imach/src/imach.c - view

File: [Local Repository] / imach / src / imach.c
Revision 1.153: download - view: text, annotated - select for diffs
Fri Jun 20 16:45:46 2014 UTC (10 years ago) by brouard
Branches: MAIN
CVS tags: HEAD

Summary: If 3 live state, convergence to period prevalence on same graph
Author: Brouard

1: /* $Id: imach.c,v 1.153 2014/06/20 16:45:46 brouard Exp $ 2: $State: Exp $ 3: $Log: imach.c,v $ 4: Revision 1.153 2014/06/20 16:45:46 brouard 5: Summary: If 3 live state, convergence to period prevalence on same graph 6: Author: Brouard 7: 8: Revision 1.152 2014/06/18 17:54:09 brouard 9: Summary: open browser, use gnuplot on same dir than imach if not found in the path 10: 11: Revision 1.151 2014/06/18 16:43:30 brouard 12: *** empty log message *** 13: 14: Revision 1.150 2014/06/18 16:42:35 brouard 15: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX) 16: Author: brouard 17: 18: Revision 1.149 2014/06/18 15:51:14 brouard 19: Summary: Some fixes in parameter files errors 20: Author: Nicolas Brouard 21: 22: Revision 1.148 2014/06/17 17:38:48 brouard 23: Summary: Nothing new 24: Author: Brouard 25: 26: Just a new packaging for OS/X version 0.98nS 27: 28: Revision 1.147 2014/06/16 10:33:11 brouard 29: *** empty log message *** 30: 31: Revision 1.146 2014/06/16 10:20:28 brouard 32: Summary: Merge 33: Author: Brouard 34: 35: Merge, before building revised version. 36: 37: Revision 1.145 2014/06/10 21:23:15 brouard 38: Summary: Debugging with valgrind 39: Author: Nicolas Brouard 40: 41: Lot of changes in order to output the results with some covariates 42: After the Edimburgh REVES conference 2014, it seems mandatory to 43: improve the code. 44: No more memory valgrind error but a lot has to be done in order to 45: continue the work of splitting the code into subroutines. 46: Also, decodemodel has been improved. Tricode is still not 47: optimal. nbcode should be improved. Documentation has been added in 48: the source code. 49: 50: Revision 1.143 2014/01/26 09:45:38 brouard 51: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising 52: 53: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested... 54: (Module): Version 0.98nR Running ok, but output format still only works for three covariates. 55: 56: Revision 1.142 2014/01/26 03:57:36 brouard 57: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2 58: 59: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested... 60: 61: Revision 1.141 2014/01/26 02:42:01 brouard 62: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested... 63: 64: Revision 1.140 2011/09/02 10:37:54 brouard 65: Summary: times.h is ok with mingw32 now. 66: 67: Revision 1.139 2010/06/14 07:50:17 brouard 68: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree. 69: I remember having already fixed agemin agemax which are pointers now but not cvs saved. 70: 71: Revision 1.138 2010/04/30 18:19:40 brouard 72: *** empty log message *** 73: 74: Revision 1.137 2010/04/29 18:11:38 brouard 75: (Module): Checking covariates for more complex models 76: than V1+V2. A lot of change to be done. Unstable. 77: 78: Revision 1.136 2010/04/26 20:30:53 brouard 79: (Module): merging some libgsl code. Fixing computation 80: of likelione (using inter/intrapolation if mle = 0) in order to 81: get same likelihood as if mle=1. 82: Some cleaning of code and comments added. 83: 84: Revision 1.135 2009/10/29 15:33:14 brouard 85: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code. 86: 87: Revision 1.134 2009/10/29 13:18:53 brouard 88: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code. 89: 90: Revision 1.133 2009/07/06 10:21:25 brouard 91: just nforces 92: 93: Revision 1.132 2009/07/06 08:22:05 brouard 94: Many tings 95: 96: Revision 1.131 2009/06/20 16:22:47 brouard 97: Some dimensions resccaled 98: 99: Revision 1.130 2009/05/26 06:44:34 brouard 100: (Module): Max Covariate is now set to 20 instead of 8. A 101: lot of cleaning with variables initialized to 0. Trying to make 102: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better. 103: 104: Revision 1.129 2007/08/31 13:49:27 lievre 105: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting 106: 107: Revision 1.128 2006/06/30 13:02:05 brouard 108: (Module): Clarifications on computing e.j 109: 110: Revision 1.127 2006/04/28 18:11:50 brouard 111: (Module): Yes the sum of survivors was wrong since 112: imach-114 because nhstepm was no more computed in the age 113: loop. Now we define nhstepma in the age loop. 114: (Module): In order to speed up (in case of numerous covariates) we 115: compute health expectancies (without variances) in a first step 116: and then all the health expectancies with variances or standard 117: deviation (needs data from the Hessian matrices) which slows the 118: computation. 119: In the future we should be able to stop the program is only health 120: expectancies and graph are needed without standard deviations. 121: 122: Revision 1.126 2006/04/28 17:23:28 brouard 123: (Module): Yes the sum of survivors was wrong since 124: imach-114 because nhstepm was no more computed in the age 125: loop. Now we define nhstepma in the age loop. 126: Version 0.98h 127: 128: Revision 1.125 2006/04/04 15:20:31 lievre 129: Errors in calculation of health expectancies. Age was not initialized. 130: Forecasting file added. 131: 132: Revision 1.124 2006/03/22 17:13:53 lievre 133: Parameters are printed with %lf instead of %f (more numbers after the comma). 134: The log-likelihood is printed in the log file 135: 136: Revision 1.123 2006/03/20 10:52:43 brouard 137: * imach.c (Module): <title> changed, corresponds to .htm file 138: name. <head> headers where missing. 139: 140: * imach.c (Module): Weights can have a decimal point as for 141: English (a comma might work with a correct LC_NUMERIC environment, 142: otherwise the weight is truncated). 143: Modification of warning when the covariates values are not 0 or 144: 1. 145: Version 0.98g 146: 147: Revision 1.122 2006/03/20 09:45:41 brouard 148: (Module): Weights can have a decimal point as for 149: English (a comma might work with a correct LC_NUMERIC environment, 150: otherwise the weight is truncated). 151: Modification of warning when the covariates values are not 0 or 152: 1. 153: Version 0.98g 154: 155: Revision 1.121 2006/03/16 17:45:01 lievre 156: * imach.c (Module): Comments concerning covariates added 157: 158: * imach.c (Module): refinements in the computation of lli if 159: status=-2 in order to have more reliable computation if stepm is 160: not 1 month. Version 0.98f 161: 162: Revision 1.120 2006/03/16 15:10:38 lievre 163: (Module): refinements in the computation of lli if 164: status=-2 in order to have more reliable computation if stepm is 165: not 1 month. Version 0.98f 166: 167: Revision 1.119 2006/03/15 17:42:26 brouard 168: (Module): Bug if status = -2, the loglikelihood was 169: computed as likelihood omitting the logarithm. Version O.98e 170: 171: Revision 1.118 2006/03/14 18:20:07 brouard 172: (Module): varevsij Comments added explaining the second 173: table of variances if popbased=1 . 174: (Module): Covariances of eij, ekl added, graphs fixed, new html link. 175: (Module): Function pstamp added 176: (Module): Version 0.98d 177: 178: Revision 1.117 2006/03/14 17:16:22 brouard 179: (Module): varevsij Comments added explaining the second 180: table of variances if popbased=1 . 181: (Module): Covariances of eij, ekl added, graphs fixed, new html link. 182: (Module): Function pstamp added 183: (Module): Version 0.98d 184: 185: Revision 1.116 2006/03/06 10:29:27 brouard 186: (Module): Variance-covariance wrong links and 187: varian-covariance of ej. is needed (Saito). 188: 189: Revision 1.115 2006/02/27 12:17:45 brouard 190: (Module): One freematrix added in mlikeli! 0.98c 191: 192: Revision 1.114 2006/02/26 12:57:58 brouard 193: (Module): Some improvements in processing parameter 194: filename with strsep. 195: 196: Revision 1.113 2006/02/24 14:20:24 brouard 197: (Module): Memory leaks checks with valgrind and: 198: datafile was not closed, some imatrix were not freed and on matrix 199: allocation too. 200: 201: Revision 1.112 2006/01/30 09:55:26 brouard 202: (Module): Back to gnuplot.exe instead of wgnuplot.exe 203: 204: Revision 1.111 2006/01/25 20:38:18 brouard 205: (Module): Lots of cleaning and bugs added (Gompertz) 206: (Module): Comments can be added in data file. Missing date values 207: can be a simple dot '.'. 208: 209: Revision 1.110 2006/01/25 00:51:50 brouard 210: (Module): Lots of cleaning and bugs added (Gompertz) 211: 212: Revision 1.109 2006/01/24 19:37:15 brouard 213: (Module): Comments (lines starting with a #) are allowed in data. 214: 215: Revision 1.108 2006/01/19 18:05:42 lievre 216: Gnuplot problem appeared... 217: To be fixed 218: 219: Revision 1.107 2006/01/19 16:20:37 brouard 220: Test existence of gnuplot in imach path 221: 222: Revision 1.106 2006/01/19 13:24:36 brouard 223: Some cleaning and links added in html output 224: 225: Revision 1.105 2006/01/05 20:23:19 lievre 226: *** empty log message *** 227: 228: Revision 1.104 2005/09/30 16:11:43 lievre 229: (Module): sump fixed, loop imx fixed, and simplifications. 230: (Module): If the status is missing at the last wave but we know 231: that the person is alive, then we can code his/her status as -2 232: (instead of missing=-1 in earlier versions) and his/her 233: contributions to the likelihood is 1 - Prob of dying from last 234: health status (= 1-p13= p11+p12 in the easiest case of somebody in 235: the healthy state at last known wave). Version is 0.98 236: 237: Revision 1.103 2005/09/30 15:54:49 lievre 238: (Module): sump fixed, loop imx fixed, and simplifications. 239: 240: Revision 1.102 2004/09/15 17:31:30 brouard 241: Add the possibility to read data file including tab characters. 242: 243: Revision 1.101 2004/09/15 10:38:38 brouard 244: Fix on curr_time 245: 246: Revision 1.100 2004/07/12 18:29:06 brouard 247: Add version for Mac OS X. Just define UNIX in Makefile 248: 249: Revision 1.99 2004/06/05 08:57:40 brouard 250: *** empty log message *** 251: 252: Revision 1.98 2004/05/16 15:05:56 brouard 253: New version 0.97 . First attempt to estimate force of mortality 254: directly from the data i.e. without the need of knowing the health 255: state at each age, but using a Gompertz model: log u =a + b*age . 256: This is the basic analysis of mortality and should be done before any 257: other analysis, in order to test if the mortality estimated from the 258: cross-longitudinal survey is different from the mortality estimated 259: from other sources like vital statistic data. 260: 261: The same imach parameter file can be used but the option for mle should be -3. 262: 263: Agnès, who wrote this part of the code, tried to keep most of the 264: former routines in order to include the new code within the former code. 265: 266: The output is very simple: only an estimate of the intercept and of 267: the slope with 95% confident intervals. 268: 269: Current limitations: 270: A) Even if you enter covariates, i.e. with the 271: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates. 272: B) There is no computation of Life Expectancy nor Life Table. 273: 274: Revision 1.97 2004/02/20 13:25:42 lievre 275: Version 0.96d. Population forecasting command line is (temporarily) 276: suppressed. 277: 278: Revision 1.96 2003/07/15 15:38:55 brouard 279: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is 280: rewritten within the same printf. Workaround: many printfs. 281: 282: Revision 1.95 2003/07/08 07:54:34 brouard 283: * imach.c (Repository): 284: (Repository): Using imachwizard code to output a more meaningful covariance 285: matrix (cov(a12,c31) instead of numbers. 286: 287: Revision 1.94 2003/06/27 13:00:02 brouard 288: Just cleaning 289: 290: Revision 1.93 2003/06/25 16:33:55 brouard 291: (Module): On windows (cygwin) function asctime_r doesn't 292: exist so I changed back to asctime which exists. 293: (Module): Version 0.96b 294: 295: Revision 1.92 2003/06/25 16:30:45 brouard 296: (Module): On windows (cygwin) function asctime_r doesn't 297: exist so I changed back to asctime which exists. 298: 299: Revision 1.91 2003/06/25 15:30:29 brouard 300: * imach.c (Repository): Duplicated warning errors corrected. 301: (Repository): Elapsed time after each iteration is now output. It 302: helps to forecast when convergence will be reached. Elapsed time 303: is stamped in powell. We created a new html file for the graphs 304: concerning matrix of covariance. It has extension -cov.htm. 305: 306: Revision 1.90 2003/06/24 12:34:15 brouard 307: (Module): Some bugs corrected for windows. Also, when 308: mle=-1 a template is output in file "or"mypar.txt with the design 309: of the covariance matrix to be input. 310: 311: Revision 1.89 2003/06/24 12:30:52 brouard 312: (Module): Some bugs corrected for windows. Also, when 313: mle=-1 a template is output in file "or"mypar.txt with the design 314: of the covariance matrix to be input. 315: 316: Revision 1.88 2003/06/23 17:54:56 brouard 317: * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things. 318: 319: Revision 1.87 2003/06/18 12:26:01 brouard 320: Version 0.96 321: 322: Revision 1.86 2003/06/17 20:04:08 brouard 323: (Module): Change position of html and gnuplot routines and added 324: routine fileappend. 325: 326: Revision 1.85 2003/06/17 13:12:43 brouard 327: * imach.c (Repository): Check when date of death was earlier that 328: current date of interview. It may happen when the death was just 329: prior to the death. In this case, dh was negative and likelihood 330: was wrong (infinity). We still send an "Error" but patch by 331: assuming that the date of death was just one stepm after the 332: interview. 333: (Repository): Because some people have very long ID (first column) 334: we changed int to long in num[] and we added a new lvector for 335: memory allocation. But we also truncated to 8 characters (left 336: truncation) 337: (Repository): No more line truncation errors. 338: 339: Revision 1.84 2003/06/13 21:44:43 brouard 340: * imach.c (Repository): Replace "freqsummary" at a correct 341: place. It differs from routine "prevalence" which may be called 342: many times. Probs is memory consuming and must be used with 343: parcimony. 344: Version 0.95a3 (should output exactly the same maximization than 0.8a2) 345: 346: Revision 1.83 2003/06/10 13:39:11 lievre 347: *** empty log message *** 348: 349: Revision 1.82 2003/06/05 15:57:20 brouard 350: Add log in imach.c and fullversion number is now printed. 351: 352: */ 353: /* 354: Interpolated Markov Chain 355: 356: Short summary of the programme: 357: 358: This program computes Healthy Life Expectancies from 359: cross-longitudinal data. Cross-longitudinal data consist in: -1- a 360: first survey ("cross") where individuals from different ages are 361: interviewed on their health status or degree of disability (in the 362: case of a health survey which is our main interest) -2- at least a 363: second wave of interviews ("longitudinal") which measure each change 364: (if any) in individual health status. Health expectancies are 365: computed from the time spent in each health state according to a 366: model. More health states you consider, more time is necessary to reach the 367: Maximum Likelihood of the parameters involved in the model. The 368: simplest model is the multinomial logistic model where pij is the 369: probability to be observed in state j at the second wave 370: conditional to be observed in state i at the first wave. Therefore 371: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where 372: 'age' is age and 'sex' is a covariate. If you want to have a more 373: complex model than "constant and age", you should modify the program 374: where the markup *Covariates have to be included here again* invites 375: you to do it. More covariates you add, slower the 376: convergence. 377: 378: The advantage of this computer programme, compared to a simple 379: multinomial logistic model, is clear when the delay between waves is not 380: identical for each individual. Also, if a individual missed an 381: intermediate interview, the information is lost, but taken into 382: account using an interpolation or extrapolation. 383: 384: hPijx is the probability to be observed in state i at age x+h 385: conditional to the observed state i at age x. The delay 'h' can be 386: split into an exact number (nh*stepm) of unobserved intermediate 387: states. This elementary transition (by month, quarter, 388: semester or year) is modelled as a multinomial logistic. The hPx 389: matrix is simply the matrix product of nh*stepm elementary matrices 390: and the contribution of each individual to the likelihood is simply 391: hPijx. 392: 393: Also this programme outputs the covariance matrix of the parameters but also 394: of the life expectancies. It also computes the period (stable) prevalence. 395: 396: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr). 397: Institut national d'études démographiques, Paris. 398: This software have been partly granted by Euro-REVES, a concerted action 399: from the European Union. 400: It is copyrighted identically to a GNU software product, ie programme and 401: software can be distributed freely for non commercial use. Latest version 402: can be accessed at http://euroreves.ined.fr/imach . 403: 404: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach 405: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so 406: 407: **********************************************************************/ 408: /* 409: main 410: read parameterfile 411: read datafile 412: concatwav 413: freqsummary 414: if (mle >= 1) 415: mlikeli 416: print results files 417: if mle==1 418: computes hessian 419: read end of parameter file: agemin, agemax, bage, fage, estepm 420: begin-prev-date,... 421: open gnuplot file 422: open html file 423: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate 424: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ****** 425: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674 426: freexexit2 possible for memory heap. 427: 428: h Pij x | pij_nom ficrestpij 429: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3 430: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000 431: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907 432: 433: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340 434: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597 435: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in () 436: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix 437: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix 438: 439: forecasting if prevfcast==1 prevforecast call prevalence() 440: health expectancies 441: Variance-covariance of DFLE 442: prevalence() 443: movingaverage() 444: varevsij() 445: if popbased==1 varevsij(,popbased) 446: total life expectancies 447: Variance of period (stable) prevalence 448: end 449: */ 450: 451: 452: 453: 454: #include <math.h> 455: #include <stdio.h> 456: #include <stdlib.h> 457: #include <string.h> 458: #include <unistd.h> 459: 460: #include <limits.h> 461: #include <sys/types.h> 462: #include <sys/stat.h> 463: #include <errno.h> 464: extern int errno; 465: 466: #ifdef LINUX 467: #include <time.h> 468: #include "timeval.h" 469: #else 470: #include <sys/time.h> 471: #endif 472: 473: #ifdef GSL 474: #include <gsl/gsl_errno.h> 475: #include <gsl/gsl_multimin.h> 476: #endif 477: 478: /* #include <libintl.h> */ 479: /* #define _(String) gettext (String) */ 480: 481: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */ 482: 483: #define GNUPLOTPROGRAM "gnuplot" 484: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/ 485: #define FILENAMELENGTH 132 486: 487: #define GLOCK_ERROR_NOPATH -1 /* empty path */ 488: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */ 489: 490: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */ 491: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */ 492: 493: #define NINTERVMAX 8 494: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */ 495: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */ 496: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */ 497: #define codtabm(h,k) 1 & (h-1) >> (k-1) ; 498: #define MAXN 20000 499: #define YEARM 12. /**< Number of months per year */ 500: #define AGESUP 130 501: #define AGEBASE 40 502: #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */ 503: #ifdef UNIX 504: #define DIRSEPARATOR '/' 505: #define CHARSEPARATOR "/" 506: #define ODIRSEPARATOR '\\' 507: #else 508: #define DIRSEPARATOR '\\' 509: #define CHARSEPARATOR "\\" 510: #define ODIRSEPARATOR '/' 511: #endif 512: 513: /* $Id: imach.c,v 1.153 2014/06/20 16:45:46 brouard Exp $ */ 514: /* $State: Exp $ */ 515: 516: char version[]="Imach version 0.98nT, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)"; 517: char fullversion[]="$Revision: 1.153 $ $Date: 2014/06/20 16:45:46 $"; 518: char strstart[80]; 519: char optionfilext[10], optionfilefiname[FILENAMELENGTH]; 520: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */ 521: int nvar=0, nforce=0; /* Number of variables, number of forces */ 522: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */ 523: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */ 524: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */ 525: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */ 526: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */ 527: int cptcovprodnoage=0; /**< Number of covariate products without age */ 528: int cptcoveff=0; /* Total number of covariates to vary for printing results */ 529: int cptcov=0; /* Working variable */ 530: int npar=NPARMAX; 531: int nlstate=2; /* Number of live states */ 532: int ndeath=1; /* Number of dead states */ 533: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */ 534: int popbased=0; 535: 536: int *wav; /* Number of waves for this individuual 0 is possible */ 537: int maxwav=0; /* Maxim number of waves */ 538: int jmin=0, jmax=0; /* min, max spacing between 2 waves */ 539: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 540: int gipmx=0, gsw=0; /* Global variables on the number of contributions 541: to the likelihood and the sum of weights (done by funcone)*/ 542: int mle=1, weightopt=0; 543: int **mw; /* mw[mi][i] is number of the mi wave for this individual */ 544: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */ 545: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between 546: * wave mi and wave mi+1 is not an exact multiple of stepm. */ 547: double jmean=1; /* Mean space between 2 waves */ 548: double **matprod2(); /* test */ 549: double **oldm, **newm, **savm; /* Working pointers to matrices */ 550: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */ 551: /*FILE *fic ; */ /* Used in readdata only */ 552: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop; 553: FILE *ficlog, *ficrespow; 554: int globpr=0; /* Global variable for printing or not */ 555: double fretone; /* Only one call to likelihood */ 556: long ipmx=0; /* Number of contributions */ 557: double sw; /* Sum of weights */ 558: char filerespow[FILENAMELENGTH]; 559: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */ 560: FILE *ficresilk; 561: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor; 562: FILE *ficresprobmorprev; 563: FILE *fichtm, *fichtmcov; /* Html File */ 564: FILE *ficreseij; 565: char filerese[FILENAMELENGTH]; 566: FILE *ficresstdeij; 567: char fileresstde[FILENAMELENGTH]; 568: FILE *ficrescveij; 569: char filerescve[FILENAMELENGTH]; 570: FILE *ficresvij; 571: char fileresv[FILENAMELENGTH]; 572: FILE *ficresvpl; 573: char fileresvpl[FILENAMELENGTH]; 574: char title[MAXLINE]; 575: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH]; 576: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH]; 577: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH]; 578: char command[FILENAMELENGTH]; 579: int outcmd=0; 580: 581: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH]; 582: 583: char filelog[FILENAMELENGTH]; /* Log file */ 584: char filerest[FILENAMELENGTH]; 585: char fileregp[FILENAMELENGTH]; 586: char popfile[FILENAMELENGTH]; 587: 588: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ; 589: 590: struct timeval start_time, end_time, curr_time, last_time, forecast_time; 591: struct timezone tzp; 592: extern int gettimeofday(); 593: struct tm tmg, tm, tmf, *gmtime(), *localtime(); 594: long time_value; 595: extern long time(); 596: char strcurr[80], strfor[80]; 597: 598: char *endptr; 599: long lval; 600: double dval; 601: 602: #define NR_END 1 603: #define FREE_ARG char* 604: #define FTOL 1.0e-10 605: 606: #define NRANSI 607: #define ITMAX 200 608: 609: #define TOL 2.0e-4 610: 611: #define CGOLD 0.3819660 612: #define ZEPS 1.0e-10 613: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 614: 615: #define GOLD 1.618034 616: #define GLIMIT 100.0 617: #define TINY 1.0e-20 618: 619: static double maxarg1,maxarg2; 620: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2)) 621: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2)) 622: 623: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a)) 624: #define rint(a) floor(a+0.5) 625: 626: static double sqrarg; 627: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg) 628: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 629: int agegomp= AGEGOMP; 630: 631: int imx; 632: int stepm=1; 633: /* Stepm, step in month: minimum step interpolation*/ 634: 635: int estepm; 636: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/ 637: 638: int m,nb; 639: long *num; 640: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens; 641: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint; 642: double **pmmij, ***probs; 643: double *ageexmed,*agecens; 644: double dateintmean=0; 645: 646: double *weight; 647: int **s; /* Status */ 648: double *agedc; 649: double **covar; /**< covar[j,i], value of jth covariate for individual i, 650: * covar=matrix(0,NCOVMAX,1,n); 651: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */ 652: double idx; 653: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */ 654: int *Ndum; /** Freq of modality (tricode */ 655: int **codtab; /**< codtab=imatrix(1,100,1,10); */ 656: int **Tvard, *Tprod, cptcovprod, *Tvaraff; 657: double *lsurv, *lpop, *tpop; 658: 659: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */ 660: double ftolhess; /**< Tolerance for computing hessian */ 661: 662: /**************** split *************************/ 663: static int split( char *path, char *dirc, char *name, char *ext, char *finame ) 664: { 665: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc) 666: the name of the file (name), its extension only (ext) and its first part of the name (finame) 667: */ 668: char *ss; /* pointer */ 669: int l1, l2; /* length counters */ 670: 671: l1 = strlen(path ); /* length of path */ 672: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH ); 673: ss= strrchr( path, DIRSEPARATOR ); /* find last / */ 674: if ( ss == NULL ) { /* no directory, so determine current directory */ 675: strcpy( name, path ); /* we got the fullname name because no directory */ 676: /*if(strrchr(path, ODIRSEPARATOR )==NULL) 677: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/ 678: /* get current working directory */ 679: /* extern char* getcwd ( char *buf , int len);*/ 680: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) { 681: return( GLOCK_ERROR_GETCWD ); 682: } 683: /* got dirc from getcwd*/ 684: printf(" DIRC = %s \n",dirc); 685: } else { /* strip direcotry from path */ 686: ss++; /* after this, the filename */ 687: l2 = strlen( ss ); /* length of filename */ 688: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH ); 689: strcpy( name, ss ); /* save file name */ 690: strncpy( dirc, path, l1 - l2 ); /* now the directory */ 691: dirc[l1-l2] = 0; /* add zero */ 692: printf(" DIRC2 = %s \n",dirc); 693: } 694: /* We add a separator at the end of dirc if not exists */ 695: l1 = strlen( dirc ); /* length of directory */ 696: if( dirc[l1-1] != DIRSEPARATOR ){ 697: dirc[l1] = DIRSEPARATOR; 698: dirc[l1+1] = 0; 699: printf(" DIRC3 = %s \n",dirc); 700: } 701: ss = strrchr( name, '.' ); /* find last / */ 702: if (ss >0){ 703: ss++; 704: strcpy(ext,ss); /* save extension */ 705: l1= strlen( name); 706: l2= strlen(ss)+1; 707: strncpy( finame, name, l1-l2); 708: finame[l1-l2]= 0; 709: } 710: 711: return( 0 ); /* we're done */ 712: } 713: 714: 715: /******************************************/ 716: 717: void replace_back_to_slash(char *s, char*t) 718: { 719: int i; 720: int lg=0; 721: i=0; 722: lg=strlen(t); 723: for(i=0; i<= lg; i++) { 724: (s[i] = t[i]); 725: if (t[i]== '\\') s[i]='/'; 726: } 727: } 728: 729: char *trimbb(char *out, char *in) 730: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */ 731: char *s; 732: s=out; 733: while (*in != '\0'){ 734: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/ 735: in++; 736: } 737: *out++ = *in++; 738: } 739: *out='\0'; 740: return s; 741: } 742: 743: char *cutl(char *blocc, char *alocc, char *in, char occ) 744: { 745: /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 746: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2') 747: gives blocc="abcdef2ghi" and alocc="j". 748: If occ is not found blocc is null and alocc is equal to in. Returns blocc 749: */ 750: char *s, *t, *bl; 751: t=in;s=in; 752: while ((*in != occ) && (*in != '\0')){ 753: *alocc++ = *in++; 754: } 755: if( *in == occ){ 756: *(alocc)='\0'; 757: s=++in; 758: } 759: 760: if (s == t) {/* occ not found */ 761: *(alocc-(in-s))='\0'; 762: in=s; 763: } 764: while ( *in != '\0'){ 765: *blocc++ = *in++; 766: } 767: 768: *blocc='\0'; 769: return t; 770: } 771: char *cutv(char *blocc, char *alocc, char *in, char occ) 772: { 773: /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 774: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2') 775: gives blocc="abcdef2ghi" and alocc="j". 776: If occ is not found blocc is null and alocc is equal to in. Returns alocc 777: */ 778: char *s, *t; 779: t=in;s=in; 780: while (*in != '\0'){ 781: while( *in == occ){ 782: *blocc++ = *in++; 783: s=in; 784: } 785: *blocc++ = *in++; 786: } 787: if (s == t) /* occ not found */ 788: *(blocc-(in-s))='\0'; 789: else 790: *(blocc-(in-s)-1)='\0'; 791: in=s; 792: while ( *in != '\0'){ 793: *alocc++ = *in++; 794: } 795: 796: *alocc='\0'; 797: return s; 798: } 799: 800: int nbocc(char *s, char occ) 801: { 802: int i,j=0; 803: int lg=20; 804: i=0; 805: lg=strlen(s); 806: for(i=0; i<= lg; i++) { 807: if (s[i] == occ ) j++; 808: } 809: return j; 810: } 811: 812: /* void cutv(char *u,char *v, char*t, char occ) */ 813: /* { */ 814: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */ 815: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */ 816: /* gives u="abcdef2ghi" and v="j" *\/ */ 817: /* int i,lg,j,p=0; */ 818: /* i=0; */ 819: /* lg=strlen(t); */ 820: /* for(j=0; j<=lg-1; j++) { */ 821: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */ 822: /* } */ 823: 824: /* for(j=0; j<p; j++) { */ 825: /* (u[j] = t[j]); */ 826: /* } */ 827: /* u[p]='\0'; */ 828: 829: /* for(j=0; j<= lg; j++) { */ 830: /* if (j>=(p+1))(v[j-p-1] = t[j]); */ 831: /* } */ 832: /* } */ 833: 834: /********************** nrerror ********************/ 835: 836: void nrerror(char error_text[]) 837: { 838: fprintf(stderr,"ERREUR ...\n"); 839: fprintf(stderr,"%s\n",error_text); 840: exit(EXIT_FAILURE); 841: } 842: /*********************** vector *******************/ 843: double *vector(int nl, int nh) 844: { 845: double *v; 846: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double))); 847: if (!v) nrerror("allocation failure in vector"); 848: return v-nl+NR_END; 849: } 850: 851: /************************ free vector ******************/ 852: void free_vector(double*v, int nl, int nh) 853: { 854: free((FREE_ARG)(v+nl-NR_END)); 855: } 856: 857: /************************ivector *******************************/ 858: int *ivector(long nl,long nh) 859: { 860: int *v; 861: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int))); 862: if (!v) nrerror("allocation failure in ivector"); 863: return v-nl+NR_END; 864: } 865: 866: /******************free ivector **************************/ 867: void free_ivector(int *v, long nl, long nh) 868: { 869: free((FREE_ARG)(v+nl-NR_END)); 870: } 871: 872: /************************lvector *******************************/ 873: long *lvector(long nl,long nh) 874: { 875: long *v; 876: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long))); 877: if (!v) nrerror("allocation failure in ivector"); 878: return v-nl+NR_END; 879: } 880: 881: /******************free lvector **************************/ 882: void free_lvector(long *v, long nl, long nh) 883: { 884: free((FREE_ARG)(v+nl-NR_END)); 885: } 886: 887: /******************* imatrix *******************************/ 888: int **imatrix(long nrl, long nrh, long ncl, long nch) 889: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 890: { 891: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 892: int **m; 893: 894: /* allocate pointers to rows */ 895: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 896: if (!m) nrerror("allocation failure 1 in matrix()"); 897: m += NR_END; 898: m -= nrl; 899: 900: 901: /* allocate rows and set pointers to them */ 902: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 903: if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 904: m[nrl] += NR_END; 905: m[nrl] -= ncl; 906: 907: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 908: 909: /* return pointer to array of pointers to rows */ 910: return m; 911: } 912: 913: /****************** free_imatrix *************************/ 914: void free_imatrix(m,nrl,nrh,ncl,nch) 915: int **m; 916: long nch,ncl,nrh,nrl; 917: /* free an int matrix allocated by imatrix() */ 918: { 919: free((FREE_ARG) (m[nrl]+ncl-NR_END)); 920: free((FREE_ARG) (m+nrl-NR_END)); 921: } 922: 923: /******************* matrix *******************************/ 924: double **matrix(long nrl, long nrh, long ncl, long nch) 925: { 926: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1; 927: double **m; 928: 929: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*))); 930: if (!m) nrerror("allocation failure 1 in matrix()"); 931: m += NR_END; 932: m -= nrl; 933: 934: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double))); 935: if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 936: m[nrl] += NR_END; 937: m[nrl] -= ncl; 938: 939: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol; 940: return m; 941: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0]) 942: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress 943: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized. 944: */ 945: } 946: 947: /*************************free matrix ************************/ 948: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch) 949: { 950: free((FREE_ARG)(m[nrl]+ncl-NR_END)); 951: free((FREE_ARG)(m+nrl-NR_END)); 952: } 953: 954: /******************* ma3x *******************************/ 955: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh) 956: { 957: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1; 958: double ***m; 959: 960: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*))); 961: if (!m) nrerror("allocation failure 1 in matrix()"); 962: m += NR_END; 963: m -= nrl; 964: 965: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double))); 966: if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 967: m[nrl] += NR_END; 968: m[nrl] -= ncl; 969: 970: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol; 971: 972: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double))); 973: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()"); 974: m[nrl][ncl] += NR_END; 975: m[nrl][ncl] -= nll; 976: for (j=ncl+1; j<=nch; j++) 977: m[nrl][j]=m[nrl][j-1]+nlay; 978: 979: for (i=nrl+1; i<=nrh; i++) { 980: m[i][ncl]=m[i-1l][ncl]+ncol*nlay; 981: for (j=ncl+1; j<=nch; j++) 982: m[i][j]=m[i][j-1]+nlay; 983: } 984: return m; 985: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1]) 986: &(m[i][j][k]) <=> *((*(m+i) + j)+k) 987: */ 988: } 989: 990: /*************************free ma3x ************************/ 991: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh) 992: { 993: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END)); 994: free((FREE_ARG)(m[nrl]+ncl-NR_END)); 995: free((FREE_ARG)(m+nrl-NR_END)); 996: } 997: 998: /*************** function subdirf ***********/ 999: char *subdirf(char fileres[]) 1000: { 1001: /* Caution optionfilefiname is hidden */ 1002: strcpy(tmpout,optionfilefiname); 1003: strcat(tmpout,"/"); /* Add to the right */ 1004: strcat(tmpout,fileres); 1005: return tmpout; 1006: } 1007: 1008: /*************** function subdirf2 ***********/ 1009: char *subdirf2(char fileres[], char *preop) 1010: { 1011: 1012: /* Caution optionfilefiname is hidden */ 1013: strcpy(tmpout,optionfilefiname); 1014: strcat(tmpout,"/"); 1015: strcat(tmpout,preop); 1016: strcat(tmpout,fileres); 1017: return tmpout; 1018: } 1019: 1020: /*************** function subdirf3 ***********/ 1021: char *subdirf3(char fileres[], char *preop, char *preop2) 1022: { 1023: 1024: /* Caution optionfilefiname is hidden */ 1025: strcpy(tmpout,optionfilefiname); 1026: strcat(tmpout,"/"); 1027: strcat(tmpout,preop); 1028: strcat(tmpout,preop2); 1029: strcat(tmpout,fileres); 1030: return tmpout; 1031: } 1032: 1033: /***************** f1dim *************************/ 1034: extern int ncom; 1035: extern double *pcom,*xicom; 1036: extern double (*nrfunc)(double []); 1037: 1038: double f1dim(double x) 1039: { 1040: int j; 1041: double f; 1042: double *xt; 1043: 1044: xt=vector(1,ncom); 1045: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 1046: f=(*nrfunc)(xt); 1047: free_vector(xt,1,ncom); 1048: return f; 1049: } 1050: 1051: /*****************brent *************************/ 1052: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin) 1053: { 1054: int iter; 1055: double a,b,d,etemp; 1056: double fu,fv,fw,fx; 1057: double ftemp; 1058: double p,q,r,tol1,tol2,u,v,w,x,xm; 1059: double e=0.0; 1060: 1061: a=(ax < cx ? ax : cx); 1062: b=(ax > cx ? ax : cx); 1063: x=w=v=bx; 1064: fw=fv=fx=(*f)(x); 1065: for (iter=1;iter<=ITMAX;iter++) { 1066: xm=0.5*(a+b); 1067: tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 1068: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/ 1069: printf(".");fflush(stdout); 1070: fprintf(ficlog,".");fflush(ficlog); 1071: #ifdef DEBUG 1072: printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol); 1073: fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol); 1074: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */ 1075: #endif 1076: if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 1077: *xmin=x; 1078: return fx; 1079: } 1080: ftemp=fu; 1081: if (fabs(e) > tol1) { 1082: r=(x-w)*(fx-fv); 1083: q=(x-v)*(fx-fw); 1084: p=(x-v)*q-(x-w)*r; 1085: q=2.0*(q-r); 1086: if (q > 0.0) p = -p; 1087: q=fabs(q); 1088: etemp=e; 1089: e=d; 1090: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 1091: d=CGOLD*(e=(x >= xm ? a-x : b-x)); 1092: else { 1093: d=p/q; 1094: u=x+d; 1095: if (u-a < tol2 || b-u < tol2) 1096: d=SIGN(tol1,xm-x); 1097: } 1098: } else { 1099: d=CGOLD*(e=(x >= xm ? a-x : b-x)); 1100: } 1101: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 1102: fu=(*f)(u); 1103: if (fu <= fx) { 1104: if (u >= x) a=x; else b=x; 1105: SHFT(v,w,x,u) 1106: SHFT(fv,fw,fx,fu) 1107: } else { 1108: if (u < x) a=u; else b=u; 1109: if (fu <= fw || w == x) { 1110: v=w; 1111: w=u; 1112: fv=fw; 1113: fw=fu; 1114: } else if (fu <= fv || v == x || v == w) { 1115: v=u; 1116: fv=fu; 1117: } 1118: } 1119: } 1120: nrerror("Too many iterations in brent"); 1121: *xmin=x; 1122: return fx; 1123: } 1124: 1125: /****************** mnbrak ***********************/ 1126: 1127: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 1128: double (*func)(double)) 1129: { 1130: double ulim,u,r,q, dum; 1131: double fu; 1132: 1133: *fa=(*func)(*ax); 1134: *fb=(*func)(*bx); 1135: if (*fb > *fa) { 1136: SHFT(dum,*ax,*bx,dum) 1137: SHFT(dum,*fb,*fa,dum) 1138: } 1139: *cx=(*bx)+GOLD*(*bx-*ax); 1140: *fc=(*func)(*cx); 1141: while (*fb > *fc) { 1142: r=(*bx-*ax)*(*fb-*fc); 1143: q=(*bx-*cx)*(*fb-*fa); 1144: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 1145: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 1146: ulim=(*bx)+GLIMIT*(*cx-*bx); 1147: if ((*bx-u)*(u-*cx) > 0.0) { 1148: fu=(*func)(u); 1149: } else if ((*cx-u)*(u-ulim) > 0.0) { 1150: fu=(*func)(u); 1151: if (fu < *fc) { 1152: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 1153: SHFT(*fb,*fc,fu,(*func)(u)) 1154: } 1155: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 1156: u=ulim; 1157: fu=(*func)(u); 1158: } else { 1159: u=(*cx)+GOLD*(*cx-*bx); 1160: fu=(*func)(u); 1161: } 1162: SHFT(*ax,*bx,*cx,u) 1163: SHFT(*fa,*fb,*fc,fu) 1164: } 1165: } 1166: 1167: /*************** linmin ************************/ 1168: 1169: int ncom; 1170: double *pcom,*xicom; 1171: double (*nrfunc)(double []); 1172: 1173: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 1174: { 1175: double brent(double ax, double bx, double cx, 1176: double (*f)(double), double tol, double *xmin); 1177: double f1dim(double x); 1178: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 1179: double *fc, double (*func)(double)); 1180: int j; 1181: double xx,xmin,bx,ax; 1182: double fx,fb,fa; 1183: 1184: ncom=n; 1185: pcom=vector(1,n); 1186: xicom=vector(1,n); 1187: nrfunc=func; 1188: for (j=1;j<=n;j++) { 1189: pcom[j]=p[j]; 1190: xicom[j]=xi[j]; 1191: } 1192: ax=0.0; 1193: xx=1.0; 1194: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 1195: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 1196: #ifdef DEBUG 1197: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin); 1198: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin); 1199: #endif 1200: for (j=1;j<=n;j++) { 1201: xi[j] *= xmin; 1202: p[j] += xi[j]; 1203: } 1204: free_vector(xicom,1,n); 1205: free_vector(pcom,1,n); 1206: } 1207: 1208: char *asc_diff_time(long time_sec, char ascdiff[]) 1209: { 1210: long sec_left, days, hours, minutes; 1211: days = (time_sec) / (60*60*24); 1212: sec_left = (time_sec) % (60*60*24); 1213: hours = (sec_left) / (60*60) ; 1214: sec_left = (sec_left) %(60*60); 1215: minutes = (sec_left) /60; 1216: sec_left = (sec_left) % (60); 1217: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left); 1218: return ascdiff; 1219: } 1220: 1221: /*************** powell ************************/ 1222: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 1223: double (*func)(double [])) 1224: { 1225: void linmin(double p[], double xi[], int n, double *fret, 1226: double (*func)(double [])); 1227: int i,ibig,j; 1228: double del,t,*pt,*ptt,*xit; 1229: double fp,fptt; 1230: double *xits; 1231: int niterf, itmp; 1232: 1233: pt=vector(1,n); 1234: ptt=vector(1,n); 1235: xit=vector(1,n); 1236: xits=vector(1,n); 1237: *fret=(*func)(p); 1238: for (j=1;j<=n;j++) pt[j]=p[j]; 1239: for (*iter=1;;++(*iter)) { 1240: fp=(*fret); 1241: ibig=0; 1242: del=0.0; 1243: last_time=curr_time; 1244: (void) gettimeofday(&curr_time,&tzp); 1245: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout); 1246: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog); 1247: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */ 1248: for (i=1;i<=n;i++) { 1249: printf(" %d %.12f",i, p[i]); 1250: fprintf(ficlog," %d %.12lf",i, p[i]); 1251: fprintf(ficrespow," %.12lf", p[i]); 1252: } 1253: printf("\n"); 1254: fprintf(ficlog,"\n"); 1255: fprintf(ficrespow,"\n");fflush(ficrespow); 1256: if(*iter <=3){ 1257: tm = *localtime(&curr_time.tv_sec); 1258: strcpy(strcurr,asctime(&tm)); 1259: /* asctime_r(&tm,strcurr); */ 1260: forecast_time=curr_time; 1261: itmp = strlen(strcurr); 1262: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */ 1263: strcurr[itmp-1]='\0'; 1264: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec); 1265: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec); 1266: for(niterf=10;niterf<=30;niterf+=10){ 1267: forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec); 1268: tmf = *localtime(&forecast_time.tv_sec); 1269: /* asctime_r(&tmf,strfor); */ 1270: strcpy(strfor,asctime(&tmf)); 1271: itmp = strlen(strfor); 1272: if(strfor[itmp-1]=='\n') 1273: strfor[itmp-1]='\0'; 1274: printf(" - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr); 1275: fprintf(ficlog," - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr); 1276: } 1277: } 1278: for (i=1;i<=n;i++) { 1279: for (j=1;j<=n;j++) xit[j]=xi[j][i]; 1280: fptt=(*fret); 1281: #ifdef DEBUG 1282: printf("fret=%lf \n",*fret); 1283: fprintf(ficlog,"fret=%lf \n",*fret); 1284: #endif 1285: printf("%d",i);fflush(stdout); 1286: fprintf(ficlog,"%d",i);fflush(ficlog); 1287: linmin(p,xit,n,fret,func); 1288: if (fabs(fptt-(*fret)) > del) { 1289: del=fabs(fptt-(*fret)); 1290: ibig=i; 1291: } 1292: #ifdef DEBUG 1293: printf("%d %.12e",i,(*fret)); 1294: fprintf(ficlog,"%d %.12e",i,(*fret)); 1295: for (j=1;j<=n;j++) { 1296: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5); 1297: printf(" x(%d)=%.12e",j,xit[j]); 1298: fprintf(ficlog," x(%d)=%.12e",j,xit[j]); 1299: } 1300: for(j=1;j<=n;j++) { 1301: printf(" p=%.12e",p[j]); 1302: fprintf(ficlog," p=%.12e",p[j]); 1303: } 1304: printf("\n"); 1305: fprintf(ficlog,"\n"); 1306: #endif 1307: } 1308: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { 1309: #ifdef DEBUG 1310: int k[2],l; 1311: k[0]=1; 1312: k[1]=-1; 1313: printf("Max: %.12e",(*func)(p)); 1314: fprintf(ficlog,"Max: %.12e",(*func)(p)); 1315: for (j=1;j<=n;j++) { 1316: printf(" %.12e",p[j]); 1317: fprintf(ficlog," %.12e",p[j]); 1318: } 1319: printf("\n"); 1320: fprintf(ficlog,"\n"); 1321: for(l=0;l<=1;l++) { 1322: for (j=1;j<=n;j++) { 1323: ptt[j]=p[j]+(p[j]-pt[j])*k[l]; 1324: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]); 1325: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]); 1326: } 1327: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p))); 1328: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p))); 1329: } 1330: #endif 1331: 1332: 1333: free_vector(xit,1,n); 1334: free_vector(xits,1,n); 1335: free_vector(ptt,1,n); 1336: free_vector(pt,1,n); 1337: return; 1338: } 1339: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 1340: for (j=1;j<=n;j++) { 1341: ptt[j]=2.0*p[j]-pt[j]; 1342: xit[j]=p[j]-pt[j]; 1343: pt[j]=p[j]; 1344: } 1345: fptt=(*func)(ptt); 1346: if (fptt < fp) { 1347: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 1348: if (t < 0.0) { 1349: linmin(p,xit,n,fret,func); 1350: for (j=1;j<=n;j++) { 1351: xi[j][ibig]=xi[j][n]; 1352: xi[j][n]=xit[j]; 1353: } 1354: #ifdef DEBUG 1355: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig); 1356: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig); 1357: for(j=1;j<=n;j++){ 1358: printf(" %.12e",xit[j]); 1359: fprintf(ficlog," %.12e",xit[j]); 1360: } 1361: printf("\n"); 1362: fprintf(ficlog,"\n"); 1363: #endif 1364: } 1365: } 1366: } 1367: } 1368: 1369: /**** Prevalence limit (stable or period prevalence) ****************/ 1370: 1371: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij) 1372: { 1373: /* Computes the prevalence limit in each live state at age x by left multiplying the unit 1374: matrix by transitions matrix until convergence is reached */ 1375: 1376: int i, ii,j,k; 1377: double min, max, maxmin, maxmax,sumnew=0.; 1378: /* double **matprod2(); */ /* test */ 1379: double **out, cov[NCOVMAX+1], **pmij(); 1380: double **newm; 1381: double agefin, delaymax=50 ; /* Max number of years to converge */ 1382: 1383: for (ii=1;ii<=nlstate+ndeath;ii++) 1384: for (j=1;j<=nlstate+ndeath;j++){ 1385: oldm[ii][j]=(ii==j ? 1.0 : 0.0); 1386: } 1387: 1388: cov[1]=1.; 1389: 1390: /* Even if hstepm = 1, at least one multiplication by the unit matrix */ 1391: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){ 1392: newm=savm; 1393: /* Covariates have to be included here again */ 1394: cov[2]=agefin; 1395: 1396: for (k=1; k<=cptcovn;k++) { 1397: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; 1398: /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/ 1399: } 1400: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */ 1401: /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */ 1402: /* cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */ 1403: 1404: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/ 1405: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/ 1406: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/ 1407: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */ 1408: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */ 1409: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */ 1410: 1411: savm=oldm; 1412: oldm=newm; 1413: maxmax=0.; 1414: for(j=1;j<=nlstate;j++){ 1415: min=1.; 1416: max=0.; 1417: for(i=1; i<=nlstate; i++) { 1418: sumnew=0; 1419: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k]; 1420: prlim[i][j]= newm[i][j]/(1-sumnew); 1421: /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/ 1422: max=FMAX(max,prlim[i][j]); 1423: min=FMIN(min,prlim[i][j]); 1424: } 1425: maxmin=max-min; 1426: maxmax=FMAX(maxmax,maxmin); 1427: } 1428: if(maxmax < ftolpl){ 1429: return prlim; 1430: } 1431: } 1432: } 1433: 1434: /*************** transition probabilities ***************/ 1435: 1436: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate ) 1437: { 1438: /* According to parameters values stored in x and the covariate's values stored in cov, 1439: computes the probability to be observed in state j being in state i by appying the 1440: model to the ncovmodel covariates (including constant and age). 1441: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc] 1442: and, according on how parameters are entered, the position of the coefficient xij(nc) of the 1443: ncth covariate in the global vector x is given by the formula: 1444: j=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel 1446: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation, 1447: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij. 1448: Outputs ps[i][j] the probability to be observed in j being in j according to 1449: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij] 1450: */ 1451: double s1, lnpijopii; 1452: /*double t34;*/ 1453: int i,j,j1, nc, ii, jj; 1454: 1455: for(i=1; i<= nlstate; i++){ 1456: for(j=1; j<i;j++){ 1457: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){ 1458: /*lnpijopii += param[i][j][nc]*cov[nc];*/ 1459: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc]; 1460: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */ 1461: } 1462: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */ 1463: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */ 1464: } 1465: for(j=i+1; j<=nlstate+ndeath;j++){ 1466: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){ 1467: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/ 1468: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc]; 1469: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */ 1470: } 1471: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */ 1472: } 1473: } 1474: 1475: for(i=1; i<= nlstate; i++){ 1476: s1=0; 1477: for(j=1; j<i; j++){ 1478: s1+=exp(ps[i][j]); /* In fact sums pij/pii */ 1479: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */ 1480: } 1481: for(j=i+1; j<=nlstate+ndeath; j++){ 1482: s1+=exp(ps[i][j]); /* In fact sums pij/pii */ 1483: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */ 1484: } 1485: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */ 1486: ps[i][i]=1./(s1+1.); 1487: /* Computing other pijs */ 1488: for(j=1; j<i; j++) 1489: ps[i][j]= exp(ps[i][j])*ps[i][i]; 1490: for(j=i+1; j<=nlstate+ndeath; j++) 1491: ps[i][j]= exp(ps[i][j])*ps[i][i]; 1492: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */ 1493: } /* end i */ 1494: 1495: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){ 1496: for(jj=1; jj<= nlstate+ndeath; jj++){ 1497: ps[ii][jj]=0; 1498: ps[ii][ii]=1; 1499: } 1500: } 1501: 1502: 1503: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */ 1504: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */ 1505: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */ 1506: /* } */ 1507: /* printf("\n "); */ 1508: /* } */ 1509: /* printf("\n ");printf("%lf ",cov[2]);*/ 1510: /* 1511: for(i=1; i<= npar; i++) printf("%f ",x[i]); 1512: goto end;*/ 1513: return ps; 1514: } 1515: 1516: /**************** Product of 2 matrices ******************/ 1517: 1518: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b) 1519: { 1520: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times 1521: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */ 1522: /* in, b, out are matrice of pointers which should have been initialized 1523: before: only the contents of out is modified. The function returns 1524: a pointer to pointers identical to out */ 1525: int i, j, k; 1526: for(i=nrl; i<= nrh; i++) 1527: for(k=ncolol; k<=ncoloh; k++){ 1528: out[i][k]=0.; 1529: for(j=ncl; j<=nch; j++) 1530: out[i][k] +=in[i][j]*b[j][k]; 1531: } 1532: return out; 1533: } 1534: 1535: 1536: /************* Higher Matrix Product ***************/ 1537: 1538: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij ) 1539: { 1540: /* Computes the transition matrix starting at age 'age' over 1541: 'nhstepm*hstepm*stepm' months (i.e. until 1542: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying 1543: nhstepm*hstepm matrices. 1544: Output is stored in matrix po[i][j][h] for h every 'hstepm' step 1545: (typically every 2 years instead of every month which is too big 1546: for the memory). 1547: Model is determined by parameters x and covariates have to be 1548: included manually here. 1549: 1550: */ 1551: 1552: int i, j, d, h, k; 1553: double **out, cov[NCOVMAX+1]; 1554: double **newm; 1555: 1556: /* Hstepm could be zero and should return the unit matrix */ 1557: for (i=1;i<=nlstate+ndeath;i++) 1558: for (j=1;j<=nlstate+ndeath;j++){ 1559: oldm[i][j]=(i==j ? 1.0 : 0.0); 1560: po[i][j][0]=(i==j ? 1.0 : 0.0); 1561: } 1562: /* Even if hstepm = 1, at least one multiplication by the unit matrix */ 1563: for(h=1; h <=nhstepm; h++){ 1564: for(d=1; d <=hstepm; d++){ 1565: newm=savm; 1566: /* Covariates have to be included here again */ 1567: cov[1]=1.; 1568: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM; 1569: for (k=1; k<=cptcovn;k++) 1570: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; 1571: for (k=1; k<=cptcovage;k++) 1572: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; 1573: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */ 1574: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; 1575: 1576: 1577: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/ 1578: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/ 1579: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 1580: pmij(pmmij,cov,ncovmodel,x,nlstate)); 1581: savm=oldm; 1582: oldm=newm; 1583: } 1584: for(i=1; i<=nlstate+ndeath; i++) 1585: for(j=1;j<=nlstate+ndeath;j++) { 1586: po[i][j][h]=newm[i][j]; 1587: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/ 1588: } 1589: /*printf("h=%d ",h);*/ 1590: } /* end h */ 1591: /* printf("\n H=%d \n",h); */ 1592: return po; 1593: } 1594: 1595: 1596: /*************** log-likelihood *************/ 1597: double func( double *x) 1598: { 1599: int i, ii, j, k, mi, d, kk; 1600: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1]; 1601: double **out; 1602: double sw; /* Sum of weights */ 1603: double lli; /* Individual log likelihood */ 1604: int s1, s2; 1605: double bbh, survp; 1606: long ipmx; 1607: /*extern weight */ 1608: /* We are differentiating ll according to initial status */ 1609: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/ 1610: /*for(i=1;i<imx;i++) 1611: printf(" %d\n",s[4][i]); 1612: */ 1613: cov[1]=1.; 1614: 1615: for(k=1; k<=nlstate; k++) ll[k]=0.; 1616: 1617: if(mle==1){ 1618: for (i=1,ipmx=0, sw=0.; i<=imx; i++){ 1619: /* Computes the values of the ncovmodel covariates of the model 1620: depending if the covariates are fixed or variying (age dependent) and stores them in cov[] 1621: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability 1622: to be observed in j being in i according to the model. 1623: */ 1624: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */ 1625: cov[2+k]=covar[Tvar[k]][i]; 1626: } 1627: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 1628: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 1629: has been calculated etc */ 1630: for(mi=1; mi<= wav[i]-1; mi++){ 1631: for (ii=1;ii<=nlstate+ndeath;ii++) 1632: for (j=1;j<=nlstate+ndeath;j++){ 1633: oldm[ii][j]=(ii==j ? 1.0 : 0.0); 1634: savm[ii][j]=(ii==j ? 1.0 : 0.0); 1635: } 1636: for(d=0; d<dh[mi][i]; d++){ 1637: newm=savm; 1638: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM; 1639: for (kk=1; kk<=cptcovage;kk++) { 1640: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */ 1641: } 1642: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, 1643: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); 1644: savm=oldm; 1645: oldm=newm; 1646: } /* end mult */ 1647: 1648: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */ 1649: /* But now since version 0.9 we anticipate for bias at large stepm. 1650: * If stepm is larger than one month (smallest stepm) and if the exact delay 1651: * (in months) between two waves is not a multiple of stepm, we rounded to 1652: * the nearest (and in case of equal distance, to the lowest) interval but now 1653: * we keep into memory the bias bh[mi][i] and also the previous matrix product 1654: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the 1655: * probability in order to take into account the bias as a fraction of the way 1656: * from savm to out if bh is negative or even beyond if bh is positive. bh varies 1657: * -stepm/2 to stepm/2 . 1658: * For stepm=1 the results are the same as for previous versions of Imach. 1659: * For stepm > 1 the results are less biased than in previous versions. 1660: */ 1661: s1=s[mw[mi][i]][i]; 1662: s2=s[mw[mi+1][i]][i]; 1663: bbh=(double)bh[mi][i]/(double)stepm; 1664: /* bias bh is positive if real duration 1665: * is higher than the multiple of stepm and negative otherwise. 1666: */ 1667: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/ 1668: if( s2 > nlstate){ 1669: /* i.e. if s2 is a death state and if the date of death is known 1670: then the contribution to the likelihood is the probability to 1671: die between last step unit time and current step unit time, 1672: which is also equal to probability to die before dh 1673: minus probability to die before dh-stepm . 1674: In version up to 0.92 likelihood was computed 1675: as if date of death was unknown. Death was treated as any other 1676: health state: the date of the interview describes the actual state 1677: and not the date of a change in health state. The former idea was 1678: to consider that at each interview the state was recorded 1679: (healthy, disable or death) and IMaCh was corrected; but when we 1680: introduced the exact date of death then we should have modified 1681: the contribution of an exact death to the likelihood. This new 1682: contribution is smaller and very dependent of the step unit 1683: stepm. It is no more the probability to die between last interview 1684: and month of death but the probability to survive from last 1685: interview up to one month before death multiplied by the 1686: probability to die within a month. Thanks to Chris 1687: Jackson for correcting this bug. Former versions increased 1688: mortality artificially. The bad side is that we add another loop 1689: which slows down the processing. The difference can be up to 10% 1690: lower mortality. 1691: */ 1692: lli=log(out[s1][s2] - savm[s1][s2]); 1693: 1694: 1695: } else if (s2==-2) { 1696: for (j=1,survp=0. ; j<=nlstate; j++) 1697: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; 1698: /*survp += out[s1][j]; */ 1699: lli= log(survp); 1700: } 1701: 1702: else if (s2==-4) { 1703: for (j=3,survp=0. ; j<=nlstate; j++) 1704: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; 1705: lli= log(survp); 1706: } 1707: 1708: else if (s2==-5) { 1709: for (j=1,survp=0. ; j<=2; j++) 1710: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; 1711: lli= log(survp); 1712: } 1713: 1714: else{ 1715: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */ 1716: /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */ 1717: } 1718: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/ 1719: /*if(lli ==000.0)*/ 1720: /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */ 1721: ipmx +=1; 1722: sw += weight[i]; 1723: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; 1724: } /* end of wave */ 1725: } /* end of individual */ 1726: } else if(mle==2){ 1727: for (i=1,ipmx=0, sw=0.; i<=imx; i++){ 1728: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i]; 1729: for(mi=1; mi<= wav[i]-1; mi++){ 1730: for (ii=1;ii<=nlstate+ndeath;ii++) 1731: for (j=1;j<=nlstate+ndeath;j++){ 1732: oldm[ii][j]=(ii==j ? 1.0 : 0.0); 1733: savm[ii][j]=(ii==j ? 1.0 : 0.0); 1734: } 1735: for(d=0; d<=dh[mi][i]; d++){ 1736: newm=savm; 1737: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM; 1738: for (kk=1; kk<=cptcovage;kk++) { 1739: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; 1740: } 1741: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, 1742: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); 1743: savm=oldm; 1744: oldm=newm; 1745: } /* end mult */ 1746: 1747: s1=s[mw[mi][i]][i]; 1748: s2=s[mw[mi+1][i]][i]; 1749: bbh=(double)bh[mi][i]/(double)stepm; 1750: lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */ 1751: ipmx +=1; 1752: sw += weight[i]; 1753: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; 1754: } /* end of wave */ 1755: } /* end of individual */ 1756: } else if(mle==3){ /* exponential inter-extrapolation */ 1757: for (i=1,ipmx=0, sw=0.; i<=imx; i++){ 1758: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i]; 1759: for(mi=1; mi<= wav[i]-1; mi++){ 1760: for (ii=1;ii<=nlstate+ndeath;ii++) 1761: for (j=1;j<=nlstate+ndeath;j++){ 1762: oldm[ii][j]=(ii==j ? 1.0 : 0.0); 1763: savm[ii][j]=(ii==j ? 1.0 : 0.0); 1764: } 1765: for(d=0; d<dh[mi][i]; d++){ 1766: newm=savm; 1767: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM; 1768: for (kk=1; kk<=cptcovage;kk++) { 1769: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; 1770: } 1771: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, 1772: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); 1773: savm=oldm; 1774: oldm=newm; 1775: } /* end mult */ 1776: 1777: s1=s[mw[mi][i]][i]; 1778: s2=s[mw[mi+1][i]][i]; 1779: bbh=(double)bh[mi][i]/(double)stepm; 1780: lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */ 1781: ipmx +=1; 1782: sw += weight[i]; 1783: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; 1784: } /* end of wave */ 1785: } /* end of individual */ 1786: }else if (mle==4){ /* ml=4 no inter-extrapolation */ 1787: for (i=1,ipmx=0, sw=0.; i<=imx; i++){ 1788: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i]; 1789: for(mi=1; mi<= wav[i]-1; mi++){ 1790: for (ii=1;ii<=nlstate+ndeath;ii++) 1791: for (j=1;j<=nlstate+ndeath;j++){ 1792: oldm[ii][j]=(ii==j ? 1.0 : 0.0); 1793: savm[ii][j]=(ii==j ? 1.0 : 0.0); 1794: } 1795: for(d=0; d<dh[mi][i]; d++){ 1796: newm=savm; 1797: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM; 1798: for (kk=1; kk<=cptcovage;kk++) { 1799: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; 1800: } 1801: 1802: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, 1803: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); 1804: savm=oldm; 1805: oldm=newm; 1806: } /* end mult */ 1807: 1808: s1=s[mw[mi][i]][i]; 1809: s2=s[mw[mi+1][i]][i]; 1810: if( s2 > nlstate){ 1811: lli=log(out[s1][s2] - savm[s1][s2]); 1812: }else{ 1813: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */ 1814: } 1815: ipmx +=1; 1816: sw += weight[i]; 1817: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; 1818: /* printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */ 1819: } /* end of wave */ 1820: } /* end of individual */ 1821: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */ 1822: for (i=1,ipmx=0, sw=0.; i<=imx; i++){ 1823: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i]; 1824: for(mi=1; mi<= wav[i]-1; mi++){ 1825: for (ii=1;ii<=nlstate+ndeath;ii++) 1826: for (j=1;j<=nlstate+ndeath;j++){ 1827: oldm[ii][j]=(ii==j ? 1.0 : 0.0); 1828: savm[ii][j]=(ii==j ? 1.0 : 0.0); 1829: } 1830: for(d=0; d<dh[mi][i]; d++){ 1831: newm=savm; 1832: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM; 1833: for (kk=1; kk<=cptcovage;kk++) { 1834: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; 1835: } 1836: 1837: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, 1838: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); 1839: savm=oldm; 1840: oldm=newm; 1841: } /* end mult */ 1842: 1843: s1=s[mw[mi][i]][i]; 1844: s2=s[mw[mi+1][i]][i]; 1845: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */ 1846: ipmx +=1; 1847: sw += weight[i]; 1848: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; 1849: /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/ 1850: } /* end of wave */ 1851: } /* end of individual */ 1852: } /* End of if */ 1853: for(k=1,l=0.; k<=nlstate; k++) l += ll[k]; 1854: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */ 1855: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */ 1856: return -l; 1857: } 1858: 1859: /*************** log-likelihood *************/ 1860: double funcone( double *x) 1861: { 1862: /* Same as likeli but slower because of a lot of printf and if */ 1863: int i, ii, j, k, mi, d, kk; 1864: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1]; 1865: double **out; 1866: double lli; /* Individual log likelihood */ 1867: double llt; 1868: int s1, s2; 1869: double bbh, survp; 1870: /*extern weight */ 1871: /* We are differentiating ll according to initial status */ 1872: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/ 1873: /*for(i=1;i<imx;i++) 1874: printf(" %d\n",s[4][i]); 1875: */ 1876: cov[1]=1.; 1877: 1878: for(k=1; k<=nlstate; k++) ll[k]=0.; 1879: 1880: for (i=1,ipmx=0, sw=0.; i<=imx; i++){ 1881: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i]; 1882: for(mi=1; mi<= wav[i]-1; mi++){ 1883: for (ii=1;ii<=nlstate+ndeath;ii++) 1884: for (j=1;j<=nlstate+ndeath;j++){ 1885: oldm[ii][j]=(ii==j ? 1.0 : 0.0); 1886: savm[ii][j]=(ii==j ? 1.0 : 0.0); 1887: } 1888: for(d=0; d<dh[mi][i]; d++){ 1889: newm=savm; 1890: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM; 1891: for (kk=1; kk<=cptcovage;kk++) { 1892: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; 1893: } 1894: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */ 1895: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, 1896: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); 1897: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */ 1898: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */ 1899: savm=oldm; 1900: oldm=newm; 1901: } /* end mult */ 1902: 1903: s1=s[mw[mi][i]][i]; 1904: s2=s[mw[mi+1][i]][i]; 1905: bbh=(double)bh[mi][i]/(double)stepm; 1906: /* bias is positive if real duration 1907: * is higher than the multiple of stepm and negative otherwise. 1908: */ 1909: if( s2 > nlstate && (mle <5) ){ /* Jackson */ 1910: lli=log(out[s1][s2] - savm[s1][s2]); 1911: } else if (s2==-2) { 1912: for (j=1,survp=0. ; j<=nlstate; j++) 1913: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; 1914: lli= log(survp); 1915: }else if (mle==1){ 1916: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */ 1917: } else if(mle==2){ 1918: lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */ 1919: } else if(mle==3){ /* exponential inter-extrapolation */ 1920: lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */ 1921: } else if (mle==4){ /* mle=4 no inter-extrapolation */ 1922: lli=log(out[s1][s2]); /* Original formula */ 1923: } else{ /* mle=0 back to 1 */ 1924: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */ 1925: /*lli=log(out[s1][s2]); */ /* Original formula */ 1926: } /* End of if */ 1927: ipmx +=1; 1928: sw += weight[i]; 1929: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; 1930: /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */ 1931: if(globpr){ 1932: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\ 1933: %11.6f %11.6f %11.6f ", \ 1934: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i], 1935: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]); 1936: for(k=1,llt=0.,l=0.; k<=nlstate; k++){ 1937: llt +=ll[k]*gipmx/gsw; 1938: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw); 1939: } 1940: fprintf(ficresilk," %10.6f\n", -llt); 1941: } 1942: } /* end of wave */ 1943: } /* end of individual */ 1944: for(k=1,l=0.; k<=nlstate; k++) l += ll[k]; 1945: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */ 1946: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */ 1947: if(globpr==0){ /* First time we count the contributions and weights */ 1948: gipmx=ipmx; 1949: gsw=sw; 1950: } 1951: return -l; 1952: } 1953: 1954: 1955: /*************** function likelione ***********/ 1956: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double [])) 1957: { 1958: /* This routine should help understanding what is done with 1959: the selection of individuals/waves and 1960: to check the exact contribution to the likelihood. 1961: Plotting could be done. 1962: */ 1963: int k; 1964: 1965: if(*globpri !=0){ /* Just counts and sums, no printings */ 1966: strcpy(fileresilk,"ilk"); 1967: strcat(fileresilk,fileres); 1968: if((ficresilk=fopen(fileresilk,"w"))==NULL) { 1969: printf("Problem with resultfile: %s\n", fileresilk); 1970: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk); 1971: } 1972: fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n"); 1973: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav "); 1974: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */ 1975: for(k=1; k<=nlstate; k++) 1976: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k); 1977: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n"); 1978: } 1979: 1980: *fretone=(*funcone)(p); 1981: if(*globpri !=0){ 1982: fclose(ficresilk); 1983: fprintf(fichtm,"\n File of contributions to the likelihood: <a href=\"%s\">%s</a> \n",subdirf(fileresilk),subdirf(fileresilk)); 1984: fflush(fichtm); 1985: } 1986: return; 1987: } 1988: 1989: 1990: /*********** Maximum Likelihood Estimation ***************/ 1991: 1992: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double [])) 1993: { 1994: int i,j, iter; 1995: double **xi; 1996: double fret; 1997: double fretone; /* Only one call to likelihood */ 1998: /* char filerespow[FILENAMELENGTH];*/ 1999: xi=matrix(1,npar,1,npar); 2000: for (i=1;i<=npar;i++) 2001: for (j=1;j<=npar;j++) 2002: xi[i][j]=(i==j ? 1.0 : 0.0); 2003: printf("Powell\n"); fprintf(ficlog,"Powell\n"); 2004: strcpy(filerespow,"pow"); 2005: strcat(filerespow,fileres); 2006: if((ficrespow=fopen(filerespow,"w"))==NULL) { 2007: printf("Problem with resultfile: %s\n", filerespow); 2008: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow); 2009: } 2010: fprintf(ficrespow,"# Powell\n# iter -2*LL"); 2011: for (i=1;i<=nlstate;i++) 2012: for(j=1;j<=nlstate+ndeath;j++) 2013: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j); 2014: fprintf(ficrespow,"\n"); 2015: 2016: powell(p,xi,npar,ftol,&iter,&fret,func); 2017: 2018: free_matrix(xi,1,npar,1,npar); 2019: fclose(ficrespow); 2020: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p)); 2021: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p)); 2022: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p)); 2023: 2024: } 2025: 2026: /**** Computes Hessian and covariance matrix ***/ 2027: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double [])) 2028: { 2029: double **a,**y,*x,pd; 2030: double **hess; 2031: int i, j,jk; 2032: int *indx; 2033: 2034: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar); 2035: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar); 2036: void lubksb(double **a, int npar, int *indx, double b[]) ; 2037: void ludcmp(double **a, int npar, int *indx, double *d) ; 2038: double gompertz(double p[]); 2039: hess=matrix(1,npar,1,npar); 2040: 2041: printf("\nCalculation of the hessian matrix. Wait...\n"); 2042: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n"); 2043: for (i=1;i<=npar;i++){ 2044: printf("%d",i);fflush(stdout); 2045: fprintf(ficlog,"%d",i);fflush(ficlog); 2046: 2047: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar); 2048: 2049: /* printf(" %f ",p[i]); 2050: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/ 2051: } 2052: 2053: for (i=1;i<=npar;i++) { 2054: for (j=1;j<=npar;j++) { 2055: if (j>i) { 2056: printf(".%d%d",i,j);fflush(stdout); 2057: fprintf(ficlog,".%d%d",i,j);fflush(ficlog); 2058: hess[i][j]=hessij(p,delti,i,j,func,npar); 2059: 2060: hess[j][i]=hess[i][j]; 2061: /*printf(" %lf ",hess[i][j]);*/ 2062: } 2063: } 2064: } 2065: printf("\n"); 2066: fprintf(ficlog,"\n"); 2067: 2068: printf("\nInverting the hessian to get the covariance matrix. Wait...\n"); 2069: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n"); 2070: 2071: a=matrix(1,npar,1,npar); 2072: y=matrix(1,npar,1,npar); 2073: x=vector(1,npar); 2074: indx=ivector(1,npar); 2075: for (i=1;i<=npar;i++) 2076: for (j=1;j<=npar;j++) a[i][j]=hess[i][j]; 2077: ludcmp(a,npar,indx,&pd); 2078: 2079: for (j=1;j<=npar;j++) { 2080: for (i=1;i<=npar;i++) x[i]=0; 2081: x[j]=1; 2082: lubksb(a,npar,indx,x); 2083: for (i=1;i<=npar;i++){ 2084: matcov[i][j]=x[i]; 2085: } 2086: } 2087: 2088: printf("\n#Hessian matrix#\n"); 2089: fprintf(ficlog,"\n#Hessian matrix#\n"); 2090: for (i=1;i<=npar;i++) { 2091: for (j=1;j<=npar;j++) { 2092: printf("%.3e ",hess[i][j]); 2093: fprintf(ficlog,"%.3e ",hess[i][j]); 2094: } 2095: printf("\n"); 2096: fprintf(ficlog,"\n"); 2097: } 2098: 2099: /* Recompute Inverse */ 2100: for (i=1;i<=npar;i++) 2101: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; 2102: ludcmp(a,npar,indx,&pd); 2103: 2104: /* printf("\n#Hessian matrix recomputed#\n"); 2105: 2106: for (j=1;j<=npar;j++) { 2107: for (i=1;i<=npar;i++) x[i]=0; 2108: x[j]=1; 2109: lubksb(a,npar,indx,x); 2110: for (i=1;i<=npar;i++){ 2111: y[i][j]=x[i]; 2112: printf("%.3e ",y[i][j]); 2113: fprintf(ficlog,"%.3e ",y[i][j]); 2114: } 2115: printf("\n"); 2116: fprintf(ficlog,"\n"); 2117: } 2118: */ 2119: 2120: free_matrix(a,1,npar,1,npar); 2121: free_matrix(y,1,npar,1,npar); 2122: free_vector(x,1,npar); 2123: free_ivector(indx,1,npar); 2124: free_matrix(hess,1,npar,1,npar); 2125: 2126: 2127: } 2128: 2129: /*************** hessian matrix ****************/ 2130: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar) 2131: { 2132: int i; 2133: int l=1, lmax=20; 2134: double k1,k2; 2135: double p2[MAXPARM+1]; /* identical to x */ 2136: double res; 2137: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; 2138: double fx; 2139: int k=0,kmax=10; 2140: double l1; 2141: 2142: fx=func(x); 2143: for (i=1;i<=npar;i++) p2[i]=x[i]; 2144: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */ 2145: l1=pow(10,l); 2146: delts=delt; 2147: for(k=1 ; k <kmax; k=k+1){ 2148: delt = delta*(l1*k); 2149: p2[theta]=x[theta] +delt; 2150: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */ 2151: p2[theta]=x[theta]-delt; 2152: k2=func(p2)-fx; 2153: /*res= (k1-2.0*fx+k2)/delt/delt; */ 2154: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */ 2155: 2156: #ifdef DEBUGHESS 2157: printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx); 2158: fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx); 2159: #endif 2160: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */ 2161: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){ 2162: k=kmax; 2163: } 2164: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */ 2165: k=kmax; l=lmax*10.; 2166: } 2167: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 2168: delts=delt; 2169: } 2170: } 2171: } 2172: delti[theta]=delts; 2173: return res; 2174: 2175: } 2176: 2177: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) 2178: { 2179: int i; 2180: int l=1, l1, lmax=20; 2181: double k1,k2,k3,k4,res,fx; 2182: double p2[MAXPARM+1]; 2183: int k; 2184: 2185: fx=func(x); 2186: for (k=1; k<=2; k++) { 2187: for (i=1;i<=npar;i++) p2[i]=x[i]; 2188: p2[thetai]=x[thetai]+delti[thetai]/k; 2189: p2[thetaj]=x[thetaj]+delti[thetaj]/k; 2190: k1=func(p2)-fx; 2191: 2192: p2[thetai]=x[thetai]+delti[thetai]/k; 2193: p2[thetaj]=x[thetaj]-delti[thetaj]/k; 2194: k2=func(p2)-fx; 2195: 2196: p2[thetai]=x[thetai]-delti[thetai]/k; 2197: p2[thetaj]=x[thetaj]+delti[thetaj]/k; 2198: k3=func(p2)-fx; 2199: 2200: p2[thetai]=x[thetai]-delti[thetai]/k; 2201: p2[thetaj]=x[thetaj]-delti[thetaj]/k; 2202: k4=func(p2)-fx; 2203: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */ 2204: #ifdef DEBUG 2205: printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); 2206: fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); 2207: #endif 2208: } 2209: return res; 2210: } 2211: 2212: /************** Inverse of matrix **************/ 2213: void ludcmp(double **a, int n, int *indx, double *d) 2214: { 2215: int i,imax,j,k; 2216: double big,dum,sum,temp; 2217: double *vv; 2218: 2219: vv=vector(1,n); 2220: *d=1.0; 2221: for (i=1;i<=n;i++) { 2222: big=0.0; 2223: for (j=1;j<=n;j++) 2224: if ((temp=fabs(a[i][j])) > big) big=temp; 2225: if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 2226: vv[i]=1.0/big; 2227: } 2228: for (j=1;j<=n;j++) { 2229: for (i=1;i<j;i++) { 2230: sum=a[i][j]; 2231: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 2232: a[i][j]=sum; 2233: } 2234: big=0.0; 2235: for (i=j;i<=n;i++) { 2236: sum=a[i][j]; 2237: for (k=1;k<j;k++) 2238: sum -= a[i][k]*a[k][j]; 2239: a[i][j]=sum; 2240: if ( (dum=vv[i]*fabs(sum)) >= big) { 2241: big=dum; 2242: imax=i; 2243: } 2244: } 2245: if (j != imax) { 2246: for (k=1;k<=n;k++) { 2247: dum=a[imax][k]; 2248: a[imax][k]=a[j][k]; 2249: a[j][k]=dum; 2250: } 2251: *d = -(*d); 2252: vv[imax]=vv[j]; 2253: } 2254: indx[j]=imax; 2255: if (a[j][j] == 0.0) a[j][j]=TINY; 2256: if (j != n) { 2257: dum=1.0/(a[j][j]); 2258: for (i=j+1;i<=n;i++) a[i][j] *= dum; 2259: } 2260: } 2261: free_vector(vv,1,n); /* Doesn't work */ 2262: ; 2263: } 2264: 2265: void lubksb(double **a, int n, int *indx, double b[]) 2266: { 2267: int i,ii=0,ip,j; 2268: double sum; 2269: 2270: for (i=1;i<=n;i++) { 2271: ip=indx[i]; 2272: sum=b[ip]; 2273: b[ip]=b[i]; 2274: if (ii) 2275: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 2276: else if (sum) ii=i; 2277: b[i]=sum; 2278: } 2279: for (i=n;i>=1;i--) { 2280: sum=b[i]; 2281: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 2282: b[i]=sum/a[i][i]; 2283: } 2284: } 2285: 2286: void pstamp(FILE *fichier) 2287: { 2288: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart); 2289: } 2290: 2291: /************ Frequencies ********************/ 2292: void freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[]) 2293: { /* Some frequencies */ 2294: 2295: int i, m, jk, k1,i1, j1, bool, z1,j; 2296: int first; 2297: double ***freq; /* Frequencies */ 2298: double *pp, **prop; 2299: double pos,posprop, k2, dateintsum=0,k2cpt=0; 2300: char fileresp[FILENAMELENGTH]; 2301: 2302: pp=vector(1,nlstate); 2303: prop=matrix(1,nlstate,iagemin,iagemax+3); 2304: strcpy(fileresp,"p"); 2305: strcat(fileresp,fileres); 2306: if((ficresp=fopen(fileresp,"w"))==NULL) { 2307: printf("Problem with prevalence resultfile: %s\n", fileresp); 2308: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp); 2309: exit(0); 2310: } 2311: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3); 2312: j1=0; 2313: 2314: j=cptcoveff; 2315: if (cptcovn<1) {j=1;ncodemax[1]=1;} 2316: 2317: first=1; 2318: 2319: /* for(k1=1; k1<=j ; k1++){ /* Loop on covariates */ 2320: /* for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */ 2321: /* j1++; 2322: */ 2323: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){ 2324: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]); 2325: scanf("%d", i);*/ 2326: for (i=-5; i<=nlstate+ndeath; i++) 2327: for (jk=-5; jk<=nlstate+ndeath; jk++) 2328: for(m=iagemin; m <= iagemax+3; m++) 2329: freq[i][jk][m]=0; 2330: 2331: for (i=1; i<=nlstate; i++) 2332: for(m=iagemin; m <= iagemax+3; m++) 2333: prop[i][m]=0; 2334: 2335: dateintsum=0; 2336: k2cpt=0; 2337: for (i=1; i<=imx; i++) { 2338: bool=1; 2339: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */ 2340: for (z1=1; z1<=cptcoveff; z1++) 2341: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){ 2342: /* Tests if the value of each of the covariates of i is equal to filter j1 */ 2343: bool=0; 2344: /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n", 2345: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1], 2346: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/ 2347: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/ 2348: } 2349: } 2350: 2351: if (bool==1){ 2352: for(m=firstpass; m<=lastpass; m++){ 2353: k2=anint[m][i]+(mint[m][i]/12.); 2354: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/ 2355: if(agev[m][i]==0) agev[m][i]=iagemax+1; 2356: if(agev[m][i]==1) agev[m][i]=iagemax+2; 2357: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i]; 2358: if (m<lastpass) { 2359: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i]; 2360: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i]; 2361: } 2362: 2363: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) { 2364: dateintsum=dateintsum+k2; 2365: k2cpt++; 2366: } 2367: /*}*/ 2368: } 2369: } 2370: } /* end i */ 2371: 2372: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/ 2373: pstamp(ficresp); 2374: if (cptcovn>0) { 2375: fprintf(ficresp, "\n#********** Variable "); 2376: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); 2377: fprintf(ficresp, "**********\n#"); 2378: fprintf(ficlog, "\n#********** Variable "); 2379: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); 2380: fprintf(ficlog, "**********\n#"); 2381: } 2382: for(i=1; i<=nlstate;i++) 2383: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i); 2384: fprintf(ficresp, "\n"); 2385: 2386: for(i=iagemin; i <= iagemax+3; i++){ 2387: if(i==iagemax+3){ 2388: fprintf(ficlog,"Total"); 2389: }else{ 2390: if(first==1){ 2391: first=0; 2392: printf("See log file for details...\n"); 2393: } 2394: fprintf(ficlog,"Age %d", i); 2395: } 2396: for(jk=1; jk <=nlstate ; jk++){ 2397: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++) 2398: pp[jk] += freq[jk][m][i]; 2399: } 2400: for(jk=1; jk <=nlstate ; jk++){ 2401: for(m=-1, pos=0; m <=0 ; m++) 2402: pos += freq[jk][m][i]; 2403: if(pp[jk]>=1.e-10){ 2404: if(first==1){ 2405: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]); 2406: } 2407: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]); 2408: }else{ 2409: if(first==1) 2410: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk); 2411: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk); 2412: } 2413: } 2414: 2415: for(jk=1; jk <=nlstate ; jk++){ 2416: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++) 2417: pp[jk] += freq[jk][m][i]; 2418: } 2419: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){ 2420: pos += pp[jk]; 2421: posprop += prop[jk][i]; 2422: } 2423: for(jk=1; jk <=nlstate ; jk++){ 2424: if(pos>=1.e-5){ 2425: if(first==1) 2426: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos); 2427: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos); 2428: }else{ 2429: if(first==1) 2430: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk); 2431: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk); 2432: } 2433: if( i <= iagemax){ 2434: if(pos>=1.e-5){ 2435: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop); 2436: /*probs[i][jk][j1]= pp[jk]/pos;*/ 2437: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/ 2438: } 2439: else 2440: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop); 2441: } 2442: } 2443: 2444: for(jk=-1; jk <=nlstate+ndeath; jk++) 2445: for(m=-1; m <=nlstate+ndeath; m++) 2446: if(freq[jk][m][i] !=0 ) { 2447: if(first==1) 2448: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]); 2449: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]); 2450: } 2451: if(i <= iagemax) 2452: fprintf(ficresp,"\n"); 2453: if(first==1) 2454: printf("Others in log...\n"); 2455: fprintf(ficlog,"\n"); 2456: } 2457: /*}*/ 2458: } 2459: dateintmean=dateintsum/k2cpt; 2460: 2461: fclose(ficresp); 2462: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3); 2463: free_vector(pp,1,nlstate); 2464: free_matrix(prop,1,nlstate,iagemin, iagemax+3); 2465: /* End of Freq */ 2466: } 2467: 2468: /************ Prevalence ********************/ 2469: void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass) 2470: { 2471: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people 2472: in each health status at the date of interview (if between dateprev1 and dateprev2). 2473: We still use firstpass and lastpass as another selection. 2474: */ 2475: 2476: int i, m, jk, k1, i1, j1, bool, z1,j; 2477: double ***freq; /* Frequencies */ 2478: double *pp, **prop; 2479: double pos,posprop; 2480: double y2; /* in fractional years */ 2481: int iagemin, iagemax; 2482: int first; /** to stop verbosity which is redirected to log file */ 2483: 2484: iagemin= (int) agemin; 2485: iagemax= (int) agemax; 2486: /*pp=vector(1,nlstate);*/ 2487: prop=matrix(1,nlstate,iagemin,iagemax+3); 2488: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/ 2489: j1=0; 2490: 2491: /*j=cptcoveff;*/ 2492: if (cptcovn<1) {j=1;ncodemax[1]=1;} 2493: 2494: first=1; 2495: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ 2496: /*for(i1=1; i1<=ncodemax[k1];i1++){ 2497: j1++;*/ 2498: 2499: for (i=1; i<=nlstate; i++) 2500: for(m=iagemin; m <= iagemax+3; m++) 2501: prop[i][m]=0.0; 2502: 2503: for (i=1; i<=imx; i++) { /* Each individual */ 2504: bool=1; 2505: if (cptcovn>0) { 2506: for (z1=1; z1<=cptcoveff; z1++) 2507: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 2508: bool=0; 2509: } 2510: if (bool==1) { 2511: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/ 2512: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */ 2513: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */ 2514: if(agev[m][i]==0) agev[m][i]=iagemax+1; 2515: if(agev[m][i]==1) agev[m][i]=iagemax+2; 2516: if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 2517: if (s[m][i]>0 && s[m][i]<=nlstate) { 2518: /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/ 2519: prop[s[m][i]][(int)agev[m][i]] += weight[i]; 2520: prop[s[m][i]][iagemax+3] += weight[i]; 2521: } 2522: } 2523: } /* end selection of waves */ 2524: } 2525: } 2526: for(i=iagemin; i <= iagemax+3; i++){ 2527: for(jk=1,posprop=0; jk <=nlstate ; jk++) { 2528: posprop += prop[jk][i]; 2529: } 2530: 2531: for(jk=1; jk <=nlstate ; jk++){ 2532: if( i <= iagemax){ 2533: if(posprop>=1.e-5){ 2534: probs[i][jk][j1]= prop[jk][i]/posprop; 2535: } else{ 2536: if(first==1){ 2537: first=0; 2538: printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]); 2539: } 2540: } 2541: } 2542: }/* end jk */ 2543: }/* end i */ 2544: /*} *//* end i1 */ 2545: } /* end j1 */ 2546: 2547: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/ 2548: /*free_vector(pp,1,nlstate);*/ 2549: free_matrix(prop,1,nlstate, iagemin,iagemax+3); 2550: } /* End of prevalence */ 2551: 2552: /************* Waves Concatenation ***************/ 2553: 2554: void concatwav(int wav[], int **dh, int **bh, int **mw, int **s, double *agedc, double **agev, int firstpass, int lastpass, int imx, int nlstate, int stepm) 2555: { 2556: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i. 2557: Death is a valid wave (if date is known). 2558: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i 2559: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i] 2560: and mw[mi+1][i]. dh depends on stepm. 2561: */ 2562: 2563: int i, mi, m; 2564: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1; 2565: double sum=0., jmean=0.;*/ 2566: int first; 2567: int j, k=0,jk, ju, jl; 2568: double sum=0.; 2569: first=0; 2570: jmin=1e+5; 2571: jmax=-1; 2572: jmean=0.; 2573: for(i=1; i<=imx; i++){ 2574: mi=0; 2575: m=firstpass; 2576: while(s[m][i] <= nlstate){ 2577: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5) 2578: mw[++mi][i]=m; 2579: if(m >=lastpass) 2580: break; 2581: else 2582: m++; 2583: }/* end while */ 2584: if (s[m][i] > nlstate){ 2585: mi++; /* Death is another wave */ 2586: /* if(mi==0) never been interviewed correctly before death */ 2587: /* Only death is a correct wave */ 2588: mw[mi][i]=m; 2589: } 2590: 2591: wav[i]=mi; 2592: if(mi==0){ 2593: nbwarn++; 2594: if(first==0){ 2595: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i); 2596: first=1; 2597: } 2598: if(first==1){ 2599: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i); 2600: } 2601: } /* end mi==0 */ 2602: } /* End individuals */ 2603: 2604: for(i=1; i<=imx; i++){ 2605: for(mi=1; mi<wav[i];mi++){ 2606: if (stepm <=0) 2607: dh[mi][i]=1; 2608: else{ 2609: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */ 2610: if (agedc[i] < 2*AGESUP) { 2611: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 2612: if(j==0) j=1; /* Survives at least one month after exam */ 2613: else if(j<0){ 2614: nberr++; 2615: printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); 2616: j=1; /* Temporary Dangerous patch */ 2617: printf(" We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm); 2618: fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); 2619: fprintf(ficlog," We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm); 2620: } 2621: k=k+1; 2622: if (j >= jmax){ 2623: jmax=j; 2624: ijmax=i; 2625: } 2626: if (j <= jmin){ 2627: jmin=j; 2628: ijmin=i; 2629: } 2630: sum=sum+j; 2631: /*if (j<0) printf("j=%d num=%d \n",j,i);*/ 2632: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/ 2633: } 2634: } 2635: else{ 2636: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12)); 2637: /* if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */ 2638: 2639: k=k+1; 2640: if (j >= jmax) { 2641: jmax=j; 2642: ijmax=i; 2643: } 2644: else if (j <= jmin){ 2645: jmin=j; 2646: ijmin=i; 2647: } 2648: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */ 2649: /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/ 2650: if(j<0){ 2651: nberr++; 2652: printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); 2653: fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); 2654: } 2655: sum=sum+j; 2656: } 2657: jk= j/stepm; 2658: jl= j -jk*stepm; 2659: ju= j -(jk+1)*stepm; 2660: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */ 2661: if(jl==0){ 2662: dh[mi][i]=jk; 2663: bh[mi][i]=0; 2664: }else{ /* We want a negative bias in order to only have interpolation ie 2665: * to avoid the price of an extra matrix product in likelihood */ 2666: dh[mi][i]=jk+1; 2667: bh[mi][i]=ju; 2668: } 2669: }else{ 2670: if(jl <= -ju){ 2671: dh[mi][i]=jk; 2672: bh[mi][i]=jl; /* bias is positive if real duration 2673: * is higher than the multiple of stepm and negative otherwise. 2674: */ 2675: } 2676: else{ 2677: dh[mi][i]=jk+1; 2678: bh[mi][i]=ju; 2679: } 2680: if(dh[mi][i]==0){ 2681: dh[mi][i]=1; /* At least one step */ 2682: bh[mi][i]=ju; /* At least one step */ 2683: /* printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/ 2684: } 2685: } /* end if mle */ 2686: } 2687: } /* end wave */ 2688: } 2689: jmean=sum/k; 2690: printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean); 2691: fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean); 2692: } 2693: 2694: /*********** Tricode ****************************/ 2695: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum) 2696: { 2697: /**< Uses cptcovn+2*cptcovprod as the number of covariates */ 2698: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 2699: /* Boring subroutine which should only output nbcode[Tvar[j]][k] 2700: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2) 2701: /* nbcode[Tvar[j]][1]= 2702: */ 2703: 2704: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX; 2705: int modmaxcovj=0; /* Modality max of covariates j */ 2706: int cptcode=0; /* Modality max of covariates j */ 2707: int modmincovj=0; /* Modality min of covariates j */ 2708: 2709: 2710: cptcoveff=0; 2711: 2712: for (k=-1; k < maxncov; k++) Ndum[k]=0; 2713: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */ 2714: 2715: /* Loop on covariates without age and products */ 2716: for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */ 2717: for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 2718: modality of this covariate Vj*/ 2719: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i 2720: * If product of Vn*Vm, still boolean *: 2721: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables 2722: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */ 2723: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the 2724: modality of the nth covariate of individual i. */ 2725: if (ij > modmaxcovj) 2726: modmaxcovj=ij; 2727: else if (ij < modmincovj) 2728: modmincovj=ij; 2729: if ((ij < -1) && (ij > NCOVMAX)){ 2730: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX ); 2731: exit(1); 2732: }else 2733: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/ 2734: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */ 2735: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/ 2736: /* getting the maximum value of the modality of the covariate 2737: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and 2738: female is 1, then modmaxcovj=1.*/ 2739: } 2740: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj); 2741: cptcode=modmaxcovj; 2742: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */ 2743: /*for (i=0; i<=cptcode; i++) {*/ 2744: for (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */ 2745: printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]); 2746: if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */ 2747: ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */ 2748: } 2749: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for 2750: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */ 2751: } /* Ndum[-1] number of undefined modalities */ 2752: 2753: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */ 2754: /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */ 2755: /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125; 2756: modmincovj=3; modmaxcovj = 7; 2757: There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3; 2758: which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 2759: variables V1_1 and V1_2. 2760: nbcode[Tvar[j]][ij]=k; 2761: nbcode[Tvar[j]][1]=0; 2762: nbcode[Tvar[j]][2]=1; 2763: nbcode[Tvar[j]][3]=2; 2764: */ 2765: ij=1; /* ij is similar to i but can jumps over null modalities */ 2766: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */ 2767: for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */ 2768: /*recode from 0 */ 2769: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */ 2770: nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode. 2771: k is a modality. If we have model=V1+V1*sex 2772: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */ 2773: ij++; 2774: } 2775: if (ij > ncodemax[j]) break; 2776: } /* end of loop on */ 2777: } /* end of loop on modality */ 2778: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/ 2779: 2780: for (k=-1; k< maxncov; k++) Ndum[k]=0; 2781: 2782: for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 2783: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 2784: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 2785: Ndum[ij]++; 2786: } 2787: 2788: ij=1; 2789: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */ 2790: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/ 2791: if((Ndum[i]!=0) && (i<=ncovcol)){ 2792: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/ 2793: Tvaraff[ij]=i; /*For printing (unclear) */ 2794: ij++; 2795: }else 2796: Tvaraff[ij]=0; 2797: } 2798: ij--; 2799: cptcoveff=ij; /*Number of total covariates*/ 2800: 2801: } 2802: 2803: 2804: /*********** Health Expectancies ****************/ 2805: 2806: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] ) 2807: 2808: { 2809: /* Health expectancies, no variances */ 2810: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2; 2811: int nhstepma, nstepma; /* Decreasing with age */ 2812: double age, agelim, hf; 2813: double ***p3mat; 2814: double eip; 2815: 2816: pstamp(ficreseij); 2817: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n"); 2818: fprintf(ficreseij,"# Age"); 2819: for(i=1; i<=nlstate;i++){ 2820: for(j=1; j<=nlstate;j++){ 2821: fprintf(ficreseij," e%1d%1d ",i,j); 2822: } 2823: fprintf(ficreseij," e%1d. ",i); 2824: } 2825: fprintf(ficreseij,"\n"); 2826: 2827: 2828: if(estepm < stepm){ 2829: printf ("Problem %d lower than %d\n",estepm, stepm); 2830: } 2831: else hstepm=estepm; 2832: /* We compute the life expectancy from trapezoids spaced every estepm months 2833: * This is mainly to measure the difference between two models: for example 2834: * if stepm=24 months pijx are given only every 2 years and by summing them 2835: * we are calculating an estimate of the Life Expectancy assuming a linear 2836: * progression in between and thus overestimating or underestimating according 2837: * to the curvature of the survival function. If, for the same date, we 2838: * estimate the model with stepm=1 month, we can keep estepm to 24 months 2839: * to compare the new estimate of Life expectancy with the same linear 2840: * hypothesis. A more precise result, taking into account a more precise 2841: * curvature will be obtained if estepm is as small as stepm. */ 2842: 2843: /* For example we decided to compute the life expectancy with the smallest unit */ 2844: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 2845: nhstepm is the number of hstepm from age to agelim 2846: nstepm is the number of stepm from age to agelin. 2847: Look at hpijx to understand the reason of that which relies in memory size 2848: and note for a fixed period like estepm months */ 2849: /* We decided (b) to get a life expectancy respecting the most precise curvature of the 2850: survival function given by stepm (the optimization length). Unfortunately it 2851: means that if the survival funtion is printed only each two years of age and if 2852: you sum them up and add 1 year (area under the trapezoids) you won't get the same 2853: results. So we changed our mind and took the option of the best precision. 2854: */ 2855: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 2856: 2857: agelim=AGESUP; 2858: /* If stepm=6 months */ 2859: /* Computed by stepm unit matrices, product of hstepm matrices, stored 2860: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */ 2861: 2862: /* nhstepm age range expressed in number of stepm */ 2863: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */ 2864: /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 2865: /* if (stepm >= YEARM) hstepm=1;*/ 2866: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */ 2867: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 2868: 2869: for (age=bage; age<=fage; age ++){ 2870: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */ 2871: /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 2872: /* if (stepm >= YEARM) hstepm=1;*/ 2873: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */ 2874: 2875: /* If stepm=6 months */ 2876: /* Computed by stepm unit matrices, product of hstepma matrices, stored 2877: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */ 2878: 2879: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij); 2880: 2881: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */ 2882: 2883: printf("%d|",(int)age);fflush(stdout); 2884: fprintf(ficlog,"%d|",(int)age);fflush(ficlog); 2885: 2886: /* Computing expectancies */ 2887: for(i=1; i<=nlstate;i++) 2888: for(j=1; j<=nlstate;j++) 2889: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){ 2890: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf; 2891: 2892: /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/ 2893: 2894: } 2895: 2896: fprintf(ficreseij,"%3.0f",age ); 2897: for(i=1; i<=nlstate;i++){ 2898: eip=0; 2899: for(j=1; j<=nlstate;j++){ 2900: eip +=eij[i][j][(int)age]; 2901: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] ); 2902: } 2903: fprintf(ficreseij,"%9.4f", eip ); 2904: } 2905: fprintf(ficreseij,"\n"); 2906: 2907: } 2908: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 2909: printf("\n"); 2910: fprintf(ficlog,"\n"); 2911: 2912: } 2913: 2914: void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] ) 2915: 2916: { 2917: /* Covariances of health expectancies eij and of total life expectancies according 2918: to initial status i, ei. . 2919: */ 2920: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji; 2921: int nhstepma, nstepma; /* Decreasing with age */ 2922: double age, agelim, hf; 2923: double ***p3matp, ***p3matm, ***varhe; 2924: double **dnewm,**doldm; 2925: double *xp, *xm; 2926: double **gp, **gm; 2927: double ***gradg, ***trgradg; 2928: int theta; 2929: 2930: double eip, vip; 2931: 2932: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage); 2933: xp=vector(1,npar); 2934: xm=vector(1,npar); 2935: dnewm=matrix(1,nlstate*nlstate,1,npar); 2936: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate); 2937: 2938: pstamp(ficresstdeij); 2939: fprintf(ficresstdeij,"# Health expectancies with standard errors\n"); 2940: fprintf(ficresstdeij,"# Age"); 2941: for(i=1; i<=nlstate;i++){ 2942: for(j=1; j<=nlstate;j++) 2943: fprintf(ficresstdeij," e%1d%1d (SE)",i,j); 2944: fprintf(ficresstdeij," e%1d. ",i); 2945: } 2946: fprintf(ficresstdeij,"\n"); 2947: 2948: pstamp(ficrescveij); 2949: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n"); 2950: fprintf(ficrescveij,"# Age"); 2951: for(i=1; i<=nlstate;i++) 2952: for(j=1; j<=nlstate;j++){ 2953: cptj= (j-1)*nlstate+i; 2954: for(i2=1; i2<=nlstate;i2++) 2955: for(j2=1; j2<=nlstate;j2++){ 2956: cptj2= (j2-1)*nlstate+i2; 2957: if(cptj2 <= cptj) 2958: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2); 2959: } 2960: } 2961: fprintf(ficrescveij,"\n"); 2962: 2963: if(estepm < stepm){ 2964: printf ("Problem %d lower than %d\n",estepm, stepm); 2965: } 2966: else hstepm=estepm; 2967: /* We compute the life expectancy from trapezoids spaced every estepm months 2968: * This is mainly to measure the difference between two models: for example 2969: * if stepm=24 months pijx are given only every 2 years and by summing them 2970: * we are calculating an estimate of the Life Expectancy assuming a linear 2971: * progression in between and thus overestimating or underestimating according 2972: * to the curvature of the survival function. If, for the same date, we 2973: * estimate the model with stepm=1 month, we can keep estepm to 24 months 2974: * to compare the new estimate of Life expectancy with the same linear 2975: * hypothesis. A more precise result, taking into account a more precise 2976: * curvature will be obtained if estepm is as small as stepm. */ 2977: 2978: /* For example we decided to compute the life expectancy with the smallest unit */ 2979: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 2980: nhstepm is the number of hstepm from age to agelim 2981: nstepm is the number of stepm from age to agelin. 2982: Look at hpijx to understand the reason of that which relies in memory size 2983: and note for a fixed period like estepm months */ 2984: /* We decided (b) to get a life expectancy respecting the most precise curvature of the 2985: survival function given by stepm (the optimization length). Unfortunately it 2986: means that if the survival funtion is printed only each two years of age and if 2987: you sum them up and add 1 year (area under the trapezoids) you won't get the same 2988: results. So we changed our mind and took the option of the best precision. 2989: */ 2990: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 2991: 2992: /* If stepm=6 months */ 2993: /* nhstepm age range expressed in number of stepm */ 2994: agelim=AGESUP; 2995: nstepm=(int) rint((agelim-bage)*YEARM/stepm); 2996: /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 2997: /* if (stepm >= YEARM) hstepm=1;*/ 2998: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */ 2999: 3000: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 3001: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 3002: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate); 3003: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar); 3004: gp=matrix(0,nhstepm,1,nlstate*nlstate); 3005: gm=matrix(0,nhstepm,1,nlstate*nlstate); 3006: 3007: for (age=bage; age<=fage; age ++){ 3008: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */ 3009: /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 3010: /* if (stepm >= YEARM) hstepm=1;*/ 3011: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */ 3012: 3013: /* If stepm=6 months */ 3014: /* Computed by stepm unit matrices, product of hstepma matrices, stored 3015: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */ 3016: 3017: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */ 3018: 3019: /* Computing Variances of health expectancies */ 3020: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to 3021: decrease memory allocation */ 3022: for(theta=1; theta <=npar; theta++){ 3023: for(i=1; i<=npar; i++){ 3024: xp[i] = x[i] + (i==theta ?delti[theta]:0); 3025: xm[i] = x[i] - (i==theta ?delti[theta]:0); 3026: } 3027: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij); 3028: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij); 3029: 3030: for(j=1; j<= nlstate; j++){ 3031: for(i=1; i<=nlstate; i++){ 3032: for(h=0; h<=nhstepm-1; h++){ 3033: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.; 3034: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.; 3035: } 3036: } 3037: } 3038: 3039: for(ij=1; ij<= nlstate*nlstate; ij++) 3040: for(h=0; h<=nhstepm-1; h++){ 3041: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta]; 3042: } 3043: }/* End theta */ 3044: 3045: 3046: for(h=0; h<=nhstepm-1; h++) 3047: for(j=1; j<=nlstate*nlstate;j++) 3048: for(theta=1; theta <=npar; theta++) 3049: trgradg[h][j][theta]=gradg[h][theta][j]; 3050: 3051: 3052: for(ij=1;ij<=nlstate*nlstate;ij++) 3053: for(ji=1;ji<=nlstate*nlstate;ji++) 3054: varhe[ij][ji][(int)age] =0.; 3055: 3056: printf("%d|",(int)age);fflush(stdout); 3057: fprintf(ficlog,"%d|",(int)age);fflush(ficlog); 3058: for(h=0;h<=nhstepm-1;h++){ 3059: for(k=0;k<=nhstepm-1;k++){ 3060: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov); 3061: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]); 3062: for(ij=1;ij<=nlstate*nlstate;ij++) 3063: for(ji=1;ji<=nlstate*nlstate;ji++) 3064: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf; 3065: } 3066: } 3067: 3068: /* Computing expectancies */ 3069: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij); 3070: for(i=1; i<=nlstate;i++) 3071: for(j=1; j<=nlstate;j++) 3072: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){ 3073: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf; 3074: 3075: /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/ 3076: 3077: } 3078: 3079: fprintf(ficresstdeij,"%3.0f",age ); 3080: for(i=1; i<=nlstate;i++){ 3081: eip=0.; 3082: vip=0.; 3083: for(j=1; j<=nlstate;j++){ 3084: eip += eij[i][j][(int)age]; 3085: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */ 3086: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age]; 3087: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) ); 3088: } 3089: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip)); 3090: } 3091: fprintf(ficresstdeij,"\n"); 3092: 3093: fprintf(ficrescveij,"%3.0f",age ); 3094: for(i=1; i<=nlstate;i++) 3095: for(j=1; j<=nlstate;j++){ 3096: cptj= (j-1)*nlstate+i; 3097: for(i2=1; i2<=nlstate;i2++) 3098: for(j2=1; j2<=nlstate;j2++){ 3099: cptj2= (j2-1)*nlstate+i2; 3100: if(cptj2 <= cptj) 3101: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]); 3102: } 3103: } 3104: fprintf(ficrescveij,"\n"); 3105: 3106: } 3107: free_matrix(gm,0,nhstepm,1,nlstate*nlstate); 3108: free_matrix(gp,0,nhstepm,1,nlstate*nlstate); 3109: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate); 3110: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar); 3111: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 3112: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 3113: printf("\n"); 3114: fprintf(ficlog,"\n"); 3115: 3116: free_vector(xm,1,npar); 3117: free_vector(xp,1,npar); 3118: free_matrix(dnewm,1,nlstate*nlstate,1,npar); 3119: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate); 3120: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage); 3121: } 3122: 3123: /************ Variance ******************/ 3124: void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[]) 3125: { 3126: /* Variance of health expectancies */ 3127: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/ 3128: /* double **newm;*/ 3129: double **dnewm,**doldm; 3130: double **dnewmp,**doldmp; 3131: int i, j, nhstepm, hstepm, h, nstepm ; 3132: int k, cptcode; 3133: double *xp; 3134: double **gp, **gm; /* for var eij */ 3135: double ***gradg, ***trgradg; /*for var eij */ 3136: double **gradgp, **trgradgp; /* for var p point j */ 3137: double *gpp, *gmp; /* for var p point j */ 3138: double **varppt; /* for var p point j nlstate to nlstate+ndeath */ 3139: double ***p3mat; 3140: double age,agelim, hf; 3141: double ***mobaverage; 3142: int theta; 3143: char digit[4]; 3144: char digitp[25]; 3145: 3146: char fileresprobmorprev[FILENAMELENGTH]; 3147: 3148: if(popbased==1){ 3149: if(mobilav!=0) 3150: strcpy(digitp,"-populbased-mobilav-"); 3151: else strcpy(digitp,"-populbased-nomobil-"); 3152: } 3153: else 3154: strcpy(digitp,"-stablbased-"); 3155: 3156: if (mobilav!=0) { 3157: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 3158: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ 3159: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); 3160: printf(" Error in movingaverage mobilav=%d\n",mobilav); 3161: } 3162: } 3163: 3164: strcpy(fileresprobmorprev,"prmorprev"); 3165: sprintf(digit,"%-d",ij); 3166: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/ 3167: strcat(fileresprobmorprev,digit); /* Tvar to be done */ 3168: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */ 3169: strcat(fileresprobmorprev,fileres); 3170: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) { 3171: printf("Problem with resultfile: %s\n", fileresprobmorprev); 3172: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev); 3173: } 3174: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); 3175: 3176: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); 3177: pstamp(ficresprobmorprev); 3178: fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm); 3179: fprintf(ficresprobmorprev,"# Age cov=%-d",ij); 3180: for(j=nlstate+1; j<=(nlstate+ndeath);j++){ 3181: fprintf(ficresprobmorprev," p.%-d SE",j); 3182: for(i=1; i<=nlstate;i++) 3183: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j); 3184: } 3185: fprintf(ficresprobmorprev,"\n"); 3186: fprintf(ficgp,"\n# Routine varevsij"); 3187: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/ 3188: fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n"); 3189: fprintf(fichtm,"\n %s \n",digitp); 3190: /* } */ 3191: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); 3192: pstamp(ficresvij); 3193: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are "); 3194: if(popbased==1) 3195: fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav); 3196: else 3197: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n"); 3198: fprintf(ficresvij,"# Age"); 3199: for(i=1; i<=nlstate;i++) 3200: for(j=1; j<=nlstate;j++) 3201: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j); 3202: fprintf(ficresvij,"\n"); 3203: 3204: xp=vector(1,npar); 3205: dnewm=matrix(1,nlstate,1,npar); 3206: doldm=matrix(1,nlstate,1,nlstate); 3207: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar); 3208: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); 3209: 3210: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath); 3211: gpp=vector(nlstate+1,nlstate+ndeath); 3212: gmp=vector(nlstate+1,nlstate+ndeath); 3213: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/ 3214: 3215: if(estepm < stepm){ 3216: printf ("Problem %d lower than %d\n",estepm, stepm); 3217: } 3218: else hstepm=estepm; 3219: /* For example we decided to compute the life expectancy with the smallest unit */ 3220: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 3221: nhstepm is the number of hstepm from age to agelim 3222: nstepm is the number of stepm from age to agelin. 3223: Look at function hpijx to understand why (it is linked to memory size questions) */ 3224: /* We decided (b) to get a life expectancy respecting the most precise curvature of the 3225: survival function given by stepm (the optimization length). Unfortunately it 3226: means that if the survival funtion is printed every two years of age and if 3227: you sum them up and add 1 year (area under the trapezoids) you won't get the same 3228: results. So we changed our mind and took the option of the best precision. 3229: */ 3230: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 3231: agelim = AGESUP; 3232: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */ 3233: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 3234: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */ 3235: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 3236: gradg=ma3x(0,nhstepm,1,npar,1,nlstate); 3237: gp=matrix(0,nhstepm,1,nlstate); 3238: gm=matrix(0,nhstepm,1,nlstate); 3239: 3240: 3241: for(theta=1; theta <=npar; theta++){ 3242: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/ 3243: xp[i] = x[i] + (i==theta ?delti[theta]:0); 3244: } 3245: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); 3246: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); 3247: 3248: if (popbased==1) { 3249: if(mobilav ==0){ 3250: for(i=1; i<=nlstate;i++) 3251: prlim[i][i]=probs[(int)age][i][ij]; 3252: }else{ /* mobilav */ 3253: for(i=1; i<=nlstate;i++) 3254: prlim[i][i]=mobaverage[(int)age][i][ij]; 3255: } 3256: } 3257: 3258: for(j=1; j<= nlstate; j++){ 3259: for(h=0; h<=nhstepm; h++){ 3260: for(i=1, gp[h][j]=0.;i<=nlstate;i++) 3261: gp[h][j] += prlim[i][i]*p3mat[i][j][h]; 3262: } 3263: } 3264: /* This for computing probability of death (h=1 means 3265: computed over hstepm matrices product = hstepm*stepm months) 3266: as a weighted average of prlim. 3267: */ 3268: for(j=nlstate+1;j<=nlstate+ndeath;j++){ 3269: for(i=1,gpp[j]=0.; i<= nlstate; i++) 3270: gpp[j] += prlim[i][i]*p3mat[i][j][1]; 3271: } 3272: /* end probability of death */ 3273: 3274: for(i=1; i<=npar; i++) /* Computes gradient x - delta */ 3275: xp[i] = x[i] - (i==theta ?delti[theta]:0); 3276: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); 3277: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); 3278: 3279: if (popbased==1) { 3280: if(mobilav ==0){ 3281: for(i=1; i<=nlstate;i++) 3282: prlim[i][i]=probs[(int)age][i][ij]; 3283: }else{ /* mobilav */ 3284: for(i=1; i<=nlstate;i++) 3285: prlim[i][i]=mobaverage[(int)age][i][ij]; 3286: } 3287: } 3288: 3289: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */ 3290: for(h=0; h<=nhstepm; h++){ 3291: for(i=1, gm[h][j]=0.;i<=nlstate;i++) 3292: gm[h][j] += prlim[i][i]*p3mat[i][j][h]; 3293: } 3294: } 3295: /* This for computing probability of death (h=1 means 3296: computed over hstepm matrices product = hstepm*stepm months) 3297: as a weighted average of prlim. 3298: */ 3299: for(j=nlstate+1;j<=nlstate+ndeath;j++){ 3300: for(i=1,gmp[j]=0.; i<= nlstate; i++) 3301: gmp[j] += prlim[i][i]*p3mat[i][j][1]; 3302: } 3303: /* end probability of death */ 3304: 3305: for(j=1; j<= nlstate; j++) /* vareij */ 3306: for(h=0; h<=nhstepm; h++){ 3307: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta]; 3308: } 3309: 3310: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */ 3311: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta]; 3312: } 3313: 3314: } /* End theta */ 3315: 3316: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */ 3317: 3318: for(h=0; h<=nhstepm; h++) /* veij */ 3319: for(j=1; j<=nlstate;j++) 3320: for(theta=1; theta <=npar; theta++) 3321: trgradg[h][j][theta]=gradg[h][theta][j]; 3322: 3323: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */ 3324: for(theta=1; theta <=npar; theta++) 3325: trgradgp[j][theta]=gradgp[theta][j]; 3326: 3327: 3328: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */ 3329: for(i=1;i<=nlstate;i++) 3330: for(j=1;j<=nlstate;j++) 3331: vareij[i][j][(int)age] =0.; 3332: 3333: for(h=0;h<=nhstepm;h++){ 3334: for(k=0;k<=nhstepm;k++){ 3335: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov); 3336: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]); 3337: for(i=1;i<=nlstate;i++) 3338: for(j=1;j<=nlstate;j++) 3339: vareij[i][j][(int)age] += doldm[i][j]*hf*hf; 3340: } 3341: } 3342: 3343: /* pptj */ 3344: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov); 3345: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp); 3346: for(j=nlstate+1;j<=nlstate+ndeath;j++) 3347: for(i=nlstate+1;i<=nlstate+ndeath;i++) 3348: varppt[j][i]=doldmp[j][i]; 3349: /* end ppptj */ 3350: /* x centered again */ 3351: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij); 3352: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij); 3353: 3354: if (popbased==1) { 3355: if(mobilav ==0){ 3356: for(i=1; i<=nlstate;i++) 3357: prlim[i][i]=probs[(int)age][i][ij]; 3358: }else{ /* mobilav */ 3359: for(i=1; i<=nlstate;i++) 3360: prlim[i][i]=mobaverage[(int)age][i][ij]; 3361: } 3362: } 3363: 3364: /* This for computing probability of death (h=1 means 3365: computed over hstepm (estepm) matrices product = hstepm*stepm months) 3366: as a weighted average of prlim. 3367: */ 3368: for(j=nlstate+1;j<=nlstate+ndeath;j++){ 3369: for(i=1,gmp[j]=0.;i<= nlstate; i++) 3370: gmp[j] += prlim[i][i]*p3mat[i][j][1]; 3371: } 3372: /* end probability of death */ 3373: 3374: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij); 3375: for(j=nlstate+1; j<=(nlstate+ndeath);j++){ 3376: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j])); 3377: for(i=1; i<=nlstate;i++){ 3378: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]); 3379: } 3380: } 3381: fprintf(ficresprobmorprev,"\n"); 3382: 3383: fprintf(ficresvij,"%.0f ",age ); 3384: for(i=1; i<=nlstate;i++) 3385: for(j=1; j<=nlstate;j++){ 3386: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]); 3387: } 3388: fprintf(ficresvij,"\n"); 3389: free_matrix(gp,0,nhstepm,1,nlstate); 3390: free_matrix(gm,0,nhstepm,1,nlstate); 3391: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate); 3392: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar); 3393: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 3394: } /* End age */ 3395: free_vector(gpp,nlstate+1,nlstate+ndeath); 3396: free_vector(gmp,nlstate+1,nlstate+ndeath); 3397: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath); 3398: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/ 3399: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); 3400: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */ 3401: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";"); 3402: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */ 3403: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */ 3404: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */ 3405: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev)); 3406: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev)); 3407: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev)); 3408: fprintf(fichtm,"\n File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev)); 3409: fprintf(fichtm,"\n Probability is computed over estepm=%d months. <img src=\"%s%s.png\"> \n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit); 3410: /* 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); 3411: */ 3412: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */ 3413: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit); 3414: 3415: free_vector(xp,1,npar); 3416: free_matrix(doldm,1,nlstate,1,nlstate); 3417: free_matrix(dnewm,1,nlstate,1,npar); 3418: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); 3419: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar); 3420: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); 3421: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 3422: fclose(ficresprobmorprev); 3423: fflush(ficgp); 3424: fflush(fichtm); 3425: } /* end varevsij */ 3426: 3427: /************ Variance of prevlim ******************/ 3428: void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[]) 3429: { 3430: /* Variance of prevalence limit */ 3431: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/ 3432: double **newm; 3433: double **dnewm,**doldm; 3434: int i, j, nhstepm, hstepm; 3435: int k, cptcode; 3436: double *xp; 3437: double *gp, *gm; 3438: double **gradg, **trgradg; 3439: double age,agelim; 3440: int theta; 3441: 3442: pstamp(ficresvpl); 3443: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n"); 3444: fprintf(ficresvpl,"# Age"); 3445: for(i=1; i<=nlstate;i++) 3446: fprintf(ficresvpl," %1d-%1d",i,i); 3447: fprintf(ficresvpl,"\n"); 3448: 3449: xp=vector(1,npar); 3450: dnewm=matrix(1,nlstate,1,npar); 3451: doldm=matrix(1,nlstate,1,nlstate); 3452: 3453: hstepm=1*YEARM; /* Every year of age */ 3454: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 3455: agelim = AGESUP; 3456: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */ 3457: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 3458: if (stepm >= YEARM) hstepm=1; 3459: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */ 3460: gradg=matrix(1,npar,1,nlstate); 3461: gp=vector(1,nlstate); 3462: gm=vector(1,nlstate); 3463: 3464: for(theta=1; theta <=npar; theta++){ 3465: for(i=1; i<=npar; i++){ /* Computes gradient */ 3466: xp[i] = x[i] + (i==theta ?delti[theta]:0); 3467: } 3468: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); 3469: for(i=1;i<=nlstate;i++) 3470: gp[i] = prlim[i][i]; 3471: 3472: for(i=1; i<=npar; i++) /* Computes gradient */ 3473: xp[i] = x[i] - (i==theta ?delti[theta]:0); 3474: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); 3475: for(i=1;i<=nlstate;i++) 3476: gm[i] = prlim[i][i]; 3477: 3478: for(i=1;i<=nlstate;i++) 3479: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta]; 3480: } /* End theta */ 3481: 3482: trgradg =matrix(1,nlstate,1,npar); 3483: 3484: for(j=1; j<=nlstate;j++) 3485: for(theta=1; theta <=npar; theta++) 3486: trgradg[j][theta]=gradg[theta][j]; 3487: 3488: for(i=1;i<=nlstate;i++) 3489: varpl[i][(int)age] =0.; 3490: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov); 3491: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg); 3492: for(i=1;i<=nlstate;i++) 3493: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */ 3494: 3495: fprintf(ficresvpl,"%.0f ",age ); 3496: for(i=1; i<=nlstate;i++) 3497: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age])); 3498: fprintf(ficresvpl,"\n"); 3499: free_vector(gp,1,nlstate); 3500: free_vector(gm,1,nlstate); 3501: free_matrix(gradg,1,npar,1,nlstate); 3502: free_matrix(trgradg,1,nlstate,1,npar); 3503: } /* End age */ 3504: 3505: free_vector(xp,1,npar); 3506: free_matrix(doldm,1,nlstate,1,npar); 3507: free_matrix(dnewm,1,nlstate,1,nlstate); 3508: 3509: } 3510: 3511: /************ Variance of one-step probabilities ******************/ 3512: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[]) 3513: { 3514: int i, j=0, i1, k1, l1, t, tj; 3515: int k2, l2, j1, z1; 3516: int k=0,l, cptcode; 3517: int first=1, first1, first2; 3518: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp; 3519: double **dnewm,**doldm; 3520: double *xp; 3521: double *gp, *gm; 3522: double **gradg, **trgradg; 3523: double **mu; 3524: double age,agelim, cov[NCOVMAX+1]; 3525: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */ 3526: int theta; 3527: char fileresprob[FILENAMELENGTH]; 3528: char fileresprobcov[FILENAMELENGTH]; 3529: char fileresprobcor[FILENAMELENGTH]; 3530: double ***varpij; 3531: 3532: strcpy(fileresprob,"prob"); 3533: strcat(fileresprob,fileres); 3534: if((ficresprob=fopen(fileresprob,"w"))==NULL) { 3535: printf("Problem with resultfile: %s\n", fileresprob); 3536: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob); 3537: } 3538: strcpy(fileresprobcov,"probcov"); 3539: strcat(fileresprobcov,fileres); 3540: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) { 3541: printf("Problem with resultfile: %s\n", fileresprobcov); 3542: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov); 3543: } 3544: strcpy(fileresprobcor,"probcor"); 3545: strcat(fileresprobcor,fileres); 3546: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) { 3547: printf("Problem with resultfile: %s\n", fileresprobcor); 3548: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor); 3549: } 3550: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob); 3551: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob); 3552: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov); 3553: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov); 3554: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor); 3555: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor); 3556: pstamp(ficresprob); 3557: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n"); 3558: fprintf(ficresprob,"# Age"); 3559: pstamp(ficresprobcov); 3560: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n"); 3561: fprintf(ficresprobcov,"# Age"); 3562: pstamp(ficresprobcor); 3563: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n"); 3564: fprintf(ficresprobcor,"# Age"); 3565: 3566: 3567: for(i=1; i<=nlstate;i++) 3568: for(j=1; j<=(nlstate+ndeath);j++){ 3569: fprintf(ficresprob," p%1d-%1d (SE)",i,j); 3570: fprintf(ficresprobcov," p%1d-%1d ",i,j); 3571: fprintf(ficresprobcor," p%1d-%1d ",i,j); 3572: } 3573: /* fprintf(ficresprob,"\n"); 3574: fprintf(ficresprobcov,"\n"); 3575: fprintf(ficresprobcor,"\n"); 3576: */ 3577: xp=vector(1,npar); 3578: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar); 3579: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath)); 3580: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage); 3581: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage); 3582: first=1; 3583: fprintf(ficgp,"\n# Routine varprob"); 3584: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n"); 3585: fprintf(fichtm,"\n"); 3586: 3587: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov); 3588: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\ 3589: file %s \n",optionfilehtmcov); 3590: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\ 3591: and drawn. It helps understanding how is the covariance between two incidences.\ 3592: They are expressed in year-1 in order to be less dependent of stepm. \n"); 3593: fprintf(fichtmcov,"\n Contour plot corresponding to x'cov-1x = 4 (where x is the column vector (pij,pkl)) are drawn. \ 3594: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \ 3595: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \ 3596: standard deviations wide on each axis. \ 3597: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\ 3598: and made the appropriate rotation to look at the uncorrelated principal directions. \ 3599: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one. \n"); 3600: 3601: cov[1]=1; 3602: /* tj=cptcoveff; */ 3603: tj = (int) pow(2,cptcoveff); 3604: if (cptcovn<1) {tj=1;ncodemax[1]=1;} 3605: j1=0; 3606: for(j1=1; j1<=tj;j1++){ 3607: /*for(i1=1; i1<=ncodemax[t];i1++){ */ 3608: /*j1++;*/ 3609: if (cptcovn>0) { 3610: fprintf(ficresprob, "\n#********** Variable "); 3611: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); 3612: fprintf(ficresprob, "**********\n#\n"); 3613: fprintf(ficresprobcov, "\n#********** Variable "); 3614: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); 3615: fprintf(ficresprobcov, "**********\n#\n"); 3616: 3617: fprintf(ficgp, "\n#********** Variable "); 3618: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); 3619: fprintf(ficgp, "**********\n#\n"); 3620: 3621: 3622: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable "); 3623: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); 3624: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">"); 3625: 3626: fprintf(ficresprobcor, "\n#********** Variable "); 3627: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); 3628: fprintf(ficresprobcor, "**********\n#"); 3629: } 3630: 3631: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath)); 3632: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar); 3633: gp=vector(1,(nlstate)*(nlstate+ndeath)); 3634: gm=vector(1,(nlstate)*(nlstate+ndeath)); 3635: for (age=bage; age<=fage; age ++){ 3636: cov[2]=age; 3637: for (k=1; k<=cptcovn;k++) { 3638: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4 3639: * 1 1 1 1 1 3640: * 2 2 1 1 1 3641: * 3 1 2 1 1 3642: */ 3643: /* nbcode[1][1]=0 nbcode[1][2]=1;*/ 3644: } 3645: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; 3646: for (k=1; k<=cptcovprod;k++) 3647: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; 3648: 3649: 3650: for(theta=1; theta <=npar; theta++){ 3651: for(i=1; i<=npar; i++) 3652: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0); 3653: 3654: pmij(pmmij,cov,ncovmodel,xp,nlstate); 3655: 3656: k=0; 3657: for(i=1; i<= (nlstate); i++){ 3658: for(j=1; j<=(nlstate+ndeath);j++){ 3659: k=k+1; 3660: gp[k]=pmmij[i][j]; 3661: } 3662: } 3663: 3664: for(i=1; i<=npar; i++) 3665: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0); 3666: 3667: pmij(pmmij,cov,ncovmodel,xp,nlstate); 3668: k=0; 3669: for(i=1; i<=(nlstate); i++){ 3670: for(j=1; j<=(nlstate+ndeath);j++){ 3671: k=k+1; 3672: gm[k]=pmmij[i][j]; 3673: } 3674: } 3675: 3676: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 3677: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta]; 3678: } 3679: 3680: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++) 3681: for(theta=1; theta <=npar; theta++) 3682: trgradg[j][theta]=gradg[theta][j]; 3683: 3684: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 3685: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg); 3686: 3687: pmij(pmmij,cov,ncovmodel,x,nlstate); 3688: 3689: k=0; 3690: for(i=1; i<=(nlstate); i++){ 3691: for(j=1; j<=(nlstate+ndeath);j++){ 3692: k=k+1; 3693: mu[k][(int) age]=pmmij[i][j]; 3694: } 3695: } 3696: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++) 3697: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++) 3698: varpij[i][j][(int)age] = doldm[i][j]; 3699: 3700: /*printf("\n%d ",(int)age); 3701: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){ 3702: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i])); 3703: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i])); 3704: }*/ 3705: 3706: fprintf(ficresprob,"\n%d ",(int)age); 3707: fprintf(ficresprobcov,"\n%d ",(int)age); 3708: fprintf(ficresprobcor,"\n%d ",(int)age); 3709: 3710: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++) 3711: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age])); 3712: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){ 3713: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]); 3714: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]); 3715: } 3716: i=0; 3717: for (k=1; k<=(nlstate);k++){ 3718: for (l=1; l<=(nlstate+ndeath);l++){ 3719: i++; 3720: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l); 3721: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l); 3722: for (j=1; j<=i;j++){ 3723: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */ 3724: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]); 3725: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age])); 3726: } 3727: } 3728: }/* end of loop for state */ 3729: } /* end of loop for age */ 3730: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath)); 3731: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath)); 3732: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar); 3733: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar); 3734: 3735: /* Confidence intervalle of pij */ 3736: /* 3737: fprintf(ficgp,"\nunset parametric;unset label"); 3738: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\""); 3739: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65"); 3740: fprintf(fichtm,"\n Probability with confidence intervals expressed in year-1 :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname); 3741: fprintf(fichtm,"\n <img src=\"pijgr%s.png\"> ",optionfilefiname); 3742: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname); 3743: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob); 3744: */ 3745: 3746: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/ 3747: first1=1;first2=2; 3748: for (k2=1; k2<=(nlstate);k2++){ 3749: for (l2=1; l2<=(nlstate+ndeath);l2++){ 3750: if(l2==k2) continue; 3751: j=(k2-1)*(nlstate+ndeath)+l2; 3752: for (k1=1; k1<=(nlstate);k1++){ 3753: for (l1=1; l1<=(nlstate+ndeath);l1++){ 3754: if(l1==k1) continue; 3755: i=(k1-1)*(nlstate+ndeath)+l1; 3756: if(i<=j) continue; 3757: for (age=bage; age<=fage; age ++){ 3758: if ((int)age %5==0){ 3759: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM; 3760: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM; 3761: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM; 3762: mu1=mu[i][(int) age]/stepm*YEARM ; 3763: mu2=mu[j][(int) age]/stepm*YEARM; 3764: c12=cv12/sqrt(v1*v2); 3765: /* Computing eigen value of matrix of covariance */ 3766: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.; 3767: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.; 3768: if ((lc2 <0) || (lc1 <0) ){ 3769: if(first2==1){ 3770: first1=0; 3771: printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor); 3772: } 3773: fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog); 3774: /* lc1=fabs(lc1); */ /* If we want to have them positive */ 3775: /* lc2=fabs(lc2); */ 3776: } 3777: 3778: /* Eigen vectors */ 3779: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12)); 3780: /*v21=sqrt(1.-v11*v11); *//* error */ 3781: v21=(lc1-v1)/cv12*v11; 3782: v12=-v21; 3783: v22=v11; 3784: tnalp=v21/v11; 3785: if(first1==1){ 3786: first1=0; 3787: printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp); 3788: } 3789: fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp); 3790: /*printf(fignu*/ 3791: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */ 3792: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */ 3793: if(first==1){ 3794: first=0; 3795: fprintf(ficgp,"\nset parametric;unset label"); 3796: fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2); 3797: fprintf(ficgp,"\nset ter png small size 320, 240"); 3798: fprintf(fichtmcov,"\n Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year-1\ 3799: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\ 3800: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\ 3801: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\ 3802: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2); 3803: fprintf(fichtmcov,"\n <img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2); 3804: fprintf(fichtmcov,"\n Correlation at age %d (%.3f),",(int) age, c12); 3805: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2); 3806: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2); 3807: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2); 3808: fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\ 3809: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\ 3810: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2)); 3811: }else{ 3812: first=0; 3813: fprintf(fichtmcov," %d (%.3f),",(int) age, c12); 3814: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2); 3815: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2); 3816: fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\ 3817: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\ 3818: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2)); 3819: }/* if first */ 3820: } /* age mod 5 */ 3821: } /* end loop age */ 3822: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2); 3823: first=1; 3824: } /*l12 */ 3825: } /* k12 */ 3826: } /*l1 */ 3827: }/* k1 */ 3828: /* } /* loop covariates */ 3829: } 3830: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage); 3831: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage); 3832: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath)); 3833: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar); 3834: free_vector(xp,1,npar); 3835: fclose(ficresprob); 3836: fclose(ficresprobcov); 3837: fclose(ficresprobcor); 3838: fflush(ficgp); 3839: fflush(fichtmcov); 3840: } 3841: 3842: 3843: /******************* Printing html file ***********/ 3844: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \ 3845: int lastpass, int stepm, int weightopt, char model[],\ 3846: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\ 3847: int popforecast, int estepm ,\ 3848: double jprev1, double mprev1,double anprev1, \ 3849: double jprev2, double mprev2,double anprev2){ 3850: int jj1, k1, i1, cpt; 3851: 3852: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \ 3853: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \ 3854: </ul>"); 3855: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \ 3856: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> \n ", 3857: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p")); 3858: fprintf(fichtm,"\ 3859: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a> \n ", 3860: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij")); 3861: fprintf(fichtm,"\ 3862: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> \n", 3863: subdirf2(fileres,"pl"),subdirf2(fileres,"pl")); 3864: fprintf(fichtm,"\ 3865: - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \ 3866: <a href=\"%s\">%s</a> \n", 3867: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e")); 3868: fprintf(fichtm,"\ 3869: - Population projections by age and states: \ 3870: <a href=\"%s\">%s</a> \n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f")); 3871: 3872: fprintf(fichtm," \n<ul><li>Graphs</li>"); 3873: 3874: m=pow(2,cptcoveff); 3875: if (cptcovn < 1) {m=1;ncodemax[1]=1;} 3876: 3877: jj1=0; 3878: for(k1=1; k1<=m;k1++){ 3879: for(i1=1; i1<=ncodemax[k1];i1++){ 3880: jj1++; 3881: if (cptcovn > 0) { 3882: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates"); 3883: for (cpt=1; cpt<=cptcoveff;cpt++) 3884: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]); 3885: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">"); 3886: } 3887: /* Pij */ 3888: fprintf(fichtm," - 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> \ 3889: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 3890: /* Quasi-incidences */ 3891: fprintf(fichtm," - Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\ 3892: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a> \ 3893: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 3894: /* Period (stable) prevalence in each health state */ 3895: for(cpt=1; cpt<nlstate;cpt++){ 3896: fprintf(fichtm," - Period (stable) prevalence in each health state : <a href=\"%s%d_%d.png\">%s%d_%d.png</a> \ 3897: <img src=\"%s%d_%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1); 3898: } 3899: for(cpt=1; cpt<=nlstate;cpt++) { 3900: fprintf(fichtm,"\n - Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> \ 3901: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1); 3902: } 3903: } /* end i1 */ 3904: }/* End k1 */ 3905: fprintf(fichtm,"</ul>"); 3906: 3907: 3908: fprintf(fichtm,"\ 3909: \n <li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\ 3910: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> \n", rfileres,rfileres); 3911: 3912: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> \n", 3913: subdirf2(fileres,"prob"),subdirf2(fileres,"prob")); 3914: fprintf(fichtm,"\ 3915: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> \n", 3916: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov")); 3917: 3918: fprintf(fichtm,"\ 3919: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> \n", 3920: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor")); 3921: fprintf(fichtm,"\ 3922: - Variances and covariances of health expectancies by age and initial health status (cov(eij,ekl)(estepm=%2d months): \ 3923: <a href=\"%s\">%s</a> \n</li>", 3924: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve")); 3925: fprintf(fichtm,"\ 3926: - (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): \ 3927: <a href=\"%s\">%s</a> \n</li>", 3928: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde")); 3929: fprintf(fichtm,"\ 3930: - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), 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", 3931: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v")); 3932: fprintf(fichtm,"\ 3933: - Total life expectancy and total health expectancies to be spent in each health state e.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", 3934: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t")); 3935: fprintf(fichtm,"\ 3936: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> \n",\ 3937: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl")); 3938: 3939: /* if(popforecast==1) fprintf(fichtm,"\n */ 3940: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> \n */ 3941: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> \n */ 3942: /* ",fileres,fileres,fileres,fileres); */ 3943: /* else */ 3944: /* fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .) </li>\n",popforecast, stepm, model); */ 3945: fflush(fichtm); 3946: fprintf(fichtm," <ul><li>Graphs</li>"); 3947: 3948: m=pow(2,cptcoveff); 3949: if (cptcovn < 1) {m=1;ncodemax[1]=1;} 3950: 3951: jj1=0; 3952: for(k1=1; k1<=m;k1++){ 3953: for(i1=1; i1<=ncodemax[k1];i1++){ 3954: jj1++; 3955: if (cptcovn > 0) { 3956: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates"); 3957: for (cpt=1; cpt<=cptcoveff;cpt++) 3958: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]); 3959: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">"); 3960: } 3961: for(cpt=1; cpt<=nlstate;cpt++) { 3962: fprintf(fichtm," - Observed (cross-sectional) and period (incidence based) \ 3963: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png \ 3964: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1); 3965: } 3966: fprintf(fichtm,"\n - Total life expectancy by age and \ 3967: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \ 3968: true period expectancies (those weighted with period prevalences are also\ 3969: drawn in addition to the population based expectancies computed using\ 3970: observed and cahotic prevalences: %s%d.png \ 3971: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1); 3972: } /* end i1 */ 3973: }/* End k1 */ 3974: fprintf(fichtm,"</ul>"); 3975: fflush(fichtm); 3976: } 3977: 3978: /******************* Gnuplot file **************/ 3979: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){ 3980: 3981: char dirfileres[132],optfileres[132]; 3982: int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0; 3983: int ng=0; 3984: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */ 3985: /* printf("Problem with file %s",optionfilegnuplot); */ 3986: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */ 3987: /* } */ 3988: 3989: /*#ifdef windows */ 3990: fprintf(ficgp,"cd \"%s\" \n",pathc); 3991: /*#endif */ 3992: m=pow(2,cptcoveff); 3993: 3994: strcpy(dirfileres,optionfilefiname); 3995: strcpy(optfileres,"vpl"); 3996: /* 1eme*/ 3997: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n"); 3998: for (cpt=1; cpt<= nlstate ; cpt ++) { 3999: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */ 4000: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1); 4001: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1); 4002: fprintf(ficgp,"set xlabel \"Age\" \n\ 4003: set ylabel \"Probability\" \n\ 4004: set ter png small size 320, 240\n\ 4005: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1); 4006: 4007: for (i=1; i<= nlstate ; i ++) { 4008: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)"); 4009: else fprintf(ficgp," \%%*lf (\%%*lf)"); 4010: } 4011: fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 4012: for (i=1; i<= nlstate ; i ++) { 4013: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)"); 4014: else fprintf(ficgp," \%%*lf (\%%*lf)"); 4015: } 4016: fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 4017: for (i=1; i<= nlstate ; i ++) { 4018: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)"); 4019: else fprintf(ficgp," \%%*lf (\%%*lf)"); 4020: } 4021: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1)); 4022: } 4023: } 4024: /*2 eme*/ 4025: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n"); 4026: for (k1=1; k1<= m ; k1 ++) { 4027: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1); 4028: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage); 4029: 4030: for (i=1; i<= nlstate+1 ; i ++) { 4031: k=2*i; 4032: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1); 4033: for (j=1; j<= nlstate+1 ; j ++) { 4034: if (j==i) fprintf(ficgp," \%%lf (\%%lf)"); 4035: else fprintf(ficgp," \%%*lf (\%%*lf)"); 4036: } 4037: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,"); 4038: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1); 4039: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1); 4040: for (j=1; j<= nlstate+1 ; j ++) { 4041: if (j==i) fprintf(ficgp," \%%lf (\%%lf)"); 4042: else fprintf(ficgp," \%%*lf (\%%*lf)"); 4043: } 4044: fprintf(ficgp,"\" t\"\" w l lt 0,"); 4045: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1); 4046: for (j=1; j<= nlstate+1 ; j ++) { 4047: if (j==i) fprintf(ficgp," \%%lf (\%%lf)"); 4048: else fprintf(ficgp," \%%*lf (\%%*lf)"); 4049: } 4050: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0"); 4051: else fprintf(ficgp,"\" t\"\" w l lt 0,"); 4052: } 4053: } 4054: 4055: /*3eme*/ 4056: 4057: for (k1=1; k1<= m ; k1 ++) { 4058: for (cpt=1; cpt<= nlstate ; cpt ++) { 4059: /* k=2+nlstate*(2*cpt-2); */ 4060: k=2+(nlstate+1)*(cpt-1); 4061: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1); 4062: fprintf(ficgp,"set ter png small size 320, 240\n\ 4063: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt); 4064: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1); 4065: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) "); 4066: fprintf(ficgp,"\" t \"e%d1\" w l",cpt); 4067: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1); 4068: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) "); 4069: fprintf(ficgp,"\" t \"e%d1\" w l",cpt); 4070: 4071: */ 4072: for (i=1; i< nlstate ; i ++) { 4073: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1); 4074: /* fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/ 4075: 4076: } 4077: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt); 4078: } 4079: } 4080: 4081: /* CV preval stable (period) */ 4082: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */ 4083: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */ 4084: k=3; 4085: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt); 4086: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1); 4087: l=(nlstate+ndeath)*(cpt-1)+1; 4088: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\ 4089: set ter png small size 320, 240\n\ 4090: unset log y\n\ 4091: plot [%.f:%.f] ", ageminpar, agemaxpar); 4092: for (i=1; i<= nlstate ; i ++){ 4093: if(i==1) 4094: fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij")); 4095: else 4096: fprintf(ficgp,", '' "); 4097: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l,k+l); 4098: for (j=1; j<= (nlstate-1) ; j ++) 4099: fprintf(ficgp,"+$%d",k+l+j); 4100: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt); 4101: } /* nlstate */ 4102: fprintf(ficgp,"\n"); 4103: } /* end cpt state*/ 4104: } /* end covariate */ 4105: 4106: /* proba elementaires */ 4107: for(i=1,jk=1; i <=nlstate; i++){ 4108: for(k=1; k <=(nlstate+ndeath); k++){ 4109: if (k != i) { 4110: for(j=1; j <=ncovmodel; j++){ 4111: fprintf(ficgp,"p%d=%f ",jk,p[jk]); 4112: jk++; 4113: fprintf(ficgp,"\n"); 4114: } 4115: } 4116: } 4117: } 4118: /*goto avoid;*/ 4119: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/ 4120: for(jk=1; jk <=m; jk++) { 4121: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 4122: if (ng==2) 4123: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n"); 4124: else 4125: fprintf(ficgp,"\nset title \"Probability\"\n"); 4126: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar); 4127: i=1; 4128: for(k2=1; k2<=nlstate; k2++) { 4129: k3=i; 4130: for(k=1; k<=(nlstate+ndeath); k++) { 4131: if (k != k2){ 4132: if(ng==2) 4133: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1); 4134: else 4135: fprintf(ficgp," exp(p%d+p%d*x",i,i+1); 4136: ij=1;/* To be checked else nbcode[0][0] wrong */ 4137: for(j=3; j <=ncovmodel; j++) { 4138: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */ 4139: /* /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */ 4140: /* ij++; */ 4141: /* } */ 4142: /* else */ 4143: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]); 4144: } 4145: fprintf(ficgp,")/(1"); 4146: 4147: for(k1=1; k1 <=nlstate; k1++){ 4148: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1); 4149: ij=1; 4150: for(j=3; j <=ncovmodel; j++){ 4151: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */ 4152: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */ 4153: /* ij++; */ 4154: /* } */ 4155: /* else */ 4156: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]); 4157: } 4158: fprintf(ficgp,")"); 4159: } 4160: fprintf(ficgp,") t \"p%d%d\" ", k2,k); 4161: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,","); 4162: i=i+ncovmodel; 4163: } 4164: } /* end k */ 4165: } /* end k2 */ 4166: } /* end jk */ 4167: } /* end ng */ 4168: avoid: 4169: fflush(ficgp); 4170: } /* end gnuplot */ 4171: 4172: 4173: /*************** Moving average **************/ 4174: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){ 4175: 4176: int i, cpt, cptcod; 4177: int modcovmax =1; 4178: int mobilavrange, mob; 4179: double age; 4180: 4181: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 4182: a covariate has 2 modalities */ 4183: if (cptcovn<1) modcovmax=1; /* At least 1 pass */ 4184: 4185: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){ 4186: if(mobilav==1) mobilavrange=5; /* default */ 4187: else mobilavrange=mobilav; 4188: for (age=bage; age<=fage; age++) 4189: for (i=1; i<=nlstate;i++) 4190: for (cptcod=1;cptcod<=modcovmax;cptcod++) 4191: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod]; 4192: /* We keep the original values on the extreme ages bage, fage and for 4193: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2 4194: we use a 5 terms etc. until the borders are no more concerned. 4195: */ 4196: for (mob=3;mob <=mobilavrange;mob=mob+2){ 4197: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ 4198: for (i=1; i<=nlstate;i++){ 4199: for (cptcod=1;cptcod<=modcovmax;cptcod++){ 4200: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod]; 4201: for (cpt=1;cpt<=(mob-1)/2;cpt++){ 4202: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod]; 4203: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod]; 4204: } 4205: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob; 4206: } 4207: } 4208: }/* end age */ 4209: }/* end mob */ 4210: }else return -1; 4211: return 0; 4212: }/* End movingaverage */ 4213: 4214: 4215: /************** Forecasting ******************/ 4216: prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){ 4217: /* proj1, year, month, day of starting projection 4218: agemin, agemax range of age 4219: dateprev1 dateprev2 range of dates during which prevalence is computed 4220: anproj2 year of en of projection (same day and month as proj1). 4221: */ 4222: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1; 4223: int *popage; 4224: double agec; /* generic age */ 4225: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; 4226: double *popeffectif,*popcount; 4227: double ***p3mat; 4228: double ***mobaverage; 4229: char fileresf[FILENAMELENGTH]; 4230: 4231: agelim=AGESUP; 4232: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); 4233: 4234: strcpy(fileresf,"f"); 4235: strcat(fileresf,fileres); 4236: if((ficresf=fopen(fileresf,"w"))==NULL) { 4237: printf("Problem with forecast resultfile: %s\n", fileresf); 4238: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf); 4239: } 4240: printf("Computing forecasting: result on file '%s' \n", fileresf); 4241: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf); 4242: 4243: if (cptcoveff==0) ncodemax[cptcoveff]=1; 4244: 4245: if (mobilav!=0) { 4246: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 4247: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ 4248: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); 4249: printf(" Error in movingaverage mobilav=%d\n",mobilav); 4250: } 4251: } 4252: 4253: stepsize=(int) (stepm+YEARM-1)/YEARM; 4254: if (stepm<=12) stepsize=1; 4255: if(estepm < stepm){ 4256: printf ("Problem %d lower than %d\n",estepm, stepm); 4257: } 4258: else hstepm=estepm; 4259: 4260: hstepm=hstepm/stepm; 4261: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and 4262: fractional in yp1 */ 4263: anprojmean=yp; 4264: yp2=modf((yp1*12),&yp); 4265: mprojmean=yp; 4266: yp1=modf((yp2*30.5),&yp); 4267: jprojmean=yp; 4268: if(jprojmean==0) jprojmean=1; 4269: if(mprojmean==0) jprojmean=1; 4270: 4271: i1=cptcoveff; 4272: if (cptcovn < 1){i1=1;} 4273: 4274: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 4275: 4276: fprintf(ficresf,"#****** Routine prevforecast **\n"); 4277: 4278: /* if (h==(int)(YEARM*yearp)){ */ 4279: for(cptcov=1, k=0;cptcov<=i1;cptcov++){ 4280: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ 4281: k=k+1; 4282: fprintf(ficresf,"\n#******"); 4283: for(j=1;j<=cptcoveff;j++) { 4284: fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 4285: } 4286: fprintf(ficresf,"******\n"); 4287: fprintf(ficresf,"# Covariate valuofcovar yearproj age"); 4288: for(j=1; j<=nlstate+ndeath;j++){ 4289: for(i=1; i<=nlstate;i++) 4290: fprintf(ficresf," p%d%d",i,j); 4291: fprintf(ficresf," p.%d",j); 4292: } 4293: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 4294: fprintf(ficresf,"\n"); 4295: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp); 4296: 4297: for (agec=fage; agec>=(ageminpar-1); agec--){ 4298: nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 4299: nhstepm = nhstepm/hstepm; 4300: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 4301: oldm=oldms;savm=savms; 4302: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k); 4303: 4304: for (h=0; h<=nhstepm; h++){ 4305: if (h*hstepm/YEARM*stepm ==yearp) { 4306: fprintf(ficresf,"\n"); 4307: for(j=1;j<=cptcoveff;j++) 4308: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 4309: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm); 4310: } 4311: for(j=1; j<=nlstate+ndeath;j++) { 4312: ppij=0.; 4313: for(i=1; i<=nlstate;i++) { 4314: if (mobilav==1) 4315: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod]; 4316: else { 4317: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod]; 4318: } 4319: if (h*hstepm/YEARM*stepm== yearp) { 4320: fprintf(ficresf," %.3f", p3mat[i][j][h]); 4321: } 4322: } /* end i */ 4323: if (h*hstepm/YEARM*stepm==yearp) { 4324: fprintf(ficresf," %.3f", ppij); 4325: } 4326: }/* end j */ 4327: } /* end h */ 4328: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 4329: } /* end agec */ 4330: } /* end yearp */ 4331: } /* end cptcod */ 4332: } /* end cptcov */ 4333: 4334: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 4335: 4336: fclose(ficresf); 4337: } 4338: 4339: /************** Forecasting *****not tested NB*************/ 4340: populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){ 4341: 4342: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; 4343: int *popage; 4344: double calagedatem, agelim, kk1, kk2; 4345: double *popeffectif,*popcount; 4346: double ***p3mat,***tabpop,***tabpopprev; 4347: double ***mobaverage; 4348: char filerespop[FILENAMELENGTH]; 4349: 4350: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 4351: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 4352: agelim=AGESUP; 4353: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; 4354: 4355: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); 4356: 4357: 4358: strcpy(filerespop,"pop"); 4359: strcat(filerespop,fileres); 4360: if((ficrespop=fopen(filerespop,"w"))==NULL) { 4361: printf("Problem with forecast resultfile: %s\n", filerespop); 4362: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); 4363: } 4364: printf("Computing forecasting: result on file '%s' \n", filerespop); 4365: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); 4366: 4367: if (cptcoveff==0) ncodemax[cptcoveff]=1; 4368: 4369: if (mobilav!=0) { 4370: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 4371: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ 4372: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); 4373: printf(" Error in movingaverage mobilav=%d\n",mobilav); 4374: } 4375: } 4376: 4377: stepsize=(int) (stepm+YEARM-1)/YEARM; 4378: if (stepm<=12) stepsize=1; 4379: 4380: agelim=AGESUP; 4381: 4382: hstepm=1; 4383: hstepm=hstepm/stepm; 4384: 4385: if (popforecast==1) { 4386: if((ficpop=fopen(popfile,"r"))==NULL) { 4387: printf("Problem with population file : %s\n",popfile);exit(0); 4388: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); 4389: } 4390: popage=ivector(0,AGESUP); 4391: popeffectif=vector(0,AGESUP); 4392: popcount=vector(0,AGESUP); 4393: 4394: i=1; 4395: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; 4396: 4397: imx=i; 4398: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i]; 4399: } 4400: 4401: for(cptcov=1,k=0;cptcov<=i2;cptcov++){ 4402: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ 4403: k=k+1; 4404: fprintf(ficrespop,"\n#******"); 4405: for(j=1;j<=cptcoveff;j++) { 4406: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 4407: } 4408: fprintf(ficrespop,"******\n"); 4409: fprintf(ficrespop,"# Age"); 4410: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j); 4411: if (popforecast==1) fprintf(ficrespop," [Population]"); 4412: 4413: for (cpt=0; cpt<=0;cpt++) { 4414: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); 4415: 4416: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 4417: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 4418: nhstepm = nhstepm/hstepm; 4419: 4420: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 4421: oldm=oldms;savm=savms; 4422: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); 4423: 4424: for (h=0; h<=nhstepm; h++){ 4425: if (h==(int) (calagedatem+YEARM*cpt)) { 4426: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); 4427: } 4428: for(j=1; j<=nlstate+ndeath;j++) { 4429: kk1=0.;kk2=0; 4430: for(i=1; i<=nlstate;i++) { 4431: if (mobilav==1) 4432: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; 4433: else { 4434: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; 4435: } 4436: } 4437: if (h==(int)(calagedatem+12*cpt)){ 4438: tabpop[(int)(agedeb)][j][cptcod]=kk1; 4439: /*fprintf(ficrespop," %.3f", kk1); 4440: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/ 4441: } 4442: } 4443: for(i=1; i<=nlstate;i++){ 4444: kk1=0.; 4445: for(j=1; j<=nlstate;j++){ 4446: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 4447: } 4448: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)]; 4449: } 4450: 4451: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 4452: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); 4453: } 4454: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 4455: } 4456: } 4457: 4458: /******/ 4459: 4460: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 4461: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); 4462: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 4463: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 4464: nhstepm = nhstepm/hstepm; 4465: 4466: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 4467: oldm=oldms;savm=savms; 4468: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); 4469: for (h=0; h<=nhstepm; h++){ 4470: if (h==(int) (calagedatem+YEARM*cpt)) { 4471: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); 4472: } 4473: for(j=1; j<=nlstate+ndeath;j++) { 4474: kk1=0.;kk2=0; 4475: for(i=1; i<=nlstate;i++) { 4476: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod]; 4477: } 4478: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1); 4479: } 4480: } 4481: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 4482: } 4483: } 4484: } 4485: } 4486: 4487: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 4488: 4489: if (popforecast==1) { 4490: free_ivector(popage,0,AGESUP); 4491: free_vector(popeffectif,0,AGESUP); 4492: free_vector(popcount,0,AGESUP); 4493: } 4494: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 4495: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 4496: fclose(ficrespop); 4497: } /* End of popforecast */ 4498: 4499: int fileappend(FILE *fichier, char *optionfich) 4500: { 4501: if((fichier=fopen(optionfich,"a"))==NULL) { 4502: printf("Problem with file: %s\n", optionfich); 4503: fprintf(ficlog,"Problem with file: %s\n", optionfich); 4504: return (0); 4505: } 4506: fflush(fichier); 4507: return (1); 4508: } 4509: 4510: 4511: /**************** function prwizard **********************/ 4512: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo) 4513: { 4514: 4515: /* Wizard to print covariance matrix template */ 4516: 4517: char ca[32], cb[32], cc[32]; 4518: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes; 4519: int numlinepar; 4520: 4521: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); 4522: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); 4523: for(i=1; i <=nlstate; i++){ 4524: jj=0; 4525: for(j=1; j <=nlstate+ndeath; j++){ 4526: if(j==i) continue; 4527: jj++; 4528: /*ca[0]= k+'a'-1;ca[1]='\0';*/ 4529: printf("%1d%1d",i,j); 4530: fprintf(ficparo,"%1d%1d",i,j); 4531: for(k=1; k<=ncovmodel;k++){ 4532: /* printf(" %lf",param[i][j][k]); */ 4533: /* fprintf(ficparo," %lf",param[i][j][k]); */ 4534: printf(" 0."); 4535: fprintf(ficparo," 0."); 4536: } 4537: printf("\n"); 4538: fprintf(ficparo,"\n"); 4539: } 4540: } 4541: printf("# Scales (for hessian or gradient estimation)\n"); 4542: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n"); 4543: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 4544: for(i=1; i <=nlstate; i++){ 4545: jj=0; 4546: for(j=1; j <=nlstate+ndeath; j++){ 4547: if(j==i) continue; 4548: jj++; 4549: fprintf(ficparo,"%1d%1d",i,j); 4550: printf("%1d%1d",i,j); 4551: fflush(stdout); 4552: for(k=1; k<=ncovmodel;k++){ 4553: /* printf(" %le",delti3[i][j][k]); */ 4554: /* fprintf(ficparo," %le",delti3[i][j][k]); */ 4555: printf(" 0."); 4556: fprintf(ficparo," 0."); 4557: } 4558: numlinepar++; 4559: printf("\n"); 4560: fprintf(ficparo,"\n"); 4561: } 4562: } 4563: printf("# Covariance matrix\n"); 4564: /* # 121 Var(a12)\n\ */ 4565: /* # 122 Cov(b12,a12) Var(b12)\n\ */ 4566: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */ 4567: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */ 4568: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */ 4569: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */ 4570: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */ 4571: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */ 4572: fflush(stdout); 4573: fprintf(ficparo,"# Covariance matrix\n"); 4574: /* # 121 Var(a12)\n\ */ 4575: /* # 122 Cov(b12,a12) Var(b12)\n\ */ 4576: /* # ...\n\ */ 4577: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */ 4578: 4579: for(itimes=1;itimes<=2;itimes++){ 4580: jj=0; 4581: for(i=1; i <=nlstate; i++){ 4582: for(j=1; j <=nlstate+ndeath; j++){ 4583: if(j==i) continue; 4584: for(k=1; k<=ncovmodel;k++){ 4585: jj++; 4586: ca[0]= k+'a'-1;ca[1]='\0'; 4587: if(itimes==1){ 4588: printf("#%1d%1d%d",i,j,k); 4589: fprintf(ficparo,"#%1d%1d%d",i,j,k); 4590: }else{ 4591: printf("%1d%1d%d",i,j,k); 4592: fprintf(ficparo,"%1d%1d%d",i,j,k); 4593: /* printf(" %.5le",matcov[i][j]); */ 4594: } 4595: ll=0; 4596: for(li=1;li <=nlstate; li++){ 4597: for(lj=1;lj <=nlstate+ndeath; lj++){ 4598: if(lj==li) continue; 4599: for(lk=1;lk<=ncovmodel;lk++){ 4600: ll++; 4601: if(ll<=jj){ 4602: cb[0]= lk +'a'-1;cb[1]='\0'; 4603: if(ll<jj){ 4604: if(itimes==1){ 4605: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj); 4606: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj); 4607: }else{ 4608: printf(" 0."); 4609: fprintf(ficparo," 0."); 4610: } 4611: }else{ 4612: if(itimes==1){ 4613: printf(" Var(%s%1d%1d)",ca,i,j); 4614: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j); 4615: }else{ 4616: printf(" 0."); 4617: fprintf(ficparo," 0."); 4618: } 4619: } 4620: } 4621: } /* end lk */ 4622: } /* end lj */ 4623: } /* end li */ 4624: printf("\n"); 4625: fprintf(ficparo,"\n"); 4626: numlinepar++; 4627: } /* end k*/ 4628: } /*end j */ 4629: } /* end i */ 4630: } /* end itimes */ 4631: 4632: } /* end of prwizard */ 4633: /******************* Gompertz Likelihood ******************************/ 4634: double gompertz(double x[]) 4635: { 4636: double A,B,L=0.0,sump=0.,num=0.; 4637: int i,n=0; /* n is the size of the sample */ 4638: 4639: for (i=0;i<=imx-1 ; i++) { 4640: sump=sump+weight[i]; 4641: /* sump=sump+1;*/ 4642: num=num+1; 4643: } 4644: 4645: 4646: /* for (i=0; i<=imx; i++) 4647: if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/ 4648: 4649: for (i=1;i<=imx ; i++) 4650: { 4651: if (cens[i] == 1 && wav[i]>1) 4652: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp))); 4653: 4654: if (cens[i] == 0 && wav[i]>1) 4655: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp))) 4656: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM); 4657: 4658: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */ 4659: if (wav[i] > 1 ) { /* ??? */ 4660: L=L+A*weight[i]; 4661: /* printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/ 4662: } 4663: } 4664: 4665: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/ 4666: 4667: return -2*L*num/sump; 4668: } 4669: 4670: #ifdef GSL 4671: /******************* Gompertz_f Likelihood ******************************/ 4672: double gompertz_f(const gsl_vector *v, void *params) 4673: { 4674: double A,B,LL=0.0,sump=0.,num=0.; 4675: double *x= (double *) v->data; 4676: int i,n=0; /* n is the size of the sample */ 4677: 4678: for (i=0;i<=imx-1 ; i++) { 4679: sump=sump+weight[i]; 4680: /* sump=sump+1;*/ 4681: num=num+1; 4682: } 4683: 4684: 4685: /* for (i=0; i<=imx; i++) 4686: if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/ 4687: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]); 4688: for (i=1;i<=imx ; i++) 4689: { 4690: if (cens[i] == 1 && wav[i]>1) 4691: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp))); 4692: 4693: if (cens[i] == 0 && wav[i]>1) 4694: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp))) 4695: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM); 4696: 4697: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */ 4698: if (wav[i] > 1 ) { /* ??? */ 4699: LL=LL+A*weight[i]; 4700: /* printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/ 4701: } 4702: } 4703: 4704: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/ 4705: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump); 4706: 4707: return -2*LL*num/sump; 4708: } 4709: #endif 4710: 4711: /******************* Printing html file ***********/ 4712: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \ 4713: int lastpass, int stepm, int weightopt, char model[],\ 4714: int imx, double p[],double **matcov,double agemortsup){ 4715: int i,k; 4716: 4717: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets): "); 4718: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year ",p[1],p[2],agegomp); 4719: for (i=1;i<=2;i++) 4720: 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])); 4721: fprintf(fichtm," <img src=\"graphmort.png\">"); 4722: fprintf(fichtm,"</ul>"); 4723: 4724: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n "); 4725: 4726: fprintf(fichtm,"\nAge l<inf>x</inf> q<inf>x</inf> d(x,x+1) L<inf>x</inf> T<inf>x</inf> e<infx</inf> "); 4727: 4728: for (k=agegomp;k<(agemortsup-2);k++) 4729: 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]); 4730: 4731: 4732: fflush(fichtm); 4733: } 4734: 4735: /******************* Gnuplot file **************/ 4736: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){ 4737: 4738: char dirfileres[132],optfileres[132]; 4739: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l; 4740: int ng; 4741: 4742: 4743: /*#ifdef windows */ 4744: fprintf(ficgp,"cd \"%s\" \n",pathc); 4745: /*#endif */ 4746: 4747: 4748: strcpy(dirfileres,optionfilefiname); 4749: strcpy(optfileres,"vpl"); 4750: fprintf(ficgp,"set out \"graphmort.png\"\n "); 4751: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 4752: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n"); 4753: /* fprintf(ficgp, "set size 0.65,0.65\n"); */ 4754: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp); 4755: 4756: } 4757: 4758: int readdata(char datafile[], int firstobs, int lastobs, int *imax) 4759: { 4760: 4761: /*-------- data file ----------*/ 4762: FILE *fic; 4763: char dummy[]=" "; 4764: int i, j, n; 4765: int linei, month, year,iout; 4766: char line[MAXLINE], linetmp[MAXLINE]; 4767: char stra[80], strb[80]; 4768: char *stratrunc; 4769: int lstra; 4770: 4771: 4772: if((fic=fopen(datafile,"r"))==NULL) { 4773: printf("Problem while opening datafile: %s\n", datafile);return 1; 4774: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1; 4775: } 4776: 4777: i=1; 4778: linei=0; 4779: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) { 4780: linei=linei+1; 4781: for(j=strlen(line); j>=0;j--){ /* Untabifies line */ 4782: if(line[j] == '\t') 4783: line[j] = ' '; 4784: } 4785: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){ 4786: ; 4787: }; 4788: line[j+1]=0; /* Trims blanks at end of line */ 4789: if(line[0]=='#'){ 4790: fprintf(ficlog,"Comment line\n%s\n",line); 4791: printf("Comment line\n%s\n",line); 4792: continue; 4793: } 4794: trimbb(linetmp,line); /* Trims multiple blanks in line */ 4795: for (j=0; line[j]!='\0';j++){ 4796: line[j]=linetmp[j]; 4797: } 4798: 4799: 4800: for (j=maxwav;j>=1;j--){ 4801: cutv(stra, strb, line, ' '); 4802: if(strb[0]=='.') { /* Missing status */ 4803: lval=-1; 4804: }else{ 4805: errno=0; 4806: lval=strtol(strb,&endptr,10); 4807: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/ 4808: if( strb[0]=='\0' || (*endptr != '\0')){ 4809: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav); 4810: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog); 4811: return 1; 4812: } 4813: } 4814: s[j][i]=lval; 4815: 4816: strcpy(line,stra); 4817: cutv(stra, strb,line,' '); 4818: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){ 4819: } 4820: else if(iout=sscanf(strb,"%s.",dummy) != 0){ 4821: month=99; 4822: year=9999; 4823: }else{ 4824: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j); 4825: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);fflush(ficlog); 4826: return 1; 4827: } 4828: anint[j][i]= (double) year; 4829: mint[j][i]= (double)month; 4830: strcpy(line,stra); 4831: } /* ENd Waves */ 4832: 4833: cutv(stra, strb,line,' '); 4834: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){ 4835: } 4836: else if(iout=sscanf(strb,"%s.",dummy) != 0){ 4837: month=99; 4838: year=9999; 4839: }else{ 4840: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line); 4841: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog); 4842: return 1; 4843: } 4844: andc[i]=(double) year; 4845: moisdc[i]=(double) month; 4846: strcpy(line,stra); 4847: 4848: cutv(stra, strb,line,' '); 4849: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){ 4850: } 4851: else if(iout=sscanf(strb,"%s.", dummy) != 0){ 4852: month=99; 4853: year=9999; 4854: }else{ 4855: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line); 4856: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog); 4857: return 1; 4858: } 4859: if (year==9999) { 4860: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line); 4861: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog); 4862: return 1; 4863: 4864: } 4865: annais[i]=(double)(year); 4866: moisnais[i]=(double)(month); 4867: strcpy(line,stra); 4868: 4869: cutv(stra, strb,line,' '); 4870: errno=0; 4871: dval=strtod(strb,&endptr); 4872: if( strb[0]=='\0' || (*endptr != '\0')){ 4873: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei); 4874: fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei); 4875: fflush(ficlog); 4876: return 1; 4877: } 4878: weight[i]=dval; 4879: strcpy(line,stra); 4880: 4881: for (j=ncovcol;j>=1;j--){ 4882: cutv(stra, strb,line,' '); 4883: if(strb[0]=='.') { /* Missing status */ 4884: lval=-1; 4885: }else{ 4886: errno=0; 4887: lval=strtol(strb,&endptr,10); 4888: if( strb[0]=='\0' || (*endptr != '\0')){ 4889: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line); 4890: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line);fflush(ficlog); 4891: return 1; 4892: } 4893: } 4894: if(lval <-1 || lval >1){ 4895: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \ 4896: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \ 4897: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \ 4898: For example, for multinomial values like 1, 2 and 3,\n \ 4899: build V1=0 V2=0 for the reference value (1),\n \ 4900: V1=1 V2=0 for (2) \n \ 4901: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \ 4902: output of IMaCh is often meaningless.\n \ 4903: Exiting.\n",lval,linei, i,line,j); 4904: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \ 4905: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \ 4906: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \ 4907: For example, for multinomial values like 1, 2 and 3,\n \ 4908: build V1=0 V2=0 for the reference value (1),\n \ 4909: V1=1 V2=0 for (2) \n \ 4910: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \ 4911: output of IMaCh is often meaningless.\n \ 4912: Exiting.\n",lval,linei, i,line,j);fflush(ficlog); 4913: return 1; 4914: } 4915: covar[j][i]=(double)(lval); 4916: strcpy(line,stra); 4917: } 4918: lstra=strlen(stra); 4919: 4920: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */ 4921: stratrunc = &(stra[lstra-9]); 4922: num[i]=atol(stratrunc); 4923: } 4924: else 4925: num[i]=atol(stra); 4926: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){ 4927: printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/ 4928: 4929: i=i+1; 4930: } /* End loop reading data */ 4931: 4932: *imax=i-1; /* Number of individuals */ 4933: fclose(fic); 4934: 4935: return (0); 4936: endread: 4937: printf("Exiting readdata: "); 4938: fclose(fic); 4939: return (1); 4940: 4941: 4942: 4943: } 4944: void removespace(char *str) { 4945: char *p1 = str, *p2 = str; 4946: do 4947: while (*p2 == ' ') 4948: p2++; 4949: while (*p1++ = *p2++); 4950: } 4951: 4952: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns: 4953: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age 4954: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 4955: * - cptcovn or number of covariates k of the models excluding age*products =6 4956: * - cptcovage number of covariates with age*products =2 4957: * - cptcovs number of simple covariates 4958: * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10 4959: * which is a new column after the 9 (ncovcol) variables. 4960: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual 4961: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage 4962: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6. 4963: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 . 4964: */ 4965: { 4966: int i, j, k, ks; 4967: int i1, j1, k1, k2; 4968: char modelsav[80]; 4969: char stra[80], strb[80], strc[80], strd[80],stre[80]; 4970: 4971: /*removespace(model);*/ 4972: if (strlen(model) >1){ /* If there is at least 1 covariate */ 4973: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0; 4974: j=nbocc(model,'+'); /**< j=Number of '+' */ 4975: j1=nbocc(model,'*'); /**< j1=Number of '*' */ 4976: cptcovs=j+1-j1; /**< Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2 */ 4977: cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/ 4978: /* including age products which are counted in cptcovage. 4979: /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */ 4980: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */ 4981: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */ 4982: strcpy(modelsav,model); 4983: if (strstr(model,"AGE") !=0){ 4984: printf("Error. AGE must be in lower case 'age' model=%s ",model); 4985: fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog); 4986: return 1; 4987: } 4988: if (strstr(model,"v") !=0){ 4989: printf("Error. 'v' must be in upper case 'V' model=%s ",model); 4990: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog); 4991: return 1; 4992: } 4993: 4994: /* Design 4995: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight 4996: * < ncovcol=8 > 4997: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 4998: * k= 1 2 3 4 5 6 7 8 4999: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8 5000: * covar[k,i], value of kth covariate if not including age for individual i: 5001: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8) 5002: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8 5003: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 5004: * Tage[++cptcovage]=k 5005: * if products, new covar are created after ncovcol with k1 5006: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11 5007: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product 5008: * Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8 5009: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2]; 5010: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted 5011: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11 5012: * < ncovcol=8 > 5013: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2 5014: * k= 1 2 3 4 5 6 7 8 9 10 11 12 5015: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8 5016: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6} 5017: * p Tprod[1]@2={ 6, 5} 5018: *p Tvard[1][1]@4= {7, 8, 5, 6} 5019: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8 5020: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; 5021: *How to reorganize? 5022: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age 5023: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6} 5024: * {2, 1, 4, 8, 5, 6, 3, 7} 5025: * Struct [] 5026: */ 5027: 5028: /* This loop fills the array Tvar from the string 'model'.*/ 5029: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */ 5030: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */ 5031: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */ 5032: /* k=3 V4 Tvar[k=3]= 4 (from V4) */ 5033: /* k=2 V1 Tvar[k=2]= 1 (from V1) */ 5034: /* k=1 Tvar[1]=2 (from V2) */ 5035: /* k=5 Tvar[5] */ 5036: /* for (k=1; k<=cptcovn;k++) { */ 5037: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */ 5038: /* } */ 5039: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */ 5040: /* 5041: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */ 5042: for(k=cptcovt; k>=1;k--) /**< Number of covariates */ 5043: Tvar[k]=0; 5044: cptcovage=0; 5045: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */ 5046: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 5047: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 5048: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */ 5049: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/ 5050: /*scanf("%d",i);*/ 5051: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */ 5052: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */ 5053: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */ 5054: /* covar is not filled and then is empty */ 5055: cptcovprod--; 5056: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */ 5057: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */ 5058: cptcovage++; /* Sums the number of covariates which include age as a product */ 5059: Tage[cptcovage]=k; /* Tage[1] = 4 */ 5060: /*printf("stre=%s ", stre);*/ 5061: } else if (strcmp(strd,"age")==0) { /* or age*Vn */ 5062: cptcovprod--; 5063: cutl(stre,strb,strc,'V'); 5064: Tvar[k]=atoi(stre); 5065: cptcovage++; 5066: Tage[cptcovage]=k; 5067: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/ 5068: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */ 5069: cptcovn++; 5070: cptcovprodnoage++;k1++; 5071: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/ 5072: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but 5073: because this model-covariate is a construction we invent a new column 5074: ncovcol + k1 5075: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2 5076: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */ 5077: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */ 5078: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */ 5079: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/ 5080: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/ 5081: k2=k2+2; 5082: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */ 5083: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */ 5084: for (i=1; i<=lastobs;i++){ 5085: /* Computes the new covariate which is a product of 5086: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */ 5087: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i]; 5088: } 5089: } /* End age is not in the model */ 5090: } /* End if model includes a product */ 5091: else { /* no more sum */ 5092: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/ 5093: /* scanf("%d",i);*/ 5094: cutl(strd,strc,strb,'V'); 5095: ks++; /**< Number of simple covariates */ 5096: cptcovn++; 5097: Tvar[k]=atoi(strd); 5098: } 5099: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 5100: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav); 5101: scanf("%d",i);*/ 5102: } /* end of loop + */ 5103: } /* end model */ 5104: 5105: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products. 5106: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/ 5107: 5108: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]); 5109: printf("cptcovprod=%d ", cptcovprod); 5110: fprintf(ficlog,"cptcovprod=%d ", cptcovprod); 5111: 5112: scanf("%d ",i);*/ 5113: 5114: 5115: return (0); /* with covar[new additional covariate if product] and Tage if age */ 5116: endread: 5117: printf("Exiting decodemodel: "); 5118: return (1); 5119: } 5120: 5121: calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn ) 5122: { 5123: int i, m; 5124: 5125: for (i=1; i<=imx; i++) { 5126: for(m=2; (m<= maxwav); m++) { 5127: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){ 5128: anint[m][i]=9999; 5129: s[m][i]=-1; 5130: } 5131: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){ 5132: *nberr++; 5133: printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i); 5134: fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i); 5135: s[m][i]=-1; 5136: } 5137: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){ 5138: *nberr++; 5139: printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 5140: fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 5141: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */ 5142: } 5143: } 5144: } 5145: 5146: for (i=1; i<=imx; i++) { 5147: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]); 5148: for(m=firstpass; (m<= lastpass); m++){ 5149: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){ 5150: if (s[m][i] >= nlstate+1) { 5151: if(agedc[i]>0) 5152: if((int)moisdc[i]!=99 && (int)andc[i]!=9999) 5153: agev[m][i]=agedc[i]; 5154: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/ 5155: else { 5156: if ((int)andc[i]!=9999){ 5157: nbwarn++; 5158: printf("Warning negative age at death: %ld line:%d\n",num[i],i); 5159: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i); 5160: agev[m][i]=-1; 5161: } 5162: } 5163: } 5164: else if(s[m][i] !=9){ /* Standard case, age in fractional 5165: years but with the precision of a month */ 5166: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]); 5167: if((int)mint[m][i]==99 || (int)anint[m][i]==9999) 5168: agev[m][i]=1; 5169: else if(agev[m][i] < *agemin){ 5170: *agemin=agev[m][i]; 5171: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin); 5172: } 5173: else if(agev[m][i] >*agemax){ 5174: *agemax=agev[m][i]; 5175: printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax); 5176: } 5177: /*agev[m][i]=anint[m][i]-annais[i];*/ 5178: /* agev[m][i] = age[i]+2*m;*/ 5179: } 5180: else { /* =9 */ 5181: agev[m][i]=1; 5182: s[m][i]=-1; 5183: } 5184: } 5185: else /*= 0 Unknown */ 5186: agev[m][i]=1; 5187: } 5188: 5189: } 5190: for (i=1; i<=imx; i++) { 5191: for(m=firstpass; (m<=lastpass); m++){ 5192: if (s[m][i] > (nlstate+ndeath)) { 5193: *nberr++; 5194: printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath); 5195: fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath); 5196: return 1; 5197: } 5198: } 5199: } 5200: 5201: /*for (i=1; i<=imx; i++){ 5202: for (m=firstpass; (m<lastpass); m++){ 5203: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]); 5204: } 5205: 5206: }*/ 5207: 5208: 5209: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 5210: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 5211: 5212: return (0); 5213: endread: 5214: printf("Exiting calandcheckages: "); 5215: return (1); 5216: } 5217: 5218: 5219: /***********************************************/ 5220: /**************** Main Program *****************/ 5221: /***********************************************/ 5222: 5223: int main(int argc, char *argv[]) 5224: { 5225: #ifdef GSL 5226: const gsl_multimin_fminimizer_type *T; 5227: size_t iteri = 0, it; 5228: int rval = GSL_CONTINUE; 5229: int status = GSL_SUCCESS; 5230: double ssval; 5231: #endif 5232: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav); 5233: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod; 5234: int linei, month, year,iout; 5235: int jj, ll, li, lj, lk, imk; 5236: int numlinepar=0; /* Current linenumber of parameter file */ 5237: int itimes; 5238: int NDIM=2; 5239: int vpopbased=0; 5240: 5241: char ca[32], cb[32], cc[32]; 5242: /* FILE *fichtm; *//* Html File */ 5243: /* FILE *ficgp;*/ /*Gnuplot File */ 5244: struct stat info; 5245: double agedeb, agefin,hf; 5246: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20; 5247: 5248: double fret; 5249: double **xi,tmp,delta; 5250: 5251: double dum; /* Dummy variable */ 5252: double ***p3mat; 5253: double ***mobaverage; 5254: int *indx; 5255: char line[MAXLINE], linepar[MAXLINE]; 5256: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE]; 5257: char pathr[MAXLINE], pathimach[MAXLINE]; 5258: char **bp, *tok, *val; /* pathtot */ 5259: int firstobs=1, lastobs=10; 5260: int sdeb, sfin; /* Status at beginning and end */ 5261: int c, h , cpt,l; 5262: int ju,jl, mi; 5263: int i1,j1, jk,aa,bb, stepsize, ij; 5264: int jnais,jdc,jint4,jint1,jint2,jint3,*tab; 5265: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */ 5266: int mobilav=0,popforecast=0; 5267: int hstepm, nhstepm; 5268: int agemortsup; 5269: float sumlpop=0.; 5270: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000; 5271: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000; 5272: 5273: double bage, fage, age, agelim, agebase; 5274: double ftolpl=FTOL; 5275: double **prlim; 5276: double ***param; /* Matrix of parameters */ 5277: double *p; 5278: double **matcov; /* Matrix of covariance */ 5279: double ***delti3; /* Scale */ 5280: double *delti; /* Scale */ 5281: double ***eij, ***vareij; 5282: double **varpl; /* Variances of prevalence limits by age */ 5283: double *epj, vepp; 5284: double kk1, kk2; 5285: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000; 5286: double **ximort; 5287: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234"; 5288: int *dcwave; 5289: 5290: char z[1]="c", occ; 5291: 5292: /*char *strt;*/ 5293: char strtend[80]; 5294: 5295: long total_usecs; 5296: 5297: /* setlocale (LC_ALL, ""); */ 5298: /* bindtextdomain (PACKAGE, LOCALEDIR); */ 5299: /* textdomain (PACKAGE); */ 5300: /* setlocale (LC_CTYPE, ""); */ 5301: /* setlocale (LC_MESSAGES, ""); */ 5302: 5303: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */ 5304: (void) gettimeofday(&start_time,&tzp); 5305: curr_time=start_time; 5306: tm = *localtime(&start_time.tv_sec); 5307: tmg = *gmtime(&start_time.tv_sec); 5308: strcpy(strstart,asctime(&tm)); 5309: 5310: /* printf("Localtime (at start)=%s",strstart); */ 5311: /* tp.tv_sec = tp.tv_sec +86400; */ 5312: /* tm = *localtime(&start_time.tv_sec); */ 5313: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */ 5314: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */ 5315: /* tmg.tm_hour=tmg.tm_hour + 1; */ 5316: /* tp.tv_sec = mktime(&tmg); */ 5317: /* strt=asctime(&tmg); */ 5318: /* printf("Time(after) =%s",strstart); */ 5319: /* (void) time (&time_value); 5320: * printf("time=%d,t-=%d\n",time_value,time_value-86400); 5321: * tm = *localtime(&time_value); 5322: * strstart=asctime(&tm); 5323: * printf("tim_value=%d,asctime=%s\n",time_value,strstart); 5324: */ 5325: 5326: nberr=0; /* Number of errors and warnings */ 5327: nbwarn=0; 5328: getcwd(pathcd, size); 5329: 5330: printf("\n%s\n%s",version,fullversion); 5331: if(argc <=1){ 5332: printf("\nEnter the parameter file name: "); 5333: fgets(pathr,FILENAMELENGTH,stdin); 5334: i=strlen(pathr); 5335: if(pathr[i-1]=='\n') 5336: pathr[i-1]='\0'; 5337: for (tok = pathr; tok != NULL; ){ 5338: printf("Pathr |%s|\n",pathr); 5339: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0'); 5340: printf("val= |%s| pathr=%s\n",val,pathr); 5341: strcpy (pathtot, val); 5342: if(pathr[0] == '\0') break; /* Dirty */ 5343: } 5344: } 5345: else{ 5346: strcpy(pathtot,argv[1]); 5347: } 5348: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/ 5349: /*cygwin_split_path(pathtot,path,optionfile); 5350: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/ 5351: /* cutv(path,optionfile,pathtot,'\\');*/ 5352: 5353: /* Split argv[0], imach program to get pathimach */ 5354: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]); 5355: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname); 5356: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname); 5357: /* strcpy(pathimach,argv[0]); */ 5358: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */ 5359: split(pathtot,path,optionfile,optionfilext,optionfilefiname); 5360: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname); 5361: chdir(path); /* Can be a relative path */ 5362: if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */ 5363: printf("Current directory %s!\n",pathcd); 5364: strcpy(command,"mkdir "); 5365: strcat(command,optionfilefiname); 5366: if((outcmd=system(command)) != 0){ 5367: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd); 5368: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */ 5369: /* fclose(ficlog); */ 5370: /* exit(1); */ 5371: } 5372: /* if((imk=mkdir(optionfilefiname))<0){ */ 5373: /* perror("mkdir"); */ 5374: /* } */ 5375: 5376: /*-------- arguments in the command line --------*/ 5377: 5378: /* Log file */ 5379: strcat(filelog, optionfilefiname); 5380: strcat(filelog,".log"); /* */ 5381: if((ficlog=fopen(filelog,"w"))==NULL) { 5382: printf("Problem with logfile %s\n",filelog); 5383: goto end; 5384: } 5385: fprintf(ficlog,"Log filename:%s\n",filelog); 5386: fprintf(ficlog,"\n%s\n%s",version,fullversion); 5387: fprintf(ficlog,"\nEnter the parameter file name: \n"); 5388: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\ 5389: path=%s \n\ 5390: optionfile=%s\n\ 5391: optionfilext=%s\n\ 5392: optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname); 5393: 5394: printf("Local time (at start):%s",strstart); 5395: fprintf(ficlog,"Local time (at start): %s",strstart); 5396: fflush(ficlog); 5397: /* (void) gettimeofday(&curr_time,&tzp); */ 5398: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */ 5399: 5400: /* */ 5401: strcpy(fileres,"r"); 5402: strcat(fileres, optionfilefiname); 5403: strcat(fileres,".txt"); /* Other files have txt extension */ 5404: 5405: /*---------arguments file --------*/ 5406: 5407: if((ficpar=fopen(optionfile,"r"))==NULL) { 5408: printf("Problem with optionfile %s with errno=%s\n",optionfile,strerror(errno)); 5409: fprintf(ficlog,"Problem with optionfile %s with errno=%s\n",optionfile,strerror(errno)); 5410: fflush(ficlog); 5411: /* goto end; */ 5412: exit(70); 5413: } 5414: 5415: 5416: 5417: strcpy(filereso,"o"); 5418: strcat(filereso,fileres); 5419: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */ 5420: printf("Problem with Output resultfile: %s\n", filereso); 5421: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso); 5422: fflush(ficlog); 5423: goto end; 5424: } 5425: 5426: /* Reads comments: lines beginning with '#' */ 5427: numlinepar=0; 5428: while((c=getc(ficpar))=='#' && c!= EOF){ 5429: ungetc(c,ficpar); 5430: fgets(line, MAXLINE, ficpar); 5431: numlinepar++; 5432: fputs(line,stdout); 5433: fputs(line,ficparo); 5434: fputs(line,ficlog); 5435: } 5436: ungetc(c,ficpar); 5437: 5438: fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); 5439: numlinepar++; 5440: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); 5441: fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model); 5442: fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model); 5443: fflush(ficlog); 5444: while((c=getc(ficpar))=='#' && c!= EOF){ 5445: ungetc(c,ficpar); 5446: fgets(line, MAXLINE, ficpar); 5447: numlinepar++; 5448: fputs(line, stdout); 5449: //puts(line); 5450: fputs(line,ficparo); 5451: fputs(line,ficlog); 5452: } 5453: ungetc(c,ficpar); 5454: 5455: 5456: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */ 5457: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/ 5458: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5 5459: v1+v2*age+v2*v3 makes cptcovn = 3 5460: */ 5461: if (strlen(model)>1) 5462: ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/ 5463: else 5464: ncovmodel=2; 5465: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */ 5466: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */ 5467: npar= nforce*ncovmodel; /* Number of parameters like aij*/ 5468: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){ 5469: printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX); 5470: fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX); 5471: fflush(stdout); 5472: fclose (ficlog); 5473: goto end; 5474: } 5475: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); 5476: delti=delti3[1][1]; 5477: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/ 5478: if(mle==-1){ /* Print a wizard for help writing covariance matrix */ 5479: prwizard(ncovmodel, nlstate, ndeath, model, ficparo); 5480: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso); 5481: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso); 5482: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 5483: fclose (ficparo); 5484: fclose (ficlog); 5485: goto end; 5486: exit(0); 5487: } 5488: else if(mle==-3) { 5489: prwizard(ncovmodel, nlstate, ndeath, model, ficparo); 5490: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso); 5491: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso); 5492: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); 5493: matcov=matrix(1,npar,1,npar); 5494: } 5495: else{ 5496: /* Read guessed parameters */ 5497: /* Reads comments: lines beginning with '#' */ 5498: while((c=getc(ficpar))=='#' && c!= EOF){ 5499: ungetc(c,ficpar); 5500: fgets(line, MAXLINE, ficpar); 5501: numlinepar++; 5502: fputs(line,stdout); 5503: fputs(line,ficparo); 5504: fputs(line,ficlog); 5505: } 5506: ungetc(c,ficpar); 5507: 5508: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); 5509: for(i=1; i <=nlstate; i++){ 5510: j=0; 5511: for(jj=1; jj <=nlstate+ndeath; jj++){ 5512: if(jj==i) continue; 5513: j++; 5514: fscanf(ficpar,"%1d%1d",&i1,&j1); 5515: if ((i1 != i) && (j1 != j)){ 5516: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \ 5517: It might be a problem of design; if ncovcol and the model are correct\n \ 5518: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1); 5519: exit(1); 5520: } 5521: fprintf(ficparo,"%1d%1d",i1,j1); 5522: if(mle==1) 5523: printf("%1d%1d",i,j); 5524: fprintf(ficlog,"%1d%1d",i,j); 5525: for(k=1; k<=ncovmodel;k++){ 5526: fscanf(ficpar," %lf",&param[i][j][k]); 5527: if(mle==1){ 5528: printf(" %lf",param[i][j][k]); 5529: fprintf(ficlog," %lf",param[i][j][k]); 5530: } 5531: else 5532: fprintf(ficlog," %lf",param[i][j][k]); 5533: fprintf(ficparo," %lf",param[i][j][k]); 5534: } 5535: fscanf(ficpar,"\n"); 5536: numlinepar++; 5537: if(mle==1) 5538: printf("\n"); 5539: fprintf(ficlog,"\n"); 5540: fprintf(ficparo,"\n"); 5541: } 5542: } 5543: fflush(ficlog); 5544: 5545: /* Reads scales values */ 5546: p=param[1][1]; 5547: 5548: /* Reads comments: lines beginning with '#' */ 5549: while((c=getc(ficpar))=='#' && c!= EOF){ 5550: ungetc(c,ficpar); 5551: fgets(line, MAXLINE, ficpar); 5552: numlinepar++; 5553: fputs(line,stdout); 5554: fputs(line,ficparo); 5555: fputs(line,ficlog); 5556: } 5557: ungetc(c,ficpar); 5558: 5559: for(i=1; i <=nlstate; i++){ 5560: for(j=1; j <=nlstate+ndeath-1; j++){ 5561: fscanf(ficpar,"%1d%1d",&i1,&j1); 5562: if ((i1-i)*(j1-j)!=0){ 5563: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1); 5564: exit(1); 5565: } 5566: printf("%1d%1d",i,j); 5567: fprintf(ficparo,"%1d%1d",i1,j1); 5568: fprintf(ficlog,"%1d%1d",i1,j1); 5569: for(k=1; k<=ncovmodel;k++){ 5570: fscanf(ficpar,"%le",&delti3[i][j][k]); 5571: printf(" %le",delti3[i][j][k]); 5572: fprintf(ficparo," %le",delti3[i][j][k]); 5573: fprintf(ficlog," %le",delti3[i][j][k]); 5574: } 5575: fscanf(ficpar,"\n"); 5576: numlinepar++; 5577: printf("\n"); 5578: fprintf(ficparo,"\n"); 5579: fprintf(ficlog,"\n"); 5580: } 5581: } 5582: fflush(ficlog); 5583: 5584: /* Reads covariance matrix */ 5585: delti=delti3[1][1]; 5586: 5587: 5588: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */ 5589: 5590: /* Reads comments: lines beginning with '#' */ 5591: while((c=getc(ficpar))=='#' && c!= EOF){ 5592: ungetc(c,ficpar); 5593: fgets(line, MAXLINE, ficpar); 5594: numlinepar++; 5595: fputs(line,stdout); 5596: fputs(line,ficparo); 5597: fputs(line,ficlog); 5598: } 5599: ungetc(c,ficpar); 5600: 5601: matcov=matrix(1,npar,1,npar); 5602: for(i=1; i <=npar; i++) 5603: for(j=1; j <=npar; j++) matcov[i][j]=0.; 5604: 5605: for(i=1; i <=npar; i++){ 5606: fscanf(ficpar,"%s",str); 5607: if(mle==1) 5608: printf("%s",str); 5609: fprintf(ficlog,"%s",str); 5610: fprintf(ficparo,"%s",str); 5611: for(j=1; j <=i; j++){ 5612: fscanf(ficpar," %le",&matcov[i][j]); 5613: if(mle==1){ 5614: printf(" %.5le",matcov[i][j]); 5615: } 5616: fprintf(ficlog," %.5le",matcov[i][j]); 5617: fprintf(ficparo," %.5le",matcov[i][j]); 5618: } 5619: fscanf(ficpar,"\n"); 5620: numlinepar++; 5621: if(mle==1) 5622: printf("\n"); 5623: fprintf(ficlog,"\n"); 5624: fprintf(ficparo,"\n"); 5625: } 5626: for(i=1; i <=npar; i++) 5627: for(j=i+1;j<=npar;j++) 5628: matcov[i][j]=matcov[j][i]; 5629: 5630: if(mle==1) 5631: printf("\n"); 5632: fprintf(ficlog,"\n"); 5633: 5634: fflush(ficlog); 5635: 5636: /*-------- Rewriting parameter file ----------*/ 5637: strcpy(rfileres,"r"); /* "Rparameterfile */ 5638: strcat(rfileres,optionfilefiname); /* Parameter file first name*/ 5639: strcat(rfileres,"."); /* */ 5640: strcat(rfileres,optionfilext); /* Other files have txt extension */ 5641: if((ficres =fopen(rfileres,"w"))==NULL) { 5642: printf("Problem writing new parameter file: %s\n", fileres);goto end; 5643: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end; 5644: } 5645: fprintf(ficres,"#%s\n",version); 5646: } /* End of mle != -3 */ 5647: 5648: 5649: n= lastobs; 5650: num=lvector(1,n); 5651: moisnais=vector(1,n); 5652: annais=vector(1,n); 5653: moisdc=vector(1,n); 5654: andc=vector(1,n); 5655: agedc=vector(1,n); 5656: cod=ivector(1,n); 5657: weight=vector(1,n); 5658: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */ 5659: mint=matrix(1,maxwav,1,n); 5660: anint=matrix(1,maxwav,1,n); 5661: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 5662: tab=ivector(1,NCOVMAX); 5663: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */ 5664: 5665: /* Reads data from file datafile */ 5666: if (readdata(datafile, firstobs, lastobs, &imx)==1) 5667: goto end; 5668: 5669: /* Calculation of the number of parameters from char model */ 5670: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 5671: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4 5672: k=3 V4 Tvar[k=3]= 4 (from V4) 5673: k=2 V1 Tvar[k=2]= 1 (from V1) 5674: k=1 Tvar[1]=2 (from V2) 5675: */ 5676: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */ 5677: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 5678: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 5679: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage. 5680: */ 5681: /* For model-covariate k tells which data-covariate to use but 5682: because this model-covariate is a construction we invent a new column 5683: ncovcol + k1 5684: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3 5685: Tvar[3=V1*V4]=4+1 etc */ 5686: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */ 5687: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3 5688: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2) 5689: */ 5690: Tvaraff=ivector(1,NCOVMAX); /* Unclear */ 5691: Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1] and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm 5692: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 5693: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */ 5694: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age 5695: 4 covariates (3 plus signs) 5696: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3 5697: */ 5698: 5699: if(decodemodel(model, lastobs) == 1) 5700: goto end; 5701: 5702: if((double)(lastobs-imx)/(double)imx > 1.10){ 5703: nbwarn++; 5704: printf("Warning: The value of parameter lastobs=%d is big compared to the \n effective number of cases imx=%d, please adjust, \n otherwise you are allocating more memory than necessary.\n",lastobs, imx); 5705: fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n effective number of cases imx=%d, please adjust, \n otherwise you are allocating more memory than necessary.\n",lastobs, imx); 5706: } 5707: /* if(mle==1){*/ 5708: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/ 5709: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */ 5710: } 5711: 5712: /*-calculation of age at interview from date of interview and age at death -*/ 5713: agev=matrix(1,maxwav,1,imx); 5714: 5715: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1) 5716: goto end; 5717: 5718: 5719: agegomp=(int)agemin; 5720: free_vector(moisnais,1,n); 5721: free_vector(annais,1,n); 5722: /* free_matrix(mint,1,maxwav,1,n); 5723: free_matrix(anint,1,maxwav,1,n);*/ 5724: free_vector(moisdc,1,n); 5725: free_vector(andc,1,n); 5726: /* */ 5727: 5728: wav=ivector(1,imx); 5729: dh=imatrix(1,lastpass-firstpass+1,1,imx); 5730: bh=imatrix(1,lastpass-firstpass+1,1,imx); 5731: mw=imatrix(1,lastpass-firstpass+1,1,imx); 5732: 5733: /* Concatenates waves */ 5734: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm); 5735: /* */ 5736: 5737: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */ 5738: 5739: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 5740: ncodemax[1]=1; 5741: Ndum =ivector(-1,NCOVMAX); 5742: if (ncovmodel > 2) 5743: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */ 5744: 5745: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */ 5746: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/ 5747: h=0; 5748: 5749: 5750: /*if (cptcovn > 0) */ 5751: 5752: 5753: m=pow(2,cptcoveff); 5754: 5755: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */ 5756: for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 5757: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/ 5758: for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 5759: h++; 5760: if (h>m) 5761: h=1; 5762: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1 5763: * h 1 2 3 4 5764: *______________________________ 5765: * 1 i=1 1 i=1 1 i=1 1 i=1 1 5766: * 2 2 1 1 1 5767: * 3 i=2 1 2 1 1 5768: * 4 2 2 1 1 5769: * 5 i=3 1 i=2 1 2 1 5770: * 6 2 1 2 1 5771: * 7 i=4 1 2 2 1 5772: * 8 2 2 2 1 5773: * 9 i=5 1 i=3 1 i=2 1 1 5774: * 10 2 1 1 1 5775: * 11 i=6 1 2 1 1 5776: * 12 2 2 1 1 5777: * 13 i=7 1 i=4 1 2 1 5778: * 14 2 1 2 1 5779: * 15 i=8 1 2 2 1 5780: * 16 2 2 2 1 5781: */ 5782: codtab[h][k]=j; 5783: /*codtab[h][Tvar[k]]=j;*/ 5784: printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]); 5785: } 5786: } 5787: } 5788: } 5789: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 5790: codtab[1][2]=1;codtab[2][2]=2; */ 5791: /* for(i=1; i <=m ;i++){ 5792: for(k=1; k <=cptcovn; k++){ 5793: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); 5794: } 5795: printf("\n"); 5796: } 5797: scanf("%d",i);*/ 5798: 5799: free_ivector(Ndum,-1,NCOVMAX); 5800: 5801: 5802: 5803: /*------------ gnuplot -------------*/ 5804: strcpy(optionfilegnuplot,optionfilefiname); 5805: if(mle==-3) 5806: strcat(optionfilegnuplot,"-mort"); 5807: strcat(optionfilegnuplot,".gp"); 5808: 5809: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) { 5810: printf("Problem with file %s",optionfilegnuplot); 5811: } 5812: else{ 5813: fprintf(ficgp,"\n# %s\n", version); 5814: fprintf(ficgp,"# %s\n", optionfilegnuplot); 5815: //fprintf(ficgp,"set missing 'NaNq'\n"); 5816: fprintf(ficgp,"set datafile missing 'NaNq'\n"); 5817: } 5818: /* fclose(ficgp);*/ 5819: /*--------- index.htm --------*/ 5820: 5821: strcpy(optionfilehtm,optionfilefiname); /* Main html file */ 5822: if(mle==-3) 5823: strcat(optionfilehtm,"-mort"); 5824: strcat(optionfilehtm,".htm"); 5825: if((fichtm=fopen(optionfilehtm,"w"))==NULL) { 5826: printf("Problem with %s \n",optionfilehtm); 5827: exit(0); 5828: } 5829: 5830: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */ 5831: strcat(optionfilehtmcov,"-cov.htm"); 5832: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) { 5833: printf("Problem with %s \n",optionfilehtmcov), exit(0); 5834: } 5835: else{ 5836: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body>%s %s \ 5837: <hr size=\"2\" color=\"#EC5E5E\"> \n\ 5838: Title=%s Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s \n",\ 5839: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model); 5840: } 5841: 5842: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body>%s %s \ 5843: <hr size=\"2\" color=\"#EC5E5E\"> \n\ 5844: Title=%s Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s \n\ 5845: \n\ 5846: <hr size=\"2\" color=\"#EC5E5E\">\ 5847: <ul><li><h4>Parameter files</h4>\n\ 5848: - Parameter file: <a href=\"%s.%s\">%s.%s</a> \n\ 5849: - Copy of the parameter file: <a href=\"o%s\">o%s</a> \n\ 5850: - Log file of the run: <a href=\"%s\">%s</a> \n\ 5851: - Gnuplot file name: <a href=\"%s\">%s</a> \n\ 5852: - Date and time at start: %s</ul>\n",\ 5853: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\ 5854: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\ 5855: fileres,fileres,\ 5856: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart); 5857: fflush(fichtm); 5858: 5859: strcpy(pathr,path); 5860: strcat(pathr,optionfilefiname); 5861: chdir(optionfilefiname); /* Move to directory named optionfile */ 5862: 5863: /* Calculates basic frequencies. Computes observed prevalence at single age 5864: and prints on file fileres'p'. */ 5865: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart); 5866: 5867: fprintf(fichtm,"\n"); 5868: fprintf(fichtm," Total number of observations=%d \n\ 5869: Youngest age at first (selected) pass %.2f, oldest age %.2f \n\ 5870: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf \n",\ 5871: imx,agemin,agemax,jmin,jmax,jmean); 5872: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ 5873: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ 5874: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ 5875: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ 5876: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */ 5877: 5878: 5879: /* For Powell, parameters are in a vector p[] starting at p[1] 5880: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */ 5881: p=param[1][1]; /* *(*(*(param +1)+1)+0) */ 5882: 5883: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/ 5884: 5885: if (mle==-3){ 5886: ximort=matrix(1,NDIM,1,NDIM); 5887: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */ 5888: cens=ivector(1,n); 5889: ageexmed=vector(1,n); 5890: agecens=vector(1,n); 5891: dcwave=ivector(1,n); 5892: 5893: for (i=1; i<=imx; i++){ 5894: dcwave[i]=-1; 5895: for (m=firstpass; m<=lastpass; m++) 5896: if (s[m][i]>nlstate) { 5897: dcwave[i]=m; 5898: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/ 5899: break; 5900: } 5901: } 5902: 5903: for (i=1; i<=imx; i++) { 5904: if (wav[i]>0){ 5905: ageexmed[i]=agev[mw[1][i]][i]; 5906: j=wav[i]; 5907: agecens[i]=1.; 5908: 5909: if (ageexmed[i]> 1 && wav[i] > 0){ 5910: agecens[i]=agev[mw[j][i]][i]; 5911: cens[i]= 1; 5912: }else if (ageexmed[i]< 1) 5913: cens[i]= -1; 5914: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass) 5915: cens[i]=0 ; 5916: } 5917: else cens[i]=-1; 5918: } 5919: 5920: for (i=1;i<=NDIM;i++) { 5921: for (j=1;j<=NDIM;j++) 5922: ximort[i][j]=(i == j ? 1.0 : 0.0); 5923: } 5924: 5925: /*p[1]=0.0268; p[NDIM]=0.083;*/ 5926: /*printf("%lf %lf", p[1], p[2]);*/ 5927: 5928: 5929: #ifdef GSL 5930: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n"); 5931: #elsedef 5932: printf("Powell\n"); fprintf(ficlog,"Powell\n"); 5933: #endif 5934: strcpy(filerespow,"pow-mort"); 5935: strcat(filerespow,fileres); 5936: if((ficrespow=fopen(filerespow,"w"))==NULL) { 5937: printf("Problem with resultfile: %s\n", filerespow); 5938: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow); 5939: } 5940: #ifdef GSL 5941: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL"); 5942: #elsedef 5943: fprintf(ficrespow,"# Powell\n# iter -2*LL"); 5944: #endif 5945: /* for (i=1;i<=nlstate;i++) 5946: for(j=1;j<=nlstate+ndeath;j++) 5947: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j); 5948: */ 5949: fprintf(ficrespow,"\n"); 5950: #ifdef GSL 5951: /* gsl starts here */ 5952: T = gsl_multimin_fminimizer_nmsimplex; 5953: gsl_multimin_fminimizer *sfm = NULL; 5954: gsl_vector *ss, *x; 5955: gsl_multimin_function minex_func; 5956: 5957: /* Initial vertex size vector */ 5958: ss = gsl_vector_alloc (NDIM); 5959: 5960: if (ss == NULL){ 5961: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0); 5962: } 5963: /* Set all step sizes to 1 */ 5964: gsl_vector_set_all (ss, 0.001); 5965: 5966: /* Starting point */ 5967: 5968: x = gsl_vector_alloc (NDIM); 5969: 5970: if (x == NULL){ 5971: gsl_vector_free(ss); 5972: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0); 5973: } 5974: 5975: /* Initialize method and iterate */ 5976: /* p[1]=0.0268; p[NDIM]=0.083; */ 5977: /* gsl_vector_set(x, 0, 0.0268); */ 5978: /* gsl_vector_set(x, 1, 0.083); */ 5979: gsl_vector_set(x, 0, p[1]); 5980: gsl_vector_set(x, 1, p[2]); 5981: 5982: minex_func.f = &gompertz_f; 5983: minex_func.n = NDIM; 5984: minex_func.params = (void *)&p; /* ??? */ 5985: 5986: sfm = gsl_multimin_fminimizer_alloc (T, NDIM); 5987: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss); 5988: 5989: printf("Iterations beginning .....\n\n"); 5990: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n"); 5991: 5992: iteri=0; 5993: while (rval == GSL_CONTINUE){ 5994: iteri++; 5995: status = gsl_multimin_fminimizer_iterate(sfm); 5996: 5997: if (status) printf("error: %s\n", gsl_strerror (status)); 5998: fflush(0); 5999: 6000: if (status) 6001: break; 6002: 6003: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6); 6004: ssval = gsl_multimin_fminimizer_size (sfm); 6005: 6006: if (rval == GSL_SUCCESS) 6007: printf ("converged to a local maximum at\n"); 6008: 6009: printf("%5d ", iteri); 6010: for (it = 0; it < NDIM; it++){ 6011: printf ("%10.5f ", gsl_vector_get (sfm->x, it)); 6012: } 6013: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval); 6014: } 6015: 6016: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n"); 6017: 6018: gsl_vector_free(x); /* initial values */ 6019: gsl_vector_free(ss); /* inital step size */ 6020: for (it=0; it<NDIM; it++){ 6021: p[it+1]=gsl_vector_get(sfm->x,it); 6022: fprintf(ficrespow," %.12lf", p[it]); 6023: } 6024: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */ 6025: #endif 6026: #ifdef POWELL 6027: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz); 6028: #endif 6029: fclose(ficrespow); 6030: 6031: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 6032: 6033: for(i=1; i <=NDIM; i++) 6034: for(j=i+1;j<=NDIM;j++) 6035: matcov[i][j]=matcov[j][i]; 6036: 6037: printf("\nCovariance matrix\n "); 6038: for(i=1; i <=NDIM; i++) { 6039: for(j=1;j<=NDIM;j++){ 6040: printf("%f ",matcov[i][j]); 6041: } 6042: printf("\n "); 6043: } 6044: 6045: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp); 6046: for (i=1;i<=NDIM;i++) 6047: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i])); 6048: 6049: lsurv=vector(1,AGESUP); 6050: lpop=vector(1,AGESUP); 6051: tpop=vector(1,AGESUP); 6052: lsurv[agegomp]=100000; 6053: 6054: for (k=agegomp;k<=AGESUP;k++) { 6055: agemortsup=k; 6056: if (p[1]*exp(p[2]*(k-agegomp))>1) break; 6057: } 6058: 6059: for (k=agegomp;k<agemortsup;k++) 6060: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp))); 6061: 6062: for (k=agegomp;k<agemortsup;k++){ 6063: lpop[k]=(lsurv[k]+lsurv[k+1])/2.; 6064: sumlpop=sumlpop+lpop[k]; 6065: } 6066: 6067: tpop[agegomp]=sumlpop; 6068: for (k=agegomp;k<(agemortsup-3);k++){ 6069: /* tpop[k+1]=2;*/ 6070: tpop[k+1]=tpop[k]-lpop[k]; 6071: } 6072: 6073: 6074: printf("\nAge lx qx dx Lx Tx e(x)\n"); 6075: for (k=agegomp;k<(agemortsup-2);k++) 6076: printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]); 6077: 6078: 6079: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */ 6080: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p); 6081: 6082: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \ 6083: stepm, weightopt,\ 6084: model,imx,p,matcov,agemortsup); 6085: 6086: free_vector(lsurv,1,AGESUP); 6087: free_vector(lpop,1,AGESUP); 6088: free_vector(tpop,1,AGESUP); 6089: #ifdef GSL 6090: free_ivector(cens,1,n); 6091: free_vector(agecens,1,n); 6092: free_ivector(dcwave,1,n); 6093: free_matrix(ximort,1,NDIM,1,NDIM); 6094: #endif 6095: } /* Endof if mle==-3 */ 6096: 6097: else{ /* For mle >=1 */ 6098: globpr=0;/* debug */ 6099: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */ 6100: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw); 6101: for (k=1; k<=npar;k++) 6102: printf(" %d %8.5f",k,p[k]); 6103: printf("\n"); 6104: globpr=1; /* to print the contributions */ 6105: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */ 6106: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw); 6107: for (k=1; k<=npar;k++) 6108: printf(" %d %8.5f",k,p[k]); 6109: printf("\n"); 6110: if(mle>=1){ /* Could be 1 or 2 */ 6111: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func); 6112: } 6113: 6114: /*--------- results files --------------*/ 6115: fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model); 6116: 6117: 6118: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); 6119: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); 6120: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); 6121: for(i=1,jk=1; i <=nlstate; i++){ 6122: for(k=1; k <=(nlstate+ndeath); k++){ 6123: if (k != i) { 6124: printf("%d%d ",i,k); 6125: fprintf(ficlog,"%d%d ",i,k); 6126: fprintf(ficres,"%1d%1d ",i,k); 6127: for(j=1; j <=ncovmodel; j++){ 6128: printf("%lf ",p[jk]); 6129: fprintf(ficlog,"%lf ",p[jk]); 6130: fprintf(ficres,"%lf ",p[jk]); 6131: jk++; 6132: } 6133: printf("\n"); 6134: fprintf(ficlog,"\n"); 6135: fprintf(ficres,"\n"); 6136: } 6137: } 6138: } 6139: if(mle!=0){ 6140: /* Computing hessian and covariance matrix */ 6141: ftolhess=ftol; /* Usually correct */ 6142: hesscov(matcov, p, npar, delti, ftolhess, func); 6143: } 6144: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n"); 6145: printf("# Scales (for hessian or gradient estimation)\n"); 6146: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n"); 6147: for(i=1,jk=1; i <=nlstate; i++){ 6148: for(j=1; j <=nlstate+ndeath; j++){ 6149: if (j!=i) { 6150: fprintf(ficres,"%1d%1d",i,j); 6151: printf("%1d%1d",i,j); 6152: fprintf(ficlog,"%1d%1d",i,j); 6153: for(k=1; k<=ncovmodel;k++){ 6154: printf(" %.5e",delti[jk]); 6155: fprintf(ficlog," %.5e",delti[jk]); 6156: fprintf(ficres," %.5e",delti[jk]); 6157: jk++; 6158: } 6159: printf("\n"); 6160: fprintf(ficlog,"\n"); 6161: fprintf(ficres,"\n"); 6162: } 6163: } 6164: } 6165: 6166: fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n"); 6167: if(mle>=1) 6168: printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n"); 6169: fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n"); 6170: /* # 121 Var(a12)\n\ */ 6171: /* # 122 Cov(b12,a12) Var(b12)\n\ */ 6172: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */ 6173: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */ 6174: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */ 6175: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */ 6176: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */ 6177: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */ 6178: 6179: 6180: /* Just to have a covariance matrix which will be more understandable 6181: even is we still don't want to manage dictionary of variables 6182: */ 6183: for(itimes=1;itimes<=2;itimes++){ 6184: jj=0; 6185: for(i=1; i <=nlstate; i++){ 6186: for(j=1; j <=nlstate+ndeath; j++){ 6187: if(j==i) continue; 6188: for(k=1; k<=ncovmodel;k++){ 6189: jj++; 6190: ca[0]= k+'a'-1;ca[1]='\0'; 6191: if(itimes==1){ 6192: if(mle>=1) 6193: printf("#%1d%1d%d",i,j,k); 6194: fprintf(ficlog,"#%1d%1d%d",i,j,k); 6195: fprintf(ficres,"#%1d%1d%d",i,j,k); 6196: }else{ 6197: if(mle>=1) 6198: printf("%1d%1d%d",i,j,k); 6199: fprintf(ficlog,"%1d%1d%d",i,j,k); 6200: fprintf(ficres,"%1d%1d%d",i,j,k); 6201: } 6202: ll=0; 6203: for(li=1;li <=nlstate; li++){ 6204: for(lj=1;lj <=nlstate+ndeath; lj++){ 6205: if(lj==li) continue; 6206: for(lk=1;lk<=ncovmodel;lk++){ 6207: ll++; 6208: if(ll<=jj){ 6209: cb[0]= lk +'a'-1;cb[1]='\0'; 6210: if(ll<jj){ 6211: if(itimes==1){ 6212: if(mle>=1) 6213: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj); 6214: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj); 6215: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj); 6216: }else{ 6217: if(mle>=1) 6218: printf(" %.5e",matcov[jj][ll]); 6219: fprintf(ficlog," %.5e",matcov[jj][ll]); 6220: fprintf(ficres," %.5e",matcov[jj][ll]); 6221: } 6222: }else{ 6223: if(itimes==1){ 6224: if(mle>=1) 6225: printf(" Var(%s%1d%1d)",ca,i,j); 6226: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j); 6227: fprintf(ficres," Var(%s%1d%1d)",ca,i,j); 6228: }else{ 6229: if(mle>=1) 6230: printf(" %.5e",matcov[jj][ll]); 6231: fprintf(ficlog," %.5e",matcov[jj][ll]); 6232: fprintf(ficres," %.5e",matcov[jj][ll]); 6233: } 6234: } 6235: } 6236: } /* end lk */ 6237: } /* end lj */ 6238: } /* end li */ 6239: if(mle>=1) 6240: printf("\n"); 6241: fprintf(ficlog,"\n"); 6242: fprintf(ficres,"\n"); 6243: numlinepar++; 6244: } /* end k*/ 6245: } /*end j */ 6246: } /* end i */ 6247: } /* end itimes */ 6248: 6249: fflush(ficlog); 6250: fflush(ficres); 6251: 6252: while((c=getc(ficpar))=='#' && c!= EOF){ 6253: ungetc(c,ficpar); 6254: fgets(line, MAXLINE, ficpar); 6255: fputs(line,stdout); 6256: fputs(line,ficparo); 6257: } 6258: ungetc(c,ficpar); 6259: 6260: estepm=0; 6261: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); 6262: if (estepm==0 || estepm < stepm) estepm=stepm; 6263: if (fage <= 2) { 6264: bage = ageminpar; 6265: fage = agemaxpar; 6266: } 6267: 6268: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n"); 6269: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm); 6270: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm); 6271: 6272: while((c=getc(ficpar))=='#' && c!= EOF){ 6273: ungetc(c,ficpar); 6274: fgets(line, MAXLINE, ficpar); 6275: fputs(line,stdout); 6276: fputs(line,ficparo); 6277: } 6278: ungetc(c,ficpar); 6279: 6280: fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav); 6281: fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav); 6282: fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav); 6283: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav); 6284: fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav); 6285: 6286: while((c=getc(ficpar))=='#' && c!= EOF){ 6287: ungetc(c,ficpar); 6288: fgets(line, MAXLINE, ficpar); 6289: fputs(line,stdout); 6290: fputs(line,ficparo); 6291: } 6292: ungetc(c,ficpar); 6293: 6294: 6295: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.; 6296: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.; 6297: 6298: fscanf(ficpar,"pop_based=%d\n",&popbased); 6299: fprintf(ficparo,"pop_based=%d\n",popbased); 6300: fprintf(ficres,"pop_based=%d\n",popbased); 6301: 6302: while((c=getc(ficpar))=='#' && c!= EOF){ 6303: ungetc(c,ficpar); 6304: fgets(line, MAXLINE, ficpar); 6305: fputs(line,stdout); 6306: fputs(line,ficparo); 6307: } 6308: ungetc(c,ficpar); 6309: 6310: fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj); 6311: fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj); 6312: printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj); 6313: fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj); 6314: fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj); 6315: /* day and month of proj2 are not used but only year anproj2.*/ 6316: 6317: 6318: 6319: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */ 6320: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */ 6321: 6322: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */ 6323: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p); 6324: 6325: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\ 6326: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\ 6327: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2); 6328: 6329: /*------------ free_vector -------------*/ 6330: /* chdir(path); */ 6331: 6332: free_ivector(wav,1,imx); 6333: free_imatrix(dh,1,lastpass-firstpass+1,1,imx); 6334: free_imatrix(bh,1,lastpass-firstpass+1,1,imx); 6335: free_imatrix(mw,1,lastpass-firstpass+1,1,imx); 6336: free_lvector(num,1,n); 6337: free_vector(agedc,1,n); 6338: /*free_matrix(covar,0,NCOVMAX,1,n);*/ 6339: /*free_matrix(covar,1,NCOVMAX,1,n);*/ 6340: fclose(ficparo); 6341: fclose(ficres); 6342: 6343: 6344: /*--------------- Prevalence limit (period or stable prevalence) --------------*/ 6345: #include "prevlim.h" /* Use ficrespl, ficlog */ 6346: fclose(ficrespl); 6347: 6348: #ifdef FREEEXIT2 6349: #include "freeexit2.h" 6350: #endif 6351: 6352: /*------------- h Pij x at various ages ------------*/ 6353: #include "hpijx.h" 6354: fclose(ficrespij); 6355: 6356: /*-------------- Variance of one-step probabilities---*/ 6357: k=1; 6358: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart); 6359: 6360: 6361: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX); 6362: for(i=1;i<=AGESUP;i++) 6363: for(j=1;j<=NCOVMAX;j++) 6364: for(k=1;k<=NCOVMAX;k++) 6365: probs[i][j][k]=0.; 6366: 6367: /*---------- Forecasting ------------------*/ 6368: /*if((stepm == 1) && (strcmp(model,".")==0)){*/ 6369: if(prevfcast==1){ 6370: /* if(stepm ==1){*/ 6371: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff); 6372: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/ 6373: /* } */ 6374: /* else{ */ 6375: /* erreur=108; */ 6376: /* printf("Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */ 6377: /* fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */ 6378: /* } */ 6379: } 6380: 6381: 6382: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */ 6383: 6384: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); 6385: /* printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d, mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\ 6386: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass); 6387: */ 6388: 6389: if (mobilav!=0) { 6390: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 6391: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ 6392: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); 6393: printf(" Error in movingaverage mobilav=%d\n",mobilav); 6394: } 6395: } 6396: 6397: 6398: /*---------- Health expectancies, no variances ------------*/ 6399: 6400: strcpy(filerese,"e"); 6401: strcat(filerese,fileres); 6402: if((ficreseij=fopen(filerese,"w"))==NULL) { 6403: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0); 6404: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0); 6405: } 6406: printf("Computing Health Expectancies: result on file '%s' \n", filerese); 6407: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese); 6408: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){ 6409: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/ 6410: 6411: for (k=1; k <= (int) pow(2,cptcoveff); k++){ 6412: fprintf(ficreseij,"\n#****** "); 6413: for(j=1;j<=cptcoveff;j++) { 6414: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 6415: } 6416: fprintf(ficreseij,"******\n"); 6417: 6418: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); 6419: oldm=oldms;savm=savms; 6420: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart); 6421: 6422: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage); 6423: /*}*/ 6424: } 6425: fclose(ficreseij); 6426: 6427: 6428: /*---------- Health expectancies and variances ------------*/ 6429: 6430: 6431: strcpy(filerest,"t"); 6432: strcat(filerest,fileres); 6433: if((ficrest=fopen(filerest,"w"))==NULL) { 6434: printf("Problem with total LE resultfile: %s\n", filerest);goto end; 6435: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end; 6436: } 6437: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 6438: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 6439: 6440: 6441: strcpy(fileresstde,"stde"); 6442: strcat(fileresstde,fileres); 6443: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) { 6444: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0); 6445: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0); 6446: } 6447: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde); 6448: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde); 6449: 6450: strcpy(filerescve,"cve"); 6451: strcat(filerescve,fileres); 6452: if((ficrescveij=fopen(filerescve,"w"))==NULL) { 6453: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0); 6454: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0); 6455: } 6456: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve); 6457: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve); 6458: 6459: strcpy(fileresv,"v"); 6460: strcat(fileresv,fileres); 6461: if((ficresvij=fopen(fileresv,"w"))==NULL) { 6462: printf("Problem with variance resultfile: %s\n", fileresv);exit(0); 6463: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0); 6464: } 6465: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv); 6466: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv); 6467: 6468: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){ 6469: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/ 6470: 6471: for (k=1; k <= (int) pow(2,cptcoveff); k++){ 6472: fprintf(ficrest,"\n#****** "); 6473: for(j=1;j<=cptcoveff;j++) 6474: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 6475: fprintf(ficrest,"******\n"); 6476: 6477: fprintf(ficresstdeij,"\n#****** "); 6478: fprintf(ficrescveij,"\n#****** "); 6479: for(j=1;j<=cptcoveff;j++) { 6480: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 6481: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 6482: } 6483: fprintf(ficresstdeij,"******\n"); 6484: fprintf(ficrescveij,"******\n"); 6485: 6486: fprintf(ficresvij,"\n#****** "); 6487: for(j=1;j<=cptcoveff;j++) 6488: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 6489: fprintf(ficresvij,"******\n"); 6490: 6491: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); 6492: oldm=oldms;savm=savms; 6493: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart); 6494: /* 6495: */ 6496: /* goto endfree; */ 6497: 6498: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); 6499: pstamp(ficrest); 6500: 6501: 6502: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/ 6503: oldm=oldms;savm=savms; /* Segmentation fault */ 6504: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); 6505: fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# (weighted average of eij where weights are "); 6506: if(vpopbased==1) 6507: fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav); 6508: else 6509: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n"); 6510: fprintf(ficrest,"# Age e.. (std) "); 6511: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i); 6512: fprintf(ficrest,"\n"); 6513: 6514: epj=vector(1,nlstate+1); 6515: for(age=bage; age <=fage ;age++){ 6516: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k); 6517: if (vpopbased==1) { 6518: if(mobilav ==0){ 6519: for(i=1; i<=nlstate;i++) 6520: prlim[i][i]=probs[(int)age][i][k]; 6521: }else{ /* mobilav */ 6522: for(i=1; i<=nlstate;i++) 6523: prlim[i][i]=mobaverage[(int)age][i][k]; 6524: } 6525: } 6526: 6527: fprintf(ficrest," %4.0f",age); 6528: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){ 6529: for(i=1, epj[j]=0.;i <=nlstate;i++) { 6530: epj[j] += prlim[i][i]*eij[i][j][(int)age]; 6531: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/ 6532: } 6533: epj[nlstate+1] +=epj[j]; 6534: } 6535: 6536: for(i=1, vepp=0.;i <=nlstate;i++) 6537: for(j=1;j <=nlstate;j++) 6538: vepp += vareij[i][j][(int)age]; 6539: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp)); 6540: for(j=1;j <=nlstate;j++){ 6541: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age])); 6542: } 6543: fprintf(ficrest,"\n"); 6544: } 6545: } 6546: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage); 6547: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage); 6548: free_vector(epj,1,nlstate+1); 6549: /*}*/ 6550: } 6551: free_vector(weight,1,n); 6552: free_imatrix(Tvard,1,NCOVMAX,1,2); 6553: free_imatrix(s,1,maxwav+1,1,n); 6554: free_matrix(anint,1,maxwav,1,n); 6555: free_matrix(mint,1,maxwav,1,n); 6556: free_ivector(cod,1,n); 6557: free_ivector(tab,1,NCOVMAX); 6558: fclose(ficresstdeij); 6559: fclose(ficrescveij); 6560: fclose(ficresvij); 6561: fclose(ficrest); 6562: fclose(ficpar); 6563: 6564: /*------- Variance of period (stable) prevalence------*/ 6565: 6566: strcpy(fileresvpl,"vpl"); 6567: strcat(fileresvpl,fileres); 6568: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) { 6569: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl); 6570: exit(0); 6571: } 6572: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl); 6573: 6574: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){ 6575: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/ 6576: 6577: for (k=1; k <= (int) pow(2,cptcoveff); k++){ 6578: fprintf(ficresvpl,"\n#****** "); 6579: for(j=1;j<=cptcoveff;j++) 6580: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 6581: fprintf(ficresvpl,"******\n"); 6582: 6583: varpl=matrix(1,nlstate,(int) bage, (int) fage); 6584: oldm=oldms;savm=savms; 6585: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart); 6586: free_matrix(varpl,1,nlstate,(int) bage, (int)fage); 6587: /*}*/ 6588: } 6589: 6590: fclose(ficresvpl); 6591: 6592: /*---------- End : free ----------------*/ 6593: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 6594: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX); 6595: } /* mle==-3 arrives here for freeing */ 6596: endfree: 6597: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */ 6598: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath); 6599: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath); 6600: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath); 6601: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath); 6602: free_matrix(covar,0,NCOVMAX,1,n); 6603: free_matrix(matcov,1,npar,1,npar); 6604: /*free_vector(delti,1,npar);*/ 6605: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 6606: free_matrix(agev,1,maxwav,1,imx); 6607: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 6608: 6609: free_ivector(ncodemax,1,NCOVMAX); 6610: free_ivector(Tvar,1,NCOVMAX); 6611: free_ivector(Tprod,1,NCOVMAX); 6612: free_ivector(Tvaraff,1,NCOVMAX); 6613: free_ivector(Tage,1,NCOVMAX); 6614: 6615: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX); 6616: free_imatrix(codtab,1,100,1,10); 6617: fflush(fichtm); 6618: fflush(ficgp); 6619: 6620: 6621: if((nberr >0) || (nbwarn>0)){ 6622: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn); 6623: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn); 6624: }else{ 6625: printf("End of Imach\n"); 6626: fprintf(ficlog,"End of Imach\n"); 6627: } 6628: printf("See log file on %s\n",filelog); 6629: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */ 6630: (void) gettimeofday(&end_time,&tzp); 6631: tm = *localtime(&end_time.tv_sec); 6632: tmg = *gmtime(&end_time.tv_sec); 6633: strcpy(strtend,asctime(&tm)); 6634: printf("Local time at start %s\nLocal time at end %s",strstart, strtend); 6635: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend); 6636: printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout)); 6637: 6638: printf("Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec); 6639: fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout)); 6640: fprintf(ficlog,"Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec); 6641: /* printf("Total time was %d uSec.\n", total_usecs);*/ 6642: /* if(fileappend(fichtm,optionfilehtm)){ */ 6643: fprintf(fichtm," Local time at start %s Local time at end %s \n</body></html>",strstart, strtend); 6644: fclose(fichtm); 6645: fprintf(fichtmcov," Local time at start %s Local time at end %s \n</body></html>",strstart, strtend); 6646: fclose(fichtmcov); 6647: fclose(ficgp); 6648: fclose(ficlog); 6649: /*------ End -----------*/ 6650: 6651: 6652: printf("Before Current directory %s!\n",pathcd); 6653: if(chdir(pathcd) != 0) 6654: printf("Can't move to directory %s!\n",path); 6655: if(getcwd(pathcd,MAXLINE) > 0) 6656: printf("Current directory %s!\n",pathcd); 6657: /*strcat(plotcmd,CHARSEPARATOR);*/ 6658: sprintf(plotcmd,"gnuplot"); 6659: #ifndef UNIX 6660: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach); 6661: #endif 6662: if(!stat(plotcmd,&info)){ 6663: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout); 6664: if(!stat(getenv("GNUPLOTBIN"),&info)){ 6665: printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout); 6666: }else 6667: strcpy(pplotcmd,plotcmd); 6668: #ifdef UNIX 6669: strcpy(plotcmd,GNUPLOTPROGRAM); 6670: if(!stat(plotcmd,&info)){ 6671: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout); 6672: }else 6673: strcpy(pplotcmd,plotcmd); 6674: #endif 6675: }else 6676: strcpy(pplotcmd,plotcmd); 6677: 6678: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot); 6679: printf("Starting graphs with: %s\n",plotcmd);fflush(stdout); 6680: 6681: if((outcmd=system(plotcmd)) != 0){ 6682: printf("\n Problem with gnuplot command %s, err=%d\n", plotcmd, outcmd); 6683: printf("\n Trying on same directory\n"); 6684: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot); 6685: if((outcmd=system(plotcmd)) != 0) 6686: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd); 6687: } 6688: printf(" Wait..."); 6689: while (z[0] != 'q') { 6690: /* chdir(path); */ 6691: printf("\nType e to edit output files, g to graph again and q for exiting: "); 6692: scanf("%s",z); 6693: /* if (z[0] == 'c') system("./imach"); */ 6694: if (z[0] == 'e') { 6695: #ifdef OSX 6696: sprintf(pplotcmd, "open %s", optionfilehtm); 6697: #else 6698: sprintf(pplotcmd, "%s", optionfilehtm); 6699: #endif 6700: printf("Starting browser with: %s",pplotcmd);fflush(stdout); 6701: system(pplotcmd); 6702: } 6703: else if (z[0] == 'g') system(plotcmd); 6704: else if (z[0] == 'q') exit(0); 6705: } 6706: end: 6707: while (z[0] != 'q') { 6708: printf("\nType q for exiting: "); 6709: scanf("%s",z); 6710: } 6711: } 6712: 6713: 6714: