1: /* $Id: imach.c,v 1.178 2015/01/04 09:35:48 brouard Exp $
2: $State: Exp $
3: $Log: imach.c,v $
4: Revision 1.178 2015/01/04 09:35:48 brouard
5: *** empty log message ***
6:
7: Revision 1.177 2015/01/03 18:40:56 brouard
8: Summary: Still testing ilc32 on OSX
9:
10: Revision 1.176 2015/01/03 16:45:04 brouard
11: *** empty log message ***
12:
13: Revision 1.175 2015/01/03 16:33:42 brouard
14: *** empty log message ***
15:
16: Revision 1.174 2015/01/03 16:15:49 brouard
17: Summary: Still in cross-compilation
18:
19: Revision 1.173 2015/01/03 12:06:26 brouard
20: Summary: trying to detect cross-compilation
21:
22: Revision 1.172 2014/12/27 12:07:47 brouard
23: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
24:
25: Revision 1.171 2014/12/23 13:26:59 brouard
26: Summary: Back from Visual C
27:
28: Still problem with utsname.h on Windows
29:
30: Revision 1.170 2014/12/23 11:17:12 brouard
31: Summary: Cleaning some \%% back to %%
32:
33: The escape was mandatory for a specific compiler (which one?), but too many warnings.
34:
35: Revision 1.169 2014/12/22 23:08:31 brouard
36: Summary: 0.98p
37:
38: Outputs some informations on compiler used, OS etc. Testing on different platforms.
39:
40: Revision 1.168 2014/12/22 15:17:42 brouard
41: Summary: update
42:
43: Revision 1.167 2014/12/22 13:50:56 brouard
44: Summary: Testing uname and compiler version and if compiled 32 or 64
45:
46: Testing on Linux 64
47:
48: Revision 1.166 2014/12/22 11:40:47 brouard
49: *** empty log message ***
50:
51: Revision 1.165 2014/12/16 11:20:36 brouard
52: Summary: After compiling on Visual C
53:
54: * imach.c (Module): Merging 1.61 to 1.162
55:
56: Revision 1.164 2014/12/16 10:52:11 brouard
57: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
58:
59: * imach.c (Module): Merging 1.61 to 1.162
60:
61: Revision 1.163 2014/12/16 10:30:11 brouard
62: * imach.c (Module): Merging 1.61 to 1.162
63:
64: Revision 1.162 2014/09/25 11:43:39 brouard
65: Summary: temporary backup 0.99!
66:
67: Revision 1.1 2014/09/16 11:06:58 brouard
68: Summary: With some code (wrong) for nlopt
69:
70: Author:
71:
72: Revision 1.161 2014/09/15 20:41:41 brouard
73: Summary: Problem with macro SQR on Intel compiler
74:
75: Revision 1.160 2014/09/02 09:24:05 brouard
76: *** empty log message ***
77:
78: Revision 1.159 2014/09/01 10:34:10 brouard
79: Summary: WIN32
80: Author: Brouard
81:
82: Revision 1.158 2014/08/27 17:11:51 brouard
83: *** empty log message ***
84:
85: Revision 1.157 2014/08/27 16:26:55 brouard
86: Summary: Preparing windows Visual studio version
87: Author: Brouard
88:
89: In order to compile on Visual studio, time.h is now correct and time_t
90: and tm struct should be used. difftime should be used but sometimes I
91: just make the differences in raw time format (time(&now).
92: Trying to suppress #ifdef LINUX
93: Add xdg-open for __linux in order to open default browser.
94:
95: Revision 1.156 2014/08/25 20:10:10 brouard
96: *** empty log message ***
97:
98: Revision 1.155 2014/08/25 18:32:34 brouard
99: Summary: New compile, minor changes
100: Author: Brouard
101:
102: Revision 1.154 2014/06/20 17:32:08 brouard
103: Summary: Outputs now all graphs of convergence to period prevalence
104:
105: Revision 1.153 2014/06/20 16:45:46 brouard
106: Summary: If 3 live state, convergence to period prevalence on same graph
107: Author: Brouard
108:
109: Revision 1.152 2014/06/18 17:54:09 brouard
110: Summary: open browser, use gnuplot on same dir than imach if not found in the path
111:
112: Revision 1.151 2014/06/18 16:43:30 brouard
113: *** empty log message ***
114:
115: Revision 1.150 2014/06/18 16:42:35 brouard
116: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
117: Author: brouard
118:
119: Revision 1.149 2014/06/18 15:51:14 brouard
120: Summary: Some fixes in parameter files errors
121: Author: Nicolas Brouard
122:
123: Revision 1.148 2014/06/17 17:38:48 brouard
124: Summary: Nothing new
125: Author: Brouard
126:
127: Just a new packaging for OS/X version 0.98nS
128:
129: Revision 1.147 2014/06/16 10:33:11 brouard
130: *** empty log message ***
131:
132: Revision 1.146 2014/06/16 10:20:28 brouard
133: Summary: Merge
134: Author: Brouard
135:
136: Merge, before building revised version.
137:
138: Revision 1.145 2014/06/10 21:23:15 brouard
139: Summary: Debugging with valgrind
140: Author: Nicolas Brouard
141:
142: Lot of changes in order to output the results with some covariates
143: After the Edimburgh REVES conference 2014, it seems mandatory to
144: improve the code.
145: No more memory valgrind error but a lot has to be done in order to
146: continue the work of splitting the code into subroutines.
147: Also, decodemodel has been improved. Tricode is still not
148: optimal. nbcode should be improved. Documentation has been added in
149: the source code.
150:
151: Revision 1.143 2014/01/26 09:45:38 brouard
152: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
153:
154: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
155: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
156:
157: Revision 1.142 2014/01/26 03:57:36 brouard
158: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
159:
160: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
161:
162: Revision 1.141 2014/01/26 02:42:01 brouard
163: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
164:
165: Revision 1.140 2011/09/02 10:37:54 brouard
166: Summary: times.h is ok with mingw32 now.
167:
168: Revision 1.139 2010/06/14 07:50:17 brouard
169: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
170: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
171:
172: Revision 1.138 2010/04/30 18:19:40 brouard
173: *** empty log message ***
174:
175: Revision 1.137 2010/04/29 18:11:38 brouard
176: (Module): Checking covariates for more complex models
177: than V1+V2. A lot of change to be done. Unstable.
178:
179: Revision 1.136 2010/04/26 20:30:53 brouard
180: (Module): merging some libgsl code. Fixing computation
181: of likelione (using inter/intrapolation if mle = 0) in order to
182: get same likelihood as if mle=1.
183: Some cleaning of code and comments added.
184:
185: Revision 1.135 2009/10/29 15:33:14 brouard
186: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
187:
188: Revision 1.134 2009/10/29 13:18:53 brouard
189: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
190:
191: Revision 1.133 2009/07/06 10:21:25 brouard
192: just nforces
193:
194: Revision 1.132 2009/07/06 08:22:05 brouard
195: Many tings
196:
197: Revision 1.131 2009/06/20 16:22:47 brouard
198: Some dimensions resccaled
199:
200: Revision 1.130 2009/05/26 06:44:34 brouard
201: (Module): Max Covariate is now set to 20 instead of 8. A
202: lot of cleaning with variables initialized to 0. Trying to make
203: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
204:
205: Revision 1.129 2007/08/31 13:49:27 lievre
206: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
207:
208: Revision 1.128 2006/06/30 13:02:05 brouard
209: (Module): Clarifications on computing e.j
210:
211: Revision 1.127 2006/04/28 18:11:50 brouard
212: (Module): Yes the sum of survivors was wrong since
213: imach-114 because nhstepm was no more computed in the age
214: loop. Now we define nhstepma in the age loop.
215: (Module): In order to speed up (in case of numerous covariates) we
216: compute health expectancies (without variances) in a first step
217: and then all the health expectancies with variances or standard
218: deviation (needs data from the Hessian matrices) which slows the
219: computation.
220: In the future we should be able to stop the program is only health
221: expectancies and graph are needed without standard deviations.
222:
223: Revision 1.126 2006/04/28 17:23:28 brouard
224: (Module): Yes the sum of survivors was wrong since
225: imach-114 because nhstepm was no more computed in the age
226: loop. Now we define nhstepma in the age loop.
227: Version 0.98h
228:
229: Revision 1.125 2006/04/04 15:20:31 lievre
230: Errors in calculation of health expectancies. Age was not initialized.
231: Forecasting file added.
232:
233: Revision 1.124 2006/03/22 17:13:53 lievre
234: Parameters are printed with %lf instead of %f (more numbers after the comma).
235: The log-likelihood is printed in the log file
236:
237: Revision 1.123 2006/03/20 10:52:43 brouard
238: * imach.c (Module): <title> changed, corresponds to .htm file
239: name. <head> headers where missing.
240:
241: * imach.c (Module): Weights can have a decimal point as for
242: English (a comma might work with a correct LC_NUMERIC environment,
243: otherwise the weight is truncated).
244: Modification of warning when the covariates values are not 0 or
245: 1.
246: Version 0.98g
247:
248: Revision 1.122 2006/03/20 09:45:41 brouard
249: (Module): Weights can have a decimal point as for
250: English (a comma might work with a correct LC_NUMERIC environment,
251: otherwise the weight is truncated).
252: Modification of warning when the covariates values are not 0 or
253: 1.
254: Version 0.98g
255:
256: Revision 1.121 2006/03/16 17:45:01 lievre
257: * imach.c (Module): Comments concerning covariates added
258:
259: * imach.c (Module): refinements in the computation of lli if
260: status=-2 in order to have more reliable computation if stepm is
261: not 1 month. Version 0.98f
262:
263: Revision 1.120 2006/03/16 15:10:38 lievre
264: (Module): refinements in the computation of lli if
265: status=-2 in order to have more reliable computation if stepm is
266: not 1 month. Version 0.98f
267:
268: Revision 1.119 2006/03/15 17:42:26 brouard
269: (Module): Bug if status = -2, the loglikelihood was
270: computed as likelihood omitting the logarithm. Version O.98e
271:
272: Revision 1.118 2006/03/14 18:20:07 brouard
273: (Module): varevsij Comments added explaining the second
274: table of variances if popbased=1 .
275: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
276: (Module): Function pstamp added
277: (Module): Version 0.98d
278:
279: Revision 1.117 2006/03/14 17:16:22 brouard
280: (Module): varevsij Comments added explaining the second
281: table of variances if popbased=1 .
282: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
283: (Module): Function pstamp added
284: (Module): Version 0.98d
285:
286: Revision 1.116 2006/03/06 10:29:27 brouard
287: (Module): Variance-covariance wrong links and
288: varian-covariance of ej. is needed (Saito).
289:
290: Revision 1.115 2006/02/27 12:17:45 brouard
291: (Module): One freematrix added in mlikeli! 0.98c
292:
293: Revision 1.114 2006/02/26 12:57:58 brouard
294: (Module): Some improvements in processing parameter
295: filename with strsep.
296:
297: Revision 1.113 2006/02/24 14:20:24 brouard
298: (Module): Memory leaks checks with valgrind and:
299: datafile was not closed, some imatrix were not freed and on matrix
300: allocation too.
301:
302: Revision 1.112 2006/01/30 09:55:26 brouard
303: (Module): Back to gnuplot.exe instead of wgnuplot.exe
304:
305: Revision 1.111 2006/01/25 20:38:18 brouard
306: (Module): Lots of cleaning and bugs added (Gompertz)
307: (Module): Comments can be added in data file. Missing date values
308: can be a simple dot '.'.
309:
310: Revision 1.110 2006/01/25 00:51:50 brouard
311: (Module): Lots of cleaning and bugs added (Gompertz)
312:
313: Revision 1.109 2006/01/24 19:37:15 brouard
314: (Module): Comments (lines starting with a #) are allowed in data.
315:
316: Revision 1.108 2006/01/19 18:05:42 lievre
317: Gnuplot problem appeared...
318: To be fixed
319:
320: Revision 1.107 2006/01/19 16:20:37 brouard
321: Test existence of gnuplot in imach path
322:
323: Revision 1.106 2006/01/19 13:24:36 brouard
324: Some cleaning and links added in html output
325:
326: Revision 1.105 2006/01/05 20:23:19 lievre
327: *** empty log message ***
328:
329: Revision 1.104 2005/09/30 16:11:43 lievre
330: (Module): sump fixed, loop imx fixed, and simplifications.
331: (Module): If the status is missing at the last wave but we know
332: that the person is alive, then we can code his/her status as -2
333: (instead of missing=-1 in earlier versions) and his/her
334: contributions to the likelihood is 1 - Prob of dying from last
335: health status (= 1-p13= p11+p12 in the easiest case of somebody in
336: the healthy state at last known wave). Version is 0.98
337:
338: Revision 1.103 2005/09/30 15:54:49 lievre
339: (Module): sump fixed, loop imx fixed, and simplifications.
340:
341: Revision 1.102 2004/09/15 17:31:30 brouard
342: Add the possibility to read data file including tab characters.
343:
344: Revision 1.101 2004/09/15 10:38:38 brouard
345: Fix on curr_time
346:
347: Revision 1.100 2004/07/12 18:29:06 brouard
348: Add version for Mac OS X. Just define UNIX in Makefile
349:
350: Revision 1.99 2004/06/05 08:57:40 brouard
351: *** empty log message ***
352:
353: Revision 1.98 2004/05/16 15:05:56 brouard
354: New version 0.97 . First attempt to estimate force of mortality
355: directly from the data i.e. without the need of knowing the health
356: state at each age, but using a Gompertz model: log u =a + b*age .
357: This is the basic analysis of mortality and should be done before any
358: other analysis, in order to test if the mortality estimated from the
359: cross-longitudinal survey is different from the mortality estimated
360: from other sources like vital statistic data.
361:
362: The same imach parameter file can be used but the option for mle should be -3.
363:
364: Agnès, who wrote this part of the code, tried to keep most of the
365: former routines in order to include the new code within the former code.
366:
367: The output is very simple: only an estimate of the intercept and of
368: the slope with 95% confident intervals.
369:
370: Current limitations:
371: A) Even if you enter covariates, i.e. with the
372: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
373: B) There is no computation of Life Expectancy nor Life Table.
374:
375: Revision 1.97 2004/02/20 13:25:42 lievre
376: Version 0.96d. Population forecasting command line is (temporarily)
377: suppressed.
378:
379: Revision 1.96 2003/07/15 15:38:55 brouard
380: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
381: rewritten within the same printf. Workaround: many printfs.
382:
383: Revision 1.95 2003/07/08 07:54:34 brouard
384: * imach.c (Repository):
385: (Repository): Using imachwizard code to output a more meaningful covariance
386: matrix (cov(a12,c31) instead of numbers.
387:
388: Revision 1.94 2003/06/27 13:00:02 brouard
389: Just cleaning
390:
391: Revision 1.93 2003/06/25 16:33:55 brouard
392: (Module): On windows (cygwin) function asctime_r doesn't
393: exist so I changed back to asctime which exists.
394: (Module): Version 0.96b
395:
396: Revision 1.92 2003/06/25 16:30:45 brouard
397: (Module): On windows (cygwin) function asctime_r doesn't
398: exist so I changed back to asctime which exists.
399:
400: Revision 1.91 2003/06/25 15:30:29 brouard
401: * imach.c (Repository): Duplicated warning errors corrected.
402: (Repository): Elapsed time after each iteration is now output. It
403: helps to forecast when convergence will be reached. Elapsed time
404: is stamped in powell. We created a new html file for the graphs
405: concerning matrix of covariance. It has extension -cov.htm.
406:
407: Revision 1.90 2003/06/24 12:34:15 brouard
408: (Module): Some bugs corrected for windows. Also, when
409: mle=-1 a template is output in file "or"mypar.txt with the design
410: of the covariance matrix to be input.
411:
412: Revision 1.89 2003/06/24 12:30:52 brouard
413: (Module): Some bugs corrected for windows. Also, when
414: mle=-1 a template is output in file "or"mypar.txt with the design
415: of the covariance matrix to be input.
416:
417: Revision 1.88 2003/06/23 17:54:56 brouard
418: * 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.
419:
420: Revision 1.87 2003/06/18 12:26:01 brouard
421: Version 0.96
422:
423: Revision 1.86 2003/06/17 20:04:08 brouard
424: (Module): Change position of html and gnuplot routines and added
425: routine fileappend.
426:
427: Revision 1.85 2003/06/17 13:12:43 brouard
428: * imach.c (Repository): Check when date of death was earlier that
429: current date of interview. It may happen when the death was just
430: prior to the death. In this case, dh was negative and likelihood
431: was wrong (infinity). We still send an "Error" but patch by
432: assuming that the date of death was just one stepm after the
433: interview.
434: (Repository): Because some people have very long ID (first column)
435: we changed int to long in num[] and we added a new lvector for
436: memory allocation. But we also truncated to 8 characters (left
437: truncation)
438: (Repository): No more line truncation errors.
439:
440: Revision 1.84 2003/06/13 21:44:43 brouard
441: * imach.c (Repository): Replace "freqsummary" at a correct
442: place. It differs from routine "prevalence" which may be called
443: many times. Probs is memory consuming and must be used with
444: parcimony.
445: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
446:
447: Revision 1.83 2003/06/10 13:39:11 lievre
448: *** empty log message ***
449:
450: Revision 1.82 2003/06/05 15:57:20 brouard
451: Add log in imach.c and fullversion number is now printed.
452:
453: */
454: /*
455: Interpolated Markov Chain
456:
457: Short summary of the programme:
458:
459: This program computes Healthy Life Expectancies from
460: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
461: first survey ("cross") where individuals from different ages are
462: interviewed on their health status or degree of disability (in the
463: case of a health survey which is our main interest) -2- at least a
464: second wave of interviews ("longitudinal") which measure each change
465: (if any) in individual health status. Health expectancies are
466: computed from the time spent in each health state according to a
467: model. More health states you consider, more time is necessary to reach the
468: Maximum Likelihood of the parameters involved in the model. The
469: simplest model is the multinomial logistic model where pij is the
470: probability to be observed in state j at the second wave
471: conditional to be observed in state i at the first wave. Therefore
472: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
473: 'age' is age and 'sex' is a covariate. If you want to have a more
474: complex model than "constant and age", you should modify the program
475: where the markup *Covariates have to be included here again* invites
476: you to do it. More covariates you add, slower the
477: convergence.
478:
479: The advantage of this computer programme, compared to a simple
480: multinomial logistic model, is clear when the delay between waves is not
481: identical for each individual. Also, if a individual missed an
482: intermediate interview, the information is lost, but taken into
483: account using an interpolation or extrapolation.
484:
485: hPijx is the probability to be observed in state i at age x+h
486: conditional to the observed state i at age x. The delay 'h' can be
487: split into an exact number (nh*stepm) of unobserved intermediate
488: states. This elementary transition (by month, quarter,
489: semester or year) is modelled as a multinomial logistic. The hPx
490: matrix is simply the matrix product of nh*stepm elementary matrices
491: and the contribution of each individual to the likelihood is simply
492: hPijx.
493:
494: Also this programme outputs the covariance matrix of the parameters but also
495: of the life expectancies. It also computes the period (stable) prevalence.
496:
497: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
498: Institut national d'études démographiques, Paris.
499: This software have been partly granted by Euro-REVES, a concerted action
500: from the European Union.
501: It is copyrighted identically to a GNU software product, ie programme and
502: software can be distributed freely for non commercial use. Latest version
503: can be accessed at http://euroreves.ined.fr/imach .
504:
505: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
506: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
507:
508: **********************************************************************/
509: /*
510: main
511: read parameterfile
512: read datafile
513: concatwav
514: freqsummary
515: if (mle >= 1)
516: mlikeli
517: print results files
518: if mle==1
519: computes hessian
520: read end of parameter file: agemin, agemax, bage, fage, estepm
521: begin-prev-date,...
522: open gnuplot file
523: open html file
524: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
525: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
526: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
527: freexexit2 possible for memory heap.
528:
529: h Pij x | pij_nom ficrestpij
530: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
531: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
532: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
533:
534: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
535: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
536: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
537: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
538: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
539:
540: forecasting if prevfcast==1 prevforecast call prevalence()
541: health expectancies
542: Variance-covariance of DFLE
543: prevalence()
544: movingaverage()
545: varevsij()
546: if popbased==1 varevsij(,popbased)
547: total life expectancies
548: Variance of period (stable) prevalence
549: end
550: */
551:
552: #define POWELL /* Instead of NLOPT */
553:
554: #include <math.h>
555: #include <stdio.h>
556: #include <stdlib.h>
557: #include <string.h>
558:
559: #ifdef _WIN32
560: #include <io.h>
561: #include <windows.h>
562: #include <tchar.h>
563: #else
564: #include <unistd.h>
565: #endif
566:
567: #include <limits.h>
568: #include <sys/types.h>
569:
570: #if defined(__GNUC__)
571: #include <sys/utsname.h> /* Doesn't work on Windows */
572: #endif
573:
574: #include <sys/stat.h>
575: #include <errno.h>
576: /* extern int errno; */
577:
578: /* #ifdef LINUX */
579: /* #include <time.h> */
580: /* #include "timeval.h" */
581: /* #else */
582: /* #include <sys/time.h> */
583: /* #endif */
584:
585: #include <time.h>
586:
587: #ifdef GSL
588: #include <gsl/gsl_errno.h>
589: #include <gsl/gsl_multimin.h>
590: #endif
591:
592:
593: #ifdef NLOPT
594: #include <nlopt.h>
595: typedef struct {
596: double (* function)(double [] );
597: } myfunc_data ;
598: #endif
599:
600: /* #include <libintl.h> */
601: /* #define _(String) gettext (String) */
602:
603: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
604:
605: #define GNUPLOTPROGRAM "gnuplot"
606: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
607: #define FILENAMELENGTH 132
608:
609: #define GLOCK_ERROR_NOPATH -1 /* empty path */
610: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
611:
612: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
613: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
614:
615: #define NINTERVMAX 8
616: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
617: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
618: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
619: #define codtabm(h,k) 1 & (h-1) >> (k-1) ;
620: #define MAXN 20000
621: #define YEARM 12. /**< Number of months per year */
622: #define AGESUP 130
623: #define AGEBASE 40
624: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
625: #ifdef _WIN32
626: #define DIRSEPARATOR '\\'
627: #define CHARSEPARATOR "\\"
628: #define ODIRSEPARATOR '/'
629: #else
630: #define DIRSEPARATOR '/'
631: #define CHARSEPARATOR "/"
632: #define ODIRSEPARATOR '\\'
633: #endif
634:
635: /* $Id: imach.c,v 1.178 2015/01/04 09:35:48 brouard Exp $ */
636: /* $State: Exp $ */
637:
638: char version[]="Imach version 0.98p, December 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
639: char fullversion[]="$Revision: 1.178 $ $Date: 2015/01/04 09:35:48 $";
640: char strstart[80];
641: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
642: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
643: int nvar=0, nforce=0; /* Number of variables, number of forces */
644: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
645: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
646: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
647: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
648: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
649: int cptcovprodnoage=0; /**< Number of covariate products without age */
650: int cptcoveff=0; /* Total number of covariates to vary for printing results */
651: int cptcov=0; /* Working variable */
652: int npar=NPARMAX;
653: int nlstate=2; /* Number of live states */
654: int ndeath=1; /* Number of dead states */
655: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
656: int popbased=0;
657:
658: int *wav; /* Number of waves for this individuual 0 is possible */
659: int maxwav=0; /* Maxim number of waves */
660: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
661: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
662: int gipmx=0, gsw=0; /* Global variables on the number of contributions
663: to the likelihood and the sum of weights (done by funcone)*/
664: int mle=1, weightopt=0;
665: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
666: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
667: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
668: * wave mi and wave mi+1 is not an exact multiple of stepm. */
669: int countcallfunc=0; /* Count the number of calls to func */
670: double jmean=1; /* Mean space between 2 waves */
671: double **matprod2(); /* test */
672: double **oldm, **newm, **savm; /* Working pointers to matrices */
673: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
674: /*FILE *fic ; */ /* Used in readdata only */
675: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
676: FILE *ficlog, *ficrespow;
677: int globpr=0; /* Global variable for printing or not */
678: double fretone; /* Only one call to likelihood */
679: long ipmx=0; /* Number of contributions */
680: double sw; /* Sum of weights */
681: char filerespow[FILENAMELENGTH];
682: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
683: FILE *ficresilk;
684: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
685: FILE *ficresprobmorprev;
686: FILE *fichtm, *fichtmcov; /* Html File */
687: FILE *ficreseij;
688: char filerese[FILENAMELENGTH];
689: FILE *ficresstdeij;
690: char fileresstde[FILENAMELENGTH];
691: FILE *ficrescveij;
692: char filerescve[FILENAMELENGTH];
693: FILE *ficresvij;
694: char fileresv[FILENAMELENGTH];
695: FILE *ficresvpl;
696: char fileresvpl[FILENAMELENGTH];
697: char title[MAXLINE];
698: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
699: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
700: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
701: char command[FILENAMELENGTH];
702: int outcmd=0;
703:
704: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
705:
706: char filelog[FILENAMELENGTH]; /* Log file */
707: char filerest[FILENAMELENGTH];
708: char fileregp[FILENAMELENGTH];
709: char popfile[FILENAMELENGTH];
710:
711: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
712:
713: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
714: /* struct timezone tzp; */
715: /* extern int gettimeofday(); */
716: struct tm tml, *gmtime(), *localtime();
717:
718: extern time_t time();
719:
720: struct tm start_time, end_time, curr_time, last_time, forecast_time;
721: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
722: struct tm tm;
723:
724: char strcurr[80], strfor[80];
725:
726: char *endptr;
727: long lval;
728: double dval;
729:
730: #define NR_END 1
731: #define FREE_ARG char*
732: #define FTOL 1.0e-10
733:
734: #define NRANSI
735: #define ITMAX 200
736:
737: #define TOL 2.0e-4
738:
739: #define CGOLD 0.3819660
740: #define ZEPS 1.0e-10
741: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
742:
743: #define GOLD 1.618034
744: #define GLIMIT 100.0
745: #define TINY 1.0e-20
746:
747: static double maxarg1,maxarg2;
748: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
749: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
750:
751: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
752: #define rint(a) floor(a+0.5)
753: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
754: /* #define mytinydouble 1.0e-16 */
755: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
756: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
757: /* static double dsqrarg; */
758: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
759: static double sqrarg;
760: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
761: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
762: int agegomp= AGEGOMP;
763:
764: int imx;
765: int stepm=1;
766: /* Stepm, step in month: minimum step interpolation*/
767:
768: int estepm;
769: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
770:
771: int m,nb;
772: long *num;
773: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
774: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
775: double **pmmij, ***probs;
776: double *ageexmed,*agecens;
777: double dateintmean=0;
778:
779: double *weight;
780: int **s; /* Status */
781: double *agedc;
782: double **covar; /**< covar[j,i], value of jth covariate for individual i,
783: * covar=matrix(0,NCOVMAX,1,n);
784: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
785: double idx;
786: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
787: int *Ndum; /** Freq of modality (tricode */
788: int **codtab; /**< codtab=imatrix(1,100,1,10); */
789: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
790: double *lsurv, *lpop, *tpop;
791:
792: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
793: double ftolhess; /**< Tolerance for computing hessian */
794:
795: /**************** split *************************/
796: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
797: {
798: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
799: the name of the file (name), its extension only (ext) and its first part of the name (finame)
800: */
801: char *ss; /* pointer */
802: int l1, l2; /* length counters */
803:
804: l1 = strlen(path ); /* length of path */
805: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
806: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
807: if ( ss == NULL ) { /* no directory, so determine current directory */
808: strcpy( name, path ); /* we got the fullname name because no directory */
809: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
810: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
811: /* get current working directory */
812: /* extern char* getcwd ( char *buf , int len);*/
813: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
814: return( GLOCK_ERROR_GETCWD );
815: }
816: /* got dirc from getcwd*/
817: printf(" DIRC = %s \n",dirc);
818: } else { /* strip direcotry from path */
819: ss++; /* after this, the filename */
820: l2 = strlen( ss ); /* length of filename */
821: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
822: strcpy( name, ss ); /* save file name */
823: strncpy( dirc, path, l1 - l2 ); /* now the directory */
824: dirc[l1-l2] = 0; /* add zero */
825: printf(" DIRC2 = %s \n",dirc);
826: }
827: /* We add a separator at the end of dirc if not exists */
828: l1 = strlen( dirc ); /* length of directory */
829: if( dirc[l1-1] != DIRSEPARATOR ){
830: dirc[l1] = DIRSEPARATOR;
831: dirc[l1+1] = 0;
832: printf(" DIRC3 = %s \n",dirc);
833: }
834: ss = strrchr( name, '.' ); /* find last / */
835: if (ss >0){
836: ss++;
837: strcpy(ext,ss); /* save extension */
838: l1= strlen( name);
839: l2= strlen(ss)+1;
840: strncpy( finame, name, l1-l2);
841: finame[l1-l2]= 0;
842: }
843:
844: return( 0 ); /* we're done */
845: }
846:
847:
848: /******************************************/
849:
850: void replace_back_to_slash(char *s, char*t)
851: {
852: int i;
853: int lg=0;
854: i=0;
855: lg=strlen(t);
856: for(i=0; i<= lg; i++) {
857: (s[i] = t[i]);
858: if (t[i]== '\\') s[i]='/';
859: }
860: }
861:
862: char *trimbb(char *out, char *in)
863: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
864: char *s;
865: s=out;
866: while (*in != '\0'){
867: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
868: in++;
869: }
870: *out++ = *in++;
871: }
872: *out='\0';
873: return s;
874: }
875:
876: char *cutl(char *blocc, char *alocc, char *in, char occ)
877: {
878: /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ'
879: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
880: gives blocc="abcdef2ghi" and alocc="j".
881: If occ is not found blocc is null and alocc is equal to in. Returns blocc
882: */
883: char *s, *t;
884: t=in;s=in;
885: while ((*in != occ) && (*in != '\0')){
886: *alocc++ = *in++;
887: }
888: if( *in == occ){
889: *(alocc)='\0';
890: s=++in;
891: }
892:
893: if (s == t) {/* occ not found */
894: *(alocc-(in-s))='\0';
895: in=s;
896: }
897: while ( *in != '\0'){
898: *blocc++ = *in++;
899: }
900:
901: *blocc='\0';
902: return t;
903: }
904: char *cutv(char *blocc, char *alocc, char *in, char occ)
905: {
906: /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
907: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
908: gives blocc="abcdef2ghi" and alocc="j".
909: If occ is not found blocc is null and alocc is equal to in. Returns alocc
910: */
911: char *s, *t;
912: t=in;s=in;
913: while (*in != '\0'){
914: while( *in == occ){
915: *blocc++ = *in++;
916: s=in;
917: }
918: *blocc++ = *in++;
919: }
920: if (s == t) /* occ not found */
921: *(blocc-(in-s))='\0';
922: else
923: *(blocc-(in-s)-1)='\0';
924: in=s;
925: while ( *in != '\0'){
926: *alocc++ = *in++;
927: }
928:
929: *alocc='\0';
930: return s;
931: }
932:
933: int nbocc(char *s, char occ)
934: {
935: int i,j=0;
936: int lg=20;
937: i=0;
938: lg=strlen(s);
939: for(i=0; i<= lg; i++) {
940: if (s[i] == occ ) j++;
941: }
942: return j;
943: }
944:
945: /* void cutv(char *u,char *v, char*t, char occ) */
946: /* { */
947: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
948: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
949: /* gives u="abcdef2ghi" and v="j" *\/ */
950: /* int i,lg,j,p=0; */
951: /* i=0; */
952: /* lg=strlen(t); */
953: /* for(j=0; j<=lg-1; j++) { */
954: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
955: /* } */
956:
957: /* for(j=0; j<p; j++) { */
958: /* (u[j] = t[j]); */
959: /* } */
960: /* u[p]='\0'; */
961:
962: /* for(j=0; j<= lg; j++) { */
963: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
964: /* } */
965: /* } */
966:
967: #ifdef _WIN32
968: char * strsep(char **pp, const char *delim)
969: {
970: char *p, *q;
971:
972: if ((p = *pp) == NULL)
973: return 0;
974: if ((q = strpbrk (p, delim)) != NULL)
975: {
976: *pp = q + 1;
977: *q = '\0';
978: }
979: else
980: *pp = 0;
981: return p;
982: }
983: #endif
984:
985: /********************** nrerror ********************/
986:
987: void nrerror(char error_text[])
988: {
989: fprintf(stderr,"ERREUR ...\n");
990: fprintf(stderr,"%s\n",error_text);
991: exit(EXIT_FAILURE);
992: }
993: /*********************** vector *******************/
994: double *vector(int nl, int nh)
995: {
996: double *v;
997: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
998: if (!v) nrerror("allocation failure in vector");
999: return v-nl+NR_END;
1000: }
1001:
1002: /************************ free vector ******************/
1003: void free_vector(double*v, int nl, int nh)
1004: {
1005: free((FREE_ARG)(v+nl-NR_END));
1006: }
1007:
1008: /************************ivector *******************************/
1009: int *ivector(long nl,long nh)
1010: {
1011: int *v;
1012: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1013: if (!v) nrerror("allocation failure in ivector");
1014: return v-nl+NR_END;
1015: }
1016:
1017: /******************free ivector **************************/
1018: void free_ivector(int *v, long nl, long nh)
1019: {
1020: free((FREE_ARG)(v+nl-NR_END));
1021: }
1022:
1023: /************************lvector *******************************/
1024: long *lvector(long nl,long nh)
1025: {
1026: long *v;
1027: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1028: if (!v) nrerror("allocation failure in ivector");
1029: return v-nl+NR_END;
1030: }
1031:
1032: /******************free lvector **************************/
1033: void free_lvector(long *v, long nl, long nh)
1034: {
1035: free((FREE_ARG)(v+nl-NR_END));
1036: }
1037:
1038: /******************* imatrix *******************************/
1039: int **imatrix(long nrl, long nrh, long ncl, long nch)
1040: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1041: {
1042: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1043: int **m;
1044:
1045: /* allocate pointers to rows */
1046: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1047: if (!m) nrerror("allocation failure 1 in matrix()");
1048: m += NR_END;
1049: m -= nrl;
1050:
1051:
1052: /* allocate rows and set pointers to them */
1053: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1054: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1055: m[nrl] += NR_END;
1056: m[nrl] -= ncl;
1057:
1058: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1059:
1060: /* return pointer to array of pointers to rows */
1061: return m;
1062: }
1063:
1064: /****************** free_imatrix *************************/
1065: void free_imatrix(m,nrl,nrh,ncl,nch)
1066: int **m;
1067: long nch,ncl,nrh,nrl;
1068: /* free an int matrix allocated by imatrix() */
1069: {
1070: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1071: free((FREE_ARG) (m+nrl-NR_END));
1072: }
1073:
1074: /******************* matrix *******************************/
1075: double **matrix(long nrl, long nrh, long ncl, long nch)
1076: {
1077: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1078: double **m;
1079:
1080: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1081: if (!m) nrerror("allocation failure 1 in matrix()");
1082: m += NR_END;
1083: m -= nrl;
1084:
1085: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1086: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1087: m[nrl] += NR_END;
1088: m[nrl] -= ncl;
1089:
1090: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1091: return m;
1092: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1093: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1094: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1095: */
1096: }
1097:
1098: /*************************free matrix ************************/
1099: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1100: {
1101: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1102: free((FREE_ARG)(m+nrl-NR_END));
1103: }
1104:
1105: /******************* ma3x *******************************/
1106: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1107: {
1108: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1109: double ***m;
1110:
1111: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1112: if (!m) nrerror("allocation failure 1 in matrix()");
1113: m += NR_END;
1114: m -= nrl;
1115:
1116: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1117: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1118: m[nrl] += NR_END;
1119: m[nrl] -= ncl;
1120:
1121: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1122:
1123: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1124: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1125: m[nrl][ncl] += NR_END;
1126: m[nrl][ncl] -= nll;
1127: for (j=ncl+1; j<=nch; j++)
1128: m[nrl][j]=m[nrl][j-1]+nlay;
1129:
1130: for (i=nrl+1; i<=nrh; i++) {
1131: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1132: for (j=ncl+1; j<=nch; j++)
1133: m[i][j]=m[i][j-1]+nlay;
1134: }
1135: return m;
1136: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1137: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1138: */
1139: }
1140:
1141: /*************************free ma3x ************************/
1142: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1143: {
1144: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1145: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1146: free((FREE_ARG)(m+nrl-NR_END));
1147: }
1148:
1149: /*************** function subdirf ***********/
1150: char *subdirf(char fileres[])
1151: {
1152: /* Caution optionfilefiname is hidden */
1153: strcpy(tmpout,optionfilefiname);
1154: strcat(tmpout,"/"); /* Add to the right */
1155: strcat(tmpout,fileres);
1156: return tmpout;
1157: }
1158:
1159: /*************** function subdirf2 ***********/
1160: char *subdirf2(char fileres[], char *preop)
1161: {
1162:
1163: /* Caution optionfilefiname is hidden */
1164: strcpy(tmpout,optionfilefiname);
1165: strcat(tmpout,"/");
1166: strcat(tmpout,preop);
1167: strcat(tmpout,fileres);
1168: return tmpout;
1169: }
1170:
1171: /*************** function subdirf3 ***********/
1172: char *subdirf3(char fileres[], char *preop, char *preop2)
1173: {
1174:
1175: /* Caution optionfilefiname is hidden */
1176: strcpy(tmpout,optionfilefiname);
1177: strcat(tmpout,"/");
1178: strcat(tmpout,preop);
1179: strcat(tmpout,preop2);
1180: strcat(tmpout,fileres);
1181: return tmpout;
1182: }
1183:
1184: char *asc_diff_time(long time_sec, char ascdiff[])
1185: {
1186: long sec_left, days, hours, minutes;
1187: days = (time_sec) / (60*60*24);
1188: sec_left = (time_sec) % (60*60*24);
1189: hours = (sec_left) / (60*60) ;
1190: sec_left = (sec_left) %(60*60);
1191: minutes = (sec_left) /60;
1192: sec_left = (sec_left) % (60);
1193: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1194: return ascdiff;
1195: }
1196:
1197: /***************** f1dim *************************/
1198: extern int ncom;
1199: extern double *pcom,*xicom;
1200: extern double (*nrfunc)(double []);
1201:
1202: double f1dim(double x)
1203: {
1204: int j;
1205: double f;
1206: double *xt;
1207:
1208: xt=vector(1,ncom);
1209: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1210: f=(*nrfunc)(xt);
1211: free_vector(xt,1,ncom);
1212: return f;
1213: }
1214:
1215: /*****************brent *************************/
1216: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1217: {
1218: int iter;
1219: double a,b,d,etemp;
1220: double fu=0,fv,fw,fx;
1221: double ftemp=0.;
1222: double p,q,r,tol1,tol2,u,v,w,x,xm;
1223: double e=0.0;
1224:
1225: a=(ax < cx ? ax : cx);
1226: b=(ax > cx ? ax : cx);
1227: x=w=v=bx;
1228: fw=fv=fx=(*f)(x);
1229: for (iter=1;iter<=ITMAX;iter++) {
1230: xm=0.5*(a+b);
1231: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1232: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1233: printf(".");fflush(stdout);
1234: fprintf(ficlog,".");fflush(ficlog);
1235: #ifdef DEBUGBRENT
1236: 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);
1237: 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);
1238: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1239: #endif
1240: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1241: *xmin=x;
1242: return fx;
1243: }
1244: ftemp=fu;
1245: if (fabs(e) > tol1) {
1246: r=(x-w)*(fx-fv);
1247: q=(x-v)*(fx-fw);
1248: p=(x-v)*q-(x-w)*r;
1249: q=2.0*(q-r);
1250: if (q > 0.0) p = -p;
1251: q=fabs(q);
1252: etemp=e;
1253: e=d;
1254: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1255: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1256: else {
1257: d=p/q;
1258: u=x+d;
1259: if (u-a < tol2 || b-u < tol2)
1260: d=SIGN(tol1,xm-x);
1261: }
1262: } else {
1263: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1264: }
1265: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1266: fu=(*f)(u);
1267: if (fu <= fx) {
1268: if (u >= x) a=x; else b=x;
1269: SHFT(v,w,x,u)
1270: SHFT(fv,fw,fx,fu)
1271: } else {
1272: if (u < x) a=u; else b=u;
1273: if (fu <= fw || w == x) {
1274: v=w;
1275: w=u;
1276: fv=fw;
1277: fw=fu;
1278: } else if (fu <= fv || v == x || v == w) {
1279: v=u;
1280: fv=fu;
1281: }
1282: }
1283: }
1284: nrerror("Too many iterations in brent");
1285: *xmin=x;
1286: return fx;
1287: }
1288:
1289: /****************** mnbrak ***********************/
1290:
1291: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1292: double (*func)(double))
1293: {
1294: double ulim,u,r,q, dum;
1295: double fu;
1296:
1297: *fa=(*func)(*ax);
1298: *fb=(*func)(*bx);
1299: if (*fb > *fa) {
1300: SHFT(dum,*ax,*bx,dum)
1301: SHFT(dum,*fb,*fa,dum)
1302: }
1303: *cx=(*bx)+GOLD*(*bx-*ax);
1304: *fc=(*func)(*cx);
1305: while (*fb > *fc) { /* Declining fa, fb, fc */
1306: r=(*bx-*ax)*(*fb-*fc);
1307: q=(*bx-*cx)*(*fb-*fa);
1308: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1309: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1310: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
1311: if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
1312: fu=(*func)(u);
1313: #ifdef DEBUG
1314: /* f(x)=A(x-u)**2+f(u) */
1315: double A, fparabu;
1316: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1317: fparabu= *fa - A*(*ax-u)*(*ax-u);
1318: 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);
1319: 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);
1320: #endif
1321: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1322: fu=(*func)(u);
1323: if (fu < *fc) {
1324: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1325: SHFT(*fb,*fc,fu,(*func)(u))
1326: }
1327: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1328: u=ulim;
1329: fu=(*func)(u);
1330: } else {
1331: u=(*cx)+GOLD*(*cx-*bx);
1332: fu=(*func)(u);
1333: }
1334: SHFT(*ax,*bx,*cx,u)
1335: SHFT(*fa,*fb,*fc,fu)
1336: }
1337: }
1338:
1339: /*************** linmin ************************/
1340: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1341: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1342: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1343: the value of func at the returned location p . This is actually all accomplished by calling the
1344: routines mnbrak and brent .*/
1345: int ncom;
1346: double *pcom,*xicom;
1347: double (*nrfunc)(double []);
1348:
1349: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1350: {
1351: double brent(double ax, double bx, double cx,
1352: double (*f)(double), double tol, double *xmin);
1353: double f1dim(double x);
1354: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1355: double *fc, double (*func)(double));
1356: int j;
1357: double xx,xmin,bx,ax;
1358: double fx,fb,fa;
1359:
1360: ncom=n;
1361: pcom=vector(1,n);
1362: xicom=vector(1,n);
1363: nrfunc=func;
1364: for (j=1;j<=n;j++) {
1365: pcom[j]=p[j];
1366: xicom[j]=xi[j];
1367: }
1368: ax=0.0;
1369: xx=1.0;
1370: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
1371: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
1372: #ifdef DEBUG
1373: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1374: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1375: #endif
1376: for (j=1;j<=n;j++) {
1377: xi[j] *= xmin;
1378: p[j] += xi[j];
1379: }
1380: free_vector(xicom,1,n);
1381: free_vector(pcom,1,n);
1382: }
1383:
1384:
1385: /*************** powell ************************/
1386: /*
1387: Minimization of a function func of n variables. Input consists of an initial starting point
1388: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1389: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1390: such that failure to decrease by more than this amount on one iteration signals doneness. On
1391: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1392: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1393: */
1394: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1395: double (*func)(double []))
1396: {
1397: void linmin(double p[], double xi[], int n, double *fret,
1398: double (*func)(double []));
1399: int i,ibig,j;
1400: double del,t,*pt,*ptt,*xit;
1401: double fp,fptt;
1402: double *xits;
1403: int niterf, itmp;
1404:
1405: pt=vector(1,n);
1406: ptt=vector(1,n);
1407: xit=vector(1,n);
1408: xits=vector(1,n);
1409: *fret=(*func)(p);
1410: for (j=1;j<=n;j++) pt[j]=p[j];
1411: rcurr_time = time(NULL);
1412: for (*iter=1;;++(*iter)) {
1413: fp=(*fret);
1414: ibig=0;
1415: del=0.0;
1416: rlast_time=rcurr_time;
1417: /* (void) gettimeofday(&curr_time,&tzp); */
1418: rcurr_time = time(NULL);
1419: curr_time = *localtime(&rcurr_time);
1420: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1421: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1422: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1423: for (i=1;i<=n;i++) {
1424: printf(" %d %.12f",i, p[i]);
1425: fprintf(ficlog," %d %.12lf",i, p[i]);
1426: fprintf(ficrespow," %.12lf", p[i]);
1427: }
1428: printf("\n");
1429: fprintf(ficlog,"\n");
1430: fprintf(ficrespow,"\n");fflush(ficrespow);
1431: if(*iter <=3){
1432: tml = *localtime(&rcurr_time);
1433: strcpy(strcurr,asctime(&tml));
1434: rforecast_time=rcurr_time;
1435: itmp = strlen(strcurr);
1436: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1437: strcurr[itmp-1]='\0';
1438: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1439: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1440: for(niterf=10;niterf<=30;niterf+=10){
1441: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1442: forecast_time = *localtime(&rforecast_time);
1443: strcpy(strfor,asctime(&forecast_time));
1444: itmp = strlen(strfor);
1445: if(strfor[itmp-1]=='\n')
1446: strfor[itmp-1]='\0';
1447: 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);
1448: 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);
1449: }
1450: }
1451: for (i=1;i<=n;i++) {
1452: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1453: fptt=(*fret);
1454: #ifdef DEBUG
1455: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1456: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1457: #endif
1458: printf("%d",i);fflush(stdout);
1459: fprintf(ficlog,"%d",i);fflush(ficlog);
1460: linmin(p,xit,n,fret,func);
1461: if (fabs(fptt-(*fret)) > del) {
1462: del=fabs(fptt-(*fret));
1463: ibig=i;
1464: }
1465: #ifdef DEBUG
1466: printf("%d %.12e",i,(*fret));
1467: fprintf(ficlog,"%d %.12e",i,(*fret));
1468: for (j=1;j<=n;j++) {
1469: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1470: printf(" x(%d)=%.12e",j,xit[j]);
1471: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1472: }
1473: for(j=1;j<=n;j++) {
1474: printf(" p(%d)=%.12e",j,p[j]);
1475: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1476: }
1477: printf("\n");
1478: fprintf(ficlog,"\n");
1479: #endif
1480: } /* end i */
1481: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1482: #ifdef DEBUG
1483: int k[2],l;
1484: k[0]=1;
1485: k[1]=-1;
1486: printf("Max: %.12e",(*func)(p));
1487: fprintf(ficlog,"Max: %.12e",(*func)(p));
1488: for (j=1;j<=n;j++) {
1489: printf(" %.12e",p[j]);
1490: fprintf(ficlog," %.12e",p[j]);
1491: }
1492: printf("\n");
1493: fprintf(ficlog,"\n");
1494: for(l=0;l<=1;l++) {
1495: for (j=1;j<=n;j++) {
1496: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1497: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1498: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1499: }
1500: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1501: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1502: }
1503: #endif
1504:
1505:
1506: free_vector(xit,1,n);
1507: free_vector(xits,1,n);
1508: free_vector(ptt,1,n);
1509: free_vector(pt,1,n);
1510: return;
1511: }
1512: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1513: for (j=1;j<=n;j++) { /* Computes an extrapolated point */
1514: ptt[j]=2.0*p[j]-pt[j];
1515: xit[j]=p[j]-pt[j];
1516: pt[j]=p[j];
1517: }
1518: fptt=(*func)(ptt);
1519: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1520: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1521: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1522: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1523: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1524: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1525: /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
1526: /* Thus we compare delta(2h) with observed f1-f3 */
1527: /* or best gain on one ancient line 'del' with total */
1528: /* gain f1-f2 = f1 - f2 - 'del' with del */
1529: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1530:
1531: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
1532: t= t- del*SQR(fp-fptt);
1533: printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
1534: fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
1535: #ifdef DEBUG
1536: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1537: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1538: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1539: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1540: 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);
1541: 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);
1542: #endif
1543: if (t < 0.0) { /* Then we use it for last direction */
1544: linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
1545: for (j=1;j<=n;j++) {
1546: xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
1547: xi[j][n]=xit[j]; /* and nth direction by the extrapolated */
1548: }
1549: printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1550: fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1551:
1552: #ifdef DEBUG
1553: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1554: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1555: for(j=1;j<=n;j++){
1556: printf(" %.12e",xit[j]);
1557: fprintf(ficlog," %.12e",xit[j]);
1558: }
1559: printf("\n");
1560: fprintf(ficlog,"\n");
1561: #endif
1562: } /* end of t negative */
1563: } /* end if (fptt < fp) */
1564: }
1565: }
1566:
1567: /**** Prevalence limit (stable or period prevalence) ****************/
1568:
1569: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1570: {
1571: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1572: matrix by transitions matrix until convergence is reached */
1573:
1574: int i, ii,j,k;
1575: double min, max, maxmin, maxmax,sumnew=0.;
1576: /* double **matprod2(); */ /* test */
1577: double **out, cov[NCOVMAX+1], **pmij();
1578: double **newm;
1579: double agefin, delaymax=50 ; /* Max number of years to converge */
1580:
1581: for (ii=1;ii<=nlstate+ndeath;ii++)
1582: for (j=1;j<=nlstate+ndeath;j++){
1583: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1584: }
1585:
1586: cov[1]=1.;
1587:
1588: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1589: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1590: newm=savm;
1591: /* Covariates have to be included here again */
1592: cov[2]=agefin;
1593:
1594: for (k=1; k<=cptcovn;k++) {
1595: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1596: /*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]]);*/
1597: }
1598: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1599: /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
1600: /* cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
1601:
1602: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1603: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1604: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1605: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1606: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1607: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1608:
1609: savm=oldm;
1610: oldm=newm;
1611: maxmax=0.;
1612: for(j=1;j<=nlstate;j++){
1613: min=1.;
1614: max=0.;
1615: for(i=1; i<=nlstate; i++) {
1616: sumnew=0;
1617: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1618: prlim[i][j]= newm[i][j]/(1-sumnew);
1619: /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
1620: max=FMAX(max,prlim[i][j]);
1621: min=FMIN(min,prlim[i][j]);
1622: }
1623: maxmin=max-min;
1624: maxmax=FMAX(maxmax,maxmin);
1625: } /* j loop */
1626: if(maxmax < ftolpl){
1627: return prlim;
1628: }
1629: } /* age loop */
1630: return prlim; /* should not reach here */
1631: }
1632:
1633: /*************** transition probabilities ***************/
1634:
1635: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1636: {
1637: /* According to parameters values stored in x and the covariate's values stored in cov,
1638: computes the probability to be observed in state j being in state i by appying the
1639: model to the ncovmodel covariates (including constant and age).
1640: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1641: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1642: ncth covariate in the global vector x is given by the formula:
1643: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1644: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1645: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1646: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1647: Outputs ps[i][j] the probability to be observed in j being in j according to
1648: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1649: */
1650: double s1, lnpijopii;
1651: /*double t34;*/
1652: int i,j, nc, ii, jj;
1653:
1654: for(i=1; i<= nlstate; i++){
1655: for(j=1; j<i;j++){
1656: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1657: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1658: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1659: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1660: }
1661: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1662: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1663: }
1664: for(j=i+1; j<=nlstate+ndeath;j++){
1665: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1666: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
1667: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
1668: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1669: }
1670: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1671: }
1672: }
1673:
1674: for(i=1; i<= nlstate; i++){
1675: s1=0;
1676: for(j=1; j<i; j++){
1677: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1678: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1679: }
1680: for(j=i+1; j<=nlstate+ndeath; j++){
1681: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1682: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1683: }
1684: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1685: ps[i][i]=1./(s1+1.);
1686: /* Computing other pijs */
1687: for(j=1; j<i; j++)
1688: ps[i][j]= exp(ps[i][j])*ps[i][i];
1689: for(j=i+1; j<=nlstate+ndeath; j++)
1690: ps[i][j]= exp(ps[i][j])*ps[i][i];
1691: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1692: } /* end i */
1693:
1694: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1695: for(jj=1; jj<= nlstate+ndeath; jj++){
1696: ps[ii][jj]=0;
1697: ps[ii][ii]=1;
1698: }
1699: }
1700:
1701:
1702: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1703: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1704: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
1705: /* } */
1706: /* printf("\n "); */
1707: /* } */
1708: /* printf("\n ");printf("%lf ",cov[2]);*/
1709: /*
1710: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1711: goto end;*/
1712: return ps;
1713: }
1714:
1715: /**************** Product of 2 matrices ******************/
1716:
1717: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1718: {
1719: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1720: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1721: /* in, b, out are matrice of pointers which should have been initialized
1722: before: only the contents of out is modified. The function returns
1723: a pointer to pointers identical to out */
1724: int i, j, k;
1725: for(i=nrl; i<= nrh; i++)
1726: for(k=ncolol; k<=ncoloh; k++){
1727: out[i][k]=0.;
1728: for(j=ncl; j<=nch; j++)
1729: out[i][k] +=in[i][j]*b[j][k];
1730: }
1731: return out;
1732: }
1733:
1734:
1735: /************* Higher Matrix Product ***************/
1736:
1737: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1738: {
1739: /* Computes the transition matrix starting at age 'age' over
1740: 'nhstepm*hstepm*stepm' months (i.e. until
1741: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1742: nhstepm*hstepm matrices.
1743: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1744: (typically every 2 years instead of every month which is too big
1745: for the memory).
1746: Model is determined by parameters x and covariates have to be
1747: included manually here.
1748:
1749: */
1750:
1751: int i, j, d, h, k;
1752: double **out, cov[NCOVMAX+1];
1753: double **newm;
1754:
1755: /* Hstepm could be zero and should return the unit matrix */
1756: for (i=1;i<=nlstate+ndeath;i++)
1757: for (j=1;j<=nlstate+ndeath;j++){
1758: oldm[i][j]=(i==j ? 1.0 : 0.0);
1759: po[i][j][0]=(i==j ? 1.0 : 0.0);
1760: }
1761: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1762: for(h=1; h <=nhstepm; h++){
1763: for(d=1; d <=hstepm; d++){
1764: newm=savm;
1765: /* Covariates have to be included here again */
1766: cov[1]=1.;
1767: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1768: for (k=1; k<=cptcovn;k++)
1769: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1770: for (k=1; k<=cptcovage;k++)
1771: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1772: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1773: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1774:
1775:
1776: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1777: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1778: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1779: pmij(pmmij,cov,ncovmodel,x,nlstate));
1780: savm=oldm;
1781: oldm=newm;
1782: }
1783: for(i=1; i<=nlstate+ndeath; i++)
1784: for(j=1;j<=nlstate+ndeath;j++) {
1785: po[i][j][h]=newm[i][j];
1786: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1787: }
1788: /*printf("h=%d ",h);*/
1789: } /* end h */
1790: /* printf("\n H=%d \n",h); */
1791: return po;
1792: }
1793:
1794: #ifdef NLOPT
1795: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
1796: double fret;
1797: double *xt;
1798: int j;
1799: myfunc_data *d2 = (myfunc_data *) pd;
1800: /* xt = (p1-1); */
1801: xt=vector(1,n);
1802: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
1803:
1804: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
1805: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
1806: printf("Function = %.12lf ",fret);
1807: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
1808: printf("\n");
1809: free_vector(xt,1,n);
1810: return fret;
1811: }
1812: #endif
1813:
1814: /*************** log-likelihood *************/
1815: double func( double *x)
1816: {
1817: int i, ii, j, k, mi, d, kk;
1818: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1819: double **out;
1820: double sw; /* Sum of weights */
1821: double lli; /* Individual log likelihood */
1822: int s1, s2;
1823: double bbh, survp;
1824: long ipmx;
1825: /*extern weight */
1826: /* We are differentiating ll according to initial status */
1827: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1828: /*for(i=1;i<imx;i++)
1829: printf(" %d\n",s[4][i]);
1830: */
1831:
1832: ++countcallfunc;
1833:
1834: cov[1]=1.;
1835:
1836: for(k=1; k<=nlstate; k++) ll[k]=0.;
1837:
1838: if(mle==1){
1839: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1840: /* Computes the values of the ncovmodel covariates of the model
1841: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
1842: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
1843: to be observed in j being in i according to the model.
1844: */
1845: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1846: cov[2+k]=covar[Tvar[k]][i];
1847: }
1848: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1849: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1850: has been calculated etc */
1851: for(mi=1; mi<= wav[i]-1; mi++){
1852: for (ii=1;ii<=nlstate+ndeath;ii++)
1853: for (j=1;j<=nlstate+ndeath;j++){
1854: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1855: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1856: }
1857: for(d=0; d<dh[mi][i]; d++){
1858: newm=savm;
1859: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1860: for (kk=1; kk<=cptcovage;kk++) {
1861: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
1862: }
1863: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1864: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1865: savm=oldm;
1866: oldm=newm;
1867: } /* end mult */
1868:
1869: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1870: /* But now since version 0.9 we anticipate for bias at large stepm.
1871: * If stepm is larger than one month (smallest stepm) and if the exact delay
1872: * (in months) between two waves is not a multiple of stepm, we rounded to
1873: * the nearest (and in case of equal distance, to the lowest) interval but now
1874: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1875: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1876: * probability in order to take into account the bias as a fraction of the way
1877: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1878: * -stepm/2 to stepm/2 .
1879: * For stepm=1 the results are the same as for previous versions of Imach.
1880: * For stepm > 1 the results are less biased than in previous versions.
1881: */
1882: s1=s[mw[mi][i]][i];
1883: s2=s[mw[mi+1][i]][i];
1884: bbh=(double)bh[mi][i]/(double)stepm;
1885: /* bias bh is positive if real duration
1886: * is higher than the multiple of stepm and negative otherwise.
1887: */
1888: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1889: if( s2 > nlstate){
1890: /* i.e. if s2 is a death state and if the date of death is known
1891: then the contribution to the likelihood is the probability to
1892: die between last step unit time and current step unit time,
1893: which is also equal to probability to die before dh
1894: minus probability to die before dh-stepm .
1895: In version up to 0.92 likelihood was computed
1896: as if date of death was unknown. Death was treated as any other
1897: health state: the date of the interview describes the actual state
1898: and not the date of a change in health state. The former idea was
1899: to consider that at each interview the state was recorded
1900: (healthy, disable or death) and IMaCh was corrected; but when we
1901: introduced the exact date of death then we should have modified
1902: the contribution of an exact death to the likelihood. This new
1903: contribution is smaller and very dependent of the step unit
1904: stepm. It is no more the probability to die between last interview
1905: and month of death but the probability to survive from last
1906: interview up to one month before death multiplied by the
1907: probability to die within a month. Thanks to Chris
1908: Jackson for correcting this bug. Former versions increased
1909: mortality artificially. The bad side is that we add another loop
1910: which slows down the processing. The difference can be up to 10%
1911: lower mortality.
1912: */
1913: lli=log(out[s1][s2] - savm[s1][s2]);
1914:
1915:
1916: } else if (s2==-2) {
1917: for (j=1,survp=0. ; j<=nlstate; j++)
1918: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1919: /*survp += out[s1][j]; */
1920: lli= log(survp);
1921: }
1922:
1923: else if (s2==-4) {
1924: for (j=3,survp=0. ; j<=nlstate; j++)
1925: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1926: lli= log(survp);
1927: }
1928:
1929: else if (s2==-5) {
1930: for (j=1,survp=0. ; j<=2; j++)
1931: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1932: lli= log(survp);
1933: }
1934:
1935: else{
1936: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1937: /* 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 */
1938: }
1939: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1940: /*if(lli ==000.0)*/
1941: /*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); */
1942: ipmx +=1;
1943: sw += weight[i];
1944: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1945: } /* end of wave */
1946: } /* end of individual */
1947: } else if(mle==2){
1948: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1949: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1950: for(mi=1; mi<= wav[i]-1; mi++){
1951: for (ii=1;ii<=nlstate+ndeath;ii++)
1952: for (j=1;j<=nlstate+ndeath;j++){
1953: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1954: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1955: }
1956: for(d=0; d<=dh[mi][i]; d++){
1957: newm=savm;
1958: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1959: for (kk=1; kk<=cptcovage;kk++) {
1960: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1961: }
1962: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1963: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1964: savm=oldm;
1965: oldm=newm;
1966: } /* end mult */
1967:
1968: s1=s[mw[mi][i]][i];
1969: s2=s[mw[mi+1][i]][i];
1970: bbh=(double)bh[mi][i]/(double)stepm;
1971: 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 */
1972: ipmx +=1;
1973: sw += weight[i];
1974: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1975: } /* end of wave */
1976: } /* end of individual */
1977: } else if(mle==3){ /* exponential inter-extrapolation */
1978: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1979: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1980: for(mi=1; mi<= wav[i]-1; mi++){
1981: for (ii=1;ii<=nlstate+ndeath;ii++)
1982: for (j=1;j<=nlstate+ndeath;j++){
1983: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1984: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1985: }
1986: for(d=0; d<dh[mi][i]; d++){
1987: newm=savm;
1988: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1989: for (kk=1; kk<=cptcovage;kk++) {
1990: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1991: }
1992: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1993: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1994: savm=oldm;
1995: oldm=newm;
1996: } /* end mult */
1997:
1998: s1=s[mw[mi][i]][i];
1999: s2=s[mw[mi+1][i]][i];
2000: bbh=(double)bh[mi][i]/(double)stepm;
2001: 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 */
2002: ipmx +=1;
2003: sw += weight[i];
2004: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2005: } /* end of wave */
2006: } /* end of individual */
2007: }else if (mle==4){ /* ml=4 no inter-extrapolation */
2008: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2009: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2010: for(mi=1; mi<= wav[i]-1; mi++){
2011: for (ii=1;ii<=nlstate+ndeath;ii++)
2012: for (j=1;j<=nlstate+ndeath;j++){
2013: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2014: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2015: }
2016: for(d=0; d<dh[mi][i]; d++){
2017: newm=savm;
2018: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2019: for (kk=1; kk<=cptcovage;kk++) {
2020: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2021: }
2022:
2023: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2024: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2025: savm=oldm;
2026: oldm=newm;
2027: } /* end mult */
2028:
2029: s1=s[mw[mi][i]][i];
2030: s2=s[mw[mi+1][i]][i];
2031: if( s2 > nlstate){
2032: lli=log(out[s1][s2] - savm[s1][s2]);
2033: }else{
2034: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2035: }
2036: ipmx +=1;
2037: sw += weight[i];
2038: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2039: /* 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]); */
2040: } /* end of wave */
2041: } /* end of individual */
2042: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
2043: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2044: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2045: for(mi=1; mi<= wav[i]-1; mi++){
2046: for (ii=1;ii<=nlstate+ndeath;ii++)
2047: for (j=1;j<=nlstate+ndeath;j++){
2048: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2049: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2050: }
2051: for(d=0; d<dh[mi][i]; d++){
2052: newm=savm;
2053: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2054: for (kk=1; kk<=cptcovage;kk++) {
2055: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2056: }
2057:
2058: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2059: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2060: savm=oldm;
2061: oldm=newm;
2062: } /* end mult */
2063:
2064: s1=s[mw[mi][i]][i];
2065: s2=s[mw[mi+1][i]][i];
2066: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2067: ipmx +=1;
2068: sw += weight[i];
2069: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2070: /*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]);*/
2071: } /* end of wave */
2072: } /* end of individual */
2073: } /* End of if */
2074: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2075: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2076: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2077: return -l;
2078: }
2079:
2080: /*************** log-likelihood *************/
2081: double funcone( double *x)
2082: {
2083: /* Same as likeli but slower because of a lot of printf and if */
2084: int i, ii, j, k, mi, d, kk;
2085: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
2086: double **out;
2087: double lli; /* Individual log likelihood */
2088: double llt;
2089: int s1, s2;
2090: double bbh, survp;
2091: /*extern weight */
2092: /* We are differentiating ll according to initial status */
2093: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2094: /*for(i=1;i<imx;i++)
2095: printf(" %d\n",s[4][i]);
2096: */
2097: cov[1]=1.;
2098:
2099: for(k=1; k<=nlstate; k++) ll[k]=0.;
2100:
2101: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2102: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2103: for(mi=1; mi<= wav[i]-1; mi++){
2104: for (ii=1;ii<=nlstate+ndeath;ii++)
2105: for (j=1;j<=nlstate+ndeath;j++){
2106: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2107: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2108: }
2109: for(d=0; d<dh[mi][i]; d++){
2110: newm=savm;
2111: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2112: for (kk=1; kk<=cptcovage;kk++) {
2113: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2114: }
2115: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2116: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2117: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2118: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2119: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
2120: savm=oldm;
2121: oldm=newm;
2122: } /* end mult */
2123:
2124: s1=s[mw[mi][i]][i];
2125: s2=s[mw[mi+1][i]][i];
2126: bbh=(double)bh[mi][i]/(double)stepm;
2127: /* bias is positive if real duration
2128: * is higher than the multiple of stepm and negative otherwise.
2129: */
2130: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2131: lli=log(out[s1][s2] - savm[s1][s2]);
2132: } else if (s2==-2) {
2133: for (j=1,survp=0. ; j<=nlstate; j++)
2134: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2135: lli= log(survp);
2136: }else if (mle==1){
2137: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2138: } else if(mle==2){
2139: 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 */
2140: } else if(mle==3){ /* exponential inter-extrapolation */
2141: 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 */
2142: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2143: lli=log(out[s1][s2]); /* Original formula */
2144: } else{ /* mle=0 back to 1 */
2145: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2146: /*lli=log(out[s1][s2]); */ /* Original formula */
2147: } /* End of if */
2148: ipmx +=1;
2149: sw += weight[i];
2150: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2151: /*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]); */
2152: if(globpr){
2153: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
2154: %11.6f %11.6f %11.6f ", \
2155: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
2156: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2157: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2158: llt +=ll[k]*gipmx/gsw;
2159: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2160: }
2161: fprintf(ficresilk," %10.6f\n", -llt);
2162: }
2163: } /* end of wave */
2164: } /* end of individual */
2165: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2166: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2167: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2168: if(globpr==0){ /* First time we count the contributions and weights */
2169: gipmx=ipmx;
2170: gsw=sw;
2171: }
2172: return -l;
2173: }
2174:
2175:
2176: /*************** function likelione ***********/
2177: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2178: {
2179: /* This routine should help understanding what is done with
2180: the selection of individuals/waves and
2181: to check the exact contribution to the likelihood.
2182: Plotting could be done.
2183: */
2184: int k;
2185:
2186: if(*globpri !=0){ /* Just counts and sums, no printings */
2187: strcpy(fileresilk,"ilk");
2188: strcat(fileresilk,fileres);
2189: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2190: printf("Problem with resultfile: %s\n", fileresilk);
2191: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2192: }
2193: 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");
2194: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
2195: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2196: for(k=1; k<=nlstate; k++)
2197: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2198: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2199: }
2200:
2201: *fretone=(*funcone)(p);
2202: if(*globpri !=0){
2203: fclose(ficresilk);
2204: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
2205: fflush(fichtm);
2206: }
2207: return;
2208: }
2209:
2210:
2211: /*********** Maximum Likelihood Estimation ***************/
2212:
2213: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2214: {
2215: int i,j, iter=0;
2216: double **xi;
2217: double fret;
2218: double fretone; /* Only one call to likelihood */
2219: /* char filerespow[FILENAMELENGTH];*/
2220:
2221: #ifdef NLOPT
2222: int creturn;
2223: nlopt_opt opt;
2224: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2225: double *lb;
2226: double minf; /* the minimum objective value, upon return */
2227: double * p1; /* Shifted parameters from 0 instead of 1 */
2228: myfunc_data dinst, *d = &dinst;
2229: #endif
2230:
2231:
2232: xi=matrix(1,npar,1,npar);
2233: for (i=1;i<=npar;i++)
2234: for (j=1;j<=npar;j++)
2235: xi[i][j]=(i==j ? 1.0 : 0.0);
2236: printf("Powell\n"); fprintf(ficlog,"Powell\n");
2237: strcpy(filerespow,"pow");
2238: strcat(filerespow,fileres);
2239: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2240: printf("Problem with resultfile: %s\n", filerespow);
2241: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2242: }
2243: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2244: for (i=1;i<=nlstate;i++)
2245: for(j=1;j<=nlstate+ndeath;j++)
2246: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2247: fprintf(ficrespow,"\n");
2248: #ifdef POWELL
2249: powell(p,xi,npar,ftol,&iter,&fret,func);
2250: #endif
2251:
2252: #ifdef NLOPT
2253: #ifdef NEWUOA
2254: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2255: #else
2256: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2257: #endif
2258: lb=vector(0,npar-1);
2259: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2260: nlopt_set_lower_bounds(opt, lb);
2261: nlopt_set_initial_step1(opt, 0.1);
2262:
2263: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2264: d->function = func;
2265: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2266: nlopt_set_min_objective(opt, myfunc, d);
2267: nlopt_set_xtol_rel(opt, ftol);
2268: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2269: printf("nlopt failed! %d\n",creturn);
2270: }
2271: else {
2272: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2273: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2274: iter=1; /* not equal */
2275: }
2276: nlopt_destroy(opt);
2277: #endif
2278: free_matrix(xi,1,npar,1,npar);
2279: fclose(ficrespow);
2280: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2281: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2282: fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2283:
2284: }
2285:
2286: /**** Computes Hessian and covariance matrix ***/
2287: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
2288: {
2289: double **a,**y,*x,pd;
2290: double **hess;
2291: int i, j;
2292: int *indx;
2293:
2294: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
2295: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
2296: void lubksb(double **a, int npar, int *indx, double b[]) ;
2297: void ludcmp(double **a, int npar, int *indx, double *d) ;
2298: double gompertz(double p[]);
2299: hess=matrix(1,npar,1,npar);
2300:
2301: printf("\nCalculation of the hessian matrix. Wait...\n");
2302: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2303: for (i=1;i<=npar;i++){
2304: printf("%d",i);fflush(stdout);
2305: fprintf(ficlog,"%d",i);fflush(ficlog);
2306:
2307: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2308:
2309: /* printf(" %f ",p[i]);
2310: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2311: }
2312:
2313: for (i=1;i<=npar;i++) {
2314: for (j=1;j<=npar;j++) {
2315: if (j>i) {
2316: printf(".%d%d",i,j);fflush(stdout);
2317: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
2318: hess[i][j]=hessij(p,delti,i,j,func,npar);
2319:
2320: hess[j][i]=hess[i][j];
2321: /*printf(" %lf ",hess[i][j]);*/
2322: }
2323: }
2324: }
2325: printf("\n");
2326: fprintf(ficlog,"\n");
2327:
2328: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2329: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2330:
2331: a=matrix(1,npar,1,npar);
2332: y=matrix(1,npar,1,npar);
2333: x=vector(1,npar);
2334: indx=ivector(1,npar);
2335: for (i=1;i<=npar;i++)
2336: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2337: ludcmp(a,npar,indx,&pd);
2338:
2339: for (j=1;j<=npar;j++) {
2340: for (i=1;i<=npar;i++) x[i]=0;
2341: x[j]=1;
2342: lubksb(a,npar,indx,x);
2343: for (i=1;i<=npar;i++){
2344: matcov[i][j]=x[i];
2345: }
2346: }
2347:
2348: printf("\n#Hessian matrix#\n");
2349: fprintf(ficlog,"\n#Hessian matrix#\n");
2350: for (i=1;i<=npar;i++) {
2351: for (j=1;j<=npar;j++) {
2352: printf("%.3e ",hess[i][j]);
2353: fprintf(ficlog,"%.3e ",hess[i][j]);
2354: }
2355: printf("\n");
2356: fprintf(ficlog,"\n");
2357: }
2358:
2359: /* Recompute Inverse */
2360: for (i=1;i<=npar;i++)
2361: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
2362: ludcmp(a,npar,indx,&pd);
2363:
2364: /* printf("\n#Hessian matrix recomputed#\n");
2365:
2366: for (j=1;j<=npar;j++) {
2367: for (i=1;i<=npar;i++) x[i]=0;
2368: x[j]=1;
2369: lubksb(a,npar,indx,x);
2370: for (i=1;i<=npar;i++){
2371: y[i][j]=x[i];
2372: printf("%.3e ",y[i][j]);
2373: fprintf(ficlog,"%.3e ",y[i][j]);
2374: }
2375: printf("\n");
2376: fprintf(ficlog,"\n");
2377: }
2378: */
2379:
2380: free_matrix(a,1,npar,1,npar);
2381: free_matrix(y,1,npar,1,npar);
2382: free_vector(x,1,npar);
2383: free_ivector(indx,1,npar);
2384: free_matrix(hess,1,npar,1,npar);
2385:
2386:
2387: }
2388:
2389: /*************** hessian matrix ****************/
2390: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2391: {
2392: int i;
2393: int l=1, lmax=20;
2394: double k1,k2;
2395: double p2[MAXPARM+1]; /* identical to x */
2396: double res;
2397: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2398: double fx;
2399: int k=0,kmax=10;
2400: double l1;
2401:
2402: fx=func(x);
2403: for (i=1;i<=npar;i++) p2[i]=x[i];
2404: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
2405: l1=pow(10,l);
2406: delts=delt;
2407: for(k=1 ; k <kmax; k=k+1){
2408: delt = delta*(l1*k);
2409: p2[theta]=x[theta] +delt;
2410: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
2411: p2[theta]=x[theta]-delt;
2412: k2=func(p2)-fx;
2413: /*res= (k1-2.0*fx+k2)/delt/delt; */
2414: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2415:
2416: #ifdef DEBUGHESS
2417: 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);
2418: 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);
2419: #endif
2420: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2421: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2422: k=kmax;
2423: }
2424: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
2425: k=kmax; l=lmax*10;
2426: }
2427: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2428: delts=delt;
2429: }
2430: }
2431: }
2432: delti[theta]=delts;
2433: return res;
2434:
2435: }
2436:
2437: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2438: {
2439: int i;
2440: int l=1, lmax=20;
2441: double k1,k2,k3,k4,res,fx;
2442: double p2[MAXPARM+1];
2443: int k;
2444:
2445: fx=func(x);
2446: for (k=1; k<=2; k++) {
2447: for (i=1;i<=npar;i++) p2[i]=x[i];
2448: p2[thetai]=x[thetai]+delti[thetai]/k;
2449: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2450: k1=func(p2)-fx;
2451:
2452: p2[thetai]=x[thetai]+delti[thetai]/k;
2453: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2454: k2=func(p2)-fx;
2455:
2456: p2[thetai]=x[thetai]-delti[thetai]/k;
2457: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2458: k3=func(p2)-fx;
2459:
2460: p2[thetai]=x[thetai]-delti[thetai]/k;
2461: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2462: k4=func(p2)-fx;
2463: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2464: #ifdef DEBUG
2465: 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);
2466: 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);
2467: #endif
2468: }
2469: return res;
2470: }
2471:
2472: /************** Inverse of matrix **************/
2473: void ludcmp(double **a, int n, int *indx, double *d)
2474: {
2475: int i,imax,j,k;
2476: double big,dum,sum,temp;
2477: double *vv;
2478:
2479: vv=vector(1,n);
2480: *d=1.0;
2481: for (i=1;i<=n;i++) {
2482: big=0.0;
2483: for (j=1;j<=n;j++)
2484: if ((temp=fabs(a[i][j])) > big) big=temp;
2485: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2486: vv[i]=1.0/big;
2487: }
2488: for (j=1;j<=n;j++) {
2489: for (i=1;i<j;i++) {
2490: sum=a[i][j];
2491: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2492: a[i][j]=sum;
2493: }
2494: big=0.0;
2495: for (i=j;i<=n;i++) {
2496: sum=a[i][j];
2497: for (k=1;k<j;k++)
2498: sum -= a[i][k]*a[k][j];
2499: a[i][j]=sum;
2500: if ( (dum=vv[i]*fabs(sum)) >= big) {
2501: big=dum;
2502: imax=i;
2503: }
2504: }
2505: if (j != imax) {
2506: for (k=1;k<=n;k++) {
2507: dum=a[imax][k];
2508: a[imax][k]=a[j][k];
2509: a[j][k]=dum;
2510: }
2511: *d = -(*d);
2512: vv[imax]=vv[j];
2513: }
2514: indx[j]=imax;
2515: if (a[j][j] == 0.0) a[j][j]=TINY;
2516: if (j != n) {
2517: dum=1.0/(a[j][j]);
2518: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2519: }
2520: }
2521: free_vector(vv,1,n); /* Doesn't work */
2522: ;
2523: }
2524:
2525: void lubksb(double **a, int n, int *indx, double b[])
2526: {
2527: int i,ii=0,ip,j;
2528: double sum;
2529:
2530: for (i=1;i<=n;i++) {
2531: ip=indx[i];
2532: sum=b[ip];
2533: b[ip]=b[i];
2534: if (ii)
2535: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2536: else if (sum) ii=i;
2537: b[i]=sum;
2538: }
2539: for (i=n;i>=1;i--) {
2540: sum=b[i];
2541: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2542: b[i]=sum/a[i][i];
2543: }
2544: }
2545:
2546: void pstamp(FILE *fichier)
2547: {
2548: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2549: }
2550:
2551: /************ Frequencies ********************/
2552: 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[])
2553: { /* Some frequencies */
2554:
2555: int i, m, jk, j1, bool, z1,j;
2556: int first;
2557: double ***freq; /* Frequencies */
2558: double *pp, **prop;
2559: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2560: char fileresp[FILENAMELENGTH];
2561:
2562: pp=vector(1,nlstate);
2563: prop=matrix(1,nlstate,iagemin,iagemax+3);
2564: strcpy(fileresp,"p");
2565: strcat(fileresp,fileres);
2566: if((ficresp=fopen(fileresp,"w"))==NULL) {
2567: printf("Problem with prevalence resultfile: %s\n", fileresp);
2568: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2569: exit(0);
2570: }
2571: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2572: j1=0;
2573:
2574: j=cptcoveff;
2575: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2576:
2577: first=1;
2578:
2579: /* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */
2580: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
2581: /* j1++; */
2582: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
2583: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2584: scanf("%d", i);*/
2585: for (i=-5; i<=nlstate+ndeath; i++)
2586: for (jk=-5; jk<=nlstate+ndeath; jk++)
2587: for(m=iagemin; m <= iagemax+3; m++)
2588: freq[i][jk][m]=0;
2589:
2590: for (i=1; i<=nlstate; i++)
2591: for(m=iagemin; m <= iagemax+3; m++)
2592: prop[i][m]=0;
2593:
2594: dateintsum=0;
2595: k2cpt=0;
2596: for (i=1; i<=imx; i++) {
2597: bool=1;
2598: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
2599: for (z1=1; z1<=cptcoveff; z1++)
2600: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
2601: /* Tests if the value of each of the covariates of i is equal to filter j1 */
2602: bool=0;
2603: /* 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",
2604: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
2605: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
2606: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
2607: }
2608: }
2609:
2610: if (bool==1){
2611: for(m=firstpass; m<=lastpass; m++){
2612: k2=anint[m][i]+(mint[m][i]/12.);
2613: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2614: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2615: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2616: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2617: if (m<lastpass) {
2618: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2619: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2620: }
2621:
2622: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2623: dateintsum=dateintsum+k2;
2624: k2cpt++;
2625: }
2626: /*}*/
2627: }
2628: }
2629: } /* end i */
2630:
2631: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2632: pstamp(ficresp);
2633: if (cptcovn>0) {
2634: fprintf(ficresp, "\n#********** Variable ");
2635: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2636: fprintf(ficresp, "**********\n#");
2637: fprintf(ficlog, "\n#********** Variable ");
2638: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2639: fprintf(ficlog, "**********\n#");
2640: }
2641: for(i=1; i<=nlstate;i++)
2642: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2643: fprintf(ficresp, "\n");
2644:
2645: for(i=iagemin; i <= iagemax+3; i++){
2646: if(i==iagemax+3){
2647: fprintf(ficlog,"Total");
2648: }else{
2649: if(first==1){
2650: first=0;
2651: printf("See log file for details...\n");
2652: }
2653: fprintf(ficlog,"Age %d", i);
2654: }
2655: for(jk=1; jk <=nlstate ; jk++){
2656: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2657: pp[jk] += freq[jk][m][i];
2658: }
2659: for(jk=1; jk <=nlstate ; jk++){
2660: for(m=-1, pos=0; m <=0 ; m++)
2661: pos += freq[jk][m][i];
2662: if(pp[jk]>=1.e-10){
2663: if(first==1){
2664: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2665: }
2666: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2667: }else{
2668: if(first==1)
2669: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2670: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2671: }
2672: }
2673:
2674: for(jk=1; jk <=nlstate ; jk++){
2675: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2676: pp[jk] += freq[jk][m][i];
2677: }
2678: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2679: pos += pp[jk];
2680: posprop += prop[jk][i];
2681: }
2682: for(jk=1; jk <=nlstate ; jk++){
2683: if(pos>=1.e-5){
2684: if(first==1)
2685: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2686: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2687: }else{
2688: if(first==1)
2689: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2690: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2691: }
2692: if( i <= iagemax){
2693: if(pos>=1.e-5){
2694: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2695: /*probs[i][jk][j1]= pp[jk]/pos;*/
2696: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2697: }
2698: else
2699: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2700: }
2701: }
2702:
2703: for(jk=-1; jk <=nlstate+ndeath; jk++)
2704: for(m=-1; m <=nlstate+ndeath; m++)
2705: if(freq[jk][m][i] !=0 ) {
2706: if(first==1)
2707: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2708: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2709: }
2710: if(i <= iagemax)
2711: fprintf(ficresp,"\n");
2712: if(first==1)
2713: printf("Others in log...\n");
2714: fprintf(ficlog,"\n");
2715: }
2716: /*}*/
2717: }
2718: dateintmean=dateintsum/k2cpt;
2719:
2720: fclose(ficresp);
2721: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2722: free_vector(pp,1,nlstate);
2723: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2724: /* End of Freq */
2725: }
2726:
2727: /************ Prevalence ********************/
2728: 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)
2729: {
2730: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2731: in each health status at the date of interview (if between dateprev1 and dateprev2).
