imach/src/imach.c - view

File: [Local Repository] / imach / src / imach.c
Revision 1.157: download - view: text, annotated - select for diffs
Wed Aug 27 16:26:55 2014 UTC (9 years, 10 months ago) by brouard
Branches: MAIN
CVS tags: HEAD

Summary: Preparing windows Visual studio version
Author: Brouard

In order to compile on Visual studio, time.h is now correct and time_t
and tm struct should be used. difftime should be used but sometimes I
just make the differences in raw time format (time(&now).
Trying to suppress #ifdef LINUX
Add xdg-open for __linux in order to open default browser.

1: /* $Id: imach.c,v 1.157 2014/08/27 16:26:55 brouard Exp $ 2: $State: Exp $ 3: $Log: imach.c,v $ 4: Revision 1.157 2014/08/27 16:26:55 brouard 5: Summary: Preparing windows Visual studio version 6: Author: Brouard 7: 8: In order to compile on Visual studio, time.h is now correct and time_t 9: and tm struct should be used. difftime should be used but sometimes I 10: just make the differences in raw time format (time(&now). 11: Trying to suppress #ifdef LINUX 12: Add xdg-open for __linux in order to open default browser. 13: 14: Revision 1.156 2014/08/25 20:10:10 brouard 15: *** empty log message *** 16: 17: Revision 1.155 2014/08/25 18:32:34 brouard 18: Summary: New compile, minor changes 19: Author: Brouard 20: 21: Revision 1.154 2014/06/20 17:32:08 brouard 22: Summary: Outputs now all graphs of convergence to period prevalence 23: 24: Revision 1.153 2014/06/20 16:45:46 brouard 25: Summary: If 3 live state, convergence to period prevalence on same graph 26: Author: Brouard 27: 28: Revision 1.152 2014/06/18 17:54:09 brouard 29: Summary: open browser, use gnuplot on same dir than imach if not found in the path 30: 31: Revision 1.151 2014/06/18 16:43:30 brouard 32: *** empty log message *** 33: 34: Revision 1.150 2014/06/18 16:42:35 brouard 35: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX) 36: Author: brouard 37: 38: Revision 1.149 2014/06/18 15:51:14 brouard 39: Summary: Some fixes in parameter files errors 40: Author: Nicolas Brouard 41: 42: Revision 1.148 2014/06/17 17:38:48 brouard 43: Summary: Nothing new 44: Author: Brouard 45: 46: Just a new packaging for OS/X version 0.98nS 47: 48: Revision 1.147 2014/06/16 10:33:11 brouard 49: *** empty log message *** 50: 51: Revision 1.146 2014/06/16 10:20:28 brouard 52: Summary: Merge 53: Author: Brouard 54: 55: Merge, before building revised version. 56: 57: Revision 1.145 2014/06/10 21:23:15 brouard 58: Summary: Debugging with valgrind 59: Author: Nicolas Brouard 60: 61: Lot of changes in order to output the results with some covariates 62: After the Edimburgh REVES conference 2014, it seems mandatory to 63: improve the code. 64: No more memory valgrind error but a lot has to be done in order to 65: continue the work of splitting the code into subroutines. 66: Also, decodemodel has been improved. Tricode is still not 67: optimal. nbcode should be improved. Documentation has been added in 68: the source code. 69: 70: Revision 1.143 2014/01/26 09:45:38 brouard 71: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising 72: 73: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested... 74: (Module): Version 0.98nR Running ok, but output format still only works for three covariates. 75: 76: Revision 1.142 2014/01/26 03:57:36 brouard 77: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2 78: 79: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested... 80: 81: Revision 1.141 2014/01/26 02:42:01 brouard 82: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested... 83: 84: Revision 1.140 2011/09/02 10:37:54 brouard 85: Summary: times.h is ok with mingw32 now. 86: 87: Revision 1.139 2010/06/14 07:50:17 brouard 88: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree. 89: I remember having already fixed agemin agemax which are pointers now but not cvs saved. 90: 91: Revision 1.138 2010/04/30 18:19:40 brouard 92: *** empty log message *** 93: 94: Revision 1.137 2010/04/29 18:11:38 brouard 95: (Module): Checking covariates for more complex models 96: than V1+V2. A lot of change to be done. Unstable. 97: 98: Revision 1.136 2010/04/26 20:30:53 brouard 99: (Module): merging some libgsl code. Fixing computation 100: of likelione (using inter/intrapolation if mle = 0) in order to 101: get same likelihood as if mle=1. 102: Some cleaning of code and comments added. 103: 104: Revision 1.135 2009/10/29 15:33:14 brouard 105: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code. 106: 107: Revision 1.134 2009/10/29 13:18:53 brouard 108: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code. 109: 110: Revision 1.133 2009/07/06 10:21:25 brouard 111: just nforces 112: 113: Revision 1.132 2009/07/06 08:22:05 brouard 114: Many tings 115: 116: Revision 1.131 2009/06/20 16:22:47 brouard 117: Some dimensions resccaled 118: 119: Revision 1.130 2009/05/26 06:44:34 brouard 120: (Module): Max Covariate is now set to 20 instead of 8. A 121: lot of cleaning with variables initialized to 0. Trying to make 122: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better. 123: 124: Revision 1.129 2007/08/31 13:49:27 lievre 125: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting 126: 127: Revision 1.128 2006/06/30 13:02:05 brouard 128: (Module): Clarifications on computing e.j 129: 130: Revision 1.127 2006/04/28 18:11:50 brouard 131: (Module): Yes the sum of survivors was wrong since 132: imach-114 because nhstepm was no more computed in the age 133: loop. Now we define nhstepma in the age loop. 134: (Module): In order to speed up (in case of numerous covariates) we 135: compute health expectancies (without variances) in a first step 136: and then all the health expectancies with variances or standard 137: deviation (needs data from the Hessian matrices) which slows the 138: computation. 139: In the future we should be able to stop the program is only health 140: expectancies and graph are needed without standard deviations. 141: 142: Revision 1.126 2006/04/28 17:23:28 brouard 143: (Module): Yes the sum of survivors was wrong since 144: imach-114 because nhstepm was no more computed in the age 145: loop. Now we define nhstepma in the age loop. 146: Version 0.98h 147: 148: Revision 1.125 2006/04/04 15:20:31 lievre 149: Errors in calculation of health expectancies. Age was not initialized. 150: Forecasting file added. 151: 152: Revision 1.124 2006/03/22 17:13:53 lievre 153: Parameters are printed with %lf instead of %f (more numbers after the comma). 154: The log-likelihood is printed in the log file 155: 156: Revision 1.123 2006/03/20 10:52:43 brouard 157: * imach.c (Module): <title> changed, corresponds to .htm file 158: name. <head> headers where missing. 159: 160: * imach.c (Module): Weights can have a decimal point as for 161: English (a comma might work with a correct LC_NUMERIC environment, 162: otherwise the weight is truncated). 163: Modification of warning when the covariates values are not 0 or 164: 1. 165: Version 0.98g 166: 167: Revision 1.122 2006/03/20 09:45:41 brouard 168: (Module): Weights can have a decimal point as for 169: English (a comma might work with a correct LC_NUMERIC environment, 170: otherwise the weight is truncated). 171: Modification of warning when the covariates values are not 0 or 172: 1. 173: Version 0.98g 174: 175: Revision 1.121 2006/03/16 17:45:01 lievre 176: * imach.c (Module): Comments concerning covariates added 177: 178: * imach.c (Module): refinements in the computation of lli if 179: status=-2 in order to have more reliable computation if stepm is 180: not 1 month. Version 0.98f 181: 182: Revision 1.120 2006/03/16 15:10:38 lievre 183: (Module): refinements in the computation of lli if 184: status=-2 in order to have more reliable computation if stepm is 185: not 1 month. Version 0.98f 186: 187: Revision 1.119 2006/03/15 17:42:26 brouard 188: (Module): Bug if status = -2, the loglikelihood was 189: computed as likelihood omitting the logarithm. Version O.98e 190: 191: Revision 1.118 2006/03/14 18:20:07 brouard 192: (Module): varevsij Comments added explaining the second 193: table of variances if popbased=1 . 194: (Module): Covariances of eij, ekl added, graphs fixed, new html link. 195: (Module): Function pstamp added 196: (Module): Version 0.98d 197: 198: Revision 1.117 2006/03/14 17:16:22 brouard 199: (Module): varevsij Comments added explaining the second 200: table of variances if popbased=1 . 201: (Module): Covariances of eij, ekl added, graphs fixed, new html link. 202: (Module): Function pstamp added 203: (Module): Version 0.98d 204: 205: Revision 1.116 2006/03/06 10:29:27 brouard 206: (Module): Variance-covariance wrong links and 207: varian-covariance of ej. is needed (Saito). 208: 209: Revision 1.115 2006/02/27 12:17:45 brouard 210: (Module): One freematrix added in mlikeli! 0.98c 211: 212: Revision 1.114 2006/02/26 12:57:58 brouard 213: (Module): Some improvements in processing parameter 214: filename with strsep. 215: 216: Revision 1.113 2006/02/24 14:20:24 brouard 217: (Module): Memory leaks checks with valgrind and: 218: datafile was not closed, some imatrix were not freed and on matrix 219: allocation too. 220: 221: Revision 1.112 2006/01/30 09:55:26 brouard 222: (Module): Back to gnuplot.exe instead of wgnuplot.exe 223: 224: Revision 1.111 2006/01/25 20:38:18 brouard 225: (Module): Lots of cleaning and bugs added (Gompertz) 226: (Module): Comments can be added in data file. Missing date values 227: can be a simple dot '.'. 228: 229: Revision 1.110 2006/01/25 00:51:50 brouard 230: (Module): Lots of cleaning and bugs added (Gompertz) 231: 232: Revision 1.109 2006/01/24 19:37:15 brouard 233: (Module): Comments (lines starting with a #) are allowed in data. 234: 235: Revision 1.108 2006/01/19 18:05:42 lievre 236: Gnuplot problem appeared... 237: To be fixed 238: 239: Revision 1.107 2006/01/19 16:20:37 brouard 240: Test existence of gnuplot in imach path 241: 242: Revision 1.106 2006/01/19 13:24:36 brouard 243: Some cleaning and links added in html output 244: 245: Revision 1.105 2006/01/05 20:23:19 lievre 246: *** empty log message *** 247: 248: Revision 1.104 2005/09/30 16:11:43 lievre 249: (Module): sump fixed, loop imx fixed, and simplifications. 250: (Module): If the status is missing at the last wave but we know 251: that the person is alive, then we can code his/her status as -2 252: (instead of missing=-1 in earlier versions) and his/her 253: contributions to the likelihood is 1 - Prob of dying from last 254: health status (= 1-p13= p11+p12 in the easiest case of somebody in 255: the healthy state at last known wave). Version is 0.98 256: 257: Revision 1.103 2005/09/30 15:54:49 lievre 258: (Module): sump fixed, loop imx fixed, and simplifications. 259: 260: Revision 1.102 2004/09/15 17:31:30 brouard 261: Add the possibility to read data file including tab characters. 262: 263: Revision 1.101 2004/09/15 10:38:38 brouard 264: Fix on curr_time 265: 266: Revision 1.100 2004/07/12 18:29:06 brouard 267: Add version for Mac OS X. Just define UNIX in Makefile 268: 269: Revision 1.99 2004/06/05 08:57:40 brouard 270: *** empty log message *** 271: 272: Revision 1.98 2004/05/16 15:05:56 brouard 273: New version 0.97 . First attempt to estimate force of mortality 274: directly from the data i.e. without the need of knowing the health 275: state at each age, but using a Gompertz model: log u =a + b*age . 276: This is the basic analysis of mortality and should be done before any 277: other analysis, in order to test if the mortality estimated from the 278: cross-longitudinal survey is different from the mortality estimated 279: from other sources like vital statistic data. 280: 281: The same imach parameter file can be used but the option for mle should be -3. 282: 283: Agnès, who wrote this part of the code, tried to keep most of the 284: former routines in order to include the new code within the former code. 285: 286: The output is very simple: only an estimate of the intercept and of 287: the slope with 95% confident intervals. 288: 289: Current limitations: 290: A) Even if you enter covariates, i.e. with the 291: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates. 292: B) There is no computation of Life Expectancy nor Life Table. 293: 294: Revision 1.97 2004/02/20 13:25:42 lievre 295: Version 0.96d. Population forecasting command line is (temporarily) 296: suppressed. 297: 298: Revision 1.96 2003/07/15 15:38:55 brouard 299: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is 300: rewritten within the same printf. Workaround: many printfs. 301: 302: Revision 1.95 2003/07/08 07:54:34 brouard 303: * imach.c (Repository): 304: (Repository): Using imachwizard code to output a more meaningful covariance 305: matrix (cov(a12,c31) instead of numbers. 306: 307: Revision 1.94 2003/06/27 13:00:02 brouard 308: Just cleaning 309: 310: Revision 1.93 2003/06/25 16:33:55 brouard 311: (Module): On windows (cygwin) function asctime_r doesn't 312: exist so I changed back to asctime which exists. 313: (Module): Version 0.96b 314: 315: Revision 1.92 2003/06/25 16:30:45 brouard 316: (Module): On windows (cygwin) function asctime_r doesn't 317: exist so I changed back to asctime which exists. 318: 319: Revision 1.91 2003/06/25 15:30:29 brouard 320: * imach.c (Repository): Duplicated warning errors corrected. 321: (Repository): Elapsed time after each iteration is now output. It 322: helps to forecast when convergence will be reached. Elapsed time 323: is stamped in powell. We created a new html file for the graphs 324: concerning matrix of covariance. It has extension -cov.htm. 325: 326: Revision 1.90 2003/06/24 12:34:15 brouard 327: (Module): Some bugs corrected for windows. Also, when 328: mle=-1 a template is output in file "or"mypar.txt with the design 329: of the covariance matrix to be input. 330: 331: Revision 1.89 2003/06/24 12:30:52 brouard 332: (Module): Some bugs corrected for windows. Also, when 333: mle=-1 a template is output in file "or"mypar.txt with the design 334: of the covariance matrix to be input. 335: 336: Revision 1.88 2003/06/23 17:54:56 brouard 337: * 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. 338: 339: Revision 1.87 2003/06/18 12:26:01 brouard 340: Version 0.96 341: 342: Revision 1.86 2003/06/17 20:04:08 brouard 343: (Module): Change position of html and gnuplot routines and added 344: routine fileappend. 345: 346: Revision 1.85 2003/06/17 13:12:43 brouard 347: * imach.c (Repository): Check when date of death was earlier that 348: current date of interview. It may happen when the death was just 349: prior to the death. In this case, dh was negative and likelihood 350: was wrong (infinity). We still send an "Error" but patch by 351: assuming that the date of death was just one stepm after the 352: interview. 353: (Repository): Because some people have very long ID (first column) 354: we changed int to long in num[] and we added a new lvector for 355: memory allocation. But we also truncated to 8 characters (left 356: truncation) 357: (Repository): No more line truncation errors. 358: 359: Revision 1.84 2003/06/13 21:44:43 brouard 360: * imach.c (Repository): Replace "freqsummary" at a correct 361: place. It differs from routine "prevalence" which may be called 362: many times. Probs is memory consuming and must be used with 363: parcimony. 364: Version 0.95a3 (should output exactly the same maximization than 0.8a2) 365: 366: Revision 1.83 2003/06/10 13:39:11 lievre 367: *** empty log message *** 368: 369: Revision 1.82 2003/06/05 15:57:20 brouard 370: Add log in imach.c and fullversion number is now printed. 371: 372: */ 373: /* 374: Interpolated Markov Chain 375: 376: Short summary of the programme: 377: 378: This program computes Healthy Life Expectancies from 379: cross-longitudinal data. Cross-longitudinal data consist in: -1- a 380: first survey ("cross") where individuals from different ages are 381: interviewed on their health status or degree of disability (in the 382: case of a health survey which is our main interest) -2- at least a 383: second wave of interviews ("longitudinal") which measure each change 384: (if any) in individual health status. Health expectancies are 385: computed from the time spent in each health state according to a 386: model. More health states you consider, more time is necessary to reach the 387: Maximum Likelihood of the parameters involved in the model. The 388: simplest model is the multinomial logistic model where pij is the 389: probability to be observed in state j at the second wave 390: conditional to be observed in state i at the first wave. Therefore 391: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where 392: 'age' is age and 'sex' is a covariate. If you want to have a more 393: complex model than "constant and age", you should modify the program 394: where the markup *Covariates have to be included here again* invites 395: you to do it. More covariates you add, slower the 396: convergence. 397: 398: The advantage of this computer programme, compared to a simple 399: multinomial logistic model, is clear when the delay between waves is not 400: identical for each individual. Also, if a individual missed an 401: intermediate interview, the information is lost, but taken into 402: account using an interpolation or extrapolation. 403: 404: hPijx is the probability to be observed in state i at age x+h 405: conditional to the observed state i at age x. The delay 'h' can be 406: split into an exact number (nh*stepm) of unobserved intermediate 407: states. This elementary transition (by month, quarter, 408: semester or year) is modelled as a multinomial logistic. The hPx 409: matrix is simply the matrix product of nh*stepm elementary matrices 410: and the contribution of each individual to the likelihood is simply 411: hPijx. 412: 413: Also this programme outputs the covariance matrix of the parameters but also 414: of the life expectancies. It also computes the period (stable) prevalence. 415: 416: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr). 417: Institut national d'études démographiques, Paris. 418: This software have been partly granted by Euro-REVES, a concerted action 419: from the European Union. 420: It is copyrighted identically to a GNU software product, ie programme and 421: software can be distributed freely for non commercial use. Latest version 422: can be accessed at http://euroreves.ined.fr/imach . 423: 424: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach 425: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so 426: 427: **********************************************************************/ 428: /* 429: main 430: read parameterfile 431: read datafile 432: concatwav 433: freqsummary 434: if (mle >= 1) 435: mlikeli 436: print results files 437: if mle==1 438: computes hessian 439: read end of parameter file: agemin, agemax, bage, fage, estepm 440: begin-prev-date,... 441: open gnuplot file 442: open html file 443: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate 444: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ****** 445: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674 446: freexexit2 possible for memory heap. 447: 448: h Pij x | pij_nom ficrestpij 449: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3 450: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000 451: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907 452: 453: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340 454: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597 455: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in () 456: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix 457: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix 458: 459: forecasting if prevfcast==1 prevforecast call prevalence() 460: health expectancies 461: Variance-covariance of DFLE 462: prevalence() 463: movingaverage() 464: varevsij() 465: if popbased==1 varevsij(,popbased) 466: total life expectancies 467: Variance of period (stable) prevalence 468: end 469: */ 470: 471: 472: 473: 474: #include <math.h> 475: #include <stdio.h> 476: #include <stdlib.h> 477: #include <string.h> 478: #include <unistd.h> 479: 480: #include <limits.h> 481: #include <sys/types.h> 482: #include <sys/stat.h> 483: #include <errno.h> 484: extern int errno; 485: 486: /* #ifdef LINUX */ 487: /* #include <time.h> */ 488: /* #include "timeval.h" */ 489: /* #else */ 490: /* #include <sys/time.h> */ 491: /* #endif */ 492: 493: #include <time.h> 494: 495: #ifdef GSL 496: #include <gsl/gsl_errno.h> 497: #include <gsl/gsl_multimin.h> 498: #endif 499: 500: /* #include <libintl.h> */ 501: /* #define _(String) gettext (String) */ 502: 503: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */ 504: 505: #define GNUPLOTPROGRAM "gnuplot" 506: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/ 507: #define FILENAMELENGTH 132 508: 509: #define GLOCK_ERROR_NOPATH -1 /* empty path */ 510: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */ 511: 512: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */ 513: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */ 514: 515: #define NINTERVMAX 8 516: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */ 517: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */ 518: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */ 519: #define codtabm(h,k) 1 & (h-1) >> (k-1) ; 520: #define MAXN 20000 521: #define YEARM 12. /**< Number of months per year */ 522: #define AGESUP 130 523: #define AGEBASE 40 524: #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */ 525: #ifdef _WIN32 526: #define DIRSEPARATOR '\\' 527: #define CHARSEPARATOR "\\" 528: #define ODIRSEPARATOR '/' 529: #else 530: #define DIRSEPARATOR '/' 531: #define CHARSEPARATOR "/" 532: #define ODIRSEPARATOR '\\' 533: #endif 534: 535: /* $Id: imach.c,v 1.157 2014/08/27 16:26:55 brouard Exp $ */ 536: /* $State: Exp $ */ 537: 538: char version[]="Imach version 0.98nX, August 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)"; 539: char fullversion[]="$Revision: 1.157 $ $Date: 2014/08/27 16:26:55 $"; 540: char strstart[80]; 541: char optionfilext[10], optionfilefiname[FILENAMELENGTH]; 542: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */ 543: int nvar=0, nforce=0; /* Number of variables, number of forces */ 544: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */ 545: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */ 546: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */ 547: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */ 548: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */ 549: int cptcovprodnoage=0; /**< Number of covariate products without age */ 550: int cptcoveff=0; /* Total number of covariates to vary for printing results */ 551: int cptcov=0; /* Working variable */ 552: int npar=NPARMAX; 553: int nlstate=2; /* Number of live states */ 554: int ndeath=1; /* Number of dead states */ 555: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */ 556: int popbased=0; 557: 558: int *wav; /* Number of waves for this individuual 0 is possible */ 559: int maxwav=0; /* Maxim number of waves */ 560: int jmin=0, jmax=0; /* min, max spacing between 2 waves */ 561: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 562: int gipmx=0, gsw=0; /* Global variables on the number of contributions 563: to the likelihood and the sum of weights (done by funcone)*/ 564: int mle=1, weightopt=0; 565: int **mw; /* mw[mi][i] is number of the mi wave for this individual */ 566: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */ 567: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between 568: * wave mi and wave mi+1 is not an exact multiple of stepm. */ 569: double jmean=1; /* Mean space between 2 waves */ 570: double **matprod2(); /* test */ 571: double **oldm, **newm, **savm; /* Working pointers to matrices */ 572: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */ 573: /*FILE *fic ; */ /* Used in readdata only */ 574: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop; 575: FILE *ficlog, *ficrespow; 576: int globpr=0; /* Global variable for printing or not */ 577: double fretone; /* Only one call to likelihood */ 578: long ipmx=0; /* Number of contributions */ 579: double sw; /* Sum of weights */ 580: char filerespow[FILENAMELENGTH]; 581: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */ 582: FILE *ficresilk; 583: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor; 584: FILE *ficresprobmorprev; 585: FILE *fichtm, *fichtmcov; /* Html File */ 586: FILE *ficreseij; 587: char filerese[FILENAMELENGTH]; 588: FILE *ficresstdeij; 589: char fileresstde[FILENAMELENGTH]; 590: FILE *ficrescveij; 591: char filerescve[FILENAMELENGTH]; 592: FILE *ficresvij; 593: char fileresv[FILENAMELENGTH]; 594: FILE *ficresvpl; 595: char fileresvpl[FILENAMELENGTH]; 596: char title[MAXLINE]; 597: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH]; 598: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH]; 599: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH]; 600: char command[FILENAMELENGTH]; 601: int outcmd=0; 602: 603: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH]; 604: 605: char filelog[FILENAMELENGTH]; /* Log file */ 606: char filerest[FILENAMELENGTH]; 607: char fileregp[FILENAMELENGTH]; 608: char popfile[FILENAMELENGTH]; 609: 610: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ; 611: 612: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */ 613: /* struct timezone tzp; */ 614: /* extern int gettimeofday(); */ 615: struct tm tml, *gmtime(), *localtime(); 616: 617: extern time_t time(); 618: 619: struct tm start_time, end_time, curr_time, last_time, forecast_time; 620: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */ 621: struct tm tm; 622: 623: char strcurr[80], strfor[80]; 624: 625: char *endptr; 626: long lval; 627: double dval; 628: 629: #define NR_END 1 630: #define FREE_ARG char* 631: #define FTOL 1.0e-10 632: 633: #define NRANSI 634: #define ITMAX 200 635: 636: #define TOL 2.0e-4 637: 638: #define CGOLD 0.3819660 639: #define ZEPS 1.0e-10 640: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 641: 642: #define GOLD 1.618034 643: #define GLIMIT 100.0 644: #define TINY 1.0e-20 645: 646: static double maxarg1,maxarg2; 647: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2)) 648: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2)) 649: 650: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a)) 651: #define rint(a) floor(a+0.5) 652: 653: static double sqrarg; 654: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg) 655: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 656: int agegomp= AGEGOMP; 657: 658: int imx; 659: int stepm=1; 660: /* Stepm, step in month: minimum step interpolation*/ 661: 662: int estepm; 663: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/ 664: 665: int m,nb; 666: long *num; 667: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens; 668: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint; 669: double **pmmij, ***probs; 670: double *ageexmed,*agecens; 671: double dateintmean=0; 672: 673: double *weight; 674: int **s; /* Status */ 675: double *agedc; 676: double **covar; /**< covar[j,i], value of jth covariate for individual i, 677: * covar=matrix(0,NCOVMAX,1,n); 678: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */ 679: double idx; 680: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */ 681: int *Ndum; /** Freq of modality (tricode */ 682: int **codtab; /**< codtab=imatrix(1,100,1,10); */ 683: int **Tvard, *Tprod, cptcovprod, *Tvaraff; 684: double *lsurv, *lpop, *tpop; 685: 686: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */ 687: double ftolhess; /**< Tolerance for computing hessian */ 688: 689: /**************** split *************************/ 690: static int split( char *path, char *dirc, char *name, char *ext, char *finame ) 691: { 692: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc) 693: the name of the file (name), its extension only (ext) and its first part of the name (finame) 694: */ 695: char *ss; /* pointer */ 696: int l1, l2; /* length counters */ 697: 698: l1 = strlen(path ); /* length of path */ 699: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH ); 700: ss= strrchr( path, DIRSEPARATOR ); /* find last / */ 701: if ( ss == NULL ) { /* no directory, so determine current directory */ 702: strcpy( name, path ); /* we got the fullname name because no directory */ 703: /*if(strrchr(path, ODIRSEPARATOR )==NULL) 704: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/ 705: /* get current working directory */ 706: /* extern char* getcwd ( char *buf , int len);*/ 707: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) { 708: return( GLOCK_ERROR_GETCWD ); 709: } 710: /* got dirc from getcwd*/ 711: printf(" DIRC = %s \n",dirc); 712: } else { /* strip direcotry from path */ 713: ss++; /* after this, the filename */ 714: l2 = strlen( ss ); /* length of filename */ 715: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH ); 716: strcpy( name, ss ); /* save file name */ 717: strncpy( dirc, path, l1 - l2 ); /* now the directory */ 718: dirc[l1-l2] = 0; /* add zero */ 719: printf(" DIRC2 = %s \n",dirc); 720: } 721: /* We add a separator at the end of dirc if not exists */ 722: l1 = strlen( dirc ); /* length of directory */ 723: if( dirc[l1-1] != DIRSEPARATOR ){ 724: dirc[l1] = DIRSEPARATOR; 725: dirc[l1+1] = 0; 726: printf(" DIRC3 = %s \n",dirc); 727: } 728: ss = strrchr( name, '.' ); /* find last / */ 729: if (ss >0){ 730: ss++; 731: strcpy(ext,ss); /* save extension */ 732: l1= strlen( name); 733: l2= strlen(ss)+1; 734: strncpy( finame, name, l1-l2); 735: finame[l1-l2]= 0; 736: } 737: 738: return( 0 ); /* we're done */ 739: } 740: 741: 742: /******************************************/ 743: 744: void replace_back_to_slash(char *s, char*t) 745: { 746: int i; 747: int lg=0; 748: i=0; 749: lg=strlen(t); 750: for(i=0; i<= lg; i++) { 751: (s[i] = t[i]); 752: if (t[i]== '\\') s[i]='/'; 753: } 754: } 755: 756: char *trimbb(char *out, char *in) 757: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */ 758: char *s; 759: s=out; 760: while (*in != '\0'){ 761: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/ 762: in++; 763: } 764: *out++ = *in++; 765: } 766: *out='\0'; 767: return s; 768: } 769: 770: char *cutl(char *blocc, char *alocc, char *in, char occ) 771: { 772: /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 773: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2') 774: gives blocc="abcdef2ghi" and alocc="j". 775: If occ is not found blocc is null and alocc is equal to in. Returns blocc 776: */ 777: char *s, *t, *bl; 778: t=in;s=in; 779: while ((*in != occ) && (*in != '\0')){ 780: *alocc++ = *in++; 781: } 782: if( *in == occ){ 783: *(alocc)='\0'; 784: s=++in; 785: } 786: 787: if (s == t) {/* occ not found */ 788: *(alocc-(in-s))='\0'; 789: in=s; 790: } 791: while ( *in != '\0'){ 792: *blocc++ = *in++; 793: } 794: 795: *blocc='\0'; 796: return t; 797: } 798: char *cutv(char *blocc, char *alocc, char *in, char occ) 799: { 800: /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 801: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2') 802: gives blocc="abcdef2ghi" and alocc="j". 803: If occ is not found blocc is null and alocc is equal to in. Returns alocc 804: */ 805: char *s, *t; 806: t=in;s=in; 807: while (*in != '\0'){ 808: while( *in == occ){ 809: *blocc++ = *in++; 810: s=in; 811: } 812: *blocc++ = *in++; 813: } 814: if (s == t) /* occ not found */ 815: *(blocc-(in-s))='\0'; 816: else 817: *(blocc-(in-s)-1)='\0'; 818: in=s; 819: while ( *in != '\0'){ 820: *alocc++ = *in++; 821: } 822: 823: *alocc='\0'; 824: return s; 825: } 826: 827: int nbocc(char *s, char occ) 828: { 829: int i,j=0; 830: int lg=20; 831: i=0; 832: lg=strlen(s); 833: for(i=0; i<= lg; i++) { 834: if (s[i] == occ ) j++; 835: } 836: return j; 837: } 838: 839: /* void cutv(char *u,char *v, char*t, char occ) */ 840: /* { */ 841: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */ 842: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */ 843: /* gives u="abcdef2ghi" and v="j" *\/ */ 844: /* int i,lg,j,p=0; */ 845: /* i=0; */ 846: /* lg=strlen(t); */ 847: /* for(j=0; j<=lg-1; j++) { */ 848: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */ 849: /* } */ 850: 851: /* for(j=0; j<p; j++) { */ 852: /* (u[j] = t[j]); */ 853: /* } */ 854: /* u[p]='\0'; */ 855: 856: /* for(j=0; j<= lg; j++) { */ 857: /* if (j>=(p+1))(v[j-p-1] = t[j]); */ 858: /* } */ 859: /* } */ 860: 861: /********************** nrerror ********************/ 862: 863: void nrerror(char error_text[]) 864: { 865: fprintf(stderr,"ERREUR ...\n"); 866: fprintf(stderr,"%s\n",error_text); 867: exit(EXIT_FAILURE); 868: } 869: /*********************** vector *******************/ 870: double *vector(int nl, int nh) 871: { 872: double *v; 873: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double))); 874: if (!v) nrerror("allocation failure in vector"); 875: return v-nl+NR_END; 876: } 877: 878: /************************ free vector ******************/ 879: void free_vector(double*v, int nl, int nh) 880: { 881: free((FREE_ARG)(v+nl-NR_END)); 882: } 883: 884: /************************ivector *******************************/ 885: int *ivector(long nl,long nh) 886: { 887: int *v; 888: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int))); 889: if (!v) nrerror("allocation failure in ivector"); 890: return v-nl+NR_END; 891: } 892: 893: /******************free ivector **************************/ 894: void free_ivector(int *v, long nl, long nh) 895: { 896: free((FREE_ARG)(v+nl-NR_END)); 897: } 898: 899: /************************lvector *******************************/ 900: long *lvector(long nl,long nh) 901: { 902: long *v; 903: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long))); 904: if (!v) nrerror("allocation failure in ivector"); 905: return v-nl+NR_END; 906: } 907: 908: /******************free lvector **************************/ 909: void free_lvector(long *v, long nl, long nh) 910: { 911: free((FREE_ARG)(v+nl-NR_END)); 912: } 913: 914: /******************* imatrix *******************************/ 915: int **imatrix(long nrl, long nrh, long ncl, long nch) 916: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 917: { 918: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 919: int **m; 920: 921: /* allocate pointers to rows */ 922: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 923: if (!m) nrerror("allocation failure 1 in matrix()"); 924: m += NR_END; 925: m -= nrl; 926: 927: 928: /* allocate rows and set pointers to them */ 929: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 930: if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 931: m[nrl] += NR_END; 932: m[nrl] -= ncl; 933: 934: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 935: 936: /* return pointer to array of pointers to rows */ 937: return m; 938: } 939: 940: /****************** free_imatrix *************************/ 941: void free_imatrix(m,nrl,nrh,ncl,nch) 942: int **m; 943: long nch,ncl,nrh,nrl; 944: /* free an int matrix allocated by imatrix() */ 945: { 946: free((FREE_ARG) (m[nrl]+ncl-NR_END)); 947: free((FREE_ARG) (m+nrl-NR_END)); 948: } 949: 950: /******************* matrix *******************************/ 951: double **matrix(long nrl, long nrh, long ncl, long nch) 952: { 953: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1; 954: double **m; 955: 956: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*))); 957: if (!m) nrerror("allocation failure 1 in matrix()"); 958: m += NR_END; 959: m -= nrl; 960: 961: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double))); 962: if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 963: m[nrl] += NR_END; 964: m[nrl] -= ncl; 965: 966: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol; 967: return m; 968: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0]) 969: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress 970: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized. 971: */ 972: } 973: 974: /*************************free matrix ************************/ 975: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch) 976: { 977: free((FREE_ARG)(m[nrl]+ncl-NR_END)); 978: free((FREE_ARG)(m+nrl-NR_END)); 979: } 980: 981: /******************* ma3x *******************************/ 982: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh) 983: { 984: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1; 985: double ***m; 986: 987: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*))); 988: if (!m) nrerror("allocation failure 1 in matrix()"); 989: m += NR_END; 990: m -= nrl; 991: 992: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double))); 993: if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 994: m[nrl] += NR_END; 995: m[nrl] -= ncl; 996: 997: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol; 998: 999: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double))); 1000: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()"); 1001: m[nrl][ncl] += NR_END; 1002: m[nrl][ncl] -= nll; 1003: for (j=ncl+1; j<=nch; j++) 1004: m[nrl][j]=m[nrl][j-1]+nlay; 1005: 1006: for (i=nrl+1; i<=nrh; i++) { 1007: m[i][ncl]=m[i-1l][ncl]+ncol*nlay; 1008: for (j=ncl+1; j<=nch; j++) 1009: m[i][j]=m[i][j-1]+nlay; 1010: } 1011: return m; 1012: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1]) 1013: &(m[i][j][k]) <=> *((*(m+i) + j)+k) 1014: */ 1015: } 1016: 1017: /*************************free ma3x ************************/ 1018: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh) 1019: { 1020: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END)); 1021: free((FREE_ARG)(m[nrl]+ncl-NR_END)); 1022: free((FREE_ARG)(m+nrl-NR_END)); 1023: } 1024: 1025: /*************** function subdirf ***********/ 1026: char *subdirf(char fileres[]) 1027: { 1028: /* Caution optionfilefiname is hidden */ 1029: strcpy(tmpout,optionfilefiname); 1030: strcat(tmpout,"/"); /* Add to the right */ 1031: strcat(tmpout,fileres); 1032: return tmpout; 1033: } 1034: 1035: /*************** function subdirf2 ***********/ 1036: char *subdirf2(char fileres[], char *preop) 1037: { 1038: 1039: /* Caution optionfilefiname is hidden */ 1040: strcpy(tmpout,optionfilefiname); 1041: strcat(tmpout,"/"); 1042: strcat(tmpout,preop); 1043: strcat(tmpout,fileres); 1044: return tmpout; 1045: } 1046: 1047: /*************** function subdirf3 ***********/ 1048: char *subdirf3(char fileres[], char *preop, char *preop2) 1049: { 1050: 1051: /* Caution optionfilefiname is hidden */ 1052: strcpy(tmpout,optionfilefiname); 1053: strcat(tmpout,"/"); 1054: strcat(tmpout,preop); 1055: strcat(tmpout,preop2); 1056: strcat(tmpout,fileres); 1057: return tmpout; 1058: } 1059: 1060: /***************** f1dim *************************/ 1061: extern int ncom; 1062: extern double *pcom,*xicom; 1063: extern double (*nrfunc)(double []); 1064: 1065: double f1dim(double x) 1066: { 1067: int j; 1068: double f; 1069: double *xt; 1070: 1071: xt=vector(1,ncom); 1072: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 1073: f=(*nrfunc)(xt); 1074: free_vector(xt,1,ncom); 1075: return f; 1076: } 1077: 1078: /*****************brent *************************/ 1079: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin) 1080: { 1081: int iter; 1082: double a,b,d,etemp; 1083: double fu,fv,fw,fx; 1084: double ftemp; 1085: double p,q,r,tol1,tol2,u,v,w,x,xm; 1086: double e=0.0; 1087: 1088: a=(ax < cx ? ax : cx); 1089: b=(ax > cx ? ax : cx); 1090: x=w=v=bx; 1091: fw=fv=fx=(*f)(x); 1092: for (iter=1;iter<=ITMAX;iter++) { 1093: xm=0.5*(a+b); 1094: tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 1095: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/ 1096: printf(".");fflush(stdout); 1097: fprintf(ficlog,".");fflush(ficlog); 1098: #ifdef DEBUG 1099: 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); 1100: 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); 1101: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */ 1102: #endif 1103: if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 1104: *xmin=x; 1105: return fx; 1106: } 1107: ftemp=fu; 1108: if (fabs(e) > tol1) { 1109: r=(x-w)*(fx-fv); 1110: q=(x-v)*(fx-fw); 1111: p=(x-v)*q-(x-w)*r; 1112: q=2.0*(q-r); 1113: if (q > 0.0) p = -p; 1114: q=fabs(q); 1115: etemp=e; 1116: e=d; 1117: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 1118: d=CGOLD*(e=(x >= xm ? a-x : b-x)); 1119: else { 1120: d=p/q; 1121: u=x+d; 1122: if (u-a < tol2 || b-u < tol2) 1123: d=SIGN(tol1,xm-x); 1124: } 1125: } else { 1126: d=CGOLD*(e=(x >= xm ? a-x : b-x)); 1127: } 1128: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 1129: fu=(*f)(u); 1130: if (fu <= fx) { 1131: if (u >= x) a=x; else b=x; 1132: SHFT(v,w,x,u) 1133: SHFT(fv,fw,fx,fu) 1134: } else { 1135: if (u < x) a=u; else b=u; 1136: if (fu <= fw || w == x) { 1137: v=w; 1138: w=u; 1139: fv=fw; 1140: fw=fu; 1141: } else if (fu <= fv || v == x || v == w) { 1142: v=u; 1143: fv=fu; 1144: } 1145: } 1146: } 1147: nrerror("Too many iterations in brent"); 1148: *xmin=x; 1149: return fx; 1150: } 1151: 1152: /****************** mnbrak ***********************/ 1153: 1154: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 1155: double (*func)(double)) 1156: { 1157: double ulim,u,r,q, dum; 1158: double fu; 1159: 1160: *fa=(*func)(*ax); 1161: *fb=(*func)(*bx); 1162: if (*fb > *fa) { 1163: SHFT(dum,*ax,*bx,dum) 1164: SHFT(dum,*fb,*fa,dum) 1165: } 1166: *cx=(*bx)+GOLD*(*bx-*ax); 1167: *fc=(*func)(*cx); 1168: while (*fb > *fc) { 1169: r=(*bx-*ax)*(*fb-*fc); 1170: q=(*bx-*cx)*(*fb-*fa); 1171: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 1172: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 1173: ulim=(*bx)+GLIMIT*(*cx-*bx); 1174: if ((*bx-u)*(u-*cx) > 0.0) { 1175: fu=(*func)(u); 1176: } else if ((*cx-u)*(u-ulim) > 0.0) { 1177: fu=(*func)(u); 1178: if (fu < *fc) { 1179: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 1180: SHFT(*fb,*fc,fu,(*func)(u)) 1181: } 1182: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 1183: u=ulim; 1184: fu=(*func)(u); 1185: } else { 1186: u=(*cx)+GOLD*(*cx-*bx); 1187: fu=(*func)(u); 1188: } 1189: SHFT(*ax,*bx,*cx,u) 1190: SHFT(*fa,*fb,*fc,fu) 1191: } 1192: } 1193: 1194: /*************** linmin ************************/ 1195: 1196: int ncom; 1197: double *pcom,*xicom; 1198: double (*nrfunc)(double []); 1199: 1200: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 1201: { 1202: double brent(double ax, double bx, double cx, 1203: double (*f)(double), double tol, double *xmin); 1204: double f1dim(double x); 1205: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 1206: double *fc, double (*func)(double)); 1207: int j; 1208: double xx,xmin,bx,ax; 1209: double fx,fb,fa; 1210: 1211: ncom=n; 1212: pcom=vector(1,n); 1213: xicom=vector(1,n); 1214: nrfunc=func; 1215: for (j=1;j<=n;j++) { 1216: pcom[j]=p[j]; 1217: xicom[j]=xi[j]; 1218: } 1219: ax=0.0; 1220: xx=1.0; 1221: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 1222: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 1223: #ifdef DEBUG 1224: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin); 1225: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin); 1226: #endif 1227: for (j=1;j<=n;j++) { 1228: xi[j] *= xmin; 1229: p[j] += xi[j]; 1230: } 1231: free_vector(xicom,1,n); 1232: free_vector(pcom,1,n); 1233: } 1234: 1235: char *asc_diff_time(long time_sec, char ascdiff[]) 1236: { 1237: long sec_left, days, hours, minutes; 1238: days = (time_sec) / (60*60*24); 1239: sec_left = (time_sec) % (60*60*24); 1240: hours = (sec_left) / (60*60) ; 1241: sec_left = (sec_left) %(60*60); 1242: minutes = (sec_left) /60; 1243: sec_left = (sec_left) % (60); 1244: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left); 1245: return ascdiff; 1246: } 1247: 1248: /*************** powell ************************/ 1249: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 1250: double (*func)(double [])) 1251: { 1252: void linmin(double p[], double xi[], int n, double *fret, 1253: double (*func)(double [])); 1254: int i,ibig,j; 1255: double del,t,*pt,*ptt,*xit; 1256: double fp,fptt; 1257: double *xits; 1258: int niterf, itmp; 1259: 1260: pt=vector(1,n); 1261: ptt=vector(1,n); 1262: xit=vector(1,n); 1263: xits=vector(1,n); 1264: *fret=(*func)(p); 1265: for (j=1;j<=n;j++) pt[j]=p[j]; 1266: rcurr_time = time(NULL); 1267: for (*iter=1;;++(*iter)) { 1268: fp=(*fret); 1269: ibig=0; 1270: del=0.0; 1271: rlast_time=rcurr_time; 1272: /* (void) gettimeofday(&curr_time,&tzp); */ 1273: rcurr_time = time(NULL); 1274: curr_time = *localtime(&rcurr_time); 1275: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout); 1276: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog); 1277: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */ 1278: for (i=1;i<=n;i++) { 1279: printf(" %d %.12f",i, p[i]); 1280: fprintf(ficlog," %d %.12lf",i, p[i]); 1281: fprintf(ficrespow," %.12lf", p[i]); 1282: } 1283: printf("\n"); 1284: fprintf(ficlog,"\n"); 1285: fprintf(ficrespow,"\n");fflush(ficrespow); 1286: if(*iter <=3){ 1287: tml = *localtime(&rcurr_time); 1288: strcpy(strcurr,asctime(&tml)); 1289: /* asctime_r(&tm,strcurr); */ 1290: rforecast_time=rcurr_time; 1291: itmp = strlen(strcurr); 1292: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */ 1293: strcurr[itmp-1]='\0'; 1294: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time); 1295: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time); 1296: for(niterf=10;niterf<=30;niterf+=10){ 1297: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time); 1298: forecast_time = *localtime(&rforecast_time); 1299: /* asctime_r(&tmf,strfor); */ 1300: strcpy(strfor,asctime(&forecast_time)); 1301: itmp = strlen(strfor); 1302: if(strfor[itmp-1]=='\n') 1303: strfor[itmp-1]='\0'; 1304: printf(" - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr); 1305: fprintf(ficlog," - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr); 1306: } 1307: } 1308: for (i=1;i<=n;i++) { 1309: for (j=1;j<=n;j++) xit[j]=xi[j][i]; 1310: fptt=(*fret); 1311: #ifdef DEBUG 1312: printf("fret=%lf \n",*fret); 1313: fprintf(ficlog,"fret=%lf \n",*fret); 1314: #endif 1315: printf("%d",i);fflush(stdout); 1316: fprintf(ficlog,"%d",i);fflush(ficlog); 1317: linmin(p,xit,n,fret,func); 1318: if (fabs(fptt-(*fret)) > del) { 1319: del=fabs(fptt-(*fret)); 1320: ibig=i; 1321: } 1322: #ifdef DEBUG 1323: printf("%d %.12e",i,(*fret)); 1324: fprintf(ficlog,"%d %.12e",i,(*fret)); 1325: for (j=1;j<=n;j++) { 1326: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5); 1327: printf(" x(%d)=%.12e",j,xit[j]); 1328: fprintf(ficlog," x(%d)=%.12e",j,xit[j]); 1329: } 1330: for(j=1;j<=n;j++) { 1331: printf(" p=%.12e",p[j]); 1332: fprintf(ficlog," p=%.12e",p[j]); 1333: } 1334: printf("\n"); 1335: fprintf(ficlog,"\n"); 1336: #endif 1337: } 1338: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { 1339: #ifdef DEBUG 1340: int k[2],l; 1341: k[0]=1; 1342: k[1]=-1; 1343: printf("Max: %.12e",(*func)(p)); 1344: fprintf(ficlog,"Max: %.12e",(*func)(p)); 1345: for (j=1;j<=n;j++) { 1346: printf(" %.12e",p[j]); 1347: fprintf(ficlog," %.12e",p[j]); 1348: } 1349: printf("\n"); 1350: fprintf(ficlog,"\n"); 1351: for(l=0;l<=1;l++) { 1352: for (j=1;j<=n;j++) { 1353: ptt[j]=p[j]+(p[j]-pt[j])*k[l]; 1354: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]); 1355: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]); 1356: } 1357: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p))); 1358: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p))); 1359: } 1360: #endif 1361: 1362: 1363: free_vector(xit,1,n); 1364: free_vector(xits,1,n); 1365: free_vector(ptt,1,n); 1366: free_vector(pt,1,n); 1367: return; 1368: } 1369: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 1370: for (j=1;j<=n;j++) { 1371: ptt[j]=2.0*p[j]-pt[j]; 1372: xit[j]=p[j]-pt[j]; 1373: pt[j]=p[j]; 1374: } 1375: fptt=(*func)(ptt); 1376: if (fptt < fp) { 1377: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 1378: if (t < 0.0) { 1379: linmin(p,xit,n,fret,func); 1380: for (j=1;j<=n;j++) { 1381: xi[j][ibig]=xi[j][n]; 1382: xi[j][n]=xit[j]; 1383: } 1384: #ifdef DEBUG 1385: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig); 1386: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig); 1387: for(j=1;j<=n;j++){ 1388: printf(" %.12e",xit[j]); 1389: fprintf(ficlog," %.12e",xit[j]); 1390: } 1391: printf("\n"); 1392: fprintf(ficlog,"\n"); 1393: #endif 1394: } 1395: } 1396: } 1397: } 1398: 1399: /**** Prevalence limit (stable or period prevalence) ****************/ 1400: 1401: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij) 1402: { 1403: /* Computes the prevalence limit in each live state at age x by left multiplying the unit 1404: matrix by transitions matrix until convergence is reached */ 1405: 1406: int i, ii,j,k; 1407: double min, max, maxmin, maxmax,sumnew=0.; 1408: /* double **matprod2(); */ /* test */ 1409: double **out, cov[NCOVMAX+1], **pmij(); 1410: double **newm; 1411: double agefin, delaymax=50 ; /* Max number of years to converge */ 1412: 1413: for (ii=1;ii<=nlstate+ndeath;ii++) 1414: for (j=1;j<=nlstate+ndeath;j++){ 1415: oldm[ii][j]=(ii==j ? 1.0 : 0.0); 1416: } 1417: 1418: cov[1]=1.; 1419: 1420: /* Even if hstepm = 1, at least one multiplication by the unit matrix */ 1421: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){ 1422: newm=savm; 1423: /* Covariates have to be included here again */ 1424: cov[2]=agefin; 1425: 1426: for (k=1; k<=cptcovn;k++) { 1427: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; 1428: /*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]]);*/ 1429: } 1430: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */ 1431: /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */ 1432: /* cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */ 1433: 1434: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/ 1435: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/ 1436: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/ 1437: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */ 1438: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */ 1439: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */ 1440: 1441: savm=oldm; 1442: oldm=newm; 1443: maxmax=0.; 1444: for(j=1;j<=nlstate;j++){ 1445: min=1.; 1446: max=0.; 1447: for(i=1; i<=nlstate; i++) { 1448: sumnew=0; 1449: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k]; 1450: prlim[i][j]= newm[i][j]/(1-sumnew); 1451: /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/ 1452: max=FMAX(max,prlim[i][j]); 1453: min=FMIN(min,prlim[i][j]); 1454: } 1455: maxmin=max-min; 1456: maxmax=FMAX(maxmax,maxmin); 1457: } 1458: if(maxmax < ftolpl){ 1459: return prlim; 1460: } 1461: } 1462: } 1463: 1464: /*************** transition probabilities ***************/ 1465: 1466: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate ) 1467: { 1468: /* According to parameters values stored in x and the covariate's values stored in cov, 1469: computes the probability to be observed in state j being in state i by appying the 1470: model to the ncovmodel covariates (including constant and age). 1471: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc] 1472: and, according on how parameters are entered, the position of the coefficient xij(nc) of the 1473: ncth covariate in the global vector x is given by the formula: 1474: j=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel 1476: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation, 1477: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij. 1478: Outputs ps[i][j] the probability to be observed in j being in j according to 1479: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij] 1480: */ 1481: double s1, lnpijopii; 1482: /*double t34;*/ 1483: int i,j,j1, nc, ii, jj; 1484: 1485: for(i=1; i<= nlstate; i++){ 1486: for(j=1; j<i;j++){ 1487: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){ 1488: /*lnpijopii += param[i][j][nc]*cov[nc];*/ 1489: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc]; 1490: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */ 1491: } 1492: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */ 1493: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */ 1494: } 1495: for(j=i+1; j<=nlstate+ndeath;j++){ 1496: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){ 1497: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/ 1498: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc]; 1499: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */ 1500: } 1501: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */ 1502: } 1503: } 1504: 1505: for(i=1; i<= nlstate; i++){ 1506: s1=0; 1507: for(j=1; j<i; j++){ 1508: s1+=exp(ps[i][j]); /* In fact sums pij/pii */ 1509: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */ 1510: } 1511: for(j=i+1; j<=nlstate+ndeath; j++){ 1512: s1+=exp(ps[i][j]); /* In fact sums pij/pii */ 1513: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */ 1514: } 1515: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */ 1516: ps[i][i]=1./(s1+1.); 1517: /* Computing other pijs */ 1518: for(j=1; j<i; j++) 1519: ps[i][j]= exp(ps[i][j])*ps[i][i]; 1520: for(j=i+1; j<=nlstate+ndeath; j++) 1521: ps[i][j]= exp(ps[i][j])*ps[i][i]; 1522: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */ 1523: } /* end i */ 1524: 1525: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){ 1526: for(jj=1; jj<= nlstate+ndeath; jj++){ 1527: ps[ii][jj]=0; 1528: ps[ii][ii]=1; 1529: } 1530: } 1531: 1532: 1533: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */ 1534: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */ 1535: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */ 1536: /* } */ 1537: /* printf("\n "); */ 1538: /* } */ 1539: /* printf("\n ");printf("%lf ",cov[2]);*/ 1540: /* 1541: for(i=1; i<= npar; i++) printf("%f ",x[i]); 1542: goto end;*/ 1543: return ps; 1544: } 1545: 1546: /**************** Product of 2 matrices ******************/ 1547: 1548: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b) 1549: { 1550: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times 1551: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */ 1552: /* in, b, out are matrice of pointers which should have been initialized 1553: before: only the contents of out is modified. The function returns 1554: a pointer to pointers identical to out */ 1555: int i, j, k; 1556: for(i=nrl; i<= nrh; i++) 1557: for(k=ncolol; k<=ncoloh; k++){ 1558: out[i][k]=0.; 1559: for(j=ncl; j<=nch; j++) 1560: out[i][k] +=in[i][j]*b[j][k]; 1561: } 1562: return out; 1563: } 1564: 1565: 1566: /************* Higher Matrix Product ***************/ 1567: 1568: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij ) 1569: { 1570: /* Computes the transition matrix starting at age 'age' over 1571: 'nhstepm*hstepm*stepm' months (i.e. until 1572: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying 1573: nhstepm*hstepm matrices. 1574: Output is stored in matrix po[i][j][h] for h every 'hstepm' step 1575: (typically every 2 years instead of every month which is too big 1576: for the memory). 1577: Model is determined by parameters x and covariates have to be 1578: included manually here. 1579: 1580: */ 1581: 1582: int i, j, d, h, k; 1583: double **out, cov[NCOVMAX+1]; 1584: double **newm; 1585: 1586: /* Hstepm could be zero and should return the unit matrix */ 1587: for (i=1;i<=nlstate+ndeath;i++) 1588: for (j=1;j<=nlstate+ndeath;j++){ 1589: oldm[i][j]=(i==j ? 1.0 : 0.0); 1590: po[i][j][0]=(i==j ? 1.0 : 0.0); 1591: } 1592: /* Even if hstepm = 1, at least one multiplication by the unit matrix */ 1593: for(h=1; h <=nhstepm; h++){ 1594: for(d=1; d <=hstepm; d++){ 1595: newm=savm; 1596: /* Covariates have to be included here again */ 1597: cov[1]=1.; 1598: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM; 1599: for (k=1; k<=cptcovn;k++) 1600: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; 1601: for (k=1; k<=cptcovage;k++) 1602: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; 1603: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */ 1604: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; 1605: 1606: 1607: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/ 1608: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/ 1609: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 1610: pmij(pmmij,cov,ncovmodel,x,nlstate)); 1611: savm=oldm; 1612: oldm=newm; 1613: } 1614: for(i=1; i<=nlstate+ndeath; i++) 1615: for(j=1;j<=nlstate+ndeath;j++) { 1616: po[i][j][h]=newm[i][j]; 1617: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/ 1618: } 1619: /*printf("h=%d ",h);*/ 1620: } /* end h */ 1621: /* printf("\n H=%d \n",h); */ 1622: return po; 1623: } 1624: 1625: 1626: /*************** log-likelihood *************/ 1627: double func( double *x) 1628: { 1629: int i, ii, j, k, mi, d, kk; 1630: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1]; 1631: double **out; 1632: double sw; /* Sum of weights */ 1633: double lli; /* Individual log likelihood */ 1634: int s1, s2; 1635: double bbh, survp; 1636: long ipmx; 1637: /*extern weight */ 1638: /* We are differentiating ll according to initial status */ 1639: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/ 1640: /*for(i=1;i<imx;i++) 1641: printf(" %d\n",s[4][i]); 1642: */ 1643: cov[1]=1.; 1644: 1645: for(k=1; k<=nlstate; k++) ll[k]=0.; 1646: 1647: if(mle==1){ 1648: for (i=1,ipmx=0, sw=0.; i<=imx; i++){ 1649: /* Computes the values of the ncovmodel covariates of the model 1650: depending if the covariates are fixed or variying (age dependent) and stores them in cov[] 1651: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability 1652: to be observed in j being in i according to the model. 1653: */ 1654: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */ 1655: cov[2+k]=covar[Tvar[k]][i]; 1656: } 1657: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 1658: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 1659: has been calculated etc */ 1660: for(mi=1; mi<= wav[i]-1; mi++){ 1661: for (ii=1;ii<=nlstate+ndeath;ii++) 1662: for (j=1;j<=nlstate+ndeath;j++){ 1663: oldm[ii][j]=(ii==j ? 1.0 : 0.0); 1664: savm[ii][j]=(ii==j ? 1.0 : 0.0); 1665: } 1666: for(d=0; d<dh[mi][i]; d++){ 1667: newm=savm; 1668: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM; 1669: for (kk=1; kk<=cptcovage;kk++) { 1670: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */ 1671: } 1672: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, 1673: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); 1674: savm=oldm; 1675: oldm=newm; 1676: } /* end mult */ 1677: 1678: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */ 1679: /* But now since version 0.9 we anticipate for bias at large stepm. 1680: * If stepm is larger than one month (smallest stepm) and if the exact delay 1681: * (in months) between two waves is not a multiple of stepm, we rounded to 1682: * the nearest (and in case of equal distance, to the lowest) interval but now 1683: * we keep into memory the bias bh[mi][i] and also the previous matrix product 1684: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the 1685: * probability in order to take into account the bias as a fraction of the way 1686: * from savm to out if bh is negative or even beyond if bh is positive. bh varies 1687: * -stepm/2 to stepm/2 . 1688: * For stepm=1 the results are the same as for previous versions of Imach. 1689: * For stepm > 1 the results are less biased than in previous versions. 1690: */ 1691: s1=s[mw[mi][i]][i]; 1692: s2=s[mw[mi+1][i]][i]; 1693: bbh=(double)bh[mi][i]/(double)stepm; 1694: /* bias bh is positive if real duration 1695: * is higher than the multiple of stepm and negative otherwise. 1696: */ 1697: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/ 1698: if( s2 > nlstate){ 1699: /* i.e. if s2 is a death state and if the date of death is known 1700: then the contribution to the likelihood is the probability to 1701: die between last step unit time and current step unit time, 1702: which is also equal to probability to die before dh 1703: minus probability to die before dh-stepm . 1704: In version up to 0.92 likelihood was computed 1705: as if date of death was unknown. Death was treated as any other 1706: health state: the date of the interview describes the actual state 1707: and not the date of a change in health state. The former idea was 1708: to consider that at each interview the state was recorded 1709: (healthy, disable or death) and IMaCh was corrected; but when we 1710: introduced the exact date of death then we should have modified 1711: the contribution of an exact death to the likelihood. This new 1712: contribution is smaller and very dependent of the step unit 1713: stepm. It is no more the probability to die between last interview 1714: and month of death but the probability to survive from last 1715: interview up to one month before death multiplied by the 1716: probability to die within a month. Thanks to Chris 1717: Jackson for correcting this bug. Former versions increased 1718: mortality artificially. The bad side is that we add another loop 1719: which slows down the processing. The difference can be up to 10% 1720: lower mortality. 1721: */ 1722: lli=log(out[s1][s2] - savm[s1][s2]); 1723: 1724: 1725: } else if (s2==-2) { 1726: for (j=1,survp=0. ; j<=nlstate; j++) 1727: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; 1728: /*survp += out[s1][j]; */ 1729: lli= log(survp); 1730: } 1731: 1732: else if (s2==-4) { 1733: for (j=3,survp=0. ; j<=nlstate; j++) 1734: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; 1735: lli= log(survp); 1736: } 1737: 1738: else if (s2==-5) { 1739: for (j=1,survp=0. ; j<=2; j++) 1740: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; 1741: lli= log(survp); 1742: } 1743: 1744: else{ 1745: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */ 1746: /* 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 */ 1747: } 1748: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/ 1749: /*if(lli ==000.0)*/ 1750: /*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); */ 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==2){ 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]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */ 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==3){ /* exponential 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: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, 1802: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); 1803: savm=oldm; 1804: oldm=newm; 1805: } /* end mult */ 1806: 1807: s1=s[mw[mi][i]][i]; 1808: s2=s[mw[mi+1][i]][i]; 1809: bbh=(double)bh[mi][i]/(double)stepm; 1810: 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 */ 1811: ipmx +=1; 1812: sw += weight[i]; 1813: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; 1814: } /* end of wave */ 1815: } /* end of individual */ 1816: }else if (mle==4){ /* ml=4 no inter-extrapolation */ 1817: for (i=1,ipmx=0, sw=0.; i<=imx; i++){ 1818: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i]; 1819: for(mi=1; mi<= wav[i]-1; mi++){ 1820: for (ii=1;ii<=nlstate+ndeath;ii++) 1821: for (j=1;j<=nlstate+ndeath;j++){ 1822: oldm[ii][j]=(ii==j ? 1.0 : 0.0); 1823: savm[ii][j]=(ii==j ? 1.0 : 0.0); 1824: } 1825: for(d=0; d<dh[mi][i]; d++){ 1826: newm=savm; 1827: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM; 1828: for (kk=1; kk<=cptcovage;kk++) { 1829: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; 1830: } 1831: 1832: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, 1833: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); 1834: savm=oldm; 1835: oldm=newm; 1836: } /* end mult */ 1837: 1838: s1=s[mw[mi][i]][i]; 1839: s2=s[mw[mi+1][i]][i]; 1840: if( s2 > nlstate){ 1841: lli=log(out[s1][s2] - savm[s1][s2]); 1842: }else{ 1843: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */ 1844: } 1845: ipmx +=1; 1846: sw += weight[i]; 1847: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; 1848: /* 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]); */ 1849: } /* end of wave */ 1850: } /* end of individual */ 1851: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */ 1852: for (i=1,ipmx=0, sw=0.; i<=imx; i++){ 1853: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i]; 1854: for(mi=1; mi<= wav[i]-1; mi++){ 1855: for (ii=1;ii<=nlstate+ndeath;ii++) 1856: for (j=1;j<=nlstate+ndeath;j++){ 1857: oldm[ii][j]=(ii==j ? 1.0 : 0.0); 1858: savm[ii][j]=(ii==j ? 1.0 : 0.0); 1859: } 1860: for(d=0; d<dh[mi][i]; d++){ 1861: newm=savm; 1862: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM; 1863: for (kk=1; kk<=cptcovage;kk++) { 1864: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; 1865: } 1866: 1867: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, 1868: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); 1869: savm=oldm; 1870: oldm=newm; 1871: } /* end mult */ 1872: 1873: s1=s[mw[mi][i]][i]; 1874: s2=s[mw[mi+1][i]][i]; 1875: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */ 1876: ipmx +=1; 1877: sw += weight[i]; 1878: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; 1879: /*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]);*/ 1880: } /* end of wave */ 1881: } /* end of individual */ 1882: } /* End of if */ 1883: for(k=1,l=0.; k<=nlstate; k++) l += ll[k]; 1884: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */ 1885: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */ 1886: return -l; 1887: } 1888: 1889: /*************** log-likelihood *************/ 1890: double funcone( double *x) 1891: { 1892: /* Same as likeli but slower because of a lot of printf and if */ 1893: int i, ii, j, k, mi, d, kk; 1894: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1]; 1895: double **out; 1896: double lli; /* Individual log likelihood */ 1897: double llt; 1898: int s1, s2; 1899: double bbh, survp; 1900: /*extern weight */ 1901: /* We are differentiating ll according to initial status */ 1902: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/ 1903: /*for(i=1;i<imx;i++) 1904: printf(" %d\n",s[4][i]); 1905: */ 1906: cov[1]=1.; 1907: 1908: for(k=1; k<=nlstate; k++) ll[k]=0.; 1909: 1910: for (i=1,ipmx=0, sw=0.; i<=imx; i++){ 1911: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i]; 1912: for(mi=1; mi<= wav[i]-1; mi++){ 1913: for (ii=1;ii<=nlstate+ndeath;ii++) 1914: for (j=1;j<=nlstate+ndeath;j++){ 1915: oldm[ii][j]=(ii==j ? 1.0 : 0.0); 1916: savm[ii][j]=(ii==j ? 1.0 : 0.0); 1917: } 1918: for(d=0; d<dh[mi][i]; d++){ 1919: newm=savm; 1920: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM; 1921: for (kk=1; kk<=cptcovage;kk++) { 1922: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; 1923: } 1924: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */ 1925: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, 1926: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); 1927: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */ 1928: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */ 1929: savm=oldm; 1930: oldm=newm; 1931: } /* end mult */ 1932: 1933: s1=s[mw[mi][i]][i]; 1934: s2=s[mw[mi+1][i]][i]; 1935: bbh=(double)bh[mi][i]/(double)stepm; 1936: /* bias is positive if real duration 1937: * is higher than the multiple of stepm and negative otherwise. 1938: */ 1939: if( s2 > nlstate && (mle <5) ){ /* Jackson */ 1940: lli=log(out[s1][s2] - savm[s1][s2]); 1941: } else if (s2==-2) { 1942: for (j=1,survp=0. ; j<=nlstate; j++) 1943: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; 1944: lli= log(survp); 1945: }else if (mle==1){ 1946: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */ 1947: } else if(mle==2){ 1948: 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 */ 1949: } else if(mle==3){ /* exponential inter-extrapolation */ 1950: 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 */ 1951: } else if (mle==4){ /* mle=4 no inter-extrapolation */ 1952: lli=log(out[s1][s2]); /* Original formula */ 1953: } else{ /* mle=0 back to 1 */ 1954: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */ 1955: /*lli=log(out[s1][s2]); */ /* Original formula */ 1956: } /* End of if */ 1957: ipmx +=1; 1958: sw += weight[i]; 1959: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; 1960: /*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]); */ 1961: if(globpr){ 1962: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\ 1963: %11.6f %11.6f %11.6f ", \ 1964: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i], 1965: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]); 1966: for(k=1,llt=0.,l=0.; k<=nlstate; k++){ 1967: llt +=ll[k]*gipmx/gsw; 1968: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw); 1969: } 1970: fprintf(ficresilk," %10.6f\n", -llt); 1971: } 1972: } /* end of wave */ 1973: } /* end of individual */ 1974: for(k=1,l=0.; k<=nlstate; k++) l += ll[k]; 1975: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */ 1976: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */ 1977: if(globpr==0){ /* First time we count the contributions and weights */ 1978: gipmx=ipmx; 1979: gsw=sw; 1980: } 1981: return -l; 1982: } 1983: 1984: 1985: /*************** function likelione ***********/ 1986: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double [])) 1987: { 1988: /* This routine should help understanding what is done with 1989: the selection of individuals/waves and 1990: to check the exact contribution to the likelihood. 1991: Plotting could be done. 1992: */ 1993: int k; 1994: 1995: if(*globpri !=0){ /* Just counts and sums, no printings */ 1996: strcpy(fileresilk,"ilk"); 1997: strcat(fileresilk,fileres); 1998: if((ficresilk=fopen(fileresilk,"w"))==NULL) { 1999: printf("Problem with resultfile: %s\n", fileresilk); 2000: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk); 2001: } 2002: 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"); 2003: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav "); 2004: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */ 2005: for(k=1; k<=nlstate; k++) 2006: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k); 2007: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n"); 2008: } 2009: 2010: *fretone=(*funcone)(p); 2011: if(*globpri !=0){ 2012: fclose(ficresilk); 2013: fprintf(fichtm,"\n File of contributions to the likelihood: <a href=\"%s\">%s</a> \n",subdirf(fileresilk),subdirf(fileresilk)); 2014: fflush(fichtm); 2015: } 2016: return; 2017: } 2018: 2019: 2020: /*********** Maximum Likelihood Estimation ***************/ 2021: 2022: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double [])) 2023: { 2024: int i,j, iter; 2025: double **xi; 2026: double fret; 2027: double fretone; /* Only one call to likelihood */ 2028: /* char filerespow[FILENAMELENGTH];*/ 2029: xi=matrix(1,npar,1,npar); 2030: for (i=1;i<=npar;i++) 2031: for (j=1;j<=npar;j++) 2032: xi[i][j]=(i==j ? 1.0 : 0.0); 2033: printf("Powell\n"); fprintf(ficlog,"Powell\n"); 2034: strcpy(filerespow,"pow"); 2035: strcat(filerespow,fileres); 2036: if((ficrespow=fopen(filerespow,"w"))==NULL) { 2037: printf("Problem with resultfile: %s\n", filerespow); 2038: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow); 2039: } 2040: fprintf(ficrespow,"# Powell\n# iter -2*LL"); 2041: for (i=1;i<=nlstate;i++) 2042: for(j=1;j<=nlstate+ndeath;j++) 2043: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j); 2044: fprintf(ficrespow,"\n"); 2045: 2046: powell(p,xi,npar,ftol,&iter,&fret,func); 2047: 2048: free_matrix(xi,1,npar,1,npar); 2049: fclose(ficrespow); 2050: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p)); 2051: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p)); 2052: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p)); 2053: 2054: } 2055: 2056: /**** Computes Hessian and covariance matrix ***/ 2057: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double [])) 2058: { 2059: double **a,**y,*x,pd; 2060: double **hess; 2061: int i, j,jk; 2062: int *indx; 2063: 2064: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar); 2065: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar); 2066: void lubksb(double **a, int npar, int *indx, double b[]) ; 2067: void ludcmp(double **a, int npar, int *indx, double *d) ; 2068: double gompertz(double p[]); 2069: hess=matrix(1,npar,1,npar); 2070: 2071: printf("\nCalculation of the hessian matrix. Wait...\n"); 2072: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n"); 2073: for (i=1;i<=npar;i++){ 2074: printf("%d",i);fflush(stdout); 2075: fprintf(ficlog,"%d",i);fflush(ficlog); 2076: 2077: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar); 2078: 2079: /* printf(" %f ",p[i]); 2080: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/ 2081: } 2082: 2083: for (i=1;i<=npar;i++) { 2084: for (j=1;j<=npar;j++) { 2085: if (j>i) { 2086: printf(".%d%d",i,j);fflush(stdout); 2087: fprintf(ficlog,".%d%d",i,j);fflush(ficlog); 2088: hess[i][j]=hessij(p,delti,i,j,func,npar); 2089: 2090: hess[j][i]=hess[i][j]; 2091: /*printf(" %lf ",hess[i][j]);*/ 2092: } 2093: } 2094: } 2095: printf("\n"); 2096: fprintf(ficlog,"\n"); 2097: 2098: printf("\nInverting the hessian to get the covariance matrix. Wait...\n"); 2099: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n"); 2100: 2101: a=matrix(1,npar,1,npar); 2102: y=matrix(1,npar,1,npar); 2103: x=vector(1,npar); 2104: indx=ivector(1,npar); 2105: for (i=1;i<=npar;i++) 2106: for (j=1;j<=npar;j++) a[i][j]=hess[i][j]; 2107: ludcmp(a,npar,indx,&pd); 2108: 2109: for (j=1;j<=npar;j++) { 2110: for (i=1;i<=npar;i++) x[i]=0; 2111: x[j]=1; 2112: lubksb(a,npar,indx,x); 2113: for (i=1;i<=npar;i++){ 2114: matcov[i][j]=x[i]; 2115: } 2116: } 2117: 2118: printf("\n#Hessian matrix#\n"); 2119: fprintf(ficlog,"\n#Hessian matrix#\n"); 2120: for (i=1;i<=npar;i++) { 2121: for (j=1;j<=npar;j++) { 2122: printf("%.3e ",hess[i][j]); 2123: fprintf(ficlog,"%.3e ",hess[i][j]); 2124: } 2125: printf("\n"); 2126: fprintf(ficlog,"\n"); 2127: } 2128: 2129: /* Recompute Inverse */ 2130: for (i=1;i<=npar;i++) 2131: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; 2132: ludcmp(a,npar,indx,&pd); 2133: 2134: /* printf("\n#Hessian matrix recomputed#\n"); 2135: 2136: for (j=1;j<=npar;j++) { 2137: for (i=1;i<=npar;i++) x[i]=0; 2138: x[j]=1; 2139: lubksb(a,npar,indx,x); 2140: for (i=1;i<=npar;i++){ 2141: y[i][j]=x[i]; 2142: printf("%.3e ",y[i][j]); 2143: fprintf(ficlog,"%.3e ",y[i][j]); 2144: } 2145: printf("\n"); 2146: fprintf(ficlog,"\n"); 2147: } 2148: */ 2149: 2150: free_matrix(a,1,npar,1,npar); 2151: free_matrix(y,1,npar,1,npar); 2152: free_vector(x,1,npar); 2153: free_ivector(indx,1,npar); 2154: free_matrix(hess,1,npar,1,npar); 2155: 2156: 2157: } 2158: 2159: /*************** hessian matrix ****************/ 2160: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar) 2161: { 2162: int i; 2163: int l=1, lmax=20; 2164: double k1,k2; 2165: double p2[MAXPARM+1]; /* identical to x */ 2166: double res; 2167: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; 2168: double fx; 2169: int k=0,kmax=10; 2170: double l1; 2171: 2172: fx=func(x); 2173: for (i=1;i<=npar;i++) p2[i]=x[i]; 2174: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */ 2175: l1=pow(10,l); 2176: delts=delt; 2177: for(k=1 ; k <kmax; k=k+1){ 2178: delt = delta*(l1*k); 2179: p2[theta]=x[theta] +delt; 2180: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */ 2181: p2[theta]=x[theta]-delt; 2182: k2=func(p2)-fx; 2183: /*res= (k1-2.0*fx+k2)/delt/delt; */ 2184: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */ 2185: 2186: #ifdef DEBUGHESS 2187: 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); 2188: 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); 2189: #endif 2190: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */ 2191: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){ 2192: k=kmax; 2193: } 2194: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */ 2195: k=kmax; l=lmax*10.; 2196: } 2197: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 2198: delts=delt; 2199: } 2200: } 2201: } 2202: delti[theta]=delts; 2203: return res; 2204: 2205: } 2206: 2207: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) 2208: { 2209: int i; 2210: int l=1, l1, lmax=20; 2211: double k1,k2,k3,k4,res,fx; 2212: double p2[MAXPARM+1]; 2213: int k; 2214: 2215: fx=func(x); 2216: for (k=1; k<=2; k++) { 2217: for (i=1;i<=npar;i++) p2[i]=x[i]; 2218: p2[thetai]=x[thetai]+delti[thetai]/k; 2219: p2[thetaj]=x[thetaj]+delti[thetaj]/k; 2220: k1=func(p2)-fx; 2221: 2222: p2[thetai]=x[thetai]+delti[thetai]/k; 2223: p2[thetaj]=x[thetaj]-delti[thetaj]/k; 2224: k2=func(p2)-fx; 2225: 2226: p2[thetai]=x[thetai]-delti[thetai]/k; 2227: p2[thetaj]=x[thetaj]+delti[thetaj]/k; 2228: k3=func(p2)-fx; 2229: 2230: p2[thetai]=x[thetai]-delti[thetai]/k; 2231: p2[thetaj]=x[thetaj]-delti[thetaj]/k; 2232: k4=func(p2)-fx; 2233: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */ 2234: #ifdef DEBUG 2235: 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); 2236: 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); 2237: #endif 2238: } 2239: return res; 2240: } 2241: 2242: /************** Inverse of matrix **************/ 2243: void ludcmp(double **a, int n, int *indx, double *d) 2244: { 2245: int i,imax,j,k; 2246: double big,dum,sum,temp; 2247: double *vv; 2248: 2249: vv=vector(1,n); 2250: *d=1.0; 2251: for (i=1;i<=n;i++) { 2252: big=0.0; 2253: for (j=1;j<=n;j++) 2254: if ((temp=fabs(a[i][j])) > big) big=temp; 2255: if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 2256: vv[i]=1.0/big; 2257: } 2258: for (j=1;j<=n;j++) { 2259: for (i=1;i<j;i++) { 2260: sum=a[i][j]; 2261: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 2262: a[i][j]=sum; 2263: } 2264: big=0.0; 2265: for (i=j;i<=n;i++) { 2266: sum=a[i][j]; 2267: for (k=1;k<j;k++) 2268: sum -= a[i][k]*a[k][j]; 2269: a[i][j]=sum; 2270: if ( (dum=vv[i]*fabs(sum)) >= big) { 2271: big=dum; 2272: imax=i; 2273: } 2274: } 2275: if (j != imax) { 2276: for (k=1;k<=n;k++) { 2277: dum=a[imax][k]; 2278: a[imax][k]=a[j][k]; 2279: a[j][k]=dum; 2280: } 2281: *d = -(*d); 2282: vv[imax]=vv[j]; 2283: } 2284: indx[j]=imax; 2285: if (a[j][j] == 0.0) a[j][j]=TINY; 2286: if (j != n) { 2287: dum=1.0/(a[j][j]); 2288: for (i=j+1;i<=n;i++) a[i][j] *= dum; 2289: } 2290: } 2291: free_vector(vv,1,n); /* Doesn't work */ 2292: ; 2293: } 2294: 2295: void lubksb(double **a, int n, int *indx, double b[]) 2296: { 2297: int i,ii=0,ip,j; 2298: double sum; 2299: 2300: for (i=1;i<=n;i++) { 2301: ip=indx[i]; 2302: sum=b[ip]; 2303: b[ip]=b[i]; 2304: if (ii) 2305: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 2306: else if (sum) ii=i; 2307: b[i]=sum; 2308: } 2309: for (i=n;i>=1;i--) { 2310: sum=b[i]; 2311: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 2312: b[i]=sum/a[i][i]; 2313: } 2314: } 2315: 2316: void pstamp(FILE *fichier) 2317: { 2318: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart); 2319: } 2320: 2321: /************ Frequencies ********************/ 2322: 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[]) 2323: { /* Some frequencies */ 2324: 2325: int i, m, jk, k1,i1, j1, bool, z1,j; 2326: int first; 2327: double ***freq; /* Frequencies */ 2328: double *pp, **prop; 2329: double pos,posprop, k2, dateintsum=0,k2cpt=0; 2330: char fileresp[FILENAMELENGTH]; 2331: 2332: pp=vector(1,nlstate); 2333: prop=matrix(1,nlstate,iagemin,iagemax+3); 2334: strcpy(fileresp,"p"); 2335: strcat(fileresp,fileres); 2336: if((ficresp=fopen(fileresp,"w"))==NULL) { 2337: printf("Problem with prevalence resultfile: %s\n", fileresp); 2338: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp); 2339: exit(0); 2340: } 2341: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3); 2342: j1=0; 2343: 2344: j=cptcoveff; 2345: if (cptcovn<1) {j=1;ncodemax[1]=1;} 2346: 2347: first=1; 2348: 2349: /* for(k1=1; k1<=j ; k1++){ /* Loop on covariates */ 2350: /* for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */ 2351: /* j1++; 2352: */ 2353: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){ 2354: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]); 2355: scanf("%d", i);*/ 2356: for (i=-5; i<=nlstate+ndeath; i++) 2357: for (jk=-5; jk<=nlstate+ndeath; jk++) 2358: for(m=iagemin; m <= iagemax+3; m++) 2359: freq[i][jk][m]=0; 2360: 2361: for (i=1; i<=nlstate; i++) 2362: for(m=iagemin; m <= iagemax+3; m++) 2363: prop[i][m]=0; 2364: 2365: dateintsum=0; 2366: k2cpt=0; 2367: for (i=1; i<=imx; i++) { 2368: bool=1; 2369: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */ 2370: for (z1=1; z1<=cptcoveff; z1++) 2371: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){ 2372: /* Tests if the value of each of the covariates of i is equal to filter j1 */ 2373: bool=0; 2374: /* 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", 2375: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1], 2376: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/ 2377: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/ 2378: } 2379: } 2380: 2381: if (bool==1){ 2382: for(m=firstpass; m<=lastpass; m++){ 2383: k2=anint[m][i]+(mint[m][i]/12.); 2384: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/ 2385: if(agev[m][i]==0) agev[m][i]=iagemax+1; 2386: if(agev[m][i]==1) agev[m][i]=iagemax+2; 2387: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i]; 2388: if (m<lastpass) { 2389: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i]; 2390: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i]; 2391: } 2392: 2393: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) { 2394: dateintsum=dateintsum+k2; 2395: k2cpt++; 2396: } 2397: /*}*/ 2398: } 2399: } 2400: } /* end i */ 2401: 2402: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/ 2403: pstamp(ficresp); 2404: if (cptcovn>0) { 2405: fprintf(ficresp, "\n#********** Variable "); 2406: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); 2407: fprintf(ficresp, "**********\n#"); 2408: fprintf(ficlog, "\n#********** Variable "); 2409: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); 2410: fprintf(ficlog, "**********\n#"); 2411: } 2412: for(i=1; i<=nlstate;i++) 2413: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i); 2414: fprintf(ficresp, "\n"); 2415: 2416: for(i=iagemin; i <= iagemax+3; i++){ 2417: if(i==iagemax+3){ 2418: fprintf(ficlog,"Total"); 2419: }else{ 2420: if(first==1){ 2421: first=0; 2422: printf("See log file for details...\n"); 2423: } 2424: fprintf(ficlog,"Age %d", i); 2425: } 2426: for(jk=1; jk <=nlstate ; jk++){ 2427: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++) 2428: pp[jk] += freq[jk][m][i]; 2429: } 2430: for(jk=1; jk <=nlstate ; jk++){ 2431: for(m=-1, pos=0; m <=0 ; m++) 2432: pos += freq[jk][m][i]; 2433: if(pp[jk]>=1.e-10){ 2434: if(first==1){ 2435: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]); 2436: } 2437: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]); 2438: }else{ 2439: if(first==1) 2440: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk); 2441: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk); 2442: } 2443: } 2444: 2445: for(jk=1; jk <=nlstate ; jk++){ 2446: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++) 2447: pp[jk] += freq[jk][m][i]; 2448: } 2449: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){ 2450: pos += pp[jk]; 2451: posprop += prop[jk][i]; 2452: } 2453: for(jk=1; jk <=nlstate ; jk++){ 2454: if(pos>=1.e-5){ 2455: if(first==1) 2456: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos); 2457: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos); 2458: }else{ 2459: if(first==1) 2460: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk); 2461: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk); 2462: } 2463: if( i <= iagemax){ 2464: if(pos>=1.e-5){ 2465: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop); 2466: /*probs[i][jk][j1]= pp[jk]/pos;*/ 2467: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/ 2468: } 2469: else 2470: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop); 2471: } 2472: } 2473: 2474: for(jk=-1; jk <=nlstate+ndeath; jk++) 2475: for(m=-1; m <=nlstate+ndeath; m++) 2476: if(freq[jk][m][i] !=0 ) { 2477: if(first==1) 2478: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]); 2479: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]); 2480: } 2481: if(i <= iagemax) 2482: fprintf(ficresp,"\n"); 2483: if(first==1) 2484: printf("Others in log...\n"); 2485: fprintf(ficlog,"\n"); 2486: } 2487: /*}*/ 2488: } 2489: dateintmean=dateintsum/k2cpt; 2490: 2491: fclose(ficresp); 2492: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3); 2493: free_vector(pp,1,nlstate); 2494: free_matrix(prop,1,nlstate,iagemin, iagemax+3); 2495: /* End of Freq */ 2496: } 2497: 2498: /************ Prevalence ********************/ 2499: 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) 2500: { 2501: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people 2502: in each health status at the date of interview (if between dateprev1 and dateprev2). 2503: We still use firstpass and lastpass as another selection. 2504: */ 2505: 2506: int i, m, jk, k1, i1, j1, bool, z1,j; 2507: double ***freq; /* Frequencies */ 2508: double *pp, **prop; 2509: double pos,posprop; 2510: double y2; /* in fractional years */ 2511: int iagemin, iagemax; 2512: int first; /** to stop verbosity which is redirected to log file */ 2513: 2514: iagemin= (int) agemin; 2515: iagemax= (int) agemax; 2516: /*pp=vector(1,nlstate);*/ 2517: prop=matrix(1,nlstate,iagemin,iagemax+3); 2518: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/ 2519: j1=0; 2520: 2521: /*j=cptcoveff;*/ 2522: if (cptcovn<1) {j=1;ncodemax[1]=1;} 2523: 2524: first=1; 2525: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ 2526: /*for(i1=1; i1<=ncodemax[k1];i1++){ 2527: j1++;*/ 2528: 2529: for (i=1; i<=nlstate; i++) 2530: for(m=iagemin; m <= iagemax+3; m++) 2531: prop[i][m]=0.0; 2532: 2533: for (i=1; i<=imx; i++) { /* Each individual */ 2534: bool=1; 2535: if (cptcovn>0) { 2536: for (z1=1; z1<=cptcoveff; z1++) 2537: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 2538: bool=0; 2539: } 2540: if (bool==1) { 2541: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/ 2542: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */ 2543: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */ 2544: if(agev[m][i]==0) agev[m][i]=iagemax+1; 2545: if(agev[m][i]==1) agev[m][i]=iagemax+2; 2546: 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); 2547: if (s[m][i]>0 && s[m][i]<=nlstate) { 2548: /*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]]);*/ 2549: prop[s[m][i]][(int)agev[m][i]] += weight[i]; 2550: prop[s[m][i]][iagemax+3] += weight[i]; 2551: } 2552: } 2553: } /* end selection of waves */ 2554: } 2555: } 2556: for(i=iagemin; i <= iagemax+3; i++){ 2557: for(jk=1,posprop=0; jk <=nlstate ; jk++) { 2558: posprop += prop[jk][i]; 2559: } 2560: 2561: for(jk=1; jk <=nlstate ; jk++){ 2562: if( i <= iagemax){ 2563: if(posprop>=1.e-5){ 2564: probs[i][jk][j1]= prop[jk][i]/posprop; 2565: } else{ 2566: if(first==1){ 2567: first=0; 2568: 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]); 2569: } 2570: } 2571: } 2572: }/* end jk */ 2573: }/* end i */ 2574: /*} *//* end i1 */ 2575: } /* end j1 */ 2576: 2577: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/ 2578: /*free_vector(pp,1,nlstate);*/ 2579: free_matrix(prop,1,nlstate, iagemin,iagemax+3); 2580: } /* End of prevalence */ 2581: 2582: /************* Waves Concatenation ***************/ 2583: 2584: 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) 2585: { 2586: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i. 2587: Death is a valid wave (if date is known). 2588: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i 2589: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i] 2590: and mw[mi+1][i]. dh depends on stepm. 2591: */ 2592: 2593: int i, mi, m; 2594: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1; 2595: double sum=0., jmean=0.;*/ 2596: int first; 2597: int j, k=0,jk, ju, jl; 2598: double sum=0.; 2599: first=0; 2600: jmin=1e+5; 2601: jmax=-1; 2602: jmean=0.; 2603: for(i=1; i<=imx; i++){ 2604: mi=0; 2605: m=firstpass; 2606: while(s[m][i] <= nlstate){ 2607: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5) 2608: mw[++mi][i]=m; 2609: if(m >=lastpass) 2610: break; 2611: else 2612: m++; 2613: }/* end while */ 2614: if (s[m][i] > nlstate){ 2615: mi++; /* Death is another wave */ 2616: /* if(mi==0) never been interviewed correctly before death */ 2617: /* Only death is a correct wave */ 2618: mw[mi][i]=m; 2619: } 2620: 2621: wav[i]=mi; 2622: if(mi==0){ 2623: nbwarn++; 2624: if(first==0){ 2625: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i); 2626: first=1; 2627: } 2628: if(first==1){ 2629: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i); 2630: } 2631: } /* end mi==0 */ 2632: } /* End individuals */ 2633: 2634: for(i=1; i<=imx; i++){ 2635: for(mi=1; mi<wav[i];mi++){ 2636: if (stepm <=0) 2637: dh[mi][i]=1; 2638: else{ 2639: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */ 2640: if (agedc[i] < 2*AGESUP) { 2641: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 2642: if(j==0) j=1; /* Survives at least one month after exam */ 2643: else if(j<0){ 2644: nberr++; 2645: 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]); 2646: j=1; /* Temporary Dangerous patch */ 2647: 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); 2648: 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]); 2649: 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); 2650: } 2651: k=k+1; 2652: if (j >= jmax){ 2653: jmax=j; 2654: ijmax=i; 2655: } 2656: if (j <= jmin){ 2657: jmin=j; 2658: ijmin=i; 2659: } 2660: sum=sum+j; 2661: /*if (j<0) printf("j=%d num=%d \n",j,i);*/ 2662: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/ 2663: } 2664: } 2665: else{ 2666: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12)); 2667: /* 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]); */ 2668: 2669: k=k+1; 2670: if (j >= jmax) { 2671: jmax=j; 2672: ijmax=i; 2673: } 2674: else if (j <= jmin){ 2675: jmin=j; 2676: ijmin=i; 2677: } 2678: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */ 2679: /*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]);*/ 2680: if(j<0){ 2681: nberr++; 2682: 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]); 2683: 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]); 2684: } 2685: sum=sum+j; 2686: } 2687: jk= j/stepm; 2688: jl= j -jk*stepm; 2689: ju= j -(jk+1)*stepm; 2690: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */ 2691: if(jl==0){ 2692: dh[mi][i]=jk; 2693: bh[mi][i]=0; 2694: }else{ /* We want a negative bias in order to only have interpolation ie 2695: * to avoid the price of an extra matrix product in likelihood */ 2696: dh[mi][i]=jk+1; 2697: bh[mi][i]=ju; 2698: } 2699: }else{ 2700: if(jl <= -ju){ 2701: dh[mi][i]=jk; 2702: bh[mi][i]=jl; /* bias is positive if real duration 2703: * is higher than the multiple of stepm and negative otherwise. 2704: */ 2705: } 2706: else{ 2707: dh[mi][i]=jk+1; 2708: bh[mi][i]=ju; 2709: } 2710: if(dh[mi][i]==0){ 2711: dh[mi][i]=1; /* At least one step */ 2712: bh[mi][i]=ju; /* At least one step */ 2713: /* 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);*/ 2714: } 2715: } /* end if mle */ 2716: } 2717: } /* end wave */ 2718: } 2719: jmean=sum/k; 2720: 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); 2721: 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); 2722: } 2723: 2724: /*********** Tricode ****************************/ 2725: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum) 2726: { 2727: /**< Uses cptcovn+2*cptcovprod as the number of covariates */ 2728: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 2729: /* Boring subroutine which should only output nbcode[Tvar[j]][k] 2730: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2) 2731: /* nbcode[Tvar[j]][1]= 2732: */ 2733: 2734: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX; 2735: int modmaxcovj=0; /* Modality max of covariates j */ 2736: int cptcode=0; /* Modality max of covariates j */ 2737: int modmincovj=0; /* Modality min of covariates j */ 2738: 2739: 2740: cptcoveff=0; 2741: 2742: for (k=-1; k < maxncov; k++) Ndum[k]=0; 2743: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */ 2744: 2745: /* Loop on covariates without age and products */ 2746: for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */ 2747: for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 2748: modality of this covariate Vj*/ 2749: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i 2750: * If product of Vn*Vm, still boolean *: 2751: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables 2752: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */ 2753: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the 2754: modality of the nth covariate of individual i. */ 2755: if (ij > modmaxcovj) 2756: modmaxcovj=ij; 2757: else if (ij < modmincovj) 2758: modmincovj=ij; 2759: if ((ij < -1) && (ij > NCOVMAX)){ 2760: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX ); 2761: exit(1); 2762: }else 2763: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/ 2764: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */ 2765: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/ 2766: /* getting the maximum value of the modality of the covariate 2767: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and 2768: female is 1, then modmaxcovj=1.*/ 2769: } 2770: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj); 2771: cptcode=modmaxcovj; 2772: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */ 2773: /*for (i=0; i<=cptcode; i++) {*/ 2774: for (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */ 2775: printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]); 2776: if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */ 2777: ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */ 2778: } 2779: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for 2780: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */ 2781: } /* Ndum[-1] number of undefined modalities */ 2782: 2783: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */ 2784: /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */ 2785: /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125; 2786: modmincovj=3; modmaxcovj = 7; 2787: There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3; 2788: which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 2789: variables V1_1 and V1_2. 2790: nbcode[Tvar[j]][ij]=k; 2791: nbcode[Tvar[j]][1]=0; 2792: nbcode[Tvar[j]][2]=1; 2793: nbcode[Tvar[j]][3]=2; 2794: */ 2795: ij=1; /* ij is similar to i but can jumps over null modalities */ 2796: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */ 2797: for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */ 2798: /*recode from 0 */ 2799: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */ 2800: nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode. 2801: k is a modality. If we have model=V1+V1*sex 2802: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */ 2803: ij++; 2804: } 2805: if (ij > ncodemax[j]) break; 2806: } /* end of loop on */ 2807: } /* end of loop on modality */ 2808: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/ 2809: 2810: for (k=-1; k< maxncov; k++) Ndum[k]=0; 2811: 2812: for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 2813: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 2814: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 2815: Ndum[ij]++; 2816: } 2817: 2818: ij=1; 2819: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */ 2820: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/ 2821: if((Ndum[i]!=0) && (i<=ncovcol)){ 2822: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/ 2823: Tvaraff[ij]=i; /*For printing (unclear) */ 2824: ij++; 2825: }else 2826: Tvaraff[ij]=0; 2827: } 2828: ij--; 2829: cptcoveff=ij; /*Number of total covariates*/ 2830: 2831: } 2832: 2833: 2834: /*********** Health Expectancies ****************/ 2835: 2836: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] ) 2837: 2838: { 2839: /* Health expectancies, no variances */ 2840: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2; 2841: int nhstepma, nstepma; /* Decreasing with age */ 2842: double age, agelim, hf; 2843: double ***p3mat; 2844: double eip; 2845: 2846: pstamp(ficreseij); 2847: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n"); 2848: fprintf(ficreseij,"# Age"); 2849: for(i=1; i<=nlstate;i++){ 2850: for(j=1; j<=nlstate;j++){ 2851: fprintf(ficreseij," e%1d%1d ",i,j); 2852: } 2853: fprintf(ficreseij," e%1d. ",i); 2854: } 2855: fprintf(ficreseij,"\n"); 2856: 2857: 2858: if(estepm < stepm){ 2859: printf ("Problem %d lower than %d\n",estepm, stepm); 2860: } 2861: else hstepm=estepm; 2862: /* We compute the life expectancy from trapezoids spaced every estepm months 2863: * This is mainly to measure the difference between two models: for example 2864: * if stepm=24 months pijx are given only every 2 years and by summing them 2865: * we are calculating an estimate of the Life Expectancy assuming a linear 2866: * progression in between and thus overestimating or underestimating according 2867: * to the curvature of the survival function. If, for the same date, we 2868: * estimate the model with stepm=1 month, we can keep estepm to 24 months 2869: * to compare the new estimate of Life expectancy with the same linear 2870: * hypothesis. A more precise result, taking into account a more precise 2871: * curvature will be obtained if estepm is as small as stepm. */ 2872: 2873: /* For example we decided to compute the life expectancy with the smallest unit */ 2874: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 2875: nhstepm is the number of hstepm from age to agelim 2876: nstepm is the number of stepm from age to agelin. 2877: Look at hpijx to understand the reason of that which relies in memory size 2878: and note for a fixed period like estepm months */ 2879: /* We decided (b) to get a life expectancy respecting the most precise curvature of the 2880: survival function given by stepm (the optimization length). Unfortunately it 2881: means that if the survival funtion is printed only each two years of age and if 2882: you sum them up and add 1 year (area under the trapezoids) you won't get the same 2883: results. So we changed our mind and took the option of the best precision. 2884: */ 2885: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 2886: 2887: agelim=AGESUP; 2888: /* If stepm=6 months */ 2889: /* Computed by stepm unit matrices, product of hstepm matrices, stored 2890: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */ 2891: 2892: /* nhstepm age range expressed in number of stepm */ 2893: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */ 2894: /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 2895: /* if (stepm >= YEARM) hstepm=1;*/ 2896: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */ 2897: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 2898: 2899: for (age=bage; age<=fage; age ++){ 2900: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */ 2901: /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 2902: /* if (stepm >= YEARM) hstepm=1;*/ 2903: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */ 2904: 2905: /* If stepm=6 months */ 2906: /* Computed by stepm unit matrices, product of hstepma matrices, stored 2907: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */ 2908: 2909: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij); 2910: 2911: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */ 2912: 2913: printf("%d|",(int)age);fflush(stdout); 2914: fprintf(ficlog,"%d|",(int)age);fflush(ficlog); 2915: 2916: /* Computing expectancies */ 2917: for(i=1; i<=nlstate;i++) 2918: for(j=1; j<=nlstate;j++) 2919: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){ 2920: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf; 2921: 2922: /* 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]);*/ 2923: 2924: } 2925: 2926: fprintf(ficreseij,"%3.0f",age ); 2927: for(i=1; i<=nlstate;i++){ 2928: eip=0; 2929: for(j=1; j<=nlstate;j++){ 2930: eip +=eij[i][j][(int)age]; 2931: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] ); 2932: } 2933: fprintf(ficreseij,"%9.4f", eip ); 2934: } 2935: fprintf(ficreseij,"\n"); 2936: 2937: } 2938: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 2939: printf("\n"); 2940: fprintf(ficlog,"\n"); 2941: 2942: } 2943: 2944: 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[] ) 2945: 2946: { 2947: /* Covariances of health expectancies eij and of total life expectancies according 2948: to initial status i, ei. . 2949: */ 2950: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji; 2951: int nhstepma, nstepma; /* Decreasing with age */ 2952: double age, agelim, hf; 2953: double ***p3matp, ***p3matm, ***varhe; 2954: double **dnewm,**doldm; 2955: double *xp, *xm; 2956: double **gp, **gm; 2957: double ***gradg, ***trgradg; 2958: int theta; 2959: 2960: double eip, vip; 2961: 2962: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage); 2963: xp=vector(1,npar); 2964: xm=vector(1,npar); 2965: dnewm=matrix(1,nlstate*nlstate,1,npar); 2966: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate); 2967: 2968: pstamp(ficresstdeij); 2969: fprintf(ficresstdeij,"# Health expectancies with standard errors\n"); 2970: fprintf(ficresstdeij,"# Age"); 2971: for(i=1; i<=nlstate;i++){ 2972: for(j=1; j<=nlstate;j++) 2973: fprintf(ficresstdeij," e%1d%1d (SE)",i,j); 2974: fprintf(ficresstdeij," e%1d. ",i); 2975: } 2976: fprintf(ficresstdeij,"\n"); 2977: 2978: pstamp(ficrescveij); 2979: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n"); 2980: fprintf(ficrescveij,"# Age"); 2981: for(i=1; i<=nlstate;i++) 2982: for(j=1; j<=nlstate;j++){ 2983: cptj= (j-1)*nlstate+i; 2984: for(i2=1; i2<=nlstate;i2++) 2985: for(j2=1; j2<=nlstate;j2++){ 2986: cptj2= (j2-1)*nlstate+i2; 2987: if(cptj2 <= cptj) 2988: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2); 2989: } 2990: } 2991: fprintf(ficrescveij,"\n"); 2992: 2993: if(estepm < stepm){ 2994: printf ("Problem %d lower than %d\n",estepm, stepm); 2995: } 2996: else hstepm=estepm; 2997: /* We compute the life expectancy from trapezoids spaced every estepm months 2998: * This is mainly to measure the difference between two models: for example 2999: * if stepm=24 months pijx are given only every 2 years and by summing them 3000: * we are calculating an estimate of the Life Expectancy assuming a linear 3001: * progression in between and thus overestimating or underestimating according 3002: * to the curvature of the survival function. If, for the same date, we 3003: * estimate the model with stepm=1 month, we can keep estepm to 24 months 3004: * to compare the new estimate of Life expectancy with the same linear 3005: * hypothesis. A more precise result, taking into account a more precise 3006: * curvature will be obtained if estepm is as small as stepm. */ 3007: 3008: /* For example we decided to compute the life expectancy with the smallest unit */ 3009: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 3010: nhstepm is the number of hstepm from age to agelim 3011: nstepm is the number of stepm from age to agelin. 3012: Look at hpijx to understand the reason of that which relies in memory size 3013: and note for a fixed period like estepm months */ 3014: /* We decided (b) to get a life expectancy respecting the most precise curvature of the 3015: survival function given by stepm (the optimization length). Unfortunately it 3016: means that if the survival funtion is printed only each two years of age and if 3017: you sum them up and add 1 year (area under the trapezoids) you won't get the same 3018: results. So we changed our mind and took the option of the best precision. 3019: */ 3020: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 3021: 3022: /* If stepm=6 months */ 3023: /* nhstepm age range expressed in number of stepm */ 3024: agelim=AGESUP; 3025: nstepm=(int) rint((agelim-bage)*YEARM/stepm); 3026: /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 3027: /* if (stepm >= YEARM) hstepm=1;*/ 3028: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */ 3029: 3030: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 3031: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 3032: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate); 3033: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar); 3034: gp=matrix(0,nhstepm,1,nlstate*nlstate); 3035: gm=matrix(0,nhstepm,1,nlstate*nlstate); 3036: 3037: for (age=bage; age<=fage; age ++){ 3038: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */ 3039: /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 3040: /* if (stepm >= YEARM) hstepm=1;*/ 3041: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */ 3042: 3043: /* If stepm=6 months */ 3044: /* Computed by stepm unit matrices, product of hstepma matrices, stored 3045: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */ 3046: 3047: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */ 3048: 3049: /* Computing Variances of health expectancies */ 3050: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to 3051: decrease memory allocation */ 3052: for(theta=1; theta <=npar; theta++){ 3053: for(i=1; i<=npar; i++){ 3054: xp[i] = x[i] + (i==theta ?delti[theta]:0); 3055: xm[i] = x[i] - (i==theta ?delti[theta]:0); 3056: } 3057: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij); 3058: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij); 3059: 3060: for(j=1; j<= nlstate; j++){ 3061: for(i=1; i<=nlstate; i++){ 3062: for(h=0; h<=nhstepm-1; h++){ 3063: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.; 3064: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.; 3065: } 3066: } 3067: } 3068: 3069: for(ij=1; ij<= nlstate*nlstate; ij++) 3070: for(h=0; h<=nhstepm-1; h++){ 3071: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta]; 3072: } 3073: }/* End theta */ 3074: 3075: 3076: for(h=0; h<=nhstepm-1; h++) 3077: for(j=1; j<=nlstate*nlstate;j++) 3078: for(theta=1; theta <=npar; theta++) 3079: trgradg[h][j][theta]=gradg[h][theta][j]; 3080: 3081: 3082: for(ij=1;ij<=nlstate*nlstate;ij++) 3083: for(ji=1;ji<=nlstate*nlstate;ji++) 3084: varhe[ij][ji][(int)age] =0.; 3085: 3086: printf("%d|",(int)age);fflush(stdout); 3087: fprintf(ficlog,"%d|",(int)age);fflush(ficlog); 3088: for(h=0;h<=nhstepm-1;h++){ 3089: for(k=0;k<=nhstepm-1;k++){ 3090: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov); 3091: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]); 3092: for(ij=1;ij<=nlstate*nlstate;ij++) 3093: for(ji=1;ji<=nlstate*nlstate;ji++) 3094: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf; 3095: } 3096: } 3097: 3098: /* Computing expectancies */ 3099: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij); 3100: for(i=1; i<=nlstate;i++) 3101: for(j=1; j<=nlstate;j++) 3102: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){ 3103: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf; 3104: 3105: /* 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]);*/ 3106: 3107: } 3108: 3109: fprintf(ficresstdeij,"%3.0f",age ); 3110: for(i=1; i<=nlstate;i++){ 3111: eip=0.; 3112: vip=0.; 3113: for(j=1; j<=nlstate;j++){ 3114: eip += eij[i][j][(int)age]; 3115: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */ 3116: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age]; 3117: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) ); 3118: } 3119: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip)); 3120: } 3121: fprintf(ficresstdeij,"\n"); 3122: 3123: fprintf(ficrescveij,"%3.0f",age ); 3124: for(i=1; i<=nlstate;i++) 3125: for(j=1; j<=nlstate;j++){ 3126: cptj= (j-1)*nlstate+i; 3127: for(i2=1; i2<=nlstate;i2++) 3128: for(j2=1; j2<=nlstate;j2++){ 3129: cptj2= (j2-1)*nlstate+i2; 3130: if(cptj2 <= cptj) 3131: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]); 3132: } 3133: } 3134: fprintf(ficrescveij,"\n"); 3135: 3136: } 3137: free_matrix(gm,0,nhstepm,1,nlstate*nlstate); 3138: free_matrix(gp,0,nhstepm,1,nlstate*nlstate); 3139: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate); 3140: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar); 3141: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 3142: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 3143: printf("\n"); 3144: fprintf(ficlog,"\n"); 3145: 3146: free_vector(xm,1,npar); 3147: free_vector(xp,1,npar); 3148: free_matrix(dnewm,1,nlstate*nlstate,1,npar); 3149: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate); 3150: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage); 3151: } 3152: 3153: /************ Variance ******************/ 3154: 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[]) 3155: { 3156: /* Variance of health expectancies */ 3157: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/ 3158: /* double **newm;*/ 3159: double **dnewm,**doldm; 3160: double **dnewmp,**doldmp; 3161: int i, j, nhstepm, hstepm, h, nstepm ; 3162: int k, cptcode; 3163: double *xp; 3164: double **gp, **gm; /* for var eij */ 3165: double ***gradg, ***trgradg; /*for var eij */ 3166: double **gradgp, **trgradgp; /* for var p point j */ 3167: double *gpp, *gmp; /* for var p point j */ 3168: double **varppt; /* for var p point j nlstate to nlstate+ndeath */ 3169: double ***p3mat; 3170: double age,agelim, hf; 3171: double ***mobaverage; 3172: int theta; 3173: char digit[4]; 3174: char digitp[25]; 3175: 3176: char fileresprobmorprev[FILENAMELENGTH]; 3177: 3178: if(popbased==1){ 3179: if(mobilav!=0) 3180: strcpy(digitp,"-populbased-mobilav-"); 3181: else strcpy(digitp,"-populbased-nomobil-"); 3182: } 3183: else 3184: strcpy(digitp,"-stablbased-"); 3185: 3186: if (mobilav!=0) { 3187: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 3188: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ 3189: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); 3190: printf(" Error in movingaverage mobilav=%d\n",mobilav); 3191: } 3192: } 3193: 3194: strcpy(fileresprobmorprev,"prmorprev"); 3195: sprintf(digit,"%-d",ij); 3196: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/ 3197: strcat(fileresprobmorprev,digit); /* Tvar to be done */ 3198: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */ 3199: strcat(fileresprobmorprev,fileres); 3200: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) { 3201: printf("Problem with resultfile: %s\n", fileresprobmorprev); 3202: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev); 3203: } 3204: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); 3205: 3206: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); 3207: pstamp(ficresprobmorprev); 3208: 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); 3209: fprintf(ficresprobmorprev,"# Age cov=%-d",ij); 3210: for(j=nlstate+1; j<=(nlstate+ndeath);j++){ 3211: fprintf(ficresprobmorprev," p.%-d SE",j); 3212: for(i=1; i<=nlstate;i++) 3213: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j); 3214: } 3215: fprintf(ficresprobmorprev,"\n"); 3216: fprintf(ficgp,"\n# Routine varevsij"); 3217: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/ 3218: 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"); 3219: fprintf(fichtm,"\n %s \n",digitp); 3220: /* } */ 3221: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); 3222: pstamp(ficresvij); 3223: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are "); 3224: if(popbased==1) 3225: 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); 3226: else 3227: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n"); 3228: fprintf(ficresvij,"# Age"); 3229: for(i=1; i<=nlstate;i++) 3230: for(j=1; j<=nlstate;j++) 3231: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j); 3232: fprintf(ficresvij,"\n"); 3233: 3234: xp=vector(1,npar); 3235: dnewm=matrix(1,nlstate,1,npar); 3236: doldm=matrix(1,nlstate,1,nlstate); 3237: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar); 3238: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); 3239: 3240: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath); 3241: gpp=vector(nlstate+1,nlstate+ndeath); 3242: gmp=vector(nlstate+1,nlstate+ndeath); 3243: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/ 3244: 3245: if(estepm < stepm){ 3246: printf ("Problem %d lower than %d\n",estepm, stepm); 3247: } 3248: else hstepm=estepm; 3249: /* For example we decided to compute the life expectancy with the smallest unit */ 3250: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 3251: nhstepm is the number of hstepm from age to agelim 3252: nstepm is the number of stepm from age to agelin. 3253: Look at function hpijx to understand why (it is linked to memory size questions) */ 3254: /* We decided (b) to get a life expectancy respecting the most precise curvature of the 3255: survival function given by stepm (the optimization length). Unfortunately it 3256: means that if the survival funtion is printed every two years of age and if 3257: you sum them up and add 1 year (area under the trapezoids) you won't get the same 3258: results. So we changed our mind and took the option of the best precision. 3259: */ 3260: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 3261: agelim = AGESUP; 3262: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */ 3263: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 3264: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */ 3265: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 3266: gradg=ma3x(0,nhstepm,1,npar,1,nlstate); 3267: gp=matrix(0,nhstepm,1,nlstate); 3268: gm=matrix(0,nhstepm,1,nlstate); 3269: 3270: 3271: for(theta=1; theta <=npar; theta++){ 3272: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/ 3273: xp[i] = x[i] + (i==theta ?delti[theta]:0); 3274: } 3275: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); 3276: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); 3277: 3278: if (popbased==1) { 3279: if(mobilav ==0){ 3280: for(i=1; i<=nlstate;i++) 3281: prlim[i][i]=probs[(int)age][i][ij]; 3282: }else{ /* mobilav */ 3283: for(i=1; i<=nlstate;i++) 3284: prlim[i][i]=mobaverage[(int)age][i][ij]; 3285: } 3286: } 3287: 3288: for(j=1; j<= nlstate; j++){ 3289: for(h=0; h<=nhstepm; h++){ 3290: for(i=1, gp[h][j]=0.;i<=nlstate;i++) 3291: gp[h][j] += prlim[i][i]*p3mat[i][j][h]; 3292: } 3293: } 3294: /* This for computing probability of death (h=1 means 3295: computed over hstepm matrices product = hstepm*stepm months) 3296: as a weighted average of prlim. 3297: */ 3298: for(j=nlstate+1;j<=nlstate+ndeath;j++){ 3299: for(i=1,gpp[j]=0.; i<= nlstate; i++) 3300: gpp[j] += prlim[i][i]*p3mat[i][j][1]; 3301: } 3302: /* end probability of death */ 3303: 3304: for(i=1; i<=npar; i++) /* Computes gradient x - delta */ 3305: xp[i] = x[i] - (i==theta ?delti[theta]:0); 3306: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); 3307: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); 3308: 3309: if (popbased==1) { 3310: if(mobilav ==0){ 3311: for(i=1; i<=nlstate;i++) 3312: prlim[i][i]=probs[(int)age][i][ij]; 3313: }else{ /* mobilav */ 3314: for(i=1; i<=nlstate;i++) 3315: prlim[i][i]=mobaverage[(int)age][i][ij]; 3316: } 3317: } 3318: 3319: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */ 3320: for(h=0; h<=nhstepm; h++){ 3321: for(i=1, gm[h][j]=0.;i<=nlstate;i++) 3322: gm[h][j] += prlim[i][i]*p3mat[i][j][h]; 3323: } 3324: } 3325: /* This for computing probability of death (h=1 means 3326: computed over hstepm matrices product = hstepm*stepm months) 3327: as a weighted average of prlim. 3328: */ 3329: for(j=nlstate+1;j<=nlstate+ndeath;j++){ 3330: for(i=1,gmp[j]=0.; i<= nlstate; i++) 3331: gmp[j] += prlim[i][i]*p3mat[i][j][1]; 3332: } 3333: /* end probability of death */ 3334: 3335: for(j=1; j<= nlstate; j++) /* vareij */ 3336: for(h=0; h<=nhstepm; h++){ 3337: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta]; 3338: } 3339: 3340: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */ 3341: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta]; 3342: } 3343: 3344: } /* End theta */ 3345: 3346: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */ 3347: 3348: for(h=0; h<=nhstepm; h++) /* veij */ 3349: for(j=1; j<=nlstate;j++) 3350: for(theta=1; theta <=npar; theta++) 3351: trgradg[h][j][theta]=gradg[h][theta][j]; 3352: 3353: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */ 3354: for(theta=1; theta <=npar; theta++) 3355: trgradgp[j][theta]=gradgp[theta][j]; 3356: 3357: 3358: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */ 3359: for(i=1;i<=nlstate;i++) 3360: for(j=1;j<=nlstate;j++) 3361: vareij[i][j][(int)age] =0.; 3362: 3363: for(h=0;h<=nhstepm;h++){ 3364: for(k=0;k<=nhstepm;k++){ 3365: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov); 3366: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]); 3367: for(i=1;i<=nlstate;i++) 3368: for(j=1;j<=nlstate;j++) 3369: vareij[i][j][(int)age] += doldm[i][j]*hf*hf; 3370: } 3371: } 3372: 3373: /* pptj */ 3374: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov); 3375: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp); 3376: for(j=nlstate+1;j<=nlstate+ndeath;j++) 3377: for(i=nlstate+1;i<=nlstate+ndeath;i++) 3378: varppt[j][i]=doldmp[j][i]; 3379: /* end ppptj */ 3380: /* x centered again */ 3381: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij); 3382: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij); 3383: 3384: if (popbased==1) { 3385: if(mobilav ==0){ 3386: for(i=1; i<=nlstate;i++) 3387: prlim[i][i]=probs[(int)age][i][ij]; 3388: }else{ /* mobilav */ 3389: for(i=1; i<=nlstate;i++) 3390: prlim[i][i]=mobaverage[(int)age][i][ij]; 3391: } 3392: } 3393: 3394: /* This for computing probability of death (h=1 means 3395: computed over hstepm (estepm) matrices product = hstepm*stepm months) 3396: as a weighted average of prlim. 