1: /* $Id: imach.c,v 1.153 2014/06/20 16:45:46 brouard Exp $
2: $State: Exp $
3: $Log: imach.c,v $
4: Revision 1.153 2014/06/20 16:45:46 brouard
5: Summary: If 3 live state, convergence to period prevalence on same graph
6: Author: Brouard
7:
8: Revision 1.152 2014/06/18 17:54:09 brouard
9: Summary: open browser, use gnuplot on same dir than imach if not found in the path
10:
11: Revision 1.151 2014/06/18 16:43:30 brouard
12: *** empty log message ***
13:
14: Revision 1.150 2014/06/18 16:42:35 brouard
15: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
16: Author: brouard
17:
18: Revision 1.149 2014/06/18 15:51:14 brouard
19: Summary: Some fixes in parameter files errors
20: Author: Nicolas Brouard
21:
22: Revision 1.148 2014/06/17 17:38:48 brouard
23: Summary: Nothing new
24: Author: Brouard
25:
26: Just a new packaging for OS/X version 0.98nS
27:
28: Revision 1.147 2014/06/16 10:33:11 brouard
29: *** empty log message ***
30:
31: Revision 1.146 2014/06/16 10:20:28 brouard
32: Summary: Merge
33: Author: Brouard
34:
35: Merge, before building revised version.
36:
37: Revision 1.145 2014/06/10 21:23:15 brouard
38: Summary: Debugging with valgrind
39: Author: Nicolas Brouard
40:
41: Lot of changes in order to output the results with some covariates
42: After the Edimburgh REVES conference 2014, it seems mandatory to
43: improve the code.
44: No more memory valgrind error but a lot has to be done in order to
45: continue the work of splitting the code into subroutines.
46: Also, decodemodel has been improved. Tricode is still not
47: optimal. nbcode should be improved. Documentation has been added in
48: the source code.
49:
50: Revision 1.143 2014/01/26 09:45:38 brouard
51: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
52:
53: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
54: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
55:
56: Revision 1.142 2014/01/26 03:57:36 brouard
57: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
58:
59: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
60:
61: Revision 1.141 2014/01/26 02:42:01 brouard
62: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
63:
64: Revision 1.140 2011/09/02 10:37:54 brouard
65: Summary: times.h is ok with mingw32 now.
66:
67: Revision 1.139 2010/06/14 07:50:17 brouard
68: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
69: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
70:
71: Revision 1.138 2010/04/30 18:19:40 brouard
72: *** empty log message ***
73:
74: Revision 1.137 2010/04/29 18:11:38 brouard
75: (Module): Checking covariates for more complex models
76: than V1+V2. A lot of change to be done. Unstable.
77:
78: Revision 1.136 2010/04/26 20:30:53 brouard
79: (Module): merging some libgsl code. Fixing computation
80: of likelione (using inter/intrapolation if mle = 0) in order to
81: get same likelihood as if mle=1.
82: Some cleaning of code and comments added.
83:
84: Revision 1.135 2009/10/29 15:33:14 brouard
85: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
86:
87: Revision 1.134 2009/10/29 13:18:53 brouard
88: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
89:
90: Revision 1.133 2009/07/06 10:21:25 brouard
91: just nforces
92:
93: Revision 1.132 2009/07/06 08:22:05 brouard
94: Many tings
95:
96: Revision 1.131 2009/06/20 16:22:47 brouard
97: Some dimensions resccaled
98:
99: Revision 1.130 2009/05/26 06:44:34 brouard
100: (Module): Max Covariate is now set to 20 instead of 8. A
101: lot of cleaning with variables initialized to 0. Trying to make
102: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
103:
104: Revision 1.129 2007/08/31 13:49:27 lievre
105: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
106:
107: Revision 1.128 2006/06/30 13:02:05 brouard
108: (Module): Clarifications on computing e.j
109:
110: Revision 1.127 2006/04/28 18:11:50 brouard
111: (Module): Yes the sum of survivors was wrong since
112: imach-114 because nhstepm was no more computed in the age
113: loop. Now we define nhstepma in the age loop.
114: (Module): In order to speed up (in case of numerous covariates) we
115: compute health expectancies (without variances) in a first step
116: and then all the health expectancies with variances or standard
117: deviation (needs data from the Hessian matrices) which slows the
118: computation.
119: In the future we should be able to stop the program is only health
120: expectancies and graph are needed without standard deviations.
121:
122: Revision 1.126 2006/04/28 17:23:28 brouard
123: (Module): Yes the sum of survivors was wrong since
124: imach-114 because nhstepm was no more computed in the age
125: loop. Now we define nhstepma in the age loop.
126: Version 0.98h
127:
128: Revision 1.125 2006/04/04 15:20:31 lievre
129: Errors in calculation of health expectancies. Age was not initialized.
130: Forecasting file added.
131:
132: Revision 1.124 2006/03/22 17:13:53 lievre
133: Parameters are printed with %lf instead of %f (more numbers after the comma).
134: The log-likelihood is printed in the log file
135:
136: Revision 1.123 2006/03/20 10:52:43 brouard
137: * imach.c (Module): <title> changed, corresponds to .htm file
138: name. <head> headers where missing.
139:
140: * imach.c (Module): Weights can have a decimal point as for
141: English (a comma might work with a correct LC_NUMERIC environment,
142: otherwise the weight is truncated).
143: Modification of warning when the covariates values are not 0 or
144: 1.
145: Version 0.98g
146:
147: Revision 1.122 2006/03/20 09:45:41 brouard
148: (Module): Weights can have a decimal point as for
149: English (a comma might work with a correct LC_NUMERIC environment,
150: otherwise the weight is truncated).
151: Modification of warning when the covariates values are not 0 or
152: 1.
153: Version 0.98g
154:
155: Revision 1.121 2006/03/16 17:45:01 lievre
156: * imach.c (Module): Comments concerning covariates added
157:
158: * imach.c (Module): refinements in the computation of lli if
159: status=-2 in order to have more reliable computation if stepm is
160: not 1 month. Version 0.98f
161:
162: Revision 1.120 2006/03/16 15:10:38 lievre
163: (Module): refinements in the computation of lli if
164: status=-2 in order to have more reliable computation if stepm is
165: not 1 month. Version 0.98f
166:
167: Revision 1.119 2006/03/15 17:42:26 brouard
168: (Module): Bug if status = -2, the loglikelihood was
169: computed as likelihood omitting the logarithm. Version O.98e
170:
171: Revision 1.118 2006/03/14 18:20:07 brouard
172: (Module): varevsij Comments added explaining the second
173: table of variances if popbased=1 .
174: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
175: (Module): Function pstamp added
176: (Module): Version 0.98d
177:
178: Revision 1.117 2006/03/14 17:16:22 brouard
179: (Module): varevsij Comments added explaining the second
180: table of variances if popbased=1 .
181: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
182: (Module): Function pstamp added
183: (Module): Version 0.98d
184:
185: Revision 1.116 2006/03/06 10:29:27 brouard
186: (Module): Variance-covariance wrong links and
187: varian-covariance of ej. is needed (Saito).
188:
189: Revision 1.115 2006/02/27 12:17:45 brouard
190: (Module): One freematrix added in mlikeli! 0.98c
191:
192: Revision 1.114 2006/02/26 12:57:58 brouard
193: (Module): Some improvements in processing parameter
194: filename with strsep.
195:
196: Revision 1.113 2006/02/24 14:20:24 brouard
197: (Module): Memory leaks checks with valgrind and:
198: datafile was not closed, some imatrix were not freed and on matrix
199: allocation too.
200:
201: Revision 1.112 2006/01/30 09:55:26 brouard
202: (Module): Back to gnuplot.exe instead of wgnuplot.exe
203:
204: Revision 1.111 2006/01/25 20:38:18 brouard
205: (Module): Lots of cleaning and bugs added (Gompertz)
206: (Module): Comments can be added in data file. Missing date values
207: can be a simple dot '.'.
208:
209: Revision 1.110 2006/01/25 00:51:50 brouard
210: (Module): Lots of cleaning and bugs added (Gompertz)
211:
212: Revision 1.109 2006/01/24 19:37:15 brouard
213: (Module): Comments (lines starting with a #) are allowed in data.
214:
215: Revision 1.108 2006/01/19 18:05:42 lievre
216: Gnuplot problem appeared...
217: To be fixed
218:
219: Revision 1.107 2006/01/19 16:20:37 brouard
220: Test existence of gnuplot in imach path
221:
222: Revision 1.106 2006/01/19 13:24:36 brouard
223: Some cleaning and links added in html output
224:
225: Revision 1.105 2006/01/05 20:23:19 lievre
226: *** empty log message ***
227:
228: Revision 1.104 2005/09/30 16:11:43 lievre
229: (Module): sump fixed, loop imx fixed, and simplifications.
230: (Module): If the status is missing at the last wave but we know
231: that the person is alive, then we can code his/her status as -2
232: (instead of missing=-1 in earlier versions) and his/her
233: contributions to the likelihood is 1 - Prob of dying from last
234: health status (= 1-p13= p11+p12 in the easiest case of somebody in
235: the healthy state at last known wave). Version is 0.98
236:
237: Revision 1.103 2005/09/30 15:54:49 lievre
238: (Module): sump fixed, loop imx fixed, and simplifications.
239:
240: Revision 1.102 2004/09/15 17:31:30 brouard
241: Add the possibility to read data file including tab characters.
242:
243: Revision 1.101 2004/09/15 10:38:38 brouard
244: Fix on curr_time
245:
246: Revision 1.100 2004/07/12 18:29:06 brouard
247: Add version for Mac OS X. Just define UNIX in Makefile
248:
249: Revision 1.99 2004/06/05 08:57:40 brouard
250: *** empty log message ***
251:
252: Revision 1.98 2004/05/16 15:05:56 brouard
253: New version 0.97 . First attempt to estimate force of mortality
254: directly from the data i.e. without the need of knowing the health
255: state at each age, but using a Gompertz model: log u =a + b*age .
256: This is the basic analysis of mortality and should be done before any
257: other analysis, in order to test if the mortality estimated from the
258: cross-longitudinal survey is different from the mortality estimated
259: from other sources like vital statistic data.
260:
261: The same imach parameter file can be used but the option for mle should be -3.
262:
263: Agnès, who wrote this part of the code, tried to keep most of the
264: former routines in order to include the new code within the former code.
265:
266: The output is very simple: only an estimate of the intercept and of
267: the slope with 95% confident intervals.
268:
269: Current limitations:
270: A) Even if you enter covariates, i.e. with the
271: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
272: B) There is no computation of Life Expectancy nor Life Table.
273:
274: Revision 1.97 2004/02/20 13:25:42 lievre
275: Version 0.96d. Population forecasting command line is (temporarily)
276: suppressed.
277:
278: Revision 1.96 2003/07/15 15:38:55 brouard
279: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
280: rewritten within the same printf. Workaround: many printfs.
281:
282: Revision 1.95 2003/07/08 07:54:34 brouard
283: * imach.c (Repository):
284: (Repository): Using imachwizard code to output a more meaningful covariance
285: matrix (cov(a12,c31) instead of numbers.
286:
287: Revision 1.94 2003/06/27 13:00:02 brouard
288: Just cleaning
289:
290: Revision 1.93 2003/06/25 16:33:55 brouard
291: (Module): On windows (cygwin) function asctime_r doesn't
292: exist so I changed back to asctime which exists.
293: (Module): Version 0.96b
294:
295: Revision 1.92 2003/06/25 16:30:45 brouard
296: (Module): On windows (cygwin) function asctime_r doesn't
297: exist so I changed back to asctime which exists.
298:
299: Revision 1.91 2003/06/25 15:30:29 brouard
300: * imach.c (Repository): Duplicated warning errors corrected.
301: (Repository): Elapsed time after each iteration is now output. It
302: helps to forecast when convergence will be reached. Elapsed time
303: is stamped in powell. We created a new html file for the graphs
304: concerning matrix of covariance. It has extension -cov.htm.
305:
306: Revision 1.90 2003/06/24 12:34:15 brouard
307: (Module): Some bugs corrected for windows. Also, when
308: mle=-1 a template is output in file "or"mypar.txt with the design
309: of the covariance matrix to be input.
310:
311: Revision 1.89 2003/06/24 12:30:52 brouard
312: (Module): Some bugs corrected for windows. Also, when
313: mle=-1 a template is output in file "or"mypar.txt with the design
314: of the covariance matrix to be input.
315:
316: Revision 1.88 2003/06/23 17:54:56 brouard
317: * 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.
318:
319: Revision 1.87 2003/06/18 12:26:01 brouard
320: Version 0.96
321:
322: Revision 1.86 2003/06/17 20:04:08 brouard
323: (Module): Change position of html and gnuplot routines and added
324: routine fileappend.
325:
326: Revision 1.85 2003/06/17 13:12:43 brouard
327: * imach.c (Repository): Check when date of death was earlier that
328: current date of interview. It may happen when the death was just
329: prior to the death. In this case, dh was negative and likelihood
330: was wrong (infinity). We still send an "Error" but patch by
331: assuming that the date of death was just one stepm after the
332: interview.
333: (Repository): Because some people have very long ID (first column)
334: we changed int to long in num[] and we added a new lvector for
335: memory allocation. But we also truncated to 8 characters (left
336: truncation)
337: (Repository): No more line truncation errors.
338:
339: Revision 1.84 2003/06/13 21:44:43 brouard
340: * imach.c (Repository): Replace "freqsummary" at a correct
341: place. It differs from routine "prevalence" which may be called
342: many times. Probs is memory consuming and must be used with
343: parcimony.
344: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
345:
346: Revision 1.83 2003/06/10 13:39:11 lievre
347: *** empty log message ***
348:
349: Revision 1.82 2003/06/05 15:57:20 brouard
350: Add log in imach.c and fullversion number is now printed.
351:
352: */
353: /*
354: Interpolated Markov Chain
355:
356: Short summary of the programme:
357:
358: This program computes Healthy Life Expectancies from
359: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
360: first survey ("cross") where individuals from different ages are
361: interviewed on their health status or degree of disability (in the
362: case of a health survey which is our main interest) -2- at least a
363: second wave of interviews ("longitudinal") which measure each change
364: (if any) in individual health status. Health expectancies are
365: computed from the time spent in each health state according to a
366: model. More health states you consider, more time is necessary to reach the
367: Maximum Likelihood of the parameters involved in the model. The
368: simplest model is the multinomial logistic model where pij is the
369: probability to be observed in state j at the second wave
370: conditional to be observed in state i at the first wave. Therefore
371: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
372: 'age' is age and 'sex' is a covariate. If you want to have a more
373: complex model than "constant and age", you should modify the program
374: where the markup *Covariates have to be included here again* invites
375: you to do it. More covariates you add, slower the
376: convergence.
377:
378: The advantage of this computer programme, compared to a simple
379: multinomial logistic model, is clear when the delay between waves is not
380: identical for each individual. Also, if a individual missed an
381: intermediate interview, the information is lost, but taken into
382: account using an interpolation or extrapolation.
383:
384: hPijx is the probability to be observed in state i at age x+h
385: conditional to the observed state i at age x. The delay 'h' can be
386: split into an exact number (nh*stepm) of unobserved intermediate
387: states. This elementary transition (by month, quarter,
388: semester or year) is modelled as a multinomial logistic. The hPx
389: matrix is simply the matrix product of nh*stepm elementary matrices
390: and the contribution of each individual to the likelihood is simply
391: hPijx.
392:
393: Also this programme outputs the covariance matrix of the parameters but also
394: of the life expectancies. It also computes the period (stable) prevalence.
395:
396: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
397: Institut national d'études démographiques, Paris.
398: This software have been partly granted by Euro-REVES, a concerted action
399: from the European Union.
400: It is copyrighted identically to a GNU software product, ie programme and
401: software can be distributed freely for non commercial use. Latest version
402: can be accessed at http://euroreves.ined.fr/imach .
403:
404: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
405: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
406:
407: **********************************************************************/
408: /*
409: main
410: read parameterfile
411: read datafile
412: concatwav
413: freqsummary
414: if (mle >= 1)
415: mlikeli
416: print results files
417: if mle==1
418: computes hessian
419: read end of parameter file: agemin, agemax, bage, fage, estepm
420: begin-prev-date,...
421: open gnuplot file
422: open html file
423: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
424: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
425: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
426: freexexit2 possible for memory heap.
427:
428: h Pij x | pij_nom ficrestpij
429: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
430: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
431: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
432:
433: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
434: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
435: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
436: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
437: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
438:
439: forecasting if prevfcast==1 prevforecast call prevalence()
440: health expectancies
441: Variance-covariance of DFLE
442: prevalence()
443: movingaverage()
444: varevsij()
445: if popbased==1 varevsij(,popbased)
446: total life expectancies
447: Variance of period (stable) prevalence
448: end
449: */
450:
451:
452:
453:
454: #include <math.h>
455: #include <stdio.h>
456: #include <stdlib.h>
457: #include <string.h>
458: #include <unistd.h>
459:
460: #include <limits.h>
461: #include <sys/types.h>
462: #include <sys/stat.h>
463: #include <errno.h>
464: extern int errno;
465:
466: #ifdef LINUX
467: #include <time.h>
468: #include "timeval.h"
469: #else
470: #include <sys/time.h>
471: #endif
472:
473: #ifdef GSL
474: #include <gsl/gsl_errno.h>
475: #include <gsl/gsl_multimin.h>
476: #endif
477:
478: /* #include <libintl.h> */
479: /* #define _(String) gettext (String) */
480:
481: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
482:
483: #define GNUPLOTPROGRAM "gnuplot"
484: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
485: #define FILENAMELENGTH 132
486:
487: #define GLOCK_ERROR_NOPATH -1 /* empty path */
488: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
489:
490: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
491: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
492:
493: #define NINTERVMAX 8
494: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
495: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
496: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
497: #define codtabm(h,k) 1 & (h-1) >> (k-1) ;
498: #define MAXN 20000
499: #define YEARM 12. /**< Number of months per year */
500: #define AGESUP 130
501: #define AGEBASE 40
502: #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */
503: #ifdef UNIX
504: #define DIRSEPARATOR '/'
505: #define CHARSEPARATOR "/"
506: #define ODIRSEPARATOR '\\'
507: #else
508: #define DIRSEPARATOR '\\'
509: #define CHARSEPARATOR "\\"
510: #define ODIRSEPARATOR '/'
511: #endif
512:
513: /* $Id: imach.c,v 1.153 2014/06/20 16:45:46 brouard Exp $ */
514: /* $State: Exp $ */
515:
516: char version[]="Imach version 0.98nT, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
517: char fullversion[]="$Revision: 1.153 $ $Date: 2014/06/20 16:45:46 $";
518: char strstart[80];
519: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
520: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
521: int nvar=0, nforce=0; /* Number of variables, number of forces */
522: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
523: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
524: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
525: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
526: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
527: int cptcovprodnoage=0; /**< Number of covariate products without age */
528: int cptcoveff=0; /* Total number of covariates to vary for printing results */
529: int cptcov=0; /* Working variable */
530: int npar=NPARMAX;
531: int nlstate=2; /* Number of live states */
532: int ndeath=1; /* Number of dead states */
533: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
534: int popbased=0;
535:
536: int *wav; /* Number of waves for this individuual 0 is possible */
537: int maxwav=0; /* Maxim number of waves */
538: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
539: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
540: int gipmx=0, gsw=0; /* Global variables on the number of contributions
541: to the likelihood and the sum of weights (done by funcone)*/
542: int mle=1, weightopt=0;
543: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
544: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
545: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
546: * wave mi and wave mi+1 is not an exact multiple of stepm. */
547: double jmean=1; /* Mean space between 2 waves */
548: double **matprod2(); /* test */
549: double **oldm, **newm, **savm; /* Working pointers to matrices */
550: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
551: /*FILE *fic ; */ /* Used in readdata only */
552: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
553: FILE *ficlog, *ficrespow;
554: int globpr=0; /* Global variable for printing or not */
555: double fretone; /* Only one call to likelihood */
556: long ipmx=0; /* Number of contributions */
557: double sw; /* Sum of weights */
558: char filerespow[FILENAMELENGTH];
559: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
560: FILE *ficresilk;
561: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
562: FILE *ficresprobmorprev;
563: FILE *fichtm, *fichtmcov; /* Html File */
564: FILE *ficreseij;
565: char filerese[FILENAMELENGTH];
566: FILE *ficresstdeij;
567: char fileresstde[FILENAMELENGTH];
568: FILE *ficrescveij;
569: char filerescve[FILENAMELENGTH];
570: FILE *ficresvij;
571: char fileresv[FILENAMELENGTH];
572: FILE *ficresvpl;
573: char fileresvpl[FILENAMELENGTH];
574: char title[MAXLINE];
575: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
576: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
577: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
578: char command[FILENAMELENGTH];
579: int outcmd=0;
580:
581: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
582:
583: char filelog[FILENAMELENGTH]; /* Log file */
584: char filerest[FILENAMELENGTH];
585: char fileregp[FILENAMELENGTH];
586: char popfile[FILENAMELENGTH];
587:
588: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
589:
590: struct timeval start_time, end_time, curr_time, last_time, forecast_time;
591: struct timezone tzp;
592: extern int gettimeofday();
593: struct tm tmg, tm, tmf, *gmtime(), *localtime();
594: long time_value;
595: extern long time();
596: char strcurr[80], strfor[80];
597:
598: char *endptr;
599: long lval;
600: double dval;
601:
602: #define NR_END 1
603: #define FREE_ARG char*
604: #define FTOL 1.0e-10
605:
606: #define NRANSI
607: #define ITMAX 200
608:
609: #define TOL 2.0e-4
610:
611: #define CGOLD 0.3819660
612: #define ZEPS 1.0e-10
613: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
614:
615: #define GOLD 1.618034
616: #define GLIMIT 100.0
617: #define TINY 1.0e-20
618:
619: static double maxarg1,maxarg2;
620: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
621: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
622:
623: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
624: #define rint(a) floor(a+0.5)
625:
626: static double sqrarg;
627: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
628: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
629: int agegomp= AGEGOMP;
630:
631: int imx;
632: int stepm=1;
633: /* Stepm, step in month: minimum step interpolation*/
634:
635: int estepm;
636: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
637:
638: int m,nb;
639: long *num;
640: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
641: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
642: double **pmmij, ***probs;
643: double *ageexmed,*agecens;
644: double dateintmean=0;
645:
646: double *weight;
647: int **s; /* Status */
648: double *agedc;
649: double **covar; /**< covar[j,i], value of jth covariate for individual i,
650: * covar=matrix(0,NCOVMAX,1,n);
651: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
652: double idx;
653: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
654: int *Ndum; /** Freq of modality (tricode */
655: int **codtab; /**< codtab=imatrix(1,100,1,10); */
656: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
657: double *lsurv, *lpop, *tpop;
658:
659: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
660: double ftolhess; /**< Tolerance for computing hessian */
661:
662: /**************** split *************************/
663: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
664: {
665: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
666: the name of the file (name), its extension only (ext) and its first part of the name (finame)
667: */
668: char *ss; /* pointer */
669: int l1, l2; /* length counters */
670:
671: l1 = strlen(path ); /* length of path */
672: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
673: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
674: if ( ss == NULL ) { /* no directory, so determine current directory */
675: strcpy( name, path ); /* we got the fullname name because no directory */
676: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
677: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
678: /* get current working directory */
679: /* extern char* getcwd ( char *buf , int len);*/
680: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
681: return( GLOCK_ERROR_GETCWD );
682: }
683: /* got dirc from getcwd*/
684: printf(" DIRC = %s \n",dirc);
685: } else { /* strip direcotry from path */
686: ss++; /* after this, the filename */
687: l2 = strlen( ss ); /* length of filename */
688: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
689: strcpy( name, ss ); /* save file name */
690: strncpy( dirc, path, l1 - l2 ); /* now the directory */
691: dirc[l1-l2] = 0; /* add zero */
692: printf(" DIRC2 = %s \n",dirc);
693: }
694: /* We add a separator at the end of dirc if not exists */
695: l1 = strlen( dirc ); /* length of directory */
696: if( dirc[l1-1] != DIRSEPARATOR ){
697: dirc[l1] = DIRSEPARATOR;
698: dirc[l1+1] = 0;
699: printf(" DIRC3 = %s \n",dirc);
700: }
701: ss = strrchr( name, '.' ); /* find last / */
702: if (ss >0){
703: ss++;
704: strcpy(ext,ss); /* save extension */
705: l1= strlen( name);
706: l2= strlen(ss)+1;
707: strncpy( finame, name, l1-l2);
708: finame[l1-l2]= 0;
709: }
710:
711: return( 0 ); /* we're done */
712: }
713:
714:
715: /******************************************/
716:
717: void replace_back_to_slash(char *s, char*t)
718: {
719: int i;
720: int lg=0;
721: i=0;
722: lg=strlen(t);
723: for(i=0; i<= lg; i++) {
724: (s[i] = t[i]);
725: if (t[i]== '\\') s[i]='/';
726: }
727: }
728:
729: char *trimbb(char *out, char *in)
730: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
731: char *s;
732: s=out;
733: while (*in != '\0'){
734: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
735: in++;
736: }
737: *out++ = *in++;
738: }
739: *out='\0';
740: return s;
741: }
742:
743: char *cutl(char *blocc, char *alocc, char *in, char occ)
744: {
745: /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ'
746: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
747: gives blocc="abcdef2ghi" and alocc="j".
748: If occ is not found blocc is null and alocc is equal to in. Returns blocc
749: */
750: char *s, *t, *bl;
751: t=in;s=in;
752: while ((*in != occ) && (*in != '\0')){
753: *alocc++ = *in++;
754: }
755: if( *in == occ){
756: *(alocc)='\0';
757: s=++in;
758: }
759:
760: if (s == t) {/* occ not found */
761: *(alocc-(in-s))='\0';
762: in=s;
763: }
764: while ( *in != '\0'){
765: *blocc++ = *in++;
766: }
767:
768: *blocc='\0';
769: return t;
770: }
771: char *cutv(char *blocc, char *alocc, char *in, char occ)
772: {
773: /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
774: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
775: gives blocc="abcdef2ghi" and alocc="j".
776: If occ is not found blocc is null and alocc is equal to in. Returns alocc
777: */
778: char *s, *t;
779: t=in;s=in;
780: while (*in != '\0'){
781: while( *in == occ){
782: *blocc++ = *in++;
783: s=in;
784: }
785: *blocc++ = *in++;
786: }
787: if (s == t) /* occ not found */
788: *(blocc-(in-s))='\0';
789: else
790: *(blocc-(in-s)-1)='\0';
791: in=s;
792: while ( *in != '\0'){
793: *alocc++ = *in++;
794: }
795:
796: *alocc='\0';
797: return s;
798: }
799:
800: int nbocc(char *s, char occ)
801: {
802: int i,j=0;
803: int lg=20;
804: i=0;
805: lg=strlen(s);
806: for(i=0; i<= lg; i++) {
807: if (s[i] == occ ) j++;
808: }
809: return j;
810: }
811:
812: /* void cutv(char *u,char *v, char*t, char occ) */
813: /* { */
814: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
815: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
816: /* gives u="abcdef2ghi" and v="j" *\/ */
817: /* int i,lg,j,p=0; */
818: /* i=0; */
819: /* lg=strlen(t); */
820: /* for(j=0; j<=lg-1; j++) { */
821: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
822: /* } */
823:
824: /* for(j=0; j<p; j++) { */
825: /* (u[j] = t[j]); */
826: /* } */
827: /* u[p]='\0'; */
828:
829: /* for(j=0; j<= lg; j++) { */
830: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
831: /* } */
832: /* } */
833:
834: /********************** nrerror ********************/
835:
836: void nrerror(char error_text[])
837: {
838: fprintf(stderr,"ERREUR ...\n");
839: fprintf(stderr,"%s\n",error_text);
840: exit(EXIT_FAILURE);
841: }
842: /*********************** vector *******************/
843: double *vector(int nl, int nh)
844: {
845: double *v;
846: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
847: if (!v) nrerror("allocation failure in vector");
848: return v-nl+NR_END;
849: }
850:
851: /************************ free vector ******************/
852: void free_vector(double*v, int nl, int nh)
853: {
854: free((FREE_ARG)(v+nl-NR_END));
855: }
856:
857: /************************ivector *******************************/
858: int *ivector(long nl,long nh)
859: {
860: int *v;
861: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
862: if (!v) nrerror("allocation failure in ivector");
863: return v-nl+NR_END;
864: }
865:
866: /******************free ivector **************************/
867: void free_ivector(int *v, long nl, long nh)
868: {
869: free((FREE_ARG)(v+nl-NR_END));
870: }
871:
872: /************************lvector *******************************/
873: long *lvector(long nl,long nh)
874: {
875: long *v;
876: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
877: if (!v) nrerror("allocation failure in ivector");
878: return v-nl+NR_END;
879: }
880:
881: /******************free lvector **************************/
882: void free_lvector(long *v, long nl, long nh)
883: {
884: free((FREE_ARG)(v+nl-NR_END));
885: }
886:
887: /******************* imatrix *******************************/
888: int **imatrix(long nrl, long nrh, long ncl, long nch)
889: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
890: {
891: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
892: int **m;
893:
894: /* allocate pointers to rows */
895: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
896: if (!m) nrerror("allocation failure 1 in matrix()");
897: m += NR_END;
898: m -= nrl;
899:
900:
901: /* allocate rows and set pointers to them */
902: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
903: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
904: m[nrl] += NR_END;
905: m[nrl] -= ncl;
906:
907: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
908:
909: /* return pointer to array of pointers to rows */
910: return m;
911: }
912:
913: /****************** free_imatrix *************************/
914: void free_imatrix(m,nrl,nrh,ncl,nch)
915: int **m;
916: long nch,ncl,nrh,nrl;
917: /* free an int matrix allocated by imatrix() */
918: {
919: free((FREE_ARG) (m[nrl]+ncl-NR_END));
920: free((FREE_ARG) (m+nrl-NR_END));
921: }
922:
923: /******************* matrix *******************************/
924: double **matrix(long nrl, long nrh, long ncl, long nch)
925: {
926: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
927: double **m;
928:
929: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
930: if (!m) nrerror("allocation failure 1 in matrix()");
931: m += NR_END;
932: m -= nrl;
933:
934: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
935: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
936: m[nrl] += NR_END;
937: m[nrl] -= ncl;
938:
939: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
940: return m;
941: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
942: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
943: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
944: */
945: }
946:
947: /*************************free matrix ************************/
948: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
949: {
950: free((FREE_ARG)(m[nrl]+ncl-NR_END));
951: free((FREE_ARG)(m+nrl-NR_END));
952: }
953:
954: /******************* ma3x *******************************/
955: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
956: {
957: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
958: double ***m;
959:
960: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
961: if (!m) nrerror("allocation failure 1 in matrix()");
962: m += NR_END;
963: m -= nrl;
964:
965: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
966: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
967: m[nrl] += NR_END;
968: m[nrl] -= ncl;
969:
970: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
971:
972: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
973: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
974: m[nrl][ncl] += NR_END;
975: m[nrl][ncl] -= nll;
976: for (j=ncl+1; j<=nch; j++)
977: m[nrl][j]=m[nrl][j-1]+nlay;
978:
979: for (i=nrl+1; i<=nrh; i++) {
980: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
981: for (j=ncl+1; j<=nch; j++)
982: m[i][j]=m[i][j-1]+nlay;
983: }
984: return m;
985: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
986: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
987: */
988: }
989:
990: /*************************free ma3x ************************/
991: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
992: {
993: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
994: free((FREE_ARG)(m[nrl]+ncl-NR_END));
995: free((FREE_ARG)(m+nrl-NR_END));
996: }
997:
998: /*************** function subdirf ***********/
999: char *subdirf(char fileres[])
1000: {
1001: /* Caution optionfilefiname is hidden */
1002: strcpy(tmpout,optionfilefiname);
1003: strcat(tmpout,"/"); /* Add to the right */
1004: strcat(tmpout,fileres);
1005: return tmpout;
1006: }
1007:
1008: /*************** function subdirf2 ***********/
1009: char *subdirf2(char fileres[], char *preop)
1010: {
1011:
1012: /* Caution optionfilefiname is hidden */
1013: strcpy(tmpout,optionfilefiname);
1014: strcat(tmpout,"/");
1015: strcat(tmpout,preop);
1016: strcat(tmpout,fileres);
1017: return tmpout;
1018: }
1019:
1020: /*************** function subdirf3 ***********/
1021: char *subdirf3(char fileres[], char *preop, char *preop2)
1022: {
1023:
1024: /* Caution optionfilefiname is hidden */
1025: strcpy(tmpout,optionfilefiname);
1026: strcat(tmpout,"/");
1027: strcat(tmpout,preop);
1028: strcat(tmpout,preop2);
1029: strcat(tmpout,fileres);
1030: return tmpout;
1031: }
1032:
1033: /***************** f1dim *************************/
1034: extern int ncom;
1035: extern double *pcom,*xicom;
1036: extern double (*nrfunc)(double []);
1037:
1038: double f1dim(double x)
1039: {
1040: int j;
1041: double f;
1042: double *xt;
1043:
1044: xt=vector(1,ncom);
1045: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1046: f=(*nrfunc)(xt);
1047: free_vector(xt,1,ncom);
1048: return f;
1049: }
1050:
1051: /*****************brent *************************/
1052: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1053: {
1054: int iter;
1055: double a,b,d,etemp;
1056: double fu,fv,fw,fx;
1057: double ftemp;
1058: double p,q,r,tol1,tol2,u,v,w,x,xm;
1059: double e=0.0;
1060:
1061: a=(ax < cx ? ax : cx);
1062: b=(ax > cx ? ax : cx);
1063: x=w=v=bx;
1064: fw=fv=fx=(*f)(x);
1065: for (iter=1;iter<=ITMAX;iter++) {
1066: xm=0.5*(a+b);
1067: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1068: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1069: printf(".");fflush(stdout);
1070: fprintf(ficlog,".");fflush(ficlog);
1071: #ifdef DEBUG
1072: 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);
1073: 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);
1074: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1075: #endif
1076: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1077: *xmin=x;
1078: return fx;
1079: }
1080: ftemp=fu;
1081: if (fabs(e) > tol1) {
1082: r=(x-w)*(fx-fv);
1083: q=(x-v)*(fx-fw);
1084: p=(x-v)*q-(x-w)*r;
1085: q=2.0*(q-r);
1086: if (q > 0.0) p = -p;
1087: q=fabs(q);
1088: etemp=e;
1089: e=d;
1090: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1091: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1092: else {
1093: d=p/q;
1094: u=x+d;
1095: if (u-a < tol2 || b-u < tol2)
1096: d=SIGN(tol1,xm-x);
1097: }
1098: } else {
1099: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1100: }
1101: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1102: fu=(*f)(u);
1103: if (fu <= fx) {
1104: if (u >= x) a=x; else b=x;
1105: SHFT(v,w,x,u)
1106: SHFT(fv,fw,fx,fu)
1107: } else {
1108: if (u < x) a=u; else b=u;
1109: if (fu <= fw || w == x) {
1110: v=w;
1111: w=u;
1112: fv=fw;
1113: fw=fu;
1114: } else if (fu <= fv || v == x || v == w) {
1115: v=u;
1116: fv=fu;
1117: }
1118: }
1119: }
1120: nrerror("Too many iterations in brent");
1121: *xmin=x;
1122: return fx;
1123: }
1124:
1125: /****************** mnbrak ***********************/
1126:
1127: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1128: double (*func)(double))
1129: {
1130: double ulim,u,r,q, dum;
1131: double fu;
1132:
1133: *fa=(*func)(*ax);
1134: *fb=(*func)(*bx);
1135: if (*fb > *fa) {
1136: SHFT(dum,*ax,*bx,dum)
1137: SHFT(dum,*fb,*fa,dum)
1138: }
1139: *cx=(*bx)+GOLD*(*bx-*ax);
1140: *fc=(*func)(*cx);
1141: while (*fb > *fc) {
1142: r=(*bx-*ax)*(*fb-*fc);
1143: q=(*bx-*cx)*(*fb-*fa);
1144: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1145: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
1146: ulim=(*bx)+GLIMIT*(*cx-*bx);
1147: if ((*bx-u)*(u-*cx) > 0.0) {
1148: fu=(*func)(u);
1149: } else if ((*cx-u)*(u-ulim) > 0.0) {
1150: fu=(*func)(u);
1151: if (fu < *fc) {
1152: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1153: SHFT(*fb,*fc,fu,(*func)(u))
1154: }
1155: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
1156: u=ulim;
1157: fu=(*func)(u);
1158: } else {
1159: u=(*cx)+GOLD*(*cx-*bx);
1160: fu=(*func)(u);
1161: }
1162: SHFT(*ax,*bx,*cx,u)
1163: SHFT(*fa,*fb,*fc,fu)
1164: }
1165: }
1166:
1167: /*************** linmin ************************/
1168:
1169: int ncom;
1170: double *pcom,*xicom;
1171: double (*nrfunc)(double []);
1172:
1173: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1174: {
1175: double brent(double ax, double bx, double cx,
1176: double (*f)(double), double tol, double *xmin);
1177: double f1dim(double x);
1178: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1179: double *fc, double (*func)(double));
1180: int j;
1181: double xx,xmin,bx,ax;
1182: double fx,fb,fa;
1183:
1184: ncom=n;
1185: pcom=vector(1,n);
1186: xicom=vector(1,n);
1187: nrfunc=func;
1188: for (j=1;j<=n;j++) {
1189: pcom[j]=p[j];
1190: xicom[j]=xi[j];
1191: }
1192: ax=0.0;
1193: xx=1.0;
1194: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
1195: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
1196: #ifdef DEBUG
1197: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1198: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1199: #endif
1200: for (j=1;j<=n;j++) {
1201: xi[j] *= xmin;
1202: p[j] += xi[j];
1203: }
1204: free_vector(xicom,1,n);
1205: free_vector(pcom,1,n);
1206: }
1207:
1208: char *asc_diff_time(long time_sec, char ascdiff[])
1209: {
1210: long sec_left, days, hours, minutes;
1211: days = (time_sec) / (60*60*24);
1212: sec_left = (time_sec) % (60*60*24);
1213: hours = (sec_left) / (60*60) ;
1214: sec_left = (sec_left) %(60*60);
1215: minutes = (sec_left) /60;
1216: sec_left = (sec_left) % (60);
1217: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1218: return ascdiff;
1219: }
1220:
1221: /*************** powell ************************/
1222: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1223: double (*func)(double []))
1224: {
1225: void linmin(double p[], double xi[], int n, double *fret,
1226: double (*func)(double []));
1227: int i,ibig,j;
1228: double del,t,*pt,*ptt,*xit;
1229: double fp,fptt;
1230: double *xits;
1231: int niterf, itmp;
1232:
1233: pt=vector(1,n);
1234: ptt=vector(1,n);
1235: xit=vector(1,n);
1236: xits=vector(1,n);
1237: *fret=(*func)(p);
1238: for (j=1;j<=n;j++) pt[j]=p[j];
1239: for (*iter=1;;++(*iter)) {
1240: fp=(*fret);
1241: ibig=0;
1242: del=0.0;
1243: last_time=curr_time;
1244: (void) gettimeofday(&curr_time,&tzp);
1245: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
1246: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog);
1247: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
1248: for (i=1;i<=n;i++) {
1249: printf(" %d %.12f",i, p[i]);
1250: fprintf(ficlog," %d %.12lf",i, p[i]);
1251: fprintf(ficrespow," %.12lf", p[i]);
1252: }
1253: printf("\n");
1254: fprintf(ficlog,"\n");
1255: fprintf(ficrespow,"\n");fflush(ficrespow);
1256: if(*iter <=3){
1257: tm = *localtime(&curr_time.tv_sec);
1258: strcpy(strcurr,asctime(&tm));
1259: /* asctime_r(&tm,strcurr); */
1260: forecast_time=curr_time;
1261: itmp = strlen(strcurr);
1262: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1263: strcurr[itmp-1]='\0';
1264: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
1265: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
1266: for(niterf=10;niterf<=30;niterf+=10){
1267: forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
1268: tmf = *localtime(&forecast_time.tv_sec);
1269: /* asctime_r(&tmf,strfor); */
1270: strcpy(strfor,asctime(&tmf));
1271: itmp = strlen(strfor);
1272: if(strfor[itmp-1]=='\n')
1273: strfor[itmp-1]='\0';
1274: 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(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
1275: 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(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
1276: }
1277: }
1278: for (i=1;i<=n;i++) {
1279: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1280: fptt=(*fret);
1281: #ifdef DEBUG
1282: printf("fret=%lf \n",*fret);
1283: fprintf(ficlog,"fret=%lf \n",*fret);
1284: #endif
1285: printf("%d",i);fflush(stdout);
1286: fprintf(ficlog,"%d",i);fflush(ficlog);
1287: linmin(p,xit,n,fret,func);
1288: if (fabs(fptt-(*fret)) > del) {
1289: del=fabs(fptt-(*fret));
1290: ibig=i;
1291: }
1292: #ifdef DEBUG
1293: printf("%d %.12e",i,(*fret));
1294: fprintf(ficlog,"%d %.12e",i,(*fret));
1295: for (j=1;j<=n;j++) {
1296: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1297: printf(" x(%d)=%.12e",j,xit[j]);
1298: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1299: }
1300: for(j=1;j<=n;j++) {
1301: printf(" p=%.12e",p[j]);
1302: fprintf(ficlog," p=%.12e",p[j]);
1303: }
1304: printf("\n");
1305: fprintf(ficlog,"\n");
1306: #endif
1307: }
1308: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1309: #ifdef DEBUG
1310: int k[2],l;
1311: k[0]=1;
1312: k[1]=-1;
1313: printf("Max: %.12e",(*func)(p));
1314: fprintf(ficlog,"Max: %.12e",(*func)(p));
1315: for (j=1;j<=n;j++) {
1316: printf(" %.12e",p[j]);
1317: fprintf(ficlog," %.12e",p[j]);
1318: }
1319: printf("\n");
1320: fprintf(ficlog,"\n");
1321: for(l=0;l<=1;l++) {
1322: for (j=1;j<=n;j++) {
1323: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1324: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1325: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1326: }
1327: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1328: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1329: }
1330: #endif
1331:
1332:
1333: free_vector(xit,1,n);
1334: free_vector(xits,1,n);
1335: free_vector(ptt,1,n);
1336: free_vector(pt,1,n);
1337: return;
1338: }
1339: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1340: for (j=1;j<=n;j++) {
1341: ptt[j]=2.0*p[j]-pt[j];
1342: xit[j]=p[j]-pt[j];
1343: pt[j]=p[j];
1344: }
1345: fptt=(*func)(ptt);
1346: if (fptt < fp) {
1347: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
1348: if (t < 0.0) {
1349: linmin(p,xit,n,fret,func);
1350: for (j=1;j<=n;j++) {
1351: xi[j][ibig]=xi[j][n];
1352: xi[j][n]=xit[j];
1353: }
1354: #ifdef DEBUG
1355: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1356: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1357: for(j=1;j<=n;j++){
1358: printf(" %.12e",xit[j]);
1359: fprintf(ficlog," %.12e",xit[j]);
1360: }
1361: printf("\n");
1362: fprintf(ficlog,"\n");
1363: #endif
1364: }
1365: }
1366: }
1367: }
1368:
1369: /**** Prevalence limit (stable or period prevalence) ****************/
1370:
1371: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1372: {
1373: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1374: matrix by transitions matrix until convergence is reached */
1375:
1376: int i, ii,j,k;
1377: double min, max, maxmin, maxmax,sumnew=0.;
1378: /* double **matprod2(); */ /* test */
1379: double **out, cov[NCOVMAX+1], **pmij();
1380: double **newm;
1381: double agefin, delaymax=50 ; /* Max number of years to converge */
1382:
1383: for (ii=1;ii<=nlstate+ndeath;ii++)
1384: for (j=1;j<=nlstate+ndeath;j++){
1385: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1386: }
1387:
1388: cov[1]=1.;
1389:
1390: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1391: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1392: newm=savm;
1393: /* Covariates have to be included here again */
1394: cov[2]=agefin;
1395:
1396: for (k=1; k<=cptcovn;k++) {
1397: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1398: /*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]]);*/
1399: }
1400: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1401: /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
1402: /* cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
1403:
1404: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1405: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1406: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1407: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1408: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1409: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1410:
1411: savm=oldm;
1412: oldm=newm;
1413: maxmax=0.;
1414: for(j=1;j<=nlstate;j++){
1415: min=1.;
1416: max=0.;
1417: for(i=1; i<=nlstate; i++) {
1418: sumnew=0;
1419: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1420: prlim[i][j]= newm[i][j]/(1-sumnew);
1421: /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
1422: max=FMAX(max,prlim[i][j]);
1423: min=FMIN(min,prlim[i][j]);
1424: }
1425: maxmin=max-min;
1426: maxmax=FMAX(maxmax,maxmin);
1427: }
1428: if(maxmax < ftolpl){
1429: return prlim;
1430: }
1431: }
1432: }
1433:
1434: /*************** transition probabilities ***************/
1435:
1436: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1437: {
1438: /* According to parameters values stored in x and the covariate's values stored in cov,
1439: computes the probability to be observed in state j being in state i by appying the
1440: model to the ncovmodel covariates (including constant and age).
1441: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1442: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1443: ncth covariate in the global vector x is given by the formula:
1444: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1445: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1446: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1447: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1448: Outputs ps[i][j] the probability to be observed in j being in j according to
1449: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1450: */
1451: double s1, lnpijopii;
1452: /*double t34;*/
1453: int i,j,j1, nc, ii, jj;
1454:
1455: for(i=1; i<= nlstate; i++){
1456: for(j=1; j<i;j++){
1457: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1458: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1459: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1460: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1461: }
1462: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1463: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1464: }
1465: for(j=i+1; j<=nlstate+ndeath;j++){
1466: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1467: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
1468: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
1469: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1470: }
1471: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1472: }
1473: }
1474:
1475: for(i=1; i<= nlstate; i++){
1476: s1=0;
1477: for(j=1; j<i; j++){
1478: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1479: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1480: }
1481: for(j=i+1; j<=nlstate+ndeath; j++){
1482: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1483: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1484: }
1485: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1486: ps[i][i]=1./(s1+1.);
1487: /* Computing other pijs */
1488: for(j=1; j<i; j++)
1489: ps[i][j]= exp(ps[i][j])*ps[i][i];
1490: for(j=i+1; j<=nlstate+ndeath; j++)
1491: ps[i][j]= exp(ps[i][j])*ps[i][i];
1492: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1493: } /* end i */
1494:
1495: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1496: for(jj=1; jj<= nlstate+ndeath; jj++){
1497: ps[ii][jj]=0;
1498: ps[ii][ii]=1;
1499: }
1500: }
1501:
1502:
1503: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1504: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1505: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
1506: /* } */
1507: /* printf("\n "); */
1508: /* } */
1509: /* printf("\n ");printf("%lf ",cov[2]);*/
1510: /*
1511: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1512: goto end;*/
1513: return ps;
1514: }
1515:
1516: /**************** Product of 2 matrices ******************/
1517:
1518: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1519: {
1520: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1521: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1522: /* in, b, out are matrice of pointers which should have been initialized
1523: before: only the contents of out is modified. The function returns
1524: a pointer to pointers identical to out */
1525: int i, j, k;
1526: for(i=nrl; i<= nrh; i++)
1527: for(k=ncolol; k<=ncoloh; k++){
1528: out[i][k]=0.;
1529: for(j=ncl; j<=nch; j++)
1530: out[i][k] +=in[i][j]*b[j][k];
1531: }
1532: return out;
1533: }
1534:
1535:
1536: /************* Higher Matrix Product ***************/
1537:
1538: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1539: {
1540: /* Computes the transition matrix starting at age 'age' over
1541: 'nhstepm*hstepm*stepm' months (i.e. until
1542: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1543: nhstepm*hstepm matrices.
1544: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1545: (typically every 2 years instead of every month which is too big
1546: for the memory).
1547: Model is determined by parameters x and covariates have to be
1548: included manually here.
1549:
1550: */
1551:
1552: int i, j, d, h, k;
1553: double **out, cov[NCOVMAX+1];
1554: double **newm;
1555:
1556: /* Hstepm could be zero and should return the unit matrix */
1557: for (i=1;i<=nlstate+ndeath;i++)
1558: for (j=1;j<=nlstate+ndeath;j++){
1559: oldm[i][j]=(i==j ? 1.0 : 0.0);
1560: po[i][j][0]=(i==j ? 1.0 : 0.0);
1561: }
1562: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1563: for(h=1; h <=nhstepm; h++){
1564: for(d=1; d <=hstepm; d++){
1565: newm=savm;
1566: /* Covariates have to be included here again */
1567: cov[1]=1.;
1568: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1569: for (k=1; k<=cptcovn;k++)
1570: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1571: for (k=1; k<=cptcovage;k++)
1572: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1573: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1574: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1575:
1576:
1577: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1578: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1579: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1580: pmij(pmmij,cov,ncovmodel,x,nlstate));
1581: savm=oldm;
1582: oldm=newm;
1583: }
1584: for(i=1; i<=nlstate+ndeath; i++)
1585: for(j=1;j<=nlstate+ndeath;j++) {
1586: po[i][j][h]=newm[i][j];
1587: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1588: }
1589: /*printf("h=%d ",h);*/
1590: } /* end h */
1591: /* printf("\n H=%d \n",h); */
1592: return po;
1593: }
1594:
1595:
1596: /*************** log-likelihood *************/
1597: double func( double *x)
1598: {
1599: int i, ii, j, k, mi, d, kk;
1600: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1601: double **out;
1602: double sw; /* Sum of weights */
1603: double lli; /* Individual log likelihood */
1604: int s1, s2;
1605: double bbh, survp;
1606: long ipmx;
1607: /*extern weight */
1608: /* We are differentiating ll according to initial status */
1609: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1610: /*for(i=1;i<imx;i++)
1611: printf(" %d\n",s[4][i]);
1612: */
1613: cov[1]=1.;
1614:
1615: for(k=1; k<=nlstate; k++) ll[k]=0.;
1616:
1617: if(mle==1){
1618: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1619: /* Computes the values of the ncovmodel covariates of the model
1620: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
1621: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
1622: to be observed in j being in i according to the model.
1623: */
1624: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1625: cov[2+k]=covar[Tvar[k]][i];
1626: }
1627: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1628: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1629: has been calculated etc */
1630: for(mi=1; mi<= wav[i]-1; mi++){
1631: for (ii=1;ii<=nlstate+ndeath;ii++)
1632: for (j=1;j<=nlstate+ndeath;j++){
1633: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1634: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1635: }
1636: for(d=0; d<dh[mi][i]; d++){
1637: newm=savm;
1638: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1639: for (kk=1; kk<=cptcovage;kk++) {
1640: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
1641: }
1642: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1643: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1644: savm=oldm;
1645: oldm=newm;
1646: } /* end mult */
1647:
1648: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1649: /* But now since version 0.9 we anticipate for bias at large stepm.
1650: * If stepm is larger than one month (smallest stepm) and if the exact delay
1651: * (in months) between two waves is not a multiple of stepm, we rounded to
1652: * the nearest (and in case of equal distance, to the lowest) interval but now
1653: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1654: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1655: * probability in order to take into account the bias as a fraction of the way
1656: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1657: * -stepm/2 to stepm/2 .
1658: * For stepm=1 the results are the same as for previous versions of Imach.
1659: * For stepm > 1 the results are less biased than in previous versions.
1660: */
1661: s1=s[mw[mi][i]][i];
1662: s2=s[mw[mi+1][i]][i];
1663: bbh=(double)bh[mi][i]/(double)stepm;
1664: /* bias bh is positive if real duration
1665: * is higher than the multiple of stepm and negative otherwise.
1666: */
1667: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1668: if( s2 > nlstate){
1669: /* i.e. if s2 is a death state and if the date of death is known
1670: then the contribution to the likelihood is the probability to
1671: die between last step unit time and current step unit time,
1672: which is also equal to probability to die before dh
1673: minus probability to die before dh-stepm .
1674: In version up to 0.92 likelihood was computed
1675: as if date of death was unknown. Death was treated as any other
1676: health state: the date of the interview describes the actual state
1677: and not the date of a change in health state. The former idea was
1678: to consider that at each interview the state was recorded
1679: (healthy, disable or death) and IMaCh was corrected; but when we
1680: introduced the exact date of death then we should have modified
1681: the contribution of an exact death to the likelihood. This new
1682: contribution is smaller and very dependent of the step unit
1683: stepm. It is no more the probability to die between last interview
1684: and month of death but the probability to survive from last
1685: interview up to one month before death multiplied by the
1686: probability to die within a month. Thanks to Chris
1687: Jackson for correcting this bug. Former versions increased
1688: mortality artificially. The bad side is that we add another loop
1689: which slows down the processing. The difference can be up to 10%
1690: lower mortality.
1691: */
1692: lli=log(out[s1][s2] - savm[s1][s2]);
1693:
1694:
1695: } else if (s2==-2) {
1696: for (j=1,survp=0. ; j<=nlstate; j++)
1697: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1698: /*survp += out[s1][j]; */
1699: lli= log(survp);
1700: }
1701:
1702: else if (s2==-4) {
1703: for (j=3,survp=0. ; j<=nlstate; j++)
1704: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1705: lli= log(survp);
1706: }
1707:
1708: else if (s2==-5) {
1709: for (j=1,survp=0. ; j<=2; j++)
1710: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1711: lli= log(survp);
1712: }
1713:
1714: else{
1715: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1716: /* 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 */
1717: }
1718: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1719: /*if(lli ==000.0)*/
1720: /*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); */
1721: ipmx +=1;
1722: sw += weight[i];
1723: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1724: } /* end of wave */
1725: } /* end of individual */
1726: } else if(mle==2){
1727: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1728: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1729: for(mi=1; mi<= wav[i]-1; mi++){
1730: for (ii=1;ii<=nlstate+ndeath;ii++)
1731: for (j=1;j<=nlstate+ndeath;j++){
1732: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1733: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1734: }
1735: for(d=0; d<=dh[mi][i]; d++){
1736: newm=savm;
1737: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1738: for (kk=1; kk<=cptcovage;kk++) {
1739: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1740: }
1741: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1742: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1743: savm=oldm;
1744: oldm=newm;
1745: } /* end mult */
1746:
1747: s1=s[mw[mi][i]][i];
1748: s2=s[mw[mi+1][i]][i];
1749: bbh=(double)bh[mi][i]/(double)stepm;
1750: 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 */
1751: ipmx +=1;
1752: sw += weight[i];
1753: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1754: } /* end of wave */
1755: } /* end of individual */
1756: } else if(mle==3){ /* exponential inter-extrapolation */
1757: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1758: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1759: for(mi=1; mi<= wav[i]-1; mi++){
1760: for (ii=1;ii<=nlstate+ndeath;ii++)
1761: for (j=1;j<=nlstate+ndeath;j++){
1762: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1763: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1764: }
1765: for(d=0; d<dh[mi][i]; d++){
1766: newm=savm;
1767: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1768: for (kk=1; kk<=cptcovage;kk++) {
1769: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1770: }
1771: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1772: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1773: savm=oldm;
1774: oldm=newm;
1775: } /* end mult */
1776:
1777: s1=s[mw[mi][i]][i];
1778: s2=s[mw[mi+1][i]][i];
1779: bbh=(double)bh[mi][i]/(double)stepm;
1780: 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 */
1781: ipmx +=1;
1782: sw += weight[i];
1783: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1784: } /* end of wave */
1785: } /* end of individual */
1786: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1787: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1788: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1789: for(mi=1; mi<= wav[i]-1; mi++){
1790: for (ii=1;ii<=nlstate+ndeath;ii++)
1791: for (j=1;j<=nlstate+ndeath;j++){
1792: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1793: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1794: }
1795: for(d=0; d<dh[mi][i]; d++){
1796: newm=savm;
1797: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1798: for (kk=1; kk<=cptcovage;kk++) {
1799: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1800: }
1801:
1802: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1803: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1804: savm=oldm;
1805: oldm=newm;
1806: } /* end mult */
1807:
1808: s1=s[mw[mi][i]][i];
1809: s2=s[mw[mi+1][i]][i];
1810: if( s2 > nlstate){
1811: lli=log(out[s1][s2] - savm[s1][s2]);
1812: }else{
1813: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1814: }
1815: ipmx +=1;
1816: sw += weight[i];
1817: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1818: /* 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]); */
1819: } /* end of wave */
1820: } /* end of individual */
1821: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1822: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1823: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1824: for(mi=1; mi<= wav[i]-1; mi++){
1825: for (ii=1;ii<=nlstate+ndeath;ii++)
1826: for (j=1;j<=nlstate+ndeath;j++){
1827: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1828: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1829: }
1830: for(d=0; d<dh[mi][i]; d++){
1831: newm=savm;
1832: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1833: for (kk=1; kk<=cptcovage;kk++) {
1834: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1835: }
1836:
1837: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1838: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1839: savm=oldm;
1840: oldm=newm;
1841: } /* end mult */
1842:
1843: s1=s[mw[mi][i]][i];
1844: s2=s[mw[mi+1][i]][i];
1845: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1846: ipmx +=1;
1847: sw += weight[i];
1848: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1849: /*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]);*/
1850: } /* end of wave */
1851: } /* end of individual */
1852: } /* End of if */
1853: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1854: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1855: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1856: return -l;
1857: }
1858:
1859: /*************** log-likelihood *************/
1860: double funcone( double *x)
1861: {
1862: /* Same as likeli but slower because of a lot of printf and if */
1863: int i, ii, j, k, mi, d, kk;
1864: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1865: double **out;
1866: double lli; /* Individual log likelihood */
1867: double llt;
1868: int s1, s2;
1869: double bbh, survp;
1870: /*extern weight */
1871: /* We are differentiating ll according to initial status */
1872: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1873: /*for(i=1;i<imx;i++)
1874: printf(" %d\n",s[4][i]);
1875: */
1876: cov[1]=1.;
1877:
1878: for(k=1; k<=nlstate; k++) ll[k]=0.;
1879:
1880: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1881: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1882: for(mi=1; mi<= wav[i]-1; mi++){
1883: for (ii=1;ii<=nlstate+ndeath;ii++)
1884: for (j=1;j<=nlstate+ndeath;j++){
1885: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1886: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1887: }
1888: for(d=0; d<dh[mi][i]; d++){
1889: newm=savm;
1890: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1891: for (kk=1; kk<=cptcovage;kk++) {
1892: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1893: }
1894: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1895: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1896: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1897: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
1898: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
1899: savm=oldm;
1900: oldm=newm;
1901: } /* end mult */
1902:
1903: s1=s[mw[mi][i]][i];
1904: s2=s[mw[mi+1][i]][i];
1905: bbh=(double)bh[mi][i]/(double)stepm;
1906: /* bias is positive if real duration
1907: * is higher than the multiple of stepm and negative otherwise.
1908: */
1909: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1910: lli=log(out[s1][s2] - savm[s1][s2]);
1911: } else if (s2==-2) {
1912: for (j=1,survp=0. ; j<=nlstate; j++)
1913: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1914: lli= log(survp);
1915: }else if (mle==1){
1916: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1917: } else if(mle==2){
1918: 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 */
1919: } else if(mle==3){ /* exponential inter-extrapolation */
1920: 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 */
1921: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1922: lli=log(out[s1][s2]); /* Original formula */
1923: } else{ /* mle=0 back to 1 */
1924: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1925: /*lli=log(out[s1][s2]); */ /* Original formula */
1926: } /* End of if */
1927: ipmx +=1;
1928: sw += weight[i];
1929: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1930: /*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]); */
1931: if(globpr){
1932: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
1933: %11.6f %11.6f %11.6f ", \
1934: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1935: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1936: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
1937: llt +=ll[k]*gipmx/gsw;
1938: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
1939: }
1940: fprintf(ficresilk," %10.6f\n", -llt);
1941: }
1942: } /* end of wave */
1943: } /* end of individual */
1944: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1945: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1946: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1947: if(globpr==0){ /* First time we count the contributions and weights */
1948: gipmx=ipmx;
1949: gsw=sw;
1950: }
1951: return -l;
1952: }
1953:
1954:
1955: /*************** function likelione ***********/
1956: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1957: {
1958: /* This routine should help understanding what is done with
1959: the selection of individuals/waves and
1960: to check the exact contribution to the likelihood.
1961: Plotting could be done.
1962: */
1963: int k;
1964:
1965: if(*globpri !=0){ /* Just counts and sums, no printings */
1966: strcpy(fileresilk,"ilk");
1967: strcat(fileresilk,fileres);
1968: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1969: printf("Problem with resultfile: %s\n", fileresilk);
1970: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1971: }
1972: 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");
1973: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1974: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1975: for(k=1; k<=nlstate; k++)
1976: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
1977: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1978: }
1979:
1980: *fretone=(*funcone)(p);
1981: if(*globpri !=0){
1982: fclose(ficresilk);
1983: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1984: fflush(fichtm);
1985: }
1986: return;
1987: }
1988:
1989:
1990: /*********** Maximum Likelihood Estimation ***************/
1991:
1992: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1993: {
1994: int i,j, iter;
1995: double **xi;
1996: double fret;
1997: double fretone; /* Only one call to likelihood */
1998: /* char filerespow[FILENAMELENGTH];*/
1999: xi=matrix(1,npar,1,npar);
2000: for (i=1;i<=npar;i++)
2001: for (j=1;j<=npar;j++)
2002: xi[i][j]=(i==j ? 1.0 : 0.0);
2003: printf("Powell\n"); fprintf(ficlog,"Powell\n");
2004: strcpy(filerespow,"pow");
2005: strcat(filerespow,fileres);
2006: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2007: printf("Problem with resultfile: %s\n", filerespow);
2008: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2009: }
2010: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2011: for (i=1;i<=nlstate;i++)
2012: for(j=1;j<=nlstate+ndeath;j++)
2013: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2014: fprintf(ficrespow,"\n");
2015:
2016: powell(p,xi,npar,ftol,&iter,&fret,func);
2017:
2018: free_matrix(xi,1,npar,1,npar);
2019: fclose(ficrespow);
2020: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
2021: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
2022: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
2023:
2024: }
2025:
2026: /**** Computes Hessian and covariance matrix ***/
2027: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
2028: {
2029: double **a,**y,*x,pd;
2030: double **hess;
2031: int i, j,jk;
2032: int *indx;
2033:
2034: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
2035: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
2036: void lubksb(double **a, int npar, int *indx, double b[]) ;
2037: void ludcmp(double **a, int npar, int *indx, double *d) ;
2038: double gompertz(double p[]);
2039: hess=matrix(1,npar,1,npar);
2040:
2041: printf("\nCalculation of the hessian matrix. Wait...\n");
2042: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2043: for (i=1;i<=npar;i++){
2044: printf("%d",i);fflush(stdout);
2045: fprintf(ficlog,"%d",i);fflush(ficlog);
2046:
2047: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2048:
2049: /* printf(" %f ",p[i]);
2050: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2051: }
2052:
2053: for (i=1;i<=npar;i++) {
2054: for (j=1;j<=npar;j++) {
2055: if (j>i) {
2056: printf(".%d%d",i,j);fflush(stdout);
2057: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
2058: hess[i][j]=hessij(p,delti,i,j,func,npar);
2059:
2060: hess[j][i]=hess[i][j];
2061: /*printf(" %lf ",hess[i][j]);*/
2062: }
2063: }
2064: }
2065: printf("\n");
2066: fprintf(ficlog,"\n");
2067:
2068: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2069: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2070:
2071: a=matrix(1,npar,1,npar);
2072: y=matrix(1,npar,1,npar);
2073: x=vector(1,npar);
2074: indx=ivector(1,npar);
2075: for (i=1;i<=npar;i++)
2076: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2077: ludcmp(a,npar,indx,&pd);
2078:
2079: for (j=1;j<=npar;j++) {
2080: for (i=1;i<=npar;i++) x[i]=0;
2081: x[j]=1;
2082: lubksb(a,npar,indx,x);
2083: for (i=1;i<=npar;i++){
2084: matcov[i][j]=x[i];
2085: }
2086: }
2087:
2088: printf("\n#Hessian matrix#\n");
2089: fprintf(ficlog,"\n#Hessian matrix#\n");
2090: for (i=1;i<=npar;i++) {
2091: for (j=1;j<=npar;j++) {
2092: printf("%.3e ",hess[i][j]);
2093: fprintf(ficlog,"%.3e ",hess[i][j]);
2094: }
2095: printf("\n");
2096: fprintf(ficlog,"\n");
2097: }
2098:
2099: /* Recompute Inverse */
2100: for (i=1;i<=npar;i++)
2101: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
2102: ludcmp(a,npar,indx,&pd);
2103:
2104: /* printf("\n#Hessian matrix recomputed#\n");
2105:
2106: for (j=1;j<=npar;j++) {
2107: for (i=1;i<=npar;i++) x[i]=0;
2108: x[j]=1;
2109: lubksb(a,npar,indx,x);
2110: for (i=1;i<=npar;i++){
2111: y[i][j]=x[i];
2112: printf("%.3e ",y[i][j]);
2113: fprintf(ficlog,"%.3e ",y[i][j]);
2114: }
2115: printf("\n");
2116: fprintf(ficlog,"\n");
2117: }
2118: */
2119:
2120: free_matrix(a,1,npar,1,npar);
2121: free_matrix(y,1,npar,1,npar);
2122: free_vector(x,1,npar);
2123: free_ivector(indx,1,npar);
2124: free_matrix(hess,1,npar,1,npar);
2125:
2126:
2127: }
2128:
2129: /*************** hessian matrix ****************/
2130: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2131: {
2132: int i;
2133: int l=1, lmax=20;
2134: double k1,k2;
2135: double p2[MAXPARM+1]; /* identical to x */
2136: double res;
2137: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2138: double fx;
2139: int k=0,kmax=10;
2140: double l1;
2141:
2142: fx=func(x);
2143: for (i=1;i<=npar;i++) p2[i]=x[i];
2144: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
2145: l1=pow(10,l);
2146: delts=delt;
2147: for(k=1 ; k <kmax; k=k+1){
2148: delt = delta*(l1*k);
2149: p2[theta]=x[theta] +delt;
2150: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
2151: p2[theta]=x[theta]-delt;
2152: k2=func(p2)-fx;
2153: /*res= (k1-2.0*fx+k2)/delt/delt; */
2154: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2155:
2156: #ifdef DEBUGHESS
2157: 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);
2158: 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);
2159: #endif
2160: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2161: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2162: k=kmax;
2163: }
2164: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
2165: k=kmax; l=lmax*10.;
2166: }
2167: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2168: delts=delt;
2169: }
2170: }
2171: }
2172: delti[theta]=delts;
2173: return res;
2174:
2175: }
2176:
2177: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2178: {
2179: int i;
2180: int l=1, l1, lmax=20;
2181: double k1,k2,k3,k4,res,fx;
2182: double p2[MAXPARM+1];
2183: int k;
2184:
2185: fx=func(x);
2186: for (k=1; k<=2; k++) {
2187: for (i=1;i<=npar;i++) p2[i]=x[i];
2188: p2[thetai]=x[thetai]+delti[thetai]/k;
2189: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2190: k1=func(p2)-fx;
2191:
2192: p2[thetai]=x[thetai]+delti[thetai]/k;
2193: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2194: k2=func(p2)-fx;
2195:
2196: p2[thetai]=x[thetai]-delti[thetai]/k;
2197: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2198: k3=func(p2)-fx;
2199:
2200: p2[thetai]=x[thetai]-delti[thetai]/k;
2201: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2202: k4=func(p2)-fx;
2203: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2204: #ifdef DEBUG
2205: 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);
2206: 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);
2207: #endif
2208: }
2209: return res;
2210: }
2211:
2212: /************** Inverse of matrix **************/
2213: void ludcmp(double **a, int n, int *indx, double *d)
2214: {
2215: int i,imax,j,k;
2216: double big,dum,sum,temp;
2217: double *vv;
2218:
2219: vv=vector(1,n);
2220: *d=1.0;
2221: for (i=1;i<=n;i++) {
2222: big=0.0;
2223: for (j=1;j<=n;j++)
2224: if ((temp=fabs(a[i][j])) > big) big=temp;
2225: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2226: vv[i]=1.0/big;
2227: }
2228: for (j=1;j<=n;j++) {
2229: for (i=1;i<j;i++) {
2230: sum=a[i][j];
2231: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2232: a[i][j]=sum;
2233: }
2234: big=0.0;
2235: for (i=j;i<=n;i++) {
2236: sum=a[i][j];
2237: for (k=1;k<j;k++)
2238: sum -= a[i][k]*a[k][j];
2239: a[i][j]=sum;
2240: if ( (dum=vv[i]*fabs(sum)) >= big) {
2241: big=dum;
2242: imax=i;
2243: }
2244: }
2245: if (j != imax) {
2246: for (k=1;k<=n;k++) {
2247: dum=a[imax][k];
2248: a[imax][k]=a[j][k];
2249: a[j][k]=dum;
2250: }
2251: *d = -(*d);
2252: vv[imax]=vv[j];
2253: }
2254: indx[j]=imax;
2255: if (a[j][j] == 0.0) a[j][j]=TINY;
2256: if (j != n) {
2257: dum=1.0/(a[j][j]);
2258: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2259: }
2260: }
2261: free_vector(vv,1,n); /* Doesn't work */
2262: ;
2263: }
2264:
2265: void lubksb(double **a, int n, int *indx, double b[])
2266: {
2267: int i,ii=0,ip,j;
2268: double sum;
2269:
2270: for (i=1;i<=n;i++) {
2271: ip=indx[i];
2272: sum=b[ip];
2273: b[ip]=b[i];
2274: if (ii)
2275: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2276: else if (sum) ii=i;
2277: b[i]=sum;
2278: }
2279: for (i=n;i>=1;i--) {
2280: sum=b[i];
2281: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2282: b[i]=sum/a[i][i];
2283: }
2284: }
2285:
2286: void pstamp(FILE *fichier)
2287: {
2288: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2289: }
2290:
2291: /************ Frequencies ********************/
2292: 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[])
2293: { /* Some frequencies */
2294:
2295: int i, m, jk, k1,i1, j1, bool, z1,j;
2296: int first;
2297: double ***freq; /* Frequencies */
2298: double *pp, **prop;
2299: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2300: char fileresp[FILENAMELENGTH];
2301:
2302: pp=vector(1,nlstate);
2303: prop=matrix(1,nlstate,iagemin,iagemax+3);
2304: strcpy(fileresp,"p");
2305: strcat(fileresp,fileres);
2306: if((ficresp=fopen(fileresp,"w"))==NULL) {
2307: printf("Problem with prevalence resultfile: %s\n", fileresp);
2308: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2309: exit(0);
2310: }
2311: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2312: j1=0;
2313:
2314: j=cptcoveff;
2315: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2316:
2317: first=1;
2318:
2319: /* for(k1=1; k1<=j ; k1++){ /* Loop on covariates */
2320: /* for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
2321: /* j1++;
2322: */
2323: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
2324: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2325: scanf("%d", i);*/
2326: for (i=-5; i<=nlstate+ndeath; i++)
2327: for (jk=-5; jk<=nlstate+ndeath; jk++)
2328: for(m=iagemin; m <= iagemax+3; m++)
2329: freq[i][jk][m]=0;
2330:
2331: for (i=1; i<=nlstate; i++)
2332: for(m=iagemin; m <= iagemax+3; m++)
2333: prop[i][m]=0;
2334:
2335: dateintsum=0;
2336: k2cpt=0;
2337: for (i=1; i<=imx; i++) {
2338: bool=1;
2339: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
2340: for (z1=1; z1<=cptcoveff; z1++)
2341: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
2342: /* Tests if the value of each of the covariates of i is equal to filter j1 */
2343: bool=0;
2344: /* 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",
2345: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
2346: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
2347: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
2348: }
2349: }
2350:
2351: if (bool==1){
2352: for(m=firstpass; m<=lastpass; m++){
2353: k2=anint[m][i]+(mint[m][i]/12.);
2354: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2355: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2356: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2357: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2358: if (m<lastpass) {
2359: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2360: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2361: }
2362:
2363: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2364: dateintsum=dateintsum+k2;
2365: k2cpt++;
2366: }
2367: /*}*/
2368: }
2369: }
2370: } /* end i */
2371:
2372: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2373: pstamp(ficresp);
2374: if (cptcovn>0) {
2375: fprintf(ficresp, "\n#********** Variable ");
2376: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2377: fprintf(ficresp, "**********\n#");
2378: fprintf(ficlog, "\n#********** Variable ");
2379: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2380: fprintf(ficlog, "**********\n#");
2381: }
2382: for(i=1; i<=nlstate;i++)
2383: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2384: fprintf(ficresp, "\n");
2385:
2386: for(i=iagemin; i <= iagemax+3; i++){
2387: if(i==iagemax+3){
2388: fprintf(ficlog,"Total");
2389: }else{
2390: if(first==1){
2391: first=0;
2392: printf("See log file for details...\n");
2393: }
2394: fprintf(ficlog,"Age %d", i);
2395: }
2396: for(jk=1; jk <=nlstate ; jk++){
2397: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2398: pp[jk] += freq[jk][m][i];
2399: }
2400: for(jk=1; jk <=nlstate ; jk++){
2401: for(m=-1, pos=0; m <=0 ; m++)
2402: pos += freq[jk][m][i];
2403: if(pp[jk]>=1.e-10){
2404: if(first==1){
2405: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2406: }
2407: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2408: }else{
2409: if(first==1)
2410: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2411: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2412: }
2413: }
2414:
2415: for(jk=1; jk <=nlstate ; jk++){
2416: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2417: pp[jk] += freq[jk][m][i];
2418: }
2419: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2420: pos += pp[jk];
2421: posprop += prop[jk][i];
2422: }
2423: for(jk=1; jk <=nlstate ; jk++){
2424: if(pos>=1.e-5){
2425: if(first==1)
2426: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2427: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2428: }else{
2429: if(first==1)
2430: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2431: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2432: }
2433: if( i <= iagemax){
2434: if(pos>=1.e-5){
2435: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2436: /*probs[i][jk][j1]= pp[jk]/pos;*/
2437: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2438: }
2439: else
2440: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2441: }
2442: }
2443:
2444: for(jk=-1; jk <=nlstate+ndeath; jk++)
2445: for(m=-1; m <=nlstate+ndeath; m++)
2446: if(freq[jk][m][i] !=0 ) {
2447: if(first==1)
2448: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2449: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2450: }
2451: if(i <= iagemax)
2452: fprintf(ficresp,"\n");
2453: if(first==1)
2454: printf("Others in log...\n");
2455: fprintf(ficlog,"\n");
2456: }
2457: /*}*/
2458: }
2459: dateintmean=dateintsum/k2cpt;
2460:
2461: fclose(ficresp);
2462: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2463: free_vector(pp,1,nlstate);
2464: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2465: /* End of Freq */
2466: }
2467:
2468: /************ Prevalence ********************/
2469: 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)
2470: {
2471: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2472: in each health status at the date of interview (if between dateprev1 and dateprev2).
2473: We still use firstpass and lastpass as another selection.
2474: */
2475:
2476: int i, m, jk, k1, i1, j1, bool, z1,j;
2477: double ***freq; /* Frequencies */
2478: double *pp, **prop;
2479: double pos,posprop;
2480: double y2; /* in fractional years */
2481: int iagemin, iagemax;
2482: int first; /** to stop verbosity which is redirected to log file */
2483:
2484: iagemin= (int) agemin;
2485: iagemax= (int) agemax;
2486: /*pp=vector(1,nlstate);*/
2487: prop=matrix(1,nlstate,iagemin,iagemax+3);
2488: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2489: j1=0;
2490:
2491: /*j=cptcoveff;*/
2492: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2493:
2494: first=1;
2495: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
2496: /*for(i1=1; i1<=ncodemax[k1];i1++){
2497: j1++;*/
2498:
2499: for (i=1; i<=nlstate; i++)
2500: for(m=iagemin; m <= iagemax+3; m++)
2501: prop[i][m]=0.0;
2502:
2503: for (i=1; i<=imx; i++) { /* Each individual */
2504: bool=1;
2505: if (cptcovn>0) {
2506: for (z1=1; z1<=cptcoveff; z1++)
2507: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2508: bool=0;
2509: }
2510: if (bool==1) {
2511: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2512: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2513: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2514: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2515: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2516: 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);
2517: if (s[m][i]>0 && s[m][i]<=nlstate) {
2518: /*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]]);*/
2519: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2520: prop[s[m][i]][iagemax+3] += weight[i];
2521: }
2522: }
2523: } /* end selection of waves */
2524: }
2525: }
2526: for(i=iagemin; i <= iagemax+3; i++){
2527: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2528: posprop += prop[jk][i];
2529: }
2530:
2531: for(jk=1; jk <=nlstate ; jk++){
2532: if( i <= iagemax){
2533: if(posprop>=1.e-5){
2534: probs[i][jk][j1]= prop[jk][i]/posprop;
2535: } else{
2536: if(first==1){
2537: first=0;
2538: 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]);
2539: }
2540: }
2541: }
2542: }/* end jk */
2543: }/* end i */
2544: /*} *//* end i1 */
2545: } /* end j1 */
2546:
2547: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2548: /*free_vector(pp,1,nlstate);*/
2549: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2550: } /* End of prevalence */
2551:
2552: /************* Waves Concatenation ***************/
2553:
2554: 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)
2555: {
2556: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2557: Death is a valid wave (if date is known).
2558: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2559: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2560: and mw[mi+1][i]. dh depends on stepm.
2561: */
2562:
2563: int i, mi, m;
2564: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2565: double sum=0., jmean=0.;*/
2566: int first;
2567: int j, k=0,jk, ju, jl;
2568: double sum=0.;
2569: first=0;
2570: jmin=1e+5;
2571: jmax=-1;
2572: jmean=0.;
2573: for(i=1; i<=imx; i++){
2574: mi=0;
2575: m=firstpass;
2576: while(s[m][i] <= nlstate){
2577: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2578: mw[++mi][i]=m;
2579: if(m >=lastpass)
2580: break;
2581: else
2582: m++;
2583: }/* end while */
2584: if (s[m][i] > nlstate){
2585: mi++; /* Death is another wave */
2586: /* if(mi==0) never been interviewed correctly before death */
2587: /* Only death is a correct wave */
2588: mw[mi][i]=m;
2589: }
2590:
2591: wav[i]=mi;
2592: if(mi==0){
2593: nbwarn++;
2594: if(first==0){
2595: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2596: first=1;
2597: }
2598: if(first==1){
2599: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2600: }
2601: } /* end mi==0 */
2602: } /* End individuals */
2603:
2604: for(i=1; i<=imx; i++){
2605: for(mi=1; mi<wav[i];mi++){
2606: if (stepm <=0)
2607: dh[mi][i]=1;
2608: else{
2609: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2610: if (agedc[i] < 2*AGESUP) {
2611: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2612: if(j==0) j=1; /* Survives at least one month after exam */
2613: else if(j<0){
2614: nberr++;
2615: 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]);
2616: j=1; /* Temporary Dangerous patch */
2617: 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);
2618: 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]);
2619: 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);
2620: }
2621: k=k+1;
2622: if (j >= jmax){
2623: jmax=j;
2624: ijmax=i;
2625: }
2626: if (j <= jmin){
2627: jmin=j;
2628: ijmin=i;
2629: }
2630: sum=sum+j;
2631: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2632: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2633: }
2634: }
2635: else{
2636: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2637: /* 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]); */
2638:
2639: k=k+1;
2640: if (j >= jmax) {
2641: jmax=j;
2642: ijmax=i;
2643: }
2644: else if (j <= jmin){
2645: jmin=j;
2646: ijmin=i;
2647: }
2648: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2649: /*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]);*/
2650: if(j<0){
2651: nberr++;
2652: 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]);
2653: 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]);
2654: }
2655: sum=sum+j;
2656: }
2657: jk= j/stepm;
2658: jl= j -jk*stepm;
2659: ju= j -(jk+1)*stepm;
2660: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2661: if(jl==0){
2662: dh[mi][i]=jk;
2663: bh[mi][i]=0;
2664: }else{ /* We want a negative bias in order to only have interpolation ie
2665: * to avoid the price of an extra matrix product in likelihood */
2666: dh[mi][i]=jk+1;
2667: bh[mi][i]=ju;
2668: }
2669: }else{
2670: if(jl <= -ju){
2671: dh[mi][i]=jk;
2672: bh[mi][i]=jl; /* bias is positive if real duration
2673: * is higher than the multiple of stepm and negative otherwise.
2674: */
2675: }
2676: else{
2677: dh[mi][i]=jk+1;
2678: bh[mi][i]=ju;
2679: }
2680: if(dh[mi][i]==0){
2681: dh[mi][i]=1; /* At least one step */
2682: bh[mi][i]=ju; /* At least one step */
2683: /* 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);*/
2684: }
2685: } /* end if mle */
2686: }
2687: } /* end wave */
2688: }
2689: jmean=sum/k;
2690: 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);
2691: 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);
2692: }
2693:
2694: /*********** Tricode ****************************/
2695: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
2696: {
2697: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
2698: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
2699: /* Boring subroutine which should only output nbcode[Tvar[j]][k]
2700: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
2701: /* nbcode[Tvar[j]][1]=
2702: */
2703:
2704: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
2705: int modmaxcovj=0; /* Modality max of covariates j */
2706: int cptcode=0; /* Modality max of covariates j */
2707: int modmincovj=0; /* Modality min of covariates j */
2708:
2709:
2710: cptcoveff=0;
2711:
2712: for (k=-1; k < maxncov; k++) Ndum[k]=0;
2713: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
2714:
2715: /* Loop on covariates without age and products */
2716: for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
2717: for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the
2718: modality of this covariate Vj*/
2719: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
2720: * If product of Vn*Vm, still boolean *:
2721: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
2722: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
2723: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
2724: modality of the nth covariate of individual i. */
2725: if (ij > modmaxcovj)
2726: modmaxcovj=ij;
2727: else if (ij < modmincovj)
2728: modmincovj=ij;
2729: if ((ij < -1) && (ij > NCOVMAX)){
2730: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
2731: exit(1);
2732: }else
2733: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
2734: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
2735: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
2736: /* getting the maximum value of the modality of the covariate
2737: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
2738: female is 1, then modmaxcovj=1.*/
2739: }
2740: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
2741: cptcode=modmaxcovj;
2742: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
2743: /*for (i=0; i<=cptcode; i++) {*/
2744: for (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
2745: printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
2746: if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
2747: ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
2748: }
2749: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
2750: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
2751: } /* Ndum[-1] number of undefined modalities */
2752:
2753: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
2754: /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
2755: /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
2756: modmincovj=3; modmaxcovj = 7;
2757: There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
2758: which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy
2759: variables V1_1 and V1_2.
2760: nbcode[Tvar[j]][ij]=k;
2761: nbcode[Tvar[j]][1]=0;
2762: nbcode[Tvar[j]][2]=1;
2763: nbcode[Tvar[j]][3]=2;
2764: */
2765: ij=1; /* ij is similar to i but can jumps over null modalities */
2766: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
2767: for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
2768: /*recode from 0 */
2769: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
2770: nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode.
2771: k is a modality. If we have model=V1+V1*sex
2772: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
2773: ij++;
2774: }
2775: if (ij > ncodemax[j]) break;
2776: } /* end of loop on */
2777: } /* end of loop on modality */
2778: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
2779:
2780: for (k=-1; k< maxncov; k++) Ndum[k]=0;
2781:
2782: for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
2783: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
2784: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
2785: Ndum[ij]++;
2786: }
2787:
2788: ij=1;
2789: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
2790: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
2791: if((Ndum[i]!=0) && (i<=ncovcol)){
2792: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
2793: Tvaraff[ij]=i; /*For printing (unclear) */
2794: ij++;
2795: }else
2796: Tvaraff[ij]=0;
2797: }
2798: ij--;
2799: cptcoveff=ij; /*Number of total covariates*/
2800:
2801: }
2802:
2803:
2804: /*********** Health Expectancies ****************/
2805:
2806: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
2807:
2808: {
2809: /* Health expectancies, no variances */
2810: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
2811: int nhstepma, nstepma; /* Decreasing with age */
2812: double age, agelim, hf;
2813: double ***p3mat;
2814: double eip;
2815:
2816: pstamp(ficreseij);
2817: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
2818: fprintf(ficreseij,"# Age");
2819: for(i=1; i<=nlstate;i++){
2820: for(j=1; j<=nlstate;j++){
2821: fprintf(ficreseij," e%1d%1d ",i,j);
2822: }
2823: fprintf(ficreseij," e%1d. ",i);
2824: }
2825: fprintf(ficreseij,"\n");
2826:
2827:
2828: if(estepm < stepm){
2829: printf ("Problem %d lower than %d\n",estepm, stepm);
2830: }
2831: else hstepm=estepm;
2832: /* We compute the life expectancy from trapezoids spaced every estepm months
2833: * This is mainly to measure the difference between two models: for example
2834: * if stepm=24 months pijx are given only every 2 years and by summing them
2835: * we are calculating an estimate of the Life Expectancy assuming a linear
2836: * progression in between and thus overestimating or underestimating according
2837: * to the curvature of the survival function. If, for the same date, we
2838: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2839: * to compare the new estimate of Life expectancy with the same linear
2840: * hypothesis. A more precise result, taking into account a more precise
2841: * curvature will be obtained if estepm is as small as stepm. */
2842:
2843: /* For example we decided to compute the life expectancy with the smallest unit */
2844: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2845: nhstepm is the number of hstepm from age to agelim
2846: nstepm is the number of stepm from age to agelin.
2847: Look at hpijx to understand the reason of that which relies in memory size
2848: and note for a fixed period like estepm months */
2849: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2850: survival function given by stepm (the optimization length). Unfortunately it
2851: means that if the survival funtion is printed only each two years of age and if
2852: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2853: results. So we changed our mind and took the option of the best precision.
2854: */
2855: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2856:
2857: agelim=AGESUP;
2858: /* If stepm=6 months */
2859: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2860: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2861:
2862: /* nhstepm age range expressed in number of stepm */
2863: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2864: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2865: /* if (stepm >= YEARM) hstepm=1;*/
2866: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2867: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2868:
2869: for (age=bage; age<=fage; age ++){
2870: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2871: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2872: /* if (stepm >= YEARM) hstepm=1;*/
2873: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
2874:
2875: /* If stepm=6 months */
2876: /* Computed by stepm unit matrices, product of hstepma matrices, stored
2877: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
2878:
2879: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
2880:
2881: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2882:
2883: printf("%d|",(int)age);fflush(stdout);
2884: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2885:
2886: /* Computing expectancies */
2887: for(i=1; i<=nlstate;i++)
2888: for(j=1; j<=nlstate;j++)
2889: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2890: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2891:
2892: /* 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]);*/
2893:
2894: }
2895:
2896: fprintf(ficreseij,"%3.0f",age );
2897: for(i=1; i<=nlstate;i++){
2898: eip=0;
2899: for(j=1; j<=nlstate;j++){
2900: eip +=eij[i][j][(int)age];
2901: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
2902: }
2903: fprintf(ficreseij,"%9.4f", eip );
2904: }
2905: fprintf(ficreseij,"\n");
2906:
2907: }
2908: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2909: printf("\n");
2910: fprintf(ficlog,"\n");
2911:
2912: }
2913:
2914: 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[] )
2915:
2916: {
2917: /* Covariances of health expectancies eij and of total life expectancies according
2918: to initial status i, ei. .
2919: */
2920: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
2921: int nhstepma, nstepma; /* Decreasing with age */
2922: double age, agelim, hf;
2923: double ***p3matp, ***p3matm, ***varhe;
2924: double **dnewm,**doldm;
2925: double *xp, *xm;
2926: double **gp, **gm;
2927: double ***gradg, ***trgradg;
2928: int theta;
2929:
2930: double eip, vip;
2931:
2932: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
2933: xp=vector(1,npar);
2934: xm=vector(1,npar);
2935: dnewm=matrix(1,nlstate*nlstate,1,npar);
2936: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
2937:
2938: pstamp(ficresstdeij);
2939: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
2940: fprintf(ficresstdeij,"# Age");
2941: for(i=1; i<=nlstate;i++){
2942: for(j=1; j<=nlstate;j++)
2943: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
2944: fprintf(ficresstdeij," e%1d. ",i);
2945: }
2946: fprintf(ficresstdeij,"\n");
2947:
2948: pstamp(ficrescveij);
2949: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
2950: fprintf(ficrescveij,"# Age");
2951: for(i=1; i<=nlstate;i++)
2952: for(j=1; j<=nlstate;j++){
2953: cptj= (j-1)*nlstate+i;
2954: for(i2=1; i2<=nlstate;i2++)
2955: for(j2=1; j2<=nlstate;j2++){
2956: cptj2= (j2-1)*nlstate+i2;
2957: if(cptj2 <= cptj)
2958: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
2959: }
2960: }
2961: fprintf(ficrescveij,"\n");
2962:
2963: if(estepm < stepm){
2964: printf ("Problem %d lower than %d\n",estepm, stepm);
2965: }
2966: else hstepm=estepm;
2967: /* We compute the life expectancy from trapezoids spaced every estepm months
2968: * This is mainly to measure the difference between two models: for example
2969: * if stepm=24 months pijx are given only every 2 years and by summing them
2970: * we are calculating an estimate of the Life Expectancy assuming a linear
2971: * progression in between and thus overestimating or underestimating according
2972: * to the curvature of the survival function. If, for the same date, we
2973: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2974: * to compare the new estimate of Life expectancy with the same linear
2975: * hypothesis. A more precise result, taking into account a more precise
2976: * curvature will be obtained if estepm is as small as stepm. */
2977:
2978: /* For example we decided to compute the life expectancy with the smallest unit */
2979: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2980: nhstepm is the number of hstepm from age to agelim
2981: nstepm is the number of stepm from age to agelin.
2982: Look at hpijx to understand the reason of that which relies in memory size
2983: and note for a fixed period like estepm months */
2984: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2985: survival function given by stepm (the optimization length). Unfortunately it
2986: means that if the survival funtion is printed only each two years of age and if
2987: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2988: results. So we changed our mind and took the option of the best precision.
2989: */
2990: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2991:
2992: /* If stepm=6 months */
2993: /* nhstepm age range expressed in number of stepm */
2994: agelim=AGESUP;
2995: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
2996: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2997: /* if (stepm >= YEARM) hstepm=1;*/
2998: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2999:
3000: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3001: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3002: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3003: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3004: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3005: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3006:
3007: for (age=bage; age<=fage; age ++){
3008: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3009: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3010: /* if (stepm >= YEARM) hstepm=1;*/
3011: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3012:
3013: /* If stepm=6 months */
3014: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3015: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3016:
3017: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3018:
3019: /* Computing Variances of health expectancies */
3020: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3021: decrease memory allocation */
3022: for(theta=1; theta <=npar; theta++){
3023: for(i=1; i<=npar; i++){
3024: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3025: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3026: }
3027: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3028: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3029:
3030: for(j=1; j<= nlstate; j++){
3031: for(i=1; i<=nlstate; i++){
3032: for(h=0; h<=nhstepm-1; h++){
3033: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3034: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3035: }
3036: }
3037: }
3038:
3039: for(ij=1; ij<= nlstate*nlstate; ij++)
3040: for(h=0; h<=nhstepm-1; h++){
3041: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3042: }
3043: }/* End theta */
3044:
3045:
3046: for(h=0; h<=nhstepm-1; h++)
3047: for(j=1; j<=nlstate*nlstate;j++)
3048: for(theta=1; theta <=npar; theta++)
3049: trgradg[h][j][theta]=gradg[h][theta][j];
3050:
3051:
3052: for(ij=1;ij<=nlstate*nlstate;ij++)
3053: for(ji=1;ji<=nlstate*nlstate;ji++)
3054: varhe[ij][ji][(int)age] =0.;
3055:
3056: printf("%d|",(int)age);fflush(stdout);
3057: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3058: for(h=0;h<=nhstepm-1;h++){
3059: for(k=0;k<=nhstepm-1;k++){
3060: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3061: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3062: for(ij=1;ij<=nlstate*nlstate;ij++)
3063: for(ji=1;ji<=nlstate*nlstate;ji++)
3064: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3065: }
3066: }
3067:
3068: /* Computing expectancies */
3069: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3070: for(i=1; i<=nlstate;i++)
3071: for(j=1; j<=nlstate;j++)
3072: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3073: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3074:
3075: /* 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]);*/
3076:
3077: }
3078:
3079: fprintf(ficresstdeij,"%3.0f",age );
3080: for(i=1; i<=nlstate;i++){
3081: eip=0.;
3082: vip=0.;
3083: for(j=1; j<=nlstate;j++){
3084: eip += eij[i][j][(int)age];
3085: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3086: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3087: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3088: }
3089: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3090: }
3091: fprintf(ficresstdeij,"\n");
3092:
3093: fprintf(ficrescveij,"%3.0f",age );
3094: for(i=1; i<=nlstate;i++)
3095: for(j=1; j<=nlstate;j++){
3096: cptj= (j-1)*nlstate+i;
3097: for(i2=1; i2<=nlstate;i2++)
3098: for(j2=1; j2<=nlstate;j2++){
3099: cptj2= (j2-1)*nlstate+i2;
3100: if(cptj2 <= cptj)
3101: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3102: }
3103: }
3104: fprintf(ficrescveij,"\n");
3105:
3106: }
3107: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3108: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3109: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3110: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3111: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3112: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3113: printf("\n");
3114: fprintf(ficlog,"\n");
3115:
3116: free_vector(xm,1,npar);
3117: free_vector(xp,1,npar);
3118: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3119: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3120: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3121: }
3122:
3123: /************ Variance ******************/
3124: 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[])
3125: {
3126: /* Variance of health expectancies */
3127: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3128: /* double **newm;*/
3129: double **dnewm,**doldm;
3130: double **dnewmp,**doldmp;
3131: int i, j, nhstepm, hstepm, h, nstepm ;
3132: int k, cptcode;
3133: double *xp;
3134: double **gp, **gm; /* for var eij */
3135: double ***gradg, ***trgradg; /*for var eij */
3136: double **gradgp, **trgradgp; /* for var p point j */
3137: double *gpp, *gmp; /* for var p point j */
3138: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3139: double ***p3mat;
3140: double age,agelim, hf;
3141: double ***mobaverage;
3142: int theta;
3143: char digit[4];
3144: char digitp[25];
3145:
3146: char fileresprobmorprev[FILENAMELENGTH];
3147:
3148: if(popbased==1){
3149: if(mobilav!=0)
3150: strcpy(digitp,"-populbased-mobilav-");
3151: else strcpy(digitp,"-populbased-nomobil-");
3152: }
3153: else
3154: strcpy(digitp,"-stablbased-");
3155:
3156: if (mobilav!=0) {
3157: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3158: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3159: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3160: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3161: }
3162: }
3163:
3164: strcpy(fileresprobmorprev,"prmorprev");
3165: sprintf(digit,"%-d",ij);
3166: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3167: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3168: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
3169: strcat(fileresprobmorprev,fileres);
3170: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3171: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3172: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3173: }
3174: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3175:
3176: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3177: pstamp(ficresprobmorprev);
3178: 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);
3179: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3180: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3181: fprintf(ficresprobmorprev," p.%-d SE",j);
3182: for(i=1; i<=nlstate;i++)
3183: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3184: }
3185: fprintf(ficresprobmorprev,"\n");
3186: fprintf(ficgp,"\n# Routine varevsij");
3187: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
3188: 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");
3189: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3190: /* } */
3191: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3192: pstamp(ficresvij);
3193: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3194: if(popbased==1)
3195: 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);
3196: else
3197: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3198: fprintf(ficresvij,"# Age");
3199: for(i=1; i<=nlstate;i++)
3200: for(j=1; j<=nlstate;j++)
3201: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3202: fprintf(ficresvij,"\n");
3203:
3204: xp=vector(1,npar);
3205: dnewm=matrix(1,nlstate,1,npar);
3206: doldm=matrix(1,nlstate,1,nlstate);
3207: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3208: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3209:
3210: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3211: gpp=vector(nlstate+1,nlstate+ndeath);
3212: gmp=vector(nlstate+1,nlstate+ndeath);
3213: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3214:
3215: if(estepm < stepm){
3216: printf ("Problem %d lower than %d\n",estepm, stepm);
3217: }
3218: else hstepm=estepm;
3219: /* For example we decided to compute the life expectancy with the smallest unit */
3220: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3221: nhstepm is the number of hstepm from age to agelim
3222: nstepm is the number of stepm from age to agelin.
3223: Look at function hpijx to understand why (it is linked to memory size questions) */
3224: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3225: survival function given by stepm (the optimization length). Unfortunately it
3226: means that if the survival funtion is printed every two years of age and if
3227: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3228: results. So we changed our mind and took the option of the best precision.
3229: */
3230: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3231: agelim = AGESUP;
3232: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3233: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3234: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3235: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3236: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3237: gp=matrix(0,nhstepm,1,nlstate);
3238: gm=matrix(0,nhstepm,1,nlstate);
3239:
3240:
3241: for(theta=1; theta <=npar; theta++){
3242: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3243: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3244: }
3245: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3246: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3247:
3248: if (popbased==1) {
3249: if(mobilav ==0){
3250: for(i=1; i<=nlstate;i++)
3251: prlim[i][i]=probs[(int)age][i][ij];
3252: }else{ /* mobilav */
3253: for(i=1; i<=nlstate;i++)
3254: prlim[i][i]=mobaverage[(int)age][i][ij];
3255: }
3256: }
3257:
3258: for(j=1; j<= nlstate; j++){
3259: for(h=0; h<=nhstepm; h++){
3260: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3261: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3262: }
3263: }
3264: /* This for computing probability of death (h=1 means
3265: computed over hstepm matrices product = hstepm*stepm months)
3266: as a weighted average of prlim.
3267: */
3268: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3269: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3270: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3271: }
3272: /* end probability of death */
3273:
3274: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3275: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3276: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3277: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3278:
3279: if (popbased==1) {
3280: if(mobilav ==0){
3281: for(i=1; i<=nlstate;i++)
3282: prlim[i][i]=probs[(int)age][i][ij];
3283: }else{ /* mobilav */
3284: for(i=1; i<=nlstate;i++)
3285: prlim[i][i]=mobaverage[(int)age][i][ij];
3286: }
3287: }
3288:
3289: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
3290: for(h=0; h<=nhstepm; h++){
3291: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3292: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3293: }
3294: }
3295: /* This for computing probability of death (h=1 means
3296: computed over hstepm matrices product = hstepm*stepm months)
3297: as a weighted average of prlim.
3298: */
3299: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3300: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3301: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3302: }
3303: /* end probability of death */
3304:
3305: for(j=1; j<= nlstate; j++) /* vareij */
3306: for(h=0; h<=nhstepm; h++){
3307: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3308: }
3309:
3310: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3311: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3312: }
3313:
3314: } /* End theta */
3315:
3316: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3317:
3318: for(h=0; h<=nhstepm; h++) /* veij */
3319: for(j=1; j<=nlstate;j++)
3320: for(theta=1; theta <=npar; theta++)
3321: trgradg[h][j][theta]=gradg[h][theta][j];
3322:
3323: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3324: for(theta=1; theta <=npar; theta++)
3325: trgradgp[j][theta]=gradgp[theta][j];
3326:
3327:
3328: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3329: for(i=1;i<=nlstate;i++)
3330: for(j=1;j<=nlstate;j++)
3331: vareij[i][j][(int)age] =0.;
3332:
3333: for(h=0;h<=nhstepm;h++){
3334: for(k=0;k<=nhstepm;k++){
3335: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3336: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3337: for(i=1;i<=nlstate;i++)
3338: for(j=1;j<=nlstate;j++)
3339: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3340: }
3341: }
3342:
3343: /* pptj */
3344: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3345: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3346: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3347: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3348: varppt[j][i]=doldmp[j][i];
3349: /* end ppptj */
3350: /* x centered again */
3351: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3352: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3353:
3354: if (popbased==1) {
3355: if(mobilav ==0){
3356: for(i=1; i<=nlstate;i++)
3357: prlim[i][i]=probs[(int)age][i][ij];
3358: }else{ /* mobilav */
3359: for(i=1; i<=nlstate;i++)
3360: prlim[i][i]=mobaverage[(int)age][i][ij];
3361: }
3362: }
3363:
3364: /* This for computing probability of death (h=1 means
3365: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3366: as a weighted average of prlim.
3367: */
3368: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3369: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3370: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3371: }
3372: /* end probability of death */
3373:
3374: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3375: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3376: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3377: for(i=1; i<=nlstate;i++){
3378: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3379: }
3380: }
3381: fprintf(ficresprobmorprev,"\n");
3382:
3383: fprintf(ficresvij,"%.0f ",age );
3384: for(i=1; i<=nlstate;i++)
3385: for(j=1; j<=nlstate;j++){
3386: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3387: }
3388: fprintf(ficresvij,"\n");
3389: free_matrix(gp,0,nhstepm,1,nlstate);
3390: free_matrix(gm,0,nhstepm,1,nlstate);
3391: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3392: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3393: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3394: } /* End age */
3395: free_vector(gpp,nlstate+1,nlstate+ndeath);
3396: free_vector(gmp,nlstate+1,nlstate+ndeath);
3397: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3398: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3399: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
3400: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
3401: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
3402: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3403: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3404: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
3405: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
3406: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
3407: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
3408: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3409: 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);
3410: /* 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);
3411: */
3412: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3413: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3414:
3415: free_vector(xp,1,npar);
3416: free_matrix(doldm,1,nlstate,1,nlstate);
3417: free_matrix(dnewm,1,nlstate,1,npar);
3418: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3419: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3420: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3421: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3422: fclose(ficresprobmorprev);
3423: fflush(ficgp);
3424: fflush(fichtm);
3425: } /* end varevsij */
3426:
3427: /************ Variance of prevlim ******************/
3428: 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[])
3429: {
3430: /* Variance of prevalence limit */
3431: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
3432: double **newm;
3433: double **dnewm,**doldm;
3434: int i, j, nhstepm, hstepm;
3435: int k, cptcode;
3436: double *xp;
3437: double *gp, *gm;
3438: double **gradg, **trgradg;
3439: double age,agelim;
3440: int theta;
3441:
3442: pstamp(ficresvpl);
3443: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3444: fprintf(ficresvpl,"# Age");
3445: for(i=1; i<=nlstate;i++)
3446: fprintf(ficresvpl," %1d-%1d",i,i);
3447: fprintf(ficresvpl,"\n");
3448:
3449: xp=vector(1,npar);
3450: dnewm=matrix(1,nlstate,1,npar);
3451: doldm=matrix(1,nlstate,1,nlstate);
3452:
3453: hstepm=1*YEARM; /* Every year of age */
3454: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3455: agelim = AGESUP;
3456: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3457: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3458: if (stepm >= YEARM) hstepm=1;
3459: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3460: gradg=matrix(1,npar,1,nlstate);
3461: gp=vector(1,nlstate);
3462: gm=vector(1,nlstate);
3463:
3464: for(theta=1; theta <=npar; theta++){
3465: for(i=1; i<=npar; i++){ /* Computes gradient */
3466: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3467: }
3468: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3469: for(i=1;i<=nlstate;i++)
3470: gp[i] = prlim[i][i];
3471:
3472: for(i=1; i<=npar; i++) /* Computes gradient */
3473: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3474: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3475: for(i=1;i<=nlstate;i++)
3476: gm[i] = prlim[i][i];
3477:
3478: for(i=1;i<=nlstate;i++)
3479: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3480: } /* End theta */
3481:
3482: trgradg =matrix(1,nlstate,1,npar);
3483:
3484: for(j=1; j<=nlstate;j++)
3485: for(theta=1; theta <=npar; theta++)
3486: trgradg[j][theta]=gradg[theta][j];
3487:
3488: for(i=1;i<=nlstate;i++)
3489: varpl[i][(int)age] =0.;
3490: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3491: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3492: for(i=1;i<=nlstate;i++)
3493: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3494:
3495: fprintf(ficresvpl,"%.0f ",age );
3496: for(i=1; i<=nlstate;i++)
3497: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3498: fprintf(ficresvpl,"\n");
3499: free_vector(gp,1,nlstate);
3500: free_vector(gm,1,nlstate);
3501: free_matrix(gradg,1,npar,1,nlstate);
3502: free_matrix(trgradg,1,nlstate,1,npar);
3503: } /* End age */
3504:
3505: free_vector(xp,1,npar);
3506: free_matrix(doldm,1,nlstate,1,npar);
3507: free_matrix(dnewm,1,nlstate,1,nlstate);
3508:
3509: }
3510:
3511: /************ Variance of one-step probabilities ******************/
3512: 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[])
3513: {
3514: int i, j=0, i1, k1, l1, t, tj;
3515: int k2, l2, j1, z1;
3516: int k=0,l, cptcode;
3517: int first=1, first1, first2;
3518: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3519: double **dnewm,**doldm;
3520: double *xp;
3521: double *gp, *gm;
3522: double **gradg, **trgradg;
3523: double **mu;
3524: double age,agelim, cov[NCOVMAX+1];
3525: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3526: int theta;
3527: char fileresprob[FILENAMELENGTH];
3528: char fileresprobcov[FILENAMELENGTH];
3529: char fileresprobcor[FILENAMELENGTH];
3530: double ***varpij;
3531:
3532: strcpy(fileresprob,"prob");
3533: strcat(fileresprob,fileres);
3534: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3535: printf("Problem with resultfile: %s\n", fileresprob);
3536: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3537: }
3538: strcpy(fileresprobcov,"probcov");
3539: strcat(fileresprobcov,fileres);
3540: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3541: printf("Problem with resultfile: %s\n", fileresprobcov);
3542: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3543: }
3544: strcpy(fileresprobcor,"probcor");
3545: strcat(fileresprobcor,fileres);
3546: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3547: printf("Problem with resultfile: %s\n", fileresprobcor);
3548: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3549: }
3550: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3551: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3552: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3553: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3554: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3555: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3556: pstamp(ficresprob);
3557: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3558: fprintf(ficresprob,"# Age");
3559: pstamp(ficresprobcov);
3560: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3561: fprintf(ficresprobcov,"# Age");
3562: pstamp(ficresprobcor);
3563: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3564: fprintf(ficresprobcor,"# Age");
3565:
3566:
3567: for(i=1; i<=nlstate;i++)
3568: for(j=1; j<=(nlstate+ndeath);j++){
3569: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3570: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3571: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3572: }
3573: /* fprintf(ficresprob,"\n");
3574: fprintf(ficresprobcov,"\n");
3575: fprintf(ficresprobcor,"\n");
3576: */
3577: xp=vector(1,npar);
3578: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3579: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3580: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3581: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3582: first=1;
3583: fprintf(ficgp,"\n# Routine varprob");
3584: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3585: fprintf(fichtm,"\n");
3586:
3587: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3588: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3589: file %s<br>\n",optionfilehtmcov);
3590: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3591: and drawn. It helps understanding how is the covariance between two incidences.\
3592: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3593: 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. \
3594: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3595: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3596: standard deviations wide on each axis. <br>\
3597: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3598: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3599: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3600:
3601: cov[1]=1;
3602: /* tj=cptcoveff; */
3603: tj = (int) pow(2,cptcoveff);
3604: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3605: j1=0;
3606: for(j1=1; j1<=tj;j1++){
3607: /*for(i1=1; i1<=ncodemax[t];i1++){ */
3608: /*j1++;*/
3609: if (cptcovn>0) {
3610: fprintf(ficresprob, "\n#********** Variable ");
3611: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3612: fprintf(ficresprob, "**********\n#\n");
3613: fprintf(ficresprobcov, "\n#********** Variable ");
3614: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3615: fprintf(ficresprobcov, "**********\n#\n");
3616:
3617: fprintf(ficgp, "\n#********** Variable ");
3618: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3619: fprintf(ficgp, "**********\n#\n");
3620:
3621:
3622: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
3623: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3624: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
3625:
3626: fprintf(ficresprobcor, "\n#********** Variable ");
3627: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3628: fprintf(ficresprobcor, "**********\n#");
3629: }
3630:
3631: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3632: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3633: gp=vector(1,(nlstate)*(nlstate+ndeath));
3634: gm=vector(1,(nlstate)*(nlstate+ndeath));
3635: for (age=bage; age<=fage; age ++){
3636: cov[2]=age;
3637: for (k=1; k<=cptcovn;k++) {
3638: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
3639: * 1 1 1 1 1
3640: * 2 2 1 1 1
3641: * 3 1 2 1 1
3642: */
3643: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
3644: }
3645: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3646: for (k=1; k<=cptcovprod;k++)
3647: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3648:
3649:
3650: for(theta=1; theta <=npar; theta++){
3651: for(i=1; i<=npar; i++)
3652: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3653:
3654: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3655:
3656: k=0;
3657: for(i=1; i<= (nlstate); i++){
3658: for(j=1; j<=(nlstate+ndeath);j++){
3659: k=k+1;
3660: gp[k]=pmmij[i][j];
3661: }
3662: }
3663:
3664: for(i=1; i<=npar; i++)
3665: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
3666:
3667: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3668: k=0;
3669: for(i=1; i<=(nlstate); i++){
3670: for(j=1; j<=(nlstate+ndeath);j++){
3671: k=k+1;
3672: gm[k]=pmmij[i][j];
3673: }
3674: }
3675:
3676: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3677: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3678: }
3679:
3680: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3681: for(theta=1; theta <=npar; theta++)
3682: trgradg[j][theta]=gradg[theta][j];
3683:
3684: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3685: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3686:
3687: pmij(pmmij,cov,ncovmodel,x,nlstate);
3688:
3689: k=0;
3690: for(i=1; i<=(nlstate); i++){
3691: for(j=1; j<=(nlstate+ndeath);j++){
3692: k=k+1;
3693: mu[k][(int) age]=pmmij[i][j];
3694: }
3695: }
3696: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3697: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3698: varpij[i][j][(int)age] = doldm[i][j];
3699:
3700: /*printf("\n%d ",(int)age);
3701: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3702: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3703: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3704: }*/
3705:
3706: fprintf(ficresprob,"\n%d ",(int)age);
3707: fprintf(ficresprobcov,"\n%d ",(int)age);
3708: fprintf(ficresprobcor,"\n%d ",(int)age);
3709:
3710: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3711: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3712: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3713: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3714: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3715: }
3716: i=0;
3717: for (k=1; k<=(nlstate);k++){
3718: for (l=1; l<=(nlstate+ndeath);l++){
3719: i++;
3720: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3721: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3722: for (j=1; j<=i;j++){
3723: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
3724: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3725: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3726: }
3727: }
3728: }/* end of loop for state */
3729: } /* end of loop for age */
3730: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3731: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3732: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3733: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3734:
3735: /* Confidence intervalle of pij */
3736: /*
3737: fprintf(ficgp,"\nunset parametric;unset label");
3738: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3739: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3740: 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);
3741: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3742: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3743: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3744: */
3745:
3746: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3747: first1=1;first2=2;
3748: for (k2=1; k2<=(nlstate);k2++){
3749: for (l2=1; l2<=(nlstate+ndeath);l2++){
3750: if(l2==k2) continue;
3751: j=(k2-1)*(nlstate+ndeath)+l2;
3752: for (k1=1; k1<=(nlstate);k1++){
3753: for (l1=1; l1<=(nlstate+ndeath);l1++){
3754: if(l1==k1) continue;
3755: i=(k1-1)*(nlstate+ndeath)+l1;
3756: if(i<=j) continue;
3757: for (age=bage; age<=fage; age ++){
3758: if ((int)age %5==0){
3759: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3760: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3761: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3762: mu1=mu[i][(int) age]/stepm*YEARM ;
3763: mu2=mu[j][(int) age]/stepm*YEARM;
3764: c12=cv12/sqrt(v1*v2);
3765: /* Computing eigen value of matrix of covariance */
3766: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3767: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3768: if ((lc2 <0) || (lc1 <0) ){
3769: if(first2==1){
3770: first1=0;
3771: 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);
3772: }
3773: 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);
3774: /* lc1=fabs(lc1); */ /* If we want to have them positive */
3775: /* lc2=fabs(lc2); */
3776: }
3777:
3778: /* Eigen vectors */
3779: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3780: /*v21=sqrt(1.-v11*v11); *//* error */
3781: v21=(lc1-v1)/cv12*v11;
3782: v12=-v21;
3783: v22=v11;
3784: tnalp=v21/v11;
3785: if(first1==1){
3786: first1=0;
3787: 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);
3788: }
3789: 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);
3790: /*printf(fignu*/
3791: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3792: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3793: if(first==1){
3794: first=0;
3795: fprintf(ficgp,"\nset parametric;unset label");
3796: 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);
3797: fprintf(ficgp,"\nset ter png small size 320, 240");
3798: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
3799: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3800: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3801: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
3802: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3803: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3804: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
3805: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3806: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3807: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3808: 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",\
3809: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3810: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3811: }else{
3812: first=0;
3813: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
3814: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3815: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3816: 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",\
3817: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3818: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3819: }/* if first */
3820: } /* age mod 5 */
3821: } /* end loop age */
3822: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3823: first=1;
3824: } /*l12 */
3825: } /* k12 */
3826: } /*l1 */
3827: }/* k1 */
3828: /* } /* loop covariates */
3829: }
3830: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3831: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
3832: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3833: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
3834: free_vector(xp,1,npar);
3835: fclose(ficresprob);
3836: fclose(ficresprobcov);
3837: fclose(ficresprobcor);
3838: fflush(ficgp);
3839: fflush(fichtmcov);
3840: }
3841:
3842:
3843: /******************* Printing html file ***********/
3844: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3845: int lastpass, int stepm, int weightopt, char model[],\
3846: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3847: int popforecast, int estepm ,\
3848: double jprev1, double mprev1,double anprev1, \
3849: double jprev2, double mprev2,double anprev2){
3850: int jj1, k1, i1, cpt;
3851:
3852: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
3853: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
3854: </ul>");
3855: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
3856: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
3857: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
3858: fprintf(fichtm,"\
3859: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
3860: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
3861: fprintf(fichtm,"\
3862: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
3863: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
3864: fprintf(fichtm,"\
3865: - (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): \
3866: <a href=\"%s\">%s</a> <br>\n",
3867: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
3868: fprintf(fichtm,"\
3869: - Population projections by age and states: \
3870: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
3871:
3872: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3873:
3874: m=pow(2,cptcoveff);
3875: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3876:
3877: jj1=0;
3878: for(k1=1; k1<=m;k1++){
3879: for(i1=1; i1<=ncodemax[k1];i1++){
3880: jj1++;
3881: if (cptcovn > 0) {
3882: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3883: for (cpt=1; cpt<=cptcoveff;cpt++)
3884: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3885: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3886: }
3887: /* Pij */
3888: 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> \
3889: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3890: /* Quasi-incidences */
3891: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
3892: 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> \
3893: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3894: /* Period (stable) prevalence in each health state */
3895: for(cpt=1; cpt<nlstate;cpt++){
3896: fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
3897: <img src=\"%s%d_%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
3898: }
3899: for(cpt=1; cpt<=nlstate;cpt++) {
3900: fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
3901: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
3902: }
3903: } /* end i1 */
3904: }/* End k1 */
3905: fprintf(fichtm,"</ul>");
3906:
3907:
3908: fprintf(fichtm,"\
3909: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
3910: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
3911:
3912: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3913: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
3914: fprintf(fichtm,"\
3915: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3916: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
3917:
3918: fprintf(fichtm,"\
3919: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3920: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
3921: fprintf(fichtm,"\
3922: - 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): \
3923: <a href=\"%s\">%s</a> <br>\n</li>",
3924: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
3925: fprintf(fichtm,"\
3926: - (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): \
3927: <a href=\"%s\">%s</a> <br>\n</li>",
3928: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
3929: fprintf(fichtm,"\
3930: - 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",
3931: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
3932: fprintf(fichtm,"\
3933: - 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",
3934: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
3935: fprintf(fichtm,"\
3936: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
3937: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
3938:
3939: /* if(popforecast==1) fprintf(fichtm,"\n */
3940: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3941: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3942: /* <br>",fileres,fileres,fileres,fileres); */
3943: /* else */
3944: /* 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); */
3945: fflush(fichtm);
3946: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
3947:
3948: m=pow(2,cptcoveff);
3949: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3950:
3951: jj1=0;
3952: for(k1=1; k1<=m;k1++){
3953: for(i1=1; i1<=ncodemax[k1];i1++){
3954: jj1++;
3955: if (cptcovn > 0) {
3956: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3957: for (cpt=1; cpt<=cptcoveff;cpt++)
3958: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3959: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3960: }
3961: for(cpt=1; cpt<=nlstate;cpt++) {
3962: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
3963: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
3964: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
3965: }
3966: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
3967: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
3968: true period expectancies (those weighted with period prevalences are also\
3969: drawn in addition to the population based expectancies computed using\
3970: observed and cahotic prevalences: %s%d.png<br>\
3971: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
3972: } /* end i1 */
3973: }/* End k1 */
3974: fprintf(fichtm,"</ul>");
3975: fflush(fichtm);
3976: }
3977:
3978: /******************* Gnuplot file **************/
3979: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
3980:
3981: char dirfileres[132],optfileres[132];
3982: int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
3983: int ng=0;
3984: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
3985: /* printf("Problem with file %s",optionfilegnuplot); */
3986: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
3987: /* } */
3988:
3989: /*#ifdef windows */
3990: fprintf(ficgp,"cd \"%s\" \n",pathc);
3991: /*#endif */
3992: m=pow(2,cptcoveff);
3993:
3994: strcpy(dirfileres,optionfilefiname);
3995: strcpy(optfileres,"vpl");
3996: /* 1eme*/
3997: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
3998: for (cpt=1; cpt<= nlstate ; cpt ++) {
3999: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
4000: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
4001: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
4002: fprintf(ficgp,"set xlabel \"Age\" \n\
4003: set ylabel \"Probability\" \n\
4004: set ter png small size 320, 240\n\
4005: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
4006:
4007: for (i=1; i<= nlstate ; i ++) {
4008: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
4009: else fprintf(ficgp," \%%*lf (\%%*lf)");
4010: }
4011: 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);
4012: for (i=1; i<= nlstate ; i ++) {
4013: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
4014: else fprintf(ficgp," \%%*lf (\%%*lf)");
4015: }
4016: fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
4017: for (i=1; i<= nlstate ; i ++) {
4018: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
4019: else fprintf(ficgp," \%%*lf (\%%*lf)");
4020: }
4021: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
4022: }
4023: }
4024: /*2 eme*/
4025: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
4026: for (k1=1; k1<= m ; k1 ++) {
4027: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
4028: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
4029:
4030: for (i=1; i<= nlstate+1 ; i ++) {
4031: k=2*i;
4032: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4033: for (j=1; j<= nlstate+1 ; j ++) {
4034: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
4035: else fprintf(ficgp," \%%*lf (\%%*lf)");
4036: }
4037: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
4038: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
4039: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4040: for (j=1; j<= nlstate+1 ; j ++) {
4041: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
4042: else fprintf(ficgp," \%%*lf (\%%*lf)");
4043: }
4044: fprintf(ficgp,"\" t\"\" w l lt 0,");
4045: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4046: for (j=1; j<= nlstate+1 ; j ++) {
4047: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
4048: else fprintf(ficgp," \%%*lf (\%%*lf)");
4049: }
4050: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4051: else fprintf(ficgp,"\" t\"\" w l lt 0,");
4052: }
4053: }
4054:
4055: /*3eme*/
4056:
4057: for (k1=1; k1<= m ; k1 ++) {
4058: for (cpt=1; cpt<= nlstate ; cpt ++) {
4059: /* k=2+nlstate*(2*cpt-2); */
4060: k=2+(nlstate+1)*(cpt-1);
4061: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
4062: fprintf(ficgp,"set ter png small size 320, 240\n\
4063: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
4064: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4065: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4066: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4067: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4068: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4069: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4070:
4071: */
4072: for (i=1; i< nlstate ; i ++) {
4073: 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);
4074: /* 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);*/
4075:
4076: }
4077: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
4078: }
4079: }
4080:
4081: /* CV preval stable (period) */
4082: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
4083: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
4084: k=3;
4085: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
4086: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
4087: l=(nlstate+ndeath)*(cpt-1)+1;
4088: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
4089: set ter png small size 320, 240\n\
4090: unset log y\n\
4091: plot [%.f:%.f] ", ageminpar, agemaxpar);
4092: for (i=1; i<= nlstate ; i ++){
4093: if(i==1)
4094: fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
4095: else
4096: fprintf(ficgp,", '' ");
4097: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l,k+l);
4098: for (j=1; j<= (nlstate-1) ; j ++)
4099: fprintf(ficgp,"+$%d",k+l+j);
4100: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
4101: } /* nlstate */
4102: fprintf(ficgp,"\n");
4103: } /* end cpt state*/
4104: } /* end covariate */
4105:
4106: /* proba elementaires */
4107: for(i=1,jk=1; i <=nlstate; i++){
4108: for(k=1; k <=(nlstate+ndeath); k++){
4109: if (k != i) {
4110: for(j=1; j <=ncovmodel; j++){
4111: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
4112: jk++;
4113: fprintf(ficgp,"\n");
4114: }
4115: }
4116: }
4117: }
4118: /*goto avoid;*/
4119: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
4120: for(jk=1; jk <=m; jk++) {
4121: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
4122: if (ng==2)
4123: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
4124: else
4125: fprintf(ficgp,"\nset title \"Probability\"\n");
4126: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
4127: i=1;
4128: for(k2=1; k2<=nlstate; k2++) {
4129: k3=i;
4130: for(k=1; k<=(nlstate+ndeath); k++) {
4131: if (k != k2){
4132: if(ng==2)
4133: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
4134: else
4135: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
4136: ij=1;/* To be checked else nbcode[0][0] wrong */
4137: for(j=3; j <=ncovmodel; j++) {
4138: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
4139: /* /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
4140: /* ij++; */
4141: /* } */
4142: /* else */
4143: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4144: }
4145: fprintf(ficgp,")/(1");
4146:
4147: for(k1=1; k1 <=nlstate; k1++){
4148: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
4149: ij=1;
4150: for(j=3; j <=ncovmodel; j++){
4151: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
4152: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
4153: /* ij++; */
4154: /* } */
4155: /* else */
4156: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4157: }
4158: fprintf(ficgp,")");
4159: }
4160: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
4161: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
4162: i=i+ncovmodel;
4163: }
4164: } /* end k */
4165: } /* end k2 */
4166: } /* end jk */
4167: } /* end ng */
4168: avoid:
4169: fflush(ficgp);
4170: } /* end gnuplot */
4171:
4172:
4173: /*************** Moving average **************/
4174: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
4175:
4176: int i, cpt, cptcod;
4177: int modcovmax =1;
4178: int mobilavrange, mob;
4179: double age;
4180:
4181: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
4182: a covariate has 2 modalities */
4183: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
4184:
4185: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
4186: if(mobilav==1) mobilavrange=5; /* default */
4187: else mobilavrange=mobilav;
4188: for (age=bage; age<=fage; age++)
4189: for (i=1; i<=nlstate;i++)
4190: for (cptcod=1;cptcod<=modcovmax;cptcod++)
4191: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
4192: /* We keep the original values on the extreme ages bage, fage and for
4193: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
4194: we use a 5 terms etc. until the borders are no more concerned.
4195: */
4196: for (mob=3;mob <=mobilavrange;mob=mob+2){
4197: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
4198: for (i=1; i<=nlstate;i++){
4199: for (cptcod=1;cptcod<=modcovmax;cptcod++){
4200: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
4201: for (cpt=1;cpt<=(mob-1)/2;cpt++){
4202: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
4203: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
4204: }
4205: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
4206: }
4207: }
4208: }/* end age */
4209: }/* end mob */
4210: }else return -1;
4211: return 0;
4212: }/* End movingaverage */
4213:
4214:
4215: /************** Forecasting ******************/
4216: 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){
4217: /* proj1, year, month, day of starting projection
4218: agemin, agemax range of age
4219: dateprev1 dateprev2 range of dates during which prevalence is computed
4220: anproj2 year of en of projection (same day and month as proj1).
4221: */
4222: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
4223: int *popage;
4224: double agec; /* generic age */
4225: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
4226: double *popeffectif,*popcount;
4227: double ***p3mat;
4228: double ***mobaverage;
4229: char fileresf[FILENAMELENGTH];
4230:
4231: agelim=AGESUP;
4232: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4233:
4234: strcpy(fileresf,"f");
4235: strcat(fileresf,fileres);
4236: if((ficresf=fopen(fileresf,"w"))==NULL) {
4237: printf("Problem with forecast resultfile: %s\n", fileresf);
4238: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
4239: }
4240: printf("Computing forecasting: result on file '%s' \n", fileresf);
4241: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
4242:
4243: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4244:
4245: if (mobilav!=0) {
4246: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4247: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4248: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4249: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4250: }
4251: }
4252:
4253: stepsize=(int) (stepm+YEARM-1)/YEARM;
4254: if (stepm<=12) stepsize=1;
4255: if(estepm < stepm){
4256: printf ("Problem %d lower than %d\n",estepm, stepm);
4257: }
4258: else hstepm=estepm;
4259:
4260: hstepm=hstepm/stepm;
4261: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
4262: fractional in yp1 */
4263: anprojmean=yp;
4264: yp2=modf((yp1*12),&yp);
4265: mprojmean=yp;
4266: yp1=modf((yp2*30.5),&yp);
4267: jprojmean=yp;
4268: if(jprojmean==0) jprojmean=1;
4269: if(mprojmean==0) jprojmean=1;
4270:
4271: i1=cptcoveff;
4272: if (cptcovn < 1){i1=1;}
4273:
4274: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4275:
4276: fprintf(ficresf,"#****** Routine prevforecast **\n");
4277:
4278: /* if (h==(int)(YEARM*yearp)){ */
4279: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4280: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4281: k=k+1;
4282: fprintf(ficresf,"\n#******");
4283: for(j=1;j<=cptcoveff;j++) {
4284: 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]]);
4285: }
4286: fprintf(ficresf,"******\n");
4287: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4288: for(j=1; j<=nlstate+ndeath;j++){
4289: for(i=1; i<=nlstate;i++)
4290: fprintf(ficresf," p%d%d",i,j);
4291: fprintf(ficresf," p.%d",j);
4292: }
4293: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4294: fprintf(ficresf,"\n");
4295: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4296:
4297: for (agec=fage; agec>=(ageminpar-1); agec--){
4298: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4299: nhstepm = nhstepm/hstepm;
4300: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4301: oldm=oldms;savm=savms;
4302: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4303:
4304: for (h=0; h<=nhstepm; h++){
4305: if (h*hstepm/YEARM*stepm ==yearp) {
4306: fprintf(ficresf,"\n");
4307: for(j=1;j<=cptcoveff;j++)
4308: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4309: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4310: }
4311: for(j=1; j<=nlstate+ndeath;j++) {
4312: ppij=0.;
4313: for(i=1; i<=nlstate;i++) {
4314: if (mobilav==1)
4315: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4316: else {
4317: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4318: }
4319: if (h*hstepm/YEARM*stepm== yearp) {
4320: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4321: }
4322: } /* end i */
4323: if (h*hstepm/YEARM*stepm==yearp) {
4324: fprintf(ficresf," %.3f", ppij);
4325: }
4326: }/* end j */
4327: } /* end h */
4328: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4329: } /* end agec */
4330: } /* end yearp */
4331: } /* end cptcod */
4332: } /* end cptcov */
4333:
4334: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4335:
4336: fclose(ficresf);
4337: }
4338:
4339: /************** Forecasting *****not tested NB*************/
4340: 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){
4341:
4342: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4343: int *popage;
4344: double calagedatem, agelim, kk1, kk2;
4345: double *popeffectif,*popcount;
4346: double ***p3mat,***tabpop,***tabpopprev;
4347: double ***mobaverage;
4348: char filerespop[FILENAMELENGTH];
4349:
4350: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4351: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4352: agelim=AGESUP;
4353: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4354:
4355: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4356:
4357:
4358: strcpy(filerespop,"pop");
4359: strcat(filerespop,fileres);
4360: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4361: printf("Problem with forecast resultfile: %s\n", filerespop);
4362: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4363: }
4364: printf("Computing forecasting: result on file '%s' \n", filerespop);
4365: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4366:
4367: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4368:
4369: if (mobilav!=0) {
4370: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4371: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4372: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4373: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4374: }
4375: }
4376:
4377: stepsize=(int) (stepm+YEARM-1)/YEARM;
4378: if (stepm<=12) stepsize=1;
4379:
4380: agelim=AGESUP;
4381:
4382: hstepm=1;
4383: hstepm=hstepm/stepm;
4384:
4385: if (popforecast==1) {
4386: if((ficpop=fopen(popfile,"r"))==NULL) {
4387: printf("Problem with population file : %s\n",popfile);exit(0);
4388: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4389: }
4390: popage=ivector(0,AGESUP);
4391: popeffectif=vector(0,AGESUP);
4392: popcount=vector(0,AGESUP);
4393:
4394: i=1;
4395: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4396:
4397: imx=i;
4398: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4399: }
4400:
4401: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4402: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4403: k=k+1;
4404: fprintf(ficrespop,"\n#******");
4405: for(j=1;j<=cptcoveff;j++) {
4406: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4407: }
4408: fprintf(ficrespop,"******\n");
4409: fprintf(ficrespop,"# Age");
4410: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4411: if (popforecast==1) fprintf(ficrespop," [Population]");
4412:
4413: for (cpt=0; cpt<=0;cpt++) {
4414: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4415:
4416: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4417: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4418: nhstepm = nhstepm/hstepm;
4419:
4420: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4421: oldm=oldms;savm=savms;
4422: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4423:
4424: for (h=0; h<=nhstepm; h++){
4425: if (h==(int) (calagedatem+YEARM*cpt)) {
4426: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4427: }
4428: for(j=1; j<=nlstate+ndeath;j++) {
4429: kk1=0.;kk2=0;
4430: for(i=1; i<=nlstate;i++) {
4431: if (mobilav==1)
4432: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4433: else {
4434: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4435: }
4436: }
4437: if (h==(int)(calagedatem+12*cpt)){
4438: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4439: /*fprintf(ficrespop," %.3f", kk1);
4440: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4441: }
4442: }
4443: for(i=1; i<=nlstate;i++){
4444: kk1=0.;
4445: for(j=1; j<=nlstate;j++){
4446: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4447: }
4448: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
4449: }
4450:
4451: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
4452: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4453: }
4454: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4455: }
4456: }
4457:
4458: /******/
4459:
4460: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4461: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4462: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4463: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4464: nhstepm = nhstepm/hstepm;
4465:
4466: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4467: oldm=oldms;savm=savms;
4468: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4469: for (h=0; h<=nhstepm; h++){
4470: if (h==(int) (calagedatem+YEARM*cpt)) {
4471: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4472: }
4473: for(j=1; j<=nlstate+ndeath;j++) {
4474: kk1=0.;kk2=0;
4475: for(i=1; i<=nlstate;i++) {
4476: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4477: }
4478: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
4479: }
4480: }
4481: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4482: }
4483: }
4484: }
4485: }
4486:
4487: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4488:
4489: if (popforecast==1) {
4490: free_ivector(popage,0,AGESUP);
4491: free_vector(popeffectif,0,AGESUP);
4492: free_vector(popcount,0,AGESUP);
4493: }
4494: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4495: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4496: fclose(ficrespop);
4497: } /* End of popforecast */
4498:
4499: int fileappend(FILE *fichier, char *optionfich)
4500: {
4501: if((fichier=fopen(optionfich,"a"))==NULL) {
4502: printf("Problem with file: %s\n", optionfich);
4503: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4504: return (0);
4505: }
4506: fflush(fichier);
4507: return (1);
4508: }
4509:
4510:
4511: /**************** function prwizard **********************/
4512: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4513: {
4514:
4515: /* Wizard to print covariance matrix template */
4516:
4517: char ca[32], cb[32], cc[32];
4518: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
4519: int numlinepar;
4520:
4521: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4522: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4523: for(i=1; i <=nlstate; i++){
4524: jj=0;
4525: for(j=1; j <=nlstate+ndeath; j++){
4526: if(j==i) continue;
4527: jj++;
4528: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4529: printf("%1d%1d",i,j);
4530: fprintf(ficparo,"%1d%1d",i,j);
4531: for(k=1; k<=ncovmodel;k++){
4532: /* printf(" %lf",param[i][j][k]); */
4533: /* fprintf(ficparo," %lf",param[i][j][k]); */
4534: printf(" 0.");
4535: fprintf(ficparo," 0.");
4536: }
4537: printf("\n");
4538: fprintf(ficparo,"\n");
4539: }
4540: }
4541: printf("# Scales (for hessian or gradient estimation)\n");
4542: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4543: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4544: for(i=1; i <=nlstate; i++){
4545: jj=0;
4546: for(j=1; j <=nlstate+ndeath; j++){
4547: if(j==i) continue;
4548: jj++;
4549: fprintf(ficparo,"%1d%1d",i,j);
4550: printf("%1d%1d",i,j);
4551: fflush(stdout);
4552: for(k=1; k<=ncovmodel;k++){
4553: /* printf(" %le",delti3[i][j][k]); */
4554: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4555: printf(" 0.");
4556: fprintf(ficparo," 0.");
4557: }
4558: numlinepar++;
4559: printf("\n");
4560: fprintf(ficparo,"\n");
4561: }
4562: }
4563: printf("# Covariance matrix\n");
4564: /* # 121 Var(a12)\n\ */
4565: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4566: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4567: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4568: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4569: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4570: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4571: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4572: fflush(stdout);
4573: fprintf(ficparo,"# Covariance matrix\n");
4574: /* # 121 Var(a12)\n\ */
4575: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4576: /* # ...\n\ */
4577: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4578:
4579: for(itimes=1;itimes<=2;itimes++){
4580: jj=0;
4581: for(i=1; i <=nlstate; i++){
4582: for(j=1; j <=nlstate+ndeath; j++){
4583: if(j==i) continue;
4584: for(k=1; k<=ncovmodel;k++){
4585: jj++;
4586: ca[0]= k+'a'-1;ca[1]='\0';
4587: if(itimes==1){
4588: printf("#%1d%1d%d",i,j,k);
4589: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4590: }else{
4591: printf("%1d%1d%d",i,j,k);
4592: fprintf(ficparo,"%1d%1d%d",i,j,k);
4593: /* printf(" %.5le",matcov[i][j]); */
4594: }
4595: ll=0;
4596: for(li=1;li <=nlstate; li++){
4597: for(lj=1;lj <=nlstate+ndeath; lj++){
4598: if(lj==li) continue;
4599: for(lk=1;lk<=ncovmodel;lk++){
4600: ll++;
4601: if(ll<=jj){
4602: cb[0]= lk +'a'-1;cb[1]='\0';
4603: if(ll<jj){
4604: if(itimes==1){
4605: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4606: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4607: }else{
4608: printf(" 0.");
4609: fprintf(ficparo," 0.");
4610: }
4611: }else{
4612: if(itimes==1){
4613: printf(" Var(%s%1d%1d)",ca,i,j);
4614: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4615: }else{
4616: printf(" 0.");
4617: fprintf(ficparo," 0.");
4618: }
4619: }
4620: }
4621: } /* end lk */
4622: } /* end lj */
4623: } /* end li */
4624: printf("\n");
4625: fprintf(ficparo,"\n");
4626: numlinepar++;
4627: } /* end k*/
4628: } /*end j */
4629: } /* end i */
4630: } /* end itimes */
4631:
4632: } /* end of prwizard */
4633: /******************* Gompertz Likelihood ******************************/
4634: double gompertz(double x[])
4635: {
4636: double A,B,L=0.0,sump=0.,num=0.;
4637: int i,n=0; /* n is the size of the sample */
4638:
4639: for (i=0;i<=imx-1 ; i++) {
4640: sump=sump+weight[i];
4641: /* sump=sump+1;*/
4642: num=num+1;
4643: }
4644:
4645:
4646: /* for (i=0; i<=imx; i++)
4647: 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]);*/
4648:
4649: for (i=1;i<=imx ; i++)
4650: {
4651: if (cens[i] == 1 && wav[i]>1)
4652: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
4653:
4654: if (cens[i] == 0 && wav[i]>1)
4655: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4656: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
4657:
4658: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4659: if (wav[i] > 1 ) { /* ??? */
4660: L=L+A*weight[i];
4661: /* 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]);*/
4662: }
4663: }
4664:
4665: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4666:
4667: return -2*L*num/sump;
4668: }
4669:
4670: #ifdef GSL
4671: /******************* Gompertz_f Likelihood ******************************/
4672: double gompertz_f(const gsl_vector *v, void *params)
4673: {
4674: double A,B,LL=0.0,sump=0.,num=0.;
4675: double *x= (double *) v->data;
4676: int i,n=0; /* n is the size of the sample */
4677:
4678: for (i=0;i<=imx-1 ; i++) {
4679: sump=sump+weight[i];
4680: /* sump=sump+1;*/
4681: num=num+1;
4682: }
4683:
4684:
4685: /* for (i=0; i<=imx; i++)
4686: 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]);*/
4687: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
4688: for (i=1;i<=imx ; i++)
4689: {
4690: if (cens[i] == 1 && wav[i]>1)
4691: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
4692:
4693: if (cens[i] == 0 && wav[i]>1)
4694: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
4695: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
4696:
4697: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4698: if (wav[i] > 1 ) { /* ??? */
4699: LL=LL+A*weight[i];
4700: /* 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]);*/
4701: }
4702: }
4703:
4704: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4705: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
4706:
4707: return -2*LL*num/sump;
4708: }
4709: #endif
4710:
4711: /******************* Printing html file ***********/
4712: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4713: int lastpass, int stepm, int weightopt, char model[],\
4714: int imx, double p[],double **matcov,double agemortsup){
4715: int i,k;
4716:
4717: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4718: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4719: for (i=1;i<=2;i++)
4720: 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]));
4721: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4722: fprintf(fichtm,"</ul>");
4723:
4724: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4725:
4726: 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>");
4727:
4728: for (k=agegomp;k<(agemortsup-2);k++)
4729: 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]);
4730:
4731:
4732: fflush(fichtm);
4733: }
4734:
4735: /******************* Gnuplot file **************/
4736: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4737:
4738: char dirfileres[132],optfileres[132];
4739: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
4740: int ng;
4741:
4742:
4743: /*#ifdef windows */
4744: fprintf(ficgp,"cd \"%s\" \n",pathc);
4745: /*#endif */
4746:
4747:
4748: strcpy(dirfileres,optionfilefiname);
4749: strcpy(optfileres,"vpl");
4750: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4751: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
4752: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
4753: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
4754: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4755:
4756: }
4757:
4758: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
4759: {
4760:
4761: /*-------- data file ----------*/
4762: FILE *fic;
4763: char dummy[]=" ";
4764: int i, j, n;
4765: int linei, month, year,iout;
4766: char line[MAXLINE], linetmp[MAXLINE];
4767: char stra[80], strb[80];
4768: char *stratrunc;
4769: int lstra;
4770:
4771:
4772: if((fic=fopen(datafile,"r"))==NULL) {
4773: printf("Problem while opening datafile: %s\n", datafile);return 1;
4774: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
4775: }
4776:
4777: i=1;
4778: linei=0;
4779: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
4780: linei=linei+1;
4781: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
4782: if(line[j] == '\t')
4783: line[j] = ' ';
4784: }
4785: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
4786: ;
4787: };
4788: line[j+1]=0; /* Trims blanks at end of line */
4789: if(line[0]=='#'){
4790: fprintf(ficlog,"Comment line\n%s\n",line);
4791: printf("Comment line\n%s\n",line);
4792: continue;
4793: }
4794: trimbb(linetmp,line); /* Trims multiple blanks in line */
4795: for (j=0; line[j]!='\0';j++){
4796: line[j]=linetmp[j];
4797: }
4798:
4799:
4800: for (j=maxwav;j>=1;j--){
4801: cutv(stra, strb, line, ' ');
4802: if(strb[0]=='.') { /* Missing status */
4803: lval=-1;
4804: }else{
4805: errno=0;
4806: lval=strtol(strb,&endptr,10);
4807: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
4808: if( strb[0]=='\0' || (*endptr != '\0')){
4809: 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);
4810: 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);
4811: return 1;
4812: }
4813: }
4814: s[j][i]=lval;
4815:
4816: strcpy(line,stra);
4817: cutv(stra, strb,line,' ');
4818: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4819: }
4820: else if(iout=sscanf(strb,"%s.",dummy) != 0){
4821: month=99;
4822: year=9999;
4823: }else{
4824: 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);
4825: 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);
4826: return 1;
4827: }
4828: anint[j][i]= (double) year;
4829: mint[j][i]= (double)month;
4830: strcpy(line,stra);
4831: } /* ENd Waves */
4832:
4833: cutv(stra, strb,line,' ');
4834: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4835: }
4836: else if(iout=sscanf(strb,"%s.",dummy) != 0){
4837: month=99;
4838: year=9999;
4839: }else{
4840: 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);
4841: 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);
4842: return 1;
4843: }
4844: andc[i]=(double) year;
4845: moisdc[i]=(double) month;
4846: strcpy(line,stra);
4847:
4848: cutv(stra, strb,line,' ');
4849: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4850: }
4851: else if(iout=sscanf(strb,"%s.", dummy) != 0){
4852: month=99;
4853: year=9999;
4854: }else{
4855: 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);
4856: 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);
4857: return 1;
4858: }
4859: if (year==9999) {
4860: 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);
4861: 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);
4862: return 1;
4863:
4864: }
4865: annais[i]=(double)(year);
4866: moisnais[i]=(double)(month);
4867: strcpy(line,stra);
4868:
4869: cutv(stra, strb,line,' ');
4870: errno=0;
4871: dval=strtod(strb,&endptr);
4872: if( strb[0]=='\0' || (*endptr != '\0')){
4873: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
4874: 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);
4875: fflush(ficlog);
4876: return 1;
4877: }
4878: weight[i]=dval;
4879: strcpy(line,stra);
4880:
4881: for (j=ncovcol;j>=1;j--){
4882: cutv(stra, strb,line,' ');
4883: if(strb[0]=='.') { /* Missing status */
4884: lval=-1;
4885: }else{
4886: errno=0;
4887: lval=strtol(strb,&endptr,10);
4888: if( strb[0]=='\0' || (*endptr != '\0')){
4889: 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);
4890: 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);
4891: return 1;
4892: }
4893: }
4894: if(lval <-1 || lval >1){
4895: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
4896: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
4897: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
4898: For example, for multinomial values like 1, 2 and 3,\n \
4899: build V1=0 V2=0 for the reference value (1),\n \
4900: V1=1 V2=0 for (2) \n \
4901: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
4902: output of IMaCh is often meaningless.\n \
4903: Exiting.\n",lval,linei, i,line,j);
4904: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
4905: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
4906: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
4907: For example, for multinomial values like 1, 2 and 3,\n \
4908: build V1=0 V2=0 for the reference value (1),\n \
4909: V1=1 V2=0 for (2) \n \
4910: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
4911: output of IMaCh is often meaningless.\n \
4912: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
4913: return 1;
4914: }
4915: covar[j][i]=(double)(lval);
4916: strcpy(line,stra);
4917: }
4918: lstra=strlen(stra);
4919:
4920: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
4921: stratrunc = &(stra[lstra-9]);
4922: num[i]=atol(stratrunc);
4923: }
4924: else
4925: num[i]=atol(stra);
4926: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
4927: 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;}*/
4928:
4929: i=i+1;
4930: } /* End loop reading data */
4931:
4932: *imax=i-1; /* Number of individuals */
4933: fclose(fic);
4934:
4935: return (0);
4936: endread:
4937: printf("Exiting readdata: ");
4938: fclose(fic);
4939: return (1);
4940:
4941:
4942:
4943: }
4944: void removespace(char *str) {
4945: char *p1 = str, *p2 = str;
4946: do
4947: while (*p2 == ' ')
4948: p2++;
4949: while (*p1++ = *p2++);
4950: }
4951:
4952: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
4953: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
4954: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
4955: * - cptcovn or number of covariates k of the models excluding age*products =6
4956: * - cptcovage number of covariates with age*products =2
4957: * - cptcovs number of simple covariates
4958: * - 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
4959: * which is a new column after the 9 (ncovcol) variables.
4960: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
4961: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
4962: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
4963: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
4964: */
4965: {
4966: int i, j, k, ks;
4967: int i1, j1, k1, k2;
4968: char modelsav[80];
4969: char stra[80], strb[80], strc[80], strd[80],stre[80];
4970:
4971: /*removespace(model);*/
4972: if (strlen(model) >1){ /* If there is at least 1 covariate */
4973: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
4974: j=nbocc(model,'+'); /**< j=Number of '+' */
4975: j1=nbocc(model,'*'); /**< j1=Number of '*' */
4976: cptcovs=j+1-j1; /**< Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2 */
4977: cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
4978: /* including age products which are counted in cptcovage.
4979: /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
4980: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
4981: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
4982: strcpy(modelsav,model);
4983: if (strstr(model,"AGE") !=0){
4984: printf("Error. AGE must be in lower case 'age' model=%s ",model);
4985: fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
4986: return 1;
4987: }
4988: if (strstr(model,"v") !=0){
4989: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
4990: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
4991: return 1;
4992: }
4993:
4994: /* Design
4995: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
4996: * < ncovcol=8 >
4997: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
4998: * k= 1 2 3 4 5 6 7 8
4999: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
5000: * covar[k,i], value of kth covariate if not including age for individual i:
5001: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
5002: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
5003: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
5004: * Tage[++cptcovage]=k
5005: * if products, new covar are created after ncovcol with k1
5006: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
5007: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
5008: * 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
5009: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
5010: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
5011: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
5012: * < ncovcol=8 >
5013: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
5014: * k= 1 2 3 4 5 6 7 8 9 10 11 12
5015: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
5016: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5017: * p Tprod[1]@2={ 6, 5}
5018: *p Tvard[1][1]@4= {7, 8, 5, 6}
5019: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
5020: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
5021: *How to reorganize?
5022: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
5023: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5024: * {2, 1, 4, 8, 5, 6, 3, 7}
5025: * Struct []
5026: */
5027:
5028: /* This loop fills the array Tvar from the string 'model'.*/
5029: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
5030: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
5031: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
5032: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
5033: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
5034: /* k=1 Tvar[1]=2 (from V2) */
5035: /* k=5 Tvar[5] */
5036: /* for (k=1; k<=cptcovn;k++) { */
5037: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
5038: /* } */
5039: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
5040: /*
5041: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
5042: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
5043: Tvar[k]=0;
5044: cptcovage=0;
5045: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
5046: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5047: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
5048: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
5049: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5050: /*scanf("%d",i);*/
5051: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
5052: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
5053: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
5054: /* covar is not filled and then is empty */
5055: cptcovprod--;
5056: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
5057: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
5058: cptcovage++; /* Sums the number of covariates which include age as a product */
5059: Tage[cptcovage]=k; /* Tage[1] = 4 */
5060: /*printf("stre=%s ", stre);*/
5061: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
5062: cptcovprod--;
5063: cutl(stre,strb,strc,'V');
5064: Tvar[k]=atoi(stre);
5065: cptcovage++;
5066: Tage[cptcovage]=k;
5067: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
5068: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
5069: cptcovn++;
5070: cptcovprodnoage++;k1++;
5071: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5072: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
5073: because this model-covariate is a construction we invent a new column
5074: ncovcol + k1
5075: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
5076: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
5077: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
5078: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
5079: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
5080: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
5081: k2=k2+2;
5082: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
5083: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
5084: for (i=1; i<=lastobs;i++){
5085: /* Computes the new covariate which is a product of
5086: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
5087: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
5088: }
5089: } /* End age is not in the model */
5090: } /* End if model includes a product */
5091: else { /* no more sum */
5092: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5093: /* scanf("%d",i);*/
5094: cutl(strd,strc,strb,'V');
5095: ks++; /**< Number of simple covariates */
5096: cptcovn++;
5097: Tvar[k]=atoi(strd);
5098: }
5099: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
5100: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5101: scanf("%d",i);*/
5102: } /* end of loop + */
5103: } /* end model */
5104:
5105: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5106: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5107:
5108: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5109: printf("cptcovprod=%d ", cptcovprod);
5110: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5111:
5112: scanf("%d ",i);*/
5113:
5114:
5115: return (0); /* with covar[new additional covariate if product] and Tage if age */
5116: endread:
5117: printf("Exiting decodemodel: ");
5118: return (1);
5119: }
5120:
5121: calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
5122: {
5123: int i, m;
5124:
5125: for (i=1; i<=imx; i++) {
5126: for(m=2; (m<= maxwav); m++) {
5127: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5128: anint[m][i]=9999;
5129: s[m][i]=-1;
5130: }
5131: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
5132: *nberr++;
5133: 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\n",(int)moisdc[i],(int)andc[i],num[i],i);
5134: 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\n",(int)moisdc[i],(int)andc[i],num[i],i);
5135: s[m][i]=-1;
5136: }
5137: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
5138: *nberr++;
5139: 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]);
5140: 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]);
5141: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5142: }
5143: }
5144: }
5145:
5146: for (i=1; i<=imx; i++) {
5147: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5148: for(m=firstpass; (m<= lastpass); m++){
5149: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5150: if (s[m][i] >= nlstate+1) {
5151: if(agedc[i]>0)
5152: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
5153: agev[m][i]=agedc[i];
5154: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
5155: else {
5156: if ((int)andc[i]!=9999){
5157: nbwarn++;
5158: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5159: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5160: agev[m][i]=-1;
5161: }
5162: }
5163: }
5164: else if(s[m][i] !=9){ /* Standard case, age in fractional
5165: years but with the precision of a month */
5166: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5167: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5168: agev[m][i]=1;
5169: else if(agev[m][i] < *agemin){
5170: *agemin=agev[m][i];
5171: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
5172: }
5173: else if(agev[m][i] >*agemax){
5174: *agemax=agev[m][i];
5175: printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);
5176: }
5177: /*agev[m][i]=anint[m][i]-annais[i];*/
5178: /* agev[m][i] = age[i]+2*m;*/
5179: }
5180: else { /* =9 */
5181: agev[m][i]=1;
5182: s[m][i]=-1;
5183: }
5184: }
5185: else /*= 0 Unknown */
5186: agev[m][i]=1;
5187: }
5188:
5189: }
5190: for (i=1; i<=imx; i++) {
5191: for(m=firstpass; (m<=lastpass); m++){
5192: if (s[m][i] > (nlstate+ndeath)) {
5193: *nberr++;
5194: 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);
5195: 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);
5196: return 1;
5197: }
5198: }
5199: }
5200:
5201: /*for (i=1; i<=imx; i++){
5202: for (m=firstpass; (m<lastpass); m++){
5203: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5204: }
5205:
5206: }*/
5207:
5208:
5209: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5210: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5211:
5212: return (0);
5213: endread:
5214: printf("Exiting calandcheckages: ");
5215: return (1);
5216: }
5217:
5218:
5219: /***********************************************/
5220: /**************** Main Program *****************/
5221: /***********************************************/
5222:
5223: int main(int argc, char *argv[])
5224: {
5225: #ifdef GSL
5226: const gsl_multimin_fminimizer_type *T;
5227: size_t iteri = 0, it;
5228: int rval = GSL_CONTINUE;
5229: int status = GSL_SUCCESS;
5230: double ssval;
5231: #endif
5232: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
5233: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
5234: int linei, month, year,iout;
5235: int jj, ll, li, lj, lk, imk;
5236: int numlinepar=0; /* Current linenumber of parameter file */
5237: int itimes;
5238: int NDIM=2;
5239: int vpopbased=0;
5240:
5241: char ca[32], cb[32], cc[32];
5242: /* FILE *fichtm; *//* Html File */
5243: /* FILE *ficgp;*/ /*Gnuplot File */
5244: struct stat info;
5245: double agedeb, agefin,hf;
5246: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
5247:
5248: double fret;
5249: double **xi,tmp,delta;
5250:
5251: double dum; /* Dummy variable */
5252: double ***p3mat;
5253: double ***mobaverage;
5254: int *indx;
5255: char line[MAXLINE], linepar[MAXLINE];
5256: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
5257: char pathr[MAXLINE], pathimach[MAXLINE];
5258: char **bp, *tok, *val; /* pathtot */
5259: int firstobs=1, lastobs=10;
5260: int sdeb, sfin; /* Status at beginning and end */
5261: int c, h , cpt,l;
5262: int ju,jl, mi;
5263: int i1,j1, jk,aa,bb, stepsize, ij;
5264: int jnais,jdc,jint4,jint1,jint2,jint3,*tab;
5265: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
5266: int mobilav=0,popforecast=0;
5267: int hstepm, nhstepm;
5268: int agemortsup;
5269: float sumlpop=0.;
5270: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
5271: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
5272:
5273: double bage, fage, age, agelim, agebase;
5274: double ftolpl=FTOL;
5275: double **prlim;
5276: double ***param; /* Matrix of parameters */
5277: double *p;
5278: double **matcov; /* Matrix of covariance */
5279: double ***delti3; /* Scale */
5280: double *delti; /* Scale */
5281: double ***eij, ***vareij;
5282: double **varpl; /* Variances of prevalence limits by age */
5283: double *epj, vepp;
5284: double kk1, kk2;
5285: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
5286: double **ximort;
5287: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
5288: int *dcwave;
5289:
5290: char z[1]="c", occ;
5291:
5292: /*char *strt;*/
5293: char strtend[80];
5294:
5295: long total_usecs;
5296:
5297: /* setlocale (LC_ALL, ""); */
5298: /* bindtextdomain (PACKAGE, LOCALEDIR); */
5299: /* textdomain (PACKAGE); */
5300: /* setlocale (LC_CTYPE, ""); */
5301: /* setlocale (LC_MESSAGES, ""); */
5302:
5303: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
5304: (void) gettimeofday(&start_time,&tzp);
5305: curr_time=start_time;
5306: tm = *localtime(&start_time.tv_sec);
5307: tmg = *gmtime(&start_time.tv_sec);
5308: strcpy(strstart,asctime(&tm));
5309:
5310: /* printf("Localtime (at start)=%s",strstart); */
5311: /* tp.tv_sec = tp.tv_sec +86400; */
5312: /* tm = *localtime(&start_time.tv_sec); */
5313: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
5314: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
5315: /* tmg.tm_hour=tmg.tm_hour + 1; */
5316: /* tp.tv_sec = mktime(&tmg); */
5317: /* strt=asctime(&tmg); */
5318: /* printf("Time(after) =%s",strstart); */
5319: /* (void) time (&time_value);
5320: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
5321: * tm = *localtime(&time_value);
5322: * strstart=asctime(&tm);
5323: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
5324: */
5325:
5326: nberr=0; /* Number of errors and warnings */
5327: nbwarn=0;
5328: getcwd(pathcd, size);
5329:
5330: printf("\n%s\n%s",version,fullversion);
5331: if(argc <=1){
5332: printf("\nEnter the parameter file name: ");
5333: fgets(pathr,FILENAMELENGTH,stdin);
5334: i=strlen(pathr);
5335: if(pathr[i-1]=='\n')
5336: pathr[i-1]='\0';
5337: for (tok = pathr; tok != NULL; ){
5338: printf("Pathr |%s|\n",pathr);
5339: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
5340: printf("val= |%s| pathr=%s\n",val,pathr);
5341: strcpy (pathtot, val);
5342: if(pathr[0] == '\0') break; /* Dirty */
5343: }
5344: }
5345: else{
5346: strcpy(pathtot,argv[1]);
5347: }
5348: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
5349: /*cygwin_split_path(pathtot,path,optionfile);
5350: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
5351: /* cutv(path,optionfile,pathtot,'\\');*/
5352:
5353: /* Split argv[0], imach program to get pathimach */
5354: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
5355: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5356: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5357: /* strcpy(pathimach,argv[0]); */
5358: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
5359: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
5360: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
5361: chdir(path); /* Can be a relative path */
5362: if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
5363: printf("Current directory %s!\n",pathcd);
5364: strcpy(command,"mkdir ");
5365: strcat(command,optionfilefiname);
5366: if((outcmd=system(command)) != 0){
5367: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
5368: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
5369: /* fclose(ficlog); */
5370: /* exit(1); */
5371: }
5372: /* if((imk=mkdir(optionfilefiname))<0){ */
5373: /* perror("mkdir"); */
5374: /* } */
5375:
5376: /*-------- arguments in the command line --------*/
5377:
5378: /* Log file */
5379: strcat(filelog, optionfilefiname);
5380: strcat(filelog,".log"); /* */
5381: if((ficlog=fopen(filelog,"w"))==NULL) {
5382: printf("Problem with logfile %s\n",filelog);
5383: goto end;
5384: }
5385: fprintf(ficlog,"Log filename:%s\n",filelog);
5386: fprintf(ficlog,"\n%s\n%s",version,fullversion);
5387: fprintf(ficlog,"\nEnter the parameter file name: \n");
5388: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
5389: path=%s \n\
5390: optionfile=%s\n\
5391: optionfilext=%s\n\
5392: optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
5393:
5394: printf("Local time (at start):%s",strstart);
5395: fprintf(ficlog,"Local time (at start): %s",strstart);
5396: fflush(ficlog);
5397: /* (void) gettimeofday(&curr_time,&tzp); */
5398: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
5399:
5400: /* */
5401: strcpy(fileres,"r");
5402: strcat(fileres, optionfilefiname);
5403: strcat(fileres,".txt"); /* Other files have txt extension */
5404:
5405: /*---------arguments file --------*/
5406:
5407: if((ficpar=fopen(optionfile,"r"))==NULL) {
5408: printf("Problem with optionfile %s with errno=%s\n",optionfile,strerror(errno));
5409: fprintf(ficlog,"Problem with optionfile %s with errno=%s\n",optionfile,strerror(errno));
5410: fflush(ficlog);
5411: /* goto end; */
5412: exit(70);
5413: }
5414:
5415:
5416:
5417: strcpy(filereso,"o");
5418: strcat(filereso,fileres);
5419: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
5420: printf("Problem with Output resultfile: %s\n", filereso);
5421: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
5422: fflush(ficlog);
5423: goto end;
5424: }
5425:
5426: /* Reads comments: lines beginning with '#' */
5427: numlinepar=0;
5428: while((c=getc(ficpar))=='#' && c!= EOF){
5429: ungetc(c,ficpar);
5430: fgets(line, MAXLINE, ficpar);
5431: numlinepar++;
5432: fputs(line,stdout);
5433: fputs(line,ficparo);
5434: fputs(line,ficlog);
5435: }
5436: ungetc(c,ficpar);
5437:
5438: 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);
5439: numlinepar++;
5440: 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);
5441: 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);
5442: 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);
5443: fflush(ficlog);
5444: while((c=getc(ficpar))=='#' && c!= EOF){
5445: ungetc(c,ficpar);
5446: fgets(line, MAXLINE, ficpar);
5447: numlinepar++;
5448: fputs(line, stdout);
5449: //puts(line);
5450: fputs(line,ficparo);
5451: fputs(line,ficlog);
5452: }
5453: ungetc(c,ficpar);
5454:
5455:
5456: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
5457: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
5458: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
5459: v1+v2*age+v2*v3 makes cptcovn = 3
5460: */
5461: if (strlen(model)>1)
5462: 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*/
5463: else
5464: ncovmodel=2;
5465: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
5466: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
5467: npar= nforce*ncovmodel; /* Number of parameters like aij*/
5468: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
5469: 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);
5470: 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);
5471: fflush(stdout);
5472: fclose (ficlog);
5473: goto end;
5474: }
5475: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5476: delti=delti3[1][1];
5477: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
5478: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
5479: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5480: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5481: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5482: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5483: fclose (ficparo);
5484: fclose (ficlog);
5485: goto end;
5486: exit(0);
5487: }
5488: else if(mle==-3) {
5489: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5490: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5491: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5492: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5493: matcov=matrix(1,npar,1,npar);
5494: }
5495: else{
5496: /* Read guessed parameters */
5497: /* Reads comments: lines beginning with '#' */
5498: while((c=getc(ficpar))=='#' && c!= EOF){
5499: ungetc(c,ficpar);
5500: fgets(line, MAXLINE, ficpar);
5501: numlinepar++;
5502: fputs(line,stdout);
5503: fputs(line,ficparo);
5504: fputs(line,ficlog);
5505: }
5506: ungetc(c,ficpar);
5507:
5508: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5509: for(i=1; i <=nlstate; i++){
5510: j=0;
5511: for(jj=1; jj <=nlstate+ndeath; jj++){
5512: if(jj==i) continue;
5513: j++;
5514: fscanf(ficpar,"%1d%1d",&i1,&j1);
5515: if ((i1 != i) && (j1 != j)){
5516: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
5517: It might be a problem of design; if ncovcol and the model are correct\n \
5518: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
5519: exit(1);
5520: }
5521: fprintf(ficparo,"%1d%1d",i1,j1);
5522: if(mle==1)
5523: printf("%1d%1d",i,j);
5524: fprintf(ficlog,"%1d%1d",i,j);
5525: for(k=1; k<=ncovmodel;k++){
5526: fscanf(ficpar," %lf",¶m[i][j][k]);
5527: if(mle==1){
5528: printf(" %lf",param[i][j][k]);
5529: fprintf(ficlog," %lf",param[i][j][k]);
5530: }
5531: else
5532: fprintf(ficlog," %lf",param[i][j][k]);
5533: fprintf(ficparo," %lf",param[i][j][k]);
5534: }
5535: fscanf(ficpar,"\n");
5536: numlinepar++;
5537: if(mle==1)
5538: printf("\n");
5539: fprintf(ficlog,"\n");
5540: fprintf(ficparo,"\n");
5541: }
5542: }
5543: fflush(ficlog);
5544:
5545: /* Reads scales values */
5546: p=param[1][1];
5547:
5548: /* Reads comments: lines beginning with '#' */
5549: while((c=getc(ficpar))=='#' && c!= EOF){
5550: ungetc(c,ficpar);
5551: fgets(line, MAXLINE, ficpar);
5552: numlinepar++;
5553: fputs(line,stdout);
5554: fputs(line,ficparo);
5555: fputs(line,ficlog);
5556: }
5557: ungetc(c,ficpar);
5558:
5559: for(i=1; i <=nlstate; i++){
5560: for(j=1; j <=nlstate+ndeath-1; j++){
5561: fscanf(ficpar,"%1d%1d",&i1,&j1);
5562: if ((i1-i)*(j1-j)!=0){
5563: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
5564: exit(1);
5565: }
5566: printf("%1d%1d",i,j);
5567: fprintf(ficparo,"%1d%1d",i1,j1);
5568: fprintf(ficlog,"%1d%1d",i1,j1);
5569: for(k=1; k<=ncovmodel;k++){
5570: fscanf(ficpar,"%le",&delti3[i][j][k]);
5571: printf(" %le",delti3[i][j][k]);
5572: fprintf(ficparo," %le",delti3[i][j][k]);
5573: fprintf(ficlog," %le",delti3[i][j][k]);
5574: }
5575: fscanf(ficpar,"\n");
5576: numlinepar++;
5577: printf("\n");
5578: fprintf(ficparo,"\n");
5579: fprintf(ficlog,"\n");
5580: }
5581: }
5582: fflush(ficlog);
5583:
5584: /* Reads covariance matrix */
5585: delti=delti3[1][1];
5586:
5587:
5588: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
5589:
5590: /* Reads comments: lines beginning with '#' */
5591: while((c=getc(ficpar))=='#' && c!= EOF){
5592: ungetc(c,ficpar);
5593: fgets(line, MAXLINE, ficpar);
5594: numlinepar++;
5595: fputs(line,stdout);
5596: fputs(line,ficparo);
5597: fputs(line,ficlog);
5598: }
5599: ungetc(c,ficpar);
5600:
5601: matcov=matrix(1,npar,1,npar);
5602: for(i=1; i <=npar; i++)
5603: for(j=1; j <=npar; j++) matcov[i][j]=0.;
5604:
5605: for(i=1; i <=npar; i++){
5606: fscanf(ficpar,"%s",str);
5607: if(mle==1)
5608: printf("%s",str);
5609: fprintf(ficlog,"%s",str);
5610: fprintf(ficparo,"%s",str);
5611: for(j=1; j <=i; j++){
5612: fscanf(ficpar," %le",&matcov[i][j]);
5613: if(mle==1){
5614: printf(" %.5le",matcov[i][j]);
5615: }
5616: fprintf(ficlog," %.5le",matcov[i][j]);
5617: fprintf(ficparo," %.5le",matcov[i][j]);
5618: }
5619: fscanf(ficpar,"\n");
5620: numlinepar++;
5621: if(mle==1)
5622: printf("\n");
5623: fprintf(ficlog,"\n");
5624: fprintf(ficparo,"\n");
5625: }
5626: for(i=1; i <=npar; i++)
5627: for(j=i+1;j<=npar;j++)
5628: matcov[i][j]=matcov[j][i];
5629:
5630: if(mle==1)
5631: printf("\n");
5632: fprintf(ficlog,"\n");
5633:
5634: fflush(ficlog);
5635:
5636: /*-------- Rewriting parameter file ----------*/
5637: strcpy(rfileres,"r"); /* "Rparameterfile */
5638: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
5639: strcat(rfileres,"."); /* */
5640: strcat(rfileres,optionfilext); /* Other files have txt extension */
5641: if((ficres =fopen(rfileres,"w"))==NULL) {
5642: printf("Problem writing new parameter file: %s\n", fileres);goto end;
5643: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
5644: }
5645: fprintf(ficres,"#%s\n",version);
5646: } /* End of mle != -3 */
5647:
5648:
5649: n= lastobs;
5650: num=lvector(1,n);
5651: moisnais=vector(1,n);
5652: annais=vector(1,n);
5653: moisdc=vector(1,n);
5654: andc=vector(1,n);
5655: agedc=vector(1,n);
5656: cod=ivector(1,n);
5657: weight=vector(1,n);
5658: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
5659: mint=matrix(1,maxwav,1,n);
5660: anint=matrix(1,maxwav,1,n);
5661: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
5662: tab=ivector(1,NCOVMAX);
5663: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
5664:
5665: /* Reads data from file datafile */
5666: if (readdata(datafile, firstobs, lastobs, &imx)==1)
5667: goto end;
5668:
5669: /* Calculation of the number of parameters from char model */
5670: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
5671: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
5672: k=3 V4 Tvar[k=3]= 4 (from V4)
5673: k=2 V1 Tvar[k=2]= 1 (from V1)
5674: k=1 Tvar[1]=2 (from V2)
5675: */
5676: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
5677: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
5678: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
5679: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
5680: */
5681: /* For model-covariate k tells which data-covariate to use but
5682: because this model-covariate is a construction we invent a new column
5683: ncovcol + k1
5684: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
5685: Tvar[3=V1*V4]=4+1 etc */
5686: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
5687: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
5688: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
5689: */
5690: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
5691: 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
5692: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
5693: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
5694: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
5695: 4 covariates (3 plus signs)
5696: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
5697: */
5698:
5699: if(decodemodel(model, lastobs) == 1)
5700: goto end;
5701:
5702: if((double)(lastobs-imx)/(double)imx > 1.10){
5703: nbwarn++;
5704: 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);
5705: 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);
5706: }
5707: /* if(mle==1){*/
5708: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
5709: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
5710: }
5711:
5712: /*-calculation of age at interview from date of interview and age at death -*/
5713: agev=matrix(1,maxwav,1,imx);
5714:
5715: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
5716: goto end;
5717:
5718:
5719: agegomp=(int)agemin;
5720: free_vector(moisnais,1,n);
5721: free_vector(annais,1,n);
5722: /* free_matrix(mint,1,maxwav,1,n);
5723: free_matrix(anint,1,maxwav,1,n);*/
5724: free_vector(moisdc,1,n);
5725: free_vector(andc,1,n);
5726: /* */
5727:
5728: wav=ivector(1,imx);
5729: dh=imatrix(1,lastpass-firstpass+1,1,imx);
5730: bh=imatrix(1,lastpass-firstpass+1,1,imx);
5731: mw=imatrix(1,lastpass-firstpass+1,1,imx);
5732:
5733: /* Concatenates waves */
5734: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
5735: /* */
5736:
5737: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
5738:
5739: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
5740: ncodemax[1]=1;
5741: Ndum =ivector(-1,NCOVMAX);
5742: if (ncovmodel > 2)
5743: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
5744:
5745: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
5746: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
5747: h=0;
5748:
5749:
5750: /*if (cptcovn > 0) */
5751:
5752:
5753: m=pow(2,cptcoveff);
5754:
5755: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
5756: 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 */
5757: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
5758: for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
5759: h++;
5760: if (h>m)
5761: h=1;
5762: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
5763: * h 1 2 3 4
5764: *______________________________
5765: * 1 i=1 1 i=1 1 i=1 1 i=1 1
5766: * 2 2 1 1 1
5767: * 3 i=2 1 2 1 1
5768: * 4 2 2 1 1
5769: * 5 i=3 1 i=2 1 2 1
5770: * 6 2 1 2 1
5771: * 7 i=4 1 2 2 1
5772: * 8 2 2 2 1
5773: * 9 i=5 1 i=3 1 i=2 1 1
5774: * 10 2 1 1 1
5775: * 11 i=6 1 2 1 1
5776: * 12 2 2 1 1
5777: * 13 i=7 1 i=4 1 2 1
5778: * 14 2 1 2 1
5779: * 15 i=8 1 2 2 1
5780: * 16 2 2 2 1
5781: */
5782: codtab[h][k]=j;
5783: /*codtab[h][Tvar[k]]=j;*/
5784: 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]]);
5785: }
5786: }
5787: }
5788: }
5789: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
5790: codtab[1][2]=1;codtab[2][2]=2; */
5791: /* for(i=1; i <=m ;i++){
5792: for(k=1; k <=cptcovn; k++){
5793: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
5794: }
5795: printf("\n");
5796: }
5797: scanf("%d",i);*/
5798:
5799: free_ivector(Ndum,-1,NCOVMAX);
5800:
5801:
5802:
5803: /*------------ gnuplot -------------*/
5804: strcpy(optionfilegnuplot,optionfilefiname);
5805: if(mle==-3)
5806: strcat(optionfilegnuplot,"-mort");
5807: strcat(optionfilegnuplot,".gp");
5808:
5809: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
5810: printf("Problem with file %s",optionfilegnuplot);
5811: }
5812: else{
5813: fprintf(ficgp,"\n# %s\n", version);
5814: fprintf(ficgp,"# %s\n", optionfilegnuplot);
5815: //fprintf(ficgp,"set missing 'NaNq'\n");
5816: fprintf(ficgp,"set datafile missing 'NaNq'\n");
5817: }
5818: /* fclose(ficgp);*/
5819: /*--------- index.htm --------*/
5820:
5821: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
5822: if(mle==-3)
5823: strcat(optionfilehtm,"-mort");
5824: strcat(optionfilehtm,".htm");
5825: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
5826: printf("Problem with %s \n",optionfilehtm);
5827: exit(0);
5828: }
5829:
5830: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
5831: strcat(optionfilehtmcov,"-cov.htm");
5832: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
5833: printf("Problem with %s \n",optionfilehtmcov), exit(0);
5834: }
5835: else{
5836: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
5837: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5838: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
5839: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
5840: }
5841:
5842: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
5843: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5844: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
5845: \n\
5846: <hr size=\"2\" color=\"#EC5E5E\">\
5847: <ul><li><h4>Parameter files</h4>\n\
5848: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
5849: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
5850: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
5851: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
5852: - Date and time at start: %s</ul>\n",\
5853: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
5854: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
5855: fileres,fileres,\
5856: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
5857: fflush(fichtm);
5858:
5859: strcpy(pathr,path);
5860: strcat(pathr,optionfilefiname);
5861: chdir(optionfilefiname); /* Move to directory named optionfile */
5862:
5863: /* Calculates basic frequencies. Computes observed prevalence at single age
5864: and prints on file fileres'p'. */
5865: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
5866:
5867: fprintf(fichtm,"\n");
5868: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
5869: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
5870: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
5871: imx,agemin,agemax,jmin,jmax,jmean);
5872: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5873: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5874: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5875: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5876: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
5877:
5878:
5879: /* For Powell, parameters are in a vector p[] starting at p[1]
5880: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
5881: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
5882:
5883: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
5884:
5885: if (mle==-3){
5886: ximort=matrix(1,NDIM,1,NDIM);
5887: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
5888: cens=ivector(1,n);
5889: ageexmed=vector(1,n);
5890: agecens=vector(1,n);
5891: dcwave=ivector(1,n);
5892:
5893: for (i=1; i<=imx; i++){
5894: dcwave[i]=-1;
5895: for (m=firstpass; m<=lastpass; m++)
5896: if (s[m][i]>nlstate) {
5897: dcwave[i]=m;
5898: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
5899: break;
5900: }
5901: }
5902:
5903: for (i=1; i<=imx; i++) {
5904: if (wav[i]>0){
5905: ageexmed[i]=agev[mw[1][i]][i];
5906: j=wav[i];
5907: agecens[i]=1.;
5908:
5909: if (ageexmed[i]> 1 && wav[i] > 0){
5910: agecens[i]=agev[mw[j][i]][i];
5911: cens[i]= 1;
5912: }else if (ageexmed[i]< 1)
5913: cens[i]= -1;
5914: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
5915: cens[i]=0 ;
5916: }
5917: else cens[i]=-1;
5918: }
5919:
5920: for (i=1;i<=NDIM;i++) {
5921: for (j=1;j<=NDIM;j++)
5922: ximort[i][j]=(i == j ? 1.0 : 0.0);
5923: }
5924:
5925: /*p[1]=0.0268; p[NDIM]=0.083;*/
5926: /*printf("%lf %lf", p[1], p[2]);*/
5927:
5928:
5929: #ifdef GSL
5930: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
5931: #elsedef
5932: printf("Powell\n"); fprintf(ficlog,"Powell\n");
5933: #endif
5934: strcpy(filerespow,"pow-mort");
5935: strcat(filerespow,fileres);
5936: if((ficrespow=fopen(filerespow,"w"))==NULL) {
5937: printf("Problem with resultfile: %s\n", filerespow);
5938: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
5939: }
5940: #ifdef GSL
5941: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
5942: #elsedef
5943: fprintf(ficrespow,"# Powell\n# iter -2*LL");
5944: #endif
5945: /* for (i=1;i<=nlstate;i++)
5946: for(j=1;j<=nlstate+ndeath;j++)
5947: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
5948: */
5949: fprintf(ficrespow,"\n");
5950: #ifdef GSL
5951: /* gsl starts here */
5952: T = gsl_multimin_fminimizer_nmsimplex;
5953: gsl_multimin_fminimizer *sfm = NULL;
5954: gsl_vector *ss, *x;
5955: gsl_multimin_function minex_func;
5956:
5957: /* Initial vertex size vector */
5958: ss = gsl_vector_alloc (NDIM);
5959:
5960: if (ss == NULL){
5961: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
5962: }
5963: /* Set all step sizes to 1 */
5964: gsl_vector_set_all (ss, 0.001);
5965:
5966: /* Starting point */
5967:
5968: x = gsl_vector_alloc (NDIM);
5969:
5970: if (x == NULL){
5971: gsl_vector_free(ss);
5972: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
5973: }
5974:
5975: /* Initialize method and iterate */
5976: /* p[1]=0.0268; p[NDIM]=0.083; */
5977: /* gsl_vector_set(x, 0, 0.0268); */
5978: /* gsl_vector_set(x, 1, 0.083); */
5979: gsl_vector_set(x, 0, p[1]);
5980: gsl_vector_set(x, 1, p[2]);
5981:
5982: minex_func.f = &gompertz_f;
5983: minex_func.n = NDIM;
5984: minex_func.params = (void *)&p; /* ??? */
5985:
5986: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
5987: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
5988:
5989: printf("Iterations beginning .....\n\n");
5990: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
5991:
5992: iteri=0;
5993: while (rval == GSL_CONTINUE){
5994: iteri++;
5995: status = gsl_multimin_fminimizer_iterate(sfm);
5996:
5997: if (status) printf("error: %s\n", gsl_strerror (status));
5998: fflush(0);
5999:
6000: if (status)
6001: break;
6002:
6003: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
6004: ssval = gsl_multimin_fminimizer_size (sfm);
6005:
6006: if (rval == GSL_SUCCESS)
6007: printf ("converged to a local maximum at\n");
6008:
6009: printf("%5d ", iteri);
6010: for (it = 0; it < NDIM; it++){
6011: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
6012: }
6013: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
6014: }
6015:
6016: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
6017:
6018: gsl_vector_free(x); /* initial values */
6019: gsl_vector_free(ss); /* inital step size */
6020: for (it=0; it<NDIM; it++){
6021: p[it+1]=gsl_vector_get(sfm->x,it);
6022: fprintf(ficrespow," %.12lf", p[it]);
6023: }
6024: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
6025: #endif
6026: #ifdef POWELL
6027: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
6028: #endif
6029: fclose(ficrespow);
6030:
6031: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
6032:
6033: for(i=1; i <=NDIM; i++)
6034: for(j=i+1;j<=NDIM;j++)
6035: matcov[i][j]=matcov[j][i];
6036:
6037: printf("\nCovariance matrix\n ");
6038: for(i=1; i <=NDIM; i++) {
6039: for(j=1;j<=NDIM;j++){
6040: printf("%f ",matcov[i][j]);
6041: }
6042: printf("\n ");
6043: }
6044:
6045: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
6046: for (i=1;i<=NDIM;i++)
6047: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
6048:
6049: lsurv=vector(1,AGESUP);
6050: lpop=vector(1,AGESUP);
6051: tpop=vector(1,AGESUP);
6052: lsurv[agegomp]=100000;
6053:
6054: for (k=agegomp;k<=AGESUP;k++) {
6055: agemortsup=k;
6056: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
6057: }
6058:
6059: for (k=agegomp;k<agemortsup;k++)
6060: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
6061:
6062: for (k=agegomp;k<agemortsup;k++){
6063: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
6064: sumlpop=sumlpop+lpop[k];
6065: }
6066:
6067: tpop[agegomp]=sumlpop;
6068: for (k=agegomp;k<(agemortsup-3);k++){
6069: /* tpop[k+1]=2;*/
6070: tpop[k+1]=tpop[k]-lpop[k];
6071: }
6072:
6073:
6074: printf("\nAge lx qx dx Lx Tx e(x)\n");
6075: for (k=agegomp;k<(agemortsup-2);k++)
6076: 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]);
6077:
6078:
6079: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6080: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6081:
6082: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
6083: stepm, weightopt,\
6084: model,imx,p,matcov,agemortsup);
6085:
6086: free_vector(lsurv,1,AGESUP);
6087: free_vector(lpop,1,AGESUP);
6088: free_vector(tpop,1,AGESUP);
6089: #ifdef GSL
6090: free_ivector(cens,1,n);
6091: free_vector(agecens,1,n);
6092: free_ivector(dcwave,1,n);
6093: free_matrix(ximort,1,NDIM,1,NDIM);
6094: #endif
6095: } /* Endof if mle==-3 */
6096:
6097: else{ /* For mle >=1 */
6098: globpr=0;/* debug */
6099: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6100: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6101: for (k=1; k<=npar;k++)
6102: printf(" %d %8.5f",k,p[k]);
6103: printf("\n");
6104: globpr=1; /* to print the contributions */
6105: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6106: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6107: for (k=1; k<=npar;k++)
6108: printf(" %d %8.5f",k,p[k]);
6109: printf("\n");
6110: if(mle>=1){ /* Could be 1 or 2 */
6111: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
6112: }
6113:
6114: /*--------- results files --------------*/
6115: 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);
6116:
6117:
6118: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6119: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6120: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6121: for(i=1,jk=1; i <=nlstate; i++){
6122: for(k=1; k <=(nlstate+ndeath); k++){
6123: if (k != i) {
6124: printf("%d%d ",i,k);
6125: fprintf(ficlog,"%d%d ",i,k);
6126: fprintf(ficres,"%1d%1d ",i,k);
6127: for(j=1; j <=ncovmodel; j++){
6128: printf("%lf ",p[jk]);
6129: fprintf(ficlog,"%lf ",p[jk]);
6130: fprintf(ficres,"%lf ",p[jk]);
6131: jk++;
6132: }
6133: printf("\n");
6134: fprintf(ficlog,"\n");
6135: fprintf(ficres,"\n");
6136: }
6137: }
6138: }
6139: if(mle!=0){
6140: /* Computing hessian and covariance matrix */
6141: ftolhess=ftol; /* Usually correct */
6142: hesscov(matcov, p, npar, delti, ftolhess, func);
6143: }
6144: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
6145: printf("# Scales (for hessian or gradient estimation)\n");
6146: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
6147: for(i=1,jk=1; i <=nlstate; i++){
6148: for(j=1; j <=nlstate+ndeath; j++){
6149: if (j!=i) {
6150: fprintf(ficres,"%1d%1d",i,j);
6151: printf("%1d%1d",i,j);
6152: fprintf(ficlog,"%1d%1d",i,j);
6153: for(k=1; k<=ncovmodel;k++){
6154: printf(" %.5e",delti[jk]);
6155: fprintf(ficlog," %.5e",delti[jk]);
6156: fprintf(ficres," %.5e",delti[jk]);
6157: jk++;
6158: }
6159: printf("\n");
6160: fprintf(ficlog,"\n");
6161: fprintf(ficres,"\n");
6162: }
6163: }
6164: }
6165:
6166: 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");
6167: if(mle>=1)
6168: 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");
6169: 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");
6170: /* # 121 Var(a12)\n\ */
6171: /* # 122 Cov(b12,a12) Var(b12)\n\ */
6172: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
6173: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
6174: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
6175: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
6176: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
6177: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
6178:
6179:
6180: /* Just to have a covariance matrix which will be more understandable
6181: even is we still don't want to manage dictionary of variables
6182: */
6183: for(itimes=1;itimes<=2;itimes++){
6184: jj=0;
6185: for(i=1; i <=nlstate; i++){
6186: for(j=1; j <=nlstate+ndeath; j++){
6187: if(j==i) continue;
6188: for(k=1; k<=ncovmodel;k++){
6189: jj++;
6190: ca[0]= k+'a'-1;ca[1]='\0';
6191: if(itimes==1){
6192: if(mle>=1)
6193: printf("#%1d%1d%d",i,j,k);
6194: fprintf(ficlog,"#%1d%1d%d",i,j,k);
6195: fprintf(ficres,"#%1d%1d%d",i,j,k);
6196: }else{
6197: if(mle>=1)
6198: printf("%1d%1d%d",i,j,k);
6199: fprintf(ficlog,"%1d%1d%d",i,j,k);
6200: fprintf(ficres,"%1d%1d%d",i,j,k);
6201: }
6202: ll=0;
6203: for(li=1;li <=nlstate; li++){
6204: for(lj=1;lj <=nlstate+ndeath; lj++){
6205: if(lj==li) continue;
6206: for(lk=1;lk<=ncovmodel;lk++){
6207: ll++;
6208: if(ll<=jj){
6209: cb[0]= lk +'a'-1;cb[1]='\0';
6210: if(ll<jj){
6211: if(itimes==1){
6212: if(mle>=1)
6213: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6214: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6215: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6216: }else{
6217: if(mle>=1)
6218: printf(" %.5e",matcov[jj][ll]);
6219: fprintf(ficlog," %.5e",matcov[jj][ll]);
6220: fprintf(ficres," %.5e",matcov[jj][ll]);
6221: }
6222: }else{
6223: if(itimes==1){
6224: if(mle>=1)
6225: printf(" Var(%s%1d%1d)",ca,i,j);
6226: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
6227: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
6228: }else{
6229: if(mle>=1)
6230: printf(" %.5e",matcov[jj][ll]);
6231: fprintf(ficlog," %.5e",matcov[jj][ll]);
6232: fprintf(ficres," %.5e",matcov[jj][ll]);
6233: }
6234: }
6235: }
6236: } /* end lk */
6237: } /* end lj */
6238: } /* end li */
6239: if(mle>=1)
6240: printf("\n");
6241: fprintf(ficlog,"\n");
6242: fprintf(ficres,"\n");
6243: numlinepar++;
6244: } /* end k*/
6245: } /*end j */
6246: } /* end i */
6247: } /* end itimes */
6248:
6249: fflush(ficlog);
6250: fflush(ficres);
6251:
6252: while((c=getc(ficpar))=='#' && c!= EOF){
6253: ungetc(c,ficpar);
6254: fgets(line, MAXLINE, ficpar);
6255: fputs(line,stdout);
6256: fputs(line,ficparo);
6257: }
6258: ungetc(c,ficpar);
6259:
6260: estepm=0;
6261: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
6262: if (estepm==0 || estepm < stepm) estepm=stepm;
6263: if (fage <= 2) {
6264: bage = ageminpar;
6265: fage = agemaxpar;
6266: }
6267:
6268: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
6269: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6270: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6271:
6272: while((c=getc(ficpar))=='#' && c!= EOF){
6273: ungetc(c,ficpar);
6274: fgets(line, MAXLINE, ficpar);
6275: fputs(line,stdout);
6276: fputs(line,ficparo);
6277: }
6278: ungetc(c,ficpar);
6279:
6280: 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);
6281: 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);
6282: 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);
6283: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
6284: 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);
6285:
6286: while((c=getc(ficpar))=='#' && c!= EOF){
6287: ungetc(c,ficpar);
6288: fgets(line, MAXLINE, ficpar);
6289: fputs(line,stdout);
6290: fputs(line,ficparo);
6291: }
6292: ungetc(c,ficpar);
6293:
6294:
6295: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
6296: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
6297:
6298: fscanf(ficpar,"pop_based=%d\n",&popbased);
6299: fprintf(ficparo,"pop_based=%d\n",popbased);
6300: fprintf(ficres,"pop_based=%d\n",popbased);
6301:
6302: while((c=getc(ficpar))=='#' && c!= EOF){
6303: ungetc(c,ficpar);
6304: fgets(line, MAXLINE, ficpar);
6305: fputs(line,stdout);
6306: fputs(line,ficparo);
6307: }
6308: ungetc(c,ficpar);
6309:
6310: 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);
6311: 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);
6312: 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);
6313: 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);
6314: 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);
6315: /* day and month of proj2 are not used but only year anproj2.*/
6316:
6317:
6318:
6319: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
6320: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
6321:
6322: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6323: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6324:
6325: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
6326: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
6327: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
6328:
6329: /*------------ free_vector -------------*/
6330: /* chdir(path); */
6331:
6332: free_ivector(wav,1,imx);
6333: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
6334: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
6335: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
6336: free_lvector(num,1,n);
6337: free_vector(agedc,1,n);
6338: /*free_matrix(covar,0,NCOVMAX,1,n);*/
6339: /*free_matrix(covar,1,NCOVMAX,1,n);*/
6340: fclose(ficparo);
6341: fclose(ficres);
6342:
6343:
6344: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6345: #include "prevlim.h" /* Use ficrespl, ficlog */
6346: fclose(ficrespl);
6347:
6348: #ifdef FREEEXIT2
6349: #include "freeexit2.h"
6350: #endif
6351:
6352: /*------------- h Pij x at various ages ------------*/
6353: #include "hpijx.h"
6354: fclose(ficrespij);
6355:
6356: /*-------------- Variance of one-step probabilities---*/
6357: k=1;
6358: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
6359:
6360:
6361: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6362: for(i=1;i<=AGESUP;i++)
6363: for(j=1;j<=NCOVMAX;j++)
6364: for(k=1;k<=NCOVMAX;k++)
6365: probs[i][j][k]=0.;
6366:
6367: /*---------- Forecasting ------------------*/
6368: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
6369: if(prevfcast==1){
6370: /* if(stepm ==1){*/
6371: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
6372: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
6373: /* } */
6374: /* else{ */
6375: /* erreur=108; */
6376: /* 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); */
6377: /* 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); */
6378: /* } */
6379: }
6380:
6381:
6382: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
6383:
6384: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
6385: /* 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",\
6386: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
6387: */
6388:
6389: if (mobilav!=0) {
6390: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6391: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
6392: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
6393: printf(" Error in movingaverage mobilav=%d\n",mobilav);
6394: }
6395: }
6396:
6397:
6398: /*---------- Health expectancies, no variances ------------*/
6399:
6400: strcpy(filerese,"e");
6401: strcat(filerese,fileres);
6402: if((ficreseij=fopen(filerese,"w"))==NULL) {
6403: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6404: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6405: }
6406: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
6407: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
6408: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6409: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6410:
6411: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6412: fprintf(ficreseij,"\n#****** ");
6413: for(j=1;j<=cptcoveff;j++) {
6414: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6415: }
6416: fprintf(ficreseij,"******\n");
6417:
6418: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6419: oldm=oldms;savm=savms;
6420: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
6421:
6422: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6423: /*}*/
6424: }
6425: fclose(ficreseij);
6426:
6427:
6428: /*---------- Health expectancies and variances ------------*/
6429:
6430:
6431: strcpy(filerest,"t");
6432: strcat(filerest,fileres);
6433: if((ficrest=fopen(filerest,"w"))==NULL) {
6434: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
6435: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
6436: }
6437: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6438: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6439:
6440:
6441: strcpy(fileresstde,"stde");
6442: strcat(fileresstde,fileres);
6443: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
6444: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6445: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6446: }
6447: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6448: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6449:
6450: strcpy(filerescve,"cve");
6451: strcat(filerescve,fileres);
6452: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
6453: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6454: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6455: }
6456: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6457: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6458:
6459: strcpy(fileresv,"v");
6460: strcat(fileresv,fileres);
6461: if((ficresvij=fopen(fileresv,"w"))==NULL) {
6462: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
6463: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
6464: }
6465: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6466: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6467:
6468: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6469: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6470:
6471: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6472: fprintf(ficrest,"\n#****** ");
6473: for(j=1;j<=cptcoveff;j++)
6474: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6475: fprintf(ficrest,"******\n");
6476:
6477: fprintf(ficresstdeij,"\n#****** ");
6478: fprintf(ficrescveij,"\n#****** ");
6479: for(j=1;j<=cptcoveff;j++) {
6480: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6481: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6482: }
6483: fprintf(ficresstdeij,"******\n");
6484: fprintf(ficrescveij,"******\n");
6485:
6486: fprintf(ficresvij,"\n#****** ");
6487: for(j=1;j<=cptcoveff;j++)
6488: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6489: fprintf(ficresvij,"******\n");
6490:
6491: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6492: oldm=oldms;savm=savms;
6493: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
6494: /*
6495: */
6496: /* goto endfree; */
6497:
6498: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6499: pstamp(ficrest);
6500:
6501:
6502: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
6503: oldm=oldms;savm=savms; /* Segmentation fault */
6504: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);
6505: 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 ");
6506: if(vpopbased==1)
6507: 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);
6508: else
6509: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
6510: fprintf(ficrest,"# Age e.. (std) ");
6511: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
6512: fprintf(ficrest,"\n");
6513:
6514: epj=vector(1,nlstate+1);
6515: for(age=bage; age <=fage ;age++){
6516: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6517: if (vpopbased==1) {
6518: if(mobilav ==0){
6519: for(i=1; i<=nlstate;i++)
6520: prlim[i][i]=probs[(int)age][i][k];
6521: }else{ /* mobilav */
6522: for(i=1; i<=nlstate;i++)
6523: prlim[i][i]=mobaverage[(int)age][i][k];
6524: }
6525: }
6526:
6527: fprintf(ficrest," %4.0f",age);
6528: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
6529: for(i=1, epj[j]=0.;i <=nlstate;i++) {
6530: epj[j] += prlim[i][i]*eij[i][j][(int)age];
6531: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
6532: }
6533: epj[nlstate+1] +=epj[j];
6534: }
6535:
6536: for(i=1, vepp=0.;i <=nlstate;i++)
6537: for(j=1;j <=nlstate;j++)
6538: vepp += vareij[i][j][(int)age];
6539: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
6540: for(j=1;j <=nlstate;j++){
6541: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
6542: }
6543: fprintf(ficrest,"\n");
6544: }
6545: }
6546: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6547: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6548: free_vector(epj,1,nlstate+1);
6549: /*}*/
6550: }
6551: free_vector(weight,1,n);
6552: free_imatrix(Tvard,1,NCOVMAX,1,2);
6553: free_imatrix(s,1,maxwav+1,1,n);
6554: free_matrix(anint,1,maxwav,1,n);
6555: free_matrix(mint,1,maxwav,1,n);
6556: free_ivector(cod,1,n);
6557: free_ivector(tab,1,NCOVMAX);
6558: fclose(ficresstdeij);
6559: fclose(ficrescveij);
6560: fclose(ficresvij);
6561: fclose(ficrest);
6562: fclose(ficpar);
6563:
6564: /*------- Variance of period (stable) prevalence------*/
6565:
6566: strcpy(fileresvpl,"vpl");
6567: strcat(fileresvpl,fileres);
6568: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
6569: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
6570: exit(0);
6571: }
6572: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
6573:
6574: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6575: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6576:
6577: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6578: fprintf(ficresvpl,"\n#****** ");
6579: for(j=1;j<=cptcoveff;j++)
6580: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6581: fprintf(ficresvpl,"******\n");
6582:
6583: varpl=matrix(1,nlstate,(int) bage, (int) fage);
6584: oldm=oldms;savm=savms;
6585: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
6586: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
6587: /*}*/
6588: }
6589:
6590: fclose(ficresvpl);
6591:
6592: /*---------- End : free ----------------*/
6593: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6594: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6595: } /* mle==-3 arrives here for freeing */
6596: endfree:
6597: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
6598: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
6599: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
6600: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
6601: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
6602: free_matrix(covar,0,NCOVMAX,1,n);
6603: free_matrix(matcov,1,npar,1,npar);
6604: /*free_vector(delti,1,npar);*/
6605: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6606: free_matrix(agev,1,maxwav,1,imx);
6607: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6608:
6609: free_ivector(ncodemax,1,NCOVMAX);
6610: free_ivector(Tvar,1,NCOVMAX);
6611: free_ivector(Tprod,1,NCOVMAX);
6612: free_ivector(Tvaraff,1,NCOVMAX);
6613: free_ivector(Tage,1,NCOVMAX);
6614:
6615: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
6616: free_imatrix(codtab,1,100,1,10);
6617: fflush(fichtm);
6618: fflush(ficgp);
6619:
6620:
6621: if((nberr >0) || (nbwarn>0)){
6622: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
6623: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
6624: }else{
6625: printf("End of Imach\n");
6626: fprintf(ficlog,"End of Imach\n");
6627: }
6628: printf("See log file on %s\n",filelog);
6629: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
6630: (void) gettimeofday(&end_time,&tzp);
6631: tm = *localtime(&end_time.tv_sec);
6632: tmg = *gmtime(&end_time.tv_sec);
6633: strcpy(strtend,asctime(&tm));
6634: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
6635: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
6636: printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
6637:
6638: printf("Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
6639: fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
6640: fprintf(ficlog,"Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
6641: /* printf("Total time was %d uSec.\n", total_usecs);*/
6642: /* if(fileappend(fichtm,optionfilehtm)){ */
6643: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6644: fclose(fichtm);
6645: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6646: fclose(fichtmcov);
6647: fclose(ficgp);
6648: fclose(ficlog);
6649: /*------ End -----------*/
6650:
6651:
6652: printf("Before Current directory %s!\n",pathcd);
6653: if(chdir(pathcd) != 0)
6654: printf("Can't move to directory %s!\n",path);
6655: if(getcwd(pathcd,MAXLINE) > 0)
6656: printf("Current directory %s!\n",pathcd);
6657: /*strcat(plotcmd,CHARSEPARATOR);*/
6658: sprintf(plotcmd,"gnuplot");
6659: #ifndef UNIX
6660: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
6661: #endif
6662: if(!stat(plotcmd,&info)){
6663: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
6664: if(!stat(getenv("GNUPLOTBIN"),&info)){
6665: printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
6666: }else
6667: strcpy(pplotcmd,plotcmd);
6668: #ifdef UNIX
6669: strcpy(plotcmd,GNUPLOTPROGRAM);
6670: if(!stat(plotcmd,&info)){
6671: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
6672: }else
6673: strcpy(pplotcmd,plotcmd);
6674: #endif
6675: }else
6676: strcpy(pplotcmd,plotcmd);
6677:
6678: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
6679: printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
6680:
6681: if((outcmd=system(plotcmd)) != 0){
6682: printf("\n Problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
6683: printf("\n Trying on same directory\n");
6684: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
6685: if((outcmd=system(plotcmd)) != 0)
6686: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
6687: }
6688: printf(" Wait...");
6689: while (z[0] != 'q') {
6690: /* chdir(path); */
6691: printf("\nType e to edit output files, g to graph again and q for exiting: ");
6692: scanf("%s",z);
6693: /* if (z[0] == 'c') system("./imach"); */
6694: if (z[0] == 'e') {
6695: #ifdef OSX
6696: sprintf(pplotcmd, "open %s", optionfilehtm);
6697: #else
6698: sprintf(pplotcmd, "%s", optionfilehtm);
6699: #endif
6700: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
6701: system(pplotcmd);
6702: }
6703: else if (z[0] == 'g') system(plotcmd);
6704: else if (z[0] == 'q') exit(0);
6705: }
6706: end:
6707: while (z[0] != 'q') {
6708: printf("\nType q for exiting: ");
6709: scanf("%s",z);
6710: }
6711: }
6712:
6713:
6714:
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