2732: We still use firstpass and lastpass as another selection.
2733: */
2734:
2735: int i, m, jk, j1, bool, z1,j;
2736:
2737: double **prop;
2738: double posprop;
2739: double y2; /* in fractional years */
2740: int iagemin, iagemax;
2741: int first; /** to stop verbosity which is redirected to log file */
2742:
2743: iagemin= (int) agemin;
2744: iagemax= (int) agemax;
2745: /*pp=vector(1,nlstate);*/
2746: prop=matrix(1,nlstate,iagemin,iagemax+3);
2747: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2748: j1=0;
2749:
2750: /*j=cptcoveff;*/
2751: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2752:
2753: first=1;
2754: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
2755: /*for(i1=1; i1<=ncodemax[k1];i1++){
2756: j1++;*/
2757:
2758: for (i=1; i<=nlstate; i++)
2759: for(m=iagemin; m <= iagemax+3; m++)
2760: prop[i][m]=0.0;
2761:
2762: for (i=1; i<=imx; i++) { /* Each individual */
2763: bool=1;
2764: if (cptcovn>0) {
2765: for (z1=1; z1<=cptcoveff; z1++)
2766: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2767: bool=0;
2768: }
2769: if (bool==1) {
2770: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2771: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2772: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2773: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2774: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2775: 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);
2776: if (s[m][i]>0 && s[m][i]<=nlstate) {
2777: /*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]]);*/
2778: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2779: prop[s[m][i]][iagemax+3] += weight[i];
2780: }
2781: }
2782: } /* end selection of waves */
2783: }
2784: }
2785: for(i=iagemin; i <= iagemax+3; i++){
2786: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2787: posprop += prop[jk][i];
2788: }
2789:
2790: for(jk=1; jk <=nlstate ; jk++){
2791: if( i <= iagemax){
2792: if(posprop>=1.e-5){
2793: probs[i][jk][j1]= prop[jk][i]/posprop;
2794: } else{
2795: if(first==1){
2796: first=0;
2797: 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]);
2798: }
2799: }
2800: }
2801: }/* end jk */
2802: }/* end i */
2803: /*} *//* end i1 */
2804: } /* end j1 */
2805:
2806: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2807: /*free_vector(pp,1,nlstate);*/
2808: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2809: } /* End of prevalence */
2810:
2811: /************* Waves Concatenation ***************/
2812:
2813: 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)
2814: {
2815: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2816: Death is a valid wave (if date is known).
2817: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2818: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2819: and mw[mi+1][i]. dh depends on stepm.
2820: */
2821:
2822: int i, mi, m;
2823: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2824: double sum=0., jmean=0.;*/
2825: int first;
2826: int j, k=0,jk, ju, jl;
2827: double sum=0.;
2828: first=0;
2829: jmin=100000;
2830: jmax=-1;
2831: jmean=0.;
2832: for(i=1; i<=imx; i++){
2833: mi=0;
2834: m=firstpass;
2835: while(s[m][i] <= nlstate){
2836: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2837: mw[++mi][i]=m;
2838: if(m >=lastpass)
2839: break;
2840: else
2841: m++;
2842: }/* end while */
2843: if (s[m][i] > nlstate){
2844: mi++; /* Death is another wave */
2845: /* if(mi==0) never been interviewed correctly before death */
2846: /* Only death is a correct wave */
2847: mw[mi][i]=m;
2848: }
2849:
2850: wav[i]=mi;
2851: if(mi==0){
2852: nbwarn++;
2853: if(first==0){
2854: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2855: first=1;
2856: }
2857: if(first==1){
2858: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2859: }
2860: } /* end mi==0 */
2861: } /* End individuals */
2862:
2863: for(i=1; i<=imx; i++){
2864: for(mi=1; mi<wav[i];mi++){
2865: if (stepm <=0)
2866: dh[mi][i]=1;
2867: else{
2868: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2869: if (agedc[i] < 2*AGESUP) {
2870: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2871: if(j==0) j=1; /* Survives at least one month after exam */
2872: else if(j<0){
2873: nberr++;
2874: 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]);
2875: j=1; /* Temporary Dangerous patch */
2876: 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);
2877: 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]);
2878: 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);
2879: }
2880: k=k+1;
2881: if (j >= jmax){
2882: jmax=j;
2883: ijmax=i;
2884: }
2885: if (j <= jmin){
2886: jmin=j;
2887: ijmin=i;
2888: }
2889: sum=sum+j;
2890: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2891: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2892: }
2893: }
2894: else{
2895: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2896: /* 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]); */
2897:
2898: k=k+1;
2899: if (j >= jmax) {
2900: jmax=j;
2901: ijmax=i;
2902: }
2903: else if (j <= jmin){
2904: jmin=j;
2905: ijmin=i;
2906: }
2907: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2908: /*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]);*/
2909: if(j<0){
2910: nberr++;
2911: 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]);
2912: 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]);
2913: }
2914: sum=sum+j;
2915: }
2916: jk= j/stepm;
2917: jl= j -jk*stepm;
2918: ju= j -(jk+1)*stepm;
2919: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2920: if(jl==0){
2921: dh[mi][i]=jk;
2922: bh[mi][i]=0;
2923: }else{ /* We want a negative bias in order to only have interpolation ie
2924: * to avoid the price of an extra matrix product in likelihood */
2925: dh[mi][i]=jk+1;
2926: bh[mi][i]=ju;
2927: }
2928: }else{
2929: if(jl <= -ju){
2930: dh[mi][i]=jk;
2931: bh[mi][i]=jl; /* bias is positive if real duration
2932: * is higher than the multiple of stepm and negative otherwise.
2933: */
2934: }
2935: else{
2936: dh[mi][i]=jk+1;
2937: bh[mi][i]=ju;
2938: }
2939: if(dh[mi][i]==0){
2940: dh[mi][i]=1; /* At least one step */
2941: bh[mi][i]=ju; /* At least one step */
2942: /* 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);*/
2943: }
2944: } /* end if mle */
2945: }
2946: } /* end wave */
2947: }
2948: jmean=sum/k;
2949: 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);
2950: 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);
2951: }
2952:
2953: /*********** Tricode ****************************/
2954: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
2955: {
2956: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
2957: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
2958: * Boring subroutine which should only output nbcode[Tvar[j]][k]
2959: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
2960: * nbcode[Tvar[j]][1]=
2961: */
2962:
2963: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
2964: int modmaxcovj=0; /* Modality max of covariates j */
2965: int cptcode=0; /* Modality max of covariates j */
2966: int modmincovj=0; /* Modality min of covariates j */
2967:
2968:
2969: cptcoveff=0;
2970:
2971: for (k=-1; k < maxncov; k++) Ndum[k]=0;
2972: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
2973:
2974: /* Loop on covariates without age and products */
2975: for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
2976: for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the
2977: modality of this covariate Vj*/
2978: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
2979: * If product of Vn*Vm, still boolean *:
2980: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
2981: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
2982: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
2983: modality of the nth covariate of individual i. */
2984: if (ij > modmaxcovj)
2985: modmaxcovj=ij;
2986: else if (ij < modmincovj)
2987: modmincovj=ij;
2988: if ((ij < -1) && (ij > NCOVMAX)){
2989: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
2990: exit(1);
2991: }else
2992: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
2993: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
2994: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
2995: /* getting the maximum value of the modality of the covariate
2996: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
2997: female is 1, then modmaxcovj=1.*/
2998: }
2999: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
3000: cptcode=modmaxcovj;
3001: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
3002: /*for (i=0; i<=cptcode; i++) {*/
3003: for (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
3004: printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
3005: if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
3006: ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
3007: }
3008: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
3009: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
3010: } /* Ndum[-1] number of undefined modalities */
3011:
3012: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
3013: /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
3014: /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
3015: modmincovj=3; modmaxcovj = 7;
3016: There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
3017: which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy
3018: variables V1_1 and V1_2.
3019: nbcode[Tvar[j]][ij]=k;
3020: nbcode[Tvar[j]][1]=0;
3021: nbcode[Tvar[j]][2]=1;
3022: nbcode[Tvar[j]][3]=2;
3023: */
3024: ij=1; /* ij is similar to i but can jumps over null modalities */
3025: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
3026: for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
3027: /*recode from 0 */
3028: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
3029: nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode.
3030: k is a modality. If we have model=V1+V1*sex
3031: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
3032: ij++;
3033: }
3034: if (ij > ncodemax[j]) break;
3035: } /* end of loop on */
3036: } /* end of loop on modality */
3037: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
3038:
3039: for (k=-1; k< maxncov; k++) Ndum[k]=0;
3040:
3041: for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
3042: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
3043: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
3044: Ndum[ij]++;
3045: }
3046:
3047: ij=1;
3048: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
3049: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
3050: if((Ndum[i]!=0) && (i<=ncovcol)){
3051: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
3052: Tvaraff[ij]=i; /*For printing (unclear) */
3053: ij++;
3054: }else
3055: Tvaraff[ij]=0;
3056: }
3057: ij--;
3058: cptcoveff=ij; /*Number of total covariates*/
3059:
3060: }
3061:
3062:
3063: /*********** Health Expectancies ****************/
3064:
3065: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
3066:
3067: {
3068: /* Health expectancies, no variances */
3069: int i, j, nhstepm, hstepm, h, nstepm;
3070: int nhstepma, nstepma; /* Decreasing with age */
3071: double age, agelim, hf;
3072: double ***p3mat;
3073: double eip;
3074:
3075: pstamp(ficreseij);
3076: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3077: fprintf(ficreseij,"# Age");
3078: for(i=1; i<=nlstate;i++){
3079: for(j=1; j<=nlstate;j++){
3080: fprintf(ficreseij," e%1d%1d ",i,j);
3081: }
3082: fprintf(ficreseij," e%1d. ",i);
3083: }
3084: fprintf(ficreseij,"\n");
3085:
3086:
3087: if(estepm < stepm){
3088: printf ("Problem %d lower than %d\n",estepm, stepm);
3089: }
3090: else hstepm=estepm;
3091: /* We compute the life expectancy from trapezoids spaced every estepm months
3092: * This is mainly to measure the difference between two models: for example
3093: * if stepm=24 months pijx are given only every 2 years and by summing them
3094: * we are calculating an estimate of the Life Expectancy assuming a linear
3095: * progression in between and thus overestimating or underestimating according
3096: * to the curvature of the survival function. If, for the same date, we
3097: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3098: * to compare the new estimate of Life expectancy with the same linear
3099: * hypothesis. A more precise result, taking into account a more precise
3100: * curvature will be obtained if estepm is as small as stepm. */
3101:
3102: /* For example we decided to compute the life expectancy with the smallest unit */
3103: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3104: nhstepm is the number of hstepm from age to agelim
3105: nstepm is the number of stepm from age to agelin.
3106: Look at hpijx to understand the reason of that which relies in memory size
3107: and note for a fixed period like estepm months */
3108: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3109: survival function given by stepm (the optimization length). Unfortunately it
3110: means that if the survival funtion is printed only each two years of age and if
3111: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3112: results. So we changed our mind and took the option of the best precision.
3113: */
3114: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3115:
3116: agelim=AGESUP;
3117: /* If stepm=6 months */
3118: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3119: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3120:
3121: /* nhstepm age range expressed in number of stepm */
3122: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3123: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3124: /* if (stepm >= YEARM) hstepm=1;*/
3125: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3126: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3127:
3128: for (age=bage; age<=fage; age ++){
3129: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3130: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3131: /* if (stepm >= YEARM) hstepm=1;*/
3132: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3133:
3134: /* If stepm=6 months */
3135: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3136: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3137:
3138: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3139:
3140: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3141:
3142: printf("%d|",(int)age);fflush(stdout);
3143: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3144:
3145: /* Computing expectancies */
3146: for(i=1; i<=nlstate;i++)
3147: for(j=1; j<=nlstate;j++)
3148: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3149: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3150:
3151: /* 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]);*/
3152:
3153: }
3154:
3155: fprintf(ficreseij,"%3.0f",age );
3156: for(i=1; i<=nlstate;i++){
3157: eip=0;
3158: for(j=1; j<=nlstate;j++){
3159: eip +=eij[i][j][(int)age];
3160: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3161: }
3162: fprintf(ficreseij,"%9.4f", eip );
3163: }
3164: fprintf(ficreseij,"\n");
3165:
3166: }
3167: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3168: printf("\n");
3169: fprintf(ficlog,"\n");
3170:
3171: }
3172:
3173: 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[] )
3174:
3175: {
3176: /* Covariances of health expectancies eij and of total life expectancies according
3177: to initial status i, ei. .
3178: */
3179: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3180: int nhstepma, nstepma; /* Decreasing with age */
3181: double age, agelim, hf;
3182: double ***p3matp, ***p3matm, ***varhe;
3183: double **dnewm,**doldm;
3184: double *xp, *xm;
3185: double **gp, **gm;
3186: double ***gradg, ***trgradg;
3187: int theta;
3188:
3189: double eip, vip;
3190:
3191: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
3192: xp=vector(1,npar);
3193: xm=vector(1,npar);
3194: dnewm=matrix(1,nlstate*nlstate,1,npar);
3195: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3196:
3197: pstamp(ficresstdeij);
3198: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3199: fprintf(ficresstdeij,"# Age");
3200: for(i=1; i<=nlstate;i++){
3201: for(j=1; j<=nlstate;j++)
3202: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3203: fprintf(ficresstdeij," e%1d. ",i);
3204: }
3205: fprintf(ficresstdeij,"\n");
3206:
3207: pstamp(ficrescveij);
3208: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3209: fprintf(ficrescveij,"# Age");
3210: for(i=1; i<=nlstate;i++)
3211: for(j=1; j<=nlstate;j++){
3212: cptj= (j-1)*nlstate+i;
3213: for(i2=1; i2<=nlstate;i2++)
3214: for(j2=1; j2<=nlstate;j2++){
3215: cptj2= (j2-1)*nlstate+i2;
3216: if(cptj2 <= cptj)
3217: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3218: }
3219: }
3220: fprintf(ficrescveij,"\n");
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: /* If stepm=6 months */
3252: /* nhstepm age range expressed in number of stepm */
3253: agelim=AGESUP;
3254: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3255: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3256: /* if (stepm >= YEARM) hstepm=1;*/
3257: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3258:
3259: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3260: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3261: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3262: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3263: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3264: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3265:
3266: for (age=bage; age<=fage; age ++){
3267: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3268: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3269: /* if (stepm >= YEARM) hstepm=1;*/
3270: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3271:
3272: /* If stepm=6 months */
3273: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3274: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3275:
3276: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3277:
3278: /* Computing Variances of health expectancies */
3279: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3280: decrease memory allocation */
3281: for(theta=1; theta <=npar; theta++){
3282: for(i=1; i<=npar; i++){
3283: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3284: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3285: }
3286: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3287: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3288:
3289: for(j=1; j<= nlstate; j++){
3290: for(i=1; i<=nlstate; i++){
3291: for(h=0; h<=nhstepm-1; h++){
3292: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3293: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3294: }
3295: }
3296: }
3297:
3298: for(ij=1; ij<= nlstate*nlstate; ij++)
3299: for(h=0; h<=nhstepm-1; h++){
3300: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3301: }
3302: }/* End theta */
3303:
3304:
3305: for(h=0; h<=nhstepm-1; h++)
3306: for(j=1; j<=nlstate*nlstate;j++)
3307: for(theta=1; theta <=npar; theta++)
3308: trgradg[h][j][theta]=gradg[h][theta][j];
3309:
3310:
3311: for(ij=1;ij<=nlstate*nlstate;ij++)
3312: for(ji=1;ji<=nlstate*nlstate;ji++)
3313: varhe[ij][ji][(int)age] =0.;
3314:
3315: printf("%d|",(int)age);fflush(stdout);
3316: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3317: for(h=0;h<=nhstepm-1;h++){
3318: for(k=0;k<=nhstepm-1;k++){
3319: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3320: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3321: for(ij=1;ij<=nlstate*nlstate;ij++)
3322: for(ji=1;ji<=nlstate*nlstate;ji++)
3323: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3324: }
3325: }
3326:
3327: /* Computing expectancies */
3328: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3329: for(i=1; i<=nlstate;i++)
3330: for(j=1; j<=nlstate;j++)
3331: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3332: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3333:
3334: /* 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]);*/
3335:
3336: }
3337:
3338: fprintf(ficresstdeij,"%3.0f",age );
3339: for(i=1; i<=nlstate;i++){
3340: eip=0.;
3341: vip=0.;
3342: for(j=1; j<=nlstate;j++){
3343: eip += eij[i][j][(int)age];
3344: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3345: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3346: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3347: }
3348: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3349: }
3350: fprintf(ficresstdeij,"\n");
3351:
3352: fprintf(ficrescveij,"%3.0f",age );
3353: for(i=1; i<=nlstate;i++)
3354: for(j=1; j<=nlstate;j++){
3355: cptj= (j-1)*nlstate+i;
3356: for(i2=1; i2<=nlstate;i2++)
3357: for(j2=1; j2<=nlstate;j2++){
3358: cptj2= (j2-1)*nlstate+i2;
3359: if(cptj2 <= cptj)
3360: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3361: }
3362: }
3363: fprintf(ficrescveij,"\n");
3364:
3365: }
3366: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3367: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3368: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3369: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3370: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3371: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3372: printf("\n");
3373: fprintf(ficlog,"\n");
3374:
3375: free_vector(xm,1,npar);
3376: free_vector(xp,1,npar);
3377: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3378: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3379: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3380: }
3381:
3382: /************ Variance ******************/
3383: 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[])
3384: {
3385: /* Variance of health expectancies */
3386: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3387: /* double **newm;*/
3388: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
3389:
3390: int movingaverage();
3391: double **dnewm,**doldm;
3392: double **dnewmp,**doldmp;
3393: int i, j, nhstepm, hstepm, h, nstepm ;
3394: int k;
3395: double *xp;
3396: double **gp, **gm; /* for var eij */
3397: double ***gradg, ***trgradg; /*for var eij */
3398: double **gradgp, **trgradgp; /* for var p point j */
3399: double *gpp, *gmp; /* for var p point j */
3400: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3401: double ***p3mat;
3402: double age,agelim, hf;
3403: double ***mobaverage;
3404: int theta;
3405: char digit[4];
3406: char digitp[25];
3407:
3408: char fileresprobmorprev[FILENAMELENGTH];
3409:
3410: if(popbased==1){
3411: if(mobilav!=0)
3412: strcpy(digitp,"-populbased-mobilav-");
3413: else strcpy(digitp,"-populbased-nomobil-");
3414: }
3415: else
3416: strcpy(digitp,"-stablbased-");
3417:
3418: if (mobilav!=0) {
3419: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3420: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3421: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3422: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3423: }
3424: }
3425:
3426: strcpy(fileresprobmorprev,"prmorprev");
3427: sprintf(digit,"%-d",ij);
3428: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3429: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3430: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
3431: strcat(fileresprobmorprev,fileres);
3432: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3433: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3434: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3435: }
3436: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3437:
3438: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3439: pstamp(ficresprobmorprev);
3440: 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);
3441: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3442: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3443: fprintf(ficresprobmorprev," p.%-d SE",j);
3444: for(i=1; i<=nlstate;i++)
3445: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3446: }
3447: fprintf(ficresprobmorprev,"\n");
3448: fprintf(ficgp,"\n# Routine varevsij");
3449: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
3450: 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");
3451: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3452: /* } */
3453: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3454: pstamp(ficresvij);
3455: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3456: if(popbased==1)
3457: 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);
3458: else
3459: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3460: fprintf(ficresvij,"# Age");
3461: for(i=1; i<=nlstate;i++)
3462: for(j=1; j<=nlstate;j++)
3463: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3464: fprintf(ficresvij,"\n");
3465:
3466: xp=vector(1,npar);
3467: dnewm=matrix(1,nlstate,1,npar);
3468: doldm=matrix(1,nlstate,1,nlstate);
3469: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3470: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3471:
3472: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3473: gpp=vector(nlstate+1,nlstate+ndeath);
3474: gmp=vector(nlstate+1,nlstate+ndeath);
3475: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3476:
3477: if(estepm < stepm){
3478: printf ("Problem %d lower than %d\n",estepm, stepm);
3479: }
3480: else hstepm=estepm;
3481: /* For example we decided to compute the life expectancy with the smallest unit */
3482: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3483: nhstepm is the number of hstepm from age to agelim
3484: nstepm is the number of stepm from age to agelin.
3485: Look at function hpijx to understand why (it is linked to memory size questions) */
3486: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3487: survival function given by stepm (the optimization length). Unfortunately it
3488: means that if the survival funtion is printed every two years of age and if
3489: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3490: results. So we changed our mind and took the option of the best precision.
3491: */
3492: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3493: agelim = AGESUP;
3494: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3495: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3496: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3497: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3498: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3499: gp=matrix(0,nhstepm,1,nlstate);
3500: gm=matrix(0,nhstepm,1,nlstate);
3501:
3502:
3503: for(theta=1; theta <=npar; theta++){
3504: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3505: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3506: }
3507: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3508: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3509:
3510: if (popbased==1) {
3511: if(mobilav ==0){
3512: for(i=1; i<=nlstate;i++)
3513: prlim[i][i]=probs[(int)age][i][ij];
3514: }else{ /* mobilav */
3515: for(i=1; i<=nlstate;i++)
3516: prlim[i][i]=mobaverage[(int)age][i][ij];
3517: }
3518: }
3519:
3520: for(j=1; j<= nlstate; j++){
3521: for(h=0; h<=nhstepm; h++){
3522: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3523: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3524: }
3525: }
3526: /* This for computing probability of death (h=1 means
3527: computed over hstepm matrices product = hstepm*stepm months)
3528: as a weighted average of prlim.
3529: */
3530: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3531: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3532: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3533: }
3534: /* end probability of death */
3535:
3536: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3537: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3538: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3539: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3540:
3541: if (popbased==1) {
3542: if(mobilav ==0){
3543: for(i=1; i<=nlstate;i++)
3544: prlim[i][i]=probs[(int)age][i][ij];
3545: }else{ /* mobilav */
3546: for(i=1; i<=nlstate;i++)
3547: prlim[i][i]=mobaverage[(int)age][i][ij];
3548: }
3549: }
3550:
3551: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
3552: for(h=0; h<=nhstepm; h++){
3553: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3554: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3555: }
3556: }
3557: /* This for computing probability of death (h=1 means
3558: computed over hstepm matrices product = hstepm*stepm months)
3559: as a weighted average of prlim.
3560: */
3561: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3562: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3563: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3564: }
3565: /* end probability of death */
3566:
3567: for(j=1; j<= nlstate; j++) /* vareij */
3568: for(h=0; h<=nhstepm; h++){
3569: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3570: }
3571:
3572: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3573: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3574: }
3575:
3576: } /* End theta */
3577:
3578: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3579:
3580: for(h=0; h<=nhstepm; h++) /* veij */
3581: for(j=1; j<=nlstate;j++)
3582: for(theta=1; theta <=npar; theta++)
3583: trgradg[h][j][theta]=gradg[h][theta][j];
3584:
3585: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3586: for(theta=1; theta <=npar; theta++)
3587: trgradgp[j][theta]=gradgp[theta][j];
3588:
3589:
3590: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3591: for(i=1;i<=nlstate;i++)
3592: for(j=1;j<=nlstate;j++)
3593: vareij[i][j][(int)age] =0.;
3594:
3595: for(h=0;h<=nhstepm;h++){
3596: for(k=0;k<=nhstepm;k++){
3597: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3598: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3599: for(i=1;i<=nlstate;i++)
3600: for(j=1;j<=nlstate;j++)
3601: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3602: }
3603: }
3604:
3605: /* pptj */
3606: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3607: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3608: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3609: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3610: varppt[j][i]=doldmp[j][i];
3611: /* end ppptj */
3612: /* x centered again */
3613: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3614: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3615:
3616: if (popbased==1) {
3617: if(mobilav ==0){
3618: for(i=1; i<=nlstate;i++)
3619: prlim[i][i]=probs[(int)age][i][ij];
3620: }else{ /* mobilav */
3621: for(i=1; i<=nlstate;i++)
3622: prlim[i][i]=mobaverage[(int)age][i][ij];
3623: }
3624: }
3625:
3626: /* This for computing probability of death (h=1 means
3627: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3628: as a weighted average of prlim.
3629: */
3630: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3631: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3632: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3633: }
3634: /* end probability of death */
3635:
3636: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3637: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3638: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3639: for(i=1; i<=nlstate;i++){
3640: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3641: }
3642: }
3643: fprintf(ficresprobmorprev,"\n");
3644:
3645: fprintf(ficresvij,"%.0f ",age );
3646: for(i=1; i<=nlstate;i++)
3647: for(j=1; j<=nlstate;j++){
3648: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3649: }
3650: fprintf(ficresvij,"\n");
3651: free_matrix(gp,0,nhstepm,1,nlstate);
3652: free_matrix(gm,0,nhstepm,1,nlstate);
3653: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3654: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3655: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3656: } /* End age */
3657: free_vector(gpp,nlstate+1,nlstate+ndeath);
3658: free_vector(gmp,nlstate+1,nlstate+ndeath);
3659: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3660: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3661: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
3662: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
3663: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
3664: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3665: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3666: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
3667: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
3668: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
3669: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
3670: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3671: 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);
3672: /* 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);
3673: */
3674: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3675: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3676:
3677: free_vector(xp,1,npar);
3678: free_matrix(doldm,1,nlstate,1,nlstate);
3679: free_matrix(dnewm,1,nlstate,1,npar);
3680: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3681: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3682: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3683: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3684: fclose(ficresprobmorprev);
3685: fflush(ficgp);
3686: fflush(fichtm);
3687: } /* end varevsij */
3688:
3689: /************ Variance of prevlim ******************/
3690: 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[])
3691: {
3692: /* Variance of prevalence limit */
3693: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
3694:
3695: double **dnewm,**doldm;
3696: int i, j, nhstepm, hstepm;
3697: double *xp;
3698: double *gp, *gm;
3699: double **gradg, **trgradg;
3700: double age,agelim;
3701: int theta;
3702:
3703: pstamp(ficresvpl);
3704: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3705: fprintf(ficresvpl,"# Age");
3706: for(i=1; i<=nlstate;i++)
3707: fprintf(ficresvpl," %1d-%1d",i,i);
3708: fprintf(ficresvpl,"\n");
3709:
3710: xp=vector(1,npar);
3711: dnewm=matrix(1,nlstate,1,npar);
3712: doldm=matrix(1,nlstate,1,nlstate);
3713:
3714: hstepm=1*YEARM; /* Every year of age */
3715: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3716: agelim = AGESUP;
3717: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3718: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3719: if (stepm >= YEARM) hstepm=1;
3720: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3721: gradg=matrix(1,npar,1,nlstate);
3722: gp=vector(1,nlstate);
3723: gm=vector(1,nlstate);
3724:
3725: for(theta=1; theta <=npar; theta++){
3726: for(i=1; i<=npar; i++){ /* Computes gradient */
3727: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3728: }
3729: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3730: for(i=1;i<=nlstate;i++)
3731: gp[i] = prlim[i][i];
3732:
3733: for(i=1; i<=npar; i++) /* Computes gradient */
3734: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3735: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3736: for(i=1;i<=nlstate;i++)
3737: gm[i] = prlim[i][i];
3738:
3739: for(i=1;i<=nlstate;i++)
3740: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3741: } /* End theta */
3742:
3743: trgradg =matrix(1,nlstate,1,npar);
3744:
3745: for(j=1; j<=nlstate;j++)
3746: for(theta=1; theta <=npar; theta++)
3747: trgradg[j][theta]=gradg[theta][j];
3748:
3749: for(i=1;i<=nlstate;i++)
3750: varpl[i][(int)age] =0.;
3751: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3752: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3753: for(i=1;i<=nlstate;i++)
3754: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3755:
3756: fprintf(ficresvpl,"%.0f ",age );
3757: for(i=1; i<=nlstate;i++)
3758: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3759: fprintf(ficresvpl,"\n");
3760: free_vector(gp,1,nlstate);
3761: free_vector(gm,1,nlstate);
3762: free_matrix(gradg,1,npar,1,nlstate);
3763: free_matrix(trgradg,1,nlstate,1,npar);
3764: } /* End age */
3765:
3766: free_vector(xp,1,npar);
3767: free_matrix(doldm,1,nlstate,1,npar);
3768: free_matrix(dnewm,1,nlstate,1,nlstate);
3769:
3770: }
3771:
3772: /************ Variance of one-step probabilities ******************/
3773: 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[])
3774: {
3775: int i, j=0, k1, l1, tj;
3776: int k2, l2, j1, z1;
3777: int k=0, l;
3778: int first=1, first1, first2;
3779: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3780: double **dnewm,**doldm;
3781: double *xp;
3782: double *gp, *gm;
3783: double **gradg, **trgradg;
3784: double **mu;
3785: double age, cov[NCOVMAX+1];
3786: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3787: int theta;
3788: char fileresprob[FILENAMELENGTH];
3789: char fileresprobcov[FILENAMELENGTH];
3790: char fileresprobcor[FILENAMELENGTH];
3791: double ***varpij;
3792:
3793: strcpy(fileresprob,"prob");
3794: strcat(fileresprob,fileres);
3795: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3796: printf("Problem with resultfile: %s\n", fileresprob);
3797: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3798: }
3799: strcpy(fileresprobcov,"probcov");
3800: strcat(fileresprobcov,fileres);
3801: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3802: printf("Problem with resultfile: %s\n", fileresprobcov);
3803: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3804: }
3805: strcpy(fileresprobcor,"probcor");
3806: strcat(fileresprobcor,fileres);
3807: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3808: printf("Problem with resultfile: %s\n", fileresprobcor);
3809: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3810: }
3811: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3812: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3813: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3814: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3815: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3816: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3817: pstamp(ficresprob);
3818: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3819: fprintf(ficresprob,"# Age");
3820: pstamp(ficresprobcov);
3821: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3822: fprintf(ficresprobcov,"# Age");
3823: pstamp(ficresprobcor);
3824: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3825: fprintf(ficresprobcor,"# Age");
3826:
3827:
3828: for(i=1; i<=nlstate;i++)
3829: for(j=1; j<=(nlstate+ndeath);j++){
3830: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3831: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3832: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3833: }
3834: /* fprintf(ficresprob,"\n");
3835: fprintf(ficresprobcov,"\n");
3836: fprintf(ficresprobcor,"\n");
3837: */
3838: xp=vector(1,npar);
3839: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3840: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3841: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3842: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3843: first=1;
3844: fprintf(ficgp,"\n# Routine varprob");
3845: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3846: fprintf(fichtm,"\n");
3847:
3848: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3849: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3850: file %s<br>\n",optionfilehtmcov);
3851: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3852: and drawn. It helps understanding how is the covariance between two incidences.\
3853: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3854: 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. \
3855: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3856: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3857: standard deviations wide on each axis. <br>\
3858: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3859: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3860: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3861:
3862: cov[1]=1;
3863: /* tj=cptcoveff; */
3864: tj = (int) pow(2,cptcoveff);
3865: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3866: j1=0;
3867: for(j1=1; j1<=tj;j1++){
3868: /*for(i1=1; i1<=ncodemax[t];i1++){ */
3869: /*j1++;*/
3870: if (cptcovn>0) {
3871: fprintf(ficresprob, "\n#********** Variable ");
3872: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3873: fprintf(ficresprob, "**********\n#\n");
3874: fprintf(ficresprobcov, "\n#********** Variable ");
3875: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3876: fprintf(ficresprobcov, "**********\n#\n");
3877:
3878: fprintf(ficgp, "\n#********** Variable ");
3879: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3880: fprintf(ficgp, "**********\n#\n");
3881:
3882:
3883: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
3884: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3885: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
3886:
3887: fprintf(ficresprobcor, "\n#********** Variable ");
3888: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3889: fprintf(ficresprobcor, "**********\n#");
3890: }
3891:
3892: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3893: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3894: gp=vector(1,(nlstate)*(nlstate+ndeath));
3895: gm=vector(1,(nlstate)*(nlstate+ndeath));
3896: for (age=bage; age<=fage; age ++){
3897: cov[2]=age;
3898: for (k=1; k<=cptcovn;k++) {
3899: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
3900: * 1 1 1 1 1
3901: * 2 2 1 1 1
3902: * 3 1 2 1 1
3903: */
3904: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
3905: }
3906: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3907: for (k=1; k<=cptcovprod;k++)
3908: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3909:
3910:
3911: for(theta=1; theta <=npar; theta++){
3912: for(i=1; i<=npar; i++)
3913: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3914:
3915: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3916:
3917: k=0;
3918: for(i=1; i<= (nlstate); i++){
3919: for(j=1; j<=(nlstate+ndeath);j++){
3920: k=k+1;
3921: gp[k]=pmmij[i][j];
3922: }
3923: }
3924:
3925: for(i=1; i<=npar; i++)
3926: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
3927:
3928: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3929: k=0;
3930: for(i=1; i<=(nlstate); i++){
3931: for(j=1; j<=(nlstate+ndeath);j++){
3932: k=k+1;
3933: gm[k]=pmmij[i][j];
3934: }
3935: }
3936:
3937: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3938: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3939: }
3940:
3941: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3942: for(theta=1; theta <=npar; theta++)
3943: trgradg[j][theta]=gradg[theta][j];
3944:
3945: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3946: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3947:
3948: pmij(pmmij,cov,ncovmodel,x,nlstate);
3949:
3950: k=0;
3951: for(i=1; i<=(nlstate); i++){
3952: for(j=1; j<=(nlstate+ndeath);j++){
3953: k=k+1;
3954: mu[k][(int) age]=pmmij[i][j];
3955: }
3956: }
3957: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3958: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3959: varpij[i][j][(int)age] = doldm[i][j];
3960:
3961: /*printf("\n%d ",(int)age);
3962: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3963: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3964: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3965: }*/
3966:
3967: fprintf(ficresprob,"\n%d ",(int)age);
3968: fprintf(ficresprobcov,"\n%d ",(int)age);
3969: fprintf(ficresprobcor,"\n%d ",(int)age);
3970:
3971: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3972: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3973: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3974: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3975: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3976: }
3977: i=0;
3978: for (k=1; k<=(nlstate);k++){
3979: for (l=1; l<=(nlstate+ndeath);l++){
3980: i++;
3981: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3982: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3983: for (j=1; j<=i;j++){
3984: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
3985: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3986: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3987: }
3988: }
3989: }/* end of loop for state */
3990: } /* end of loop for age */
3991: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3992: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3993: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3994: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3995:
3996: /* Confidence intervalle of pij */
3997: /*
3998: fprintf(ficgp,"\nunset parametric;unset label");
3999: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
4000: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
4001: 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);
4002: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
4003: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
4004: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
4005: */
4006:
4007: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
4008: first1=1;first2=2;
4009: for (k2=1; k2<=(nlstate);k2++){
4010: for (l2=1; l2<=(nlstate+ndeath);l2++){
4011: if(l2==k2) continue;
4012: j=(k2-1)*(nlstate+ndeath)+l2;
4013: for (k1=1; k1<=(nlstate);k1++){
4014: for (l1=1; l1<=(nlstate+ndeath);l1++){
4015: if(l1==k1) continue;
4016: i=(k1-1)*(nlstate+ndeath)+l1;
4017: if(i<=j) continue;
4018: for (age=bage; age<=fage; age ++){
4019: if ((int)age %5==0){
4020: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
4021: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
4022: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
4023: mu1=mu[i][(int) age]/stepm*YEARM ;
4024: mu2=mu[j][(int) age]/stepm*YEARM;
4025: c12=cv12/sqrt(v1*v2);
4026: /* Computing eigen value of matrix of covariance */
4027: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4028: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4029: if ((lc2 <0) || (lc1 <0) ){
4030: if(first2==1){
4031: first1=0;
4032: 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);
4033: }
4034: 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);
4035: /* lc1=fabs(lc1); */ /* If we want to have them positive */
4036: /* lc2=fabs(lc2); */
4037: }
4038:
4039: /* Eigen vectors */
4040: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
4041: /*v21=sqrt(1.-v11*v11); *//* error */
4042: v21=(lc1-v1)/cv12*v11;
4043: v12=-v21;
4044: v22=v11;
4045: tnalp=v21/v11;
4046: if(first1==1){
4047: first1=0;
4048: 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);
4049: }
4050: 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);
4051: /*printf(fignu*/
4052: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
4053: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
4054: if(first==1){
4055: first=0;
4056: fprintf(ficgp,"\nset parametric;unset label");
4057: 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);
4058: fprintf(ficgp,"\nset ter png small size 320, 240");
4059: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
4060: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
4061: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
4062: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
4063: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4064: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4065: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
4066: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4067: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4068: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4069: 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",\
4070: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4071: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4072: }else{
4073: first=0;
4074: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4075: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4076: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4077: 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",\
4078: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4079: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4080: }/* if first */
4081: } /* age mod 5 */
4082: } /* end loop age */
4083: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4084: first=1;
4085: } /*l12 */
4086: } /* k12 */
4087: } /*l1 */
4088: }/* k1 */
4089: /* } */ /* loop covariates */
4090: }
4091: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4092: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4093: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4094: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4095: free_vector(xp,1,npar);
4096: fclose(ficresprob);
4097: fclose(ficresprobcov);
4098: fclose(ficresprobcor);
4099: fflush(ficgp);
4100: fflush(fichtmcov);
4101: }
4102:
4103:
4104: /******************* Printing html file ***********/
4105: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
4106: int lastpass, int stepm, int weightopt, char model[],\
4107: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
4108: int popforecast, int estepm ,\
4109: double jprev1, double mprev1,double anprev1, \
4110: double jprev2, double mprev2,double anprev2){
4111: int jj1, k1, i1, cpt;
4112:
4113: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4114: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4115: </ul>");
4116: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
4117: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
4118: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
4119: fprintf(fichtm,"\
4120: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
4121: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
4122: fprintf(fichtm,"\
4123: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
4124: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
4125: fprintf(fichtm,"\
4126: - (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): \
4127: <a href=\"%s\">%s</a> <br>\n",
4128: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
4129: fprintf(fichtm,"\
4130: - Population projections by age and states: \
4131: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
4132:
4133: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4134:
4135: m=pow(2,cptcoveff);
4136: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4137:
4138: jj1=0;
4139: for(k1=1; k1<=m;k1++){
4140: for(i1=1; i1<=ncodemax[k1];i1++){
4141: jj1++;
4142: if (cptcovn > 0) {
4143: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4144: for (cpt=1; cpt<=cptcoveff;cpt++)
4145: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4146: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4147: }
4148: /* Pij */
4149: 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> \
4150: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
4151: /* Quasi-incidences */
4152: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
4153: 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> \
4154: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
4155: /* Period (stable) prevalence in each health state */
4156: for(cpt=1; cpt<=nlstate;cpt++){
4157: 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> \
4158: <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
4159: }
4160: for(cpt=1; cpt<=nlstate;cpt++) {
4161: 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> \
4162: <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
4163: }
4164: } /* end i1 */
4165: }/* End k1 */
4166: fprintf(fichtm,"</ul>");
4167:
4168:
4169: fprintf(fichtm,"\
4170: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
4171: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
4172:
4173: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4174: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
4175: fprintf(fichtm,"\
4176: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4177: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
4178:
4179: fprintf(fichtm,"\
4180: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4181: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
4182: fprintf(fichtm,"\
4183: - 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): \
4184: <a href=\"%s\">%s</a> <br>\n</li>",
4185: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
4186: fprintf(fichtm,"\
4187: - (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): \
4188: <a href=\"%s\">%s</a> <br>\n</li>",
4189: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
4190: fprintf(fichtm,"\
4191: - 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",
4192: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
4193: fprintf(fichtm,"\
4194: - 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",
4195: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
4196: fprintf(fichtm,"\
4197: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
4198: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
4199:
4200: /* if(popforecast==1) fprintf(fichtm,"\n */
4201: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4202: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4203: /* <br>",fileres,fileres,fileres,fileres); */
4204: /* else */
4205: /* 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); */
4206: fflush(fichtm);
4207: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4208:
4209: m=pow(2,cptcoveff);
4210: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4211:
4212: jj1=0;
4213: for(k1=1; k1<=m;k1++){
4214: for(i1=1; i1<=ncodemax[k1];i1++){
4215: jj1++;
4216: if (cptcovn > 0) {
4217: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4218: for (cpt=1; cpt<=cptcoveff;cpt++)
4219: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4220: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4221: }
4222: for(cpt=1; cpt<=nlstate;cpt++) {
4223: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
4224: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
4225: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
4226: }
4227: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
4228: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4229: true period expectancies (those weighted with period prevalences are also\
4230: drawn in addition to the population based expectancies computed using\
4231: observed and cahotic prevalences: %s%d.png<br>\
4232: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
4233: } /* end i1 */
4234: }/* End k1 */
4235: fprintf(fichtm,"</ul>");
4236: fflush(fichtm);
4237: }
4238:
4239: /******************* Gnuplot file **************/
4240: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4241:
4242: char dirfileres[132],optfileres[132];
4243: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
4244: int ng=0;
4245: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4246: /* printf("Problem with file %s",optionfilegnuplot); */
4247: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4248: /* } */
4249:
4250: /*#ifdef windows */
4251: fprintf(ficgp,"cd \"%s\" \n",pathc);
4252: /*#endif */
4253: m=pow(2,cptcoveff);
4254:
4255: strcpy(dirfileres,optionfilefiname);
4256: strcpy(optfileres,"vpl");
4257: /* 1eme*/
4258: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
4259: for (cpt=1; cpt<= nlstate ; cpt ++) {
4260: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
4261: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
4262: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
4263: fprintf(ficgp,"set xlabel \"Age\" \n\
4264: set ylabel \"Probability\" \n\
4265: set ter png small size 320, 240\n\
4266: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
4267:
4268: for (i=1; i<= nlstate ; i ++) {
4269: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4270: else fprintf(ficgp," %%*lf (%%*lf)");
4271: }
4272: 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);
4273: for (i=1; i<= nlstate ; i ++) {
4274: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4275: else fprintf(ficgp," %%*lf (%%*lf)");
4276: }
4277: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
4278: for (i=1; i<= nlstate ; i ++) {
4279: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4280: else fprintf(ficgp," %%*lf (%%*lf)");
4281: }
4282: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
4283: }
4284: }
4285: /*2 eme*/
4286: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
4287: for (k1=1; k1<= m ; k1 ++) {
4288: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
4289: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
4290:
4291: for (i=1; i<= nlstate+1 ; i ++) {
4292: k=2*i;
4293: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4294: for (j=1; j<= nlstate+1 ; j ++) {
4295: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4296: else fprintf(ficgp," %%*lf (%%*lf)");
4297: }
4298: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
4299: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
4300: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4301: for (j=1; j<= nlstate+1 ; j ++) {
4302: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4303: else fprintf(ficgp," %%*lf (%%*lf)");
4304: }
4305: fprintf(ficgp,"\" t\"\" w l lt 0,");
4306: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4307: for (j=1; j<= nlstate+1 ; j ++) {
4308: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4309: else fprintf(ficgp," %%*lf (%%*lf)");
4310: }
4311: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4312: else fprintf(ficgp,"\" t\"\" w l lt 0,");
4313: }
4314: }
4315:
4316: /*3eme*/
4317:
4318: for (k1=1; k1<= m ; k1 ++) {
4319: for (cpt=1; cpt<= nlstate ; cpt ++) {
4320: /* k=2+nlstate*(2*cpt-2); */
4321: k=2+(nlstate+1)*(cpt-1);
4322: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
4323: fprintf(ficgp,"set ter png small size 320, 240\n\
4324: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
4325: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4326: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4327: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4328: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4329: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4330: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4331:
4332: */
4333: for (i=1; i< nlstate ; i ++) {
4334: 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);
4335: /* 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);*/
4336:
4337: }
4338: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
4339: }
4340: }
4341:
4342: /* CV preval stable (period) */
4343: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
4344: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
4345: k=3;
4346: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
4347: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
4348: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
4349: set ter png small size 320, 240\n\
4350: unset log y\n\
4351: plot [%.f:%.f] ", ageminpar, agemaxpar);
4352: for (i=1; i<= nlstate ; i ++){
4353: if(i==1)
4354: fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
4355: else
4356: fprintf(ficgp,", '' ");
4357: l=(nlstate+ndeath)*(i-1)+1;
4358: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
4359: for (j=1; j<= (nlstate-1) ; j ++)
4360: fprintf(ficgp,"+$%d",k+l+j);
4361: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
4362: } /* nlstate */
4363: fprintf(ficgp,"\n");
4364: } /* end cpt state*/
4365: } /* end covariate */
4366:
4367: /* proba elementaires */
4368: for(i=1,jk=1; i <=nlstate; i++){
4369: for(k=1; k <=(nlstate+ndeath); k++){
4370: if (k != i) {
4371: for(j=1; j <=ncovmodel; j++){
4372: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
4373: jk++;
4374: fprintf(ficgp,"\n");
4375: }
4376: }
4377: }
4378: }
4379: /*goto avoid;*/
4380: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
4381: for(jk=1; jk <=m; jk++) {
4382: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
4383: if (ng==2)
4384: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
4385: else
4386: fprintf(ficgp,"\nset title \"Probability\"\n");
4387: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
4388: i=1;
4389: for(k2=1; k2<=nlstate; k2++) {
4390: k3=i;
4391: for(k=1; k<=(nlstate+ndeath); k++) {
4392: if (k != k2){
4393: if(ng==2)
4394: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
4395: else
4396: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
4397: ij=1;/* To be checked else nbcode[0][0] wrong */
4398: for(j=3; j <=ncovmodel; j++) {
4399: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
4400: /* /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
4401: /* ij++; */
4402: /* } */
4403: /* else */
4404: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4405: }
4406: fprintf(ficgp,")/(1");
4407:
4408: for(k1=1; k1 <=nlstate; k1++){
4409: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
4410: ij=1;
4411: for(j=3; j <=ncovmodel; j++){
4412: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
4413: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
4414: /* ij++; */
4415: /* } */
4416: /* else */
4417: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4418: }
4419: fprintf(ficgp,")");
4420: }
4421: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
4422: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
4423: i=i+ncovmodel;
4424: }
4425: } /* end k */
4426: } /* end k2 */
4427: } /* end jk */
4428: } /* end ng */
4429: /* avoid: */
4430: fflush(ficgp);
4431: } /* end gnuplot */
4432:
4433:
4434: /*************** Moving average **************/
4435: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
4436:
4437: int i, cpt, cptcod;
4438: int modcovmax =1;
4439: int mobilavrange, mob;
4440: double age;
4441:
4442: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
4443: a covariate has 2 modalities */
4444: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
4445:
4446: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
4447: if(mobilav==1) mobilavrange=5; /* default */
4448: else mobilavrange=mobilav;
4449: for (age=bage; age<=fage; age++)
4450: for (i=1; i<=nlstate;i++)
4451: for (cptcod=1;cptcod<=modcovmax;cptcod++)
4452: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
4453: /* We keep the original values on the extreme ages bage, fage and for
4454: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
4455: we use a 5 terms etc. until the borders are no more concerned.
4456: */
4457: for (mob=3;mob <=mobilavrange;mob=mob+2){
4458: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
4459: for (i=1; i<=nlstate;i++){
4460: for (cptcod=1;cptcod<=modcovmax;cptcod++){
4461: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
4462: for (cpt=1;cpt<=(mob-1)/2;cpt++){
4463: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
4464: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
4465: }
4466: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
4467: }
4468: }
4469: }/* end age */
4470: }/* end mob */
4471: }else return -1;
4472: return 0;
4473: }/* End movingaverage */
4474:
4475:
4476: /************** Forecasting ******************/
4477: 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){
4478: /* proj1, year, month, day of starting projection
4479: agemin, agemax range of age
4480: dateprev1 dateprev2 range of dates during which prevalence is computed
4481: anproj2 year of en of projection (same day and month as proj1).
4482: */
4483: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
4484: double agec; /* generic age */
4485: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
4486: double *popeffectif,*popcount;
4487: double ***p3mat;
4488: double ***mobaverage;
4489: char fileresf[FILENAMELENGTH];
4490:
4491: agelim=AGESUP;
4492: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4493:
4494: strcpy(fileresf,"f");
4495: strcat(fileresf,fileres);
4496: if((ficresf=fopen(fileresf,"w"))==NULL) {
4497: printf("Problem with forecast resultfile: %s\n", fileresf);
4498: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
4499: }
4500: printf("Computing forecasting: result on file '%s' \n", fileresf);
4501: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
4502:
4503: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4504:
4505: if (mobilav!=0) {
4506: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4507: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4508: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4509: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4510: }
4511: }
4512:
4513: stepsize=(int) (stepm+YEARM-1)/YEARM;
4514: if (stepm<=12) stepsize=1;
4515: if(estepm < stepm){
4516: printf ("Problem %d lower than %d\n",estepm, stepm);
4517: }
4518: else hstepm=estepm;
4519:
4520: hstepm=hstepm/stepm;
4521: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
4522: fractional in yp1 */
4523: anprojmean=yp;
4524: yp2=modf((yp1*12),&yp);
4525: mprojmean=yp;
4526: yp1=modf((yp2*30.5),&yp);
4527: jprojmean=yp;
4528: if(jprojmean==0) jprojmean=1;
4529: if(mprojmean==0) jprojmean=1;
4530:
4531: i1=cptcoveff;
4532: if (cptcovn < 1){i1=1;}
4533:
4534: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4535:
4536: fprintf(ficresf,"#****** Routine prevforecast **\n");
4537:
4538: /* if (h==(int)(YEARM*yearp)){ */
4539: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4540: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4541: k=k+1;
4542: fprintf(ficresf,"\n#******");
4543: for(j=1;j<=cptcoveff;j++) {
4544: 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]]);
4545: }
4546: fprintf(ficresf,"******\n");
4547: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4548: for(j=1; j<=nlstate+ndeath;j++){
4549: for(i=1; i<=nlstate;i++)
4550: fprintf(ficresf," p%d%d",i,j);
4551: fprintf(ficresf," p.%d",j);
4552: }
4553: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4554: fprintf(ficresf,"\n");
4555: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4556:
4557: for (agec=fage; agec>=(ageminpar-1); agec--){
4558: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4559: nhstepm = nhstepm/hstepm;
4560: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4561: oldm=oldms;savm=savms;
4562: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4563:
4564: for (h=0; h<=nhstepm; h++){
4565: if (h*hstepm/YEARM*stepm ==yearp) {
4566: fprintf(ficresf,"\n");
4567: for(j=1;j<=cptcoveff;j++)
4568: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4569: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4570: }
4571: for(j=1; j<=nlstate+ndeath;j++) {
4572: ppij=0.;
4573: for(i=1; i<=nlstate;i++) {
4574: if (mobilav==1)
4575: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4576: else {
4577: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4578: }
4579: if (h*hstepm/YEARM*stepm== yearp) {
4580: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4581: }
4582: } /* end i */
4583: if (h*hstepm/YEARM*stepm==yearp) {
4584: fprintf(ficresf," %.3f", ppij);
4585: }
4586: }/* end j */
4587: } /* end h */
4588: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4589: } /* end agec */
4590: } /* end yearp */
4591: } /* end cptcod */
4592: } /* end cptcov */
4593:
4594: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4595:
4596: fclose(ficresf);
4597: }
4598:
4599: /************** Forecasting *****not tested NB*************/
4600: 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){
4601:
4602: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4603: int *popage;
4604: double calagedatem, agelim, kk1, kk2;
4605: double *popeffectif,*popcount;
4606: double ***p3mat,***tabpop,***tabpopprev;
4607: double ***mobaverage;
4608: char filerespop[FILENAMELENGTH];
4609:
4610: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4611: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4612: agelim=AGESUP;
4613: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4614:
4615: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4616:
4617:
4618: strcpy(filerespop,"pop");
4619: strcat(filerespop,fileres);
4620: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4621: printf("Problem with forecast resultfile: %s\n", filerespop);
4622: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4623: }
4624: printf("Computing forecasting: result on file '%s' \n", filerespop);
4625: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4626:
4627: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4628:
4629: if (mobilav!=0) {
4630: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4631: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4632: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4633: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4634: }
4635: }
4636:
4637: stepsize=(int) (stepm+YEARM-1)/YEARM;
4638: if (stepm<=12) stepsize=1;
4639:
4640: agelim=AGESUP;
4641:
4642: hstepm=1;
4643: hstepm=hstepm/stepm;
4644:
4645: if (popforecast==1) {
4646: if((ficpop=fopen(popfile,"r"))==NULL) {
4647: printf("Problem with population file : %s\n",popfile);exit(0);
4648: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4649: }
4650: popage=ivector(0,AGESUP);
4651: popeffectif=vector(0,AGESUP);
4652: popcount=vector(0,AGESUP);
4653:
4654: i=1;
4655: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4656:
4657: imx=i;
4658: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4659: }
4660:
4661: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4662: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4663: k=k+1;
4664: fprintf(ficrespop,"\n#******");
4665: for(j=1;j<=cptcoveff;j++) {
4666: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4667: }
4668: fprintf(ficrespop,"******\n");
4669: fprintf(ficrespop,"# Age");
4670: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4671: if (popforecast==1) fprintf(ficrespop," [Population]");
4672:
4673: for (cpt=0; cpt<=0;cpt++) {
4674: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4675:
4676: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4677: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4678: nhstepm = nhstepm/hstepm;
4679:
4680: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4681: oldm=oldms;savm=savms;
4682: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4683:
4684: for (h=0; h<=nhstepm; h++){
4685: if (h==(int) (calagedatem+YEARM*cpt)) {
4686: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4687: }
4688: for(j=1; j<=nlstate+ndeath;j++) {
4689: kk1=0.;kk2=0;
4690: for(i=1; i<=nlstate;i++) {
4691: if (mobilav==1)
4692: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4693: else {
4694: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4695: }
4696: }
4697: if (h==(int)(calagedatem+12*cpt)){
4698: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4699: /*fprintf(ficrespop," %.3f", kk1);
4700: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4701: }
4702: }
4703: for(i=1; i<=nlstate;i++){
4704: kk1=0.;
4705: for(j=1; j<=nlstate;j++){
4706: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4707: }
4708: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
4709: }
4710:
4711: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
4712: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4713: }
4714: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4715: }
4716: }
4717:
4718: /******/
4719:
4720: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4721: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4722: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4723: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4724: nhstepm = nhstepm/hstepm;
4725:
4726: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4727: oldm=oldms;savm=savms;
4728: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4729: for (h=0; h<=nhstepm; h++){
4730: if (h==(int) (calagedatem+YEARM*cpt)) {
4731: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4732: }
4733: for(j=1; j<=nlstate+ndeath;j++) {
4734: kk1=0.;kk2=0;
4735: for(i=1; i<=nlstate;i++) {
4736: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4737: }
4738: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
4739: }
4740: }
4741: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4742: }
4743: }
4744: }
4745: }
4746:
4747: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4748:
4749: if (popforecast==1) {
4750: free_ivector(popage,0,AGESUP);
4751: free_vector(popeffectif,0,AGESUP);
4752: free_vector(popcount,0,AGESUP);
4753: }
4754: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4755: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4756: fclose(ficrespop);
4757: } /* End of popforecast */
4758:
4759: int fileappend(FILE *fichier, char *optionfich)
4760: {
4761: if((fichier=fopen(optionfich,"a"))==NULL) {
4762: printf("Problem with file: %s\n", optionfich);
4763: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4764: return (0);
4765: }
4766: fflush(fichier);
4767: return (1);
4768: }
4769:
4770:
4771: /**************** function prwizard **********************/
4772: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4773: {
4774:
4775: /* Wizard to print covariance matrix template */
4776:
4777: char ca[32], cb[32];
4778: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
4779: int numlinepar;
4780:
4781: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4782: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4783: for(i=1; i <=nlstate; i++){
4784: jj=0;
4785: for(j=1; j <=nlstate+ndeath; j++){
4786: if(j==i) continue;
4787: jj++;
4788: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4789: printf("%1d%1d",i,j);
4790: fprintf(ficparo,"%1d%1d",i,j);
4791: for(k=1; k<=ncovmodel;k++){
4792: /* printf(" %lf",param[i][j][k]); */
4793: /* fprintf(ficparo," %lf",param[i][j][k]); */
4794: printf(" 0.");
4795: fprintf(ficparo," 0.");
4796: }
4797: printf("\n");
4798: fprintf(ficparo,"\n");
4799: }
4800: }
4801: printf("# Scales (for hessian or gradient estimation)\n");
4802: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4803: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4804: for(i=1; i <=nlstate; i++){
4805: jj=0;
4806: for(j=1; j <=nlstate+ndeath; j++){
4807: if(j==i) continue;
4808: jj++;
4809: fprintf(ficparo,"%1d%1d",i,j);
4810: printf("%1d%1d",i,j);
4811: fflush(stdout);
4812: for(k=1; k<=ncovmodel;k++){
4813: /* printf(" %le",delti3[i][j][k]); */
4814: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4815: printf(" 0.");
4816: fprintf(ficparo," 0.");
4817: }
4818: numlinepar++;
4819: printf("\n");
4820: fprintf(ficparo,"\n");
4821: }
4822: }
4823: printf("# Covariance matrix\n");
4824: /* # 121 Var(a12)\n\ */
4825: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4826: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4827: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4828: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4829: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4830: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4831: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4832: fflush(stdout);
4833: fprintf(ficparo,"# Covariance matrix\n");
4834: /* # 121 Var(a12)\n\ */
4835: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4836: /* # ...\n\ */
4837: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4838:
4839: for(itimes=1;itimes<=2;itimes++){
4840: jj=0;
4841: for(i=1; i <=nlstate; i++){
4842: for(j=1; j <=nlstate+ndeath; j++){
4843: if(j==i) continue;
4844: for(k=1; k<=ncovmodel;k++){
4845: jj++;
4846: ca[0]= k+'a'-1;ca[1]='\0';
4847: if(itimes==1){
4848: printf("#%1d%1d%d",i,j,k);
4849: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4850: }else{
4851: printf("%1d%1d%d",i,j,k);
4852: fprintf(ficparo,"%1d%1d%d",i,j,k);
4853: /* printf(" %.5le",matcov[i][j]); */
4854: }
4855: ll=0;
4856: for(li=1;li <=nlstate; li++){
4857: for(lj=1;lj <=nlstate+ndeath; lj++){
4858: if(lj==li) continue;
4859: for(lk=1;lk<=ncovmodel;lk++){
4860: ll++;
4861: if(ll<=jj){
4862: cb[0]= lk +'a'-1;cb[1]='\0';
4863: if(ll<jj){
4864: if(itimes==1){
4865: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4866: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4867: }else{
4868: printf(" 0.");
4869: fprintf(ficparo," 0.");
4870: }
4871: }else{
4872: if(itimes==1){
4873: printf(" Var(%s%1d%1d)",ca,i,j);
4874: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4875: }else{
4876: printf(" 0.");
4877: fprintf(ficparo," 0.");
4878: }
4879: }
4880: }
4881: } /* end lk */
4882: } /* end lj */
4883: } /* end li */
4884: printf("\n");
4885: fprintf(ficparo,"\n");
4886: numlinepar++;
4887: } /* end k*/
4888: } /*end j */
4889: } /* end i */
4890: } /* end itimes */
4891:
4892: } /* end of prwizard */
4893: /******************* Gompertz Likelihood ******************************/
4894: double gompertz(double x[])
4895: {
4896: double A,B,L=0.0,sump=0.,num=0.;
4897: int i,n=0; /* n is the size of the sample */
4898:
4899: for (i=0;i<=imx-1 ; i++) {
4900: sump=sump+weight[i];
4901: /* sump=sump+1;*/
4902: num=num+1;
4903: }
4904:
4905:
4906: /* for (i=0; i<=imx; i++)
4907: 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]);*/
4908:
4909: for (i=1;i<=imx ; i++)
4910: {
4911: if (cens[i] == 1 && wav[i]>1)
4912: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
4913:
4914: if (cens[i] == 0 && wav[i]>1)
4915: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4916: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
4917:
4918: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4919: if (wav[i] > 1 ) { /* ??? */
4920: L=L+A*weight[i];
4921: /* 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]);*/
4922: }
4923: }
4924:
4925: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4926:
4927: return -2*L*num/sump;
4928: }
4929:
4930: #ifdef GSL
4931: /******************* Gompertz_f Likelihood ******************************/
4932: double gompertz_f(const gsl_vector *v, void *params)
4933: {
4934: double A,B,LL=0.0,sump=0.,num=0.;
4935: double *x= (double *) v->data;
4936: int i,n=0; /* n is the size of the sample */
4937:
4938: for (i=0;i<=imx-1 ; i++) {
4939: sump=sump+weight[i];
4940: /* sump=sump+1;*/
4941: num=num+1;
4942: }
4943:
4944:
4945: /* for (i=0; i<=imx; i++)
4946: 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]);*/
4947: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
4948: for (i=1;i<=imx ; i++)
4949: {
4950: if (cens[i] == 1 && wav[i]>1)
4951: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
4952:
4953: if (cens[i] == 0 && wav[i]>1)
4954: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
4955: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
4956:
4957: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4958: if (wav[i] > 1 ) { /* ??? */
4959: LL=LL+A*weight[i];
4960: /* 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]);*/
4961: }
4962: }
4963:
4964: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4965: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
4966:
4967: return -2*LL*num/sump;
4968: }
4969: #endif
4970:
4971: /******************* Printing html file ***********/
4972: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4973: int lastpass, int stepm, int weightopt, char model[],\
4974: int imx, double p[],double **matcov,double agemortsup){
4975: int i,k;
4976:
4977: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4978: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4979: for (i=1;i<=2;i++)
4980: 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]));
4981: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4982: fprintf(fichtm,"</ul>");
4983:
4984: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4985:
4986: 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>");
4987:
4988: for (k=agegomp;k<(agemortsup-2);k++)
4989: 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]);
4990:
4991:
4992: fflush(fichtm);
4993: }
4994:
4995: /******************* Gnuplot file **************/
4996: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4997:
4998: char dirfileres[132],optfileres[132];
4999:
5000: int ng;
5001:
5002:
5003: /*#ifdef windows */
5004: fprintf(ficgp,"cd \"%s\" \n",pathc);
5005: /*#endif */
5006:
5007:
5008: strcpy(dirfileres,optionfilefiname);
5009: strcpy(optfileres,"vpl");
5010: fprintf(ficgp,"set out \"graphmort.png\"\n ");
5011: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
5012: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
5013: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
5014: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
5015:
5016: }
5017:
5018: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
5019: {
5020:
5021: /*-------- data file ----------*/
5022: FILE *fic;
5023: char dummy[]=" ";
5024: int i=0, j=0, n=0;
5025: int linei, month, year,iout;
5026: char line[MAXLINE], linetmp[MAXLINE];
5027: char stra[MAXLINE], strb[MAXLINE];
5028: char *stratrunc;
5029: int lstra;
5030:
5031:
5032: if((fic=fopen(datafile,"r"))==NULL) {
5033: printf("Problem while opening datafile: %s\n", datafile);return 1;
5034: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
5035: }
5036:
5037: i=1;
5038: linei=0;
5039: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
5040: linei=linei+1;
5041: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
5042: if(line[j] == '\t')
5043: line[j] = ' ';
5044: }
5045: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
5046: ;
5047: };
5048: line[j+1]=0; /* Trims blanks at end of line */
5049: if(line[0]=='#'){
5050: fprintf(ficlog,"Comment line\n%s\n",line);
5051: printf("Comment line\n%s\n",line);
5052: continue;
5053: }
5054: trimbb(linetmp,line); /* Trims multiple blanks in line */
5055: strcpy(line, linetmp);
5056:
5057:
5058: for (j=maxwav;j>=1;j--){
5059: cutv(stra, strb, line, ' ');
5060: if(strb[0]=='.') { /* Missing status */
5061: lval=-1;
5062: }else{
5063: errno=0;
5064: lval=strtol(strb,&endptr,10);
5065: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
5066: if( strb[0]=='\0' || (*endptr != '\0')){
5067: 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);
5068: 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);
5069: return 1;
5070: }
5071: }
5072: s[j][i]=lval;
5073:
5074: strcpy(line,stra);
5075: cutv(stra, strb,line,' ');
5076: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
5077: }
5078: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
5079: month=99;
5080: year=9999;
5081: }else{
5082: 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);
5083: 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);
5084: return 1;
5085: }
5086: anint[j][i]= (double) year;
5087: mint[j][i]= (double)month;
5088: strcpy(line,stra);
5089: } /* ENd Waves */
5090:
5091: cutv(stra, strb,line,' ');
5092: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
5093: }
5094: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
5095: month=99;
5096: year=9999;
5097: }else{
5098: 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);
5099: 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);
5100: return 1;
5101: }
5102: andc[i]=(double) year;
5103: moisdc[i]=(double) month;
5104: strcpy(line,stra);
5105:
5106: cutv(stra, strb,line,' ');
5107: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
5108: }
5109: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
5110: month=99;
5111: year=9999;
5112: }else{
5113: 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);
5114: 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);
5115: return 1;
5116: }
5117: if (year==9999) {
5118: 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);
5119: 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);
5120: return 1;
5121:
5122: }
5123: annais[i]=(double)(year);
5124: moisnais[i]=(double)(month);
5125: strcpy(line,stra);
5126:
5127: cutv(stra, strb,line,' ');
5128: errno=0;
5129: dval=strtod(strb,&endptr);
5130: if( strb[0]=='\0' || (*endptr != '\0')){
5131: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
5132: 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);
5133: fflush(ficlog);
5134: return 1;
5135: }
5136: weight[i]=dval;
5137: strcpy(line,stra);
5138:
5139: for (j=ncovcol;j>=1;j--){
5140: cutv(stra, strb,line,' ');
5141: if(strb[0]=='.') { /* Missing status */
5142: lval=-1;
5143: }else{
5144: errno=0;
5145: lval=strtol(strb,&endptr,10);
5146: if( strb[0]=='\0' || (*endptr != '\0')){
5147: 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);
5148: 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);
5149: return 1;
5150: }
5151: }
5152: if(lval <-1 || lval >1){
5153: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
5154: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5155: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5156: For example, for multinomial values like 1, 2 and 3,\n \
5157: build V1=0 V2=0 for the reference value (1),\n \
5158: V1=1 V2=0 for (2) \n \
5159: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5160: output of IMaCh is often meaningless.\n \
5161: Exiting.\n",lval,linei, i,line,j);
5162: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
5163: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5164: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5165: For example, for multinomial values like 1, 2 and 3,\n \
5166: build V1=0 V2=0 for the reference value (1),\n \
5167: V1=1 V2=0 for (2) \n \
5168: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5169: output of IMaCh is often meaningless.\n \
5170: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
5171: return 1;
5172: }
5173: covar[j][i]=(double)(lval);
5174: strcpy(line,stra);
5175: }
5176: lstra=strlen(stra);
5177:
5178: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
5179: stratrunc = &(stra[lstra-9]);
5180: num[i]=atol(stratrunc);
5181: }
5182: else
5183: num[i]=atol(stra);
5184: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
5185: 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;}*/
5186:
5187: i=i+1;
5188: } /* End loop reading data */
5189:
5190: *imax=i-1; /* Number of individuals */
5191: fclose(fic);
5192:
5193: return (0);
5194: /* endread: */
5195: printf("Exiting readdata: ");
5196: fclose(fic);
5197: return (1);
5198:
5199:
5200:
5201: }
5202: void removespace(char *str) {
5203: char *p1 = str, *p2 = str;
5204: do
5205: while (*p2 == ' ')
5206: p2++;
5207: while (*p1++ == *p2++);
5208: }
5209:
5210: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
5211: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
5212: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
5213: * - cptcovn or number of covariates k of the models excluding age*products =6
5214: * - cptcovage number of covariates with age*products =2
5215: * - cptcovs number of simple covariates
5216: * - 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
5217: * which is a new column after the 9 (ncovcol) variables.
5218: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
5219: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
5220: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
5221: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
5222: */
5223: {
5224: int i, j, k, ks;
5225: int j1, k1, k2;
5226: char modelsav[80];
5227: char stra[80], strb[80], strc[80], strd[80],stre[80];
5228:
5229: /*removespace(model);*/
5230: if (strlen(model) >1){ /* If there is at least 1 covariate */
5231: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
5232: j=nbocc(model,'+'); /**< j=Number of '+' */
5233: j1=nbocc(model,'*'); /**< j1=Number of '*' */
5234: cptcovs=j+1-j1; /**< Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2 */
5235: cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
5236: /* including age products which are counted in cptcovage.
5237: * but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
5238: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
5239: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
5240: strcpy(modelsav,model);
5241: if (strstr(model,"AGE") !=0){
5242: printf("Error. AGE must be in lower case 'age' model=%s ",model);
5243: fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
5244: return 1;
5245: }
5246: if (strstr(model,"v") !=0){
5247: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
5248: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
5249: return 1;
5250: }
5251:
5252: /* Design
5253: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
5254: * < ncovcol=8 >
5255: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
5256: * k= 1 2 3 4 5 6 7 8
5257: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
5258: * covar[k,i], value of kth covariate if not including age for individual i:
5259: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
5260: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
5261: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
5262: * Tage[++cptcovage]=k
5263: * if products, new covar are created after ncovcol with k1
5264: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
5265: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
5266: * 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
5267: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
5268: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
5269: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
5270: * < ncovcol=8 >
5271: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
5272: * k= 1 2 3 4 5 6 7 8 9 10 11 12
5273: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
5274: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5275: * p Tprod[1]@2={ 6, 5}
5276: *p Tvard[1][1]@4= {7, 8, 5, 6}
5277: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
5278: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
5279: *How to reorganize?
5280: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
5281: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5282: * {2, 1, 4, 8, 5, 6, 3, 7}
5283: * Struct []
5284: */
5285:
5286: /* This loop fills the array Tvar from the string 'model'.*/
5287: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
5288: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
5289: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
5290: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
5291: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
5292: /* k=1 Tvar[1]=2 (from V2) */
5293: /* k=5 Tvar[5] */
5294: /* for (k=1; k<=cptcovn;k++) { */
5295: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
5296: /* } */
5297: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
5298: /*
5299: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
5300: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
5301: Tvar[k]=0;
5302: cptcovage=0;
5303: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
5304: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5305: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
5306: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
5307: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5308: /*scanf("%d",i);*/
5309: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
5310: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
5311: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
5312: /* covar is not filled and then is empty */
5313: cptcovprod--;
5314: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
5315: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
5316: cptcovage++; /* Sums the number of covariates which include age as a product */
5317: Tage[cptcovage]=k; /* Tage[1] = 4 */
5318: /*printf("stre=%s ", stre);*/
5319: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
5320: cptcovprod--;
5321: cutl(stre,strb,strc,'V');
5322: Tvar[k]=atoi(stre);
5323: cptcovage++;
5324: Tage[cptcovage]=k;
5325: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
5326: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
5327: cptcovn++;
5328: cptcovprodnoage++;k1++;
5329: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5330: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
5331: because this model-covariate is a construction we invent a new column
5332: ncovcol + k1
5333: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
5334: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
5335: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
5336: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
5337: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
5338: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
5339: k2=k2+2;
5340: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
5341: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
5342: for (i=1; i<=lastobs;i++){
5343: /* Computes the new covariate which is a product of
5344: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
5345: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
5346: }
5347: } /* End age is not in the model */
5348: } /* End if model includes a product */
5349: else { /* no more sum */
5350: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5351: /* scanf("%d",i);*/
5352: cutl(strd,strc,strb,'V');
5353: ks++; /**< Number of simple covariates */
5354: cptcovn++;
5355: Tvar[k]=atoi(strd);
5356: }
5357: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
5358: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5359: scanf("%d",i);*/
5360: } /* end of loop + */
5361: } /* end model */
5362:
5363: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5364: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5365:
5366: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5367: printf("cptcovprod=%d ", cptcovprod);
5368: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5369:
5370: scanf("%d ",i);*/
5371:
5372:
5373: return (0); /* with covar[new additional covariate if product] and Tage if age */
5374: /*endread:*/
5375: printf("Exiting decodemodel: ");
5376: return (1);
5377: }
5378:
5379: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
5380: {
5381: int i, m;
5382:
5383: for (i=1; i<=imx; i++) {
5384: for(m=2; (m<= maxwav); m++) {
5385: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5386: anint[m][i]=9999;
5387: s[m][i]=-1;
5388: }
5389: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
5390: *nberr = *nberr + 1;
5391: 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);
5392: 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);
5393: s[m][i]=-1;
5394: }
5395: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
5396: (*nberr)++;
5397: 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]);
5398: 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]);
5399: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5400: }
5401: }
5402: }
5403:
5404: for (i=1; i<=imx; i++) {
5405: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5406: for(m=firstpass; (m<= lastpass); m++){
5407: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5408: if (s[m][i] >= nlstate+1) {
5409: if(agedc[i]>0){
5410: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
5411: agev[m][i]=agedc[i];
5412: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
5413: }else {
5414: if ((int)andc[i]!=9999){
5415: nbwarn++;
5416: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5417: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5418: agev[m][i]=-1;
5419: }
5420: }
5421: } /* agedc > 0 */
5422: }
5423: else if(s[m][i] !=9){ /* Standard case, age in fractional
5424: years but with the precision of a month */
5425: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5426: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5427: agev[m][i]=1;
5428: else if(agev[m][i] < *agemin){
5429: *agemin=agev[m][i];
5430: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
5431: }
5432: else if(agev[m][i] >*agemax){
5433: *agemax=agev[m][i];
5434: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
5435: }
5436: /*agev[m][i]=anint[m][i]-annais[i];*/
5437: /* agev[m][i] = age[i]+2*m;*/
5438: }
5439: else { /* =9 */
5440: agev[m][i]=1;
5441: s[m][i]=-1;
5442: }
5443: }
5444: else /*= 0 Unknown */
5445: agev[m][i]=1;
5446: }
5447:
5448: }
5449: for (i=1; i<=imx; i++) {
5450: for(m=firstpass; (m<=lastpass); m++){
5451: if (s[m][i] > (nlstate+ndeath)) {
5452: (*nberr)++;
5453: 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);
5454: 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);
5455: return 1;
5456: }
5457: }
5458: }
5459:
5460: /*for (i=1; i<=imx; i++){
5461: for (m=firstpass; (m<lastpass); m++){
5462: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5463: }
5464:
5465: }*/
5466:
5467:
5468: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5469: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5470:
5471: return (0);
5472: /* endread:*/
5473: printf("Exiting calandcheckages: ");
5474: return (1);
5475: }
5476:
5477: #if defined(_MSC_VER)
5478: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5479: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5480: //#include "stdafx.h"
5481: //#include <stdio.h>
5482: //#include <tchar.h>
5483: //#include <windows.h>
5484: //#include <iostream>
5485: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
5486:
5487: LPFN_ISWOW64PROCESS fnIsWow64Process;
5488:
5489: BOOL IsWow64()
5490: {
5491: BOOL bIsWow64 = FALSE;
5492:
5493: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
5494: // (HANDLE, PBOOL);
5495:
5496: //LPFN_ISWOW64PROCESS fnIsWow64Process;
5497:
5498: HMODULE module = GetModuleHandle(_T("kernel32"));
5499: const char funcName[] = "IsWow64Process";
5500: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
5501: GetProcAddress(module, funcName);
5502:
5503: if (NULL != fnIsWow64Process)
5504: {
5505: if (!fnIsWow64Process(GetCurrentProcess(),
5506: &bIsWow64))
5507: //throw std::exception("Unknown error");
5508: printf("Unknown error\n");
5509: }
5510: return bIsWow64 != FALSE;
5511: }
5512: #endif
5513:
5514: void syscompilerinfo()
5515: {
5516: /* #include "syscompilerinfo.h"*/
5517:
5518: #if defined __INTEL_COMPILER
5519: #if defined(__GNUC__)
5520: struct utsname sysInfo; /* For Intel on Linux and OS/X */
5521: #endif
5522: #elif defined(__GNUC__)
5523: #include <gnu/libc-version.h> /* Only on gnu */
5524: struct utsname sysInfo;
5525: int cross = CROSS;
5526: if (cross){
5527: printf("Cross-");
5528: fprintf(ficlog, "Cross-");
5529: }
5530: #endif
5531:
5532: #include <stdint.h>
5533:
5534: printf("Compiled with:");fprintf(ficlog,"Compiled with:");
5535: #if defined(__clang__)
5536: printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
5537: #endif
5538: #if defined(__ICC) || defined(__INTEL_COMPILER)
5539: printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
5540: #endif
5541: #if defined(__GNUC__) || defined(__GNUG__)
5542: printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
5543: #endif
5544: #if defined(__HP_cc) || defined(__HP_aCC)
5545: printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
5546: #endif
5547: #if defined(__IBMC__) || defined(__IBMCPP__)
5548: printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
5549: #endif
5550: #if defined(_MSC_VER)
5551: printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
5552: #endif
5553: #if defined(__PGI)
5554: printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
5555: #endif
5556: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
5557: printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
5558: #endif
5559: printf(" for ");fprintf(ficlog," for ");
5560:
5561: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
5562: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
5563: // Windows (x64 and x86)
5564: printf("Windows (x64 and x86) ");fprintf(ficlog,"Windows (x64 and x86) ");
5565: #elif __unix__ // all unices, not all compilers
5566: // Unix
5567: printf("Unix ");fprintf(ficlog,"Unix ");
5568: #elif __linux__
5569: // linux
5570: printf("linux ");fprintf(ficlog,"linux ");
5571: #elif __APPLE__
5572: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
5573: printf("Mac OS ");fprintf(ficlog,"Mac OS ");
5574: #endif
5575:
5576: /* __MINGW32__ */
5577: /* __CYGWIN__ */
5578: /* __MINGW64__ */
5579: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
5580: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
5581: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
5582: /* _WIN64 // Defined for applications for Win64. */
5583: /* _M_X64 // Defined for compilations that target x64 processors. */
5584: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
5585:
5586: #if UINTPTR_MAX == 0xffffffff
5587: printf(" 32-bit"); fprintf(ficlog," 32-bit");/* 32-bit */
5588: #elif UINTPTR_MAX == 0xffffffffffffffff
5589: printf(" 64-bit"); fprintf(ficlog," 64-bit");/* 64-bit */
5590: #else
5591: printf(" wtf-bit"); fprintf(ficlog," wtf-bit");/* wtf */
5592: #endif
5593:
5594: #if defined(__GNUC__)
5595: # if defined(__GNUC_PATCHLEVEL__)
5596: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
5597: + __GNUC_MINOR__ * 100 \
5598: + __GNUC_PATCHLEVEL__)
5599: # else
5600: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
5601: + __GNUC_MINOR__ * 100)
5602: # endif
5603: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
5604: fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
5605:
5606: if (uname(&sysInfo) != -1) {
5607: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
5608: fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
5609: }
5610: else
5611: perror("uname() error");
5612: #ifndef __INTEL_COMPILER
5613: printf("GNU libc version: %s\n", gnu_get_libc_version());
5614: fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
5615: #endif
5616: #endif
5617:
5618: // void main()
5619: // {
5620: #if defined(_MSC_VER)
5621: if (IsWow64()){
5622: printf("The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
5623: fprintf(ficlog, "The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
5624: }
5625: else{
5626: printf("The process is not running under WOW64 (i.e probably on a 64bit Windows).\n");
5627: fprintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
5628: }
5629: // printf("\nPress Enter to continue...");
5630: // getchar();
5631: // }
5632:
5633: #endif
5634:
5635:
5636: }
5637:
5638: /***********************************************/
5639: /**************** Main Program *****************/
5640: /***********************************************/
5641:
5642: int main(int argc, char *argv[])
5643: {
5644: #ifdef GSL
5645: const gsl_multimin_fminimizer_type *T;
5646: size_t iteri = 0, it;
5647: int rval = GSL_CONTINUE;
5648: int status = GSL_SUCCESS;
5649: double ssval;
5650: #endif
5651: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
5652: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
5653:
5654: int jj, ll, li, lj, lk;
5655: int numlinepar=0; /* Current linenumber of parameter file */
5656: int itimes;
5657: int NDIM=2;
5658: int vpopbased=0;
5659:
5660: char ca[32], cb[32];
5661: /* FILE *fichtm; *//* Html File */
5662: /* FILE *ficgp;*/ /*Gnuplot File */
5663: struct stat info;
5664: double agedeb;
5665: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
5666:
5667: double fret;
5668: double dum; /* Dummy variable */
5669: double ***p3mat;
5670: double ***mobaverage;
5671:
5672: char line[MAXLINE];
5673: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
5674: char pathr[MAXLINE], pathimach[MAXLINE];
5675: char *tok, *val; /* pathtot */
5676: int firstobs=1, lastobs=10;
5677: int c, h , cpt;
5678: int jl;
5679: int i1, j1, jk, stepsize;
5680: int *tab;
5681: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
5682: int mobilav=0,popforecast=0;
5683: int hstepm, nhstepm;
5684: int agemortsup;
5685: float sumlpop=0.;
5686: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
5687: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
5688:
5689: double bage=0, fage=110, age, agelim, agebase;
5690: double ftolpl=FTOL;
5691: double **prlim;
5692: double ***param; /* Matrix of parameters */
5693: double *p;
5694: double **matcov; /* Matrix of covariance */
5695: double ***delti3; /* Scale */
5696: double *delti; /* Scale */
5697: double ***eij, ***vareij;
5698: double **varpl; /* Variances of prevalence limits by age */
5699: double *epj, vepp;
5700:
5701: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
5702: double **ximort;
5703: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
5704: int *dcwave;
5705:
5706: char z[1]="c";
5707:
5708: /*char *strt;*/
5709: char strtend[80];
5710:
5711:
5712: /* setlocale (LC_ALL, ""); */
5713: /* bindtextdomain (PACKAGE, LOCALEDIR); */
5714: /* textdomain (PACKAGE); */
5715: /* setlocale (LC_CTYPE, ""); */
5716: /* setlocale (LC_MESSAGES, ""); */
5717:
5718: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
5719: rstart_time = time(NULL);
5720: /* (void) gettimeofday(&start_time,&tzp);*/
5721: start_time = *localtime(&rstart_time);
5722: curr_time=start_time;
5723: /*tml = *localtime(&start_time.tm_sec);*/
5724: /* strcpy(strstart,asctime(&tml)); */
5725: strcpy(strstart,asctime(&start_time));
5726:
5727: /* printf("Localtime (at start)=%s",strstart); */
5728: /* tp.tm_sec = tp.tm_sec +86400; */
5729: /* tm = *localtime(&start_time.tm_sec); */
5730: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
5731: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
5732: /* tmg.tm_hour=tmg.tm_hour + 1; */
5733: /* tp.tm_sec = mktime(&tmg); */
5734: /* strt=asctime(&tmg); */
5735: /* printf("Time(after) =%s",strstart); */
5736: /* (void) time (&time_value);
5737: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
5738: * tm = *localtime(&time_value);
5739: * strstart=asctime(&tm);
5740: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
5741: */
5742:
5743: nberr=0; /* Number of errors and warnings */
5744: nbwarn=0;
5745: getcwd(pathcd, size);
5746:
5747: printf("\n%s\n%s",version,fullversion);
5748: if(argc <=1){
5749: printf("\nEnter the parameter file name: ");
5750: fgets(pathr,FILENAMELENGTH,stdin);
5751: i=strlen(pathr);
5752: if(pathr[i-1]=='\n')
5753: pathr[i-1]='\0';
5754: i=strlen(pathr);
5755: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
5756: pathr[i-1]='\0';
5757: for (tok = pathr; tok != NULL; ){
5758: printf("Pathr |%s|\n",pathr);
5759: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
5760: printf("val= |%s| pathr=%s\n",val,pathr);
5761: strcpy (pathtot, val);
5762: if(pathr[0] == '\0') break; /* Dirty */
5763: }
5764: }
5765: else{
5766: strcpy(pathtot,argv[1]);
5767: }
5768: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
5769: /*cygwin_split_path(pathtot,path,optionfile);
5770: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
5771: /* cutv(path,optionfile,pathtot,'\\');*/
5772:
5773: /* Split argv[0], imach program to get pathimach */
5774: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
5775: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5776: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5777: /* strcpy(pathimach,argv[0]); */
5778: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
5779: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
5780: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
5781: chdir(path); /* Can be a relative path */
5782: if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
5783: printf("Current directory %s!\n",pathcd);
5784: strcpy(command,"mkdir ");
5785: strcat(command,optionfilefiname);
5786: if((outcmd=system(command)) != 0){
5787: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
5788: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
5789: /* fclose(ficlog); */
5790: /* exit(1); */
5791: }
5792: /* if((imk=mkdir(optionfilefiname))<0){ */
5793: /* perror("mkdir"); */
5794: /* } */
5795:
5796: /*-------- arguments in the command line --------*/
5797:
5798: /* Log file */
5799: strcat(filelog, optionfilefiname);
5800: strcat(filelog,".log"); /* */
5801: if((ficlog=fopen(filelog,"w"))==NULL) {
5802: printf("Problem with logfile %s\n",filelog);
5803: goto end;
5804: }
5805: fprintf(ficlog,"Log filename:%s\n",filelog);
5806: fprintf(ficlog,"\n%s\n%s",version,fullversion);
5807: fprintf(ficlog,"\nEnter the parameter file name: \n");
5808: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
5809: path=%s \n\
5810: optionfile=%s\n\
5811: optionfilext=%s\n\
5812: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
5813:
5814: syscompilerinfo();
5815:
5816: printf("Local time (at start):%s",strstart);
5817: fprintf(ficlog,"Local time (at start): %s",strstart);
5818: fflush(ficlog);
5819: /* (void) gettimeofday(&curr_time,&tzp); */
5820: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
5821:
5822: /* */
5823: strcpy(fileres,"r");
5824: strcat(fileres, optionfilefiname);
5825: strcat(fileres,".txt"); /* Other files have txt extension */
5826:
5827: /*---------arguments file --------*/
5828:
5829: if((ficpar=fopen(optionfile,"r"))==NULL) {
5830: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
5831: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
5832: fflush(ficlog);
5833: /* goto end; */
5834: exit(70);
5835: }
5836:
5837:
5838:
5839: strcpy(filereso,"o");
5840: strcat(filereso,fileres);
5841: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
5842: printf("Problem with Output resultfile: %s\n", filereso);
5843: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
5844: fflush(ficlog);
5845: goto end;
5846: }
5847:
5848: /* Reads comments: lines beginning with '#' */
5849: numlinepar=0;
5850: while((c=getc(ficpar))=='#' && c!= EOF){
5851: ungetc(c,ficpar);
5852: fgets(line, MAXLINE, ficpar);
5853: numlinepar++;
5854: fputs(line,stdout);
5855: fputs(line,ficparo);
5856: fputs(line,ficlog);
5857: }
5858: ungetc(c,ficpar);
5859:
5860: 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);
5861: numlinepar++;
5862: 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);
5863: 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);
5864: 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);
5865: fflush(ficlog);
5866: while((c=getc(ficpar))=='#' && c!= EOF){
5867: ungetc(c,ficpar);
5868: fgets(line, MAXLINE, ficpar);
5869: numlinepar++;
5870: fputs(line, stdout);
5871: //puts(line);
5872: fputs(line,ficparo);
5873: fputs(line,ficlog);
5874: }
5875: ungetc(c,ficpar);
5876:
5877:
5878: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
5879: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
5880: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
5881: v1+v2*age+v2*v3 makes cptcovn = 3
5882: */
5883: if (strlen(model)>1)
5884: 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*/
5885: else
5886: ncovmodel=2;
5887: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
5888: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
5889: npar= nforce*ncovmodel; /* Number of parameters like aij*/
5890: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
5891: 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);
5892: 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);
5893: fflush(stdout);
5894: fclose (ficlog);
5895: goto end;
5896: }
5897: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5898: delti=delti3[1][1];
5899: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
5900: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
5901: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5902: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5903: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5904: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5905: fclose (ficparo);
5906: fclose (ficlog);
5907: goto end;
5908: exit(0);
5909: }
5910: else if(mle==-3) {
5911: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5912: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5913: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5914: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5915: matcov=matrix(1,npar,1,npar);
5916: }
5917: else{
5918: /* Read guessed parameters */
5919: /* Reads comments: lines beginning with '#' */
5920: while((c=getc(ficpar))=='#' && c!= EOF){
5921: ungetc(c,ficpar);
5922: fgets(line, MAXLINE, ficpar);
5923: numlinepar++;
5924: fputs(line,stdout);
5925: fputs(line,ficparo);
5926: fputs(line,ficlog);
5927: }
5928: ungetc(c,ficpar);
5929:
5930: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5931: for(i=1; i <=nlstate; i++){
5932: j=0;
5933: for(jj=1; jj <=nlstate+ndeath; jj++){
5934: if(jj==i) continue;
5935: j++;
5936: fscanf(ficpar,"%1d%1d",&i1,&j1);
5937: if ((i1 != i) && (j1 != j)){
5938: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
5939: It might be a problem of design; if ncovcol and the model are correct\n \
5940: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
5941: exit(1);
5942: }
5943: fprintf(ficparo,"%1d%1d",i1,j1);
5944: if(mle==1)
5945: printf("%1d%1d",i,j);
5946: fprintf(ficlog,"%1d%1d",i,j);
5947: for(k=1; k<=ncovmodel;k++){
5948: fscanf(ficpar," %lf",¶m[i][j][k]);
5949: if(mle==1){
5950: printf(" %lf",param[i][j][k]);
5951: fprintf(ficlog," %lf",param[i][j][k]);
5952: }
5953: else
5954: fprintf(ficlog," %lf",param[i][j][k]);
5955: fprintf(ficparo," %lf",param[i][j][k]);
5956: }
5957: fscanf(ficpar,"\n");
5958: numlinepar++;
5959: if(mle==1)
5960: printf("\n");
5961: fprintf(ficlog,"\n");
5962: fprintf(ficparo,"\n");
5963: }
5964: }
5965: fflush(ficlog);
5966:
5967: /* Reads scales values */
5968: p=param[1][1];
5969:
5970: /* Reads comments: lines beginning with '#' */
5971: while((c=getc(ficpar))=='#' && c!= EOF){
5972: ungetc(c,ficpar);
5973: fgets(line, MAXLINE, ficpar);
5974: numlinepar++;
5975: fputs(line,stdout);
5976: fputs(line,ficparo);
5977: fputs(line,ficlog);
5978: }
5979: ungetc(c,ficpar);
5980:
5981: for(i=1; i <=nlstate; i++){
5982: for(j=1; j <=nlstate+ndeath-1; j++){
5983: fscanf(ficpar,"%1d%1d",&i1,&j1);
5984: if ( (i1-i) * (j1-j) != 0){
5985: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
5986: exit(1);
5987: }
5988: printf("%1d%1d",i,j);
5989: fprintf(ficparo,"%1d%1d",i1,j1);
5990: fprintf(ficlog,"%1d%1d",i1,j1);
5991: for(k=1; k<=ncovmodel;k++){
5992: fscanf(ficpar,"%le",&delti3[i][j][k]);
5993: printf(" %le",delti3[i][j][k]);
5994: fprintf(ficparo," %le",delti3[i][j][k]);
5995: fprintf(ficlog," %le",delti3[i][j][k]);
5996: }
5997: fscanf(ficpar,"\n");
5998: numlinepar++;
5999: printf("\n");
6000: fprintf(ficparo,"\n");
6001: fprintf(ficlog,"\n");
6002: }
6003: }
6004: fflush(ficlog);
6005:
6006: /* Reads covariance matrix */
6007: delti=delti3[1][1];
6008:
6009:
6010: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
6011:
6012: /* Reads comments: lines beginning with '#' */
6013: while((c=getc(ficpar))=='#' && c!= EOF){
6014: ungetc(c,ficpar);
6015: fgets(line, MAXLINE, ficpar);
6016: numlinepar++;
6017: fputs(line,stdout);
6018: fputs(line,ficparo);
6019: fputs(line,ficlog);
6020: }
6021: ungetc(c,ficpar);
6022:
6023: matcov=matrix(1,npar,1,npar);
6024: for(i=1; i <=npar; i++)
6025: for(j=1; j <=npar; j++) matcov[i][j]=0.;
6026:
6027: for(i=1; i <=npar; i++){
6028: fscanf(ficpar,"%s",str);
6029: if(mle==1)
6030: printf("%s",str);
6031: fprintf(ficlog,"%s",str);
6032: fprintf(ficparo,"%s",str);
6033: for(j=1; j <=i; j++){
6034: fscanf(ficpar," %le",&matcov[i][j]);
6035: if(mle==1){
6036: printf(" %.5le",matcov[i][j]);
6037: }
6038: fprintf(ficlog," %.5le",matcov[i][j]);
6039: fprintf(ficparo," %.5le",matcov[i][j]);
6040: }
6041: fscanf(ficpar,"\n");
6042: numlinepar++;
6043: if(mle==1)
6044: printf("\n");
6045: fprintf(ficlog,"\n");
6046: fprintf(ficparo,"\n");
6047: }
6048: for(i=1; i <=npar; i++)
6049: for(j=i+1;j<=npar;j++)
6050: matcov[i][j]=matcov[j][i];
6051:
6052: if(mle==1)
6053: printf("\n");
6054: fprintf(ficlog,"\n");
6055:
6056: fflush(ficlog);
6057:
6058: /*-------- Rewriting parameter file ----------*/
6059: strcpy(rfileres,"r"); /* "Rparameterfile */
6060: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
6061: strcat(rfileres,"."); /* */
6062: strcat(rfileres,optionfilext); /* Other files have txt extension */
6063: if((ficres =fopen(rfileres,"w"))==NULL) {
6064: printf("Problem writing new parameter file: %s\n", fileres);goto end;
6065: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
6066: }
6067: fprintf(ficres,"#%s\n",version);
6068: } /* End of mle != -3 */
6069:
6070:
6071: n= lastobs;
6072: num=lvector(1,n);
6073: moisnais=vector(1,n);
6074: annais=vector(1,n);
6075: moisdc=vector(1,n);
6076: andc=vector(1,n);
6077: agedc=vector(1,n);
6078: cod=ivector(1,n);
6079: weight=vector(1,n);
6080: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
6081: mint=matrix(1,maxwav,1,n);
6082: anint=matrix(1,maxwav,1,n);
6083: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
6084: tab=ivector(1,NCOVMAX);
6085: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
6086:
6087: /* Reads data from file datafile */
6088: if (readdata(datafile, firstobs, lastobs, &imx)==1)
6089: goto end;
6090:
6091: /* Calculation of the number of parameters from char model */
6092: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
6093: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
6094: k=3 V4 Tvar[k=3]= 4 (from V4)
6095: k=2 V1 Tvar[k=2]= 1 (from V1)
6096: k=1 Tvar[1]=2 (from V2)
6097: */
6098: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
6099: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
6100: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
6101: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
6102: */
6103: /* For model-covariate k tells which data-covariate to use but
6104: because this model-covariate is a construction we invent a new column
6105: ncovcol + k1
6106: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
6107: Tvar[3=V1*V4]=4+1 etc */
6108: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
6109: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
6110: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
6111: */
6112: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
6113: 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
6114: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
6115: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
6116: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
6117: 4 covariates (3 plus signs)
6118: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
6119: */
6120:
6121: if(decodemodel(model, lastobs) == 1)
6122: goto end;
6123:
6124: if((double)(lastobs-imx)/(double)imx > 1.10){
6125: nbwarn++;
6126: 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);
6127: 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);
6128: }
6129: /* if(mle==1){*/
6130: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
6131: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
6132: }
6133:
6134: /*-calculation of age at interview from date of interview and age at death -*/
6135: agev=matrix(1,maxwav,1,imx);
6136:
6137: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
6138: goto end;
6139:
6140:
6141: agegomp=(int)agemin;
6142: free_vector(moisnais,1,n);
6143: free_vector(annais,1,n);
6144: /* free_matrix(mint,1,maxwav,1,n);
6145: free_matrix(anint,1,maxwav,1,n);*/
6146: free_vector(moisdc,1,n);
6147: free_vector(andc,1,n);
6148: /* */
6149:
6150: wav=ivector(1,imx);
6151: dh=imatrix(1,lastpass-firstpass+1,1,imx);
6152: bh=imatrix(1,lastpass-firstpass+1,1,imx);
6153: mw=imatrix(1,lastpass-firstpass+1,1,imx);
6154:
6155: /* Concatenates waves */
6156: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
6157: /* */
6158:
6159: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
6160:
6161: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
6162: ncodemax[1]=1;
6163: Ndum =ivector(-1,NCOVMAX);
6164: if (ncovmodel > 2)
6165: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
6166:
6167: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
6168: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
6169: h=0;
6170:
6171:
6172: /*if (cptcovn > 0) */
6173:
6174:
6175: m=pow(2,cptcoveff);
6176:
6177: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
6178: 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 */
6179: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
6180: for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
6181: h++;
6182: if (h>m)
6183: h=1;
6184: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
6185: * h 1 2 3 4
6186: *______________________________
6187: * 1 i=1 1 i=1 1 i=1 1 i=1 1
6188: * 2 2 1 1 1
6189: * 3 i=2 1 2 1 1
6190: * 4 2 2 1 1
6191: * 5 i=3 1 i=2 1 2 1
6192: * 6 2 1 2 1
6193: * 7 i=4 1 2 2 1
6194: * 8 2 2 2 1
6195: * 9 i=5 1 i=3 1 i=2 1 1
6196: * 10 2 1 1 1
6197: * 11 i=6 1 2 1 1
6198: * 12 2 2 1 1
6199: * 13 i=7 1 i=4 1 2 1
6200: * 14 2 1 2 1
6201: * 15 i=8 1 2 2 1
6202: * 16 2 2 2 1
6203: */
6204: codtab[h][k]=j;
6205: /*codtab[h][Tvar[k]]=j;*/
6206: 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]]);
6207: }
6208: }
6209: }
6210: }
6211: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
6212: codtab[1][2]=1;codtab[2][2]=2; */
6213: /* for(i=1; i <=m ;i++){
6214: for(k=1; k <=cptcovn; k++){
6215: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
6216: }
6217: printf("\n");
6218: }
6219: scanf("%d",i);*/
6220:
6221: free_ivector(Ndum,-1,NCOVMAX);
6222:
6223:
6224:
6225: /*------------ gnuplot -------------*/
6226: strcpy(optionfilegnuplot,optionfilefiname);
6227: if(mle==-3)
6228: strcat(optionfilegnuplot,"-mort");
6229: strcat(optionfilegnuplot,".gp");
6230:
6231: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
6232: printf("Problem with file %s",optionfilegnuplot);
6233: }
6234: else{
6235: fprintf(ficgp,"\n# %s\n", version);
6236: fprintf(ficgp,"# %s\n", optionfilegnuplot);
6237: //fprintf(ficgp,"set missing 'NaNq'\n");
6238: fprintf(ficgp,"set datafile missing 'NaNq'\n");
6239: }
6240: /* fclose(ficgp);*/
6241: /*--------- index.htm --------*/
6242:
6243: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
6244: if(mle==-3)
6245: strcat(optionfilehtm,"-mort");
6246: strcat(optionfilehtm,".htm");
6247: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
6248: printf("Problem with %s \n",optionfilehtm);
6249: exit(0);
6250: }
6251:
6252: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
6253: strcat(optionfilehtmcov,"-cov.htm");
6254: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
6255: printf("Problem with %s \n",optionfilehtmcov), exit(0);
6256: }
6257: else{
6258: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6259: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6260: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
6261: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
6262: }
6263:
6264: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6265: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6266: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
6267: \n\
6268: <hr size=\"2\" color=\"#EC5E5E\">\
6269: <ul><li><h4>Parameter files</h4>\n\
6270: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
6271: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
6272: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
6273: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
6274: - Date and time at start: %s</ul>\n",\
6275: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
6276: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
6277: fileres,fileres,\
6278: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
6279: fflush(fichtm);
6280:
6281: strcpy(pathr,path);
6282: strcat(pathr,optionfilefiname);
6283: chdir(optionfilefiname); /* Move to directory named optionfile */
6284:
6285: /* Calculates basic frequencies. Computes observed prevalence at single age
6286: and prints on file fileres'p'. */
6287: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
6288:
6289: fprintf(fichtm,"\n");
6290: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
6291: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
6292: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
6293: imx,agemin,agemax,jmin,jmax,jmean);
6294: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6295: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6296: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6297: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6298: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
6299:
6300:
6301: /* For Powell, parameters are in a vector p[] starting at p[1]
6302: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
6303: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
6304:
6305: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
6306:
6307: if (mle==-3){
6308: ximort=matrix(1,NDIM,1,NDIM);
6309: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
6310: cens=ivector(1,n);
6311: ageexmed=vector(1,n);
6312: agecens=vector(1,n);
6313: dcwave=ivector(1,n);
6314:
6315: for (i=1; i<=imx; i++){
6316: dcwave[i]=-1;
6317: for (m=firstpass; m<=lastpass; m++)
6318: if (s[m][i]>nlstate) {
6319: dcwave[i]=m;
6320: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
6321: break;
6322: }
6323: }
6324:
6325: for (i=1; i<=imx; i++) {
6326: if (wav[i]>0){
6327: ageexmed[i]=agev[mw[1][i]][i];
6328: j=wav[i];
6329: agecens[i]=1.;
6330:
6331: if (ageexmed[i]> 1 && wav[i] > 0){
6332: agecens[i]=agev[mw[j][i]][i];
6333: cens[i]= 1;
6334: }else if (ageexmed[i]< 1)
6335: cens[i]= -1;
6336: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
6337: cens[i]=0 ;
6338: }
6339: else cens[i]=-1;
6340: }
6341:
6342: for (i=1;i<=NDIM;i++) {
6343: for (j=1;j<=NDIM;j++)
6344: ximort[i][j]=(i == j ? 1.0 : 0.0);
6345: }
6346:
6347: /*p[1]=0.0268; p[NDIM]=0.083;*/
6348: /*printf("%lf %lf", p[1], p[2]);*/
6349:
6350:
6351: #ifdef GSL
6352: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
6353: #else
6354: printf("Powell\n"); fprintf(ficlog,"Powell\n");
6355: #endif
6356: strcpy(filerespow,"pow-mort");
6357: strcat(filerespow,fileres);
6358: if((ficrespow=fopen(filerespow,"w"))==NULL) {
6359: printf("Problem with resultfile: %s\n", filerespow);
6360: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
6361: }
6362: #ifdef GSL
6363: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
6364: #else
6365: fprintf(ficrespow,"# Powell\n# iter -2*LL");
6366: #endif
6367: /* for (i=1;i<=nlstate;i++)
6368: for(j=1;j<=nlstate+ndeath;j++)
6369: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
6370: */
6371: fprintf(ficrespow,"\n");
6372: #ifdef GSL
6373: /* gsl starts here */
6374: T = gsl_multimin_fminimizer_nmsimplex;
6375: gsl_multimin_fminimizer *sfm = NULL;
6376: gsl_vector *ss, *x;
6377: gsl_multimin_function minex_func;
6378:
6379: /* Initial vertex size vector */
6380: ss = gsl_vector_alloc (NDIM);
6381:
6382: if (ss == NULL){
6383: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
6384: }
6385: /* Set all step sizes to 1 */
6386: gsl_vector_set_all (ss, 0.001);
6387:
6388: /* Starting point */
6389:
6390: x = gsl_vector_alloc (NDIM);
6391:
6392: if (x == NULL){
6393: gsl_vector_free(ss);
6394: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
6395: }
6396:
6397: /* Initialize method and iterate */
6398: /* p[1]=0.0268; p[NDIM]=0.083; */
6399: /* gsl_vector_set(x, 0, 0.0268); */
6400: /* gsl_vector_set(x, 1, 0.083); */
6401: gsl_vector_set(x, 0, p[1]);
6402: gsl_vector_set(x, 1, p[2]);
6403:
6404: minex_func.f = &gompertz_f;
6405: minex_func.n = NDIM;
6406: minex_func.params = (void *)&p; /* ??? */
6407:
6408: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
6409: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
6410:
6411: printf("Iterations beginning .....\n\n");
6412: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
6413:
6414: iteri=0;
6415: while (rval == GSL_CONTINUE){
6416: iteri++;
6417: status = gsl_multimin_fminimizer_iterate(sfm);
6418:
6419: if (status) printf("error: %s\n", gsl_strerror (status));
6420: fflush(0);
6421:
6422: if (status)
6423: break;
6424:
6425: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
6426: ssval = gsl_multimin_fminimizer_size (sfm);
6427:
6428: if (rval == GSL_SUCCESS)
6429: printf ("converged to a local maximum at\n");
6430:
6431: printf("%5d ", iteri);
6432: for (it = 0; it < NDIM; it++){
6433: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
6434: }
6435: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
6436: }
6437:
6438: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
6439:
6440: gsl_vector_free(x); /* initial values */
6441: gsl_vector_free(ss); /* inital step size */
6442: for (it=0; it<NDIM; it++){
6443: p[it+1]=gsl_vector_get(sfm->x,it);
6444: fprintf(ficrespow," %.12lf", p[it]);
6445: }
6446: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
6447: #endif
6448: #ifdef POWELL
6449: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
6450: #endif
6451: fclose(ficrespow);
6452:
6453: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
6454:
6455: for(i=1; i <=NDIM; i++)
6456: for(j=i+1;j<=NDIM;j++)
6457: matcov[i][j]=matcov[j][i];
6458:
6459: printf("\nCovariance matrix\n ");
6460: for(i=1; i <=NDIM; i++) {
6461: for(j=1;j<=NDIM;j++){
6462: printf("%f ",matcov[i][j]);
6463: }
6464: printf("\n ");
6465: }
6466:
6467: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
6468: for (i=1;i<=NDIM;i++)
6469: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
6470:
6471: lsurv=vector(1,AGESUP);
6472: lpop=vector(1,AGESUP);
6473: tpop=vector(1,AGESUP);
6474: lsurv[agegomp]=100000;
6475:
6476: for (k=agegomp;k<=AGESUP;k++) {
6477: agemortsup=k;
6478: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
6479: }
6480:
6481: for (k=agegomp;k<agemortsup;k++)
6482: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
6483:
6484: for (k=agegomp;k<agemortsup;k++){
6485: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
6486: sumlpop=sumlpop+lpop[k];
6487: }
6488:
6489: tpop[agegomp]=sumlpop;
6490: for (k=agegomp;k<(agemortsup-3);k++){
6491: /* tpop[k+1]=2;*/
6492: tpop[k+1]=tpop[k]-lpop[k];
6493: }
6494:
6495:
6496: printf("\nAge lx qx dx Lx Tx e(x)\n");
6497: for (k=agegomp;k<(agemortsup-2);k++)
6498: 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]);
6499:
6500:
6501: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6502: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6503:
6504: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
6505: stepm, weightopt,\
6506: model,imx,p,matcov,agemortsup);
6507:
6508: free_vector(lsurv,1,AGESUP);
6509: free_vector(lpop,1,AGESUP);
6510: free_vector(tpop,1,AGESUP);
6511: #ifdef GSL
6512: free_ivector(cens,1,n);
6513: free_vector(agecens,1,n);
6514: free_ivector(dcwave,1,n);
6515: free_matrix(ximort,1,NDIM,1,NDIM);
6516: #endif
6517: } /* Endof if mle==-3 */
6518:
6519: else{ /* For mle >=1 */
6520: globpr=0;/* debug */
6521: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6522: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6523: for (k=1; k<=npar;k++)
6524: printf(" %d %8.5f",k,p[k]);
6525: printf("\n");
6526: globpr=1; /* to print the contributions */
6527: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6528: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6529: for (k=1; k<=npar;k++)
6530: printf(" %d %8.5f",k,p[k]);
6531: printf("\n");
6532: if(mle>=1){ /* Could be 1 or 2 */
6533: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
6534: }
6535:
6536: /*--------- results files --------------*/
6537: 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);
6538:
6539:
6540: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6541: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6542: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6543: for(i=1,jk=1; i <=nlstate; i++){
6544: for(k=1; k <=(nlstate+ndeath); k++){
6545: if (k != i) {
6546: printf("%d%d ",i,k);
6547: fprintf(ficlog,"%d%d ",i,k);
6548: fprintf(ficres,"%1d%1d ",i,k);
6549: for(j=1; j <=ncovmodel; j++){
6550: printf("%lf ",p[jk]);
6551: fprintf(ficlog,"%lf ",p[jk]);
6552: fprintf(ficres,"%lf ",p[jk]);
6553: jk++;
6554: }
6555: printf("\n");
6556: fprintf(ficlog,"\n");
6557: fprintf(ficres,"\n");
6558: }
6559: }
6560: }
6561: if(mle!=0){
6562: /* Computing hessian and covariance matrix */
6563: ftolhess=ftol; /* Usually correct */
6564: hesscov(matcov, p, npar, delti, ftolhess, func);
6565: }
6566: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
6567: printf("# Scales (for hessian or gradient estimation)\n");
6568: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
6569: for(i=1,jk=1; i <=nlstate; i++){
6570: for(j=1; j <=nlstate+ndeath; j++){
6571: if (j!=i) {
6572: fprintf(ficres,"%1d%1d",i,j);
6573: printf("%1d%1d",i,j);
6574: fprintf(ficlog,"%1d%1d",i,j);
6575: for(k=1; k<=ncovmodel;k++){
6576: printf(" %.5e",delti[jk]);
6577: fprintf(ficlog," %.5e",delti[jk]);
6578: fprintf(ficres," %.5e",delti[jk]);
6579: jk++;
6580: }
6581: printf("\n");
6582: fprintf(ficlog,"\n");
6583: fprintf(ficres,"\n");
6584: }
6585: }
6586: }
6587:
6588: 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");
6589: if(mle>=1)
6590: 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");
6591: 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");
6592: /* # 121 Var(a12)\n\ */
6593: /* # 122 Cov(b12,a12) Var(b12)\n\ */
6594: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
6595: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
6596: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
6597: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
6598: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
6599: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
6600:
6601:
6602: /* Just to have a covariance matrix which will be more understandable
6603: even is we still don't want to manage dictionary of variables
6604: */
6605: for(itimes=1;itimes<=2;itimes++){
6606: jj=0;
6607: for(i=1; i <=nlstate; i++){
6608: for(j=1; j <=nlstate+ndeath; j++){
6609: if(j==i) continue;
6610: for(k=1; k<=ncovmodel;k++){
6611: jj++;
6612: ca[0]= k+'a'-1;ca[1]='\0';
6613: if(itimes==1){
6614: if(mle>=1)
6615: printf("#%1d%1d%d",i,j,k);
6616: fprintf(ficlog,"#%1d%1d%d",i,j,k);
6617: fprintf(ficres,"#%1d%1d%d",i,j,k);
6618: }else{
6619: if(mle>=1)
6620: printf("%1d%1d%d",i,j,k);
6621: fprintf(ficlog,"%1d%1d%d",i,j,k);
6622: fprintf(ficres,"%1d%1d%d",i,j,k);
6623: }
6624: ll=0;
6625: for(li=1;li <=nlstate; li++){
6626: for(lj=1;lj <=nlstate+ndeath; lj++){
6627: if(lj==li) continue;
6628: for(lk=1;lk<=ncovmodel;lk++){
6629: ll++;
6630: if(ll<=jj){
6631: cb[0]= lk +'a'-1;cb[1]='\0';
6632: if(ll<jj){
6633: if(itimes==1){
6634: if(mle>=1)
6635: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6636: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6637: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6638: }else{
6639: if(mle>=1)
6640: printf(" %.5e",matcov[jj][ll]);
6641: fprintf(ficlog," %.5e",matcov[jj][ll]);
6642: fprintf(ficres," %.5e",matcov[jj][ll]);
6643: }
6644: }else{
6645: if(itimes==1){
6646: if(mle>=1)
6647: printf(" Var(%s%1d%1d)",ca,i,j);
6648: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
6649: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
6650: }else{
6651: if(mle>=1)
6652: printf(" %.5e",matcov[jj][ll]);
6653: fprintf(ficlog," %.5e",matcov[jj][ll]);
6654: fprintf(ficres," %.5e",matcov[jj][ll]);
6655: }
6656: }
6657: }
6658: } /* end lk */
6659: } /* end lj */
6660: } /* end li */
6661: if(mle>=1)
6662: printf("\n");
6663: fprintf(ficlog,"\n");
6664: fprintf(ficres,"\n");
6665: numlinepar++;
6666: } /* end k*/
6667: } /*end j */
6668: } /* end i */
6669: } /* end itimes */
6670:
6671: fflush(ficlog);
6672: fflush(ficres);
6673:
6674: while((c=getc(ficpar))=='#' && c!= EOF){
6675: ungetc(c,ficpar);
6676: fgets(line, MAXLINE, ficpar);
6677: fputs(line,stdout);
6678: fputs(line,ficparo);
6679: }
6680: ungetc(c,ficpar);
6681:
6682: estepm=0;
6683: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
6684: if (estepm==0 || estepm < stepm) estepm=stepm;
6685: if (fage <= 2) {
6686: bage = ageminpar;
6687: fage = agemaxpar;
6688: }
6689:
6690: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
6691: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6692: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6693:
6694: while((c=getc(ficpar))=='#' && c!= EOF){
6695: ungetc(c,ficpar);
6696: fgets(line, MAXLINE, ficpar);
6697: fputs(line,stdout);
6698: fputs(line,ficparo);
6699: }
6700: ungetc(c,ficpar);
6701:
6702: 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);
6703: 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);
6704: 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);
6705: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
6706: 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);
6707:
6708: while((c=getc(ficpar))=='#' && c!= EOF){
6709: ungetc(c,ficpar);
6710: fgets(line, MAXLINE, ficpar);
6711: fputs(line,stdout);
6712: fputs(line,ficparo);
6713: }
6714: ungetc(c,ficpar);
6715:
6716:
6717: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
6718: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
6719:
6720: fscanf(ficpar,"pop_based=%d\n",&popbased);
6721: fprintf(ficparo,"pop_based=%d\n",popbased);
6722: fprintf(ficres,"pop_based=%d\n",popbased);
6723:
6724: while((c=getc(ficpar))=='#' && c!= EOF){
6725: ungetc(c,ficpar);
6726: fgets(line, MAXLINE, ficpar);
6727: fputs(line,stdout);
6728: fputs(line,ficparo);
6729: }
6730: ungetc(c,ficpar);
6731:
6732: 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);
6733: 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);
6734: 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);
6735: 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);
6736: 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);
6737: /* day and month of proj2 are not used but only year anproj2.*/
6738:
6739:
6740:
6741: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
6742: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
6743:
6744: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6745: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6746:
6747: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
6748: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
6749: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
6750:
6751: /*------------ free_vector -------------*/
6752: /* chdir(path); */
6753:
6754: free_ivector(wav,1,imx);
6755: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
6756: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
6757: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
6758: free_lvector(num,1,n);
6759: free_vector(agedc,1,n);
6760: /*free_matrix(covar,0,NCOVMAX,1,n);*/
6761: /*free_matrix(covar,1,NCOVMAX,1,n);*/
6762: fclose(ficparo);
6763: fclose(ficres);
6764:
6765:
6766: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6767: #include "prevlim.h" /* Use ficrespl, ficlog */
6768: fclose(ficrespl);
6769:
6770: #ifdef FREEEXIT2
6771: #include "freeexit2.h"
6772: #endif
6773:
6774: /*------------- h Pij x at various ages ------------*/
6775: #include "hpijx.h"
6776: fclose(ficrespij);
6777:
6778: /*-------------- Variance of one-step probabilities---*/
6779: k=1;
6780: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
6781:
6782:
6783: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6784: for(i=1;i<=AGESUP;i++)
6785: for(j=1;j<=NCOVMAX;j++)
6786: for(k=1;k<=NCOVMAX;k++)
6787: probs[i][j][k]=0.;
6788:
6789: /*---------- Forecasting ------------------*/
6790: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
6791: if(prevfcast==1){
6792: /* if(stepm ==1){*/
6793: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
6794: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
6795: /* } */
6796: /* else{ */
6797: /* erreur=108; */
6798: /* 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); */
6799: /* 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); */
6800: /* } */
6801: }
6802:
6803:
6804: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
6805:
6806: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
6807: /* 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",\
6808: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
6809: */
6810:
6811: if (mobilav!=0) {
6812: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6813: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
6814: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
6815: printf(" Error in movingaverage mobilav=%d\n",mobilav);
6816: }
6817: }
6818:
6819:
6820: /*---------- Health expectancies, no variances ------------*/
6821:
6822: strcpy(filerese,"e");
6823: strcat(filerese,fileres);
6824: if((ficreseij=fopen(filerese,"w"))==NULL) {
6825: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6826: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6827: }
6828: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
6829: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
6830: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6831: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6832:
6833: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6834: fprintf(ficreseij,"\n#****** ");
6835: for(j=1;j<=cptcoveff;j++) {
6836: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6837: }
6838: fprintf(ficreseij,"******\n");
6839:
6840: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6841: oldm=oldms;savm=savms;
6842: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
6843:
6844: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6845: /*}*/
6846: }
6847: fclose(ficreseij);
6848:
6849:
6850: /*---------- Health expectancies and variances ------------*/
6851:
6852:
6853: strcpy(filerest,"t");
6854: strcat(filerest,fileres);
6855: if((ficrest=fopen(filerest,"w"))==NULL) {
6856: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
6857: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
6858: }
6859: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6860: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6861:
6862:
6863: strcpy(fileresstde,"stde");
6864: strcat(fileresstde,fileres);
6865: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
6866: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6867: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6868: }
6869: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6870: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6871:
6872: strcpy(filerescve,"cve");
6873: strcat(filerescve,fileres);
6874: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
6875: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6876: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6877: }
6878: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6879: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6880:
6881: strcpy(fileresv,"v");
6882: strcat(fileresv,fileres);
6883: if((ficresvij=fopen(fileresv,"w"))==NULL) {
6884: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
6885: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
6886: }
6887: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6888: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6889:
6890: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6891: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6892:
6893: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6894: fprintf(ficrest,"\n#****** ");
6895: for(j=1;j<=cptcoveff;j++)
6896: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6897: fprintf(ficrest,"******\n");
6898:
6899: fprintf(ficresstdeij,"\n#****** ");
6900: fprintf(ficrescveij,"\n#****** ");
6901: for(j=1;j<=cptcoveff;j++) {
6902: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6903: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6904: }
6905: fprintf(ficresstdeij,"******\n");
6906: fprintf(ficrescveij,"******\n");
6907:
6908: fprintf(ficresvij,"\n#****** ");
6909: for(j=1;j<=cptcoveff;j++)
6910: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6911: fprintf(ficresvij,"******\n");
6912:
6913: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6914: oldm=oldms;savm=savms;
6915: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
6916: /*
6917: */
6918: /* goto endfree; */
6919:
6920: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6921: pstamp(ficrest);
6922:
6923:
6924: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
6925: oldm=oldms;savm=savms; /* Segmentation fault */
6926: cptcod= 0; /* To be deleted */
6927: 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 */
6928: 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 ");
6929: if(vpopbased==1)
6930: 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);
6931: else
6932: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
6933: fprintf(ficrest,"# Age e.. (std) ");
6934: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
6935: fprintf(ficrest,"\n");
6936:
6937: epj=vector(1,nlstate+1);
6938: for(age=bage; age <=fage ;age++){
6939: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6940: if (vpopbased==1) {
6941: if(mobilav ==0){
6942: for(i=1; i<=nlstate;i++)
6943: prlim[i][i]=probs[(int)age][i][k];
6944: }else{ /* mobilav */
6945: for(i=1; i<=nlstate;i++)
6946: prlim[i][i]=mobaverage[(int)age][i][k];
6947: }
6948: }
6949:
6950: fprintf(ficrest," %4.0f",age);
6951: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
6952: for(i=1, epj[j]=0.;i <=nlstate;i++) {
6953: epj[j] += prlim[i][i]*eij[i][j][(int)age];
6954: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
6955: }
6956: epj[nlstate+1] +=epj[j];
6957: }
6958:
6959: for(i=1, vepp=0.;i <=nlstate;i++)
6960: for(j=1;j <=nlstate;j++)
6961: vepp += vareij[i][j][(int)age];
6962: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
6963: for(j=1;j <=nlstate;j++){
6964: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
6965: }
6966: fprintf(ficrest,"\n");
6967: }
6968: }
6969: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6970: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6971: free_vector(epj,1,nlstate+1);
6972: /*}*/
6973: }
6974: free_vector(weight,1,n);
6975: free_imatrix(Tvard,1,NCOVMAX,1,2);
6976: free_imatrix(s,1,maxwav+1,1,n);
6977: free_matrix(anint,1,maxwav,1,n);
6978: free_matrix(mint,1,maxwav,1,n);
6979: free_ivector(cod,1,n);
6980: free_ivector(tab,1,NCOVMAX);
6981: fclose(ficresstdeij);
6982: fclose(ficrescveij);
6983: fclose(ficresvij);
6984: fclose(ficrest);
6985: fclose(ficpar);
6986:
6987: /*------- Variance of period (stable) prevalence------*/
6988:
6989: strcpy(fileresvpl,"vpl");
6990: strcat(fileresvpl,fileres);
6991: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
6992: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
6993: exit(0);
6994: }
6995: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
6996:
6997: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6998: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6999:
7000: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7001: fprintf(ficresvpl,"\n#****** ");
7002: for(j=1;j<=cptcoveff;j++)
7003: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7004: fprintf(ficresvpl,"******\n");
7005:
7006: varpl=matrix(1,nlstate,(int) bage, (int) fage);
7007: oldm=oldms;savm=savms;
7008: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
7009: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
7010: /*}*/
7011: }
7012:
7013: fclose(ficresvpl);
7014:
7015: /*---------- End : free ----------------*/
7016: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7017: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7018: } /* mle==-3 arrives here for freeing */
7019: /* endfree:*/
7020: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
7021: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
7022: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
7023: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
7024: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
7025: free_matrix(covar,0,NCOVMAX,1,n);
7026: free_matrix(matcov,1,npar,1,npar);
7027: /*free_vector(delti,1,npar);*/
7028: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7029: free_matrix(agev,1,maxwav,1,imx);
7030: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7031:
7032: free_ivector(ncodemax,1,NCOVMAX);
7033: free_ivector(Tvar,1,NCOVMAX);
7034: free_ivector(Tprod,1,NCOVMAX);
7035: free_ivector(Tvaraff,1,NCOVMAX);
7036: free_ivector(Tage,1,NCOVMAX);
7037:
7038: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
7039: free_imatrix(codtab,1,100,1,10);
7040: fflush(fichtm);
7041: fflush(ficgp);
7042:
7043:
7044: if((nberr >0) || (nbwarn>0)){
7045: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
7046: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
7047: }else{
7048: printf("End of Imach\n");
7049: fprintf(ficlog,"End of Imach\n");
7050: }
7051: printf("See log file on %s\n",filelog);
7052: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
7053: /*(void) gettimeofday(&end_time,&tzp);*/
7054: rend_time = time(NULL);
7055: end_time = *localtime(&rend_time);
7056: /* tml = *localtime(&end_time.tm_sec); */
7057: strcpy(strtend,asctime(&end_time));
7058: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
7059: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
7060: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
7061:
7062: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
7063: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
7064: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
7065: /* printf("Total time was %d uSec.\n", total_usecs);*/
7066: /* if(fileappend(fichtm,optionfilehtm)){ */
7067: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7068: fclose(fichtm);
7069: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7070: fclose(fichtmcov);
7071: fclose(ficgp);
7072: fclose(ficlog);
7073: /*------ End -----------*/
7074:
7075:
7076: printf("Before Current directory %s!\n",pathcd);
7077: if(chdir(pathcd) != 0)
7078: printf("Can't move to directory %s!\n",path);
7079: if(getcwd(pathcd,MAXLINE) > 0)
7080: printf("Current directory %s!\n",pathcd);
7081: /*strcat(plotcmd,CHARSEPARATOR);*/
7082: sprintf(plotcmd,"gnuplot");
7083: #ifdef _WIN32
7084: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
7085: #endif
7086: if(!stat(plotcmd,&info)){
7087: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
7088: if(!stat(getenv("GNUPLOTBIN"),&info)){
7089: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
7090: }else
7091: strcpy(pplotcmd,plotcmd);
7092: #ifdef __unix
7093: strcpy(plotcmd,GNUPLOTPROGRAM);
7094: if(!stat(plotcmd,&info)){
7095: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
7096: }else
7097: strcpy(pplotcmd,plotcmd);
7098: #endif
7099: }else
7100: strcpy(pplotcmd,plotcmd);
7101:
7102: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
7103: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
7104:
7105: if((outcmd=system(plotcmd)) != 0){
7106: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
7107: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
7108: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
7109: if((outcmd=system(plotcmd)) != 0)
7110: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
7111: }
7112: printf(" Successful, please wait...");
7113: while (z[0] != 'q') {
7114: /* chdir(path); */
7115: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
7116: scanf("%s",z);
7117: /* if (z[0] == 'c') system("./imach"); */
7118: if (z[0] == 'e') {
7119: #ifdef __APPLE__
7120: sprintf(pplotcmd, "open %s", optionfilehtm);
7121: #elif __linux
7122: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
7123: #else
7124: sprintf(pplotcmd, "%s", optionfilehtm);
7125: #endif
7126: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
7127: system(pplotcmd);
7128: }
7129: else if (z[0] == 'g') system(plotcmd);
7130: else if (z[0] == 'q') exit(0);
7131: }
7132: end:
7133: while (z[0] != 'q') {
7134: printf("\nType q for exiting: ");
7135: scanf("%s",z);
7136: }
7137: }
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