5140: /*#endif */
5141:
5142:
5143: strcpy(dirfileres,optionfilefiname);
5144: strcpy(optfileres,"vpl");
5145: fprintf(ficgp,"set out \"graphmort.png\"\n ");
5146: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
5147: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
5148: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
5149: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
5150:
5151: }
5152:
5153: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
5154: {
5155:
5156: /*-------- data file ----------*/
5157: FILE *fic;
5158: char dummy[]=" ";
5159: int i=0, j=0, n=0;
5160: int linei, month, year,iout;
5161: char line[MAXLINE], linetmp[MAXLINE];
5162: char stra[MAXLINE], strb[MAXLINE];
5163: char *stratrunc;
5164: int lstra;
5165:
5166:
5167: if((fic=fopen(datafile,"r"))==NULL) {
5168: printf("Problem while opening datafile: %s\n", datafile);return 1;
5169: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
5170: }
5171:
5172: i=1;
5173: linei=0;
5174: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
5175: linei=linei+1;
5176: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
5177: if(line[j] == '\t')
5178: line[j] = ' ';
5179: }
5180: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
5181: ;
5182: };
5183: line[j+1]=0; /* Trims blanks at end of line */
5184: if(line[0]=='#'){
5185: fprintf(ficlog,"Comment line\n%s\n",line);
5186: printf("Comment line\n%s\n",line);
5187: continue;
5188: }
5189: trimbb(linetmp,line); /* Trims multiple blanks in line */
5190: strcpy(line, linetmp);
5191:
5192:
5193: for (j=maxwav;j>=1;j--){
5194: cutv(stra, strb, line, ' ');
5195: if(strb[0]=='.') { /* Missing status */
5196: lval=-1;
5197: }else{
5198: errno=0;
5199: lval=strtol(strb,&endptr,10);
5200: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
5201: if( strb[0]=='\0' || (*endptr != '\0')){
5202: 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);
5203: 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);
5204: return 1;
5205: }
5206: }
5207: s[j][i]=lval;
5208:
5209: strcpy(line,stra);
5210: cutv(stra, strb,line,' ');
5211: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
5212: }
5213: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
5214: month=99;
5215: year=9999;
5216: }else{
5217: 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);
5218: 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);
5219: return 1;
5220: }
5221: anint[j][i]= (double) year;
5222: mint[j][i]= (double)month;
5223: strcpy(line,stra);
5224: } /* ENd Waves */
5225:
5226: cutv(stra, strb,line,' ');
5227: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
5228: }
5229: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
5230: month=99;
5231: year=9999;
5232: }else{
5233: 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);
5234: 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);
5235: return 1;
5236: }
5237: andc[i]=(double) year;
5238: moisdc[i]=(double) month;
5239: strcpy(line,stra);
5240:
5241: cutv(stra, strb,line,' ');
5242: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
5243: }
5244: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
5245: month=99;
5246: year=9999;
5247: }else{
5248: 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);
5249: 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);
5250: return 1;
5251: }
5252: if (year==9999) {
5253: 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);
5254: 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);
5255: return 1;
5256:
5257: }
5258: annais[i]=(double)(year);
5259: moisnais[i]=(double)(month);
5260: strcpy(line,stra);
5261:
5262: cutv(stra, strb,line,' ');
5263: errno=0;
5264: dval=strtod(strb,&endptr);
5265: if( strb[0]=='\0' || (*endptr != '\0')){
5266: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
5267: 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);
5268: fflush(ficlog);
5269: return 1;
5270: }
5271: weight[i]=dval;
5272: strcpy(line,stra);
5273:
5274: for (j=ncovcol;j>=1;j--){
5275: cutv(stra, strb,line,' ');
5276: if(strb[0]=='.') { /* Missing status */
5277: lval=-1;
5278: }else{
5279: errno=0;
5280: lval=strtol(strb,&endptr,10);
5281: if( strb[0]=='\0' || (*endptr != '\0')){
5282: 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);
5283: 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);
5284: return 1;
5285: }
5286: }
5287: if(lval <-1 || lval >1){
5288: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
5289: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5290: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5291: For example, for multinomial values like 1, 2 and 3,\n \
5292: build V1=0 V2=0 for the reference value (1),\n \
5293: V1=1 V2=0 for (2) \n \
5294: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5295: output of IMaCh is often meaningless.\n \
5296: Exiting.\n",lval,linei, i,line,j);
5297: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
5298: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5299: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5300: For example, for multinomial values like 1, 2 and 3,\n \
5301: build V1=0 V2=0 for the reference value (1),\n \
5302: V1=1 V2=0 for (2) \n \
5303: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5304: output of IMaCh is often meaningless.\n \
5305: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
5306: return 1;
5307: }
5308: covar[j][i]=(double)(lval);
5309: strcpy(line,stra);
5310: }
5311: lstra=strlen(stra);
5312:
5313: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
5314: stratrunc = &(stra[lstra-9]);
5315: num[i]=atol(stratrunc);
5316: }
5317: else
5318: num[i]=atol(stra);
5319: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
5320: 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;}*/
5321:
5322: i=i+1;
5323: } /* End loop reading data */
5324:
5325: *imax=i-1; /* Number of individuals */
5326: fclose(fic);
5327:
5328: return (0);
5329: /* endread: */
5330: printf("Exiting readdata: ");
5331: fclose(fic);
5332: return (1);
5333:
5334:
5335:
5336: }
5337: void removespace(char *str) {
5338: char *p1 = str, *p2 = str;
5339: do
5340: while (*p2 == ' ')
5341: p2++;
5342: while (*p1++ == *p2++);
5343: }
5344:
5345: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
5346: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
5347: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
5348: * - cptcovn or number of covariates k of the models excluding age*products =6
5349: * - cptcovage number of covariates with age*products =2
5350: * - cptcovs number of simple covariates
5351: * - 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
5352: * which is a new column after the 9 (ncovcol) variables.
5353: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
5354: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
5355: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
5356: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
5357: */
5358: {
5359: int i, j, k, ks;
5360: int j1, k1, k2;
5361: char modelsav[80];
5362: char stra[80], strb[80], strc[80], strd[80],stre[80];
5363:
5364: /*removespace(model);*/
5365: if (strlen(model) >1){ /* If there is at least 1 covariate */
5366: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
5367: j=nbocc(model,'+'); /**< j=Number of '+' */
5368: j1=nbocc(model,'*'); /**< j1=Number of '*' */
5369: cptcovs=j+1-j1; /**< Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2 */
5370: cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
5371: /* including age products which are counted in cptcovage.
5372: * but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
5373: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
5374: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
5375: strcpy(modelsav,model);
5376: if (strstr(model,"AGE") !=0){
5377: printf("Error. AGE must be in lower case 'age' model=%s ",model);
5378: fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
5379: return 1;
5380: }
5381: if (strstr(model,"v") !=0){
5382: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
5383: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
5384: return 1;
5385: }
5386:
5387: /* Design
5388: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
5389: * < ncovcol=8 >
5390: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
5391: * k= 1 2 3 4 5 6 7 8
5392: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
5393: * covar[k,i], value of kth covariate if not including age for individual i:
5394: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
5395: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
5396: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
5397: * Tage[++cptcovage]=k
5398: * if products, new covar are created after ncovcol with k1
5399: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
5400: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
5401: * 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
5402: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
5403: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
5404: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
5405: * < ncovcol=8 >
5406: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
5407: * k= 1 2 3 4 5 6 7 8 9 10 11 12
5408: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
5409: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5410: * p Tprod[1]@2={ 6, 5}
5411: *p Tvard[1][1]@4= {7, 8, 5, 6}
5412: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
5413: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
5414: *How to reorganize?
5415: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
5416: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5417: * {2, 1, 4, 8, 5, 6, 3, 7}
5418: * Struct []
5419: */
5420:
5421: /* This loop fills the array Tvar from the string 'model'.*/
5422: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
5423: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
5424: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
5425: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
5426: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
5427: /* k=1 Tvar[1]=2 (from V2) */
5428: /* k=5 Tvar[5] */
5429: /* for (k=1; k<=cptcovn;k++) { */
5430: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
5431: /* } */
5432: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
5433: /*
5434: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
5435: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
5436: Tvar[k]=0;
5437: cptcovage=0;
5438: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
5439: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5440: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
5441: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
5442: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5443: /*scanf("%d",i);*/
5444: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
5445: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
5446: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
5447: /* covar is not filled and then is empty */
5448: cptcovprod--;
5449: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
5450: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
5451: cptcovage++; /* Sums the number of covariates which include age as a product */
5452: Tage[cptcovage]=k; /* Tage[1] = 4 */
5453: /*printf("stre=%s ", stre);*/
5454: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
5455: cptcovprod--;
5456: cutl(stre,strb,strc,'V');
5457: Tvar[k]=atoi(stre);
5458: cptcovage++;
5459: Tage[cptcovage]=k;
5460: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
5461: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
5462: cptcovn++;
5463: cptcovprodnoage++;k1++;
5464: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5465: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
5466: because this model-covariate is a construction we invent a new column
5467: ncovcol + k1
5468: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
5469: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
5470: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
5471: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
5472: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
5473: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
5474: k2=k2+2;
5475: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
5476: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
5477: for (i=1; i<=lastobs;i++){
5478: /* Computes the new covariate which is a product of
5479: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
5480: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
5481: }
5482: } /* End age is not in the model */
5483: } /* End if model includes a product */
5484: else { /* no more sum */
5485: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5486: /* scanf("%d",i);*/
5487: cutl(strd,strc,strb,'V');
5488: ks++; /**< Number of simple covariates */
5489: cptcovn++;
5490: Tvar[k]=atoi(strd);
5491: }
5492: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
5493: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5494: scanf("%d",i);*/
5495: } /* end of loop + */
5496: } /* end model */
5497:
5498: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5499: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5500:
5501: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5502: printf("cptcovprod=%d ", cptcovprod);
5503: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5504:
5505: scanf("%d ",i);*/
5506:
5507:
5508: return (0); /* with covar[new additional covariate if product] and Tage if age */
5509: /*endread:*/
5510: printf("Exiting decodemodel: ");
5511: return (1);
5512: }
5513:
5514: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
5515: {
5516: int i, m;
5517:
5518: for (i=1; i<=imx; i++) {
5519: for(m=2; (m<= maxwav); m++) {
5520: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5521: anint[m][i]=9999;
5522: s[m][i]=-1;
5523: }
5524: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
5525: *nberr = *nberr + 1;
5526: 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);
5527: 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);
5528: s[m][i]=-1;
5529: }
5530: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
5531: (*nberr)++;
5532: 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]);
5533: 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]);
5534: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5535: }
5536: }
5537: }
5538:
5539: for (i=1; i<=imx; i++) {
5540: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5541: for(m=firstpass; (m<= lastpass); m++){
5542: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5543: if (s[m][i] >= nlstate+1) {
5544: if(agedc[i]>0){
5545: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
5546: agev[m][i]=agedc[i];
5547: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
5548: }else {
5549: if ((int)andc[i]!=9999){
5550: nbwarn++;
5551: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5552: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5553: agev[m][i]=-1;
5554: }
5555: }
5556: } /* agedc > 0 */
5557: }
5558: else if(s[m][i] !=9){ /* Standard case, age in fractional
5559: years but with the precision of a month */
5560: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5561: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5562: agev[m][i]=1;
5563: else if(agev[m][i] < *agemin){
5564: *agemin=agev[m][i];
5565: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
5566: }
5567: else if(agev[m][i] >*agemax){
5568: *agemax=agev[m][i];
5569: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
5570: }
5571: /*agev[m][i]=anint[m][i]-annais[i];*/
5572: /* agev[m][i] = age[i]+2*m;*/
5573: }
5574: else { /* =9 */
5575: agev[m][i]=1;
5576: s[m][i]=-1;
5577: }
5578: }
5579: else /*= 0 Unknown */
5580: agev[m][i]=1;
5581: }
5582:
5583: }
5584: for (i=1; i<=imx; i++) {
5585: for(m=firstpass; (m<=lastpass); m++){
5586: if (s[m][i] > (nlstate+ndeath)) {
5587: (*nberr)++;
5588: 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);
5589: 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);
5590: return 1;
5591: }
5592: }
5593: }
5594:
5595: /*for (i=1; i<=imx; i++){
5596: for (m=firstpass; (m<lastpass); m++){
5597: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5598: }
5599:
5600: }*/
5601:
5602:
5603: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5604: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5605:
5606: return (0);
5607: /* endread:*/
5608: printf("Exiting calandcheckages: ");
5609: return (1);
5610: }
5611:
5612: #if defined(_MSC_VER)
5613: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5614: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5615: //#include "stdafx.h"
5616: //#include <stdio.h>
5617: //#include <tchar.h>
5618: //#include <windows.h>
5619: //#include <iostream>
5620: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
5621:
5622: LPFN_ISWOW64PROCESS fnIsWow64Process;
5623:
5624: BOOL IsWow64()
5625: {
5626: BOOL bIsWow64 = FALSE;
5627:
5628: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
5629: // (HANDLE, PBOOL);
5630:
5631: //LPFN_ISWOW64PROCESS fnIsWow64Process;
5632:
5633: HMODULE module = GetModuleHandle(_T("kernel32"));
5634: const char funcName[] = "IsWow64Process";
5635: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
5636: GetProcAddress(module, funcName);
5637:
5638: if (NULL != fnIsWow64Process)
5639: {
5640: if (!fnIsWow64Process(GetCurrentProcess(),
5641: &bIsWow64))
5642: //throw std::exception("Unknown error");
5643: printf("Unknown error\n");
5644: }
5645: return bIsWow64 != FALSE;
5646: }
5647: #endif
5648:
5649: void syscompilerinfo()
5650: {
5651: /* #include "syscompilerinfo.h"*/
5652: /* command line Intel compiler 32bit windows, XP compatible:*/
5653: /* /GS /W3 /Gy
5654: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
5655: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
5656: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
5657: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
5658: /* 64 bits */
5659: /*
5660: /GS /W3 /Gy
5661: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
5662: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
5663: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
5664: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
5665: /* Optimization are useless and O3 is slower than O2 */
5666: /*
5667: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
5668: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
5669: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
5670: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
5671: */
5672: /* Link is $/ /* /OUT:"visual studio
5673: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
5674: /PDB:"visual studio
5675: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
5676: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
5677: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
5678: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
5679: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
5680: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
5681: uiAccess='false'"
5682: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
5683: /NOLOGO /TLBID:1
5684: */
5685: #if defined __INTEL_COMPILER
5686: #if defined(__GNUC__)
5687: struct utsname sysInfo; /* For Intel on Linux and OS/X */
5688: #endif
5689: #elif defined(__GNUC__)
5690: #ifndef __APPLE__
5691: #include <gnu/libc-version.h> /* Only on gnu */
5692: #endif
5693: struct utsname sysInfo;
5694: int cross = CROSS;
5695: if (cross){
5696: printf("Cross-");
5697: fprintf(ficlog, "Cross-");
5698: }
5699: #endif
5700:
5701: #include <stdint.h>
5702:
5703: printf("Compiled with:");fprintf(ficlog,"Compiled with:");
5704: #if defined(__clang__)
5705: printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
5706: #endif
5707: #if defined(__ICC) || defined(__INTEL_COMPILER)
5708: printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
5709: #endif
5710: #if defined(__GNUC__) || defined(__GNUG__)
5711: printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
5712: #endif
5713: #if defined(__HP_cc) || defined(__HP_aCC)
5714: printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
5715: #endif
5716: #if defined(__IBMC__) || defined(__IBMCPP__)
5717: printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
5718: #endif
5719: #if defined(_MSC_VER)
5720: printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
5721: #endif
5722: #if defined(__PGI)
5723: printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
5724: #endif
5725: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
5726: printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
5727: #endif
5728: printf(" for ");fprintf(ficlog," for ");
5729:
5730: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
5731: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
5732: // Windows (x64 and x86)
5733: printf("Windows (x64 and x86) ");fprintf(ficlog,"Windows (x64 and x86) ");
5734: #elif __unix__ // all unices, not all compilers
5735: // Unix
5736: printf("Unix ");fprintf(ficlog,"Unix ");
5737: #elif __linux__
5738: // linux
5739: printf("linux ");fprintf(ficlog,"linux ");
5740: #elif __APPLE__
5741: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
5742: printf("Mac OS ");fprintf(ficlog,"Mac OS ");
5743: #endif
5744:
5745: /* __MINGW32__ */
5746: /* __CYGWIN__ */
5747: /* __MINGW64__ */
5748: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
5749: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
5750: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
5751: /* _WIN64 // Defined for applications for Win64. */
5752: /* _M_X64 // Defined for compilations that target x64 processors. */
5753: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
5754:
5755: #if UINTPTR_MAX == 0xffffffff
5756: printf(" 32-bit"); fprintf(ficlog," 32-bit");/* 32-bit */
5757: #elif UINTPTR_MAX == 0xffffffffffffffff
5758: printf(" 64-bit"); fprintf(ficlog," 64-bit");/* 64-bit */
5759: #else
5760: printf(" wtf-bit"); fprintf(ficlog," wtf-bit");/* wtf */
5761: #endif
5762:
5763: #if defined(__GNUC__)
5764: # if defined(__GNUC_PATCHLEVEL__)
5765: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
5766: + __GNUC_MINOR__ * 100 \
5767: + __GNUC_PATCHLEVEL__)
5768: # else
5769: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
5770: + __GNUC_MINOR__ * 100)
5771: # endif
5772: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
5773: fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
5774:
5775: if (uname(&sysInfo) != -1) {
5776: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
5777: fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
5778: }
5779: else
5780: perror("uname() error");
5781: //#ifndef __INTEL_COMPILER
5782: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
5783: printf("GNU libc version: %s\n", gnu_get_libc_version());
5784: fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
5785: #endif
5786: #endif
5787:
5788: // void main()
5789: // {
5790: #if defined(_MSC_VER)
5791: if (IsWow64()){
5792: printf("The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
5793: fprintf(ficlog, "The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
5794: }
5795: else{
5796: printf("The process is not running under WOW64 (i.e probably on a 64bit Windows).\n");
5797: fprintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
5798: }
5799: // printf("\nPress Enter to continue...");
5800: // getchar();
5801: // }
5802:
5803: #endif
5804:
5805:
5806: }
5807:
5808: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){
5809: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
5810: int i, j, k, i1 ;
5811: double ftolpl = 1.e-10;
5812: double age, agebase, agelim;
5813:
5814: strcpy(filerespl,"pl");
5815: strcat(filerespl,fileres);
5816: if((ficrespl=fopen(filerespl,"w"))==NULL) {
5817: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
5818: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
5819: }
5820: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
5821: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
5822: pstamp(ficrespl);
5823: fprintf(ficrespl,"# Period (stable) prevalence \n");
5824: fprintf(ficrespl,"#Age ");
5825: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
5826: fprintf(ficrespl,"\n");
5827:
5828: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
5829:
5830: agebase=ageminpar;
5831: agelim=agemaxpar;
5832:
5833: i1=pow(2,cptcoveff);
5834: if (cptcovn < 1){i1=1;}
5835:
5836: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5837: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
5838: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5839: k=k+1;
5840: /* to clean */
5841: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);
5842: fprintf(ficrespl,"\n#******");
5843: printf("\n#******");
5844: fprintf(ficlog,"\n#******");
5845: for(j=1;j<=cptcoveff;j++) {
5846: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5847: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5848: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5849: }
5850: fprintf(ficrespl,"******\n");
5851: printf("******\n");
5852: fprintf(ficlog,"******\n");
5853:
5854: fprintf(ficrespl,"#Age ");
5855: for(j=1;j<=cptcoveff;j++) {
5856: fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5857: }
5858: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
5859: fprintf(ficrespl,"\n");
5860:
5861: for (age=agebase; age<=agelim; age++){
5862: /* for (age=agebase; age<=agebase; age++){ */
5863: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5864: fprintf(ficrespl,"%.0f ",age );
5865: for(j=1;j<=cptcoveff;j++)
5866: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5867: for(i=1; i<=nlstate;i++)
5868: fprintf(ficrespl," %.5f", prlim[i][i]);
5869: fprintf(ficrespl,"\n");
5870: } /* Age */
5871: /* was end of cptcod */
5872: } /* cptcov */
5873: return 0;
5874: }
5875:
5876: int hPijx(double *p, int bage, int fage){
5877: /*------------- h Pij x at various ages ------------*/
5878:
5879: int stepsize;
5880: int agelim;
5881: int hstepm;
5882: int nhstepm;
5883: int h, i, i1, j, k;
5884:
5885: double agedeb;
5886: double ***p3mat;
5887:
5888: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
5889: if((ficrespij=fopen(filerespij,"w"))==NULL) {
5890: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
5891: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
5892: }
5893: printf("Computing pij: result on file '%s' \n", filerespij);
5894: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
5895:
5896: stepsize=(int) (stepm+YEARM-1)/YEARM;
5897: /*if (stepm<=24) stepsize=2;*/
5898:
5899: agelim=AGESUP;
5900: hstepm=stepsize*YEARM; /* Every year of age */
5901: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
5902:
5903: /* hstepm=1; aff par mois*/
5904: pstamp(ficrespij);
5905: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
5906: i1= pow(2,cptcoveff);
5907: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
5908: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
5909: /* k=k+1; */
5910: for (k=1; k <= (int) pow(2,cptcoveff); k++){
5911: fprintf(ficrespij,"\n#****** ");
5912: for(j=1;j<=cptcoveff;j++)
5913: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5914: fprintf(ficrespij,"******\n");
5915:
5916: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
5917: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5918: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
5919:
5920: /* nhstepm=nhstepm*YEARM; aff par mois*/
5921:
5922: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5923: oldm=oldms;savm=savms;
5924: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5925: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
5926: for(i=1; i<=nlstate;i++)
5927: for(j=1; j<=nlstate+ndeath;j++)
5928: fprintf(ficrespij," %1d-%1d",i,j);
5929: fprintf(ficrespij,"\n");
5930: for (h=0; h<=nhstepm; h++){
5931: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
5932: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
5933: for(i=1; i<=nlstate;i++)
5934: for(j=1; j<=nlstate+ndeath;j++)
5935: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
5936: fprintf(ficrespij,"\n");
5937: }
5938: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5939: fprintf(ficrespij,"\n");
5940: }
5941: /*}*/
5942: }
5943: return 0;
5944: }
5945:
5946:
5947: /***********************************************/
5948: /**************** Main Program *****************/
5949: /***********************************************/
5950:
5951: int main(int argc, char *argv[])
5952: {
5953: #ifdef GSL
5954: const gsl_multimin_fminimizer_type *T;
5955: size_t iteri = 0, it;
5956: int rval = GSL_CONTINUE;
5957: int status = GSL_SUCCESS;
5958: double ssval;
5959: #endif
5960: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
5961: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
5962:
5963: int jj, ll, li, lj, lk;
5964: int numlinepar=0; /* Current linenumber of parameter file */
5965: int itimes;
5966: int NDIM=2;
5967: int vpopbased=0;
5968:
5969: char ca[32], cb[32];
5970: /* FILE *fichtm; *//* Html File */
5971: /* FILE *ficgp;*/ /*Gnuplot File */
5972: struct stat info;
5973: double agedeb;
5974: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
5975:
5976: double fret;
5977: double dum; /* Dummy variable */
5978: double ***p3mat;
5979: double ***mobaverage;
5980:
5981: char line[MAXLINE];
5982: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
5983: char pathr[MAXLINE], pathimach[MAXLINE];
5984: char *tok, *val; /* pathtot */
5985: int firstobs=1, lastobs=10;
5986: int c, h , cpt;
5987: int jl;
5988: int i1, j1, jk, stepsize;
5989: int *tab;
5990: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
5991: int mobilav=0,popforecast=0;
5992: int hstepm, nhstepm;
5993: int agemortsup;
5994: float sumlpop=0.;
5995: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
5996: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
5997:
5998: double bage=0, fage=110, age, agelim, agebase;
5999: double ftolpl=FTOL;
6000: double **prlim;
6001: double ***param; /* Matrix of parameters */
6002: double *p;
6003: double **matcov; /* Matrix of covariance */
6004: double ***delti3; /* Scale */
6005: double *delti; /* Scale */
6006: double ***eij, ***vareij;
6007: double **varpl; /* Variances of prevalence limits by age */
6008: double *epj, vepp;
6009:
6010: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
6011: double **ximort;
6012: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
6013: int *dcwave;
6014:
6015: char z[1]="c";
6016:
6017: /*char *strt;*/
6018: char strtend[80];
6019:
6020:
6021: /* setlocale (LC_ALL, ""); */
6022: /* bindtextdomain (PACKAGE, LOCALEDIR); */
6023: /* textdomain (PACKAGE); */
6024: /* setlocale (LC_CTYPE, ""); */
6025: /* setlocale (LC_MESSAGES, ""); */
6026:
6027: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
6028: rstart_time = time(NULL);
6029: /* (void) gettimeofday(&start_time,&tzp);*/
6030: start_time = *localtime(&rstart_time);
6031: curr_time=start_time;
6032: /*tml = *localtime(&start_time.tm_sec);*/
6033: /* strcpy(strstart,asctime(&tml)); */
6034: strcpy(strstart,asctime(&start_time));
6035:
6036: /* printf("Localtime (at start)=%s",strstart); */
6037: /* tp.tm_sec = tp.tm_sec +86400; */
6038: /* tm = *localtime(&start_time.tm_sec); */
6039: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
6040: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
6041: /* tmg.tm_hour=tmg.tm_hour + 1; */
6042: /* tp.tm_sec = mktime(&tmg); */
6043: /* strt=asctime(&tmg); */
6044: /* printf("Time(after) =%s",strstart); */
6045: /* (void) time (&time_value);
6046: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
6047: * tm = *localtime(&time_value);
6048: * strstart=asctime(&tm);
6049: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
6050: */
6051:
6052: nberr=0; /* Number of errors and warnings */
6053: nbwarn=0;
6054: #ifdef WIN32
6055: _getcwd(pathcd, size);
6056: #else
6057: getcwd(pathcd, size);
6058: #endif
6059:
6060: printf("\n%s\n%s",version,fullversion);
6061: if(argc <=1){
6062: printf("\nEnter the parameter file name: ");
6063: fgets(pathr,FILENAMELENGTH,stdin);
6064: i=strlen(pathr);
6065: if(pathr[i-1]=='\n')
6066: pathr[i-1]='\0';
6067: i=strlen(pathr);
6068: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
6069: pathr[i-1]='\0';
6070: for (tok = pathr; tok != NULL; ){
6071: printf("Pathr |%s|\n",pathr);
6072: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
6073: printf("val= |%s| pathr=%s\n",val,pathr);
6074: strcpy (pathtot, val);
6075: if(pathr[0] == '\0') break; /* Dirty */
6076: }
6077: }
6078: else{
6079: strcpy(pathtot,argv[1]);
6080: }
6081: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
6082: /*cygwin_split_path(pathtot,path,optionfile);
6083: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
6084: /* cutv(path,optionfile,pathtot,'\\');*/
6085:
6086: /* Split argv[0], imach program to get pathimach */
6087: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
6088: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6089: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6090: /* strcpy(pathimach,argv[0]); */
6091: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
6092: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
6093: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
6094: #ifdef WIN32
6095: _chdir(path); /* Can be a relative path */
6096: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
6097: #else
6098: chdir(path); /* Can be a relative path */
6099: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
6100: #endif
6101: printf("Current directory %s!\n",pathcd);
6102: strcpy(command,"mkdir ");
6103: strcat(command,optionfilefiname);
6104: if((outcmd=system(command)) != 0){
6105: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
6106: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
6107: /* fclose(ficlog); */
6108: /* exit(1); */
6109: }
6110: /* if((imk=mkdir(optionfilefiname))<0){ */
6111: /* perror("mkdir"); */
6112: /* } */
6113:
6114: /*-------- arguments in the command line --------*/
6115:
6116: /* Log file */
6117: strcat(filelog, optionfilefiname);
6118: strcat(filelog,".log"); /* */
6119: if((ficlog=fopen(filelog,"w"))==NULL) {
6120: printf("Problem with logfile %s\n",filelog);
6121: goto end;
6122: }
6123: fprintf(ficlog,"Log filename:%s\n",filelog);
6124: fprintf(ficlog,"\n%s\n%s",version,fullversion);
6125: fprintf(ficlog,"\nEnter the parameter file name: \n");
6126: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
6127: path=%s \n\
6128: optionfile=%s\n\
6129: optionfilext=%s\n\
6130: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
6131:
6132: syscompilerinfo();
6133:
6134: printf("Local time (at start):%s",strstart);
6135: fprintf(ficlog,"Local time (at start): %s",strstart);
6136: fflush(ficlog);
6137: /* (void) gettimeofday(&curr_time,&tzp); */
6138: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
6139:
6140: /* */
6141: strcpy(fileres,"r");
6142: strcat(fileres, optionfilefiname);
6143: strcat(fileres,".txt"); /* Other files have txt extension */
6144:
6145: /*---------arguments file --------*/
6146:
6147: if((ficpar=fopen(optionfile,"r"))==NULL) {
6148: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
6149: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
6150: fflush(ficlog);
6151: /* goto end; */
6152: exit(70);
6153: }
6154:
6155:
6156:
6157: strcpy(filereso,"o");
6158: strcat(filereso,fileres);
6159: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
6160: printf("Problem with Output resultfile: %s\n", filereso);
6161: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
6162: fflush(ficlog);
6163: goto end;
6164: }
6165:
6166: /* Reads comments: lines beginning with '#' */
6167: numlinepar=0;
6168: while((c=getc(ficpar))=='#' && c!= EOF){
6169: ungetc(c,ficpar);
6170: fgets(line, MAXLINE, ficpar);
6171: numlinepar++;
6172: fputs(line,stdout);
6173: fputs(line,ficparo);
6174: fputs(line,ficlog);
6175: }
6176: ungetc(c,ficpar);
6177:
6178: 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=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
6179: numlinepar++;
6180: 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=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
6181: 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=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
6182: 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=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
6183: fflush(ficlog);
6184: while((c=getc(ficpar))=='#' && c!= EOF){
6185: ungetc(c,ficpar);
6186: fgets(line, MAXLINE, ficpar);
6187: numlinepar++;
6188: fputs(line, stdout);
6189: //puts(line);
6190: fputs(line,ficparo);
6191: fputs(line,ficlog);
6192: }
6193: ungetc(c,ficpar);
6194:
6195:
6196: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
6197: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
6198: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
6199: v1+v2*age+v2*v3 makes cptcovn = 3
6200: */
6201: if (strlen(model)>1)
6202: 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*/
6203: else
6204: ncovmodel=2;
6205: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
6206: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
6207: npar= nforce*ncovmodel; /* Number of parameters like aij*/
6208: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
6209: 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);
6210: 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);
6211: fflush(stdout);
6212: fclose (ficlog);
6213: goto end;
6214: }
6215: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6216: delti=delti3[1][1];
6217: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
6218: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
6219: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
6220: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
6221: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
6222: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6223: fclose (ficparo);
6224: fclose (ficlog);
6225: goto end;
6226: exit(0);
6227: }
6228: else if(mle==-3) {
6229: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
6230: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
6231: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
6232: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6233: matcov=matrix(1,npar,1,npar);
6234: }
6235: else{
6236: /* Read guessed parameters */
6237: /* Reads comments: lines beginning with '#' */
6238: while((c=getc(ficpar))=='#' && c!= EOF){
6239: ungetc(c,ficpar);
6240: fgets(line, MAXLINE, ficpar);
6241: numlinepar++;
6242: fputs(line,stdout);
6243: fputs(line,ficparo);
6244: fputs(line,ficlog);
6245: }
6246: ungetc(c,ficpar);
6247:
6248: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6249: for(i=1; i <=nlstate; i++){
6250: j=0;
6251: for(jj=1; jj <=nlstate+ndeath; jj++){
6252: if(jj==i) continue;
6253: j++;
6254: fscanf(ficpar,"%1d%1d",&i1,&j1);
6255: if ((i1 != i) && (j1 != j)){
6256: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
6257: It might be a problem of design; if ncovcol and the model are correct\n \
6258: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
6259: exit(1);
6260: }
6261: fprintf(ficparo,"%1d%1d",i1,j1);
6262: if(mle==1)
6263: printf("%1d%1d",i,j);
6264: fprintf(ficlog,"%1d%1d",i,j);
6265: for(k=1; k<=ncovmodel;k++){
6266: fscanf(ficpar," %lf",¶m[i][j][k]);
6267: if(mle==1){
6268: printf(" %lf",param[i][j][k]);
6269: fprintf(ficlog," %lf",param[i][j][k]);
6270: }
6271: else
6272: fprintf(ficlog," %lf",param[i][j][k]);
6273: fprintf(ficparo," %lf",param[i][j][k]);
6274: }
6275: fscanf(ficpar,"\n");
6276: numlinepar++;
6277: if(mle==1)
6278: printf("\n");
6279: fprintf(ficlog,"\n");
6280: fprintf(ficparo,"\n");
6281: }
6282: }
6283: fflush(ficlog);
6284:
6285: /* Reads scales values */
6286: p=param[1][1];
6287:
6288: /* Reads comments: lines beginning with '#' */
6289: while((c=getc(ficpar))=='#' && c!= EOF){
6290: ungetc(c,ficpar);
6291: fgets(line, MAXLINE, ficpar);
6292: numlinepar++;
6293: fputs(line,stdout);
6294: fputs(line,ficparo);
6295: fputs(line,ficlog);
6296: }
6297: ungetc(c,ficpar);
6298:
6299: for(i=1; i <=nlstate; i++){
6300: for(j=1; j <=nlstate+ndeath-1; j++){
6301: fscanf(ficpar,"%1d%1d",&i1,&j1);
6302: if ( (i1-i) * (j1-j) != 0){
6303: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
6304: exit(1);
6305: }
6306: printf("%1d%1d",i,j);
6307: fprintf(ficparo,"%1d%1d",i1,j1);
6308: fprintf(ficlog,"%1d%1d",i1,j1);
6309: for(k=1; k<=ncovmodel;k++){
6310: fscanf(ficpar,"%le",&delti3[i][j][k]);
6311: printf(" %le",delti3[i][j][k]);
6312: fprintf(ficparo," %le",delti3[i][j][k]);
6313: fprintf(ficlog," %le",delti3[i][j][k]);
6314: }
6315: fscanf(ficpar,"\n");
6316: numlinepar++;
6317: printf("\n");
6318: fprintf(ficparo,"\n");
6319: fprintf(ficlog,"\n");
6320: }
6321: }
6322: fflush(ficlog);
6323:
6324: /* Reads covariance matrix */
6325: delti=delti3[1][1];
6326:
6327:
6328: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
6329:
6330: /* Reads comments: lines beginning with '#' */
6331: while((c=getc(ficpar))=='#' && c!= EOF){
6332: ungetc(c,ficpar);
6333: fgets(line, MAXLINE, ficpar);
6334: numlinepar++;
6335: fputs(line,stdout);
6336: fputs(line,ficparo);
6337: fputs(line,ficlog);
6338: }
6339: ungetc(c,ficpar);
6340:
6341: matcov=matrix(1,npar,1,npar);
6342: for(i=1; i <=npar; i++)
6343: for(j=1; j <=npar; j++) matcov[i][j]=0.;
6344:
6345: for(i=1; i <=npar; i++){
6346: fscanf(ficpar,"%s",str);
6347: if(mle==1)
6348: printf("%s",str);
6349: fprintf(ficlog,"%s",str);
6350: fprintf(ficparo,"%s",str);
6351: for(j=1; j <=i; j++){
6352: fscanf(ficpar," %le",&matcov[i][j]);
6353: if(mle==1){
6354: printf(" %.5le",matcov[i][j]);
6355: }
6356: fprintf(ficlog," %.5le",matcov[i][j]);
6357: fprintf(ficparo," %.5le",matcov[i][j]);
6358: }
6359: fscanf(ficpar,"\n");
6360: numlinepar++;
6361: if(mle==1)
6362: printf("\n");
6363: fprintf(ficlog,"\n");
6364: fprintf(ficparo,"\n");
6365: }
6366: for(i=1; i <=npar; i++)
6367: for(j=i+1;j<=npar;j++)
6368: matcov[i][j]=matcov[j][i];
6369:
6370: if(mle==1)
6371: printf("\n");
6372: fprintf(ficlog,"\n");
6373:
6374: fflush(ficlog);
6375:
6376: /*-------- Rewriting parameter file ----------*/
6377: strcpy(rfileres,"r"); /* "Rparameterfile */
6378: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
6379: strcat(rfileres,"."); /* */
6380: strcat(rfileres,optionfilext); /* Other files have txt extension */
6381: if((ficres =fopen(rfileres,"w"))==NULL) {
6382: printf("Problem writing new parameter file: %s\n", fileres);goto end;
6383: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
6384: }
6385: fprintf(ficres,"#%s\n",version);
6386: } /* End of mle != -3 */
6387:
6388:
6389: n= lastobs;
6390: num=lvector(1,n);
6391: moisnais=vector(1,n);
6392: annais=vector(1,n);
6393: moisdc=vector(1,n);
6394: andc=vector(1,n);
6395: agedc=vector(1,n);
6396: cod=ivector(1,n);
6397: weight=vector(1,n);
6398: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
6399: mint=matrix(1,maxwav,1,n);
6400: anint=matrix(1,maxwav,1,n);
6401: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
6402: tab=ivector(1,NCOVMAX);
6403: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
6404:
6405: /* Reads data from file datafile */
6406: if (readdata(datafile, firstobs, lastobs, &imx)==1)
6407: goto end;
6408:
6409: /* Calculation of the number of parameters from char model */
6410: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
6411: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
6412: k=3 V4 Tvar[k=3]= 4 (from V4)
6413: k=2 V1 Tvar[k=2]= 1 (from V1)
6414: k=1 Tvar[1]=2 (from V2)
6415: */
6416: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
6417: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
6418: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
6419: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
6420: */
6421: /* For model-covariate k tells which data-covariate to use but
6422: because this model-covariate is a construction we invent a new column
6423: ncovcol + k1
6424: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
6425: Tvar[3=V1*V4]=4+1 etc */
6426: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
6427: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
6428: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
6429: */
6430: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
6431: 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
6432: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
6433: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
6434: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
6435: 4 covariates (3 plus signs)
6436: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
6437: */
6438:
6439: if(decodemodel(model, lastobs) == 1)
6440: goto end;
6441:
6442: if((double)(lastobs-imx)/(double)imx > 1.10){
6443: nbwarn++;
6444: 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);
6445: 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);
6446: }
6447: /* if(mle==1){*/
6448: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
6449: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
6450: }
6451:
6452: /*-calculation of age at interview from date of interview and age at death -*/
6453: agev=matrix(1,maxwav,1,imx);
6454:
6455: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
6456: goto end;
6457:
6458:
6459: agegomp=(int)agemin;
6460: free_vector(moisnais,1,n);
6461: free_vector(annais,1,n);
6462: /* free_matrix(mint,1,maxwav,1,n);
6463: free_matrix(anint,1,maxwav,1,n);*/
6464: free_vector(moisdc,1,n);
6465: free_vector(andc,1,n);
6466: /* */
6467:
6468: wav=ivector(1,imx);
6469: dh=imatrix(1,lastpass-firstpass+1,1,imx);
6470: bh=imatrix(1,lastpass-firstpass+1,1,imx);
6471: mw=imatrix(1,lastpass-firstpass+1,1,imx);
6472:
6473: /* Concatenates waves */
6474: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
6475: /* */
6476:
6477: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
6478:
6479: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
6480: ncodemax[1]=1;
6481: Ndum =ivector(-1,NCOVMAX);
6482: if (ncovmodel > 2)
6483: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
6484:
6485: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
6486: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
6487: h=0;
6488:
6489:
6490: /*if (cptcovn > 0) */
6491:
6492:
6493: m=pow(2,cptcoveff);
6494:
6495: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
6496: 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 */
6497: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
6498: for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
6499: h++;
6500: if (h>m)
6501: h=1;
6502: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
6503: * h 1 2 3 4
6504: *______________________________
6505: * 1 i=1 1 i=1 1 i=1 1 i=1 1
6506: * 2 2 1 1 1
6507: * 3 i=2 1 2 1 1
6508: * 4 2 2 1 1
6509: * 5 i=3 1 i=2 1 2 1
6510: * 6 2 1 2 1
6511: * 7 i=4 1 2 2 1
6512: * 8 2 2 2 1
6513: * 9 i=5 1 i=3 1 i=2 1 1
6514: * 10 2 1 1 1
6515: * 11 i=6 1 2 1 1
6516: * 12 2 2 1 1
6517: * 13 i=7 1 i=4 1 2 1
6518: * 14 2 1 2 1
6519: * 15 i=8 1 2 2 1
6520: * 16 2 2 2 1
6521: */
6522: codtab[h][k]=j;
6523: /*codtab[h][Tvar[k]]=j;*/
6524: 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]]);
6525: }
6526: }
6527: }
6528: }
6529: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
6530: codtab[1][2]=1;codtab[2][2]=2; */
6531: /* for(i=1; i <=m ;i++){
6532: for(k=1; k <=cptcovn; k++){
6533: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
6534: }
6535: printf("\n");
6536: }
6537: scanf("%d",i);*/
6538:
6539: free_ivector(Ndum,-1,NCOVMAX);
6540:
6541:
6542:
6543: /*------------ gnuplot -------------*/
6544: strcpy(optionfilegnuplot,optionfilefiname);
6545: if(mle==-3)
6546: strcat(optionfilegnuplot,"-mort");
6547: strcat(optionfilegnuplot,".gp");
6548:
6549: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
6550: printf("Problem with file %s",optionfilegnuplot);
6551: }
6552: else{
6553: fprintf(ficgp,"\n# %s\n", version);
6554: fprintf(ficgp,"# %s\n", optionfilegnuplot);
6555: //fprintf(ficgp,"set missing 'NaNq'\n");
6556: fprintf(ficgp,"set datafile missing 'NaNq'\n");
6557: }
6558: /* fclose(ficgp);*/
6559: /*--------- index.htm --------*/
6560:
6561: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
6562: if(mle==-3)
6563: strcat(optionfilehtm,"-mort");
6564: strcat(optionfilehtm,".htm");
6565: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
6566: printf("Problem with %s \n",optionfilehtm);
6567: exit(0);
6568: }
6569:
6570: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
6571: strcat(optionfilehtmcov,"-cov.htm");
6572: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
6573: printf("Problem with %s \n",optionfilehtmcov), exit(0);
6574: }
6575: else{
6576: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6577: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6578: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
6579: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
6580: }
6581:
6582: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6583: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6584: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
6585: \n\
6586: <hr size=\"2\" color=\"#EC5E5E\">\
6587: <ul><li><h4>Parameter files</h4>\n\
6588: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
6589: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
6590: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
6591: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
6592: - Date and time at start: %s</ul>\n",\
6593: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
6594: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
6595: fileres,fileres,\
6596: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
6597: fflush(fichtm);
6598:
6599: strcpy(pathr,path);
6600: strcat(pathr,optionfilefiname);
6601: #ifdef WIN32
6602: _chdir(optionfilefiname); /* Move to directory named optionfile */
6603: #else
6604: chdir(optionfilefiname); /* Move to directory named optionfile */
6605: #endif
6606:
6607:
6608: /* Calculates basic frequencies. Computes observed prevalence at single age
6609: and prints on file fileres'p'. */
6610: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
6611:
6612: fprintf(fichtm,"\n");
6613: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
6614: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
6615: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
6616: imx,agemin,agemax,jmin,jmax,jmean);
6617: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6618: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6619: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6620: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6621: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
6622:
6623:
6624: /* For Powell, parameters are in a vector p[] starting at p[1]
6625: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
6626: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
6627:
6628: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
6629:
6630: if (mle==-3){
6631: ximort=matrix(1,NDIM,1,NDIM);
6632: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
6633: cens=ivector(1,n);
6634: ageexmed=vector(1,n);
6635: agecens=vector(1,n);
6636: dcwave=ivector(1,n);
6637:
6638: for (i=1; i<=imx; i++){
6639: dcwave[i]=-1;
6640: for (m=firstpass; m<=lastpass; m++)
6641: if (s[m][i]>nlstate) {
6642: dcwave[i]=m;
6643: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
6644: break;
6645: }
6646: }
6647:
6648: for (i=1; i<=imx; i++) {
6649: if (wav[i]>0){
6650: ageexmed[i]=agev[mw[1][i]][i];
6651: j=wav[i];
6652: agecens[i]=1.;
6653:
6654: if (ageexmed[i]> 1 && wav[i] > 0){
6655: agecens[i]=agev[mw[j][i]][i];
6656: cens[i]= 1;
6657: }else if (ageexmed[i]< 1)
6658: cens[i]= -1;
6659: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
6660: cens[i]=0 ;
6661: }
6662: else cens[i]=-1;
6663: }
6664:
6665: for (i=1;i<=NDIM;i++) {
6666: for (j=1;j<=NDIM;j++)
6667: ximort[i][j]=(i == j ? 1.0 : 0.0);
6668: }
6669:
6670: /*p[1]=0.0268; p[NDIM]=0.083;*/
6671: /*printf("%lf %lf", p[1], p[2]);*/
6672:
6673:
6674: #ifdef GSL
6675: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
6676: #else
6677: printf("Powell\n"); fprintf(ficlog,"Powell\n");
6678: #endif
6679: strcpy(filerespow,"pow-mort");
6680: strcat(filerespow,fileres);
6681: if((ficrespow=fopen(filerespow,"w"))==NULL) {
6682: printf("Problem with resultfile: %s\n", filerespow);
6683: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
6684: }
6685: #ifdef GSL
6686: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
6687: #else
6688: fprintf(ficrespow,"# Powell\n# iter -2*LL");
6689: #endif
6690: /* for (i=1;i<=nlstate;i++)
6691: for(j=1;j<=nlstate+ndeath;j++)
6692: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
6693: */
6694: fprintf(ficrespow,"\n");
6695: #ifdef GSL
6696: /* gsl starts here */
6697: T = gsl_multimin_fminimizer_nmsimplex;
6698: gsl_multimin_fminimizer *sfm = NULL;
6699: gsl_vector *ss, *x;
6700: gsl_multimin_function minex_func;
6701:
6702: /* Initial vertex size vector */
6703: ss = gsl_vector_alloc (NDIM);
6704:
6705: if (ss == NULL){
6706: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
6707: }
6708: /* Set all step sizes to 1 */
6709: gsl_vector_set_all (ss, 0.001);
6710:
6711: /* Starting point */
6712:
6713: x = gsl_vector_alloc (NDIM);
6714:
6715: if (x == NULL){
6716: gsl_vector_free(ss);
6717: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
6718: }
6719:
6720: /* Initialize method and iterate */
6721: /* p[1]=0.0268; p[NDIM]=0.083; */
6722: /* gsl_vector_set(x, 0, 0.0268); */
6723: /* gsl_vector_set(x, 1, 0.083); */
6724: gsl_vector_set(x, 0, p[1]);
6725: gsl_vector_set(x, 1, p[2]);
6726:
6727: minex_func.f = &gompertz_f;
6728: minex_func.n = NDIM;
6729: minex_func.params = (void *)&p; /* ??? */
6730:
6731: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
6732: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
6733:
6734: printf("Iterations beginning .....\n\n");
6735: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
6736:
6737: iteri=0;
6738: while (rval == GSL_CONTINUE){
6739: iteri++;
6740: status = gsl_multimin_fminimizer_iterate(sfm);
6741:
6742: if (status) printf("error: %s\n", gsl_strerror (status));
6743: fflush(0);
6744:
6745: if (status)
6746: break;
6747:
6748: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
6749: ssval = gsl_multimin_fminimizer_size (sfm);
6750:
6751: if (rval == GSL_SUCCESS)
6752: printf ("converged to a local maximum at\n");
6753:
6754: printf("%5d ", iteri);
6755: for (it = 0; it < NDIM; it++){
6756: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
6757: }
6758: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
6759: }
6760:
6761: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
6762:
6763: gsl_vector_free(x); /* initial values */
6764: gsl_vector_free(ss); /* inital step size */
6765: for (it=0; it<NDIM; it++){
6766: p[it+1]=gsl_vector_get(sfm->x,it);
6767: fprintf(ficrespow," %.12lf", p[it]);
6768: }
6769: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
6770: #endif
6771: #ifdef POWELL
6772: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
6773: #endif
6774: fclose(ficrespow);
6775:
6776: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
6777:
6778: for(i=1; i <=NDIM; i++)
6779: for(j=i+1;j<=NDIM;j++)
6780: matcov[i][j]=matcov[j][i];
6781:
6782: printf("\nCovariance matrix\n ");
6783: for(i=1; i <=NDIM; i++) {
6784: for(j=1;j<=NDIM;j++){
6785: printf("%f ",matcov[i][j]);
6786: }
6787: printf("\n ");
6788: }
6789:
6790: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
6791: for (i=1;i<=NDIM;i++)
6792: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
6793:
6794: lsurv=vector(1,AGESUP);
6795: lpop=vector(1,AGESUP);
6796: tpop=vector(1,AGESUP);
6797: lsurv[agegomp]=100000;
6798:
6799: for (k=agegomp;k<=AGESUP;k++) {
6800: agemortsup=k;
6801: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
6802: }
6803:
6804: for (k=agegomp;k<agemortsup;k++)
6805: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
6806:
6807: for (k=agegomp;k<agemortsup;k++){
6808: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
6809: sumlpop=sumlpop+lpop[k];
6810: }
6811:
6812: tpop[agegomp]=sumlpop;
6813: for (k=agegomp;k<(agemortsup-3);k++){
6814: /* tpop[k+1]=2;*/
6815: tpop[k+1]=tpop[k]-lpop[k];
6816: }
6817:
6818:
6819: printf("\nAge lx qx dx Lx Tx e(x)\n");
6820: for (k=agegomp;k<(agemortsup-2);k++)
6821: 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]);
6822:
6823:
6824: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6825: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6826:
6827: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
6828: stepm, weightopt,\
6829: model,imx,p,matcov,agemortsup);
6830:
6831: free_vector(lsurv,1,AGESUP);
6832: free_vector(lpop,1,AGESUP);
6833: free_vector(tpop,1,AGESUP);
6834: #ifdef GSL
6835: free_ivector(cens,1,n);
6836: free_vector(agecens,1,n);
6837: free_ivector(dcwave,1,n);
6838: free_matrix(ximort,1,NDIM,1,NDIM);
6839: #endif
6840: } /* Endof if mle==-3 */
6841:
6842: else{ /* For mle >=1 */
6843: globpr=0;/* debug */
6844: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6845: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6846: for (k=1; k<=npar;k++)
6847: printf(" %d %8.5f",k,p[k]);
6848: printf("\n");
6849: globpr=1; /* to print the contributions */
6850: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6851: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6852: for (k=1; k<=npar;k++)
6853: printf(" %d %8.5f",k,p[k]);
6854: printf("\n");
6855: if(mle>=1){ /* Could be 1 or 2 */
6856: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
6857: }
6858:
6859: /*--------- results files --------------*/
6860: 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=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
6861:
6862:
6863: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6864: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6865: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6866: for(i=1,jk=1; i <=nlstate; i++){
6867: for(k=1; k <=(nlstate+ndeath); k++){
6868: if (k != i) {
6869: printf("%d%d ",i,k);
6870: fprintf(ficlog,"%d%d ",i,k);
6871: fprintf(ficres,"%1d%1d ",i,k);
6872: for(j=1; j <=ncovmodel; j++){
6873: printf("%lf ",p[jk]);
6874: fprintf(ficlog,"%lf ",p[jk]);
6875: fprintf(ficres,"%lf ",p[jk]);
6876: jk++;
6877: }
6878: printf("\n");
6879: fprintf(ficlog,"\n");
6880: fprintf(ficres,"\n");
6881: }
6882: }
6883: }
6884: if(mle!=0){
6885: /* Computing hessian and covariance matrix */
6886: ftolhess=ftol; /* Usually correct */
6887: hesscov(matcov, p, npar, delti, ftolhess, func);
6888: }
6889: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
6890: printf("# Scales (for hessian or gradient estimation)\n");
6891: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
6892: for(i=1,jk=1; i <=nlstate; i++){
6893: for(j=1; j <=nlstate+ndeath; j++){
6894: if (j!=i) {
6895: fprintf(ficres,"%1d%1d",i,j);
6896: printf("%1d%1d",i,j);
6897: fprintf(ficlog,"%1d%1d",i,j);
6898: for(k=1; k<=ncovmodel;k++){
6899: printf(" %.5e",delti[jk]);
6900: fprintf(ficlog," %.5e",delti[jk]);
6901: fprintf(ficres," %.5e",delti[jk]);
6902: jk++;
6903: }
6904: printf("\n");
6905: fprintf(ficlog,"\n");
6906: fprintf(ficres,"\n");
6907: }
6908: }
6909: }
6910:
6911: 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");
6912: if(mle>=1)
6913: 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");
6914: 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");
6915: /* # 121 Var(a12)\n\ */
6916: /* # 122 Cov(b12,a12) Var(b12)\n\ */
6917: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
6918: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
6919: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
6920: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
6921: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
6922: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
6923:
6924:
6925: /* Just to have a covariance matrix which will be more understandable
6926: even is we still don't want to manage dictionary of variables
6927: */
6928: for(itimes=1;itimes<=2;itimes++){
6929: jj=0;
6930: for(i=1; i <=nlstate; i++){
6931: for(j=1; j <=nlstate+ndeath; j++){
6932: if(j==i) continue;
6933: for(k=1; k<=ncovmodel;k++){
6934: jj++;
6935: ca[0]= k+'a'-1;ca[1]='\0';
6936: if(itimes==1){
6937: if(mle>=1)
6938: printf("#%1d%1d%d",i,j,k);
6939: fprintf(ficlog,"#%1d%1d%d",i,j,k);
6940: fprintf(ficres,"#%1d%1d%d",i,j,k);
6941: }else{
6942: if(mle>=1)
6943: printf("%1d%1d%d",i,j,k);
6944: fprintf(ficlog,"%1d%1d%d",i,j,k);
6945: fprintf(ficres,"%1d%1d%d",i,j,k);
6946: }
6947: ll=0;
6948: for(li=1;li <=nlstate; li++){
6949: for(lj=1;lj <=nlstate+ndeath; lj++){
6950: if(lj==li) continue;
6951: for(lk=1;lk<=ncovmodel;lk++){
6952: ll++;
6953: if(ll<=jj){
6954: cb[0]= lk +'a'-1;cb[1]='\0';
6955: if(ll<jj){
6956: if(itimes==1){
6957: if(mle>=1)
6958: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6959: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6960: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6961: }else{
6962: if(mle>=1)
6963: printf(" %.5e",matcov[jj][ll]);
6964: fprintf(ficlog," %.5e",matcov[jj][ll]);
6965: fprintf(ficres," %.5e",matcov[jj][ll]);
6966: }
6967: }else{
6968: if(itimes==1){
6969: if(mle>=1)
6970: printf(" Var(%s%1d%1d)",ca,i,j);
6971: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
6972: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
6973: }else{
6974: if(mle>=1)
6975: printf(" %.5e",matcov[jj][ll]);
6976: fprintf(ficlog," %.5e",matcov[jj][ll]);
6977: fprintf(ficres," %.5e",matcov[jj][ll]);
6978: }
6979: }
6980: }
6981: } /* end lk */
6982: } /* end lj */
6983: } /* end li */
6984: if(mle>=1)
6985: printf("\n");
6986: fprintf(ficlog,"\n");
6987: fprintf(ficres,"\n");
6988: numlinepar++;
6989: } /* end k*/
6990: } /*end j */
6991: } /* end i */
6992: } /* end itimes */
6993:
6994: fflush(ficlog);
6995: fflush(ficres);
6996:
6997: while((c=getc(ficpar))=='#' && c!= EOF){
6998: ungetc(c,ficpar);
6999: fgets(line, MAXLINE, ficpar);
7000: fputs(line,stdout);
7001: fputs(line,ficparo);
7002: }
7003: ungetc(c,ficpar);
7004:
7005: estepm=0;
7006: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
7007: if (estepm==0 || estepm < stepm) estepm=stepm;
7008: if (fage <= 2) {
7009: bage = ageminpar;
7010: fage = agemaxpar;
7011: }
7012:
7013: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
7014: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
7015: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
7016:
7017: while((c=getc(ficpar))=='#' && c!= EOF){
7018: ungetc(c,ficpar);
7019: fgets(line, MAXLINE, ficpar);
7020: fputs(line,stdout);
7021: fputs(line,ficparo);
7022: }
7023: ungetc(c,ficpar);
7024:
7025: 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);
7026: 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);
7027: 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);
7028: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
7029: 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);
7030:
7031: while((c=getc(ficpar))=='#' && c!= EOF){
7032: ungetc(c,ficpar);
7033: fgets(line, MAXLINE, ficpar);
7034: fputs(line,stdout);
7035: fputs(line,ficparo);
7036: }
7037: ungetc(c,ficpar);
7038:
7039:
7040: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
7041: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
7042:
7043: fscanf(ficpar,"pop_based=%d\n",&popbased);
7044: fprintf(ficparo,"pop_based=%d\n",popbased);
7045: fprintf(ficres,"pop_based=%d\n",popbased);
7046:
7047: while((c=getc(ficpar))=='#' && c!= EOF){
7048: ungetc(c,ficpar);
7049: fgets(line, MAXLINE, ficpar);
7050: fputs(line,stdout);
7051: fputs(line,ficparo);
7052: }
7053: ungetc(c,ficpar);
7054:
7055: 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);
7056: 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);
7057: 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);
7058: 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);
7059: 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);
7060: /* day and month of proj2 are not used but only year anproj2.*/
7061:
7062:
7063:
7064: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
7065: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
7066:
7067: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
7068: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
7069:
7070: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
7071: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
7072: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
7073:
7074: /*------------ free_vector -------------*/
7075: /* chdir(path); */
7076:
7077: free_ivector(wav,1,imx);
7078: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
7079: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
7080: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
7081: free_lvector(num,1,n);
7082: free_vector(agedc,1,n);
7083: /*free_matrix(covar,0,NCOVMAX,1,n);*/
7084: /*free_matrix(covar,1,NCOVMAX,1,n);*/
7085: fclose(ficparo);
7086: fclose(ficres);
7087:
7088:
7089: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
7090: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
7091: prlim=matrix(1,nlstate,1,nlstate);
7092: prevalence_limit(p, prlim, ageminpar, agemaxpar);
7093: fclose(ficrespl);
7094:
7095: #ifdef FREEEXIT2
7096: #include "freeexit2.h"
7097: #endif
7098:
7099: /*------------- h Pij x at various ages ------------*/
7100: /*#include "hpijx.h"*/
7101: hPijx(p, bage, fage);
7102: fclose(ficrespij);
7103:
7104: /*-------------- Variance of one-step probabilities---*/
7105: k=1;
7106: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
7107:
7108:
7109: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7110: for(i=1;i<=AGESUP;i++)
7111: for(j=1;j<=NCOVMAX;j++)
7112: for(k=1;k<=NCOVMAX;k++)
7113: probs[i][j][k]=0.;
7114:
7115: /*---------- Forecasting ------------------*/
7116: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
7117: if(prevfcast==1){
7118: /* if(stepm ==1){*/
7119: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
7120: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
7121: /* } */
7122: /* else{ */
7123: /* erreur=108; */
7124: /* 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); */
7125: /* 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); */
7126: /* } */
7127: }
7128:
7129:
7130: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
7131:
7132: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
7133: /* 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",\
7134: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
7135: */
7136:
7137: if (mobilav!=0) {
7138: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7139: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
7140: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
7141: printf(" Error in movingaverage mobilav=%d\n",mobilav);
7142: }
7143: }
7144:
7145:
7146: /*---------- Health expectancies, no variances ------------*/
7147:
7148: strcpy(filerese,"e");
7149: strcat(filerese,fileres);
7150: if((ficreseij=fopen(filerese,"w"))==NULL) {
7151: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
7152: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
7153: }
7154: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
7155: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
7156: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7157: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7158:
7159: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7160: fprintf(ficreseij,"\n#****** ");
7161: for(j=1;j<=cptcoveff;j++) {
7162: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7163: }
7164: fprintf(ficreseij,"******\n");
7165:
7166: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7167: oldm=oldms;savm=savms;
7168: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
7169:
7170: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
7171: /*}*/
7172: }
7173: fclose(ficreseij);
7174:
7175:
7176: /*---------- Health expectancies and variances ------------*/
7177:
7178:
7179: strcpy(filerest,"t");
7180: strcat(filerest,fileres);
7181: if((ficrest=fopen(filerest,"w"))==NULL) {
7182: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
7183: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
7184: }
7185: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
7186: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
7187:
7188:
7189: strcpy(fileresstde,"stde");
7190: strcat(fileresstde,fileres);
7191: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
7192: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
7193: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
7194: }
7195: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
7196: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
7197:
7198: strcpy(filerescve,"cve");
7199: strcat(filerescve,fileres);
7200: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
7201: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
7202: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
7203: }
7204: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
7205: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
7206:
7207: strcpy(fileresv,"v");
7208: strcat(fileresv,fileres);
7209: if((ficresvij=fopen(fileresv,"w"))==NULL) {
7210: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
7211: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
7212: }
7213: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
7214: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
7215:
7216: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7217: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7218:
7219: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7220: fprintf(ficrest,"\n#****** ");
7221: for(j=1;j<=cptcoveff;j++)
7222: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7223: fprintf(ficrest,"******\n");
7224:
7225: fprintf(ficresstdeij,"\n#****** ");
7226: fprintf(ficrescveij,"\n#****** ");
7227: for(j=1;j<=cptcoveff;j++) {
7228: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7229: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7230: }
7231: fprintf(ficresstdeij,"******\n");
7232: fprintf(ficrescveij,"******\n");
7233:
7234: fprintf(ficresvij,"\n#****** ");
7235: for(j=1;j<=cptcoveff;j++)
7236: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7237: fprintf(ficresvij,"******\n");
7238:
7239: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7240: oldm=oldms;savm=savms;
7241: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
7242: /*
7243: */
7244: /* goto endfree; */
7245:
7246: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7247: pstamp(ficrest);
7248:
7249:
7250: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
7251: oldm=oldms;savm=savms; /* Segmentation fault */
7252: cptcod= 0; /* To be deleted */
7253: 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 */
7254: 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 ");
7255: if(vpopbased==1)
7256: 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);
7257: else
7258: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
7259: fprintf(ficrest,"# Age e.. (std) ");
7260: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
7261: fprintf(ficrest,"\n");
7262:
7263: epj=vector(1,nlstate+1);
7264: for(age=bage; age <=fage ;age++){
7265: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
7266: if (vpopbased==1) {
7267: if(mobilav ==0){
7268: for(i=1; i<=nlstate;i++)
7269: prlim[i][i]=probs[(int)age][i][k];
7270: }else{ /* mobilav */
7271: for(i=1; i<=nlstate;i++)
7272: prlim[i][i]=mobaverage[(int)age][i][k];
7273: }
7274: }
7275:
7276: fprintf(ficrest," %4.0f",age);
7277: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
7278: for(i=1, epj[j]=0.;i <=nlstate;i++) {
7279: epj[j] += prlim[i][i]*eij[i][j][(int)age];
7280: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
7281: }
7282: epj[nlstate+1] +=epj[j];
7283: }
7284:
7285: for(i=1, vepp=0.;i <=nlstate;i++)
7286: for(j=1;j <=nlstate;j++)
7287: vepp += vareij[i][j][(int)age];
7288: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
7289: for(j=1;j <=nlstate;j++){
7290: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
7291: }
7292: fprintf(ficrest,"\n");
7293: }
7294: }
7295: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
7296: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
7297: free_vector(epj,1,nlstate+1);
7298: /*}*/
7299: }
7300: free_vector(weight,1,n);
7301: free_imatrix(Tvard,1,NCOVMAX,1,2);
7302: free_imatrix(s,1,maxwav+1,1,n);
7303: free_matrix(anint,1,maxwav,1,n);
7304: free_matrix(mint,1,maxwav,1,n);
7305: free_ivector(cod,1,n);
7306: free_ivector(tab,1,NCOVMAX);
7307: fclose(ficresstdeij);
7308: fclose(ficrescveij);
7309: fclose(ficresvij);
7310: fclose(ficrest);
7311: fclose(ficpar);
7312:
7313: /*------- Variance of period (stable) prevalence------*/
7314:
7315: strcpy(fileresvpl,"vpl");
7316: strcat(fileresvpl,fileres);
7317: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
7318: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
7319: exit(0);
7320: }
7321: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
7322:
7323: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7324: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7325:
7326: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7327: fprintf(ficresvpl,"\n#****** ");
7328: for(j=1;j<=cptcoveff;j++)
7329: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7330: fprintf(ficresvpl,"******\n");
7331:
7332: varpl=matrix(1,nlstate,(int) bage, (int) fage);
7333: oldm=oldms;savm=savms;
7334: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
7335: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
7336: /*}*/
7337: }
7338:
7339: fclose(ficresvpl);
7340:
7341: /*---------- End : free ----------------*/
7342: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7343: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7344: } /* mle==-3 arrives here for freeing */
7345: /* endfree:*/
7346: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
7347: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
7348: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
7349: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
7350: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
7351: free_matrix(covar,0,NCOVMAX,1,n);
7352: free_matrix(matcov,1,npar,1,npar);
7353: /*free_vector(delti,1,npar);*/
7354: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7355: free_matrix(agev,1,maxwav,1,imx);
7356: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7357:
7358: free_ivector(ncodemax,1,NCOVMAX);
7359: free_ivector(Tvar,1,NCOVMAX);
7360: free_ivector(Tprod,1,NCOVMAX);
7361: free_ivector(Tvaraff,1,NCOVMAX);
7362: free_ivector(Tage,1,NCOVMAX);
7363:
7364: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
7365: free_imatrix(codtab,1,100,1,10);
7366: fflush(fichtm);
7367: fflush(ficgp);
7368:
7369:
7370: if((nberr >0) || (nbwarn>0)){
7371: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
7372: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
7373: }else{
7374: printf("End of Imach\n");
7375: fprintf(ficlog,"End of Imach\n");
7376: }
7377: printf("See log file on %s\n",filelog);
7378: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
7379: /*(void) gettimeofday(&end_time,&tzp);*/
7380: rend_time = time(NULL);
7381: end_time = *localtime(&rend_time);
7382: /* tml = *localtime(&end_time.tm_sec); */
7383: strcpy(strtend,asctime(&end_time));
7384: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
7385: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
7386: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
7387:
7388: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
7389: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
7390: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
7391: /* printf("Total time was %d uSec.\n", total_usecs);*/
7392: /* if(fileappend(fichtm,optionfilehtm)){ */
7393: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7394: fclose(fichtm);
7395: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7396: fclose(fichtmcov);
7397: fclose(ficgp);
7398: fclose(ficlog);
7399: /*------ End -----------*/
7400:
7401:
7402: printf("Before Current directory %s!\n",pathcd);
7403: #ifdef WIN32
7404: if (_chdir(pathcd) != 0)
7405: printf("Can't move to directory %s!\n",path);
7406: if(_getcwd(pathcd,MAXLINE) > 0)
7407: #else
7408: if(chdir(pathcd) != 0)
7409: printf("Can't move to directory %s!\n", path);
7410: if (getcwd(pathcd, MAXLINE) > 0)
7411: #endif
7412: printf("Current directory %s!\n",pathcd);
7413: /*strcat(plotcmd,CHARSEPARATOR);*/
7414: sprintf(plotcmd,"gnuplot");
7415: #ifdef _WIN32
7416: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
7417: #endif
7418: if(!stat(plotcmd,&info)){
7419: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
7420: if(!stat(getenv("GNUPLOTBIN"),&info)){
7421: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
7422: }else
7423: strcpy(pplotcmd,plotcmd);
7424: #ifdef __unix
7425: strcpy(plotcmd,GNUPLOTPROGRAM);
7426: if(!stat(plotcmd,&info)){
7427: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
7428: }else
7429: strcpy(pplotcmd,plotcmd);
7430: #endif
7431: }else
7432: strcpy(pplotcmd,plotcmd);
7433:
7434: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
7435: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
7436:
7437: if((outcmd=system(plotcmd)) != 0){
7438: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
7439: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
7440: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
7441: if((outcmd=system(plotcmd)) != 0)
7442: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
7443: }
7444: printf(" Successful, please wait...");
7445: while (z[0] != 'q') {
7446: /* chdir(path); */
7447: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
7448: scanf("%s",z);
7449: /* if (z[0] == 'c') system("./imach"); */
7450: if (z[0] == 'e') {
7451: #ifdef __APPLE__
7452: sprintf(pplotcmd, "open %s", optionfilehtm);
7453: #elif __linux
7454: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
7455: #else
7456: sprintf(pplotcmd, "%s", optionfilehtm);
7457: #endif
7458: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
7459: system(pplotcmd);
7460: }
7461: else if (z[0] == 'g') system(plotcmd);
7462: else if (z[0] == 'q') exit(0);
7463: }
7464: end:
7465: while (z[0] != 'q') {
7466: printf("\nType q for exiting: ");
7467: scanf("%s",z);
7468: }
7469: }
FreeBSD-CVSweb <freebsd-cvsweb@FreeBSD.org>
![[BACK]](/icons/small/back.gif){kind=icon}
Return to imach.c CVS log ![[TXT]](/icons/small/text.gif){kind=icon}
![[DIR]](/icons/small/dir.gif){kind=icon}
Up to [Local Repository] / imach / src