3397: */ 3398: for(j=nlstate+1;j<=nlstate+ndeath;j++){ 3399: for(i=1,gmp[j]=0.;i<= nlstate; i++) 3400: gmp[j] += prlim[i][i]*p3mat[i][j][1]; 3401: } 3402: /* end probability of death */ 3403: 3404: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij); 3405: for(j=nlstate+1; j<=(nlstate+ndeath);j++){ 3406: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j])); 3407: for(i=1; i<=nlstate;i++){ 3408: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]); 3409: } 3410: } 3411: fprintf(ficresprobmorprev,"\n"); 3412: 3413: fprintf(ficresvij,"%.0f ",age ); 3414: for(i=1; i<=nlstate;i++) 3415: for(j=1; j<=nlstate;j++){ 3416: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]); 3417: } 3418: fprintf(ficresvij,"\n"); 3419: free_matrix(gp,0,nhstepm,1,nlstate); 3420: free_matrix(gm,0,nhstepm,1,nlstate); 3421: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate); 3422: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar); 3423: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 3424: } /* End age */ 3425: free_vector(gpp,nlstate+1,nlstate+ndeath); 3426: free_vector(gmp,nlstate+1,nlstate+ndeath); 3427: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath); 3428: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/ 3429: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); 3430: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */ 3431: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";"); 3432: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */ 3433: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */ 3434: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */ 3435: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev)); 3436: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev)); 3437: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev)); 3438: fprintf(fichtm,"\n File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev)); 3439: fprintf(fichtm,"\n Probability is computed over estepm=%d months. <img src=\"%s%s.png\"> \n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit); 3440: /* fprintf(fichtm,"\n 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 <img src=\"varmuptjgr%s%s.png\"> \n", stepm,YEARM,digitp,digit); 3441: */ 3442: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */ 3443: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit); 3444: 3445: free_vector(xp,1,npar); 3446: free_matrix(doldm,1,nlstate,1,nlstate); 3447: free_matrix(dnewm,1,nlstate,1,npar); 3448: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); 3449: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar); 3450: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); 3451: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 3452: fclose(ficresprobmorprev); 3453: fflush(ficgp); 3454: fflush(fichtm); 3455: } /* end varevsij */ 3456: 3457: /************ Variance of prevlim ******************/ 3458: 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[]) 3459: { 3460: /* Variance of prevalence limit */ 3461: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/ 3462: double **newm; 3463: double **dnewm,**doldm; 3464: int i, j, nhstepm, hstepm; 3465: int k, cptcode; 3466: double *xp; 3467: double *gp, *gm; 3468: double **gradg, **trgradg; 3469: double age,agelim; 3470: int theta; 3471: 3472: pstamp(ficresvpl); 3473: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n"); 3474: fprintf(ficresvpl,"# Age"); 3475: for(i=1; i<=nlstate;i++) 3476: fprintf(ficresvpl," %1d-%1d",i,i); 3477: fprintf(ficresvpl,"\n"); 3478: 3479: xp=vector(1,npar); 3480: dnewm=matrix(1,nlstate,1,npar); 3481: doldm=matrix(1,nlstate,1,nlstate); 3482: 3483: hstepm=1*YEARM; /* Every year of age */ 3484: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 3485: agelim = AGESUP; 3486: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */ 3487: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 3488: if (stepm >= YEARM) hstepm=1; 3489: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */ 3490: gradg=matrix(1,npar,1,nlstate); 3491: gp=vector(1,nlstate); 3492: gm=vector(1,nlstate); 3493: 3494: for(theta=1; theta <=npar; theta++){ 3495: for(i=1; i<=npar; i++){ /* Computes gradient */ 3496: xp[i] = x[i] + (i==theta ?delti[theta]:0); 3497: } 3498: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); 3499: for(i=1;i<=nlstate;i++) 3500: gp[i] = prlim[i][i]; 3501: 3502: for(i=1; i<=npar; i++) /* Computes gradient */ 3503: xp[i] = x[i] - (i==theta ?delti[theta]:0); 3504: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); 3505: for(i=1;i<=nlstate;i++) 3506: gm[i] = prlim[i][i]; 3507: 3508: for(i=1;i<=nlstate;i++) 3509: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta]; 3510: } /* End theta */ 3511: 3512: trgradg =matrix(1,nlstate,1,npar); 3513: 3514: for(j=1; j<=nlstate;j++) 3515: for(theta=1; theta <=npar; theta++) 3516: trgradg[j][theta]=gradg[theta][j]; 3517: 3518: for(i=1;i<=nlstate;i++) 3519: varpl[i][(int)age] =0.; 3520: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov); 3521: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg); 3522: for(i=1;i<=nlstate;i++) 3523: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */ 3524: 3525: fprintf(ficresvpl,"%.0f ",age ); 3526: for(i=1; i<=nlstate;i++) 3527: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age])); 3528: fprintf(ficresvpl,"\n"); 3529: free_vector(gp,1,nlstate); 3530: free_vector(gm,1,nlstate); 3531: free_matrix(gradg,1,npar,1,nlstate); 3532: free_matrix(trgradg,1,nlstate,1,npar); 3533: } /* End age */ 3534: 3535: free_vector(xp,1,npar); 3536: free_matrix(doldm,1,nlstate,1,npar); 3537: free_matrix(dnewm,1,nlstate,1,nlstate); 3538: 3539: } 3540: 3541: /************ Variance of one-step probabilities ******************/ 3542: 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[]) 3543: { 3544: int i, j=0, i1, k1, l1, t, tj; 3545: int k2, l2, j1, z1; 3546: int k=0,l, cptcode; 3547: int first=1, first1, first2; 3548: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp; 3549: double **dnewm,**doldm; 3550: double *xp; 3551: double *gp, *gm; 3552: double **gradg, **trgradg; 3553: double **mu; 3554: double age,agelim, cov[NCOVMAX+1]; 3555: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */ 3556: int theta; 3557: char fileresprob[FILENAMELENGTH]; 3558: char fileresprobcov[FILENAMELENGTH]; 3559: char fileresprobcor[FILENAMELENGTH]; 3560: double ***varpij; 3561: 3562: strcpy(fileresprob,"prob"); 3563: strcat(fileresprob,fileres); 3564: if((ficresprob=fopen(fileresprob,"w"))==NULL) { 3565: printf("Problem with resultfile: %s\n", fileresprob); 3566: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob); 3567: } 3568: strcpy(fileresprobcov,"probcov"); 3569: strcat(fileresprobcov,fileres); 3570: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) { 3571: printf("Problem with resultfile: %s\n", fileresprobcov); 3572: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov); 3573: } 3574: strcpy(fileresprobcor,"probcor"); 3575: strcat(fileresprobcor,fileres); 3576: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) { 3577: printf("Problem with resultfile: %s\n", fileresprobcor); 3578: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor); 3579: } 3580: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob); 3581: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob); 3582: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov); 3583: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov); 3584: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor); 3585: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor); 3586: pstamp(ficresprob); 3587: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n"); 3588: fprintf(ficresprob,"# Age"); 3589: pstamp(ficresprobcov); 3590: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n"); 3591: fprintf(ficresprobcov,"# Age"); 3592: pstamp(ficresprobcor); 3593: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n"); 3594: fprintf(ficresprobcor,"# Age"); 3595: 3596: 3597: for(i=1; i<=nlstate;i++) 3598: for(j=1; j<=(nlstate+ndeath);j++){ 3599: fprintf(ficresprob," p%1d-%1d (SE)",i,j); 3600: fprintf(ficresprobcov," p%1d-%1d ",i,j); 3601: fprintf(ficresprobcor," p%1d-%1d ",i,j); 3602: } 3603: /* fprintf(ficresprob,"\n"); 3604: fprintf(ficresprobcov,"\n"); 3605: fprintf(ficresprobcor,"\n"); 3606: */ 3607: xp=vector(1,npar); 3608: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar); 3609: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath)); 3610: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage); 3611: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage); 3612: first=1; 3613: fprintf(ficgp,"\n# Routine varprob"); 3614: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n"); 3615: fprintf(fichtm,"\n"); 3616: 3617: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov); 3618: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\ 3619: file %s \n",optionfilehtmcov); 3620: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\ 3621: and drawn. It helps understanding how is the covariance between two incidences.\ 3622: They are expressed in year-1 in order to be less dependent of stepm. \n"); 3623: fprintf(fichtmcov,"\n Contour plot corresponding to x'cov-1x = 4 (where x is the column vector (pij,pkl)) are drawn. \ 3624: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \ 3625: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \ 3626: standard deviations wide on each axis. \ 3627: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\ 3628: and made the appropriate rotation to look at the uncorrelated principal directions. \ 3629: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one. \n"); 3630: 3631: cov[1]=1; 3632: /* tj=cptcoveff; */ 3633: tj = (int) pow(2,cptcoveff); 3634: if (cptcovn<1) {tj=1;ncodemax[1]=1;} 3635: j1=0; 3636: for(j1=1; j1<=tj;j1++){ 3637: /*for(i1=1; i1<=ncodemax[t];i1++){ */ 3638: /*j1++;*/ 3639: if (cptcovn>0) { 3640: fprintf(ficresprob, "\n#********** Variable "); 3641: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); 3642: fprintf(ficresprob, "**********\n#\n"); 3643: fprintf(ficresprobcov, "\n#********** Variable "); 3644: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); 3645: fprintf(ficresprobcov, "**********\n#\n"); 3646: 3647: fprintf(ficgp, "\n#********** Variable "); 3648: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); 3649: fprintf(ficgp, "**********\n#\n"); 3650: 3651: 3652: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable "); 3653: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); 3654: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">"); 3655: 3656: fprintf(ficresprobcor, "\n#********** Variable "); 3657: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); 3658: fprintf(ficresprobcor, "**********\n#"); 3659: } 3660: 3661: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath)); 3662: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar); 3663: gp=vector(1,(nlstate)*(nlstate+ndeath)); 3664: gm=vector(1,(nlstate)*(nlstate+ndeath)); 3665: for (age=bage; age<=fage; age ++){ 3666: cov[2]=age; 3667: for (k=1; k<=cptcovn;k++) { 3668: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4 3669: * 1 1 1 1 1 3670: * 2 2 1 1 1 3671: * 3 1 2 1 1 3672: */ 3673: /* nbcode[1][1]=0 nbcode[1][2]=1;*/ 3674: } 3675: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; 3676: for (k=1; k<=cptcovprod;k++) 3677: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; 3678: 3679: 3680: for(theta=1; theta <=npar; theta++){ 3681: for(i=1; i<=npar; i++) 3682: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0); 3683: 3684: pmij(pmmij,cov,ncovmodel,xp,nlstate); 3685: 3686: k=0; 3687: for(i=1; i<= (nlstate); i++){ 3688: for(j=1; j<=(nlstate+ndeath);j++){ 3689: k=k+1; 3690: gp[k]=pmmij[i][j]; 3691: } 3692: } 3693: 3694: for(i=1; i<=npar; i++) 3695: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0); 3696: 3697: pmij(pmmij,cov,ncovmodel,xp,nlstate); 3698: k=0; 3699: for(i=1; i<=(nlstate); i++){ 3700: for(j=1; j<=(nlstate+ndeath);j++){ 3701: k=k+1; 3702: gm[k]=pmmij[i][j]; 3703: } 3704: } 3705: 3706: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 3707: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta]; 3708: } 3709: 3710: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++) 3711: for(theta=1; theta <=npar; theta++) 3712: trgradg[j][theta]=gradg[theta][j]; 3713: 3714: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 3715: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg); 3716: 3717: pmij(pmmij,cov,ncovmodel,x,nlstate); 3718: 3719: k=0; 3720: for(i=1; i<=(nlstate); i++){ 3721: for(j=1; j<=(nlstate+ndeath);j++){ 3722: k=k+1; 3723: mu[k][(int) age]=pmmij[i][j]; 3724: } 3725: } 3726: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++) 3727: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++) 3728: varpij[i][j][(int)age] = doldm[i][j]; 3729: 3730: /*printf("\n%d ",(int)age); 3731: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){ 3732: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i])); 3733: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i])); 3734: }*/ 3735: 3736: fprintf(ficresprob,"\n%d ",(int)age); 3737: fprintf(ficresprobcov,"\n%d ",(int)age); 3738: fprintf(ficresprobcor,"\n%d ",(int)age); 3739: 3740: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++) 3741: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age])); 3742: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){ 3743: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]); 3744: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]); 3745: } 3746: i=0; 3747: for (k=1; k<=(nlstate);k++){ 3748: for (l=1; l<=(nlstate+ndeath);l++){ 3749: i++; 3750: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l); 3751: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l); 3752: for (j=1; j<=i;j++){ 3753: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */ 3754: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]); 3755: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age])); 3756: } 3757: } 3758: }/* end of loop for state */ 3759: } /* end of loop for age */ 3760: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath)); 3761: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath)); 3762: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar); 3763: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar); 3764: 3765: /* Confidence intervalle of pij */ 3766: /* 3767: fprintf(ficgp,"\nunset parametric;unset label"); 3768: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\""); 3769: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65"); 3770: fprintf(fichtm,"\n Probability with confidence intervals expressed in year-1 :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname); 3771: fprintf(fichtm,"\n <img src=\"pijgr%s.png\"> ",optionfilefiname); 3772: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname); 3773: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob); 3774: */ 3775: 3776: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/ 3777: first1=1;first2=2; 3778: for (k2=1; k2<=(nlstate);k2++){ 3779: for (l2=1; l2<=(nlstate+ndeath);l2++){ 3780: if(l2==k2) continue; 3781: j=(k2-1)*(nlstate+ndeath)+l2; 3782: for (k1=1; k1<=(nlstate);k1++){ 3783: for (l1=1; l1<=(nlstate+ndeath);l1++){ 3784: if(l1==k1) continue; 3785: i=(k1-1)*(nlstate+ndeath)+l1; 3786: if(i<=j) continue; 3787: for (age=bage; age<=fage; age ++){ 3788: if ((int)age %5==0){ 3789: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM; 3790: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM; 3791: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM; 3792: mu1=mu[i][(int) age]/stepm*YEARM ; 3793: mu2=mu[j][(int) age]/stepm*YEARM; 3794: c12=cv12/sqrt(v1*v2); 3795: /* Computing eigen value of matrix of covariance */ 3796: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.; 3797: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.; 3798: if ((lc2 <0) || (lc1 <0) ){ 3799: if(first2==1){ 3800: first1=0; 3801: 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); 3802: } 3803: 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); 3804: /* lc1=fabs(lc1); */ /* If we want to have them positive */ 3805: /* lc2=fabs(lc2); */ 3806: } 3807: 3808: /* Eigen vectors */ 3809: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12)); 3810: /*v21=sqrt(1.-v11*v11); *//* error */ 3811: v21=(lc1-v1)/cv12*v11; 3812: v12=-v21; 3813: v22=v11; 3814: tnalp=v21/v11; 3815: if(first1==1){ 3816: first1=0; 3817: 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); 3818: } 3819: 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); 3820: /*printf(fignu*/ 3821: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */ 3822: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */ 3823: if(first==1){ 3824: first=0; 3825: fprintf(ficgp,"\nset parametric;unset label"); 3826: 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); 3827: fprintf(ficgp,"\nset ter png small size 320, 240"); 3828: fprintf(fichtmcov,"\n Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year-1\ 3829: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\ 3830: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\ 3831: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\ 3832: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2); 3833: fprintf(fichtmcov,"\n <img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2); 3834: fprintf(fichtmcov,"\n Correlation at age %d (%.3f),",(int) age, c12); 3835: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2); 3836: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2); 3837: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2); 3838: 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",\ 3839: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\ 3840: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2)); 3841: }else{ 3842: first=0; 3843: fprintf(fichtmcov," %d (%.3f),",(int) age, c12); 3844: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2); 3845: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2); 3846: 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",\ 3847: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\ 3848: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2)); 3849: }/* if first */ 3850: } /* age mod 5 */ 3851: } /* end loop age */ 3852: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2); 3853: first=1; 3854: } /*l12 */ 3855: } /* k12 */ 3856: } /*l1 */ 3857: }/* k1 */ 3858: /* } /* loop covariates */ 3859: } 3860: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage); 3861: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage); 3862: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath)); 3863: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar); 3864: free_vector(xp,1,npar); 3865: fclose(ficresprob); 3866: fclose(ficresprobcov); 3867: fclose(ficresprobcor); 3868: fflush(ficgp); 3869: fflush(fichtmcov); 3870: } 3871: 3872: 3873: /******************* Printing html file ***********/ 3874: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \ 3875: int lastpass, int stepm, int weightopt, char model[],\ 3876: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\ 3877: int popforecast, int estepm ,\ 3878: double jprev1, double mprev1,double anprev1, \ 3879: double jprev2, double mprev2,double anprev2){ 3880: int jj1, k1, i1, cpt; 3881: 3882: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \ 3883: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \ 3884: </ul>"); 3885: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \ 3886: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> \n ", 3887: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p")); 3888: fprintf(fichtm,"\ 3889: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a> \n ", 3890: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij")); 3891: fprintf(fichtm,"\ 3892: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> \n", 3893: subdirf2(fileres,"pl"),subdirf2(fileres,"pl")); 3894: fprintf(fichtm,"\ 3895: - (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): \ 3896: <a href=\"%s\">%s</a> \n", 3897: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e")); 3898: fprintf(fichtm,"\ 3899: - Population projections by age and states: \ 3900: <a href=\"%s\">%s</a> \n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f")); 3901: 3902: fprintf(fichtm," \n<ul><li>Graphs</li>"); 3903: 3904: m=pow(2,cptcoveff); 3905: if (cptcovn < 1) {m=1;ncodemax[1]=1;} 3906: 3907: jj1=0; 3908: for(k1=1; k1<=m;k1++){ 3909: for(i1=1; i1<=ncodemax[k1];i1++){ 3910: jj1++; 3911: if (cptcovn > 0) { 3912: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates"); 3913: for (cpt=1; cpt<=cptcoveff;cpt++) 3914: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]); 3915: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">"); 3916: } 3917: /* Pij */ 3918: fprintf(fichtm," - 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> \ 3919: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 3920: /* Quasi-incidences */ 3921: fprintf(fichtm," - Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\ 3922: 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> \ 3923: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 3924: /* Period (stable) prevalence in each health state */ 3925: for(cpt=1; cpt<=nlstate;cpt++){ 3926: fprintf(fichtm," - Convergence from each state (1 to %d) to period (stable) prevalence in state %d <a href=\"%s%d_%d.png\">%s%d_%d.png</a> \ 3927: <img src=\"%s%d_%d.png\">",nlstate, cpt, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1); 3928: } 3929: for(cpt=1; cpt<=nlstate;cpt++) { 3930: fprintf(fichtm,"\n - Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> \ 3931: <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1); 3932: } 3933: } /* end i1 */ 3934: }/* End k1 */ 3935: fprintf(fichtm,"</ul>"); 3936: 3937: 3938: fprintf(fichtm,"\ 3939: \n <li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\ 3940: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> \n", rfileres,rfileres); 3941: 3942: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> \n", 3943: subdirf2(fileres,"prob"),subdirf2(fileres,"prob")); 3944: fprintf(fichtm,"\ 3945: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> \n", 3946: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov")); 3947: 3948: fprintf(fichtm,"\ 3949: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> \n", 3950: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor")); 3951: fprintf(fichtm,"\ 3952: - Variances and covariances of health expectancies by age and initial health status (cov(eij,ekl)(estepm=%2d months): \ 3953: <a href=\"%s\">%s</a> \n</li>", 3954: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve")); 3955: fprintf(fichtm,"\ 3956: - (a) Health expectancies by health status at initial age (eij) and standard errors (in parentheses) (b) life expectancies and standard errors (ei.=ei1+ei2+...)(estepm=%2d months): \ 3957: <a href=\"%s\">%s</a> \n</li>", 3958: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde")); 3959: fprintf(fichtm,"\ 3960: - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), eij 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> \n", 3961: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v")); 3962: fprintf(fichtm,"\ 3963: - Total life expectancy and total health expectancies to be spent in each health state e.j 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> \n", 3964: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t")); 3965: fprintf(fichtm,"\ 3966: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> \n",\ 3967: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl")); 3968: 3969: /* if(popforecast==1) fprintf(fichtm,"\n */ 3970: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> \n */ 3971: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> \n */ 3972: /* ",fileres,fileres,fileres,fileres); */ 3973: /* else */ 3974: /* fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .) </li>\n",popforecast, stepm, model); */ 3975: fflush(fichtm); 3976: fprintf(fichtm," <ul><li>Graphs</li>"); 3977: 3978: m=pow(2,cptcoveff); 3979: if (cptcovn < 1) {m=1;ncodemax[1]=1;} 3980: 3981: jj1=0; 3982: for(k1=1; k1<=m;k1++){ 3983: for(i1=1; i1<=ncodemax[k1];i1++){ 3984: jj1++; 3985: if (cptcovn > 0) { 3986: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates"); 3987: for (cpt=1; cpt<=cptcoveff;cpt++) 3988: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]); 3989: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">"); 3990: } 3991: for(cpt=1; cpt<=nlstate;cpt++) { 3992: fprintf(fichtm," - Observed (cross-sectional) and period (incidence based) \ 3993: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png \ 3994: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1); 3995: } 3996: fprintf(fichtm,"\n - Total life expectancy by age and \ 3997: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \ 3998: true period expectancies (those weighted with period prevalences are also\ 3999: drawn in addition to the population based expectancies computed using\ 4000: observed and cahotic prevalences: %s%d.png \ 4001: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1); 4002: } /* end i1 */ 4003: }/* End k1 */ 4004: fprintf(fichtm,"</ul>"); 4005: fflush(fichtm); 4006: } 4007: 4008: /******************* Gnuplot file **************/ 4009: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){ 4010: 4011: char dirfileres[132],optfileres[132]; 4012: int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0; 4013: int ng=0; 4014: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */ 4015: /* printf("Problem with file %s",optionfilegnuplot); */ 4016: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */ 4017: /* } */ 4018: 4019: /*#ifdef windows */ 4020: fprintf(ficgp,"cd \"%s\" \n",pathc); 4021: /*#endif */ 4022: m=pow(2,cptcoveff); 4023: 4024: strcpy(dirfileres,optionfilefiname); 4025: strcpy(optfileres,"vpl"); 4026: /* 1eme*/ 4027: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n"); 4028: for (cpt=1; cpt<= nlstate ; cpt ++) { 4029: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */ 4030: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1); 4031: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1); 4032: fprintf(ficgp,"set xlabel \"Age\" \n\ 4033: set ylabel \"Probability\" \n\ 4034: set ter png small size 320, 240\n\ 4035: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1); 4036: 4037: for (i=1; i<= nlstate ; i ++) { 4038: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)"); 4039: else fprintf(ficgp," \%%*lf (\%%*lf)"); 4040: } 4041: 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); 4042: for (i=1; i<= nlstate ; i ++) { 4043: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)"); 4044: else fprintf(ficgp," \%%*lf (\%%*lf)"); 4045: } 4046: fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 4047: for (i=1; i<= nlstate ; i ++) { 4048: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)"); 4049: else fprintf(ficgp," \%%*lf (\%%*lf)"); 4050: } 4051: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1)); 4052: } 4053: } 4054: /*2 eme*/ 4055: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n"); 4056: for (k1=1; k1<= m ; k1 ++) { 4057: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1); 4058: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage); 4059: 4060: for (i=1; i<= nlstate+1 ; i ++) { 4061: k=2*i; 4062: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1); 4063: for (j=1; j<= nlstate+1 ; j ++) { 4064: if (j==i) fprintf(ficgp," \%%lf (\%%lf)"); 4065: else fprintf(ficgp," \%%*lf (\%%*lf)"); 4066: } 4067: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,"); 4068: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1); 4069: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1); 4070: for (j=1; j<= nlstate+1 ; j ++) { 4071: if (j==i) fprintf(ficgp," \%%lf (\%%lf)"); 4072: else fprintf(ficgp," \%%*lf (\%%*lf)"); 4073: } 4074: fprintf(ficgp,"\" t\"\" w l lt 0,"); 4075: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1); 4076: for (j=1; j<= nlstate+1 ; j ++) { 4077: if (j==i) fprintf(ficgp," \%%lf (\%%lf)"); 4078: else fprintf(ficgp," \%%*lf (\%%*lf)"); 4079: } 4080: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0"); 4081: else fprintf(ficgp,"\" t\"\" w l lt 0,"); 4082: } 4083: } 4084: 4085: /*3eme*/ 4086: 4087: for (k1=1; k1<= m ; k1 ++) { 4088: for (cpt=1; cpt<= nlstate ; cpt ++) { 4089: /* k=2+nlstate*(2*cpt-2); */ 4090: k=2+(nlstate+1)*(cpt-1); 4091: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1); 4092: fprintf(ficgp,"set ter png small size 320, 240\n\ 4093: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt); 4094: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1); 4095: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) "); 4096: fprintf(ficgp,"\" t \"e%d1\" w l",cpt); 4097: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1); 4098: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) "); 4099: fprintf(ficgp,"\" t \"e%d1\" w l",cpt); 4100: 4101: */ 4102: for (i=1; i< nlstate ; i ++) { 4103: 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); 4104: /* 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);*/ 4105: 4106: } 4107: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt); 4108: } 4109: } 4110: 4111: /* CV preval stable (period) */ 4112: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */ 4113: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */ 4114: k=3; 4115: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt); 4116: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1); 4117: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\ 4118: set ter png small size 320, 240\n\ 4119: unset log y\n\ 4120: plot [%.f:%.f] ", ageminpar, agemaxpar); 4121: for (i=1; i<= nlstate ; i ++){ 4122: if(i==1) 4123: fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij")); 4124: else 4125: fprintf(ficgp,", '' "); 4126: l=(nlstate+ndeath)*(i-1)+1; 4127: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); 4128: for (j=1; j<= (nlstate-1) ; j ++) 4129: fprintf(ficgp,"+$%d",k+l+j); 4130: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt); 4131: } /* nlstate */ 4132: fprintf(ficgp,"\n"); 4133: } /* end cpt state*/ 4134: } /* end covariate */ 4135: 4136: /* proba elementaires */ 4137: for(i=1,jk=1; i <=nlstate; i++){ 4138: for(k=1; k <=(nlstate+ndeath); k++){ 4139: if (k != i) { 4140: for(j=1; j <=ncovmodel; j++){ 4141: fprintf(ficgp,"p%d=%f ",jk,p[jk]); 4142: jk++; 4143: fprintf(ficgp,"\n"); 4144: } 4145: } 4146: } 4147: } 4148: /*goto avoid;*/ 4149: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/ 4150: for(jk=1; jk <=m; jk++) { 4151: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 4152: if (ng==2) 4153: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n"); 4154: else 4155: fprintf(ficgp,"\nset title \"Probability\"\n"); 4156: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar); 4157: i=1; 4158: for(k2=1; k2<=nlstate; k2++) { 4159: k3=i; 4160: for(k=1; k<=(nlstate+ndeath); k++) { 4161: if (k != k2){ 4162: if(ng==2) 4163: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1); 4164: else 4165: fprintf(ficgp," exp(p%d+p%d*x",i,i+1); 4166: ij=1;/* To be checked else nbcode[0][0] wrong */ 4167: for(j=3; j <=ncovmodel; j++) { 4168: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */ 4169: /* /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */ 4170: /* ij++; */ 4171: /* } */ 4172: /* else */ 4173: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]); 4174: } 4175: fprintf(ficgp,")/(1"); 4176: 4177: for(k1=1; k1 <=nlstate; k1++){ 4178: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1); 4179: ij=1; 4180: for(j=3; j <=ncovmodel; j++){ 4181: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */ 4182: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */ 4183: /* ij++; */ 4184: /* } */ 4185: /* else */ 4186: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]); 4187: } 4188: fprintf(ficgp,")"); 4189: } 4190: fprintf(ficgp,") t \"p%d%d\" ", k2,k); 4191: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,","); 4192: i=i+ncovmodel; 4193: } 4194: } /* end k */ 4195: } /* end k2 */ 4196: } /* end jk */ 4197: } /* end ng */ 4198: avoid: 4199: fflush(ficgp); 4200: } /* end gnuplot */ 4201: 4202: 4203: /*************** Moving average **************/ 4204: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){ 4205: 4206: int i, cpt, cptcod; 4207: int modcovmax =1; 4208: int mobilavrange, mob; 4209: double age; 4210: 4211: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 4212: a covariate has 2 modalities */ 4213: if (cptcovn<1) modcovmax=1; /* At least 1 pass */ 4214: 4215: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){ 4216: if(mobilav==1) mobilavrange=5; /* default */ 4217: else mobilavrange=mobilav; 4218: for (age=bage; age<=fage; age++) 4219: for (i=1; i<=nlstate;i++) 4220: for (cptcod=1;cptcod<=modcovmax;cptcod++) 4221: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod]; 4222: /* We keep the original values on the extreme ages bage, fage and for 4223: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2 4224: we use a 5 terms etc. until the borders are no more concerned. 4225: */ 4226: for (mob=3;mob <=mobilavrange;mob=mob+2){ 4227: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ 4228: for (i=1; i<=nlstate;i++){ 4229: for (cptcod=1;cptcod<=modcovmax;cptcod++){ 4230: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod]; 4231: for (cpt=1;cpt<=(mob-1)/2;cpt++){ 4232: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod]; 4233: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod]; 4234: } 4235: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob; 4236: } 4237: } 4238: }/* end age */ 4239: }/* end mob */ 4240: }else return -1; 4241: return 0; 4242: }/* End movingaverage */ 4243: 4244: 4245: /************** Forecasting ******************/ 4246: 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){ 4247: /* proj1, year, month, day of starting projection 4248: agemin, agemax range of age 4249: dateprev1 dateprev2 range of dates during which prevalence is computed 4250: anproj2 year of en of projection (same day and month as proj1). 4251: */ 4252: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1; 4253: int *popage; 4254: double agec; /* generic age */ 4255: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; 4256: double *popeffectif,*popcount; 4257: double ***p3mat; 4258: double ***mobaverage; 4259: char fileresf[FILENAMELENGTH]; 4260: 4261: agelim=AGESUP; 4262: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); 4263: 4264: strcpy(fileresf,"f"); 4265: strcat(fileresf,fileres); 4266: if((ficresf=fopen(fileresf,"w"))==NULL) { 4267: printf("Problem with forecast resultfile: %s\n", fileresf); 4268: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf); 4269: } 4270: printf("Computing forecasting: result on file '%s' \n", fileresf); 4271: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf); 4272: 4273: if (cptcoveff==0) ncodemax[cptcoveff]=1; 4274: 4275: if (mobilav!=0) { 4276: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 4277: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ 4278: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); 4279: printf(" Error in movingaverage mobilav=%d\n",mobilav); 4280: } 4281: } 4282: 4283: stepsize=(int) (stepm+YEARM-1)/YEARM; 4284: if (stepm<=12) stepsize=1; 4285: if(estepm < stepm){ 4286: printf ("Problem %d lower than %d\n",estepm, stepm); 4287: } 4288: else hstepm=estepm; 4289: 4290: hstepm=hstepm/stepm; 4291: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and 4292: fractional in yp1 */ 4293: anprojmean=yp; 4294: yp2=modf((yp1*12),&yp); 4295: mprojmean=yp; 4296: yp1=modf((yp2*30.5),&yp); 4297: jprojmean=yp; 4298: if(jprojmean==0) jprojmean=1; 4299: if(mprojmean==0) jprojmean=1; 4300: 4301: i1=cptcoveff; 4302: if (cptcovn < 1){i1=1;} 4303: 4304: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 4305: 4306: fprintf(ficresf,"#****** Routine prevforecast **\n"); 4307: 4308: /* if (h==(int)(YEARM*yearp)){ */ 4309: for(cptcov=1, k=0;cptcov<=i1;cptcov++){ 4310: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ 4311: k=k+1; 4312: fprintf(ficresf,"\n#******"); 4313: for(j=1;j<=cptcoveff;j++) { 4314: 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]]); 4315: } 4316: fprintf(ficresf,"******\n"); 4317: fprintf(ficresf,"# Covariate valuofcovar yearproj age"); 4318: for(j=1; j<=nlstate+ndeath;j++){ 4319: for(i=1; i<=nlstate;i++) 4320: fprintf(ficresf," p%d%d",i,j); 4321: fprintf(ficresf," p.%d",j); 4322: } 4323: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 4324: fprintf(ficresf,"\n"); 4325: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp); 4326: 4327: for (agec=fage; agec>=(ageminpar-1); agec--){ 4328: nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 4329: nhstepm = nhstepm/hstepm; 4330: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 4331: oldm=oldms;savm=savms; 4332: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k); 4333: 4334: for (h=0; h<=nhstepm; h++){ 4335: if (h*hstepm/YEARM*stepm ==yearp) { 4336: fprintf(ficresf,"\n"); 4337: for(j=1;j<=cptcoveff;j++) 4338: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 4339: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm); 4340: } 4341: for(j=1; j<=nlstate+ndeath;j++) { 4342: ppij=0.; 4343: for(i=1; i<=nlstate;i++) { 4344: if (mobilav==1) 4345: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod]; 4346: else { 4347: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod]; 4348: } 4349: if (h*hstepm/YEARM*stepm== yearp) { 4350: fprintf(ficresf," %.3f", p3mat[i][j][h]); 4351: } 4352: } /* end i */ 4353: if (h*hstepm/YEARM*stepm==yearp) { 4354: fprintf(ficresf," %.3f", ppij); 4355: } 4356: }/* end j */ 4357: } /* end h */ 4358: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 4359: } /* end agec */ 4360: } /* end yearp */ 4361: } /* end cptcod */ 4362: } /* end cptcov */ 4363: 4364: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 4365: 4366: fclose(ficresf); 4367: } 4368: 4369: /************** Forecasting *****not tested NB*************/ 4370: 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){ 4371: 4372: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; 4373: int *popage; 4374: double calagedatem, agelim, kk1, kk2; 4375: double *popeffectif,*popcount; 4376: double ***p3mat,***tabpop,***tabpopprev; 4377: double ***mobaverage; 4378: char filerespop[FILENAMELENGTH]; 4379: 4380: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 4381: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 4382: agelim=AGESUP; 4383: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; 4384: 4385: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); 4386: 4387: 4388: strcpy(filerespop,"pop"); 4389: strcat(filerespop,fileres); 4390: if((ficrespop=fopen(filerespop,"w"))==NULL) { 4391: printf("Problem with forecast resultfile: %s\n", filerespop); 4392: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); 4393: } 4394: printf("Computing forecasting: result on file '%s' \n", filerespop); 4395: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); 4396: 4397: if (cptcoveff==0) ncodemax[cptcoveff]=1; 4398: 4399: if (mobilav!=0) { 4400: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 4401: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ 4402: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); 4403: printf(" Error in movingaverage mobilav=%d\n",mobilav); 4404: } 4405: } 4406: 4407: stepsize=(int) (stepm+YEARM-1)/YEARM; 4408: if (stepm<=12) stepsize=1; 4409: 4410: agelim=AGESUP; 4411: 4412: hstepm=1; 4413: hstepm=hstepm/stepm; 4414: 4415: if (popforecast==1) { 4416: if((ficpop=fopen(popfile,"r"))==NULL) { 4417: printf("Problem with population file : %s\n",popfile);exit(0); 4418: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); 4419: } 4420: popage=ivector(0,AGESUP); 4421: popeffectif=vector(0,AGESUP); 4422: popcount=vector(0,AGESUP); 4423: 4424: i=1; 4425: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; 4426: 4427: imx=i; 4428: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i]; 4429: } 4430: 4431: for(cptcov=1,k=0;cptcov<=i2;cptcov++){ 4432: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ 4433: k=k+1; 4434: fprintf(ficrespop,"\n#******"); 4435: for(j=1;j<=cptcoveff;j++) { 4436: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 4437: } 4438: fprintf(ficrespop,"******\n"); 4439: fprintf(ficrespop,"# Age"); 4440: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j); 4441: if (popforecast==1) fprintf(ficrespop," [Population]"); 4442: 4443: for (cpt=0; cpt<=0;cpt++) { 4444: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); 4445: 4446: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 4447: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 4448: nhstepm = nhstepm/hstepm; 4449: 4450: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 4451: oldm=oldms;savm=savms; 4452: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); 4453: 4454: for (h=0; h<=nhstepm; h++){ 4455: if (h==(int) (calagedatem+YEARM*cpt)) { 4456: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); 4457: } 4458: for(j=1; j<=nlstate+ndeath;j++) { 4459: kk1=0.;kk2=0; 4460: for(i=1; i<=nlstate;i++) { 4461: if (mobilav==1) 4462: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; 4463: else { 4464: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; 4465: } 4466: } 4467: if (h==(int)(calagedatem+12*cpt)){ 4468: tabpop[(int)(agedeb)][j][cptcod]=kk1; 4469: /*fprintf(ficrespop," %.3f", kk1); 4470: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/ 4471: } 4472: } 4473: for(i=1; i<=nlstate;i++){ 4474: kk1=0.; 4475: for(j=1; j<=nlstate;j++){ 4476: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 4477: } 4478: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)]; 4479: } 4480: 4481: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 4482: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); 4483: } 4484: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 4485: } 4486: } 4487: 4488: /******/ 4489: 4490: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 4491: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); 4492: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 4493: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 4494: nhstepm = nhstepm/hstepm; 4495: 4496: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 4497: oldm=oldms;savm=savms; 4498: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); 4499: for (h=0; h<=nhstepm; h++){ 4500: if (h==(int) (calagedatem+YEARM*cpt)) { 4501: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); 4502: } 4503: for(j=1; j<=nlstate+ndeath;j++) { 4504: kk1=0.;kk2=0; 4505: for(i=1; i<=nlstate;i++) { 4506: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod]; 4507: } 4508: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1); 4509: } 4510: } 4511: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 4512: } 4513: } 4514: } 4515: } 4516: 4517: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 4518: 4519: if (popforecast==1) { 4520: free_ivector(popage,0,AGESUP); 4521: free_vector(popeffectif,0,AGESUP); 4522: free_vector(popcount,0,AGESUP); 4523: } 4524: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 4525: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 4526: fclose(ficrespop); 4527: } /* End of popforecast */ 4528: 4529: int fileappend(FILE *fichier, char *optionfich) 4530: { 4531: if((fichier=fopen(optionfich,"a"))==NULL) { 4532: printf("Problem with file: %s\n", optionfich); 4533: fprintf(ficlog,"Problem with file: %s\n", optionfich); 4534: return (0); 4535: } 4536: fflush(fichier); 4537: return (1); 4538: } 4539: 4540: 4541: /**************** function prwizard **********************/ 4542: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo) 4543: { 4544: 4545: /* Wizard to print covariance matrix template */ 4546: 4547: char ca[32], cb[32], cc[32]; 4548: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes; 4549: int numlinepar; 4550: 4551: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); 4552: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); 4553: for(i=1; i <=nlstate; i++){ 4554: jj=0; 4555: for(j=1; j <=nlstate+ndeath; j++){ 4556: if(j==i) continue; 4557: jj++; 4558: /*ca[0]= k+'a'-1;ca[1]='\0';*/ 4559: printf("%1d%1d",i,j); 4560: fprintf(ficparo,"%1d%1d",i,j); 4561: for(k=1; k<=ncovmodel;k++){ 4562: /* printf(" %lf",param[i][j][k]); */ 4563: /* fprintf(ficparo," %lf",param[i][j][k]); */ 4564: printf(" 0."); 4565: fprintf(ficparo," 0."); 4566: } 4567: printf("\n"); 4568: fprintf(ficparo,"\n"); 4569: } 4570: } 4571: printf("# Scales (for hessian or gradient estimation)\n"); 4572: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n"); 4573: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 4574: for(i=1; i <=nlstate; i++){ 4575: jj=0; 4576: for(j=1; j <=nlstate+ndeath; j++){ 4577: if(j==i) continue; 4578: jj++; 4579: fprintf(ficparo,"%1d%1d",i,j); 4580: printf("%1d%1d",i,j); 4581: fflush(stdout); 4582: for(k=1; k<=ncovmodel;k++){ 4583: /* printf(" %le",delti3[i][j][k]); */ 4584: /* fprintf(ficparo," %le",delti3[i][j][k]); */ 4585: printf(" 0."); 4586: fprintf(ficparo," 0."); 4587: } 4588: numlinepar++; 4589: printf("\n"); 4590: fprintf(ficparo,"\n"); 4591: } 4592: } 4593: printf("# Covariance matrix\n"); 4594: /* # 121 Var(a12)\n\ */ 4595: /* # 122 Cov(b12,a12) Var(b12)\n\ */ 4596: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */ 4597: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */ 4598: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */ 4599: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */ 4600: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */ 4601: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */ 4602: fflush(stdout); 4603: fprintf(ficparo,"# Covariance matrix\n"); 4604: /* # 121 Var(a12)\n\ */ 4605: /* # 122 Cov(b12,a12) Var(b12)\n\ */ 4606: /* # ...\n\ */ 4607: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */ 4608: 4609: for(itimes=1;itimes<=2;itimes++){ 4610: jj=0; 4611: for(i=1; i <=nlstate; i++){ 4612: for(j=1; j <=nlstate+ndeath; j++){ 4613: if(j==i) continue; 4614: for(k=1; k<=ncovmodel;k++){ 4615: jj++; 4616: ca[0]= k+'a'-1;ca[1]='\0'; 4617: if(itimes==1){ 4618: printf("#%1d%1d%d",i,j,k); 4619: fprintf(ficparo,"#%1d%1d%d",i,j,k); 4620: }else{ 4621: printf("%1d%1d%d",i,j,k); 4622: fprintf(ficparo,"%1d%1d%d",i,j,k); 4623: /* printf(" %.5le",matcov[i][j]); */ 4624: } 4625: ll=0; 4626: for(li=1;li <=nlstate; li++){ 4627: for(lj=1;lj <=nlstate+ndeath; lj++){ 4628: if(lj==li) continue; 4629: for(lk=1;lk<=ncovmodel;lk++){ 4630: ll++; 4631: if(ll<=jj){ 4632: cb[0]= lk +'a'-1;cb[1]='\0'; 4633: if(ll<jj){ 4634: if(itimes==1){ 4635: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj); 4636: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj); 4637: }else{ 4638: printf(" 0."); 4639: fprintf(ficparo," 0."); 4640: } 4641: }else{ 4642: if(itimes==1){ 4643: printf(" Var(%s%1d%1d)",ca,i,j); 4644: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j); 4645: }else{ 4646: printf(" 0."); 4647: fprintf(ficparo," 0."); 4648: } 4649: } 4650: } 4651: } /* end lk */ 4652: } /* end lj */ 4653: } /* end li */ 4654: printf("\n"); 4655: fprintf(ficparo,"\n"); 4656: numlinepar++; 4657: } /* end k*/ 4658: } /*end j */ 4659: } /* end i */ 4660: } /* end itimes */ 4661: 4662: } /* end of prwizard */ 4663: /******************* Gompertz Likelihood ******************************/ 4664: double gompertz(double x[]) 4665: { 4666: double A,B,L=0.0,sump=0.,num=0.; 4667: int i,n=0; /* n is the size of the sample */ 4668: 4669: for (i=0;i<=imx-1 ; i++) { 4670: sump=sump+weight[i]; 4671: /* sump=sump+1;*/ 4672: num=num+1; 4673: } 4674: 4675: 4676: /* for (i=0; i<=imx; i++) 4677: 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]);*/ 4678: 4679: for (i=1;i<=imx ; i++) 4680: { 4681: if (cens[i] == 1 && wav[i]>1) 4682: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp))); 4683: 4684: if (cens[i] == 0 && wav[i]>1) 4685: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp))) 4686: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM); 4687: 4688: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */ 4689: if (wav[i] > 1 ) { /* ??? */ 4690: L=L+A*weight[i]; 4691: /* 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]);*/ 4692: } 4693: } 4694: 4695: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/ 4696: 4697: return -2*L*num/sump; 4698: } 4699: 4700: #ifdef GSL 4701: /******************* Gompertz_f Likelihood ******************************/ 4702: double gompertz_f(const gsl_vector *v, void *params) 4703: { 4704: double A,B,LL=0.0,sump=0.,num=0.; 4705: double *x= (double *) v->data; 4706: int i,n=0; /* n is the size of the sample */ 4707: 4708: for (i=0;i<=imx-1 ; i++) { 4709: sump=sump+weight[i]; 4710: /* sump=sump+1;*/ 4711: num=num+1; 4712: } 4713: 4714: 4715: /* for (i=0; i<=imx; i++) 4716: 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]);*/ 4717: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]); 4718: for (i=1;i<=imx ; i++) 4719: { 4720: if (cens[i] == 1 && wav[i]>1) 4721: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp))); 4722: 4723: if (cens[i] == 0 && wav[i]>1) 4724: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp))) 4725: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM); 4726: 4727: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */ 4728: if (wav[i] > 1 ) { /* ??? */ 4729: LL=LL+A*weight[i]; 4730: /* 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]);*/ 4731: } 4732: } 4733: 4734: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/ 4735: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump); 4736: 4737: return -2*LL*num/sump; 4738: } 4739: #endif 4740: 4741: /******************* Printing html file ***********/ 4742: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \ 4743: int lastpass, int stepm, int weightopt, char model[],\ 4744: int imx, double p[],double **matcov,double agemortsup){ 4745: int i,k; 4746: 4747: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets): "); 4748: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year ",p[1],p[2],agegomp); 4749: for (i=1;i<=2;i++) 4750: fprintf(fichtm," p[%d] = %lf [%f ; %f] \n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i])); 4751: fprintf(fichtm," <img src=\"graphmort.png\">"); 4752: fprintf(fichtm,"</ul>"); 4753: 4754: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n "); 4755: 4756: 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> "); 4757: 4758: for (k=agegomp;k<(agemortsup-2);k++) 4759: fprintf(fichtm,"%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]); 4760: 4761: 4762: fflush(fichtm); 4763: } 4764: 4765: /******************* Gnuplot file **************/ 4766: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){ 4767: 4768: char dirfileres[132],optfileres[132]; 4769: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l; 4770: int ng; 4771: 4772: 4773: /*#ifdef windows */ 4774: fprintf(ficgp,"cd \"%s\" \n",pathc); 4775: /*#endif */ 4776: 4777: 4778: strcpy(dirfileres,optionfilefiname); 4779: strcpy(optfileres,"vpl"); 4780: fprintf(ficgp,"set out \"graphmort.png\"\n "); 4781: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 4782: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n"); 4783: /* fprintf(ficgp, "set size 0.65,0.65\n"); */ 4784: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp); 4785: 4786: } 4787: 4788: int readdata(char datafile[], int firstobs, int lastobs, int *imax) 4789: { 4790: 4791: /*-------- data file ----------*/ 4792: FILE *fic; 4793: char dummy[]=" "; 4794: int i, j, n; 4795: int linei, month, year,iout; 4796: char line[MAXLINE], linetmp[MAXLINE]; 4797: char stra[80], strb[80]; 4798: char *stratrunc; 4799: int lstra; 4800: 4801: 4802: if((fic=fopen(datafile,"r"))==NULL) { 4803: printf("Problem while opening datafile: %s\n", datafile);return 1; 4804: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1; 4805: } 4806: 4807: i=1; 4808: linei=0; 4809: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) { 4810: linei=linei+1; 4811: for(j=strlen(line); j>=0;j--){ /* Untabifies line */ 4812: if(line[j] == '\t') 4813: line[j] = ' '; 4814: } 4815: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){ 4816: ; 4817: }; 4818: line[j+1]=0; /* Trims blanks at end of line */ 4819: if(line[0]=='#'){ 4820: fprintf(ficlog,"Comment line\n%s\n",line); 4821: printf("Comment line\n%s\n",line); 4822: continue; 4823: } 4824: trimbb(linetmp,line); /* Trims multiple blanks in line */ 4825: for (j=0; line[j]!='\0';j++){ 4826: line[j]=linetmp[j]; 4827: } 4828: 4829: 4830: for (j=maxwav;j>=1;j--){ 4831: cutv(stra, strb, line, ' '); 4832: if(strb[0]=='.') { /* Missing status */ 4833: lval=-1; 4834: }else{ 4835: errno=0; 4836: lval=strtol(strb,&endptr,10); 4837: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/ 4838: if( strb[0]=='\0' || (*endptr != '\0')){ 4839: 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); 4840: 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); 4841: return 1; 4842: } 4843: } 4844: s[j][i]=lval; 4845: 4846: strcpy(line,stra); 4847: cutv(stra, strb,line,' '); 4848: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){ 4849: } 4850: else if(iout=sscanf(strb,"%s.",dummy) != 0){ 4851: month=99; 4852: year=9999; 4853: }else{ 4854: 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); 4855: 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); 4856: return 1; 4857: } 4858: anint[j][i]= (double) year; 4859: mint[j][i]= (double)month; 4860: strcpy(line,stra); 4861: } /* ENd Waves */ 4862: 4863: cutv(stra, strb,line,' '); 4864: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){ 4865: } 4866: else if(iout=sscanf(strb,"%s.",dummy) != 0){ 4867: month=99; 4868: year=9999; 4869: }else{ 4870: 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); 4871: 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); 4872: return 1; 4873: } 4874: andc[i]=(double) year; 4875: moisdc[i]=(double) month; 4876: strcpy(line,stra); 4877: 4878: cutv(stra, strb,line,' '); 4879: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){ 4880: } 4881: else if(iout=sscanf(strb,"%s.", dummy) != 0){ 4882: month=99; 4883: year=9999; 4884: }else{ 4885: 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); 4886: 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); 4887: return 1; 4888: } 4889: if (year==9999) { 4890: 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); 4891: 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); 4892: return 1; 4893: 4894: } 4895: annais[i]=(double)(year); 4896: moisnais[i]=(double)(month); 4897: strcpy(line,stra); 4898: 4899: cutv(stra, strb,line,' '); 4900: errno=0; 4901: dval=strtod(strb,&endptr); 4902: if( strb[0]=='\0' || (*endptr != '\0')){ 4903: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei); 4904: 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); 4905: fflush(ficlog); 4906: return 1; 4907: } 4908: weight[i]=dval; 4909: strcpy(line,stra); 4910: 4911: for (j=ncovcol;j>=1;j--){ 4912: cutv(stra, strb,line,' '); 4913: if(strb[0]=='.') { /* Missing status */ 4914: lval=-1; 4915: }else{ 4916: errno=0; 4917: lval=strtol(strb,&endptr,10); 4918: if( strb[0]=='\0' || (*endptr != '\0')){ 4919: 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); 4920: 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); 4921: return 1; 4922: } 4923: } 4924: if(lval <-1 || lval >1){ 4925: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \ 4926: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \ 4927: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \ 4928: For example, for multinomial values like 1, 2 and 3,\n \ 4929: build V1=0 V2=0 for the reference value (1),\n \ 4930: V1=1 V2=0 for (2) \n \ 4931: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \ 4932: output of IMaCh is often meaningless.\n \ 4933: Exiting.\n",lval,linei, i,line,j); 4934: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \ 4935: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \ 4936: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \ 4937: For example, for multinomial values like 1, 2 and 3,\n \ 4938: build V1=0 V2=0 for the reference value (1),\n \ 4939: V1=1 V2=0 for (2) \n \ 4940: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \ 4941: output of IMaCh is often meaningless.\n \ 4942: Exiting.\n",lval,linei, i,line,j);fflush(ficlog); 4943: return 1; 4944: } 4945: covar[j][i]=(double)(lval); 4946: strcpy(line,stra); 4947: } 4948: lstra=strlen(stra); 4949: 4950: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */ 4951: stratrunc = &(stra[lstra-9]); 4952: num[i]=atol(stratrunc); 4953: } 4954: else 4955: num[i]=atol(stra); 4956: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){ 4957: 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;}*/ 4958: 4959: i=i+1; 4960: } /* End loop reading data */ 4961: 4962: *imax=i-1; /* Number of individuals */ 4963: fclose(fic); 4964: 4965: return (0); 4966: endread: 4967: printf("Exiting readdata: "); 4968: fclose(fic); 4969: return (1); 4970: 4971: 4972: 4973: } 4974: void removespace(char *str) { 4975: char *p1 = str, *p2 = str; 4976: do 4977: while (*p2 == ' ') 4978: p2++; 4979: while (*p1++ = *p2++); 4980: } 4981: 4982: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns: 4983: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age 4984: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 4985: * - cptcovn or number of covariates k of the models excluding age*products =6 4986: * - cptcovage number of covariates with age*products =2 4987: * - cptcovs number of simple covariates 4988: * - 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 4989: * which is a new column after the 9 (ncovcol) variables. 4990: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual 4991: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage 4992: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6. 4993: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 . 4994: */ 4995: { 4996: int i, j, k, ks; 4997: int i1, j1, k1, k2; 4998: char modelsav[80]; 4999: char stra[80], strb[80], strc[80], strd[80],stre[80]; 5000: 5001: /*removespace(model);*/ 5002: if (strlen(model) >1){ /* If there is at least 1 covariate */ 5003: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0; 5004: j=nbocc(model,'+'); /**< j=Number of '+' */ 5005: j1=nbocc(model,'*'); /**< j1=Number of '*' */ 5006: cptcovs=j+1-j1; /**< Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2 */ 5007: cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/ 5008: /* including age products which are counted in cptcovage. 5009: /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */ 5010: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */ 5011: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */ 5012: strcpy(modelsav,model); 5013: if (strstr(model,"AGE") !=0){ 5014: printf("Error. AGE must be in lower case 'age' model=%s ",model); 5015: fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog); 5016: return 1; 5017: } 5018: if (strstr(model,"v") !=0){ 5019: printf("Error. 'v' must be in upper case 'V' model=%s ",model); 5020: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog); 5021: return 1; 5022: } 5023: 5024: /* Design 5025: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight 5026: * < ncovcol=8 > 5027: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 5028: * k= 1 2 3 4 5 6 7 8 5029: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8 5030: * covar[k,i], value of kth covariate if not including age for individual i: 5031: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8) 5032: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8 5033: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 5034: * Tage[++cptcovage]=k 5035: * if products, new covar are created after ncovcol with k1 5036: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11 5037: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product 5038: * 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 5039: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2]; 5040: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted 5041: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11 5042: * < ncovcol=8 > 5043: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2 5044: * k= 1 2 3 4 5 6 7 8 9 10 11 12 5045: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8 5046: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6} 5047: * p Tprod[1]@2={ 6, 5} 5048: *p Tvard[1][1]@4= {7, 8, 5, 6} 5049: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8 5050: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; 5051: *How to reorganize? 5052: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age 5053: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6} 5054: * {2, 1, 4, 8, 5, 6, 3, 7} 5055: * Struct [] 5056: */ 5057: 5058: /* This loop fills the array Tvar from the string 'model'.*/ 5059: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */ 5060: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */ 5061: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */ 5062: /* k=3 V4 Tvar[k=3]= 4 (from V4) */ 5063: /* k=2 V1 Tvar[k=2]= 1 (from V1) */ 5064: /* k=1 Tvar[1]=2 (from V2) */ 5065: /* k=5 Tvar[5] */ 5066: /* for (k=1; k<=cptcovn;k++) { */ 5067: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */ 5068: /* } */ 5069: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */ 5070: /* 5071: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */ 5072: for(k=cptcovt; k>=1;k--) /**< Number of covariates */ 5073: Tvar[k]=0; 5074: cptcovage=0; 5075: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */ 5076: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 5077: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 5078: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */ 5079: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/ 5080: /*scanf("%d",i);*/ 5081: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */ 5082: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */ 5083: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */ 5084: /* covar is not filled and then is empty */ 5085: cptcovprod--; 5086: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */ 5087: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */ 5088: cptcovage++; /* Sums the number of covariates which include age as a product */ 5089: Tage[cptcovage]=k; /* Tage[1] = 4 */ 5090: /*printf("stre=%s ", stre);*/ 5091: } else if (strcmp(strd,"age")==0) { /* or age*Vn */ 5092: cptcovprod--; 5093: cutl(stre,strb,strc,'V'); 5094: Tvar[k]=atoi(stre); 5095: cptcovage++; 5096: Tage[cptcovage]=k; 5097: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/ 5098: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */ 5099: cptcovn++; 5100: cptcovprodnoage++;k1++; 5101: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/ 5102: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but 5103: because this model-covariate is a construction we invent a new column 5104: ncovcol + k1 5105: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2 5106: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */ 5107: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */ 5108: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */ 5109: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/ 5110: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/ 5111: k2=k2+2; 5112: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */ 5113: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */ 5114: for (i=1; i<=lastobs;i++){ 5115: /* Computes the new covariate which is a product of 5116: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */ 5117: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i]; 5118: } 5119: } /* End age is not in the model */ 5120: } /* End if model includes a product */ 5121: else { /* no more sum */ 5122: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/ 5123: /* scanf("%d",i);*/ 5124: cutl(strd,strc,strb,'V'); 5125: ks++; /**< Number of simple covariates */ 5126: cptcovn++; 5127: Tvar[k]=atoi(strd); 5128: } 5129: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 5130: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav); 5131: scanf("%d",i);*/ 5132: } /* end of loop + */ 5133: } /* end model */ 5134: 5135: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products. 5136: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/ 5137: 5138: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]); 5139: printf("cptcovprod=%d ", cptcovprod); 5140: fprintf(ficlog,"cptcovprod=%d ", cptcovprod); 5141: 5142: scanf("%d ",i);*/ 5143: 5144: 5145: return (0); /* with covar[new additional covariate if product] and Tage if age */ 5146: endread: 5147: printf("Exiting decodemodel: "); 5148: return (1); 5149: } 5150: 5151: calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn ) 5152: { 5153: int i, m; 5154: 5155: for (i=1; i<=imx; i++) { 5156: for(m=2; (m<= maxwav); m++) { 5157: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){ 5158: anint[m][i]=9999; 5159: s[m][i]=-1; 5160: } 5161: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){ 5162: *nberr++; 5163: 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); 5164: 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); 5165: s[m][i]=-1; 5166: } 5167: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){ 5168: *nberr++; 5169: 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]); 5170: 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]); 5171: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */ 5172: } 5173: } 5174: } 5175: 5176: for (i=1; i<=imx; i++) { 5177: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]); 5178: for(m=firstpass; (m<= lastpass); m++){ 5179: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){ 5180: if (s[m][i] >= nlstate+1) { 5181: if(agedc[i]>0) 5182: if((int)moisdc[i]!=99 && (int)andc[i]!=9999) 5183: agev[m][i]=agedc[i]; 5184: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/ 5185: else { 5186: if ((int)andc[i]!=9999){ 5187: nbwarn++; 5188: printf("Warning negative age at death: %ld line:%d\n",num[i],i); 5189: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i); 5190: agev[m][i]=-1; 5191: } 5192: } 5193: } 5194: else if(s[m][i] !=9){ /* Standard case, age in fractional 5195: years but with the precision of a month */ 5196: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]); 5197: if((int)mint[m][i]==99 || (int)anint[m][i]==9999) 5198: agev[m][i]=1; 5199: else if(agev[m][i] < *agemin){ 5200: *agemin=agev[m][i]; 5201: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin); 5202: } 5203: else if(agev[m][i] >*agemax){ 5204: *agemax=agev[m][i]; 5205: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/ 5206: } 5207: /*agev[m][i]=anint[m][i]-annais[i];*/ 5208: /* agev[m][i] = age[i]+2*m;*/ 5209: } 5210: else { /* =9 */ 5211: agev[m][i]=1; 5212: s[m][i]=-1; 5213: } 5214: } 5215: else /*= 0 Unknown */ 5216: agev[m][i]=1; 5217: } 5218: 5219: } 5220: for (i=1; i<=imx; i++) { 5221: for(m=firstpass; (m<=lastpass); m++){ 5222: if (s[m][i] > (nlstate+ndeath)) { 5223: *nberr++; 5224: 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); 5225: 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); 5226: return 1; 5227: } 5228: } 5229: } 5230: 5231: /*for (i=1; i<=imx; i++){ 5232: for (m=firstpass; (m<lastpass); m++){ 5233: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]); 5234: } 5235: 5236: }*/ 5237: 5238: 5239: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 5240: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 5241: 5242: return (0); 5243: endread: 5244: printf("Exiting calandcheckages: "); 5245: return (1); 5246: } 5247: 5248: 5249: /***********************************************/ 5250: /**************** Main Program *****************/ 5251: /***********************************************/ 5252: 5253: int main(int argc, char *argv[]) 5254: { 5255: #ifdef GSL 5256: const gsl_multimin_fminimizer_type *T; 5257: size_t iteri = 0, it; 5258: int rval = GSL_CONTINUE; 5259: int status = GSL_SUCCESS; 5260: double ssval; 5261: #endif 5262: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav); 5263: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod; 5264: int linei, month, year,iout; 5265: int jj, ll, li, lj, lk, imk; 5266: int numlinepar=0; /* Current linenumber of parameter file */ 5267: int itimes; 5268: int NDIM=2; 5269: int vpopbased=0; 5270: 5271: char ca[32], cb[32], cc[32]; 5272: /* FILE *fichtm; *//* Html File */ 5273: /* FILE *ficgp;*/ /*Gnuplot File */ 5274: struct stat info; 5275: double agedeb, agefin,hf; 5276: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20; 5277: 5278: double fret; 5279: double **xi,tmp,delta; 5280: 5281: double dum; /* Dummy variable */ 5282: double ***p3mat; 5283: double ***mobaverage; 5284: int *indx; 5285: char line[MAXLINE], linepar[MAXLINE]; 5286: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE]; 5287: char pathr[MAXLINE], pathimach[MAXLINE]; 5288: char **bp, *tok, *val; /* pathtot */ 5289: int firstobs=1, lastobs=10; 5290: int sdeb, sfin; /* Status at beginning and end */ 5291: int c, h , cpt,l; 5292: int ju,jl, mi; 5293: int i1,j1, jk,aa,bb, stepsize, ij; 5294: int jnais,jdc,jint4,jint1,jint2,jint3,*tab; 5295: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */ 5296: int mobilav=0,popforecast=0; 5297: int hstepm, nhstepm; 5298: int agemortsup; 5299: float sumlpop=0.; 5300: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000; 5301: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000; 5302: 5303: double bage, fage, age, agelim, agebase; 5304: double ftolpl=FTOL; 5305: double **prlim; 5306: double ***param; /* Matrix of parameters */ 5307: double *p; 5308: double **matcov; /* Matrix of covariance */ 5309: double ***delti3; /* Scale */ 5310: double *delti; /* Scale */ 5311: double ***eij, ***vareij; 5312: double **varpl; /* Variances of prevalence limits by age */ 5313: double *epj, vepp; 5314: double kk1, kk2; 5315: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000; 5316: double **ximort; 5317: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234"; 5318: int *dcwave; 5319: 5320: char z[1]="c", occ; 5321: 5322: /*char *strt;*/ 5323: char strtend[80]; 5324: 5325: long total_usecs; 5326: 5327: /* setlocale (LC_ALL, ""); */ 5328: /* bindtextdomain (PACKAGE, LOCALEDIR); */ 5329: /* textdomain (PACKAGE); */ 5330: /* setlocale (LC_CTYPE, ""); */ 5331: /* setlocale (LC_MESSAGES, ""); */ 5332: 5333: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */ 5334: rstart_time = time(NULL); 5335: /* (void) gettimeofday(&start_time,&tzp);*/ 5336: start_time = *localtime(&rstart_time); 5337: curr_time=start_time; 5338: /*tml = *localtime(&start_time.tm_sec);*/ 5339: /* strcpy(strstart,asctime(&tml)); */ 5340: strcpy(strstart,asctime(&start_time)); 5341: 5342: /* printf("Localtime (at start)=%s",strstart); */ 5343: /* tp.tm_sec = tp.tm_sec +86400; */ 5344: /* tm = *localtime(&start_time.tm_sec); */ 5345: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */ 5346: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */ 5347: /* tmg.tm_hour=tmg.tm_hour + 1; */ 5348: /* tp.tm_sec = mktime(&tmg); */ 5349: /* strt=asctime(&tmg); */ 5350: /* printf("Time(after) =%s",strstart); */ 5351: /* (void) time (&time_value); 5352: * printf("time=%d,t-=%d\n",time_value,time_value-86400); 5353: * tm = *localtime(&time_value); 5354: * strstart=asctime(&tm); 5355: * printf("tim_value=%d,asctime=%s\n",time_value,strstart); 5356: */ 5357: 5358: nberr=0; /* Number of errors and warnings */ 5359: nbwarn=0; 5360: getcwd(pathcd, size); 5361: 5362: printf("\n%s\n%s",version,fullversion); 5363: if(argc <=1){ 5364: printf("\nEnter the parameter file name: "); 5365: fgets(pathr,FILENAMELENGTH,stdin); 5366: i=strlen(pathr); 5367: if(pathr[i-1]=='\n') 5368: pathr[i-1]='\0'; 5369: i=strlen(pathr); 5370: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */ 5371: pathr[i-1]='\0'; 5372: for (tok = pathr; tok != NULL; ){ 5373: printf("Pathr |%s|\n",pathr); 5374: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0'); 5375: printf("val= |%s| pathr=%s\n",val,pathr); 5376: strcpy (pathtot, val); 5377: if(pathr[0] == '\0') break; /* Dirty */ 5378: } 5379: } 5380: else{ 5381: strcpy(pathtot,argv[1]); 5382: } 5383: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/ 5384: /*cygwin_split_path(pathtot,path,optionfile); 5385: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/ 5386: /* cutv(path,optionfile,pathtot,'\\');*/ 5387: 5388: /* Split argv[0], imach program to get pathimach */ 5389: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]); 5390: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname); 5391: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname); 5392: /* strcpy(pathimach,argv[0]); */ 5393: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */ 5394: split(pathtot,path,optionfile,optionfilext,optionfilefiname); 5395: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname); 5396: chdir(path); /* Can be a relative path */ 5397: if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */ 5398: printf("Current directory %s!\n",pathcd); 5399: strcpy(command,"mkdir "); 5400: strcat(command,optionfilefiname); 5401: if((outcmd=system(command)) != 0){ 5402: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd); 5403: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */ 5404: /* fclose(ficlog); */ 5405: /* exit(1); */ 5406: } 5407: /* if((imk=mkdir(optionfilefiname))<0){ */ 5408: /* perror("mkdir"); */ 5409: /* } */ 5410: 5411: /*-------- arguments in the command line --------*/ 5412: 5413: /* Log file */ 5414: strcat(filelog, optionfilefiname); 5415: strcat(filelog,".log"); /* */ 5416: if((ficlog=fopen(filelog,"w"))==NULL) { 5417: printf("Problem with logfile %s\n",filelog); 5418: goto end; 5419: } 5420: fprintf(ficlog,"Log filename:%s\n",filelog); 5421: fprintf(ficlog,"\n%s\n%s",version,fullversion); 5422: fprintf(ficlog,"\nEnter the parameter file name: \n"); 5423: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\ 5424: path=%s \n\ 5425: optionfile=%s\n\ 5426: optionfilext=%s\n\ 5427: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname); 5428: 5429: printf("Local time (at start):%s",strstart); 5430: fprintf(ficlog,"Local time (at start): %s",strstart); 5431: fflush(ficlog); 5432: /* (void) gettimeofday(&curr_time,&tzp); */ 5433: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */ 5434: 5435: /* */ 5436: strcpy(fileres,"r"); 5437: strcat(fileres, optionfilefiname); 5438: strcat(fileres,".txt"); /* Other files have txt extension */ 5439: 5440: /*---------arguments file --------*/ 5441: 5442: if((ficpar=fopen(optionfile,"r"))==NULL) { 5443: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno)); 5444: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno)); 5445: fflush(ficlog); 5446: /* goto end; */ 5447: exit(70); 5448: } 5449: 5450: 5451: 5452: strcpy(filereso,"o"); 5453: strcat(filereso,fileres); 5454: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */ 5455: printf("Problem with Output resultfile: %s\n", filereso); 5456: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso); 5457: fflush(ficlog); 5458: goto end; 5459: } 5460: 5461: /* Reads comments: lines beginning with '#' */ 5462: numlinepar=0; 5463: while((c=getc(ficpar))=='#' && c!= EOF){ 5464: ungetc(c,ficpar); 5465: fgets(line, MAXLINE, ficpar); 5466: numlinepar++; 5467: fputs(line,stdout); 5468: fputs(line,ficparo); 5469: fputs(line,ficlog); 5470: } 5471: ungetc(c,ficpar); 5472: 5473: 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); 5474: numlinepar++; 5475: 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); 5476: 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); 5477: 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); 5478: fflush(ficlog); 5479: while((c=getc(ficpar))=='#' && c!= EOF){ 5480: ungetc(c,ficpar); 5481: fgets(line, MAXLINE, ficpar); 5482: numlinepar++; 5483: fputs(line, stdout); 5484: //puts(line); 5485: fputs(line,ficparo); 5486: fputs(line,ficlog); 5487: } 5488: ungetc(c,ficpar); 5489: 5490: 5491: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */ 5492: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/ 5493: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5 5494: v1+v2*age+v2*v3 makes cptcovn = 3 5495: */ 5496: if (strlen(model)>1) 5497: 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*/ 5498: else 5499: ncovmodel=2; 5500: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */ 5501: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */ 5502: npar= nforce*ncovmodel; /* Number of parameters like aij*/ 5503: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){ 5504: 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); 5505: 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); 5506: fflush(stdout); 5507: fclose (ficlog); 5508: goto end; 5509: } 5510: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); 5511: delti=delti3[1][1]; 5512: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/ 5513: if(mle==-1){ /* Print a wizard for help writing covariance matrix */ 5514: prwizard(ncovmodel, nlstate, ndeath, model, ficparo); 5515: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso); 5516: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso); 5517: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 5518: fclose (ficparo); 5519: fclose (ficlog); 5520: goto end; 5521: exit(0); 5522: } 5523: else if(mle==-3) { 5524: prwizard(ncovmodel, nlstate, ndeath, model, ficparo); 5525: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso); 5526: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso); 5527: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); 5528: matcov=matrix(1,npar,1,npar); 5529: } 5530: else{ 5531: /* Read guessed parameters */ 5532: /* Reads comments: lines beginning with '#' */ 5533: while((c=getc(ficpar))=='#' && c!= EOF){ 5534: ungetc(c,ficpar); 5535: fgets(line, MAXLINE, ficpar); 5536: numlinepar++; 5537: fputs(line,stdout); 5538: fputs(line,ficparo); 5539: fputs(line,ficlog); 5540: } 5541: ungetc(c,ficpar); 5542: 5543: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); 5544: for(i=1; i <=nlstate; i++){ 5545: j=0; 5546: for(jj=1; jj <=nlstate+ndeath; jj++){ 5547: if(jj==i) continue; 5548: j++; 5549: fscanf(ficpar,"%1d%1d",&i1,&j1); 5550: if ((i1 != i) && (j1 != j)){ 5551: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \ 5552: It might be a problem of design; if ncovcol and the model are correct\n \ 5553: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1); 5554: exit(1); 5555: } 5556: fprintf(ficparo,"%1d%1d",i1,j1); 5557: if(mle==1) 5558: printf("%1d%1d",i,j); 5559: fprintf(ficlog,"%1d%1d",i,j); 5560: for(k=1; k<=ncovmodel;k++){ 5561: fscanf(ficpar," %lf",&param[i][j][k]); 5562: if(mle==1){ 5563: printf(" %lf",param[i][j][k]); 5564: fprintf(ficlog," %lf",param[i][j][k]); 5565: } 5566: else 5567: fprintf(ficlog," %lf",param[i][j][k]); 5568: fprintf(ficparo," %lf",param[i][j][k]); 5569: } 5570: fscanf(ficpar,"\n"); 5571: numlinepar++; 5572: if(mle==1) 5573: printf("\n"); 5574: fprintf(ficlog,"\n"); 5575: fprintf(ficparo,"\n"); 5576: } 5577: } 5578: fflush(ficlog); 5579: 5580: /* Reads scales values */ 5581: p=param[1][1]; 5582: 5583: /* Reads comments: lines beginning with '#' */ 5584: while((c=getc(ficpar))=='#' && c!= EOF){ 5585: ungetc(c,ficpar); 5586: fgets(line, MAXLINE, ficpar); 5587: numlinepar++; 5588: fputs(line,stdout); 5589: fputs(line,ficparo); 5590: fputs(line,ficlog); 5591: } 5592: ungetc(c,ficpar); 5593: 5594: for(i=1; i <=nlstate; i++){ 5595: for(j=1; j <=nlstate+ndeath-1; j++){ 5596: fscanf(ficpar,"%1d%1d",&i1,&j1); 5597: if ((i1-i)*(j1-j)!=0){ 5598: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1); 5599: exit(1); 5600: } 5601: printf("%1d%1d",i,j); 5602: fprintf(ficparo,"%1d%1d",i1,j1); 5603: fprintf(ficlog,"%1d%1d",i1,j1); 5604: for(k=1; k<=ncovmodel;k++){ 5605: fscanf(ficpar,"%le",&delti3[i][j][k]); 5606: printf(" %le",delti3[i][j][k]); 5607: fprintf(ficparo," %le",delti3[i][j][k]); 5608: fprintf(ficlog," %le",delti3[i][j][k]); 5609: } 5610: fscanf(ficpar,"\n"); 5611: numlinepar++; 5612: printf("\n"); 5613: fprintf(ficparo,"\n"); 5614: fprintf(ficlog,"\n"); 5615: } 5616: } 5617: fflush(ficlog); 5618: 5619: /* Reads covariance matrix */ 5620: delti=delti3[1][1]; 5621: 5622: 5623: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */ 5624: 5625: /* Reads comments: lines beginning with '#' */ 5626: while((c=getc(ficpar))=='#' && c!= EOF){ 5627: ungetc(c,ficpar); 5628: fgets(line, MAXLINE, ficpar); 5629: numlinepar++; 5630: fputs(line,stdout); 5631: fputs(line,ficparo); 5632: fputs(line,ficlog); 5633: } 5634: ungetc(c,ficpar); 5635: 5636: matcov=matrix(1,npar,1,npar); 5637: for(i=1; i <=npar; i++) 5638: for(j=1; j <=npar; j++) matcov[i][j]=0.; 5639: 5640: for(i=1; i <=npar; i++){ 5641: fscanf(ficpar,"%s",str); 5642: if(mle==1) 5643: printf("%s",str); 5644: fprintf(ficlog,"%s",str); 5645: fprintf(ficparo,"%s",str); 5646: for(j=1; j <=i; j++){ 5647: fscanf(ficpar," %le",&matcov[i][j]); 5648: if(mle==1){ 5649: printf(" %.5le",matcov[i][j]); 5650: } 5651: fprintf(ficlog," %.5le",matcov[i][j]); 5652: fprintf(ficparo," %.5le",matcov[i][j]); 5653: } 5654: fscanf(ficpar,"\n"); 5655: numlinepar++; 5656: if(mle==1) 5657: printf("\n"); 5658: fprintf(ficlog,"\n"); 5659: fprintf(ficparo,"\n"); 5660: } 5661: for(i=1; i <=npar; i++) 5662: for(j=i+1;j<=npar;j++) 5663: matcov[i][j]=matcov[j][i]; 5664: 5665: if(mle==1) 5666: printf("\n"); 5667: fprintf(ficlog,"\n"); 5668: 5669: fflush(ficlog); 5670: 5671: /*-------- Rewriting parameter file ----------*/ 5672: strcpy(rfileres,"r"); /* "Rparameterfile */ 5673: strcat(rfileres,optionfilefiname); /* Parameter file first name*/ 5674: strcat(rfileres,"."); /* */ 5675: strcat(rfileres,optionfilext); /* Other files have txt extension */ 5676: if((ficres =fopen(rfileres,"w"))==NULL) { 5677: printf("Problem writing new parameter file: %s\n", fileres);goto end; 5678: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end; 5679: } 5680: fprintf(ficres,"#%s\n",version); 5681: } /* End of mle != -3 */ 5682: 5683: 5684: n= lastobs; 5685: num=lvector(1,n); 5686: moisnais=vector(1,n); 5687: annais=vector(1,n); 5688: moisdc=vector(1,n); 5689: andc=vector(1,n); 5690: agedc=vector(1,n); 5691: cod=ivector(1,n); 5692: weight=vector(1,n); 5693: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */ 5694: mint=matrix(1,maxwav,1,n); 5695: anint=matrix(1,maxwav,1,n); 5696: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 5697: tab=ivector(1,NCOVMAX); 5698: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */ 5699: 5700: /* Reads data from file datafile */ 5701: if (readdata(datafile, firstobs, lastobs, &imx)==1) 5702: goto end; 5703: 5704: /* Calculation of the number of parameters from char model */ 5705: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 5706: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4 5707: k=3 V4 Tvar[k=3]= 4 (from V4) 5708: k=2 V1 Tvar[k=2]= 1 (from V1) 5709: k=1 Tvar[1]=2 (from V2) 5710: */ 5711: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */ 5712: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 5713: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 5714: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage. 5715: */ 5716: /* For model-covariate k tells which data-covariate to use but 5717: because this model-covariate is a construction we invent a new column 5718: ncovcol + k1 5719: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3 5720: Tvar[3=V1*V4]=4+1 etc */ 5721: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */ 5722: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3 5723: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2) 5724: */ 5725: Tvaraff=ivector(1,NCOVMAX); /* Unclear */ 5726: 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 5727: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 5728: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */ 5729: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age 5730: 4 covariates (3 plus signs) 5731: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3 5732: */ 5733: 5734: if(decodemodel(model, lastobs) == 1) 5735: goto end; 5736: 5737: if((double)(lastobs-imx)/(double)imx > 1.10){ 5738: nbwarn++; 5739: 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); 5740: 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); 5741: } 5742: /* if(mle==1){*/ 5743: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/ 5744: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */ 5745: } 5746: 5747: /*-calculation of age at interview from date of interview and age at death -*/ 5748: agev=matrix(1,maxwav,1,imx); 5749: 5750: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1) 5751: goto end; 5752: 5753: 5754: agegomp=(int)agemin; 5755: free_vector(moisnais,1,n); 5756: free_vector(annais,1,n); 5757: /* free_matrix(mint,1,maxwav,1,n); 5758: free_matrix(anint,1,maxwav,1,n);*/ 5759: free_vector(moisdc,1,n); 5760: free_vector(andc,1,n); 5761: /* */ 5762: 5763: wav=ivector(1,imx); 5764: dh=imatrix(1,lastpass-firstpass+1,1,imx); 5765: bh=imatrix(1,lastpass-firstpass+1,1,imx); 5766: mw=imatrix(1,lastpass-firstpass+1,1,imx); 5767: 5768: /* Concatenates waves */ 5769: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm); 5770: /* */ 5771: 5772: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */ 5773: 5774: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 5775: ncodemax[1]=1; 5776: Ndum =ivector(-1,NCOVMAX); 5777: if (ncovmodel > 2) 5778: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */ 5779: 5780: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */ 5781: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/ 5782: h=0; 5783: 5784: 5785: /*if (cptcovn > 0) */ 5786: 5787: 5788: m=pow(2,cptcoveff); 5789: 5790: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */ 5791: 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 */ 5792: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/ 5793: for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 5794: h++; 5795: if (h>m) 5796: h=1; 5797: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1 5798: * h 1 2 3 4 5799: *______________________________ 5800: * 1 i=1 1 i=1 1 i=1 1 i=1 1 5801: * 2 2 1 1 1 5802: * 3 i=2 1 2 1 1 5803: * 4 2 2 1 1 5804: * 5 i=3 1 i=2 1 2 1 5805: * 6 2 1 2 1 5806: * 7 i=4 1 2 2 1 5807: * 8 2 2 2 1 5808: * 9 i=5 1 i=3 1 i=2 1 1 5809: * 10 2 1 1 1 5810: * 11 i=6 1 2 1 1 5811: * 12 2 2 1 1 5812: * 13 i=7 1 i=4 1 2 1 5813: * 14 2 1 2 1 5814: * 15 i=8 1 2 2 1 5815: * 16 2 2 2 1 5816: */ 5817: codtab[h][k]=j; 5818: /*codtab[h][Tvar[k]]=j;*/ 5819: 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]]); 5820: } 5821: } 5822: } 5823: } 5824: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 5825: codtab[1][2]=1;codtab[2][2]=2; */ 5826: /* for(i=1; i <=m ;i++){ 5827: for(k=1; k <=cptcovn; k++){ 5828: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); 5829: } 5830: printf("\n"); 5831: } 5832: scanf("%d",i);*/ 5833: 5834: free_ivector(Ndum,-1,NCOVMAX); 5835: 5836: 5837: 5838: /*------------ gnuplot -------------*/ 5839: strcpy(optionfilegnuplot,optionfilefiname); 5840: if(mle==-3) 5841: strcat(optionfilegnuplot,"-mort"); 5842: strcat(optionfilegnuplot,".gp"); 5843: 5844: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) { 5845: printf("Problem with file %s",optionfilegnuplot); 5846: } 5847: else{ 5848: fprintf(ficgp,"\n# %s\n", version); 5849: fprintf(ficgp,"# %s\n", optionfilegnuplot); 5850: //fprintf(ficgp,"set missing 'NaNq'\n"); 5851: fprintf(ficgp,"set datafile missing 'NaNq'\n"); 5852: } 5853: /* fclose(ficgp);*/ 5854: /*--------- index.htm --------*/ 5855: 5856: strcpy(optionfilehtm,optionfilefiname); /* Main html file */ 5857: if(mle==-3) 5858: strcat(optionfilehtm,"-mort"); 5859: strcat(optionfilehtm,".htm"); 5860: if((fichtm=fopen(optionfilehtm,"w"))==NULL) { 5861: printf("Problem with %s \n",optionfilehtm); 5862: exit(0); 5863: } 5864: 5865: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */ 5866: strcat(optionfilehtmcov,"-cov.htm"); 5867: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) { 5868: printf("Problem with %s \n",optionfilehtmcov), exit(0); 5869: } 5870: else{ 5871: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body>%s %s \ 5872: <hr size=\"2\" color=\"#EC5E5E\"> \n\ 5873: Title=%s Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s \n",\ 5874: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model); 5875: } 5876: 5877: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body>%s %s \ 5878: <hr size=\"2\" color=\"#EC5E5E\"> \n\ 5879: Title=%s Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s \n\ 5880: \n\ 5881: <hr size=\"2\" color=\"#EC5E5E\">\ 5882: <ul><li><h4>Parameter files</h4>\n\ 5883: - Parameter file: <a href=\"%s.%s\">%s.%s</a> \n\ 5884: - Copy of the parameter file: <a href=\"o%s\">o%s</a> \n\ 5885: - Log file of the run: <a href=\"%s\">%s</a> \n\ 5886: - Gnuplot file name: <a href=\"%s\">%s</a> \n\ 5887: - Date and time at start: %s</ul>\n",\ 5888: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\ 5889: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\ 5890: fileres,fileres,\ 5891: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart); 5892: fflush(fichtm); 5893: 5894: strcpy(pathr,path); 5895: strcat(pathr,optionfilefiname); 5896: chdir(optionfilefiname); /* Move to directory named optionfile */ 5897: 5898: /* Calculates basic frequencies. Computes observed prevalence at single age 5899: and prints on file fileres'p'. */ 5900: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart); 5901: 5902: fprintf(fichtm,"\n"); 5903: fprintf(fichtm," Total number of observations=%d \n\ 5904: Youngest age at first (selected) pass %.2f, oldest age %.2f \n\ 5905: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf \n",\ 5906: imx,agemin,agemax,jmin,jmax,jmean); 5907: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ 5908: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ 5909: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ 5910: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ 5911: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */ 5912: 5913: 5914: /* For Powell, parameters are in a vector p[] starting at p[1] 5915: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */ 5916: p=param[1][1]; /* *(*(*(param +1)+1)+0) */ 5917: 5918: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/ 5919: 5920: if (mle==-3){ 5921: ximort=matrix(1,NDIM,1,NDIM); 5922: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */ 5923: cens=ivector(1,n); 5924: ageexmed=vector(1,n); 5925: agecens=vector(1,n); 5926: dcwave=ivector(1,n); 5927: 5928: for (i=1; i<=imx; i++){ 5929: dcwave[i]=-1; 5930: for (m=firstpass; m<=lastpass; m++) 5931: if (s[m][i]>nlstate) { 5932: dcwave[i]=m; 5933: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/ 5934: break; 5935: } 5936: } 5937: 5938: for (i=1; i<=imx; i++) { 5939: if (wav[i]>0){ 5940: ageexmed[i]=agev[mw[1][i]][i]; 5941: j=wav[i]; 5942: agecens[i]=1.; 5943: 5944: if (ageexmed[i]> 1 && wav[i] > 0){ 5945: agecens[i]=agev[mw[j][i]][i]; 5946: cens[i]= 1; 5947: }else if (ageexmed[i]< 1) 5948: cens[i]= -1; 5949: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass) 5950: cens[i]=0 ; 5951: } 5952: else cens[i]=-1; 5953: } 5954: 5955: for (i=1;i<=NDIM;i++) { 5956: for (j=1;j<=NDIM;j++) 5957: ximort[i][j]=(i == j ? 1.0 : 0.0); 5958: } 5959: 5960: /*p[1]=0.0268; p[NDIM]=0.083;*/ 5961: /*printf("%lf %lf", p[1], p[2]);*/ 5962: 5963: 5964: #ifdef GSL 5965: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n"); 5966: #elsedef 5967: printf("Powell\n"); fprintf(ficlog,"Powell\n"); 5968: #endif 5969: strcpy(filerespow,"pow-mort"); 5970: strcat(filerespow,fileres); 5971: if((ficrespow=fopen(filerespow,"w"))==NULL) { 5972: printf("Problem with resultfile: %s\n", filerespow); 5973: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow); 5974: } 5975: #ifdef GSL 5976: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL"); 5977: #elsedef 5978: fprintf(ficrespow,"# Powell\n# iter -2*LL"); 5979: #endif 5980: /* for (i=1;i<=nlstate;i++) 5981: for(j=1;j<=nlstate+ndeath;j++) 5982: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j); 5983: */ 5984: fprintf(ficrespow,"\n"); 5985: #ifdef GSL 5986: /* gsl starts here */ 5987: T = gsl_multimin_fminimizer_nmsimplex; 5988: gsl_multimin_fminimizer *sfm = NULL; 5989: gsl_vector *ss, *x; 5990: gsl_multimin_function minex_func; 5991: 5992: /* Initial vertex size vector */ 5993: ss = gsl_vector_alloc (NDIM); 5994: 5995: if (ss == NULL){ 5996: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0); 5997: } 5998: /* Set all step sizes to 1 */ 5999: gsl_vector_set_all (ss, 0.001); 6000: 6001: /* Starting point */ 6002: 6003: x = gsl_vector_alloc (NDIM); 6004: 6005: if (x == NULL){ 6006: gsl_vector_free(ss); 6007: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0); 6008: } 6009: 6010: /* Initialize method and iterate */ 6011: /* p[1]=0.0268; p[NDIM]=0.083; */ 6012: /* gsl_vector_set(x, 0, 0.0268); */ 6013: /* gsl_vector_set(x, 1, 0.083); */ 6014: gsl_vector_set(x, 0, p[1]); 6015: gsl_vector_set(x, 1, p[2]); 6016: 6017: minex_func.f = &gompertz_f; 6018: minex_func.n = NDIM; 6019: minex_func.params = (void *)&p; /* ??? */ 6020: 6021: sfm = gsl_multimin_fminimizer_alloc (T, NDIM); 6022: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss); 6023: 6024: printf("Iterations beginning .....\n\n"); 6025: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n"); 6026: 6027: iteri=0; 6028: while (rval == GSL_CONTINUE){ 6029: iteri++; 6030: status = gsl_multimin_fminimizer_iterate(sfm); 6031: 6032: if (status) printf("error: %s\n", gsl_strerror (status)); 6033: fflush(0); 6034: 6035: if (status) 6036: break; 6037: 6038: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6); 6039: ssval = gsl_multimin_fminimizer_size (sfm); 6040: 6041: if (rval == GSL_SUCCESS) 6042: printf ("converged to a local maximum at\n"); 6043: 6044: printf("%5d ", iteri); 6045: for (it = 0; it < NDIM; it++){ 6046: printf ("%10.5f ", gsl_vector_get (sfm->x, it)); 6047: } 6048: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval); 6049: } 6050: 6051: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n"); 6052: 6053: gsl_vector_free(x); /* initial values */ 6054: gsl_vector_free(ss); /* inital step size */ 6055: for (it=0; it<NDIM; it++){ 6056: p[it+1]=gsl_vector_get(sfm->x,it); 6057: fprintf(ficrespow," %.12lf", p[it]); 6058: } 6059: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */ 6060: #endif 6061: #ifdef POWELL 6062: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz); 6063: #endif 6064: fclose(ficrespow); 6065: 6066: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 6067: 6068: for(i=1; i <=NDIM; i++) 6069: for(j=i+1;j<=NDIM;j++) 6070: matcov[i][j]=matcov[j][i]; 6071: 6072: printf("\nCovariance matrix\n "); 6073: for(i=1; i <=NDIM; i++) { 6074: for(j=1;j<=NDIM;j++){ 6075: printf("%f ",matcov[i][j]); 6076: } 6077: printf("\n "); 6078: } 6079: 6080: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp); 6081: for (i=1;i<=NDIM;i++) 6082: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i])); 6083: 6084: lsurv=vector(1,AGESUP); 6085: lpop=vector(1,AGESUP); 6086: tpop=vector(1,AGESUP); 6087: lsurv[agegomp]=100000; 6088: 6089: for (k=agegomp;k<=AGESUP;k++) { 6090: agemortsup=k; 6091: if (p[1]*exp(p[2]*(k-agegomp))>1) break; 6092: } 6093: 6094: for (k=agegomp;k<agemortsup;k++) 6095: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp))); 6096: 6097: for (k=agegomp;k<agemortsup;k++){ 6098: lpop[k]=(lsurv[k]+lsurv[k+1])/2.; 6099: sumlpop=sumlpop+lpop[k]; 6100: } 6101: 6102: tpop[agegomp]=sumlpop; 6103: for (k=agegomp;k<(agemortsup-3);k++){ 6104: /* tpop[k+1]=2;*/ 6105: tpop[k+1]=tpop[k]-lpop[k]; 6106: } 6107: 6108: 6109: printf("\nAge lx qx dx Lx Tx e(x)\n"); 6110: for (k=agegomp;k<(agemortsup-2);k++) 6111: 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]); 6112: 6113: 6114: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */ 6115: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p); 6116: 6117: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \ 6118: stepm, weightopt,\ 6119: model,imx,p,matcov,agemortsup); 6120: 6121: free_vector(lsurv,1,AGESUP); 6122: free_vector(lpop,1,AGESUP); 6123: free_vector(tpop,1,AGESUP); 6124: #ifdef GSL 6125: free_ivector(cens,1,n); 6126: free_vector(agecens,1,n); 6127: free_ivector(dcwave,1,n); 6128: free_matrix(ximort,1,NDIM,1,NDIM); 6129: #endif 6130: } /* Endof if mle==-3 */ 6131: 6132: else{ /* For mle >=1 */ 6133: globpr=0;/* debug */ 6134: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */ 6135: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw); 6136: for (k=1; k<=npar;k++) 6137: printf(" %d %8.5f",k,p[k]); 6138: printf("\n"); 6139: globpr=1; /* to print the contributions */ 6140: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */ 6141: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw); 6142: for (k=1; k<=npar;k++) 6143: printf(" %d %8.5f",k,p[k]); 6144: printf("\n"); 6145: if(mle>=1){ /* Could be 1 or 2 */ 6146: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func); 6147: } 6148: 6149: /*--------- results files --------------*/ 6150: 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); 6151: 6152: 6153: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); 6154: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); 6155: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); 6156: for(i=1,jk=1; i <=nlstate; i++){ 6157: for(k=1; k <=(nlstate+ndeath); k++){ 6158: if (k != i) { 6159: printf("%d%d ",i,k); 6160: fprintf(ficlog,"%d%d ",i,k); 6161: fprintf(ficres,"%1d%1d ",i,k); 6162: for(j=1; j <=ncovmodel; j++){ 6163: printf("%lf ",p[jk]); 6164: fprintf(ficlog,"%lf ",p[jk]); 6165: fprintf(ficres,"%lf ",p[jk]); 6166: jk++; 6167: } 6168: printf("\n"); 6169: fprintf(ficlog,"\n"); 6170: fprintf(ficres,"\n"); 6171: } 6172: } 6173: } 6174: if(mle!=0){ 6175: /* Computing hessian and covariance matrix */ 6176: ftolhess=ftol; /* Usually correct */ 6177: hesscov(matcov, p, npar, delti, ftolhess, func); 6178: } 6179: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n"); 6180: printf("# Scales (for hessian or gradient estimation)\n"); 6181: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n"); 6182: for(i=1,jk=1; i <=nlstate; i++){ 6183: for(j=1; j <=nlstate+ndeath; j++){ 6184: if (j!=i) { 6185: fprintf(ficres,"%1d%1d",i,j); 6186: printf("%1d%1d",i,j); 6187: fprintf(ficlog,"%1d%1d",i,j); 6188: for(k=1; k<=ncovmodel;k++){ 6189: printf(" %.5e",delti[jk]); 6190: fprintf(ficlog," %.5e",delti[jk]); 6191: fprintf(ficres," %.5e",delti[jk]); 6192: jk++; 6193: } 6194: printf("\n"); 6195: fprintf(ficlog,"\n"); 6196: fprintf(ficres,"\n"); 6197: } 6198: } 6199: } 6200: 6201: 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"); 6202: if(mle>=1) 6203: 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"); 6204: 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"); 6205: /* # 121 Var(a12)\n\ */ 6206: /* # 122 Cov(b12,a12) Var(b12)\n\ */ 6207: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */ 6208: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */ 6209: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */ 6210: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */ 6211: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */ 6212: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */ 6213: 6214: 6215: /* Just to have a covariance matrix which will be more understandable 6216: even is we still don't want to manage dictionary of variables 6217: */ 6218: for(itimes=1;itimes<=2;itimes++){ 6219: jj=0; 6220: for(i=1; i <=nlstate; i++){ 6221: for(j=1; j <=nlstate+ndeath; j++){ 6222: if(j==i) continue; 6223: for(k=1; k<=ncovmodel;k++){ 6224: jj++; 6225: ca[0]= k+'a'-1;ca[1]='\0'; 6226: if(itimes==1){ 6227: if(mle>=1) 6228: printf("#%1d%1d%d",i,j,k); 6229: fprintf(ficlog,"#%1d%1d%d",i,j,k); 6230: fprintf(ficres,"#%1d%1d%d",i,j,k); 6231: }else{ 6232: if(mle>=1) 6233: printf("%1d%1d%d",i,j,k); 6234: fprintf(ficlog,"%1d%1d%d",i,j,k); 6235: fprintf(ficres,"%1d%1d%d",i,j,k); 6236: } 6237: ll=0; 6238: for(li=1;li <=nlstate; li++){ 6239: for(lj=1;lj <=nlstate+ndeath; lj++){ 6240: if(lj==li) continue; 6241: for(lk=1;lk<=ncovmodel;lk++){ 6242: ll++; 6243: if(ll<=jj){ 6244: cb[0]= lk +'a'-1;cb[1]='\0'; 6245: if(ll<jj){ 6246: if(itimes==1){ 6247: if(mle>=1) 6248: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj); 6249: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj); 6250: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj); 6251: }else{ 6252: if(mle>=1) 6253: printf(" %.5e",matcov[jj][ll]); 6254: fprintf(ficlog," %.5e",matcov[jj][ll]); 6255: fprintf(ficres," %.5e",matcov[jj][ll]); 6256: } 6257: }else{ 6258: if(itimes==1){ 6259: if(mle>=1) 6260: printf(" Var(%s%1d%1d)",ca,i,j); 6261: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j); 6262: fprintf(ficres," Var(%s%1d%1d)",ca,i,j); 6263: }else{ 6264: if(mle>=1) 6265: printf(" %.5e",matcov[jj][ll]); 6266: fprintf(ficlog," %.5e",matcov[jj][ll]); 6267: fprintf(ficres," %.5e",matcov[jj][ll]); 6268: } 6269: } 6270: } 6271: } /* end lk */ 6272: } /* end lj */ 6273: } /* end li */ 6274: if(mle>=1) 6275: printf("\n"); 6276: fprintf(ficlog,"\n"); 6277: fprintf(ficres,"\n"); 6278: numlinepar++; 6279: } /* end k*/ 6280: } /*end j */ 6281: } /* end i */ 6282: } /* end itimes */ 6283: 6284: fflush(ficlog); 6285: fflush(ficres); 6286: 6287: while((c=getc(ficpar))=='#' && c!= EOF){ 6288: ungetc(c,ficpar); 6289: fgets(line, MAXLINE, ficpar); 6290: fputs(line,stdout); 6291: fputs(line,ficparo); 6292: } 6293: ungetc(c,ficpar); 6294: 6295: estepm=0; 6296: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); 6297: if (estepm==0 || estepm < stepm) estepm=stepm; 6298: if (fage <= 2) { 6299: bage = ageminpar; 6300: fage = agemaxpar; 6301: } 6302: 6303: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n"); 6304: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm); 6305: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm); 6306: 6307: while((c=getc(ficpar))=='#' && c!= EOF){ 6308: ungetc(c,ficpar); 6309: fgets(line, MAXLINE, ficpar); 6310: fputs(line,stdout); 6311: fputs(line,ficparo); 6312: } 6313: ungetc(c,ficpar); 6314: 6315: 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); 6316: 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); 6317: 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); 6318: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav); 6319: 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); 6320: 6321: while((c=getc(ficpar))=='#' && c!= EOF){ 6322: ungetc(c,ficpar); 6323: fgets(line, MAXLINE, ficpar); 6324: fputs(line,stdout); 6325: fputs(line,ficparo); 6326: } 6327: ungetc(c,ficpar); 6328: 6329: 6330: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.; 6331: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.; 6332: 6333: fscanf(ficpar,"pop_based=%d\n",&popbased); 6334: fprintf(ficparo,"pop_based=%d\n",popbased); 6335: fprintf(ficres,"pop_based=%d\n",popbased); 6336: 6337: while((c=getc(ficpar))=='#' && c!= EOF){ 6338: ungetc(c,ficpar); 6339: fgets(line, MAXLINE, ficpar); 6340: fputs(line,stdout); 6341: fputs(line,ficparo); 6342: } 6343: ungetc(c,ficpar); 6344: 6345: 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); 6346: 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); 6347: 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); 6348: 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); 6349: 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); 6350: /* day and month of proj2 are not used but only year anproj2.*/ 6351: 6352: 6353: 6354: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */ 6355: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */ 6356: 6357: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */ 6358: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p); 6359: 6360: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\ 6361: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\ 6362: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2); 6363: 6364: /*------------ free_vector -------------*/ 6365: /* chdir(path); */ 6366: 6367: free_ivector(wav,1,imx); 6368: free_imatrix(dh,1,lastpass-firstpass+1,1,imx); 6369: free_imatrix(bh,1,lastpass-firstpass+1,1,imx); 6370: free_imatrix(mw,1,lastpass-firstpass+1,1,imx); 6371: free_lvector(num,1,n); 6372: free_vector(agedc,1,n); 6373: /*free_matrix(covar,0,NCOVMAX,1,n);*/ 6374: /*free_matrix(covar,1,NCOVMAX,1,n);*/ 6375: fclose(ficparo); 6376: fclose(ficres); 6377: 6378: 6379: /*--------------- Prevalence limit (period or stable prevalence) --------------*/ 6380: #include "prevlim.h" /* Use ficrespl, ficlog */ 6381: fclose(ficrespl); 6382: 6383: #ifdef FREEEXIT2 6384: #include "freeexit2.h" 6385: #endif 6386: 6387: /*------------- h Pij x at various ages ------------*/ 6388: #include "hpijx.h" 6389: fclose(ficrespij); 6390: 6391: /*-------------- Variance of one-step probabilities---*/ 6392: k=1; 6393: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart); 6394: 6395: 6396: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX); 6397: for(i=1;i<=AGESUP;i++) 6398: for(j=1;j<=NCOVMAX;j++) 6399: for(k=1;k<=NCOVMAX;k++) 6400: probs[i][j][k]=0.; 6401: 6402: /*---------- Forecasting ------------------*/ 6403: /*if((stepm == 1) && (strcmp(model,".")==0)){*/ 6404: if(prevfcast==1){ 6405: /* if(stepm ==1){*/ 6406: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff); 6407: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/ 6408: /* } */ 6409: /* else{ */ 6410: /* erreur=108; */ 6411: /* 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); */ 6412: /* 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); */ 6413: /* } */ 6414: } 6415: 6416: 6417: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */ 6418: 6419: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); 6420: /* 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",\ 6421: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass); 6422: */ 6423: 6424: if (mobilav!=0) { 6425: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 6426: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ 6427: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); 6428: printf(" Error in movingaverage mobilav=%d\n",mobilav); 6429: } 6430: } 6431: 6432: 6433: /*---------- Health expectancies, no variances ------------*/ 6434: 6435: strcpy(filerese,"e"); 6436: strcat(filerese,fileres); 6437: if((ficreseij=fopen(filerese,"w"))==NULL) { 6438: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0); 6439: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0); 6440: } 6441: printf("Computing Health Expectancies: result on file '%s' \n", filerese); 6442: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese); 6443: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){ 6444: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/ 6445: 6446: for (k=1; k <= (int) pow(2,cptcoveff); k++){ 6447: fprintf(ficreseij,"\n#****** "); 6448: for(j=1;j<=cptcoveff;j++) { 6449: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 6450: } 6451: fprintf(ficreseij,"******\n"); 6452: 6453: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); 6454: oldm=oldms;savm=savms; 6455: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart); 6456: 6457: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage); 6458: /*}*/ 6459: } 6460: fclose(ficreseij); 6461: 6462: 6463: /*---------- Health expectancies and variances ------------*/ 6464: 6465: 6466: strcpy(filerest,"t"); 6467: strcat(filerest,fileres); 6468: if((ficrest=fopen(filerest,"w"))==NULL) { 6469: printf("Problem with total LE resultfile: %s\n", filerest);goto end; 6470: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end; 6471: } 6472: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 6473: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 6474: 6475: 6476: strcpy(fileresstde,"stde"); 6477: strcat(fileresstde,fileres); 6478: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) { 6479: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0); 6480: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0); 6481: } 6482: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde); 6483: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde); 6484: 6485: strcpy(filerescve,"cve"); 6486: strcat(filerescve,fileres); 6487: if((ficrescveij=fopen(filerescve,"w"))==NULL) { 6488: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0); 6489: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0); 6490: } 6491: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve); 6492: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve); 6493: 6494: strcpy(fileresv,"v"); 6495: strcat(fileresv,fileres); 6496: if((ficresvij=fopen(fileresv,"w"))==NULL) { 6497: printf("Problem with variance resultfile: %s\n", fileresv);exit(0); 6498: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0); 6499: } 6500: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv); 6501: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv); 6502: 6503: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){ 6504: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/ 6505: 6506: for (k=1; k <= (int) pow(2,cptcoveff); k++){ 6507: fprintf(ficrest,"\n#****** "); 6508: for(j=1;j<=cptcoveff;j++) 6509: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 6510: fprintf(ficrest,"******\n"); 6511: 6512: fprintf(ficresstdeij,"\n#****** "); 6513: fprintf(ficrescveij,"\n#****** "); 6514: for(j=1;j<=cptcoveff;j++) { 6515: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 6516: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 6517: } 6518: fprintf(ficresstdeij,"******\n"); 6519: fprintf(ficrescveij,"******\n"); 6520: 6521: fprintf(ficresvij,"\n#****** "); 6522: for(j=1;j<=cptcoveff;j++) 6523: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 6524: fprintf(ficresvij,"******\n"); 6525: 6526: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); 6527: oldm=oldms;savm=savms; 6528: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart); 6529: /* 6530: */ 6531: /* goto endfree; */ 6532: 6533: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); 6534: pstamp(ficrest); 6535: 6536: 6537: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/ 6538: oldm=oldms;savm=savms; /* Segmentation fault */ 6539: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); 6540: 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 "); 6541: if(vpopbased==1) 6542: 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); 6543: else 6544: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n"); 6545: fprintf(ficrest,"# Age e.. (std) "); 6546: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i); 6547: fprintf(ficrest,"\n"); 6548: 6549: epj=vector(1,nlstate+1); 6550: for(age=bage; age <=fage ;age++){ 6551: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k); 6552: if (vpopbased==1) { 6553: if(mobilav ==0){ 6554: for(i=1; i<=nlstate;i++) 6555: prlim[i][i]=probs[(int)age][i][k]; 6556: }else{ /* mobilav */ 6557: for(i=1; i<=nlstate;i++) 6558: prlim[i][i]=mobaverage[(int)age][i][k]; 6559: } 6560: } 6561: 6562: fprintf(ficrest," %4.0f",age); 6563: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){ 6564: for(i=1, epj[j]=0.;i <=nlstate;i++) { 6565: epj[j] += prlim[i][i]*eij[i][j][(int)age]; 6566: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/ 6567: } 6568: epj[nlstate+1] +=epj[j]; 6569: } 6570: 6571: for(i=1, vepp=0.;i <=nlstate;i++) 6572: for(j=1;j <=nlstate;j++) 6573: vepp += vareij[i][j][(int)age]; 6574: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp)); 6575: for(j=1;j <=nlstate;j++){ 6576: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age])); 6577: } 6578: fprintf(ficrest,"\n"); 6579: } 6580: } 6581: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage); 6582: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage); 6583: free_vector(epj,1,nlstate+1); 6584: /*}*/ 6585: } 6586: free_vector(weight,1,n); 6587: free_imatrix(Tvard,1,NCOVMAX,1,2); 6588: free_imatrix(s,1,maxwav+1,1,n); 6589: free_matrix(anint,1,maxwav,1,n); 6590: free_matrix(mint,1,maxwav,1,n); 6591: free_ivector(cod,1,n); 6592: free_ivector(tab,1,NCOVMAX); 6593: fclose(ficresstdeij); 6594: fclose(ficrescveij); 6595: fclose(ficresvij); 6596: fclose(ficrest); 6597: fclose(ficpar); 6598: 6599: /*------- Variance of period (stable) prevalence------*/ 6600: 6601: strcpy(fileresvpl,"vpl"); 6602: strcat(fileresvpl,fileres); 6603: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) { 6604: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl); 6605: exit(0); 6606: } 6607: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl); 6608: 6609: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){ 6610: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/ 6611: 6612: for (k=1; k <= (int) pow(2,cptcoveff); k++){ 6613: fprintf(ficresvpl,"\n#****** "); 6614: for(j=1;j<=cptcoveff;j++) 6615: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 6616: fprintf(ficresvpl,"******\n"); 6617: 6618: varpl=matrix(1,nlstate,(int) bage, (int) fage); 6619: oldm=oldms;savm=savms; 6620: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart); 6621: free_matrix(varpl,1,nlstate,(int) bage, (int)fage); 6622: /*}*/ 6623: } 6624: 6625: fclose(ficresvpl); 6626: 6627: /*---------- End : free ----------------*/ 6628: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 6629: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX); 6630: } /* mle==-3 arrives here for freeing */ 6631: endfree: 6632: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */ 6633: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath); 6634: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath); 6635: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath); 6636: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath); 6637: free_matrix(covar,0,NCOVMAX,1,n); 6638: free_matrix(matcov,1,npar,1,npar); 6639: /*free_vector(delti,1,npar);*/ 6640: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 6641: free_matrix(agev,1,maxwav,1,imx); 6642: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 6643: 6644: free_ivector(ncodemax,1,NCOVMAX); 6645: free_ivector(Tvar,1,NCOVMAX); 6646: free_ivector(Tprod,1,NCOVMAX); 6647: free_ivector(Tvaraff,1,NCOVMAX); 6648: free_ivector(Tage,1,NCOVMAX); 6649: 6650: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX); 6651: free_imatrix(codtab,1,100,1,10); 6652: fflush(fichtm); 6653: fflush(ficgp); 6654: 6655: 6656: if((nberr >0) || (nbwarn>0)){ 6657: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn); 6658: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn); 6659: }else{ 6660: printf("End of Imach\n"); 6661: fprintf(ficlog,"End of Imach\n"); 6662: } 6663: printf("See log file on %s\n",filelog); 6664: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */ 6665: /*(void) gettimeofday(&end_time,&tzp);*/ 6666: rend_time = time(NULL); 6667: end_time = *localtime(&rend_time); 6668: /* tml = *localtime(&end_time.tm_sec); */ 6669: strcpy(strtend,asctime(&end_time)); 6670: printf("Local time at start %s\nLocal time at end %s",strstart, strtend); 6671: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend); 6672: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout)); 6673: 6674: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time)); 6675: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout)); 6676: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time)); 6677: /* printf("Total time was %d uSec.\n", total_usecs);*/ 6678: /* if(fileappend(fichtm,optionfilehtm)){ */ 6679: fprintf(fichtm," Local time at start %s Local time at end %s \n</body></html>",strstart, strtend); 6680: fclose(fichtm); 6681: fprintf(fichtmcov," Local time at start %s Local time at end %s \n</body></html>",strstart, strtend); 6682: fclose(fichtmcov); 6683: fclose(ficgp); 6684: fclose(ficlog); 6685: /*------ End -----------*/ 6686: 6687: 6688: printf("Before Current directory %s!\n",pathcd); 6689: if(chdir(pathcd) != 0) 6690: printf("Can't move to directory %s!\n",path); 6691: if(getcwd(pathcd,MAXLINE) > 0) 6692: printf("Current directory %s!\n",pathcd); 6693: /*strcat(plotcmd,CHARSEPARATOR);*/ 6694: sprintf(plotcmd,"gnuplot"); 6695: #ifdef _WIN32 6696: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach); 6697: #endif 6698: if(!stat(plotcmd,&info)){ 6699: printf("Error or gnuplot program not found: %s\n",plotcmd);fflush(stdout); 6700: if(!stat(getenv("GNUPLOTBIN"),&info)){ 6701: printf("Error or gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout); 6702: }else 6703: strcpy(pplotcmd,plotcmd); 6704: #ifdef __unix 6705: strcpy(plotcmd,GNUPLOTPROGRAM); 6706: if(!stat(plotcmd,&info)){ 6707: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout); 6708: }else 6709: strcpy(pplotcmd,plotcmd); 6710: #endif 6711: }else 6712: strcpy(pplotcmd,plotcmd); 6713: 6714: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot); 6715: printf("Starting graphs with: %s\n",plotcmd);fflush(stdout); 6716: 6717: if((outcmd=system(plotcmd)) != 0){ 6718: printf("gnuplot command might not be in your path: %s, err=%d\n", plotcmd, outcmd); 6719: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n"); 6720: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot); 6721: if((outcmd=system(plotcmd)) != 0) 6722: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd); 6723: } 6724: printf(" Successul, please wait..."); 6725: while (z[0] != 'q') { 6726: /* chdir(path); */ 6727: printf("\nType e to edit results with your browser, g to graph again and q for exit: "); 6728: scanf("%s",z); 6729: /* if (z[0] == 'c') system("./imach"); */ 6730: if (z[0] == 'e') { 6731: #ifdef _APPLE_ 6732: sprintf(pplotcmd, "open %s", optionfilehtm); 6733: #elif __linux 6734: sprintf(pplotcmd, "xdg-open %s", optionfilehtm); 6735: #else 6736: sprintf(pplotcmd, "%s", optionfilehtm); 6737: #endif 6738: printf("Starting browser with: %s",pplotcmd);fflush(stdout); 6739: system(pplotcmd); 6740: } 6741: else if (z[0] == 'g') system(plotcmd); 6742: else if (z[0] == 'q') exit(0); 6743: } 6744: end: 6745: while (z[0] != 'q') { 6746: printf("\nType q for exiting: "); 6747: scanf("%s",z); 6748: } 6749: } 6750: 6751: 6752: