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Wed Apr 29 09:11:15 2015 UTC (9 years, 1 month ago) by brouard
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1: /* $Id: imach.c,v 1.187 2015/04/29 09:11:15 brouard Exp $ 2: $State: Exp $ 3: $Log: imach.c,v $ 4: Revision 1.187 2015/04/29 09:11:15 brouard 5: *** empty log message *** 6: 7: Revision 1.186 2015/04/23 12:01:52 brouard 8: Summary: V1*age is working now, version 0.98q1 9: 10: Some codes had been disabled in order to simplify and Vn*age was 11: working in the optimization phase, ie, giving correct MLE parameters, 12: but, as usual, outputs were not correct and program core dumped. 13: 14: Revision 1.185 2015/03/11 13:26:42 brouard 15: Summary: Inclusion of compile and links command line for Intel Compiler 16: 17: Revision 1.184 2015/03/11 11:52:39 brouard 18: Summary: Back from Windows 8. Intel Compiler 19: 20: Revision 1.183 2015/03/10 20:34:32 brouard 21: Summary: 0.98q0, trying with directest, mnbrak fixed 22: 23: We use directest instead of original Powell test; probably no 24: incidence on the results, but better justifications; 25: We fixed Numerical Recipes mnbrak routine which was wrong and gave 26: wrong results. 27: 28: Revision 1.182 2015/02/12 08:19:57 brouard 29: Summary: Trying to keep directest which seems simpler and more general 30: Author: Nicolas Brouard 31: 32: Revision 1.181 2015/02/11 23:22:24 brouard 33: Summary: Comments on Powell added 34: 35: Author: 36: 37: Revision 1.180 2015/02/11 17:33:45 brouard 38: Summary: Finishing move from main to function (hpijx and prevalence_limit) 39: 40: Revision 1.179 2015/01/04 09:57:06 brouard 41: Summary: back to OS/X 42: 43: Revision 1.178 2015/01/04 09:35:48 brouard 44: *** empty log message *** 45: 46: Revision 1.177 2015/01/03 18:40:56 brouard 47: Summary: Still testing ilc32 on OSX 48: 49: Revision 1.176 2015/01/03 16:45:04 brouard 50: *** empty log message *** 51: 52: Revision 1.175 2015/01/03 16:33:42 brouard 53: *** empty log message *** 54: 55: Revision 1.174 2015/01/03 16:15:49 brouard 56: Summary: Still in cross-compilation 57: 58: Revision 1.173 2015/01/03 12:06:26 brouard 59: Summary: trying to detect cross-compilation 60: 61: Revision 1.172 2014/12/27 12:07:47 brouard 62: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP 63: 64: Revision 1.171 2014/12/23 13:26:59 brouard 65: Summary: Back from Visual C 66: 67: Still problem with utsname.h on Windows 68: 69: Revision 1.170 2014/12/23 11:17:12 brouard 70: Summary: Cleaning some \%% back to %% 71: 72: The escape was mandatory for a specific compiler (which one?), but too many warnings. 73: 74: Revision 1.169 2014/12/22 23:08:31 brouard 75: Summary: 0.98p 76: 77: Outputs some informations on compiler used, OS etc. Testing on different platforms. 78: 79: Revision 1.168 2014/12/22 15:17:42 brouard 80: Summary: update 81: 82: Revision 1.167 2014/12/22 13:50:56 brouard 83: Summary: Testing uname and compiler version and if compiled 32 or 64 84: 85: Testing on Linux 64 86: 87: Revision 1.166 2014/12/22 11:40:47 brouard 88: *** empty log message *** 89: 90: Revision 1.165 2014/12/16 11:20:36 brouard 91: Summary: After compiling on Visual C 92: 93: * imach.c (Module): Merging 1.61 to 1.162 94: 95: Revision 1.164 2014/12/16 10:52:11 brouard 96: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn 97: 98: * imach.c (Module): Merging 1.61 to 1.162 99: 100: Revision 1.163 2014/12/16 10:30:11 brouard 101: * imach.c (Module): Merging 1.61 to 1.162 102: 103: Revision 1.162 2014/09/25 11:43:39 brouard 104: Summary: temporary backup 0.99! 105: 106: Revision 1.1 2014/09/16 11:06:58 brouard 107: Summary: With some code (wrong) for nlopt 108: 109: Author: 110: 111: Revision 1.161 2014/09/15 20:41:41 brouard 112: Summary: Problem with macro SQR on Intel compiler 113: 114: Revision 1.160 2014/09/02 09:24:05 brouard 115: *** empty log message *** 116: 117: Revision 1.159 2014/09/01 10:34:10 brouard 118: Summary: WIN32 119: Author: Brouard 120: 121: Revision 1.158 2014/08/27 17:11:51 brouard 122: *** empty log message *** 123: 124: Revision 1.157 2014/08/27 16:26:55 brouard 125: Summary: Preparing windows Visual studio version 126: Author: Brouard 127: 128: In order to compile on Visual studio, time.h is now correct and time_t 129: and tm struct should be used. difftime should be used but sometimes I 130: just make the differences in raw time format (time(&now). 131: Trying to suppress #ifdef LINUX 132: Add xdg-open for __linux in order to open default browser. 133: 134: Revision 1.156 2014/08/25 20:10:10 brouard 135: *** empty log message *** 136: 137: Revision 1.155 2014/08/25 18:32:34 brouard 138: Summary: New compile, minor changes 139: Author: Brouard 140: 141: Revision 1.154 2014/06/20 17:32:08 brouard 142: Summary: Outputs now all graphs of convergence to period prevalence 143: 144: Revision 1.153 2014/06/20 16:45:46 brouard 145: Summary: If 3 live state, convergence to period prevalence on same graph 146: Author: Brouard 147: 148: Revision 1.152 2014/06/18 17:54:09 brouard 149: Summary: open browser, use gnuplot on same dir than imach if not found in the path 150: 151: Revision 1.151 2014/06/18 16:43:30 brouard 152: *** empty log message *** 153: 154: Revision 1.150 2014/06/18 16:42:35 brouard 155: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX) 156: Author: brouard 157: 158: Revision 1.149 2014/06/18 15:51:14 brouard 159: Summary: Some fixes in parameter files errors 160: Author: Nicolas Brouard 161: 162: Revision 1.148 2014/06/17 17:38:48 brouard 163: Summary: Nothing new 164: Author: Brouard 165: 166: Just a new packaging for OS/X version 0.98nS 167: 168: Revision 1.147 2014/06/16 10:33:11 brouard 169: *** empty log message *** 170: 171: Revision 1.146 2014/06/16 10:20:28 brouard 172: Summary: Merge 173: Author: Brouard 174: 175: Merge, before building revised version. 176: 177: Revision 1.145 2014/06/10 21:23:15 brouard 178: Summary: Debugging with valgrind 179: Author: Nicolas Brouard 180: 181: Lot of changes in order to output the results with some covariates 182: After the Edimburgh REVES conference 2014, it seems mandatory to 183: improve the code. 184: No more memory valgrind error but a lot has to be done in order to 185: continue the work of splitting the code into subroutines. 186: Also, decodemodel has been improved. Tricode is still not 187: optimal. nbcode should be improved. Documentation has been added in 188: the source code. 189: 190: Revision 1.143 2014/01/26 09:45:38 brouard 191: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising 192: 193: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested... 194: (Module): Version 0.98nR Running ok, but output format still only works for three covariates. 195: 196: Revision 1.142 2014/01/26 03:57:36 brouard 197: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2 198: 199: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested... 200: 201: Revision 1.141 2014/01/26 02:42:01 brouard 202: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested... 203: 204: Revision 1.140 2011/09/02 10:37:54 brouard 205: Summary: times.h is ok with mingw32 now. 206: 207: Revision 1.139 2010/06/14 07:50:17 brouard 208: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree. 209: I remember having already fixed agemin agemax which are pointers now but not cvs saved. 210: 211: Revision 1.138 2010/04/30 18:19:40 brouard 212: *** empty log message *** 213: 214: Revision 1.137 2010/04/29 18:11:38 brouard 215: (Module): Checking covariates for more complex models 216: than V1+V2. A lot of change to be done. Unstable. 217: 218: Revision 1.136 2010/04/26 20:30:53 brouard 219: (Module): merging some libgsl code. Fixing computation 220: of likelione (using inter/intrapolation if mle = 0) in order to 221: get same likelihood as if mle=1. 222: Some cleaning of code and comments added. 223: 224: Revision 1.135 2009/10/29 15:33:14 brouard 225: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code. 226: 227: Revision 1.134 2009/10/29 13:18:53 brouard 228: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code. 229: 230: Revision 1.133 2009/07/06 10:21:25 brouard 231: just nforces 232: 233: Revision 1.132 2009/07/06 08:22:05 brouard 234: Many tings 235: 236: Revision 1.131 2009/06/20 16:22:47 brouard 237: Some dimensions resccaled 238: 239: Revision 1.130 2009/05/26 06:44:34 brouard 240: (Module): Max Covariate is now set to 20 instead of 8. A 241: lot of cleaning with variables initialized to 0. Trying to make 242: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better. 243: 244: Revision 1.129 2007/08/31 13:49:27 lievre 245: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting 246: 247: Revision 1.128 2006/06/30 13:02:05 brouard 248: (Module): Clarifications on computing e.j 249: 250: Revision 1.127 2006/04/28 18:11:50 brouard 251: (Module): Yes the sum of survivors was wrong since 252: imach-114 because nhstepm was no more computed in the age 253: loop. Now we define nhstepma in the age loop. 254: (Module): In order to speed up (in case of numerous covariates) we 255: compute health expectancies (without variances) in a first step 256: and then all the health expectancies with variances or standard 257: deviation (needs data from the Hessian matrices) which slows the 258: computation. 259: In the future we should be able to stop the program is only health 260: expectancies and graph are needed without standard deviations. 261: 262: Revision 1.126 2006/04/28 17:23:28 brouard 263: (Module): Yes the sum of survivors was wrong since 264: imach-114 because nhstepm was no more computed in the age 265: loop. Now we define nhstepma in the age loop. 266: Version 0.98h 267: 268: Revision 1.125 2006/04/04 15:20:31 lievre 269: Errors in calculation of health expectancies. Age was not initialized. 270: Forecasting file added. 271: 272: Revision 1.124 2006/03/22 17:13:53 lievre 273: Parameters are printed with %lf instead of %f (more numbers after the comma). 274: The log-likelihood is printed in the log file 275: 276: Revision 1.123 2006/03/20 10:52:43 brouard 277: * imach.c (Module): <title> changed, corresponds to .htm file 278: name. <head> headers where missing. 279: 280: * imach.c (Module): Weights can have a decimal point as for 281: English (a comma might work with a correct LC_NUMERIC environment, 282: otherwise the weight is truncated). 283: Modification of warning when the covariates values are not 0 or 284: 1. 285: Version 0.98g 286: 287: Revision 1.122 2006/03/20 09:45:41 brouard 288: (Module): Weights can have a decimal point as for 289: English (a comma might work with a correct LC_NUMERIC environment, 290: otherwise the weight is truncated). 291: Modification of warning when the covariates values are not 0 or 292: 1. 293: Version 0.98g 294: 295: Revision 1.121 2006/03/16 17:45:01 lievre 296: * imach.c (Module): Comments concerning covariates added 297: 298: * imach.c (Module): refinements in the computation of lli if 299: status=-2 in order to have more reliable computation if stepm is 300: not 1 month. Version 0.98f 301: 302: Revision 1.120 2006/03/16 15:10:38 lievre 303: (Module): refinements in the computation of lli if 304: status=-2 in order to have more reliable computation if stepm is 305: not 1 month. Version 0.98f 306: 307: Revision 1.119 2006/03/15 17:42:26 brouard 308: (Module): Bug if status = -2, the loglikelihood was 309: computed as likelihood omitting the logarithm. Version O.98e 310: 311: Revision 1.118 2006/03/14 18:20:07 brouard 312: (Module): varevsij Comments added explaining the second 313: table of variances if popbased=1 . 314: (Module): Covariances of eij, ekl added, graphs fixed, new html link. 315: (Module): Function pstamp added 316: (Module): Version 0.98d 317: 318: Revision 1.117 2006/03/14 17:16:22 brouard 319: (Module): varevsij Comments added explaining the second 320: table of variances if popbased=1 . 321: (Module): Covariances of eij, ekl added, graphs fixed, new html link. 322: (Module): Function pstamp added 323: (Module): Version 0.98d 324: 325: Revision 1.116 2006/03/06 10:29:27 brouard 326: (Module): Variance-covariance wrong links and 327: varian-covariance of ej. is needed (Saito). 328: 329: Revision 1.115 2006/02/27 12:17:45 brouard 330: (Module): One freematrix added in mlikeli! 0.98c 331: 332: Revision 1.114 2006/02/26 12:57:58 brouard 333: (Module): Some improvements in processing parameter 334: filename with strsep. 335: 336: Revision 1.113 2006/02/24 14:20:24 brouard 337: (Module): Memory leaks checks with valgrind and: 338: datafile was not closed, some imatrix were not freed and on matrix 339: allocation too. 340: 341: Revision 1.112 2006/01/30 09:55:26 brouard 342: (Module): Back to gnuplot.exe instead of wgnuplot.exe 343: 344: Revision 1.111 2006/01/25 20:38:18 brouard 345: (Module): Lots of cleaning and bugs added (Gompertz) 346: (Module): Comments can be added in data file. Missing date values 347: can be a simple dot '.'. 348: 349: Revision 1.110 2006/01/25 00:51:50 brouard 350: (Module): Lots of cleaning and bugs added (Gompertz) 351: 352: Revision 1.109 2006/01/24 19:37:15 brouard 353: (Module): Comments (lines starting with a #) are allowed in data. 354: 355: Revision 1.108 2006/01/19 18:05:42 lievre 356: Gnuplot problem appeared... 357: To be fixed 358: 359: Revision 1.107 2006/01/19 16:20:37 brouard 360: Test existence of gnuplot in imach path 361: 362: Revision 1.106 2006/01/19 13:24:36 brouard 363: Some cleaning and links added in html output 364: 365: Revision 1.105 2006/01/05 20:23:19 lievre 366: *** empty log message *** 367: 368: Revision 1.104 2005/09/30 16:11:43 lievre 369: (Module): sump fixed, loop imx fixed, and simplifications. 370: (Module): If the status is missing at the last wave but we know 371: that the person is alive, then we can code his/her status as -2 372: (instead of missing=-1 in earlier versions) and his/her 373: contributions to the likelihood is 1 - Prob of dying from last 374: health status (= 1-p13= p11+p12 in the easiest case of somebody in 375: the healthy state at last known wave). Version is 0.98 376: 377: Revision 1.103 2005/09/30 15:54:49 lievre 378: (Module): sump fixed, loop imx fixed, and simplifications. 379: 380: Revision 1.102 2004/09/15 17:31:30 brouard 381: Add the possibility to read data file including tab characters. 382: 383: Revision 1.101 2004/09/15 10:38:38 brouard 384: Fix on curr_time 385: 386: Revision 1.100 2004/07/12 18:29:06 brouard 387: Add version for Mac OS X. Just define UNIX in Makefile 388: 389: Revision 1.99 2004/06/05 08:57:40 brouard 390: *** empty log message *** 391: 392: Revision 1.98 2004/05/16 15:05:56 brouard 393: New version 0.97 . First attempt to estimate force of mortality 394: directly from the data i.e. without the need of knowing the health 395: state at each age, but using a Gompertz model: log u =a + b*age . 396: This is the basic analysis of mortality and should be done before any 397: other analysis, in order to test if the mortality estimated from the 398: cross-longitudinal survey is different from the mortality estimated 399: from other sources like vital statistic data. 400: 401: The same imach parameter file can be used but the option for mle should be -3. 402: 403: Agnès, who wrote this part of the code, tried to keep most of the 404: former routines in order to include the new code within the former code. 405: 406: The output is very simple: only an estimate of the intercept and of 407: the slope with 95% confident intervals. 408: 409: Current limitations: 410: A) Even if you enter covariates, i.e. with the 411: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates. 412: B) There is no computation of Life Expectancy nor Life Table. 413: 414: Revision 1.97 2004/02/20 13:25:42 lievre 415: Version 0.96d. Population forecasting command line is (temporarily) 416: suppressed. 417: 418: Revision 1.96 2003/07/15 15:38:55 brouard 419: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is 420: rewritten within the same printf. Workaround: many printfs. 421: 422: Revision 1.95 2003/07/08 07:54:34 brouard 423: * imach.c (Repository): 424: (Repository): Using imachwizard code to output a more meaningful covariance 425: matrix (cov(a12,c31) instead of numbers. 426: 427: Revision 1.94 2003/06/27 13:00:02 brouard 428: Just cleaning 429: 430: Revision 1.93 2003/06/25 16:33:55 brouard 431: (Module): On windows (cygwin) function asctime_r doesn't 432: exist so I changed back to asctime which exists. 433: (Module): Version 0.96b 434: 435: Revision 1.92 2003/06/25 16:30:45 brouard 436: (Module): On windows (cygwin) function asctime_r doesn't 437: exist so I changed back to asctime which exists. 438: 439: Revision 1.91 2003/06/25 15:30:29 brouard 440: * imach.c (Repository): Duplicated warning errors corrected. 441: (Repository): Elapsed time after each iteration is now output. It 442: helps to forecast when convergence will be reached. Elapsed time 443: is stamped in powell. We created a new html file for the graphs 444: concerning matrix of covariance. It has extension -cov.htm. 445: 446: Revision 1.90 2003/06/24 12:34:15 brouard 447: (Module): Some bugs corrected for windows. Also, when 448: mle=-1 a template is output in file "or"mypar.txt with the design 449: of the covariance matrix to be input. 450: 451: Revision 1.89 2003/06/24 12:30:52 brouard 452: (Module): Some bugs corrected for windows. Also, when 453: mle=-1 a template is output in file "or"mypar.txt with the design 454: of the covariance matrix to be input. 455: 456: Revision 1.88 2003/06/23 17:54:56 brouard 457: * 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. 458: 459: Revision 1.87 2003/06/18 12:26:01 brouard 460: Version 0.96 461: 462: Revision 1.86 2003/06/17 20:04:08 brouard 463: (Module): Change position of html and gnuplot routines and added 464: routine fileappend. 465: 466: Revision 1.85 2003/06/17 13:12:43 brouard 467: * imach.c (Repository): Check when date of death was earlier that 468: current date of interview. It may happen when the death was just 469: prior to the death. In this case, dh was negative and likelihood 470: was wrong (infinity). We still send an "Error" but patch by 471: assuming that the date of death was just one stepm after the 472: interview. 473: (Repository): Because some people have very long ID (first column) 474: we changed int to long in num[] and we added a new lvector for 475: memory allocation. But we also truncated to 8 characters (left 476: truncation) 477: (Repository): No more line truncation errors. 478: 479: Revision 1.84 2003/06/13 21:44:43 brouard 480: * imach.c (Repository): Replace "freqsummary" at a correct 481: place. It differs from routine "prevalence" which may be called 482: many times. Probs is memory consuming and must be used with 483: parcimony. 484: Version 0.95a3 (should output exactly the same maximization than 0.8a2) 485: 486: Revision 1.83 2003/06/10 13:39:11 lievre 487: *** empty log message *** 488: 489: Revision 1.82 2003/06/05 15:57:20 brouard 490: Add log in imach.c and fullversion number is now printed. 491: 492: */ 493: /* 494: Interpolated Markov Chain 495: 496: Short summary of the programme: 497: 498: This program computes Healthy Life Expectancies from 499: cross-longitudinal data. Cross-longitudinal data consist in: -1- a 500: first survey ("cross") where individuals from different ages are 501: interviewed on their health status or degree of disability (in the 502: case of a health survey which is our main interest) -2- at least a 503: second wave of interviews ("longitudinal") which measure each change 504: (if any) in individual health status. Health expectancies are 505: computed from the time spent in each health state according to a 506: model. More health states you consider, more time is necessary to reach the 507: Maximum Likelihood of the parameters involved in the model. The 508: simplest model is the multinomial logistic model where pij is the 509: probability to be observed in state j at the second wave 510: conditional to be observed in state i at the first wave. Therefore 511: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where 512: 'age' is age and 'sex' is a covariate. If you want to have a more 513: complex model than "constant and age", you should modify the program 514: where the markup *Covariates have to be included here again* invites 515: you to do it. More covariates you add, slower the 516: convergence. 517: 518: The advantage of this computer programme, compared to a simple 519: multinomial logistic model, is clear when the delay between waves is not 520: identical for each individual. Also, if a individual missed an 521: intermediate interview, the information is lost, but taken into 522: account using an interpolation or extrapolation. 523: 524: hPijx is the probability to be observed in state i at age x+h 525: conditional to the observed state i at age x. The delay 'h' can be 526: split into an exact number (nh*stepm) of unobserved intermediate 527: states. This elementary transition (by month, quarter, 528: semester or year) is modelled as a multinomial logistic. The hPx 529: matrix is simply the matrix product of nh*stepm elementary matrices 530: and the contribution of each individual to the likelihood is simply 531: hPijx. 532: 533: Also this programme outputs the covariance matrix of the parameters but also 534: of the life expectancies. It also computes the period (stable) prevalence. 535: 536: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr). 537: Institut national d'études démographiques, Paris. 538: This software have been partly granted by Euro-REVES, a concerted action 539: from the European Union. 540: It is copyrighted identically to a GNU software product, ie programme and 541: software can be distributed freely for non commercial use. Latest version 542: can be accessed at http://euroreves.ined.fr/imach . 543: 544: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach 545: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so 546: 547: **********************************************************************/ 548: /* 549: main 550: read parameterfile 551: read datafile 552: concatwav 553: freqsummary 554: if (mle >= 1) 555: mlikeli 556: print results files 557: if mle==1 558: computes hessian 559: read end of parameter file: agemin, agemax, bage, fage, estepm 560: begin-prev-date,... 561: open gnuplot file 562: open html file 563: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate 564: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ****** 565: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674 566: freexexit2 possible for memory heap. 567: 568: h Pij x | pij_nom ficrestpij 569: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3 570: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000 571: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907 572: 573: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340 574: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597 575: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in () 576: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix 577: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix 578: 579: forecasting if prevfcast==1 prevforecast call prevalence() 580: health expectancies 581: Variance-covariance of DFLE 582: prevalence() 583: movingaverage() 584: varevsij() 585: if popbased==1 varevsij(,popbased) 586: total life expectancies 587: Variance of period (stable) prevalence 588: end 589: */ 590: 591: /* #define DEBUG */ 592: /* #define DEBUGBRENT */ 593: #define POWELL /* Instead of NLOPT */ 594: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */ 595: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */ 596: 597: #include <math.h> 598: #include <stdio.h> 599: #include <stdlib.h> 600: #include <string.h> 601: 602: #ifdef _WIN32 603: #include <io.h> 604: #include <windows.h> 605: #include <tchar.h> 606: #else 607: #include <unistd.h> 608: #endif 609: 610: #include <limits.h> 611: #include <sys/types.h> 612: 613: #if defined(__GNUC__) 614: #include <sys/utsname.h> /* Doesn't work on Windows */ 615: #endif 616: 617: #include <sys/stat.h> 618: #include <errno.h> 619: /* extern int errno; */ 620: 621: /* #ifdef LINUX */ 622: /* #include <time.h> */ 623: /* #include "timeval.h" */ 624: /* #else */ 625: /* #include <sys/time.h> */ 626: /* #endif */ 627: 628: #include <time.h> 629: 630: #ifdef GSL 631: #include <gsl/gsl_errno.h> 632: #include <gsl/gsl_multimin.h> 633: #endif 634: 635: 636: #ifdef NLOPT 637: #include <nlopt.h> 638: typedef struct { 639: double (* function)(double [] ); 640: } myfunc_data ; 641: #endif 642: 643: /* #include <libintl.h> */ 644: /* #define _(String) gettext (String) */ 645: 646: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */ 647: 648: #define GNUPLOTPROGRAM "gnuplot" 649: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/ 650: #define FILENAMELENGTH 132 651: 652: #define GLOCK_ERROR_NOPATH -1 /* empty path */ 653: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */ 654: 655: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */ 656: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */ 657: 658: #define NINTERVMAX 8 659: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */ 660: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */ 661: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */ 662: #define codtabm(h,k) 1 & (h-1) >> (k-1) ; 663: #define MAXN 20000 664: #define YEARM 12. /**< Number of months per year */ 665: #define AGESUP 130 666: #define AGEBASE 40 667: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */ 668: #ifdef _WIN32 669: #define DIRSEPARATOR '\\' 670: #define CHARSEPARATOR "\\" 671: #define ODIRSEPARATOR '/' 672: #else 673: #define DIRSEPARATOR '/' 674: #define CHARSEPARATOR "/" 675: #define ODIRSEPARATOR '\\' 676: #endif 677: 678: /* $Id: imach.c,v 1.187 2015/04/29 09:11:15 brouard Exp $ */ 679: /* $State: Exp $ */ 680: 681: char version[]="Imach version 0.98q1, April 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015"; 682: char fullversion[]="$Revision: 1.187 $ $Date: 2015/04/29 09:11:15 $"; 683: char strstart[80]; 684: char optionfilext[10], optionfilefiname[FILENAMELENGTH]; 685: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */ 686: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */ 687: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */ 688: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */ 689: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */ 690: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */ 691: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */ 692: int cptcovprodnoage=0; /**< Number of covariate products without age */ 693: int cptcoveff=0; /* Total number of covariates to vary for printing results */ 694: int cptcov=0; /* Working variable */ 695: int npar=NPARMAX; 696: int nlstate=2; /* Number of live states */ 697: int ndeath=1; /* Number of dead states */ 698: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */ 699: int popbased=0; 700: 701: int *wav; /* Number of waves for this individuual 0 is possible */ 702: int maxwav=0; /* Maxim number of waves */ 703: int jmin=0, jmax=0; /* min, max spacing between 2 waves */ 704: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 705: int gipmx=0, gsw=0; /* Global variables on the number of contributions 706: to the likelihood and the sum of weights (done by funcone)*/ 707: int mle=1, weightopt=0; 708: int **mw; /* mw[mi][i] is number of the mi wave for this individual */ 709: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */ 710: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between 711: * wave mi and wave mi+1 is not an exact multiple of stepm. */ 712: int countcallfunc=0; /* Count the number of calls to func */ 713: double jmean=1; /* Mean space between 2 waves */ 714: double **matprod2(); /* test */ 715: double **oldm, **newm, **savm; /* Working pointers to matrices */ 716: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */ 717: /*FILE *fic ; */ /* Used in readdata only */ 718: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop; 719: FILE *ficlog, *ficrespow; 720: int globpr=0; /* Global variable for printing or not */ 721: double fretone; /* Only one call to likelihood */ 722: long ipmx=0; /* Number of contributions */ 723: double sw; /* Sum of weights */ 724: char filerespow[FILENAMELENGTH]; 725: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */ 726: FILE *ficresilk; 727: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor; 728: FILE *ficresprobmorprev; 729: FILE *fichtm, *fichtmcov; /* Html File */ 730: FILE *ficreseij; 731: char filerese[FILENAMELENGTH]; 732: FILE *ficresstdeij; 733: char fileresstde[FILENAMELENGTH]; 734: FILE *ficrescveij; 735: char filerescve[FILENAMELENGTH]; 736: FILE *ficresvij; 737: char fileresv[FILENAMELENGTH]; 738: FILE *ficresvpl; 739: char fileresvpl[FILENAMELENGTH]; 740: char title[MAXLINE]; 741: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH]; 742: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH]; 743: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH]; 744: char command[FILENAMELENGTH]; 745: int outcmd=0; 746: 747: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH]; 748: 749: char filelog[FILENAMELENGTH]; /* Log file */ 750: char filerest[FILENAMELENGTH]; 751: char fileregp[FILENAMELENGTH]; 752: char popfile[FILENAMELENGTH]; 753: 754: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ; 755: 756: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */ 757: /* struct timezone tzp; */ 758: /* extern int gettimeofday(); */ 759: struct tm tml, *gmtime(), *localtime(); 760: 761: extern time_t time(); 762: 763: struct tm start_time, end_time, curr_time, last_time, forecast_time; 764: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */ 765: struct tm tm; 766: 767: char strcurr[80], strfor[80]; 768: 769: char *endptr; 770: long lval; 771: double dval; 772: 773: #define NR_END 1 774: #define FREE_ARG char* 775: #define FTOL 1.0e-10 776: 777: #define NRANSI 778: #define ITMAX 200 779: 780: #define TOL 2.0e-4 781: 782: #define CGOLD 0.3819660 783: #define ZEPS 1.0e-10 784: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 785: 786: #define GOLD 1.618034 787: #define GLIMIT 100.0 788: #define TINY 1.0e-20 789: 790: static double maxarg1,maxarg2; 791: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2)) 792: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2)) 793: 794: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a)) 795: #define rint(a) floor(a+0.5) 796: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */ 797: #define mytinydouble 1.0e-16 798: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */ 799: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */ 800: /* static double dsqrarg; */ 801: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */ 802: static double sqrarg; 803: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg) 804: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 805: int agegomp= AGEGOMP; 806: 807: int imx; 808: int stepm=1; 809: /* Stepm, step in month: minimum step interpolation*/ 810: 811: int estepm; 812: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/ 813: 814: int m,nb; 815: long *num; 816: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens; 817: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint; 818: double **pmmij, ***probs; 819: double *ageexmed,*agecens; 820: double dateintmean=0; 821: 822: double *weight; 823: int **s; /* Status */ 824: double *agedc; 825: double **covar; /**< covar[j,i], value of jth covariate for individual i, 826: * covar=matrix(0,NCOVMAX,1,n); 827: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */ 828: double idx; 829: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */ 830: int *Ndum; /** Freq of modality (tricode */ 831: int **codtab; /**< codtab=imatrix(1,100,1,10); */ 832: int **Tvard, *Tprod, cptcovprod, *Tvaraff; 833: double *lsurv, *lpop, *tpop; 834: 835: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */ 836: double ftolhess; /**< Tolerance for computing hessian */ 837: 838: /**************** split *************************/ 839: static int split( char *path, char *dirc, char *name, char *ext, char *finame ) 840: { 841: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc) 842: the name of the file (name), its extension only (ext) and its first part of the name (finame) 843: */ 844: char *ss; /* pointer */ 845: int l1=0, l2=0; /* length counters */ 846: 847: l1 = strlen(path ); /* length of path */ 848: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH ); 849: ss= strrchr( path, DIRSEPARATOR ); /* find last / */ 850: if ( ss == NULL ) { /* no directory, so determine current directory */ 851: strcpy( name, path ); /* we got the fullname name because no directory */ 852: /*if(strrchr(path, ODIRSEPARATOR )==NULL) 853: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/ 854: /* get current working directory */ 855: /* extern char* getcwd ( char *buf , int len);*/ 856: #ifdef WIN32 857: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) { 858: #else 859: if (getcwd(dirc, FILENAME_MAX) == NULL) { 860: #endif 861: return( GLOCK_ERROR_GETCWD ); 862: } 863: /* got dirc from getcwd*/ 864: printf(" DIRC = %s \n",dirc); 865: } else { /* strip direcotry from path */ 866: ss++; /* after this, the filename */ 867: l2 = strlen( ss ); /* length of filename */ 868: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH ); 869: strcpy( name, ss ); /* save file name */ 870: strncpy( dirc, path, l1 - l2 ); /* now the directory */ 871: dirc[l1-l2] = '\0'; /* add zero */ 872: printf(" DIRC2 = %s \n",dirc); 873: } 874: /* We add a separator at the end of dirc if not exists */ 875: l1 = strlen( dirc ); /* length of directory */ 876: if( dirc[l1-1] != DIRSEPARATOR ){ 877: dirc[l1] = DIRSEPARATOR; 878: dirc[l1+1] = 0; 879: printf(" DIRC3 = %s \n",dirc); 880: } 881: ss = strrchr( name, '.' ); /* find last / */ 882: if (ss >0){ 883: ss++; 884: strcpy(ext,ss); /* save extension */ 885: l1= strlen( name); 886: l2= strlen(ss)+1; 887: strncpy( finame, name, l1-l2); 888: finame[l1-l2]= 0; 889: } 890: 891: return( 0 ); /* we're done */ 892: } 893: 894: 895: /******************************************/ 896: 897: void replace_back_to_slash(char *s, char*t) 898: { 899: int i; 900: int lg=0; 901: i=0; 902: lg=strlen(t); 903: for(i=0; i<= lg; i++) { 904: (s[i] = t[i]); 905: if (t[i]== '\\') s[i]='/'; 906: } 907: } 908: 909: char *trimbb(char *out, char *in) 910: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */ 911: char *s; 912: s=out; 913: while (*in != '\0'){ 914: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/ 915: in++; 916: } 917: *out++ = *in++; 918: } 919: *out='\0'; 920: return s; 921: } 922: 923: /* char *substrchaine(char *out, char *in, char *chain) */ 924: /* { */ 925: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */ 926: /* char *s, *t; */ 927: /* t=in;s=out; */ 928: /* while ((*in != *chain) && (*in != '\0')){ */ 929: /* *out++ = *in++; */ 930: /* } */ 931: 932: /* /\* *in matches *chain *\/ */ 933: /* while ((*in++ == *chain++) && (*in != '\0')){ */ 934: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */ 935: /* } */ 936: /* in--; chain--; */ 937: /* while ( (*in != '\0')){ */ 938: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */ 939: /* *out++ = *in++; */ 940: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */ 941: /* } */ 942: /* *out='\0'; */ 943: /* out=s; */ 944: /* return out; */ 945: /* } */ 946: char *substrchaine(char *out, char *in, char *chain) 947: { 948: /* Substract chain 'chain' from 'in', return and output 'out' */ 949: /* in="V1+V1*age+age*age+V2", chain="age*age" */ 950: 951: char *strloc; 952: 953: strcpy (out, in); 954: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */ 955: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out); 956: if(strloc != NULL){ 957: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */ 958: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1); 959: /* strcpy (strloc, strloc +strlen(chain));*/ 960: } 961: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out); 962: return out; 963: } 964: 965: 966: char *cutl(char *blocc, char *alocc, char *in, char occ) 967: { 968: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ' 969: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2') 970: gives blocc="abcdef" and alocc="ghi2j". 971: If occ is not found blocc is null and alocc is equal to in. Returns blocc 972: */ 973: char *s, *t; 974: t=in;s=in; 975: while ((*in != occ) && (*in != '\0')){ 976: *alocc++ = *in++; 977: } 978: if( *in == occ){ 979: *(alocc)='\0'; 980: s=++in; 981: } 982: 983: if (s == t) {/* occ not found */ 984: *(alocc-(in-s))='\0'; 985: in=s; 986: } 987: while ( *in != '\0'){ 988: *blocc++ = *in++; 989: } 990: 991: *blocc='\0'; 992: return t; 993: } 994: char *cutv(char *blocc, char *alocc, char *in, char occ) 995: { 996: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ' 997: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2') 998: gives blocc="abcdef2ghi" and alocc="j". 999: If occ is not found blocc is null and alocc is equal to in. Returns alocc 1000: */ 1001: char *s, *t; 1002: t=in;s=in; 1003: while (*in != '\0'){ 1004: while( *in == occ){ 1005: *blocc++ = *in++; 1006: s=in; 1007: } 1008: *blocc++ = *in++; 1009: } 1010: if (s == t) /* occ not found */ 1011: *(blocc-(in-s))='\0'; 1012: else 1013: *(blocc-(in-s)-1)='\0'; 1014: in=s; 1015: while ( *in != '\0'){ 1016: *alocc++ = *in++; 1017: } 1018: 1019: *alocc='\0'; 1020: return s; 1021: } 1022: 1023: int nbocc(char *s, char occ) 1024: { 1025: int i,j=0; 1026: int lg=20; 1027: i=0; 1028: lg=strlen(s); 1029: for(i=0; i<= lg; i++) { 1030: if (s[i] == occ ) j++; 1031: } 1032: return j; 1033: } 1034: 1035: /* void cutv(char *u,char *v, char*t, char occ) */ 1036: /* { */ 1037: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */ 1038: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */ 1039: /* gives u="abcdef2ghi" and v="j" *\/ */ 1040: /* int i,lg,j,p=0; */ 1041: /* i=0; */ 1042: /* lg=strlen(t); */ 1043: /* for(j=0; j<=lg-1; j++) { */ 1044: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */ 1045: /* } */ 1046: 1047: /* for(j=0; j<p; j++) { */ 1048: /* (u[j] = t[j]); */ 1049: /* } */ 1050: /* u[p]='\0'; */ 1051: 1052: /* for(j=0; j<= lg; j++) { */ 1053: /* if (j>=(p+1))(v[j-p-1] = t[j]); */ 1054: /* } */ 1055: /* } */ 1056: 1057: #ifdef _WIN32 1058: char * strsep(char **pp, const char *delim) 1059: { 1060: char *p, *q; 1061: 1062: if ((p = *pp) == NULL) 1063: return 0; 1064: if ((q = strpbrk (p, delim)) != NULL) 1065: { 1066: *pp = q + 1; 1067: *q = '\0'; 1068: } 1069: else 1070: *pp = 0; 1071: return p; 1072: } 1073: #endif 1074: 1075: /********************** nrerror ********************/ 1076: 1077: void nrerror(char error_text[]) 1078: { 1079: fprintf(stderr,"ERREUR ...\n"); 1080: fprintf(stderr,"%s\n",error_text); 1081: exit(EXIT_FAILURE); 1082: } 1083: /*********************** vector *******************/ 1084: double *vector(int nl, int nh) 1085: { 1086: double *v; 1087: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double))); 1088: if (!v) nrerror("allocation failure in vector"); 1089: return v-nl+NR_END; 1090: } 1091: 1092: /************************ free vector ******************/ 1093: void free_vector(double*v, int nl, int nh) 1094: { 1095: free((FREE_ARG)(v+nl-NR_END)); 1096: } 1097: 1098: /************************ivector *******************************/ 1099: int *ivector(long nl,long nh) 1100: { 1101: int *v; 1102: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int))); 1103: if (!v) nrerror("allocation failure in ivector"); 1104: return v-nl+NR_END; 1105: } 1106: 1107: /******************free ivector **************************/ 1108: void free_ivector(int *v, long nl, long nh) 1109: { 1110: free((FREE_ARG)(v+nl-NR_END)); 1111: } 1112: 1113: /************************lvector *******************************/ 1114: long *lvector(long nl,long nh) 1115: { 1116: long *v; 1117: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long))); 1118: if (!v) nrerror("allocation failure in ivector"); 1119: return v-nl+NR_END; 1120: } 1121: 1122: /******************free lvector **************************/ 1123: void free_lvector(long *v, long nl, long nh) 1124: { 1125: free((FREE_ARG)(v+nl-NR_END)); 1126: } 1127: 1128: /******************* imatrix *******************************/ 1129: int **imatrix(long nrl, long nrh, long ncl, long nch) 1130: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 1131: { 1132: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 1133: int **m; 1134: 1135: /* allocate pointers to rows */ 1136: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 1137: if (!m) nrerror("allocation failure 1 in matrix()"); 1138: m += NR_END; 1139: m -= nrl; 1140: 1141: 1142: /* allocate rows and set pointers to them */ 1143: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 1144: if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 1145: m[nrl] += NR_END; 1146: m[nrl] -= ncl; 1147: 1148: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 1149: 1150: /* return pointer to array of pointers to rows */ 1151: return m; 1152: } 1153: 1154: /****************** free_imatrix *************************/ 1155: void free_imatrix(m,nrl,nrh,ncl,nch) 1156: int **m; 1157: long nch,ncl,nrh,nrl; 1158: /* free an int matrix allocated by imatrix() */ 1159: { 1160: free((FREE_ARG) (m[nrl]+ncl-NR_END)); 1161: free((FREE_ARG) (m+nrl-NR_END)); 1162: } 1163: 1164: /******************* matrix *******************************/ 1165: double **matrix(long nrl, long nrh, long ncl, long nch) 1166: { 1167: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1; 1168: double **m; 1169: 1170: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*))); 1171: if (!m) nrerror("allocation failure 1 in matrix()"); 1172: m += NR_END; 1173: m -= nrl; 1174: 1175: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double))); 1176: if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 1177: m[nrl] += NR_END; 1178: m[nrl] -= ncl; 1179: 1180: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol; 1181: return m; 1182: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0]) 1183: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress 1184: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized. 1185: */ 1186: } 1187: 1188: /*************************free matrix ************************/ 1189: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch) 1190: { 1191: free((FREE_ARG)(m[nrl]+ncl-NR_END)); 1192: free((FREE_ARG)(m+nrl-NR_END)); 1193: } 1194: 1195: /******************* ma3x *******************************/ 1196: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh) 1197: { 1198: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1; 1199: double ***m; 1200: 1201: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*))); 1202: if (!m) nrerror("allocation failure 1 in matrix()"); 1203: m += NR_END; 1204: m -= nrl; 1205: 1206: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double))); 1207: if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 1208: m[nrl] += NR_END; 1209: m[nrl] -= ncl; 1210: 1211: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol; 1212: 1213: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double))); 1214: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()"); 1215: m[nrl][ncl] += NR_END; 1216: m[nrl][ncl] -= nll; 1217: for (j=ncl+1; j<=nch; j++) 1218: m[nrl][j]=m[nrl][j-1]+nlay; 1219: 1220: for (i=nrl+1; i<=nrh; i++) { 1221: m[i][ncl]=m[i-1l][ncl]+ncol*nlay; 1222: for (j=ncl+1; j<=nch; j++) 1223: m[i][j]=m[i][j-1]+nlay; 1224: } 1225: return m; 1226: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1]) 1227: &(m[i][j][k]) <=> *((*(m+i) + j)+k) 1228: */ 1229: } 1230: 1231: /*************************free ma3x ************************/ 1232: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh) 1233: { 1234: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END)); 1235: free((FREE_ARG)(m[nrl]+ncl-NR_END)); 1236: free((FREE_ARG)(m+nrl-NR_END)); 1237: } 1238: 1239: /*************** function subdirf ***********/ 1240: char *subdirf(char fileres[]) 1241: { 1242: /* Caution optionfilefiname is hidden */ 1243: strcpy(tmpout,optionfilefiname); 1244: strcat(tmpout,"/"); /* Add to the right */ 1245: strcat(tmpout,fileres); 1246: return tmpout; 1247: } 1248: 1249: /*************** function subdirf2 ***********/ 1250: char *subdirf2(char fileres[], char *preop) 1251: { 1252: 1253: /* Caution optionfilefiname is hidden */ 1254: strcpy(tmpout,optionfilefiname); 1255: strcat(tmpout,"/"); 1256: strcat(tmpout,preop); 1257: strcat(tmpout,fileres); 1258: return tmpout; 1259: } 1260: 1261: /*************** function subdirf3 ***********/ 1262: char *subdirf3(char fileres[], char *preop, char *preop2) 1263: { 1264: 1265: /* Caution optionfilefiname is hidden */ 1266: strcpy(tmpout,optionfilefiname); 1267: strcat(tmpout,"/"); 1268: strcat(tmpout,preop); 1269: strcat(tmpout,preop2); 1270: strcat(tmpout,fileres); 1271: return tmpout; 1272: } 1273: 1274: char *asc_diff_time(long time_sec, char ascdiff[]) 1275: { 1276: long sec_left, days, hours, minutes; 1277: days = (time_sec) / (60*60*24); 1278: sec_left = (time_sec) % (60*60*24); 1279: hours = (sec_left) / (60*60) ; 1280: sec_left = (sec_left) %(60*60); 1281: minutes = (sec_left) /60; 1282: sec_left = (sec_left) % (60); 1283: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left); 1284: return ascdiff; 1285: } 1286: 1287: /***************** f1dim *************************/ 1288: extern int ncom; 1289: extern double *pcom,*xicom; 1290: extern double (*nrfunc)(double []); 1291: 1292: double f1dim(double x) 1293: { 1294: int j; 1295: double f; 1296: double *xt; 1297: 1298: xt=vector(1,ncom); 1299: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 1300: f=(*nrfunc)(xt); 1301: free_vector(xt,1,ncom); 1302: return f; 1303: } 1304: 1305: /*****************brent *************************/ 1306: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin) 1307: { 1308: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is 1309: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates 1310: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of 1311: * the minimum is returned as xmin, and the minimum function value is returned as brent , the 1312: * returned function value. 1313: */ 1314: int iter; 1315: double a,b,d,etemp; 1316: double fu=0,fv,fw,fx; 1317: double ftemp=0.; 1318: double p,q,r,tol1,tol2,u,v,w,x,xm; 1319: double e=0.0; 1320: 1321: a=(ax < cx ? ax : cx); 1322: b=(ax > cx ? ax : cx); 1323: x=w=v=bx; 1324: fw=fv=fx=(*f)(x); 1325: for (iter=1;iter<=ITMAX;iter++) { 1326: xm=0.5*(a+b); 1327: tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 1328: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/ 1329: printf(".");fflush(stdout); 1330: fprintf(ficlog,".");fflush(ficlog); 1331: #ifdef DEBUGBRENT 1332: 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); 1333: 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); 1334: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */ 1335: #endif 1336: if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 1337: *xmin=x; 1338: return fx; 1339: } 1340: ftemp=fu; 1341: if (fabs(e) > tol1) { 1342: r=(x-w)*(fx-fv); 1343: q=(x-v)*(fx-fw); 1344: p=(x-v)*q-(x-w)*r; 1345: q=2.0*(q-r); 1346: if (q > 0.0) p = -p; 1347: q=fabs(q); 1348: etemp=e; 1349: e=d; 1350: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 1351: d=CGOLD*(e=(x >= xm ? a-x : b-x)); 1352: else { 1353: d=p/q; 1354: u=x+d; 1355: if (u-a < tol2 || b-u < tol2) 1356: d=SIGN(tol1,xm-x); 1357: } 1358: } else { 1359: d=CGOLD*(e=(x >= xm ? a-x : b-x)); 1360: } 1361: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 1362: fu=(*f)(u); 1363: if (fu <= fx) { 1364: if (u >= x) a=x; else b=x; 1365: SHFT(v,w,x,u) 1366: SHFT(fv,fw,fx,fu) 1367: } else { 1368: if (u < x) a=u; else b=u; 1369: if (fu <= fw || w == x) { 1370: v=w; 1371: w=u; 1372: fv=fw; 1373: fw=fu; 1374: } else if (fu <= fv || v == x || v == w) { 1375: v=u; 1376: fv=fu; 1377: } 1378: } 1379: } 1380: nrerror("Too many iterations in brent"); 1381: *xmin=x; 1382: return fx; 1383: } 1384: 1385: /****************** mnbrak ***********************/ 1386: 1387: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 1388: double (*func)(double)) 1389: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in 1390: the downhill direction (defined by the function as evaluated at the initial points) and returns 1391: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function 1392: values at the three points, fa, fb , and fc such that fa > fb and fb < fc. 1393: */ 1394: double ulim,u,r,q, dum; 1395: double fu; 1396: 1397: double scale=10.; 1398: int iterscale=0; 1399: 1400: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/ 1401: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */ 1402: 1403: 1404: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */ 1405: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */ 1406: /* *bx = *ax - (*ax - *bx)/scale; */ 1407: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */ 1408: /* } */ 1409: 1410: if (*fb > *fa) { 1411: SHFT(dum,*ax,*bx,dum) 1412: SHFT(dum,*fb,*fa,dum) 1413: } 1414: *cx=(*bx)+GOLD*(*bx-*ax); 1415: *fc=(*func)(*cx); 1416: #ifdef DEBUG 1417: printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc); 1418: fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc); 1419: #endif 1420: while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */ 1421: r=(*bx-*ax)*(*fb-*fc); 1422: q=(*bx-*cx)*(*fb-*fa); 1423: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 1424: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */ 1425: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */ 1426: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */ 1427: fu=(*func)(u); 1428: #ifdef DEBUG 1429: /* f(x)=A(x-u)**2+f(u) */ 1430: double A, fparabu; 1431: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u); 1432: fparabu= *fa - A*(*ax-u)*(*ax-u); 1433: printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu); 1434: fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu); 1435: /* And thus,it can be that fu > *fc even if fparabu < *fc */ 1436: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489), 1437: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */ 1438: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/ 1439: #endif 1440: #ifdef MNBRAKORIGINAL 1441: #else 1442: if (fu > *fc) { 1443: #ifdef DEBUG 1444: printf("mnbrak4 fu > fc \n"); 1445: fprintf(ficlog, "mnbrak4 fu > fc\n"); 1446: #endif 1447: /* SHFT(u,*cx,*cx,u) /\* ie a=c, c=u and u=c; in that case, next SHFT(a,b,c,u) will give a=b=b, b=c=u, c=u=c and *\/ */ 1448: /* SHFT(*fa,*fc,fu,*fc) /\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\/ */ 1449: dum=u; /* Shifting c and u */ 1450: u = *cx; 1451: *cx = dum; 1452: dum = fu; 1453: fu = *fc; 1454: *fc =dum; 1455: } else { /* end */ 1456: #ifdef DEBUG 1457: printf("mnbrak3 fu < fc \n"); 1458: fprintf(ficlog, "mnbrak3 fu < fc\n"); 1459: #endif 1460: dum=u; /* Shifting c and u */ 1461: u = *cx; 1462: *cx = dum; 1463: dum = fu; 1464: fu = *fc; 1465: *fc =dum; 1466: } 1467: #endif 1468: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */ 1469: #ifdef DEBUG 1470: printf("mnbrak2 u after c but before ulim\n"); 1471: fprintf(ficlog, "mnbrak2 u after c but before ulim\n"); 1472: #endif 1473: fu=(*func)(u); 1474: if (fu < *fc) { 1475: #ifdef DEBUG 1476: printf("mnbrak2 u after c but before ulim AND fu < fc\n"); 1477: fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n"); 1478: #endif 1479: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 1480: SHFT(*fb,*fc,fu,(*func)(u)) 1481: } 1482: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */ 1483: #ifdef DEBUG 1484: printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n"); 1485: fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n"); 1486: #endif 1487: u=ulim; 1488: fu=(*func)(u); 1489: } else { /* u could be left to b (if r > q parabola has a maximum) */ 1490: #ifdef DEBUG 1491: printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n"); 1492: fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n"); 1493: #endif 1494: u=(*cx)+GOLD*(*cx-*bx); 1495: fu=(*func)(u); 1496: } /* end tests */ 1497: SHFT(*ax,*bx,*cx,u) 1498: SHFT(*fa,*fb,*fc,fu) 1499: #ifdef DEBUG 1500: printf("mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu); 1501: fprintf(ficlog, "mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu); 1502: #endif 1503: } /* end while; ie return (a, b, c, fa, fb, fc) such that a f(b) and fb < f(c) */ 1504: } 1505: 1506: /*************** linmin ************************/ 1507: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and 1508: resets p to where the function func(p) takes on a minimum along the direction xi from p , 1509: and replaces xi by the actual vector displacement that p was moved. Also returns as fret 1510: the value of func at the returned location p . This is actually all accomplished by calling the 1511: routines mnbrak and brent .*/ 1512: int ncom; 1513: double *pcom,*xicom; 1514: double (*nrfunc)(double []); 1515: 1516: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 1517: { 1518: double brent(double ax, double bx, double cx, 1519: double (*f)(double), double tol, double *xmin); 1520: double f1dim(double x); 1521: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 1522: double *fc, double (*func)(double)); 1523: int j; 1524: double xx,xmin,bx,ax; 1525: double fx,fb,fa; 1526: 1527: double scale=10., axs, xxs, xxss; /* Scale added for infinity */ 1528: 1529: ncom=n; 1530: pcom=vector(1,n); 1531: xicom=vector(1,n); 1532: nrfunc=func; 1533: for (j=1;j<=n;j++) { 1534: pcom[j]=p[j]; 1535: xicom[j]=xi[j]; 1536: } 1537: 1538: axs=0.0; 1539: xxss=1; /* 1 and using scale */ 1540: xxs=1; 1541: do{ 1542: ax=0.; 1543: xx= xxs; 1544: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */ 1545: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */ 1546: /* xt[x,j]=pcom[j]+x*xicom[j] f(ax) = f(xt(a,j=1,n)) = f(p(j) + 0 * xi(j)) and f(xx) = f(xt(x, j=1,n)) = f(p(j) + 1 * xi(j)) */ 1547: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */ 1548: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */ 1549: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */ 1550: /* Find a bracket a,x,b in direction n=xi ie xicom, order may change. Scale is [0:xxs*xi[j]] et non plus [0:xi[j]]*/ 1551: if (fx != fx){ 1552: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */ 1553: printf("\nLinmin NAN : input [axs=%lf:xxs=%lf], mnbrak outputs fx=%lf <(fb=%lf and fa=%lf) with xx=%lf in [ax=%lf:bx=%lf] \n", axs, xxs, fx,fb, fa, xx, ax, bx); 1554: } 1555: }while(fx != fx); 1556: 1557: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/ 1558: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */ 1559: /* fmin = f(p[j] + xmin * xi[j]) */ 1560: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */ 1561: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */ 1562: #ifdef DEBUG 1563: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin); 1564: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin); 1565: #endif 1566: printf("linmin end "); 1567: for (j=1;j<=n;j++) { 1568: printf(" before xi[%d]=%12.8f", j,xi[j]); 1569: xi[j] *= xmin; /* xi rescaled by xmin: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */ 1570: if(xxs <1.0) 1571: printf(" after xi[%d]=%12.8f, xmin=%12.8f, ax=%12.8f, xx=%12.8f, bx=%12.8f, xxs=%12.8f", j,xi[j], xmin, ax, xx, bx,xxs ); 1572: p[j] += xi[j]; /* Parameters values are updated accordingly */ 1573: } 1574: printf("\n"); 1575: free_vector(xicom,1,n); 1576: free_vector(pcom,1,n); 1577: } 1578: 1579: 1580: /*************** powell ************************/ 1581: /* 1582: Minimization of a function func of n variables. Input consists of an initial starting point 1583: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di- 1584: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value 1585: such that failure to decrease by more than this amount on one iteration signals doneness. On 1586: output, p is set to the best point found, xi is the then-current direction set, fret is the returned 1587: function value at p , and iter is the number of iterations taken. The routine linmin is used. 1588: */ 1589: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 1590: double (*func)(double [])) 1591: { 1592: void linmin(double p[], double xi[], int n, double *fret, 1593: double (*func)(double [])); 1594: int i,ibig,j; 1595: double del,t,*pt,*ptt,*xit; 1596: double directest; 1597: double fp,fptt; 1598: double *xits; 1599: int niterf, itmp; 1600: 1601: pt=vector(1,n); 1602: ptt=vector(1,n); 1603: xit=vector(1,n); 1604: xits=vector(1,n); 1605: *fret=(*func)(p); 1606: for (j=1;j<=n;j++) pt[j]=p[j]; 1607: rcurr_time = time(NULL); 1608: for (*iter=1;;++(*iter)) { 1609: fp=(*fret); /* From former iteration or initial value */ 1610: ibig=0; 1611: del=0.0; 1612: rlast_time=rcurr_time; 1613: /* (void) gettimeofday(&curr_time,&tzp); */ 1614: rcurr_time = time(NULL); 1615: curr_time = *localtime(&rcurr_time); 1616: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout); 1617: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog); 1618: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */ 1619: for (i=1;i<=n;i++) { 1620: printf(" %d %.12f",i, p[i]); 1621: fprintf(ficlog," %d %.12lf",i, p[i]); 1622: fprintf(ficrespow," %.12lf", p[i]); 1623: } 1624: printf("\n"); 1625: fprintf(ficlog,"\n"); 1626: fprintf(ficrespow,"\n");fflush(ficrespow); 1627: if(*iter <=3){ 1628: tml = *localtime(&rcurr_time); 1629: strcpy(strcurr,asctime(&tml)); 1630: rforecast_time=rcurr_time; 1631: itmp = strlen(strcurr); 1632: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */ 1633: strcurr[itmp-1]='\0'; 1634: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time); 1635: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time); 1636: for(niterf=10;niterf<=30;niterf+=10){ 1637: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time); 1638: forecast_time = *localtime(&rforecast_time); 1639: strcpy(strfor,asctime(&forecast_time)); 1640: itmp = strlen(strfor); 1641: if(strfor[itmp-1]=='\n') 1642: strfor[itmp-1]='\0'; 1643: printf(" - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr); 1644: fprintf(ficlog," - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr); 1645: } 1646: } 1647: for (i=1;i<=n;i++) { /* For each direction i */ 1648: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */ 1649: fptt=(*fret); 1650: #ifdef DEBUG 1651: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret); 1652: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret); 1653: #endif 1654: printf("%d",i);fflush(stdout); /* print direction (parameter) i */ 1655: fprintf(ficlog,"%d",i);fflush(ficlog); 1656: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input. Outputs are fret(new point p) p is updated and xit rescaled */ 1657: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions 1658: because that direction will be replaced unless the gain del is small 1659: in comparison with the 'probable' gain, mu^2, with the last average direction. 1660: Unless the n directions are conjugate some gain in the determinant may be obtained 1661: with the new direction. 1662: */ 1663: del=fabs(fptt-(*fret)); 1664: ibig=i; 1665: } 1666: #ifdef DEBUG 1667: printf("%d %.12e",i,(*fret)); 1668: fprintf(ficlog,"%d %.12e",i,(*fret)); 1669: for (j=1;j<=n;j++) { 1670: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5); 1671: printf(" x(%d)=%.12e",j,xit[j]); 1672: fprintf(ficlog," x(%d)=%.12e",j,xit[j]); 1673: } 1674: for(j=1;j<=n;j++) { 1675: printf(" p(%d)=%.12e",j,p[j]); 1676: fprintf(ficlog," p(%d)=%.12e",j,p[j]); 1677: } 1678: printf("\n"); 1679: fprintf(ficlog,"\n"); 1680: #endif 1681: } /* end loop on each direction i */ 1682: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */ 1683: /* But p and xit have been updated at the end of linmin and do not produce *fret any more! */ 1684: /* New value of last point Pn is not computed, P(n-1) */ 1685: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */ 1686: #ifdef DEBUG 1687: int k[2],l; 1688: k[0]=1; 1689: k[1]=-1; 1690: printf("Max: %.12e",(*func)(p)); 1691: fprintf(ficlog,"Max: %.12e",(*func)(p)); 1692: for (j=1;j<=n;j++) { 1693: printf(" %.12e",p[j]); 1694: fprintf(ficlog," %.12e",p[j]); 1695: } 1696: printf("\n"); 1697: fprintf(ficlog,"\n"); 1698: for(l=0;l<=1;l++) { 1699: for (j=1;j<=n;j++) { 1700: ptt[j]=p[j]+(p[j]-pt[j])*k[l]; 1701: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]); 1702: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]); 1703: } 1704: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p))); 1705: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p))); 1706: } 1707: #endif 1708: 1709: 1710: free_vector(xit,1,n); 1711: free_vector(xits,1,n); 1712: free_vector(ptt,1,n); 1713: free_vector(pt,1,n); 1714: return; 1715: } 1716: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 1717: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */ 1718: ptt[j]=2.0*p[j]-pt[j]; 1719: xit[j]=p[j]-pt[j]; 1720: pt[j]=p[j]; 1721: } 1722: fptt=(*func)(ptt); /* f_3 */ 1723: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */ 1724: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */ 1725: /* From x1 (P0) distance of x2 is at h and x3 is 2h */ 1726: /* Let f"(x2) be the 2nd derivative equal everywhere. */ 1727: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */ 1728: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */ 1729: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */ 1730: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */ 1731: #ifdef NRCORIGINAL 1732: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/ 1733: #else 1734: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */ 1735: t= t- del*SQR(fp-fptt); 1736: #endif 1737: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */ 1738: #ifdef DEBUG 1739: printf("t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest); 1740: fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest); 1741: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt), 1742: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt)); 1743: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt), 1744: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt)); 1745: printf("tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t); 1746: fprintf(ficlog, "tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t); 1747: #endif 1748: #ifdef POWELLORIGINAL 1749: if (t < 0.0) { /* Then we use it for new direction */ 1750: #else 1751: if (directest*t < 0.0) { /* Contradiction between both tests */ 1752: printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del); 1753: printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt); 1754: fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del); 1755: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt); 1756: } 1757: if (directest < 0.0) { /* Then we use it for new direction */ 1758: #endif 1759: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/ 1760: for (j=1;j<=n;j++) { 1761: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */ 1762: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */ 1763: } 1764: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig); 1765: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig); 1766: 1767: #ifdef DEBUG 1768: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig); 1769: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig); 1770: for(j=1;j<=n;j++){ 1771: printf(" %.12e",xit[j]); 1772: fprintf(ficlog," %.12e",xit[j]); 1773: } 1774: printf("\n"); 1775: fprintf(ficlog,"\n"); 1776: #endif 1777: } /* end of t negative */ 1778: } /* end if (fptt < fp) */ 1779: } 1780: } 1781: 1782: /**** Prevalence limit (stable or period prevalence) ****************/ 1783: 1784: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij) 1785: { 1786: /* Computes the prevalence limit in each live state at age x by left multiplying the unit 1787: matrix by transitions matrix until convergence is reached */ 1788: 1789: int i, ii,j,k; 1790: double min, max, maxmin, maxmax,sumnew=0.; 1791: /* double **matprod2(); */ /* test */ 1792: double **out, cov[NCOVMAX+1], **pmij(); 1793: double **newm; 1794: double agefin, delaymax=50 ; /* Max number of years to converge */ 1795: 1796: for (ii=1;ii<=nlstate+ndeath;ii++) 1797: for (j=1;j<=nlstate+ndeath;j++){ 1798: oldm[ii][j]=(ii==j ? 1.0 : 0.0); 1799: } 1800: 1801: cov[1]=1.; 1802: 1803: /* Even if hstepm = 1, at least one multiplication by the unit matrix */ 1804: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){ 1805: newm=savm; 1806: /* Covariates have to be included here again */ 1807: cov[2]=agefin; 1808: if(nagesqr==1) 1809: cov[3]= agefin*agefin;; 1810: for (k=1; k<=cptcovn;k++) { 1811: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; 1812: /*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]]);*/ 1813: } 1814: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */ 1815: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]*cov[2]; 1816: for (k=1; k<=cptcovprod;k++) /* Useless */ 1817: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; 1818: 1819: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/ 1820: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/ 1821: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/ 1822: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */ 1823: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */ 1824: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */ 1825: 1826: savm=oldm; 1827: oldm=newm; 1828: maxmax=0.; 1829: for(j=1;j<=nlstate;j++){ 1830: min=1.; 1831: max=0.; 1832: for(i=1; i<=nlstate; i++) { 1833: sumnew=0; 1834: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k]; 1835: prlim[i][j]= newm[i][j]/(1-sumnew); 1836: /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/ 1837: max=FMAX(max,prlim[i][j]); 1838: min=FMIN(min,prlim[i][j]); 1839: } 1840: maxmin=max-min; 1841: maxmax=FMAX(maxmax,maxmin); 1842: } /* j loop */ 1843: if(maxmax < ftolpl){ 1844: return prlim; 1845: } 1846: } /* age loop */ 1847: return prlim; /* should not reach here */ 1848: } 1849: 1850: /*************** transition probabilities ***************/ 1851: 1852: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate ) 1853: { 1854: /* According to parameters values stored in x and the covariate's values stored in cov, 1855: computes the probability to be observed in state j being in state i by appying the 1856: model to the ncovmodel covariates (including constant and age). 1857: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc] 1858: and, according on how parameters are entered, the position of the coefficient xij(nc) of the 1859: ncth covariate in the global vector x is given by the formula: 1860: j=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel 1862: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation, 1863: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij. 1864: Outputs ps[i][j] the probability to be observed in j being in j according to 1865: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij] 1866: */ 1867: double s1, lnpijopii; 1868: /*double t34;*/ 1869: int i,j, nc, ii, jj; 1870: 1871: for(i=1; i<= nlstate; i++){ 1872: for(j=1; j<i;j++){ 1873: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){ 1874: /*lnpijopii += param[i][j][nc]*cov[nc];*/ 1875: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc]; 1876: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */ 1877: } 1878: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */ 1879: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */ 1880: } 1881: for(j=i+1; j<=nlstate+ndeath;j++){ 1882: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){ 1883: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/ 1884: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc]; 1885: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */ 1886: } 1887: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */ 1888: } 1889: } 1890: 1891: for(i=1; i<= nlstate; i++){ 1892: s1=0; 1893: for(j=1; j<i; j++){ 1894: s1+=exp(ps[i][j]); /* In fact sums pij/pii */ 1895: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */ 1896: } 1897: for(j=i+1; j<=nlstate+ndeath; j++){ 1898: s1+=exp(ps[i][j]); /* In fact sums pij/pii */ 1899: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */ 1900: } 1901: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */ 1902: ps[i][i]=1./(s1+1.); 1903: /* Computing other pijs */ 1904: for(j=1; j<i; j++) 1905: ps[i][j]= exp(ps[i][j])*ps[i][i]; 1906: for(j=i+1; j<=nlstate+ndeath; j++) 1907: ps[i][j]= exp(ps[i][j])*ps[i][i]; 1908: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */ 1909: } /* end i */ 1910: 1911: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){ 1912: for(jj=1; jj<= nlstate+ndeath; jj++){ 1913: ps[ii][jj]=0; 1914: ps[ii][ii]=1; 1915: } 1916: } 1917: 1918: 1919: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */ 1920: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */ 1921: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */ 1922: /* } */ 1923: /* printf("\n "); */ 1924: /* } */ 1925: /* printf("\n ");printf("%lf ",cov[2]);*/ 1926: /* 1927: for(i=1; i<= npar; i++) printf("%f ",x[i]); 1928: goto end;*/ 1929: return ps; 1930: } 1931: 1932: /**************** Product of 2 matrices ******************/ 1933: 1934: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b) 1935: { 1936: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times 1937: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */ 1938: /* in, b, out are matrice of pointers which should have been initialized 1939: before: only the contents of out is modified. The function returns 1940: a pointer to pointers identical to out */ 1941: int i, j, k; 1942: for(i=nrl; i<= nrh; i++) 1943: for(k=ncolol; k<=ncoloh; k++){ 1944: out[i][k]=0.; 1945: for(j=ncl; j<=nch; j++) 1946: out[i][k] +=in[i][j]*b[j][k]; 1947: } 1948: return out; 1949: } 1950: 1951: 1952: /************* Higher Matrix Product ***************/ 1953: 1954: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij ) 1955: { 1956: /* Computes the transition matrix starting at age 'age' over 1957: 'nhstepm*hstepm*stepm' months (i.e. until 1958: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying 1959: nhstepm*hstepm matrices. 1960: Output is stored in matrix po[i][j][h] for h every 'hstepm' step 1961: (typically every 2 years instead of every month which is too big 1962: for the memory). 1963: Model is determined by parameters x and covariates have to be 1964: included manually here. 1965: 1966: */ 1967: 1968: int i, j, d, h, k; 1969: double **out, cov[NCOVMAX+1]; 1970: double **newm; 1971: double agexact; 1972: 1973: /* Hstepm could be zero and should return the unit matrix */ 1974: for (i=1;i<=nlstate+ndeath;i++) 1975: for (j=1;j<=nlstate+ndeath;j++){ 1976: oldm[i][j]=(i==j ? 1.0 : 0.0); 1977: po[i][j][0]=(i==j ? 1.0 : 0.0); 1978: } 1979: /* Even if hstepm = 1, at least one multiplication by the unit matrix */ 1980: for(h=1; h <=nhstepm; h++){ 1981: for(d=1; d <=hstepm; d++){ 1982: newm=savm; 1983: /* Covariates have to be included here again */ 1984: cov[1]=1.; 1985: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; 1986: cov[2]=agexact; 1987: if(nagesqr==1) 1988: cov[3]= agexact*agexact; 1989: for (k=1; k<=cptcovn;k++) 1990: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; 1991: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */ 1992: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */ 1993: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2]; 1994: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */ 1995: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; 1996: 1997: 1998: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/ 1999: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/ 2000: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 2001: pmij(pmmij,cov,ncovmodel,x,nlstate)); 2002: savm=oldm; 2003: oldm=newm; 2004: } 2005: for(i=1; i<=nlstate+ndeath; i++) 2006: for(j=1;j<=nlstate+ndeath;j++) { 2007: po[i][j][h]=newm[i][j]; 2008: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/ 2009: } 2010: /*printf("h=%d ",h);*/ 2011: } /* end h */ 2012: /* printf("\n H=%d \n",h); */ 2013: return po; 2014: } 2015: 2016: #ifdef NLOPT 2017: double myfunc(unsigned n, const double *p1, double *grad, void *pd){ 2018: double fret; 2019: double *xt; 2020: int j; 2021: myfunc_data *d2 = (myfunc_data *) pd; 2022: /* xt = (p1-1); */ 2023: xt=vector(1,n); 2024: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */ 2025: 2026: fret=(d2->function)(xt); /* p xt[1]@8 is fine */ 2027: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */ 2028: printf("Function = %.12lf ",fret); 2029: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 2030: printf("\n"); 2031: free_vector(xt,1,n); 2032: return fret; 2033: } 2034: #endif 2035: 2036: /*************** log-likelihood *************/ 2037: double func( double *x) 2038: { 2039: int i, ii, j, k, mi, d, kk; 2040: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1]; 2041: double **out; 2042: double sw; /* Sum of weights */ 2043: double lli; /* Individual log likelihood */ 2044: int s1, s2; 2045: double bbh, survp; 2046: long ipmx; 2047: double agexact; 2048: /*extern weight */ 2049: /* We are differentiating ll according to initial status */ 2050: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/ 2051: /*for(i=1;i<imx;i++) 2052: printf(" %d\n",s[4][i]); 2053: */ 2054: 2055: ++countcallfunc; 2056: 2057: cov[1]=1.; 2058: 2059: for(k=1; k<=nlstate; k++) ll[k]=0.; 2060: 2061: if(mle==1){ 2062: for (i=1,ipmx=0, sw=0.; i<=imx; i++){ 2063: /* Computes the values of the ncovmodel covariates of the model 2064: depending if the covariates are fixed or variying (age dependent) and stores them in cov[] 2065: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability 2066: to be observed in j being in i according to the model. 2067: */ 2068: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */ 2069: cov[2+nagesqr+k]=covar[Tvar[k]][i]; 2070: } 2071: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 2072: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 2073: has been calculated etc */ 2074: for(mi=1; mi<= wav[i]-1; mi++){ 2075: for (ii=1;ii<=nlstate+ndeath;ii++) 2076: for (j=1;j<=nlstate+ndeath;j++){ 2077: oldm[ii][j]=(ii==j ? 1.0 : 0.0); 2078: savm[ii][j]=(ii==j ? 1.0 : 0.0); 2079: } 2080: for(d=0; d<dh[mi][i]; d++){ 2081: newm=savm; 2082: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; 2083: cov[2]=agexact; 2084: if(nagesqr==1) 2085: cov[3]= agexact*agexact; 2086: for (kk=1; kk<=cptcovage;kk++) { 2087: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */ 2088: } 2089: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, 2090: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); 2091: savm=oldm; 2092: oldm=newm; 2093: } /* end mult */ 2094: 2095: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */ 2096: /* But now since version 0.9 we anticipate for bias at large stepm. 2097: * If stepm is larger than one month (smallest stepm) and if the exact delay 2098: * (in months) between two waves is not a multiple of stepm, we rounded to 2099: * the nearest (and in case of equal distance, to the lowest) interval but now 2100: * we keep into memory the bias bh[mi][i] and also the previous matrix product 2101: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the 2102: * probability in order to take into account the bias as a fraction of the way 2103: * from savm to out if bh is negative or even beyond if bh is positive. bh varies 2104: * -stepm/2 to stepm/2 . 2105: * For stepm=1 the results are the same as for previous versions of Imach. 2106: * For stepm > 1 the results are less biased than in previous versions. 2107: */ 2108: s1=s[mw[mi][i]][i]; 2109: s2=s[mw[mi+1][i]][i]; 2110: bbh=(double)bh[mi][i]/(double)stepm; 2111: /* bias bh is positive if real duration 2112: * is higher than the multiple of stepm and negative otherwise. 2113: */ 2114: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/ 2115: if( s2 > nlstate){ 2116: /* i.e. if s2 is a death state and if the date of death is known 2117: then the contribution to the likelihood is the probability to 2118: die between last step unit time and current step unit time, 2119: which is also equal to probability to die before dh 2120: minus probability to die before dh-stepm . 2121: In version up to 0.92 likelihood was computed 2122: as if date of death was unknown. Death was treated as any other 2123: health state: the date of the interview describes the actual state 2124: and not the date of a change in health state. The former idea was 2125: to consider that at each interview the state was recorded 2126: (healthy, disable or death) and IMaCh was corrected; but when we 2127: introduced the exact date of death then we should have modified 2128: the contribution of an exact death to the likelihood. This new 2129: contribution is smaller and very dependent of the step unit 2130: stepm. It is no more the probability to die between last interview 2131: and month of death but the probability to survive from last 2132: interview up to one month before death multiplied by the 2133: probability to die within a month. Thanks to Chris 2134: Jackson for correcting this bug. Former versions increased 2135: mortality artificially. The bad side is that we add another loop 2136: which slows down the processing. The difference can be up to 10% 2137: lower mortality. 2138: */ 2139: /* If, at the beginning of the maximization mostly, the 2140: cumulative probability or probability to be dead is 2141: constant (ie = 1) over time d, the difference is equal to 2142: 0. out[s1][3] = savm[s1][3]: probability, being at state 2143: s1 at precedent wave, to be dead a month before current 2144: wave is equal to probability, being at state s1 at 2145: precedent wave, to be dead at mont of the current 2146: wave. Then the observed probability (that this person died) 2147: is null according to current estimated parameter. In fact, 2148: it should be very low but not zero otherwise the log go to 2149: infinity. 2150: */ 2151: /* #ifdef INFINITYORIGINAL */ 2152: /* lli=log(out[s1][s2] - savm[s1][s2]); */ 2153: /* #else */ 2154: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */ 2155: /* lli=log(mytinydouble); */ 2156: /* else */ 2157: /* lli=log(out[s1][s2] - savm[s1][s2]); */ 2158: /* #endif */ 2159: lli=log(out[s1][s2] - savm[s1][s2]); 2160: 2161: } else if (s2==-2) { 2162: for (j=1,survp=0. ; j<=nlstate; j++) 2163: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; 2164: /*survp += out[s1][j]; */ 2165: lli= log(survp); 2166: } 2167: 2168: else if (s2==-4) { 2169: for (j=3,survp=0. ; j<=nlstate; j++) 2170: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; 2171: lli= log(survp); 2172: } 2173: 2174: else if (s2==-5) { 2175: for (j=1,survp=0. ; j<=2; j++) 2176: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; 2177: lli= log(survp); 2178: } 2179: 2180: else{ 2181: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */ 2182: /* 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 */ 2183: } 2184: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/ 2185: /*if(lli ==000.0)*/ 2186: /*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); */ 2187: ipmx +=1; 2188: sw += weight[i]; 2189: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; 2190: /* if (lli < log(mytinydouble)){ */ 2191: /* printf("Close to inf lli = %.10lf < %.10lf i= %d mi= %d, s[%d][i]=%d s1=%d s2=%d\n", lli,log(mytinydouble), i, mi,mw[mi][i], s[mw[mi][i]][i], s1,s2); */ 2192: /* fprintf(ficlog,"Close to inf lli = %.10lf i= %d mi= %d, s[mw[mi][i]][i]=%d\n", lli, i, mi,s[mw[mi][i]][i]); */ 2193: /* } */ 2194: } /* end of wave */ 2195: } /* end of individual */ 2196: } else if(mle==2){ 2197: for (i=1,ipmx=0, sw=0.; i<=imx; i++){ 2198: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; 2199: for(mi=1; mi<= wav[i]-1; mi++){ 2200: for (ii=1;ii<=nlstate+ndeath;ii++) 2201: for (j=1;j<=nlstate+ndeath;j++){ 2202: oldm[ii][j]=(ii==j ? 1.0 : 0.0); 2203: savm[ii][j]=(ii==j ? 1.0 : 0.0); 2204: } 2205: for(d=0; d<=dh[mi][i]; d++){ 2206: newm=savm; 2207: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; 2208: cov[2]=agexact; 2209: if(nagesqr==1) 2210: cov[3]= agexact*agexact; 2211: for (kk=1; kk<=cptcovage;kk++) { 2212: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; 2213: } 2214: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, 2215: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); 2216: savm=oldm; 2217: oldm=newm; 2218: } /* end mult */ 2219: 2220: s1=s[mw[mi][i]][i]; 2221: s2=s[mw[mi+1][i]][i]; 2222: bbh=(double)bh[mi][i]/(double)stepm; 2223: 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 */ 2224: ipmx +=1; 2225: sw += weight[i]; 2226: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; 2227: } /* end of wave */ 2228: } /* end of individual */ 2229: } else if(mle==3){ /* exponential inter-extrapolation */ 2230: for (i=1,ipmx=0, sw=0.; i<=imx; i++){ 2231: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; 2232: for(mi=1; mi<= wav[i]-1; mi++){ 2233: for (ii=1;ii<=nlstate+ndeath;ii++) 2234: for (j=1;j<=nlstate+ndeath;j++){ 2235: oldm[ii][j]=(ii==j ? 1.0 : 0.0); 2236: savm[ii][j]=(ii==j ? 1.0 : 0.0); 2237: } 2238: for(d=0; d<dh[mi][i]; d++){ 2239: newm=savm; 2240: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; 2241: cov[2]=agexact; 2242: if(nagesqr==1) 2243: cov[3]= agexact*agexact; 2244: for (kk=1; kk<=cptcovage;kk++) { 2245: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; 2246: } 2247: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, 2248: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); 2249: savm=oldm; 2250: oldm=newm; 2251: } /* end mult */ 2252: 2253: s1=s[mw[mi][i]][i]; 2254: s2=s[mw[mi+1][i]][i]; 2255: bbh=(double)bh[mi][i]/(double)stepm; 2256: 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 */ 2257: ipmx +=1; 2258: sw += weight[i]; 2259: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; 2260: } /* end of wave */ 2261: } /* end of individual */ 2262: }else if (mle==4){ /* ml=4 no inter-extrapolation */ 2263: for (i=1,ipmx=0, sw=0.; i<=imx; i++){ 2264: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; 2265: for(mi=1; mi<= wav[i]-1; mi++){ 2266: for (ii=1;ii<=nlstate+ndeath;ii++) 2267: for (j=1;j<=nlstate+ndeath;j++){ 2268: oldm[ii][j]=(ii==j ? 1.0 : 0.0); 2269: savm[ii][j]=(ii==j ? 1.0 : 0.0); 2270: } 2271: for(d=0; d<dh[mi][i]; d++){ 2272: newm=savm; 2273: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; 2274: cov[2]=agexact; 2275: if(nagesqr==1) 2276: cov[3]= agexact*agexact; 2277: for (kk=1; kk<=cptcovage;kk++) { 2278: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; 2279: } 2280: 2281: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, 2282: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); 2283: savm=oldm; 2284: oldm=newm; 2285: } /* end mult */ 2286: 2287: s1=s[mw[mi][i]][i]; 2288: s2=s[mw[mi+1][i]][i]; 2289: if( s2 > nlstate){ 2290: lli=log(out[s1][s2] - savm[s1][s2]); 2291: }else{ 2292: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */ 2293: } 2294: ipmx +=1; 2295: sw += weight[i]; 2296: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; 2297: /* 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]); */ 2298: } /* end of wave */ 2299: } /* end of individual */ 2300: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */ 2301: for (i=1,ipmx=0, sw=0.; i<=imx; i++){ 2302: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; 2303: for(mi=1; mi<= wav[i]-1; mi++){ 2304: for (ii=1;ii<=nlstate+ndeath;ii++) 2305: for (j=1;j<=nlstate+ndeath;j++){ 2306: oldm[ii][j]=(ii==j ? 1.0 : 0.0); 2307: savm[ii][j]=(ii==j ? 1.0 : 0.0); 2308: } 2309: for(d=0; d<dh[mi][i]; d++){ 2310: newm=savm; 2311: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; 2312: cov[2]=agexact; 2313: if(nagesqr==1) 2314: cov[3]= agexact*agexact; 2315: for (kk=1; kk<=cptcovage;kk++) { 2316: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; 2317: } 2318: 2319: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, 2320: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); 2321: savm=oldm; 2322: oldm=newm; 2323: } /* end mult */ 2324: 2325: s1=s[mw[mi][i]][i]; 2326: s2=s[mw[mi+1][i]][i]; 2327: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */ 2328: ipmx +=1; 2329: sw += weight[i]; 2330: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; 2331: /*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]);*/ 2332: } /* end of wave */ 2333: } /* end of individual */ 2334: } /* End of if */ 2335: for(k=1,l=0.; k<=nlstate; k++) l += ll[k]; 2336: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */ 2337: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */ 2338: return -l; 2339: } 2340: 2341: /*************** log-likelihood *************/ 2342: double funcone( double *x) 2343: { 2344: /* Same as likeli but slower because of a lot of printf and if */ 2345: int i, ii, j, k, mi, d, kk; 2346: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1]; 2347: double **out; 2348: double lli; /* Individual log likelihood */ 2349: double llt; 2350: int s1, s2; 2351: double bbh, survp; 2352: double agexact; 2353: /*extern weight */ 2354: /* We are differentiating ll according to initial status */ 2355: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/ 2356: /*for(i=1;i<imx;i++) 2357: printf(" %d\n",s[4][i]); 2358: */ 2359: cov[1]=1.; 2360: 2361: for(k=1; k<=nlstate; k++) ll[k]=0.; 2362: 2363: for (i=1,ipmx=0, sw=0.; i<=imx; i++){ 2364: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; 2365: for(mi=1; mi<= wav[i]-1; mi++){ 2366: for (ii=1;ii<=nlstate+ndeath;ii++) 2367: for (j=1;j<=nlstate+ndeath;j++){ 2368: oldm[ii][j]=(ii==j ? 1.0 : 0.0); 2369: savm[ii][j]=(ii==j ? 1.0 : 0.0); 2370: } 2371: for(d=0; d<dh[mi][i]; d++){ 2372: newm=savm; 2373: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; 2374: cov[2]=agexact; 2375: if(nagesqr==1) 2376: cov[3]= agexact*agexact; 2377: for (kk=1; kk<=cptcovage;kk++) { 2378: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; 2379: } 2380: 2381: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */ 2382: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, 2383: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); 2384: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */ 2385: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */ 2386: savm=oldm; 2387: oldm=newm; 2388: } /* end mult */ 2389: 2390: s1=s[mw[mi][i]][i]; 2391: s2=s[mw[mi+1][i]][i]; 2392: bbh=(double)bh[mi][i]/(double)stepm; 2393: /* bias is positive if real duration 2394: * is higher than the multiple of stepm and negative otherwise. 2395: */ 2396: if( s2 > nlstate && (mle <5) ){ /* Jackson */ 2397: lli=log(out[s1][s2] - savm[s1][s2]); 2398: } else if (s2==-2) { 2399: for (j=1,survp=0. ; j<=nlstate; j++) 2400: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; 2401: lli= log(survp); 2402: }else if (mle==1){ 2403: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */ 2404: } else if(mle==2){ 2405: 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 */ 2406: } else if(mle==3){ /* exponential inter-extrapolation */ 2407: 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 */ 2408: } else if (mle==4){ /* mle=4 no inter-extrapolation */ 2409: lli=log(out[s1][s2]); /* Original formula */ 2410: } else{ /* mle=0 back to 1 */ 2411: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */ 2412: /*lli=log(out[s1][s2]); */ /* Original formula */ 2413: } /* End of if */ 2414: ipmx +=1; 2415: sw += weight[i]; 2416: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; 2417: /*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]); */ 2418: if(globpr){ 2419: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\ 2420: %11.6f %11.6f %11.6f ", \ 2421: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i], 2422: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]); 2423: for(k=1,llt=0.,l=0.; k<=nlstate; k++){ 2424: llt +=ll[k]*gipmx/gsw; 2425: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw); 2426: } 2427: fprintf(ficresilk," %10.6f\n", -llt); 2428: } 2429: } /* end of wave */ 2430: } /* end of individual */ 2431: for(k=1,l=0.; k<=nlstate; k++) l += ll[k]; 2432: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */ 2433: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */ 2434: if(globpr==0){ /* First time we count the contributions and weights */ 2435: gipmx=ipmx; 2436: gsw=sw; 2437: } 2438: return -l; 2439: } 2440: 2441: 2442: /*************** function likelione ***********/ 2443: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double [])) 2444: { 2445: /* This routine should help understanding what is done with 2446: the selection of individuals/waves and 2447: to check the exact contribution to the likelihood. 2448: Plotting could be done. 2449: */ 2450: int k; 2451: 2452: if(*globpri !=0){ /* Just counts and sums, no printings */ 2453: strcpy(fileresilk,"ilk"); 2454: strcat(fileresilk,fileres); 2455: if((ficresilk=fopen(fileresilk,"w"))==NULL) { 2456: printf("Problem with resultfile: %s\n", fileresilk); 2457: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk); 2458: } 2459: 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"); 2460: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav "); 2461: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */ 2462: for(k=1; k<=nlstate; k++) 2463: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k); 2464: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n"); 2465: } 2466: 2467: *fretone=(*funcone)(p); 2468: if(*globpri !=0){ 2469: fclose(ficresilk); 2470: fprintf(fichtm,"\n File of contributions to the likelihood: <a href=\"%s\">%s</a> \n",subdirf(fileresilk),subdirf(fileresilk)); 2471: fflush(fichtm); 2472: } 2473: return; 2474: } 2475: 2476: 2477: /*********** Maximum Likelihood Estimation ***************/ 2478: 2479: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double [])) 2480: { 2481: int i,j, iter=0; 2482: double **xi; 2483: double fret; 2484: double fretone; /* Only one call to likelihood */ 2485: /* char filerespow[FILENAMELENGTH];*/ 2486: 2487: #ifdef NLOPT 2488: int creturn; 2489: nlopt_opt opt; 2490: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */ 2491: double *lb; 2492: double minf; /* the minimum objective value, upon return */ 2493: double * p1; /* Shifted parameters from 0 instead of 1 */ 2494: myfunc_data dinst, *d = &dinst; 2495: #endif 2496: 2497: 2498: xi=matrix(1,npar,1,npar); 2499: for (i=1;i<=npar;i++) 2500: for (j=1;j<=npar;j++) 2501: xi[i][j]=(i==j ? 1.0 : 0.0); 2502: printf("Powell\n"); fprintf(ficlog,"Powell\n"); 2503: strcpy(filerespow,"pow"); 2504: strcat(filerespow,fileres); 2505: if((ficrespow=fopen(filerespow,"w"))==NULL) { 2506: printf("Problem with resultfile: %s\n", filerespow); 2507: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow); 2508: } 2509: fprintf(ficrespow,"# Powell\n# iter -2*LL"); 2510: for (i=1;i<=nlstate;i++) 2511: for(j=1;j<=nlstate+ndeath;j++) 2512: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j); 2513: fprintf(ficrespow,"\n"); 2514: #ifdef POWELL 2515: powell(p,xi,npar,ftol,&iter,&fret,func); 2516: #endif 2517: 2518: #ifdef NLOPT 2519: #ifdef NEWUOA 2520: opt = nlopt_create(NLOPT_LN_NEWUOA,npar); 2521: #else 2522: opt = nlopt_create(NLOPT_LN_BOBYQA,npar); 2523: #endif 2524: lb=vector(0,npar-1); 2525: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL; 2526: nlopt_set_lower_bounds(opt, lb); 2527: nlopt_set_initial_step1(opt, 0.1); 2528: 2529: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */ 2530: d->function = func; 2531: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d)); 2532: nlopt_set_min_objective(opt, myfunc, d); 2533: nlopt_set_xtol_rel(opt, ftol); 2534: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) { 2535: printf("nlopt failed! %d\n",creturn); 2536: } 2537: else { 2538: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT); 2539: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf); 2540: iter=1; /* not equal */ 2541: } 2542: nlopt_destroy(opt); 2543: #endif 2544: free_matrix(xi,1,npar,1,npar); 2545: fclose(ficrespow); 2546: printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p)); 2547: fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p)); 2548: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p)); 2549: 2550: } 2551: 2552: /**** Computes Hessian and covariance matrix ***/ 2553: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double [])) 2554: { 2555: double **a,**y,*x,pd; 2556: double **hess; 2557: int i, j; 2558: int *indx; 2559: 2560: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar); 2561: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar); 2562: void lubksb(double **a, int npar, int *indx, double b[]) ; 2563: void ludcmp(double **a, int npar, int *indx, double *d) ; 2564: double gompertz(double p[]); 2565: hess=matrix(1,npar,1,npar); 2566: 2567: printf("\nCalculation of the hessian matrix. Wait...\n"); 2568: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n"); 2569: for (i=1;i<=npar;i++){ 2570: printf("%d",i);fflush(stdout); 2571: fprintf(ficlog,"%d",i);fflush(ficlog); 2572: 2573: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar); 2574: 2575: /* printf(" %f ",p[i]); 2576: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/ 2577: } 2578: 2579: for (i=1;i<=npar;i++) { 2580: for (j=1;j<=npar;j++) { 2581: if (j>i) { 2582: printf(".%d%d",i,j);fflush(stdout); 2583: fprintf(ficlog,".%d%d",i,j);fflush(ficlog); 2584: hess[i][j]=hessij(p,delti,i,j,func,npar); 2585: 2586: hess[j][i]=hess[i][j]; 2587: /*printf(" %lf ",hess[i][j]);*/ 2588: } 2589: } 2590: } 2591: printf("\n"); 2592: fprintf(ficlog,"\n"); 2593: 2594: printf("\nInverting the hessian to get the covariance matrix. Wait...\n"); 2595: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n"); 2596: 2597: a=matrix(1,npar,1,npar); 2598: y=matrix(1,npar,1,npar); 2599: x=vector(1,npar); 2600: indx=ivector(1,npar); 2601: for (i=1;i<=npar;i++) 2602: for (j=1;j<=npar;j++) a[i][j]=hess[i][j]; 2603: ludcmp(a,npar,indx,&pd); 2604: 2605: for (j=1;j<=npar;j++) { 2606: for (i=1;i<=npar;i++) x[i]=0; 2607: x[j]=1; 2608: lubksb(a,npar,indx,x); 2609: for (i=1;i<=npar;i++){ 2610: matcov[i][j]=x[i]; 2611: } 2612: } 2613: 2614: printf("\n#Hessian matrix#\n"); 2615: fprintf(ficlog,"\n#Hessian matrix#\n"); 2616: for (i=1;i<=npar;i++) { 2617: for (j=1;j<=npar;j++) { 2618: printf("%.3e ",hess[i][j]); 2619: fprintf(ficlog,"%.3e ",hess[i][j]); 2620: } 2621: printf("\n"); 2622: fprintf(ficlog,"\n"); 2623: } 2624: 2625: /* Recompute Inverse */ 2626: for (i=1;i<=npar;i++) 2627: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; 2628: ludcmp(a,npar,indx,&pd); 2629: 2630: /* printf("\n#Hessian matrix recomputed#\n"); 2631: 2632: for (j=1;j<=npar;j++) { 2633: for (i=1;i<=npar;i++) x[i]=0; 2634: x[j]=1; 2635: lubksb(a,npar,indx,x); 2636: for (i=1;i<=npar;i++){ 2637: y[i][j]=x[i]; 2638: printf("%.3e ",y[i][j]); 2639: fprintf(ficlog,"%.3e ",y[i][j]); 2640: } 2641: printf("\n"); 2642: fprintf(ficlog,"\n"); 2643: } 2644: */ 2645: 2646: free_matrix(a,1,npar,1,npar); 2647: free_matrix(y,1,npar,1,npar); 2648: free_vector(x,1,npar); 2649: free_ivector(indx,1,npar); 2650: free_matrix(hess,1,npar,1,npar); 2651: 2652: 2653: } 2654: 2655: /*************** hessian matrix ****************/ 2656: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar) 2657: { 2658: int i; 2659: int l=1, lmax=20; 2660: double k1,k2; 2661: double p2[MAXPARM+1]; /* identical to x */ 2662: double res; 2663: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; 2664: double fx; 2665: int k=0,kmax=10; 2666: double l1; 2667: 2668: fx=func(x); 2669: for (i=1;i<=npar;i++) p2[i]=x[i]; 2670: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */ 2671: l1=pow(10,l); 2672: delts=delt; 2673: for(k=1 ; k <kmax; k=k+1){ 2674: delt = delta*(l1*k); 2675: p2[theta]=x[theta] +delt; 2676: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */ 2677: p2[theta]=x[theta]-delt; 2678: k2=func(p2)-fx; 2679: /*res= (k1-2.0*fx+k2)/delt/delt; */ 2680: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */ 2681: 2682: #ifdef DEBUGHESS 2683: 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); 2684: 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); 2685: #endif 2686: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */ 2687: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){ 2688: k=kmax; 2689: } 2690: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */ 2691: k=kmax; l=lmax*10; 2692: } 2693: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 2694: delts=delt; 2695: } 2696: } 2697: } 2698: delti[theta]=delts; 2699: return res; 2700: 2701: } 2702: 2703: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) 2704: { 2705: int i; 2706: int l=1, lmax=20; 2707: double k1,k2,k3,k4,res,fx; 2708: double p2[MAXPARM+1]; 2709: int k; 2710: 2711: fx=func(x); 2712: for (k=1; k<=2; k++) { 2713: for (i=1;i<=npar;i++) p2[i]=x[i]; 2714: p2[thetai]=x[thetai]+delti[thetai]/k; 2715: p2[thetaj]=x[thetaj]+delti[thetaj]/k; 2716: k1=func(p2)-fx; 2717: 2718: p2[thetai]=x[thetai]+delti[thetai]/k; 2719: p2[thetaj]=x[thetaj]-delti[thetaj]/k; 2720: k2=func(p2)-fx; 2721: 2722: p2[thetai]=x[thetai]-delti[thetai]/k; 2723: p2[thetaj]=x[thetaj]+delti[thetaj]/k; 2724: k3=func(p2)-fx; 2725: 2726: p2[thetai]=x[thetai]-delti[thetai]/k; 2727: p2[thetaj]=x[thetaj]-delti[thetaj]/k; 2728: k4=func(p2)-fx; 2729: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */ 2730: #ifdef DEBUG 2731: 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); 2732: 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); 2733: #endif 2734: } 2735: return res; 2736: } 2737: 2738: /************** Inverse of matrix **************/ 2739: void ludcmp(double **a, int n, int *indx, double *d) 2740: { 2741: int i,imax,j,k; 2742: double big,dum,sum,temp; 2743: double *vv; 2744: 2745: vv=vector(1,n); 2746: *d=1.0; 2747: for (i=1;i<=n;i++) { 2748: big=0.0; 2749: for (j=1;j<=n;j++) 2750: if ((temp=fabs(a[i][j])) > big) big=temp; 2751: if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 2752: vv[i]=1.0/big; 2753: } 2754: for (j=1;j<=n;j++) { 2755: for (i=1;i<j;i++) { 2756: sum=a[i][j]; 2757: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 2758: a[i][j]=sum; 2759: } 2760: big=0.0; 2761: for (i=j;i<=n;i++) { 2762: sum=a[i][j]; 2763: for (k=1;k<j;k++) 2764: sum -= a[i][k]*a[k][j]; 2765: a[i][j]=sum; 2766: if ( (dum=vv[i]*fabs(sum)) >= big) { 2767: big=dum; 2768: imax=i; 2769: } 2770: } 2771: if (j != imax) { 2772: for (k=1;k<=n;k++) { 2773: dum=a[imax][k]; 2774: a[imax][k]=a[j][k]; 2775: a[j][k]=dum; 2776: } 2777: *d = -(*d); 2778: vv[imax]=vv[j]; 2779: } 2780: indx[j]=imax; 2781: if (a[j][j] == 0.0) a[j][j]=TINY; 2782: if (j != n) { 2783: dum=1.0/(a[j][j]); 2784: for (i=j+1;i<=n;i++) a[i][j] *= dum; 2785: } 2786: } 2787: free_vector(vv,1,n); /* Doesn't work */ 2788: ; 2789: } 2790: 2791: void lubksb(double **a, int n, int *indx, double b[]) 2792: { 2793: int i,ii=0,ip,j; 2794: double sum; 2795: 2796: for (i=1;i<=n;i++) { 2797: ip=indx[i]; 2798: sum=b[ip]; 2799: b[ip]=b[i]; 2800: if (ii) 2801: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 2802: else if (sum) ii=i; 2803: b[i]=sum; 2804: } 2805: for (i=n;i>=1;i--) { 2806: sum=b[i]; 2807: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 2808: b[i]=sum/a[i][i]; 2809: } 2810: } 2811: 2812: void pstamp(FILE *fichier) 2813: { 2814: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart); 2815: } 2816: 2817: /************ Frequencies ********************/ 2818: 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[]) 2819: { /* Some frequencies */ 2820: 2821: int i, m, jk, j1, bool, z1,j; 2822: int first; 2823: double ***freq; /* Frequencies */ 2824: double *pp, **prop; 2825: double pos,posprop, k2, dateintsum=0,k2cpt=0; 2826: char fileresp[FILENAMELENGTH]; 2827: 2828: pp=vector(1,nlstate); 2829: prop=matrix(1,nlstate,iagemin,iagemax+3); 2830: strcpy(fileresp,"p"); 2831: strcat(fileresp,fileres); 2832: if((ficresp=fopen(fileresp,"w"))==NULL) { 2833: printf("Problem with prevalence resultfile: %s\n", fileresp); 2834: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp); 2835: exit(0); 2836: } 2837: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3); 2838: j1=0; 2839: 2840: j=cptcoveff; 2841: if (cptcovn<1) {j=1;ncodemax[1]=1;} 2842: 2843: first=1; 2844: 2845: /* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */ 2846: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */ 2847: /* j1++; */ 2848: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){ 2849: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]); 2850: scanf("%d", i);*/ 2851: for (i=-5; i<=nlstate+ndeath; i++) 2852: for (jk=-5; jk<=nlstate+ndeath; jk++) 2853: for(m=iagemin; m <= iagemax+3; m++) 2854: freq[i][jk][m]=0; 2855: 2856: for (i=1; i<=nlstate; i++) 2857: for(m=iagemin; m <= iagemax+3; m++) 2858: prop[i][m]=0; 2859: 2860: dateintsum=0; 2861: k2cpt=0; 2862: for (i=1; i<=imx; i++) { 2863: bool=1; 2864: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */ 2865: for (z1=1; z1<=cptcoveff; z1++) 2866: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){ 2867: /* Tests if the value of each of the covariates of i is equal to filter j1 */ 2868: bool=0; 2869: /* 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", 2870: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1], 2871: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/ 2872: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/ 2873: } 2874: } 2875: 2876: if (bool==1){ 2877: for(m=firstpass; m<=lastpass; m++){ 2878: k2=anint[m][i]+(mint[m][i]/12.); 2879: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/ 2880: if(agev[m][i]==0) agev[m][i]=iagemax+1; 2881: if(agev[m][i]==1) agev[m][i]=iagemax+2; 2882: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i]; 2883: if (m<lastpass) { 2884: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i]; 2885: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i]; 2886: } 2887: 2888: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) { 2889: dateintsum=dateintsum+k2; 2890: k2cpt++; 2891: } 2892: /*}*/ 2893: } 2894: } 2895: } /* end i */ 2896: 2897: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/ 2898: pstamp(ficresp); 2899: if (cptcovn>0) { 2900: fprintf(ficresp, "\n#********** Variable "); 2901: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); 2902: fprintf(ficresp, "**********\n#"); 2903: fprintf(ficlog, "\n#********** Variable "); 2904: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); 2905: fprintf(ficlog, "**********\n#"); 2906: } 2907: for(i=1; i<=nlstate;i++) 2908: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i); 2909: fprintf(ficresp, "\n"); 2910: 2911: for(i=iagemin; i <= iagemax+3; i++){ 2912: if(i==iagemax+3){ 2913: fprintf(ficlog,"Total"); 2914: }else{ 2915: if(first==1){ 2916: first=0; 2917: printf("See log file for details...\n"); 2918: } 2919: fprintf(ficlog,"Age %d", i); 2920: } 2921: for(jk=1; jk <=nlstate ; jk++){ 2922: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++) 2923: pp[jk] += freq[jk][m][i]; 2924: } 2925: for(jk=1; jk <=nlstate ; jk++){ 2926: for(m=-1, pos=0; m <=0 ; m++) 2927: pos += freq[jk][m][i]; 2928: if(pp[jk]>=1.e-10){ 2929: if(first==1){ 2930: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]); 2931: } 2932: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]); 2933: }else{ 2934: if(first==1) 2935: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk); 2936: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk); 2937: } 2938: } 2939: 2940: for(jk=1; jk <=nlstate ; jk++){ 2941: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++) 2942: pp[jk] += freq[jk][m][i]; 2943: } 2944: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){ 2945: pos += pp[jk]; 2946: posprop += prop[jk][i]; 2947: } 2948: for(jk=1; jk <=nlstate ; jk++){ 2949: if(pos>=1.e-5){ 2950: if(first==1) 2951: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos); 2952: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos); 2953: }else{ 2954: if(first==1) 2955: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk); 2956: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk); 2957: } 2958: if( i <= iagemax){ 2959: if(pos>=1.e-5){ 2960: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop); 2961: /*probs[i][jk][j1]= pp[jk]/pos;*/ 2962: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/ 2963: } 2964: else 2965: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop); 2966: } 2967: } 2968: 2969: for(jk=-1; jk <=nlstate+ndeath; jk++) 2970: for(m=-1; m <=nlstate+ndeath; m++) 2971: if(freq[jk][m][i] !=0 ) { 2972: if(first==1) 2973: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]); 2974: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]); 2975: } 2976: if(i <= iagemax) 2977: fprintf(ficresp,"\n"); 2978: if(first==1) 2979: printf("Others in log...\n"); 2980: fprintf(ficlog,"\n"); 2981: } 2982: /*}*/ 2983: } 2984: dateintmean=dateintsum/k2cpt; 2985: 2986: fclose(ficresp); 2987: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3); 2988: free_vector(pp,1,nlstate); 2989: free_matrix(prop,1,nlstate,iagemin, iagemax+3); 2990: /* End of Freq */ 2991: } 2992: 2993: /************ Prevalence ********************/ 2994: 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) 2995: { 2996: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people 2997: in each health status at the date of interview (if between dateprev1 and dateprev2). 2998: We still use firstpass and lastpass as another selection. 2999: */ 3000: 3001: int i, m, jk, j1, bool, z1,j; 3002: 3003: double **prop; 3004: double posprop; 3005: double y2; /* in fractional years */ 3006: int iagemin, iagemax; 3007: int first; /** to stop verbosity which is redirected to log file */ 3008: 3009: iagemin= (int) agemin; 3010: iagemax= (int) agemax; 3011: /*pp=vector(1,nlstate);*/ 3012: prop=matrix(1,nlstate,iagemin,iagemax+3); 3013: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/ 3014: j1=0; 3015: 3016: /*j=cptcoveff;*/ 3017: if (cptcovn<1) {j=1;ncodemax[1]=1;} 3018: 3019: first=1; 3020: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ 3021: /*for(i1=1; i1<=ncodemax[k1];i1++){ 3022: j1++;*/ 3023: 3024: for (i=1; i<=nlstate; i++) 3025: for(m=iagemin; m <= iagemax+3; m++) 3026: prop[i][m]=0.0; 3027: 3028: for (i=1; i<=imx; i++) { /* Each individual */ 3029: bool=1; 3030: if (cptcovn>0) { 3031: for (z1=1; z1<=cptcoveff; z1++) 3032: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 3033: bool=0; 3034: } 3035: if (bool==1) { 3036: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/ 3037: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */ 3038: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */ 3039: if(agev[m][i]==0) agev[m][i]=iagemax+1; 3040: if(agev[m][i]==1) agev[m][i]=iagemax+2; 3041: 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); 3042: if (s[m][i]>0 && s[m][i]<=nlstate) { 3043: /*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]]);*/ 3044: prop[s[m][i]][(int)agev[m][i]] += weight[i]; 3045: prop[s[m][i]][iagemax+3] += weight[i]; 3046: } 3047: } 3048: } /* end selection of waves */ 3049: } 3050: } 3051: for(i=iagemin; i <= iagemax+3; i++){ 3052: for(jk=1,posprop=0; jk <=nlstate ; jk++) { 3053: posprop += prop[jk][i]; 3054: } 3055: 3056: for(jk=1; jk <=nlstate ; jk++){ 3057: if( i <= iagemax){ 3058: if(posprop>=1.e-5){ 3059: probs[i][jk][j1]= prop[jk][i]/posprop; 3060: } else{ 3061: if(first==1){ 3062: first=0; 3063: 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]); 3064: } 3065: } 3066: } 3067: }/* end jk */ 3068: }/* end i */ 3069: /*} *//* end i1 */ 3070: } /* end j1 */ 3071: 3072: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/ 3073: /*free_vector(pp,1,nlstate);*/ 3074: free_matrix(prop,1,nlstate, iagemin,iagemax+3); 3075: } /* End of prevalence */ 3076: 3077: /************* Waves Concatenation ***************/ 3078: 3079: 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) 3080: { 3081: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i. 3082: Death is a valid wave (if date is known). 3083: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i 3084: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i] 3085: and mw[mi+1][i]. dh depends on stepm. 3086: */ 3087: 3088: int i, mi, m; 3089: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1; 3090: double sum=0., jmean=0.;*/ 3091: int first; 3092: int j, k=0,jk, ju, jl; 3093: double sum=0.; 3094: first=0; 3095: jmin=100000; 3096: jmax=-1; 3097: jmean=0.; 3098: for(i=1; i<=imx; i++){ 3099: mi=0; 3100: m=firstpass; 3101: while(s[m][i] <= nlstate){ 3102: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5) 3103: mw[++mi][i]=m; 3104: if(m >=lastpass) 3105: break; 3106: else 3107: m++; 3108: }/* end while */ 3109: if (s[m][i] > nlstate){ 3110: mi++; /* Death is another wave */ 3111: /* if(mi==0) never been interviewed correctly before death */ 3112: /* Only death is a correct wave */ 3113: mw[mi][i]=m; 3114: } 3115: 3116: wav[i]=mi; 3117: if(mi==0){ 3118: nbwarn++; 3119: if(first==0){ 3120: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i); 3121: first=1; 3122: } 3123: if(first==1){ 3124: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i); 3125: } 3126: } /* end mi==0 */ 3127: } /* End individuals */ 3128: 3129: for(i=1; i<=imx; i++){ 3130: for(mi=1; mi<wav[i];mi++){ 3131: if (stepm <=0) 3132: dh[mi][i]=1; 3133: else{ 3134: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */ 3135: if (agedc[i] < 2*AGESUP) { 3136: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 3137: if(j==0) j=1; /* Survives at least one month after exam */ 3138: else if(j<0){ 3139: nberr++; 3140: 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]); 3141: j=1; /* Temporary Dangerous patch */ 3142: 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); 3143: 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]); 3144: 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); 3145: } 3146: k=k+1; 3147: if (j >= jmax){ 3148: jmax=j; 3149: ijmax=i; 3150: } 3151: if (j <= jmin){ 3152: jmin=j; 3153: ijmin=i; 3154: } 3155: sum=sum+j; 3156: /*if (j<0) printf("j=%d num=%d \n",j,i);*/ 3157: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/ 3158: } 3159: } 3160: else{ 3161: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12)); 3162: /* 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]); */ 3163: 3164: k=k+1; 3165: if (j >= jmax) { 3166: jmax=j; 3167: ijmax=i; 3168: } 3169: else if (j <= jmin){ 3170: jmin=j; 3171: ijmin=i; 3172: } 3173: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */ 3174: /*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]);*/ 3175: if(j<0){ 3176: nberr++; 3177: 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]); 3178: 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]); 3179: } 3180: sum=sum+j; 3181: } 3182: jk= j/stepm; 3183: jl= j -jk*stepm; 3184: ju= j -(jk+1)*stepm; 3185: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */ 3186: if(jl==0){ 3187: dh[mi][i]=jk; 3188: bh[mi][i]=0; 3189: }else{ /* We want a negative bias in order to only have interpolation ie 3190: * to avoid the price of an extra matrix product in likelihood */ 3191: dh[mi][i]=jk+1; 3192: bh[mi][i]=ju; 3193: } 3194: }else{ 3195: if(jl <= -ju){ 3196: dh[mi][i]=jk; 3197: bh[mi][i]=jl; /* bias is positive if real duration 3198: * is higher than the multiple of stepm and negative otherwise. 3199: */ 3200: } 3201: else{ 3202: dh[mi][i]=jk+1; 3203: bh[mi][i]=ju; 3204: } 3205: if(dh[mi][i]==0){ 3206: dh[mi][i]=1; /* At least one step */ 3207: bh[mi][i]=ju; /* At least one step */ 3208: /* 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);*/ 3209: } 3210: } /* end if mle */ 3211: } 3212: } /* end wave */ 3213: } 3214: jmean=sum/k; 3215: 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); 3216: 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); 3217: } 3218: 3219: /*********** Tricode ****************************/ 3220: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum) 3221: { 3222: /**< Uses cptcovn+2*cptcovprod as the number of covariates */ 3223: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 3224: * Boring subroutine which should only output nbcode[Tvar[j]][k] 3225: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2) 3226: * nbcode[Tvar[j]][1]= 3227: */ 3228: 3229: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX; 3230: int modmaxcovj=0; /* Modality max of covariates j */ 3231: int cptcode=0; /* Modality max of covariates j */ 3232: int modmincovj=0; /* Modality min of covariates j */ 3233: 3234: 3235: cptcoveff=0; 3236: 3237: for (k=-1; k < maxncov; k++) Ndum[k]=0; 3238: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */ 3239: 3240: /* Loop on covariates without age and products */ 3241: for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */ 3242: for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the 3243: modality of this covariate Vj*/ 3244: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i 3245: * If product of Vn*Vm, still boolean *: 3246: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables 3247: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */ 3248: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the 3249: modality of the nth covariate of individual i. */ 3250: if (ij > modmaxcovj) 3251: modmaxcovj=ij; 3252: else if (ij < modmincovj) 3253: modmincovj=ij; 3254: if ((ij < -1) && (ij > NCOVMAX)){ 3255: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX ); 3256: exit(1); 3257: }else 3258: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/ 3259: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */ 3260: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/ 3261: /* getting the maximum value of the modality of the covariate 3262: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and 3263: female is 1, then modmaxcovj=1.*/ 3264: } /* end for loop on individuals */ 3265: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj); 3266: cptcode=modmaxcovj; 3267: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */ 3268: /*for (i=0; i<=cptcode; i++) {*/ 3269: for (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */ 3270: printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], i, Ndum[i]); 3271: if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */ 3272: ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */ 3273: } 3274: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for 3275: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */ 3276: } /* Ndum[-1] number of undefined modalities */ 3277: 3278: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */ 3279: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. 3280: If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; 3281: modmincovj=3; modmaxcovj = 7; 3282: There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3; 3283: which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10; 3284: defining two dummy variables: variables V1_1 and V1_2. 3285: nbcode[Tvar[j]][ij]=k; 3286: nbcode[Tvar[j]][1]=0; 3287: nbcode[Tvar[j]][2]=1; 3288: nbcode[Tvar[j]][3]=2; 3289: */ 3290: ij=1; /* ij is similar to i but can jumps over null modalities */ 3291: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */ 3292: for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */ 3293: /*recode from 0 */ 3294: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */ 3295: nbcode[Tvar[j]][ij]=k; /* stores the modality k in an array nbcode. 3296: k is a modality. If we have model=V1+V1*sex 3297: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */ 3298: ij++; 3299: } 3300: if (ij > ncodemax[j]) break; 3301: } /* end of loop on */ 3302: } /* end of loop on modality */ 3303: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/ 3304: 3305: for (k=-1; k< maxncov; k++) Ndum[k]=0; 3306: 3307: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */ 3308: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 3309: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 3310: Ndum[ij]++; /* Might be supersed V1 + V1*age */ 3311: } 3312: 3313: ij=1; 3314: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */ 3315: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/ 3316: if((Ndum[i]!=0) && (i<=ncovcol)){ 3317: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/ 3318: Tvaraff[ij]=i; /*For printing (unclear) */ 3319: ij++; 3320: }else 3321: Tvaraff[ij]=0; 3322: } 3323: ij--; 3324: cptcoveff=ij; /*Number of total covariates*/ 3325: 3326: } 3327: 3328: 3329: /*********** Health Expectancies ****************/ 3330: 3331: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] ) 3332: 3333: { 3334: /* Health expectancies, no variances */ 3335: int i, j, nhstepm, hstepm, h, nstepm; 3336: int nhstepma, nstepma; /* Decreasing with age */ 3337: double age, agelim, hf; 3338: double ***p3mat; 3339: double eip; 3340: 3341: pstamp(ficreseij); 3342: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n"); 3343: fprintf(ficreseij,"# Age"); 3344: for(i=1; i<=nlstate;i++){ 3345: for(j=1; j<=nlstate;j++){ 3346: fprintf(ficreseij," e%1d%1d ",i,j); 3347: } 3348: fprintf(ficreseij," e%1d. ",i); 3349: } 3350: fprintf(ficreseij,"\n"); 3351: 3352: 3353: if(estepm < stepm){ 3354: printf ("Problem %d lower than %d\n",estepm, stepm); 3355: } 3356: else hstepm=estepm; 3357: /* We compute the life expectancy from trapezoids spaced every estepm months 3358: * This is mainly to measure the difference between two models: for example 3359: * if stepm=24 months pijx are given only every 2 years and by summing them 3360: * we are calculating an estimate of the Life Expectancy assuming a linear 3361: * progression in between and thus overestimating or underestimating according 3362: * to the curvature of the survival function. If, for the same date, we 3363: * estimate the model with stepm=1 month, we can keep estepm to 24 months 3364: * to compare the new estimate of Life expectancy with the same linear 3365: * hypothesis. A more precise result, taking into account a more precise 3366: * curvature will be obtained if estepm is as small as stepm. */ 3367: 3368: /* For example we decided to compute the life expectancy with the smallest unit */ 3369: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 3370: nhstepm is the number of hstepm from age to agelim 3371: nstepm is the number of stepm from age to agelin. 3372: Look at hpijx to understand the reason of that which relies in memory size 3373: and note for a fixed period like estepm months */ 3374: /* We decided (b) to get a life expectancy respecting the most precise curvature of the 3375: survival function given by stepm (the optimization length). Unfortunately it 3376: means that if the survival funtion is printed only each two years of age and if 3377: you sum them up and add 1 year (area under the trapezoids) you won't get the same 3378: results. So we changed our mind and took the option of the best precision. 3379: */ 3380: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 3381: 3382: agelim=AGESUP; 3383: /* If stepm=6 months */ 3384: /* Computed by stepm unit matrices, product of hstepm matrices, stored 3385: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */ 3386: 3387: /* nhstepm age range expressed in number of stepm */ 3388: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */ 3389: /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 3390: /* if (stepm >= YEARM) hstepm=1;*/ 3391: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */ 3392: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 3393: 3394: for (age=bage; age<=fage; age ++){ 3395: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */ 3396: /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 3397: /* if (stepm >= YEARM) hstepm=1;*/ 3398: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */ 3399: 3400: /* If stepm=6 months */ 3401: /* Computed by stepm unit matrices, product of hstepma matrices, stored 3402: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */ 3403: 3404: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij); 3405: 3406: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */ 3407: 3408: printf("%d|",(int)age);fflush(stdout); 3409: fprintf(ficlog,"%d|",(int)age);fflush(ficlog); 3410: 3411: /* Computing expectancies */ 3412: for(i=1; i<=nlstate;i++) 3413: for(j=1; j<=nlstate;j++) 3414: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){ 3415: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf; 3416: 3417: /* 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]);*/ 3418: 3419: } 3420: 3421: fprintf(ficreseij,"%3.0f",age ); 3422: for(i=1; i<=nlstate;i++){ 3423: eip=0; 3424: for(j=1; j<=nlstate;j++){ 3425: eip +=eij[i][j][(int)age]; 3426: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] ); 3427: } 3428: fprintf(ficreseij,"%9.4f", eip ); 3429: } 3430: fprintf(ficreseij,"\n"); 3431: 3432: } 3433: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 3434: printf("\n"); 3435: fprintf(ficlog,"\n"); 3436: 3437: } 3438: 3439: 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[] ) 3440: 3441: { 3442: /* Covariances of health expectancies eij and of total life expectancies according 3443: to initial status i, ei. . 3444: */ 3445: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji; 3446: int nhstepma, nstepma; /* Decreasing with age */ 3447: double age, agelim, hf; 3448: double ***p3matp, ***p3matm, ***varhe; 3449: double **dnewm,**doldm; 3450: double *xp, *xm; 3451: double **gp, **gm; 3452: double ***gradg, ***trgradg; 3453: int theta; 3454: 3455: double eip, vip; 3456: 3457: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage); 3458: xp=vector(1,npar); 3459: xm=vector(1,npar); 3460: dnewm=matrix(1,nlstate*nlstate,1,npar); 3461: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate); 3462: 3463: pstamp(ficresstdeij); 3464: fprintf(ficresstdeij,"# Health expectancies with standard errors\n"); 3465: fprintf(ficresstdeij,"# Age"); 3466: for(i=1; i<=nlstate;i++){ 3467: for(j=1; j<=nlstate;j++) 3468: fprintf(ficresstdeij," e%1d%1d (SE)",i,j); 3469: fprintf(ficresstdeij," e%1d. ",i); 3470: } 3471: fprintf(ficresstdeij,"\n"); 3472: 3473: pstamp(ficrescveij); 3474: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n"); 3475: fprintf(ficrescveij,"# Age"); 3476: for(i=1; i<=nlstate;i++) 3477: for(j=1; j<=nlstate;j++){ 3478: cptj= (j-1)*nlstate+i; 3479: for(i2=1; i2<=nlstate;i2++) 3480: for(j2=1; j2<=nlstate;j2++){ 3481: cptj2= (j2-1)*nlstate+i2; 3482: if(cptj2 <= cptj) 3483: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2); 3484: } 3485: } 3486: fprintf(ficrescveij,"\n"); 3487: 3488: if(estepm < stepm){ 3489: printf ("Problem %d lower than %d\n",estepm, stepm); 3490: } 3491: else hstepm=estepm; 3492: /* We compute the life expectancy from trapezoids spaced every estepm months 3493: * This is mainly to measure the difference between two models: for example 3494: * if stepm=24 months pijx are given only every 2 years and by summing them 3495: * we are calculating an estimate of the Life Expectancy assuming a linear 3496: * progression in between and thus overestimating or underestimating according 3497: * to the curvature of the survival function. If, for the same date, we 3498: * estimate the model with stepm=1 month, we can keep estepm to 24 months 3499: * to compare the new estimate of Life expectancy with the same linear 3500: * hypothesis. A more precise result, taking into account a more precise 3501: * curvature will be obtained if estepm is as small as stepm. */ 3502: 3503: /* For example we decided to compute the life expectancy with the smallest unit */ 3504: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 3505: nhstepm is the number of hstepm from age to agelim 3506: nstepm is the number of stepm from age to agelin. 3507: Look at hpijx to understand the reason of that which relies in memory size 3508: and note for a fixed period like estepm months */ 3509: /* We decided (b) to get a life expectancy respecting the most precise curvature of the 3510: survival function given by stepm (the optimization length). Unfortunately it 3511: means that if the survival funtion is printed only each two years of age and if 3512: you sum them up and add 1 year (area under the trapezoids) you won't get the same 3513: results. So we changed our mind and took the option of the best precision. 3514: */ 3515: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 3516: 3517: /* If stepm=6 months */ 3518: /* nhstepm age range expressed in number of stepm */ 3519: agelim=AGESUP; 3520: nstepm=(int) rint((agelim-bage)*YEARM/stepm); 3521: /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 3522: /* if (stepm >= YEARM) hstepm=1;*/ 3523: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */ 3524: 3525: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 3526: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 3527: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate); 3528: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar); 3529: gp=matrix(0,nhstepm,1,nlstate*nlstate); 3530: gm=matrix(0,nhstepm,1,nlstate*nlstate); 3531: 3532: for (age=bage; age<=fage; age ++){ 3533: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */ 3534: /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 3535: /* if (stepm >= YEARM) hstepm=1;*/ 3536: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */ 3537: 3538: /* If stepm=6 months */ 3539: /* Computed by stepm unit matrices, product of hstepma matrices, stored 3540: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */ 3541: 3542: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */ 3543: 3544: /* Computing Variances of health expectancies */ 3545: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to 3546: decrease memory allocation */ 3547: for(theta=1; theta <=npar; theta++){ 3548: for(i=1; i<=npar; i++){ 3549: xp[i] = x[i] + (i==theta ?delti[theta]:0); 3550: xm[i] = x[i] - (i==theta ?delti[theta]:0); 3551: } 3552: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij); 3553: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij); 3554: 3555: for(j=1; j<= nlstate; j++){ 3556: for(i=1; i<=nlstate; i++){ 3557: for(h=0; h<=nhstepm-1; h++){ 3558: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.; 3559: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.; 3560: } 3561: } 3562: } 3563: 3564: for(ij=1; ij<= nlstate*nlstate; ij++) 3565: for(h=0; h<=nhstepm-1; h++){ 3566: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta]; 3567: } 3568: }/* End theta */ 3569: 3570: 3571: for(h=0; h<=nhstepm-1; h++) 3572: for(j=1; j<=nlstate*nlstate;j++) 3573: for(theta=1; theta <=npar; theta++) 3574: trgradg[h][j][theta]=gradg[h][theta][j]; 3575: 3576: 3577: for(ij=1;ij<=nlstate*nlstate;ij++) 3578: for(ji=1;ji<=nlstate*nlstate;ji++) 3579: varhe[ij][ji][(int)age] =0.; 3580: 3581: printf("%d|",(int)age);fflush(stdout); 3582: fprintf(ficlog,"%d|",(int)age);fflush(ficlog); 3583: for(h=0;h<=nhstepm-1;h++){ 3584: for(k=0;k<=nhstepm-1;k++){ 3585: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov); 3586: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]); 3587: for(ij=1;ij<=nlstate*nlstate;ij++) 3588: for(ji=1;ji<=nlstate*nlstate;ji++) 3589: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf; 3590: } 3591: } 3592: 3593: /* Computing expectancies */ 3594: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij); 3595: for(i=1; i<=nlstate;i++) 3596: for(j=1; j<=nlstate;j++) 3597: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){ 3598: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf; 3599: 3600: /* 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]);*/ 3601: 3602: } 3603: 3604: fprintf(ficresstdeij,"%3.0f",age ); 3605: for(i=1; i<=nlstate;i++){ 3606: eip=0.; 3607: vip=0.; 3608: for(j=1; j<=nlstate;j++){ 3609: eip += eij[i][j][(int)age]; 3610: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */ 3611: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age]; 3612: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) ); 3613: } 3614: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip)); 3615: } 3616: fprintf(ficresstdeij,"\n"); 3617: 3618: fprintf(ficrescveij,"%3.0f",age ); 3619: for(i=1; i<=nlstate;i++) 3620: for(j=1; j<=nlstate;j++){ 3621: cptj= (j-1)*nlstate+i; 3622: for(i2=1; i2<=nlstate;i2++) 3623: for(j2=1; j2<=nlstate;j2++){ 3624: cptj2= (j2-1)*nlstate+i2; 3625: if(cptj2 <= cptj) 3626: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]); 3627: } 3628: } 3629: fprintf(ficrescveij,"\n"); 3630: 3631: } 3632: free_matrix(gm,0,nhstepm,1,nlstate*nlstate); 3633: free_matrix(gp,0,nhstepm,1,nlstate*nlstate); 3634: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate); 3635: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar); 3636: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 3637: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 3638: printf("\n"); 3639: fprintf(ficlog,"\n"); 3640: 3641: free_vector(xm,1,npar); 3642: free_vector(xp,1,npar); 3643: free_matrix(dnewm,1,nlstate*nlstate,1,npar); 3644: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate); 3645: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage); 3646: } 3647: 3648: /************ Variance ******************/ 3649: 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[]) 3650: { 3651: /* Variance of health expectancies */ 3652: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/ 3653: /* double **newm;*/ 3654: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/ 3655: 3656: int movingaverage(); 3657: double **dnewm,**doldm; 3658: double **dnewmp,**doldmp; 3659: int i, j, nhstepm, hstepm, h, nstepm ; 3660: int k; 3661: double *xp; 3662: double **gp, **gm; /* for var eij */ 3663: double ***gradg, ***trgradg; /*for var eij */ 3664: double **gradgp, **trgradgp; /* for var p point j */ 3665: double *gpp, *gmp; /* for var p point j */ 3666: double **varppt; /* for var p point j nlstate to nlstate+ndeath */ 3667: double ***p3mat; 3668: double age,agelim, hf; 3669: double ***mobaverage; 3670: int theta; 3671: char digit[4]; 3672: char digitp[25]; 3673: 3674: char fileresprobmorprev[FILENAMELENGTH]; 3675: 3676: if(popbased==1){ 3677: if(mobilav!=0) 3678: strcpy(digitp,"-populbased-mobilav-"); 3679: else strcpy(digitp,"-populbased-nomobil-"); 3680: } 3681: else 3682: strcpy(digitp,"-stablbased-"); 3683: 3684: if (mobilav!=0) { 3685: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 3686: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ 3687: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); 3688: printf(" Error in movingaverage mobilav=%d\n",mobilav); 3689: } 3690: } 3691: 3692: strcpy(fileresprobmorprev,"prmorprev"); 3693: sprintf(digit,"%-d",ij); 3694: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/ 3695: strcat(fileresprobmorprev,digit); /* Tvar to be done */ 3696: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */ 3697: strcat(fileresprobmorprev,fileres); 3698: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) { 3699: printf("Problem with resultfile: %s\n", fileresprobmorprev); 3700: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev); 3701: } 3702: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); 3703: 3704: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); 3705: pstamp(ficresprobmorprev); 3706: 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); 3707: fprintf(ficresprobmorprev,"# Age cov=%-d",ij); 3708: for(j=nlstate+1; j<=(nlstate+ndeath);j++){ 3709: fprintf(ficresprobmorprev," p.%-d SE",j); 3710: for(i=1; i<=nlstate;i++) 3711: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j); 3712: } 3713: fprintf(ficresprobmorprev,"\n"); 3714: fprintf(ficgp,"\n# Routine varevsij"); 3715: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/ 3716: 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"); 3717: fprintf(fichtm,"\n %s \n",digitp); 3718: /* } */ 3719: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); 3720: pstamp(ficresvij); 3721: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are "); 3722: if(popbased==1) 3723: 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); 3724: else 3725: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n"); 3726: fprintf(ficresvij,"# Age"); 3727: for(i=1; i<=nlstate;i++) 3728: for(j=1; j<=nlstate;j++) 3729: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j); 3730: fprintf(ficresvij,"\n"); 3731: 3732: xp=vector(1,npar); 3733: dnewm=matrix(1,nlstate,1,npar); 3734: doldm=matrix(1,nlstate,1,nlstate); 3735: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar); 3736: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); 3737: 3738: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath); 3739: gpp=vector(nlstate+1,nlstate+ndeath); 3740: gmp=vector(nlstate+1,nlstate+ndeath); 3741: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/ 3742: 3743: if(estepm < stepm){ 3744: printf ("Problem %d lower than %d\n",estepm, stepm); 3745: } 3746: else hstepm=estepm; 3747: /* For example we decided to compute the life expectancy with the smallest unit */ 3748: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 3749: nhstepm is the number of hstepm from age to agelim 3750: nstepm is the number of stepm from age to agelin. 3751: Look at function hpijx to understand why (it is linked to memory size questions) */ 3752: /* We decided (b) to get a life expectancy respecting the most precise curvature of the 3753: survival function given by stepm (the optimization length). Unfortunately it 3754: means that if the survival funtion is printed every two years of age and if 3755: you sum them up and add 1 year (area under the trapezoids) you won't get the same 3756: results. So we changed our mind and took the option of the best precision. 3757: */ 3758: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 3759: agelim = AGESUP; 3760: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */ 3761: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 3762: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */ 3763: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 3764: gradg=ma3x(0,nhstepm,1,npar,1,nlstate); 3765: gp=matrix(0,nhstepm,1,nlstate); 3766: gm=matrix(0,nhstepm,1,nlstate); 3767: 3768: 3769: for(theta=1; theta <=npar; theta++){ 3770: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/ 3771: xp[i] = x[i] + (i==theta ?delti[theta]:0); 3772: } 3773: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); 3774: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); 3775: 3776: if (popbased==1) { 3777: if(mobilav ==0){ 3778: for(i=1; i<=nlstate;i++) 3779: prlim[i][i]=probs[(int)age][i][ij]; 3780: }else{ /* mobilav */ 3781: for(i=1; i<=nlstate;i++) 3782: prlim[i][i]=mobaverage[(int)age][i][ij]; 3783: } 3784: } 3785: 3786: for(j=1; j<= nlstate; j++){ 3787: for(h=0; h<=nhstepm; h++){ 3788: for(i=1, gp[h][j]=0.;i<=nlstate;i++) 3789: gp[h][j] += prlim[i][i]*p3mat[i][j][h]; 3790: } 3791: } 3792: /* This for computing probability of death (h=1 means 3793: computed over hstepm matrices product = hstepm*stepm months) 3794: as a weighted average of prlim. 3795: */ 3796: for(j=nlstate+1;j<=nlstate+ndeath;j++){ 3797: for(i=1,gpp[j]=0.; i<= nlstate; i++) 3798: gpp[j] += prlim[i][i]*p3mat[i][j][1]; 3799: } 3800: /* end probability of death */ 3801: 3802: for(i=1; i<=npar; i++) /* Computes gradient x - delta */ 3803: xp[i] = x[i] - (i==theta ?delti[theta]:0); 3804: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); 3805: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); 3806: 3807: if (popbased==1) { 3808: if(mobilav ==0){ 3809: for(i=1; i<=nlstate;i++) 3810: prlim[i][i]=probs[(int)age][i][ij]; 3811: }else{ /* mobilav */ 3812: for(i=1; i<=nlstate;i++) 3813: prlim[i][i]=mobaverage[(int)age][i][ij]; 3814: } 3815: } 3816: 3817: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */ 3818: for(h=0; h<=nhstepm; h++){ 3819: for(i=1, gm[h][j]=0.;i<=nlstate;i++) 3820: gm[h][j] += prlim[i][i]*p3mat[i][j][h]; 3821: } 3822: } 3823: /* This for computing probability of death (h=1 means 3824: computed over hstepm matrices product = hstepm*stepm months) 3825: as a weighted average of prlim. 3826: */ 3827: for(j=nlstate+1;j<=nlstate+ndeath;j++){ 3828: for(i=1,gmp[j]=0.; i<= nlstate; i++) 3829: gmp[j] += prlim[i][i]*p3mat[i][j][1]; 3830: } 3831: /* end probability of death */ 3832: 3833: for(j=1; j<= nlstate; j++) /* vareij */ 3834: for(h=0; h<=nhstepm; h++){ 3835: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta]; 3836: } 3837: 3838: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */ 3839: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta]; 3840: } 3841: 3842: } /* End theta */ 3843: 3844: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */ 3845: 3846: for(h=0; h<=nhstepm; h++) /* veij */ 3847: for(j=1; j<=nlstate;j++) 3848: for(theta=1; theta <=npar; theta++) 3849: trgradg[h][j][theta]=gradg[h][theta][j]; 3850: 3851: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */ 3852: for(theta=1; theta <=npar; theta++) 3853: trgradgp[j][theta]=gradgp[theta][j]; 3854: 3855: 3856: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */ 3857: for(i=1;i<=nlstate;i++) 3858: for(j=1;j<=nlstate;j++) 3859: vareij[i][j][(int)age] =0.; 3860: 3861: for(h=0;h<=nhstepm;h++){ 3862: for(k=0;k<=nhstepm;k++){ 3863: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov); 3864: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]); 3865: for(i=1;i<=nlstate;i++) 3866: for(j=1;j<=nlstate;j++) 3867: vareij[i][j][(int)age] += doldm[i][j]*hf*hf; 3868: } 3869: } 3870: 3871: /* pptj */ 3872: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov); 3873: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp); 3874: for(j=nlstate+1;j<=nlstate+ndeath;j++) 3875: for(i=nlstate+1;i<=nlstate+ndeath;i++) 3876: varppt[j][i]=doldmp[j][i]; 3877: /* end ppptj */ 3878: /* x centered again */ 3879: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij); 3880: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij); 3881: 3882: if (popbased==1) { 3883: if(mobilav ==0){ 3884: for(i=1; i<=nlstate;i++) 3885: prlim[i][i]=probs[(int)age][i][ij]; 3886: }else{ /* mobilav */ 3887: for(i=1; i<=nlstate;i++) 3888: prlim[i][i]=mobaverage[(int)age][i][ij]; 3889: } 3890: } 3891: 3892: /* This for computing probability of death (h=1 means 3893: computed over hstepm (estepm) matrices product = hstepm*stepm months) 3894: as a weighted average of prlim. 3895: */ 3896: for(j=nlstate+1;j<=nlstate+ndeath;j++){ 3897: for(i=1,gmp[j]=0.;i<= nlstate; i++) 3898: gmp[j] += prlim[i][i]*p3mat[i][j][1]; 3899: } 3900: /* end probability of death */ 3901: 3902: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij); 3903: for(j=nlstate+1; j<=(nlstate+ndeath);j++){ 3904: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j])); 3905: for(i=1; i<=nlstate;i++){ 3906: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]); 3907: } 3908: } 3909: fprintf(ficresprobmorprev,"\n"); 3910: 3911: fprintf(ficresvij,"%.0f ",age ); 3912: for(i=1; i<=nlstate;i++) 3913: for(j=1; j<=nlstate;j++){ 3914: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]); 3915: } 3916: fprintf(ficresvij,"\n"); 3917: free_matrix(gp,0,nhstepm,1,nlstate); 3918: free_matrix(gm,0,nhstepm,1,nlstate); 3919: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate); 3920: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar); 3921: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 3922: } /* End age */ 3923: free_vector(gpp,nlstate+1,nlstate+ndeath); 3924: free_vector(gmp,nlstate+1,nlstate+ndeath); 3925: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath); 3926: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/ 3927: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); 3928: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */ 3929: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";"); 3930: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */ 3931: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */ 3932: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */ 3933: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev)); 3934: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev)); 3935: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev)); 3936: fprintf(fichtm,"\n File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev)); 3937: fprintf(fichtm,"\n Probability is computed over estepm=%d months. <img src=\"%s%s.png\"> \n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit); 3938: /* 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); 3939: */ 3940: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */ 3941: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit); 3942: 3943: free_vector(xp,1,npar); 3944: free_matrix(doldm,1,nlstate,1,nlstate); 3945: free_matrix(dnewm,1,nlstate,1,npar); 3946: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); 3947: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar); 3948: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); 3949: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 3950: fclose(ficresprobmorprev); 3951: fflush(ficgp); 3952: fflush(fichtm); 3953: } /* end varevsij */ 3954: 3955: /************ Variance of prevlim ******************/ 3956: 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[]) 3957: { 3958: /* Variance of prevalence limit */ 3959: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/ 3960: 3961: double **dnewm,**doldm; 3962: int i, j, nhstepm, hstepm; 3963: double *xp; 3964: double *gp, *gm; 3965: double **gradg, **trgradg; 3966: double age,agelim; 3967: int theta; 3968: 3969: pstamp(ficresvpl); 3970: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n"); 3971: fprintf(ficresvpl,"# Age"); 3972: for(i=1; i<=nlstate;i++) 3973: fprintf(ficresvpl," %1d-%1d",i,i); 3974: fprintf(ficresvpl,"\n"); 3975: 3976: xp=vector(1,npar); 3977: dnewm=matrix(1,nlstate,1,npar); 3978: doldm=matrix(1,nlstate,1,nlstate); 3979: 3980: hstepm=1*YEARM; /* Every year of age */ 3981: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 3982: agelim = AGESUP; 3983: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */ 3984: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 3985: if (stepm >= YEARM) hstepm=1; 3986: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */ 3987: gradg=matrix(1,npar,1,nlstate); 3988: gp=vector(1,nlstate); 3989: gm=vector(1,nlstate); 3990: 3991: for(theta=1; theta <=npar; theta++){ 3992: for(i=1; i<=npar; i++){ /* Computes gradient */ 3993: xp[i] = x[i] + (i==theta ?delti[theta]:0); 3994: } 3995: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); 3996: for(i=1;i<=nlstate;i++) 3997: gp[i] = prlim[i][i]; 3998: 3999: for(i=1; i<=npar; i++) /* Computes gradient */ 4000: xp[i] = x[i] - (i==theta ?delti[theta]:0); 4001: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); 4002: for(i=1;i<=nlstate;i++) 4003: gm[i] = prlim[i][i]; 4004: 4005: for(i=1;i<=nlstate;i++) 4006: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta]; 4007: } /* End theta */ 4008: 4009: trgradg =matrix(1,nlstate,1,npar); 4010: 4011: for(j=1; j<=nlstate;j++) 4012: for(theta=1; theta <=npar; theta++) 4013: trgradg[j][theta]=gradg[theta][j]; 4014: 4015: for(i=1;i<=nlstate;i++) 4016: varpl[i][(int)age] =0.; 4017: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov); 4018: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg); 4019: for(i=1;i<=nlstate;i++) 4020: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */ 4021: 4022: fprintf(ficresvpl,"%.0f ",age ); 4023: for(i=1; i<=nlstate;i++) 4024: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age])); 4025: fprintf(ficresvpl,"\n"); 4026: free_vector(gp,1,nlstate); 4027: free_vector(gm,1,nlstate); 4028: free_matrix(gradg,1,npar,1,nlstate); 4029: free_matrix(trgradg,1,nlstate,1,npar); 4030: } /* End age */ 4031: 4032: free_vector(xp,1,npar); 4033: free_matrix(doldm,1,nlstate,1,npar); 4034: free_matrix(dnewm,1,nlstate,1,nlstate); 4035: 4036: } 4037: 4038: /************ Variance of one-step probabilities ******************/ 4039: 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[]) 4040: { 4041: int i, j=0, k1, l1, tj; 4042: int k2, l2, j1, z1; 4043: int k=0, l; 4044: int first=1, first1, first2; 4045: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp; 4046: double **dnewm,**doldm; 4047: double *xp; 4048: double *gp, *gm; 4049: double **gradg, **trgradg; 4050: double **mu; 4051: double age, cov[NCOVMAX+1]; 4052: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */ 4053: int theta; 4054: char fileresprob[FILENAMELENGTH]; 4055: char fileresprobcov[FILENAMELENGTH]; 4056: char fileresprobcor[FILENAMELENGTH]; 4057: double ***varpij; 4058: 4059: strcpy(fileresprob,"prob"); 4060: strcat(fileresprob,fileres); 4061: if((ficresprob=fopen(fileresprob,"w"))==NULL) { 4062: printf("Problem with resultfile: %s\n", fileresprob); 4063: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob); 4064: } 4065: strcpy(fileresprobcov,"probcov"); 4066: strcat(fileresprobcov,fileres); 4067: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) { 4068: printf("Problem with resultfile: %s\n", fileresprobcov); 4069: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov); 4070: } 4071: strcpy(fileresprobcor,"probcor"); 4072: strcat(fileresprobcor,fileres); 4073: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) { 4074: printf("Problem with resultfile: %s\n", fileresprobcor); 4075: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor); 4076: } 4077: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob); 4078: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob); 4079: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov); 4080: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov); 4081: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor); 4082: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor); 4083: pstamp(ficresprob); 4084: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n"); 4085: fprintf(ficresprob,"# Age"); 4086: pstamp(ficresprobcov); 4087: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n"); 4088: fprintf(ficresprobcov,"# Age"); 4089: pstamp(ficresprobcor); 4090: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n"); 4091: fprintf(ficresprobcor,"# Age"); 4092: 4093: 4094: for(i=1; i<=nlstate;i++) 4095: for(j=1; j<=(nlstate+ndeath);j++){ 4096: fprintf(ficresprob," p%1d-%1d (SE)",i,j); 4097: fprintf(ficresprobcov," p%1d-%1d ",i,j); 4098: fprintf(ficresprobcor," p%1d-%1d ",i,j); 4099: } 4100: /* fprintf(ficresprob,"\n"); 4101: fprintf(ficresprobcov,"\n"); 4102: fprintf(ficresprobcor,"\n"); 4103: */ 4104: xp=vector(1,npar); 4105: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar); 4106: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath)); 4107: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage); 4108: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage); 4109: first=1; 4110: fprintf(ficgp,"\n# Routine varprob"); 4111: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n"); 4112: fprintf(fichtm,"\n"); 4113: 4114: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov); 4115: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\ 4116: file %s \n",optionfilehtmcov); 4117: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\ 4118: and drawn. It helps understanding how is the covariance between two incidences.\ 4119: They are expressed in year-1 in order to be less dependent of stepm. \n"); 4120: fprintf(fichtmcov,"\n Contour plot corresponding to x'cov-1x = 4 (where x is the column vector (pij,pkl)) are drawn. \ 4121: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \ 4122: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \ 4123: standard deviations wide on each axis. \ 4124: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\ 4125: and made the appropriate rotation to look at the uncorrelated principal directions. \ 4126: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one. \n"); 4127: 4128: cov[1]=1; 4129: /* tj=cptcoveff; */ 4130: tj = (int) pow(2,cptcoveff); 4131: if (cptcovn<1) {tj=1;ncodemax[1]=1;} 4132: j1=0; 4133: for(j1=1; j1<=tj;j1++){ 4134: /*for(i1=1; i1<=ncodemax[t];i1++){ */ 4135: /*j1++;*/ 4136: if (cptcovn>0) { 4137: fprintf(ficresprob, "\n#********** Variable "); 4138: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); 4139: fprintf(ficresprob, "**********\n#\n"); 4140: fprintf(ficresprobcov, "\n#********** Variable "); 4141: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); 4142: fprintf(ficresprobcov, "**********\n#\n"); 4143: 4144: fprintf(ficgp, "\n#********** Variable "); 4145: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); 4146: fprintf(ficgp, "**********\n#\n"); 4147: 4148: 4149: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable "); 4150: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); 4151: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">"); 4152: 4153: fprintf(ficresprobcor, "\n#********** Variable "); 4154: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); 4155: fprintf(ficresprobcor, "**********\n#"); 4156: } 4157: 4158: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath)); 4159: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar); 4160: gp=vector(1,(nlstate)*(nlstate+ndeath)); 4161: gm=vector(1,(nlstate)*(nlstate+ndeath)); 4162: for (age=bage; age<=fage; age ++){ 4163: cov[2]=age; 4164: if(nagesqr==1) 4165: cov[3]= age*age; 4166: for (k=1; k<=cptcovn;k++) { 4167: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4 4168: * 1 1 1 1 1 4169: * 2 2 1 1 1 4170: * 3 1 2 1 1 4171: */ 4172: /* nbcode[1][1]=0 nbcode[1][2]=1;*/ 4173: } 4174: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */ 4175: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2]; 4176: for (k=1; k<=cptcovprod;k++) 4177: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; 4178: 4179: 4180: for(theta=1; theta <=npar; theta++){ 4181: for(i=1; i<=npar; i++) 4182: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0); 4183: 4184: pmij(pmmij,cov,ncovmodel,xp,nlstate); 4185: 4186: k=0; 4187: for(i=1; i<= (nlstate); i++){ 4188: for(j=1; j<=(nlstate+ndeath);j++){ 4189: k=k+1; 4190: gp[k]=pmmij[i][j]; 4191: } 4192: } 4193: 4194: for(i=1; i<=npar; i++) 4195: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0); 4196: 4197: pmij(pmmij,cov,ncovmodel,xp,nlstate); 4198: k=0; 4199: for(i=1; i<=(nlstate); i++){ 4200: for(j=1; j<=(nlstate+ndeath);j++){ 4201: k=k+1; 4202: gm[k]=pmmij[i][j]; 4203: } 4204: } 4205: 4206: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 4207: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta]; 4208: } 4209: 4210: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++) 4211: for(theta=1; theta <=npar; theta++) 4212: trgradg[j][theta]=gradg[theta][j]; 4213: 4214: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 4215: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg); 4216: 4217: pmij(pmmij,cov,ncovmodel,x,nlstate); 4218: 4219: k=0; 4220: for(i=1; i<=(nlstate); i++){ 4221: for(j=1; j<=(nlstate+ndeath);j++){ 4222: k=k+1; 4223: mu[k][(int) age]=pmmij[i][j]; 4224: } 4225: } 4226: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++) 4227: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++) 4228: varpij[i][j][(int)age] = doldm[i][j]; 4229: 4230: /*printf("\n%d ",(int)age); 4231: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){ 4232: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i])); 4233: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i])); 4234: }*/ 4235: 4236: fprintf(ficresprob,"\n%d ",(int)age); 4237: fprintf(ficresprobcov,"\n%d ",(int)age); 4238: fprintf(ficresprobcor,"\n%d ",(int)age); 4239: 4240: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++) 4241: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age])); 4242: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){ 4243: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]); 4244: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]); 4245: } 4246: i=0; 4247: for (k=1; k<=(nlstate);k++){ 4248: for (l=1; l<=(nlstate+ndeath);l++){ 4249: i++; 4250: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l); 4251: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l); 4252: for (j=1; j<=i;j++){ 4253: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */ 4254: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]); 4255: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age])); 4256: } 4257: } 4258: }/* end of loop for state */ 4259: } /* end of loop for age */ 4260: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath)); 4261: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath)); 4262: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar); 4263: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar); 4264: 4265: /* Confidence intervalle of pij */ 4266: /* 4267: fprintf(ficgp,"\nunset parametric;unset label"); 4268: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\""); 4269: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65"); 4270: fprintf(fichtm,"\n Probability with confidence intervals expressed in year-1 :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname); 4271: fprintf(fichtm,"\n <img src=\"pijgr%s.png\"> ",optionfilefiname); 4272: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname); 4273: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob); 4274: */ 4275: 4276: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/ 4277: first1=1;first2=2; 4278: for (k2=1; k2<=(nlstate);k2++){ 4279: for (l2=1; l2<=(nlstate+ndeath);l2++){ 4280: if(l2==k2) continue; 4281: j=(k2-1)*(nlstate+ndeath)+l2; 4282: for (k1=1; k1<=(nlstate);k1++){ 4283: for (l1=1; l1<=(nlstate+ndeath);l1++){ 4284: if(l1==k1) continue; 4285: i=(k1-1)*(nlstate+ndeath)+l1; 4286: if(i<=j) continue; 4287: for (age=bage; age<=fage; age ++){ 4288: if ((int)age %5==0){ 4289: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM; 4290: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM; 4291: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM; 4292: mu1=mu[i][(int) age]/stepm*YEARM ; 4293: mu2=mu[j][(int) age]/stepm*YEARM; 4294: c12=cv12/sqrt(v1*v2); 4295: /* Computing eigen value of matrix of covariance */ 4296: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.; 4297: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.; 4298: if ((lc2 <0) || (lc1 <0) ){ 4299: if(first2==1){ 4300: first1=0; 4301: 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); 4302: } 4303: 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); 4304: /* lc1=fabs(lc1); */ /* If we want to have them positive */ 4305: /* lc2=fabs(lc2); */ 4306: } 4307: 4308: /* Eigen vectors */ 4309: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12)); 4310: /*v21=sqrt(1.-v11*v11); *//* error */ 4311: v21=(lc1-v1)/cv12*v11; 4312: v12=-v21; 4313: v22=v11; 4314: tnalp=v21/v11; 4315: if(first1==1){ 4316: first1=0; 4317: 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); 4318: } 4319: 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); 4320: /*printf(fignu*/ 4321: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */ 4322: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */ 4323: if(first==1){ 4324: first=0; 4325: fprintf(ficgp,"\nset parametric;unset label"); 4326: 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); 4327: fprintf(ficgp,"\nset ter png small size 320, 240"); 4328: fprintf(fichtmcov,"\n Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year-1\ 4329: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\ 4330: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\ 4331: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\ 4332: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2); 4333: fprintf(fichtmcov,"\n <img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2); 4334: fprintf(fichtmcov,"\n Correlation at age %d (%.3f),",(int) age, c12); 4335: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2); 4336: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2); 4337: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2); 4338: 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",\ 4339: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\ 4340: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2)); 4341: }else{ 4342: first=0; 4343: fprintf(fichtmcov," %d (%.3f),",(int) age, c12); 4344: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2); 4345: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2); 4346: 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",\ 4347: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\ 4348: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2)); 4349: }/* if first */ 4350: } /* age mod 5 */ 4351: } /* end loop age */ 4352: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2); 4353: first=1; 4354: } /*l12 */ 4355: } /* k12 */ 4356: } /*l1 */ 4357: }/* k1 */ 4358: /* } */ /* loop covariates */ 4359: } 4360: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage); 4361: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage); 4362: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath)); 4363: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar); 4364: free_vector(xp,1,npar); 4365: fclose(ficresprob); 4366: fclose(ficresprobcov); 4367: fclose(ficresprobcor); 4368: fflush(ficgp); 4369: fflush(fichtmcov); 4370: } 4371: 4372: 4373: /******************* Printing html file ***********/ 4374: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \ 4375: int lastpass, int stepm, int weightopt, char model[],\ 4376: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\ 4377: int popforecast, int estepm ,\ 4378: double jprev1, double mprev1,double anprev1, \ 4379: double jprev2, double mprev2,double anprev2){ 4380: int jj1, k1, i1, cpt; 4381: 4382: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \ 4383: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \ 4384: </ul>"); 4385: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \ 4386: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> \n ", 4387: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p")); 4388: fprintf(fichtm,"\ 4389: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a> \n ", 4390: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij")); 4391: fprintf(fichtm,"\ 4392: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> \n", 4393: subdirf2(fileres,"pl"),subdirf2(fileres,"pl")); 4394: fprintf(fichtm,"\ 4395: - (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): \ 4396: <a href=\"%s\">%s</a> \n", 4397: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e")); 4398: fprintf(fichtm,"\ 4399: - Population projections by age and states: \ 4400: <a href=\"%s\">%s</a> \n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f")); 4401: 4402: fprintf(fichtm," \n<ul><li>Graphs</li>"); 4403: 4404: m=pow(2,cptcoveff); 4405: if (cptcovn < 1) {m=1;ncodemax[1]=1;} 4406: 4407: jj1=0; 4408: for(k1=1; k1<=m;k1++){ 4409: for(i1=1; i1<=ncodemax[k1];i1++){ 4410: jj1++; 4411: if (cptcovn > 0) { 4412: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates"); 4413: for (cpt=1; cpt<=cptcoveff;cpt++) 4414: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]); 4415: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">"); 4416: } 4417: /* Pij */ 4418: 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> \ 4419: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 4420: /* Quasi-incidences */ 4421: fprintf(fichtm," - Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\ 4422: 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> \ 4423: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 4424: /* Period (stable) prevalence in each health state */ 4425: for(cpt=1; cpt<=nlstate;cpt++){ 4426: fprintf(fichtm," - Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.png\">%s%d_%d.png</a> \ 4427: <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1); 4428: } 4429: for(cpt=1; cpt<=nlstate;cpt++) { 4430: fprintf(fichtm,"\n - Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> \ 4431: <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1); 4432: } 4433: } /* end i1 */ 4434: }/* End k1 */ 4435: fprintf(fichtm,"</ul>"); 4436: 4437: 4438: fprintf(fichtm,"\ 4439: \n <li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\ 4440: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> \n", rfileres,rfileres); 4441: 4442: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> \n", 4443: subdirf2(fileres,"prob"),subdirf2(fileres,"prob")); 4444: fprintf(fichtm,"\ 4445: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> \n", 4446: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov")); 4447: 4448: fprintf(fichtm,"\ 4449: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> \n", 4450: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor")); 4451: fprintf(fichtm,"\ 4452: - Variances and covariances of health expectancies by age and initial health status (cov(eij,ekl)(estepm=%2d months): \ 4453: <a href=\"%s\">%s</a> \n</li>", 4454: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve")); 4455: fprintf(fichtm,"\ 4456: - (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): \ 4457: <a href=\"%s\">%s</a> \n</li>", 4458: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde")); 4459: fprintf(fichtm,"\ 4460: - 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", 4461: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v")); 4462: fprintf(fichtm,"\ 4463: - 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", 4464: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t")); 4465: fprintf(fichtm,"\ 4466: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> \n",\ 4467: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl")); 4468: 4469: /* if(popforecast==1) fprintf(fichtm,"\n */ 4470: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> \n */ 4471: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> \n */ 4472: /* ",fileres,fileres,fileres,fileres); */ 4473: /* else */ 4474: /* 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); */ 4475: fflush(fichtm); 4476: fprintf(fichtm," <ul><li>Graphs</li>"); 4477: 4478: m=pow(2,cptcoveff); 4479: if (cptcovn < 1) {m=1;ncodemax[1]=1;} 4480: 4481: jj1=0; 4482: for(k1=1; k1<=m;k1++){ 4483: for(i1=1; i1<=ncodemax[k1];i1++){ 4484: jj1++; 4485: if (cptcovn > 0) { 4486: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates"); 4487: for (cpt=1; cpt<=cptcoveff;cpt++) 4488: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]); 4489: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">"); 4490: } 4491: for(cpt=1; cpt<=nlstate;cpt++) { 4492: fprintf(fichtm," - Observed (cross-sectional) and period (incidence based) \ 4493: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png \ 4494: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1); 4495: } 4496: fprintf(fichtm,"\n - Total life expectancy by age and \ 4497: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \ 4498: true period expectancies (those weighted with period prevalences are also\ 4499: drawn in addition to the population based expectancies computed using\ 4500: observed and cahotic prevalences: %s%d.png \ 4501: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1); 4502: } /* end i1 */ 4503: }/* End k1 */ 4504: fprintf(fichtm,"</ul>"); 4505: fflush(fichtm); 4506: } 4507: 4508: /******************* Gnuplot file **************/ 4509: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){ 4510: 4511: char dirfileres[132],optfileres[132]; 4512: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0; 4513: int ng=0; 4514: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */ 4515: /* printf("Problem with file %s",optionfilegnuplot); */ 4516: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */ 4517: /* } */ 4518: 4519: /*#ifdef windows */ 4520: fprintf(ficgp,"cd \"%s\" \n",pathc); 4521: /*#endif */ 4522: m=pow(2,cptcoveff); 4523: 4524: strcpy(dirfileres,optionfilefiname); 4525: strcpy(optfileres,"vpl"); 4526: /* 1eme*/ 4527: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n"); 4528: for (cpt=1; cpt<= nlstate ; cpt ++) { 4529: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */ 4530: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1); 4531: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1); 4532: fprintf(ficgp,"set xlabel \"Age\" \n\ 4533: set ylabel \"Probability\" \n\ 4534: set ter png small size 320, 240\n\ 4535: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1); 4536: 4537: for (i=1; i<= nlstate ; i ++) { 4538: if (i==cpt) fprintf(ficgp," %%lf (%%lf)"); 4539: else fprintf(ficgp," %%*lf (%%*lf)"); 4540: } 4541: 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); 4542: for (i=1; i<= nlstate ; i ++) { 4543: if (i==cpt) fprintf(ficgp," %%lf (%%lf)"); 4544: else fprintf(ficgp," %%*lf (%%*lf)"); 4545: } 4546: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 4547: for (i=1; i<= nlstate ; i ++) { 4548: if (i==cpt) fprintf(ficgp," %%lf (%%lf)"); 4549: else fprintf(ficgp," %%*lf (%%*lf)"); 4550: } 4551: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1)); 4552: } 4553: } 4554: /*2 eme*/ 4555: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n"); 4556: for (k1=1; k1<= m ; k1 ++) { 4557: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1); 4558: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage); 4559: 4560: for (i=1; i<= nlstate+1 ; i ++) { 4561: k=2*i; 4562: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1); 4563: for (j=1; j<= nlstate+1 ; j ++) { 4564: if (j==i) fprintf(ficgp," %%lf (%%lf)"); 4565: else fprintf(ficgp," %%*lf (%%*lf)"); 4566: } 4567: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,"); 4568: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1); 4569: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1); 4570: for (j=1; j<= nlstate+1 ; j ++) { 4571: if (j==i) fprintf(ficgp," %%lf (%%lf)"); 4572: else fprintf(ficgp," %%*lf (%%*lf)"); 4573: } 4574: fprintf(ficgp,"\" t\"\" w l lt 0,"); 4575: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1); 4576: for (j=1; j<= nlstate+1 ; j ++) { 4577: if (j==i) fprintf(ficgp," %%lf (%%lf)"); 4578: else fprintf(ficgp," %%*lf (%%*lf)"); 4579: } 4580: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0"); 4581: else fprintf(ficgp,"\" t\"\" w l lt 0,"); 4582: } 4583: } 4584: 4585: /*3eme*/ 4586: 4587: for (k1=1; k1<= m ; k1 ++) { 4588: for (cpt=1; cpt<= nlstate ; cpt ++) { 4589: /* k=2+nlstate*(2*cpt-2); */ 4590: k=2+(nlstate+1)*(cpt-1); 4591: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1); 4592: fprintf(ficgp,"set ter png small size 320, 240\n\ 4593: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt); 4594: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1); 4595: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) "); 4596: fprintf(ficgp,"\" t \"e%d1\" w l",cpt); 4597: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1); 4598: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) "); 4599: fprintf(ficgp,"\" t \"e%d1\" w l",cpt); 4600: 4601: */ 4602: for (i=1; i< nlstate ; i ++) { 4603: 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); 4604: /* 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);*/ 4605: 4606: } 4607: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt); 4608: } 4609: } 4610: 4611: /* CV preval stable (period) */ 4612: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */ 4613: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */ 4614: k=3; 4615: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt); 4616: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1); 4617: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\ 4618: set ter png small size 320, 240\n\ 4619: unset log y\n\ 4620: plot [%.f:%.f] ", ageminpar, agemaxpar); 4621: for (i=1; i<= nlstate ; i ++){ 4622: if(i==1) 4623: fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij")); 4624: else 4625: fprintf(ficgp,", '' "); 4626: l=(nlstate+ndeath)*(i-1)+1; 4627: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); 4628: for (j=1; j<= (nlstate-1) ; j ++) 4629: fprintf(ficgp,"+$%d",k+l+j); 4630: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt); 4631: } /* nlstate */ 4632: fprintf(ficgp,"\n"); 4633: } /* end cpt state*/ 4634: } /* end covariate */ 4635: 4636: /* proba elementaires */ 4637: fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n"); 4638: for(i=1,jk=1; i <=nlstate; i++){ 4639: fprintf(ficgp,"# initial state %d\n",i); 4640: for(k=1; k <=(nlstate+ndeath); k++){ 4641: if (k != i) { 4642: fprintf(ficgp,"# current state %d\n",k); 4643: for(j=1; j <=ncovmodel; j++){ 4644: fprintf(ficgp,"p%d=%f; ",jk,p[jk]); 4645: jk++; 4646: } 4647: fprintf(ficgp,"\n"); 4648: } 4649: } 4650: } 4651: fprintf(ficgp,"##############\n#\n"); 4652: 4653: /*goto avoid;*/ 4654: fprintf(ficgp,"\n##############\n#Graphics of of probabilities or incidences\n#############\n"); 4655: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n"); 4656: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n"); 4657: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n"); 4658: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n"); 4659: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n"); 4660: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n"); 4661: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n"); 4662: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n"); 4663: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n"); 4664: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n"); 4665: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n"); 4666: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n"); 4667: fprintf(ficgp,"#\n"); 4668: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/ 4669: fprintf(ficgp,"# ng=%d\n",ng); 4670: fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m); 4671: for(jk=1; jk <=m; jk++) { 4672: fprintf(ficgp,"# jk=%d\n",jk); 4673: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 4674: if (ng==2) 4675: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n"); 4676: else 4677: fprintf(ficgp,"\nset title \"Probability\"\n"); 4678: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar); 4679: i=1; 4680: for(k2=1; k2<=nlstate; k2++) { 4681: k3=i; 4682: for(k=1; k<=(nlstate+ndeath); k++) { 4683: if (k != k2){ 4684: if(ng==2) 4685: if(nagesqr==0) 4686: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1); 4687: else /* nagesqr =1 */ 4688: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr); 4689: else 4690: if(nagesqr==0) 4691: fprintf(ficgp," exp(p%d+p%d*x",i,i+1); 4692: else /* nagesqr =1 */ 4693: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr); 4694: ij=1;/* To be checked else nbcode[0][0] wrong */ 4695: for(j=3; j <=ncovmodel-nagesqr; j++) { 4696: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /* Bug valgrind */ 4697: fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); 4698: ij++; 4699: } 4700: else 4701: fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]); 4702: } 4703: fprintf(ficgp,")/(1"); 4704: 4705: for(k1=1; k1 <=nlstate; k1++){ 4706: if(nagesqr==0) 4707: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1); 4708: else /* nagesqr =1 */ 4709: fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr); 4710: 4711: ij=1; 4712: for(j=3; j <=ncovmodel-nagesqr; j++){ 4713: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { 4714: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); 4715: ij++; 4716: } 4717: else 4718: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][j-2]]); 4719: } 4720: fprintf(ficgp,")"); 4721: } 4722: fprintf(ficgp,") t \"p%d%d\" ", k2,k); 4723: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,","); 4724: i=i+ncovmodel; 4725: } 4726: } /* end k */ 4727: } /* end k2 */ 4728: } /* end jk */ 4729: } /* end ng */ 4730: /* avoid: */ 4731: fflush(ficgp); 4732: } /* end gnuplot */ 4733: 4734: 4735: /*************** Moving average **************/ 4736: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){ 4737: 4738: int i, cpt, cptcod; 4739: int modcovmax =1; 4740: int mobilavrange, mob; 4741: double age; 4742: 4743: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 4744: a covariate has 2 modalities */ 4745: if (cptcovn<1) modcovmax=1; /* At least 1 pass */ 4746: 4747: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){ 4748: if(mobilav==1) mobilavrange=5; /* default */ 4749: else mobilavrange=mobilav; 4750: for (age=bage; age<=fage; age++) 4751: for (i=1; i<=nlstate;i++) 4752: for (cptcod=1;cptcod<=modcovmax;cptcod++) 4753: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod]; 4754: /* We keep the original values on the extreme ages bage, fage and for 4755: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2 4756: we use a 5 terms etc. until the borders are no more concerned. 4757: */ 4758: for (mob=3;mob <=mobilavrange;mob=mob+2){ 4759: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ 4760: for (i=1; i<=nlstate;i++){ 4761: for (cptcod=1;cptcod<=modcovmax;cptcod++){ 4762: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod]; 4763: for (cpt=1;cpt<=(mob-1)/2;cpt++){ 4764: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod]; 4765: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod]; 4766: } 4767: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob; 4768: } 4769: } 4770: }/* end age */ 4771: }/* end mob */ 4772: }else return -1; 4773: return 0; 4774: }/* End movingaverage */ 4775: 4776: 4777: /************** Forecasting ******************/ 4778: void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){ 4779: /* proj1, year, month, day of starting projection 4780: agemin, agemax range of age 4781: dateprev1 dateprev2 range of dates during which prevalence is computed 4782: anproj2 year of en of projection (same day and month as proj1). 4783: */ 4784: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1; 4785: double agec; /* generic age */ 4786: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; 4787: double *popeffectif,*popcount; 4788: double ***p3mat; 4789: double ***mobaverage; 4790: char fileresf[FILENAMELENGTH]; 4791: 4792: agelim=AGESUP; 4793: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); 4794: 4795: strcpy(fileresf,"f"); 4796: strcat(fileresf,fileres); 4797: if((ficresf=fopen(fileresf,"w"))==NULL) { 4798: printf("Problem with forecast resultfile: %s\n", fileresf); 4799: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf); 4800: } 4801: printf("Computing forecasting: result on file '%s' \n", fileresf); 4802: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf); 4803: 4804: if (cptcoveff==0) ncodemax[cptcoveff]=1; 4805: 4806: if (mobilav!=0) { 4807: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 4808: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ 4809: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); 4810: printf(" Error in movingaverage mobilav=%d\n",mobilav); 4811: } 4812: } 4813: 4814: stepsize=(int) (stepm+YEARM-1)/YEARM; 4815: if (stepm<=12) stepsize=1; 4816: if(estepm < stepm){ 4817: printf ("Problem %d lower than %d\n",estepm, stepm); 4818: } 4819: else hstepm=estepm; 4820: 4821: hstepm=hstepm/stepm; 4822: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and 4823: fractional in yp1 */ 4824: anprojmean=yp; 4825: yp2=modf((yp1*12),&yp); 4826: mprojmean=yp; 4827: yp1=modf((yp2*30.5),&yp); 4828: jprojmean=yp; 4829: if(jprojmean==0) jprojmean=1; 4830: if(mprojmean==0) jprojmean=1; 4831: 4832: i1=cptcoveff; 4833: if (cptcovn < 1){i1=1;} 4834: 4835: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 4836: 4837: fprintf(ficresf,"#****** Routine prevforecast **\n"); 4838: 4839: /* if (h==(int)(YEARM*yearp)){ */ 4840: for(cptcov=1, k=0;cptcov<=i1;cptcov++){ 4841: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ 4842: k=k+1; 4843: fprintf(ficresf,"\n#******"); 4844: for(j=1;j<=cptcoveff;j++) { 4845: 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]]); 4846: } 4847: fprintf(ficresf,"******\n"); 4848: fprintf(ficresf,"# Covariate valuofcovar yearproj age"); 4849: for(j=1; j<=nlstate+ndeath;j++){ 4850: for(i=1; i<=nlstate;i++) 4851: fprintf(ficresf," p%d%d",i,j); 4852: fprintf(ficresf," p.%d",j); 4853: } 4854: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 4855: fprintf(ficresf,"\n"); 4856: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp); 4857: 4858: for (agec=fage; agec>=(ageminpar-1); agec--){ 4859: nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 4860: nhstepm = nhstepm/hstepm; 4861: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 4862: oldm=oldms;savm=savms; 4863: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k); 4864: 4865: for (h=0; h<=nhstepm; h++){ 4866: if (h*hstepm/YEARM*stepm ==yearp) { 4867: fprintf(ficresf,"\n"); 4868: for(j=1;j<=cptcoveff;j++) 4869: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 4870: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm); 4871: } 4872: for(j=1; j<=nlstate+ndeath;j++) { 4873: ppij=0.; 4874: for(i=1; i<=nlstate;i++) { 4875: if (mobilav==1) 4876: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod]; 4877: else { 4878: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod]; 4879: } 4880: if (h*hstepm/YEARM*stepm== yearp) { 4881: fprintf(ficresf," %.3f", p3mat[i][j][h]); 4882: } 4883: } /* end i */ 4884: if (h*hstepm/YEARM*stepm==yearp) { 4885: fprintf(ficresf," %.3f", ppij); 4886: } 4887: }/* end j */ 4888: } /* end h */ 4889: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 4890: } /* end agec */ 4891: } /* end yearp */ 4892: } /* end cptcod */ 4893: } /* end cptcov */ 4894: 4895: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 4896: 4897: fclose(ficresf); 4898: } 4899: 4900: /************** Forecasting *****not tested NB*************/ 4901: void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){ 4902: 4903: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; 4904: int *popage; 4905: double calagedatem, agelim, kk1, kk2; 4906: double *popeffectif,*popcount; 4907: double ***p3mat,***tabpop,***tabpopprev; 4908: double ***mobaverage; 4909: char filerespop[FILENAMELENGTH]; 4910: 4911: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 4912: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 4913: agelim=AGESUP; 4914: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; 4915: 4916: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); 4917: 4918: 4919: strcpy(filerespop,"pop"); 4920: strcat(filerespop,fileres); 4921: if((ficrespop=fopen(filerespop,"w"))==NULL) { 4922: printf("Problem with forecast resultfile: %s\n", filerespop); 4923: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); 4924: } 4925: printf("Computing forecasting: result on file '%s' \n", filerespop); 4926: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); 4927: 4928: if (cptcoveff==0) ncodemax[cptcoveff]=1; 4929: 4930: if (mobilav!=0) { 4931: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 4932: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ 4933: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); 4934: printf(" Error in movingaverage mobilav=%d\n",mobilav); 4935: } 4936: } 4937: 4938: stepsize=(int) (stepm+YEARM-1)/YEARM; 4939: if (stepm<=12) stepsize=1; 4940: 4941: agelim=AGESUP; 4942: 4943: hstepm=1; 4944: hstepm=hstepm/stepm; 4945: 4946: if (popforecast==1) { 4947: if((ficpop=fopen(popfile,"r"))==NULL) { 4948: printf("Problem with population file : %s\n",popfile);exit(0); 4949: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); 4950: } 4951: popage=ivector(0,AGESUP); 4952: popeffectif=vector(0,AGESUP); 4953: popcount=vector(0,AGESUP); 4954: 4955: i=1; 4956: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; 4957: 4958: imx=i; 4959: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i]; 4960: } 4961: 4962: for(cptcov=1,k=0;cptcov<=i2;cptcov++){ 4963: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ 4964: k=k+1; 4965: fprintf(ficrespop,"\n#******"); 4966: for(j=1;j<=cptcoveff;j++) { 4967: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 4968: } 4969: fprintf(ficrespop,"******\n"); 4970: fprintf(ficrespop,"# Age"); 4971: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j); 4972: if (popforecast==1) fprintf(ficrespop," [Population]"); 4973: 4974: for (cpt=0; cpt<=0;cpt++) { 4975: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); 4976: 4977: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 4978: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 4979: nhstepm = nhstepm/hstepm; 4980: 4981: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 4982: oldm=oldms;savm=savms; 4983: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); 4984: 4985: for (h=0; h<=nhstepm; h++){ 4986: if (h==(int) (calagedatem+YEARM*cpt)) { 4987: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); 4988: } 4989: for(j=1; j<=nlstate+ndeath;j++) { 4990: kk1=0.;kk2=0; 4991: for(i=1; i<=nlstate;i++) { 4992: if (mobilav==1) 4993: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; 4994: else { 4995: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; 4996: } 4997: } 4998: if (h==(int)(calagedatem+12*cpt)){ 4999: tabpop[(int)(agedeb)][j][cptcod]=kk1; 5000: /*fprintf(ficrespop," %.3f", kk1); 5001: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/ 5002: } 5003: } 5004: for(i=1; i<=nlstate;i++){ 5005: kk1=0.; 5006: for(j=1; j<=nlstate;j++){ 5007: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 5008: } 5009: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)]; 5010: } 5011: 5012: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 5013: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); 5014: } 5015: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 5016: } 5017: } 5018: 5019: /******/ 5020: 5021: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 5022: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); 5023: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 5024: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 5025: nhstepm = nhstepm/hstepm; 5026: 5027: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 5028: oldm=oldms;savm=savms; 5029: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); 5030: for (h=0; h<=nhstepm; h++){ 5031: if (h==(int) (calagedatem+YEARM*cpt)) { 5032: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); 5033: } 5034: for(j=1; j<=nlstate+ndeath;j++) { 5035: kk1=0.;kk2=0; 5036: for(i=1; i<=nlstate;i++) { 5037: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod]; 5038: } 5039: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1); 5040: } 5041: } 5042: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 5043: } 5044: } 5045: } 5046: } 5047: 5048: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 5049: 5050: if (popforecast==1) { 5051: free_ivector(popage,0,AGESUP); 5052: free_vector(popeffectif,0,AGESUP); 5053: free_vector(popcount,0,AGESUP); 5054: } 5055: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 5056: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 5057: fclose(ficrespop); 5058: } /* End of popforecast */ 5059: 5060: int fileappend(FILE *fichier, char *optionfich) 5061: { 5062: if((fichier=fopen(optionfich,"a"))==NULL) { 5063: printf("Problem with file: %s\n", optionfich); 5064: fprintf(ficlog,"Problem with file: %s\n", optionfich); 5065: return (0); 5066: } 5067: fflush(fichier); 5068: return (1); 5069: } 5070: 5071: 5072: /**************** function prwizard **********************/ 5073: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo) 5074: { 5075: 5076: /* Wizard to print covariance matrix template */ 5077: 5078: char ca[32], cb[32]; 5079: int i,j, k, li, lj, lk, ll, jj, npar, itimes; 5080: int numlinepar; 5081: 5082: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); 5083: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); 5084: for(i=1; i <=nlstate; i++){ 5085: jj=0; 5086: for(j=1; j <=nlstate+ndeath; j++){ 5087: if(j==i) continue; 5088: jj++; 5089: /*ca[0]= k+'a'-1;ca[1]='\0';*/ 5090: printf("%1d%1d",i,j); 5091: fprintf(ficparo,"%1d%1d",i,j); 5092: for(k=1; k<=ncovmodel;k++){ 5093: /* printf(" %lf",param[i][j][k]); */ 5094: /* fprintf(ficparo," %lf",param[i][j][k]); */ 5095: printf(" 0."); 5096: fprintf(ficparo," 0."); 5097: } 5098: printf("\n"); 5099: fprintf(ficparo,"\n"); 5100: } 5101: } 5102: printf("# Scales (for hessian or gradient estimation)\n"); 5103: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n"); 5104: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 5105: for(i=1; i <=nlstate; i++){ 5106: jj=0; 5107: for(j=1; j <=nlstate+ndeath; j++){ 5108: if(j==i) continue; 5109: jj++; 5110: fprintf(ficparo,"%1d%1d",i,j); 5111: printf("%1d%1d",i,j); 5112: fflush(stdout); 5113: for(k=1; k<=ncovmodel;k++){ 5114: /* printf(" %le",delti3[i][j][k]); */ 5115: /* fprintf(ficparo," %le",delti3[i][j][k]); */ 5116: printf(" 0."); 5117: fprintf(ficparo," 0."); 5118: } 5119: numlinepar++; 5120: printf("\n"); 5121: fprintf(ficparo,"\n"); 5122: } 5123: } 5124: printf("# Covariance matrix\n"); 5125: /* # 121 Var(a12)\n\ */ 5126: /* # 122 Cov(b12,a12) Var(b12)\n\ */ 5127: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */ 5128: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */ 5129: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */ 5130: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */ 5131: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */ 5132: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */ 5133: fflush(stdout); 5134: fprintf(ficparo,"# Covariance matrix\n"); 5135: /* # 121 Var(a12)\n\ */ 5136: /* # 122 Cov(b12,a12) Var(b12)\n\ */ 5137: /* # ...\n\ */ 5138: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */ 5139: 5140: for(itimes=1;itimes<=2;itimes++){ 5141: jj=0; 5142: for(i=1; i <=nlstate; i++){ 5143: for(j=1; j <=nlstate+ndeath; j++){ 5144: if(j==i) continue; 5145: for(k=1; k<=ncovmodel;k++){ 5146: jj++; 5147: ca[0]= k+'a'-1;ca[1]='\0'; 5148: if(itimes==1){ 5149: printf("#%1d%1d%d",i,j,k); 5150: fprintf(ficparo,"#%1d%1d%d",i,j,k); 5151: }else{ 5152: printf("%1d%1d%d",i,j,k); 5153: fprintf(ficparo,"%1d%1d%d",i,j,k); 5154: /* printf(" %.5le",matcov[i][j]); */ 5155: } 5156: ll=0; 5157: for(li=1;li <=nlstate; li++){ 5158: for(lj=1;lj <=nlstate+ndeath; lj++){ 5159: if(lj==li) continue; 5160: for(lk=1;lk<=ncovmodel;lk++){ 5161: ll++; 5162: if(ll<=jj){ 5163: cb[0]= lk +'a'-1;cb[1]='\0'; 5164: if(ll<jj){ 5165: if(itimes==1){ 5166: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj); 5167: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj); 5168: }else{ 5169: printf(" 0."); 5170: fprintf(ficparo," 0."); 5171: } 5172: }else{ 5173: if(itimes==1){ 5174: printf(" Var(%s%1d%1d)",ca,i,j); 5175: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j); 5176: }else{ 5177: printf(" 0."); 5178: fprintf(ficparo," 0."); 5179: } 5180: } 5181: } 5182: } /* end lk */ 5183: } /* end lj */ 5184: } /* end li */ 5185: printf("\n"); 5186: fprintf(ficparo,"\n"); 5187: numlinepar++; 5188: } /* end k*/ 5189: } /*end j */ 5190: } /* end i */ 5191: } /* end itimes */ 5192: 5193: } /* end of prwizard */ 5194: /******************* Gompertz Likelihood ******************************/ 5195: double gompertz(double x[]) 5196: { 5197: double A,B,L=0.0,sump=0.,num=0.; 5198: int i,n=0; /* n is the size of the sample */ 5199: 5200: for (i=0;i<=imx-1 ; i++) { 5201: sump=sump+weight[i]; 5202: /* sump=sump+1;*/ 5203: num=num+1; 5204: } 5205: 5206: 5207: /* for (i=0; i<=imx; i++) 5208: 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]);*/ 5209: 5210: for (i=1;i<=imx ; i++) 5211: { 5212: if (cens[i] == 1 && wav[i]>1) 5213: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp))); 5214: 5215: if (cens[i] == 0 && wav[i]>1) 5216: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp))) 5217: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM); 5218: 5219: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */ 5220: if (wav[i] > 1 ) { /* ??? */ 5221: L=L+A*weight[i]; 5222: /* 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]);*/ 5223: } 5224: } 5225: 5226: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/ 5227: 5228: return -2*L*num/sump; 5229: } 5230: 5231: #ifdef GSL 5232: /******************* Gompertz_f Likelihood ******************************/ 5233: double gompertz_f(const gsl_vector *v, void *params) 5234: { 5235: double A,B,LL=0.0,sump=0.,num=0.; 5236: double *x= (double *) v->data; 5237: int i,n=0; /* n is the size of the sample */ 5238: 5239: for (i=0;i<=imx-1 ; i++) { 5240: sump=sump+weight[i]; 5241: /* sump=sump+1;*/ 5242: num=num+1; 5243: } 5244: 5245: 5246: /* for (i=0; i<=imx; i++) 5247: 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]);*/ 5248: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]); 5249: for (i=1;i<=imx ; i++) 5250: { 5251: if (cens[i] == 1 && wav[i]>1) 5252: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp))); 5253: 5254: if (cens[i] == 0 && wav[i]>1) 5255: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp))) 5256: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM); 5257: 5258: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */ 5259: if (wav[i] > 1 ) { /* ??? */ 5260: LL=LL+A*weight[i]; 5261: /* 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]);*/ 5262: } 5263: } 5264: 5265: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/ 5266: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump); 5267: 5268: return -2*LL*num/sump; 5269: } 5270: #endif 5271: 5272: /******************* Printing html file ***********/ 5273: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \ 5274: int lastpass, int stepm, int weightopt, char model[],\ 5275: int imx, double p[],double **matcov,double agemortsup){ 5276: int i,k; 5277: 5278: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets): "); 5279: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year ",p[1],p[2],agegomp); 5280: for (i=1;i<=2;i++) 5281: 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])); 5282: fprintf(fichtm," <img src=\"graphmort.png\">"); 5283: fprintf(fichtm,"</ul>"); 5284: 5285: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n "); 5286: 5287: 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> "); 5288: 5289: for (k=agegomp;k<(agemortsup-2);k++) 5290: 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]); 5291: 5292: 5293: fflush(fichtm); 5294: } 5295: 5296: /******************* Gnuplot file **************/ 5297: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){ 5298: 5299: char dirfileres[132],optfileres[132]; 5300: 5301: int ng; 5302: 5303: 5304: /*#ifdef windows */ 5305: fprintf(ficgp,"cd \"%s\" \n",pathc); 5306: /*#endif */ 5307: 5308: 5309: strcpy(dirfileres,optionfilefiname); 5310: strcpy(optfileres,"vpl"); 5311: fprintf(ficgp,"set out \"graphmort.png\"\n "); 5312: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 5313: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n"); 5314: /* fprintf(ficgp, "set size 0.65,0.65\n"); */ 5315: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp); 5316: 5317: } 5318: 5319: int readdata(char datafile[], int firstobs, int lastobs, int *imax) 5320: { 5321: 5322: /*-------- data file ----------*/ 5323: FILE *fic; 5324: char dummy[]=" "; 5325: int i=0, j=0, n=0; 5326: int linei, month, year,iout; 5327: char line[MAXLINE], linetmp[MAXLINE]; 5328: char stra[MAXLINE], strb[MAXLINE]; 5329: char *stratrunc; 5330: int lstra; 5331: 5332: 5333: if((fic=fopen(datafile,"r"))==NULL) { 5334: printf("Problem while opening datafile: %s\n", datafile);return 1; 5335: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1; 5336: } 5337: 5338: i=1; 5339: linei=0; 5340: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) { 5341: linei=linei+1; 5342: for(j=strlen(line); j>=0;j--){ /* Untabifies line */ 5343: if(line[j] == '\t') 5344: line[j] = ' '; 5345: } 5346: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){ 5347: ; 5348: }; 5349: line[j+1]=0; /* Trims blanks at end of line */ 5350: if(line[0]=='#'){ 5351: fprintf(ficlog,"Comment line\n%s\n",line); 5352: printf("Comment line\n%s\n",line); 5353: continue; 5354: } 5355: trimbb(linetmp,line); /* Trims multiple blanks in line */ 5356: strcpy(line, linetmp); 5357: 5358: 5359: for (j=maxwav;j>=1;j--){ 5360: cutv(stra, strb, line, ' '); 5361: if(strb[0]=='.') { /* Missing status */ 5362: lval=-1; 5363: }else{ 5364: errno=0; 5365: lval=strtol(strb,&endptr,10); 5366: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/ 5367: if( strb[0]=='\0' || (*endptr != '\0')){ 5368: 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); 5369: 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); 5370: return 1; 5371: } 5372: } 5373: s[j][i]=lval; 5374: 5375: strcpy(line,stra); 5376: cutv(stra, strb,line,' '); 5377: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){ 5378: } 5379: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){ 5380: month=99; 5381: year=9999; 5382: }else{ 5383: 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); 5384: 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); 5385: return 1; 5386: } 5387: anint[j][i]= (double) year; 5388: mint[j][i]= (double)month; 5389: strcpy(line,stra); 5390: } /* ENd Waves */ 5391: 5392: cutv(stra, strb,line,' '); 5393: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){ 5394: } 5395: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){ 5396: month=99; 5397: year=9999; 5398: }else{ 5399: 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); 5400: 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); 5401: return 1; 5402: } 5403: andc[i]=(double) year; 5404: moisdc[i]=(double) month; 5405: strcpy(line,stra); 5406: 5407: cutv(stra, strb,line,' '); 5408: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){ 5409: } 5410: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){ 5411: month=99; 5412: year=9999; 5413: }else{ 5414: 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); 5415: 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); 5416: return 1; 5417: } 5418: if (year==9999) { 5419: 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); 5420: 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); 5421: return 1; 5422: 5423: } 5424: annais[i]=(double)(year); 5425: moisnais[i]=(double)(month); 5426: strcpy(line,stra); 5427: 5428: cutv(stra, strb,line,' '); 5429: errno=0; 5430: dval=strtod(strb,&endptr); 5431: if( strb[0]=='\0' || (*endptr != '\0')){ 5432: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei); 5433: 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); 5434: fflush(ficlog); 5435: return 1; 5436: } 5437: weight[i]=dval; 5438: strcpy(line,stra); 5439: 5440: for (j=ncovcol;j>=1;j--){ 5441: cutv(stra, strb,line,' '); 5442: if(strb[0]=='.') { /* Missing status */ 5443: lval=-1; 5444: }else{ 5445: errno=0; 5446: lval=strtol(strb,&endptr,10); 5447: if( strb[0]=='\0' || (*endptr != '\0')){ 5448: 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); 5449: 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); 5450: return 1; 5451: } 5452: } 5453: if(lval <-1 || lval >1){ 5454: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \ 5455: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \ 5456: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \ 5457: For example, for multinomial values like 1, 2 and 3,\n \ 5458: build V1=0 V2=0 for the reference value (1),\n \ 5459: V1=1 V2=0 for (2) \n \ 5460: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \ 5461: output of IMaCh is often meaningless.\n \ 5462: Exiting.\n",lval,linei, i,line,j); 5463: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \ 5464: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \ 5465: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \ 5466: For example, for multinomial values like 1, 2 and 3,\n \ 5467: build V1=0 V2=0 for the reference value (1),\n \ 5468: V1=1 V2=0 for (2) \n \ 5469: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \ 5470: output of IMaCh is often meaningless.\n \ 5471: Exiting.\n",lval,linei, i,line,j);fflush(ficlog); 5472: return 1; 5473: } 5474: covar[j][i]=(double)(lval); 5475: strcpy(line,stra); 5476: } 5477: lstra=strlen(stra); 5478: 5479: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */ 5480: stratrunc = &(stra[lstra-9]); 5481: num[i]=atol(stratrunc); 5482: } 5483: else 5484: num[i]=atol(stra); 5485: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){ 5486: 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;}*/ 5487: 5488: i=i+1; 5489: } /* End loop reading data */ 5490: 5491: *imax=i-1; /* Number of individuals */ 5492: fclose(fic); 5493: 5494: return (0); 5495: /* endread: */ 5496: printf("Exiting readdata: "); 5497: fclose(fic); 5498: return (1); 5499: 5500: 5501: 5502: } 5503: void removespace(char *str) { 5504: char *p1 = str, *p2 = str; 5505: do 5506: while (*p2 == ' ') 5507: p2++; 5508: while (*p1++ == *p2++); 5509: } 5510: 5511: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns: 5512: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age 5513: * - nagesqr = 1 if age*age in the model, otherwise 0. 5514: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age 5515: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age 5516: * - cptcovage number of covariates with age*products =2 5517: * - cptcovs number of simple covariates 5518: * - 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 5519: * which is a new column after the 9 (ncovcol) variables. 5520: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual 5521: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage 5522: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6. 5523: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 . 5524: */ 5525: { 5526: int i, j, k, ks; 5527: int j1, k1, k2; 5528: char modelsav[80]; 5529: char stra[80], strb[80], strc[80], strd[80],stre[80]; 5530: char *strpt; 5531: 5532: /*removespace(model);*/ 5533: if (strlen(model) >1){ /* If there is at least 1 covariate */ 5534: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0; 5535: if (strstr(model,"AGE") !=0){ 5536: printf("Error. AGE must be in lower case 'age' model=1+age+%s ",model); 5537: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s ",model);fflush(ficlog); 5538: return 1; 5539: } 5540: if (strstr(model,"v") !=0){ 5541: printf("Error. 'v' must be in upper case 'V' model=%s ",model); 5542: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog); 5543: return 1; 5544: } 5545: strcpy(modelsav,model); 5546: if ((strpt=strstr(model,"age*age")) !=0){ 5547: printf(" strpt=%s, model=%s\n",strpt, model); 5548: if(strpt != model){ 5549: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \ 5550: 'model=1+age+age*age+V1' or 'model=1+age+age*age+V1+V1*age', please swap as well as \n \ 5551: corresponding column of parameters.\n",model); 5552: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \ 5553: 'model=1+age+age*age+V1' or 'model=1+age+age*age+V1+V1*age', please swap as well as \n \ 5554: corresponding column of parameters.\n",model); fflush(ficlog); 5555: return 1; 5556: } 5557: 5558: nagesqr=1; 5559: if (strstr(model,"+age*age") !=0) 5560: substrchaine(modelsav, model, "+age*age"); 5561: else if (strstr(model,"age*age+") !=0) 5562: substrchaine(modelsav, model, "age*age+"); 5563: else 5564: substrchaine(modelsav, model, "age*age"); 5565: }else 5566: nagesqr=0; 5567: if (strlen(modelsav) >1){ 5568: j=nbocc(modelsav,'+'); /**< j=Number of '+' */ 5569: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */ 5570: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2 */ 5571: cptcovt= j+1; /* Number of total covariates in the model, not including 5572: * cst, age and age*age 5573: * V1+V1*age+ V3 + V3*V4+age*age=> 4*/ 5574: /* including age products which are counted in cptcovage. 5575: * but the covariates which are products must be treated 5576: * separately: ncovn=4- 2=2 (V1+V3). */ 5577: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */ 5578: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */ 5579: 5580: 5581: /* Design 5582: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight 5583: * < ncovcol=8 > 5584: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 5585: * k= 1 2 3 4 5 6 7 8 5586: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8 5587: * covar[k,i], value of kth covariate if not including age for individual i: 5588: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8) 5589: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8 5590: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 5591: * Tage[++cptcovage]=k 5592: * if products, new covar are created after ncovcol with k1 5593: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11 5594: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product 5595: * 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 5596: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2]; 5597: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted 5598: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11 5599: * < ncovcol=8 > 5600: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2 5601: * k= 1 2 3 4 5 6 7 8 9 10 11 12 5602: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8 5603: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6} 5604: * p Tprod[1]@2={ 6, 5} 5605: *p Tvard[1][1]@4= {7, 8, 5, 6} 5606: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8 5607: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; 5608: *How to reorganize? 5609: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age 5610: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6} 5611: * {2, 1, 4, 8, 5, 6, 3, 7} 5612: * Struct [] 5613: */ 5614: 5615: /* This loop fills the array Tvar from the string 'model'.*/ 5616: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */ 5617: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */ 5618: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */ 5619: /* k=3 V4 Tvar[k=3]= 4 (from V4) */ 5620: /* k=2 V1 Tvar[k=2]= 1 (from V1) */ 5621: /* k=1 Tvar[1]=2 (from V2) */ 5622: /* k=5 Tvar[5] */ 5623: /* for (k=1; k<=cptcovn;k++) { */ 5624: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */ 5625: /* } */ 5626: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2]; */ 5627: /* 5628: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */ 5629: for(k=cptcovt; k>=1;k--) /**< Number of covariates */ 5630: Tvar[k]=0; 5631: cptcovage=0; 5632: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */ 5633: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 5634: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 5635: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */ 5636: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/ 5637: /*scanf("%d",i);*/ 5638: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */ 5639: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */ 5640: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */ 5641: /* covar is not filled and then is empty */ 5642: cptcovprod--; 5643: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */ 5644: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */ 5645: cptcovage++; /* Sums the number of covariates which include age as a product */ 5646: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */ 5647: /*printf("stre=%s ", stre);*/ 5648: } else if (strcmp(strd,"age")==0) { /* or age*Vn */ 5649: cptcovprod--; 5650: cutl(stre,strb,strc,'V'); 5651: Tvar[k]=atoi(stre); 5652: cptcovage++; 5653: Tage[cptcovage]=k; 5654: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/ 5655: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */ 5656: cptcovn++; 5657: cptcovprodnoage++;k1++; 5658: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/ 5659: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but 5660: because this model-covariate is a construction we invent a new column 5661: ncovcol + k1 5662: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2 5663: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */ 5664: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */ 5665: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */ 5666: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/ 5667: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/ 5668: k2=k2+2; 5669: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */ 5670: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */ 5671: for (i=1; i<=lastobs;i++){ 5672: /* Computes the new covariate which is a product of 5673: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */ 5674: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i]; 5675: } 5676: } /* End age is not in the model */ 5677: } /* End if model includes a product */ 5678: else { /* no more sum */ 5679: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/ 5680: /* scanf("%d",i);*/ 5681: cutl(strd,strc,strb,'V'); 5682: ks++; /**< Number of simple covariates */ 5683: cptcovn++; 5684: Tvar[k]=atoi(strd); 5685: } 5686: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 5687: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav); 5688: scanf("%d",i);*/ 5689: } /* end of loop + on total covariates */ 5690: } /* end if strlen(modelsave == 0) age*age might exist */ 5691: } /* end if strlen(model == 0) */ 5692: 5693: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products. 5694: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/ 5695: 5696: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]); 5697: printf("cptcovprod=%d ", cptcovprod); 5698: fprintf(ficlog,"cptcovprod=%d ", cptcovprod); 5699: 5700: scanf("%d ",i);*/ 5701: 5702: 5703: return (0); /* with covar[new additional covariate if product] and Tage if age */ 5704: /*endread:*/ 5705: printf("Exiting decodemodel: "); 5706: return (1); 5707: } 5708: 5709: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn ) 5710: { 5711: int i, m; 5712: 5713: for (i=1; i<=imx; i++) { 5714: for(m=2; (m<= maxwav); m++) { 5715: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){ 5716: anint[m][i]=9999; 5717: s[m][i]=-1; 5718: } 5719: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){ 5720: *nberr = *nberr + 1; 5721: printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr); 5722: fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr); 5723: s[m][i]=-1; 5724: } 5725: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){ 5726: (*nberr)++; 5727: 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]); 5728: 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]); 5729: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */ 5730: } 5731: } 5732: } 5733: 5734: for (i=1; i<=imx; i++) { 5735: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]); 5736: for(m=firstpass; (m<= lastpass); m++){ 5737: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){ 5738: if (s[m][i] >= nlstate+1) { 5739: if(agedc[i]>0){ 5740: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){ 5741: agev[m][i]=agedc[i]; 5742: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/ 5743: }else { 5744: if ((int)andc[i]!=9999){ 5745: nbwarn++; 5746: printf("Warning negative age at death: %ld line:%d\n",num[i],i); 5747: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i); 5748: agev[m][i]=-1; 5749: } 5750: } 5751: } /* agedc > 0 */ 5752: } 5753: else if(s[m][i] !=9){ /* Standard case, age in fractional 5754: years but with the precision of a month */ 5755: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]); 5756: if((int)mint[m][i]==99 || (int)anint[m][i]==9999) 5757: agev[m][i]=1; 5758: else if(agev[m][i] < *agemin){ 5759: *agemin=agev[m][i]; 5760: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin); 5761: } 5762: else if(agev[m][i] >*agemax){ 5763: *agemax=agev[m][i]; 5764: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/ 5765: } 5766: /*agev[m][i]=anint[m][i]-annais[i];*/ 5767: /* agev[m][i] = age[i]+2*m;*/ 5768: } 5769: else { /* =9 */ 5770: agev[m][i]=1; 5771: s[m][i]=-1; 5772: } 5773: } 5774: else /*= 0 Unknown */ 5775: agev[m][i]=1; 5776: } 5777: 5778: } 5779: for (i=1; i<=imx; i++) { 5780: for(m=firstpass; (m<=lastpass); m++){ 5781: if (s[m][i] > (nlstate+ndeath)) { 5782: (*nberr)++; 5783: 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); 5784: 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); 5785: return 1; 5786: } 5787: } 5788: } 5789: 5790: /*for (i=1; i<=imx; i++){ 5791: for (m=firstpass; (m<lastpass); m++){ 5792: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]); 5793: } 5794: 5795: }*/ 5796: 5797: 5798: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 5799: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 5800: 5801: return (0); 5802: /* endread:*/ 5803: printf("Exiting calandcheckages: "); 5804: return (1); 5805: } 5806: 5807: #if defined(_MSC_VER) 5808: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/ 5809: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/ 5810: //#include "stdafx.h" 5811: //#include <stdio.h> 5812: //#include <tchar.h> 5813: //#include <windows.h> 5814: //#include <iostream> 5815: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL); 5816: 5817: LPFN_ISWOW64PROCESS fnIsWow64Process; 5818: 5819: BOOL IsWow64() 5820: { 5821: BOOL bIsWow64 = FALSE; 5822: 5823: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS) 5824: // (HANDLE, PBOOL); 5825: 5826: //LPFN_ISWOW64PROCESS fnIsWow64Process; 5827: 5828: HMODULE module = GetModuleHandle(_T("kernel32")); 5829: const char funcName[] = "IsWow64Process"; 5830: fnIsWow64Process = (LPFN_ISWOW64PROCESS) 5831: GetProcAddress(module, funcName); 5832: 5833: if (NULL != fnIsWow64Process) 5834: { 5835: if (!fnIsWow64Process(GetCurrentProcess(), 5836: &bIsWow64)) 5837: //throw std::exception("Unknown error"); 5838: printf("Unknown error\n"); 5839: } 5840: return bIsWow64 != FALSE; 5841: } 5842: #endif 5843: 5844: void syscompilerinfo() 5845: { 5846: /* #include "syscompilerinfo.h"*/ 5847: /* command line Intel compiler 32bit windows, XP compatible:*/ 5848: /* /GS /W3 /Gy 5849: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D 5850: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D 5851: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo 5852: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch" 5853: */ 5854: /* 64 bits */ 5855: /* 5856: /GS /W3 /Gy 5857: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG" 5858: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope 5859: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir 5860: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */ 5861: /* Optimization are useless and O3 is slower than O2 */ 5862: /* 5863: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32" 5864: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo 5865: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel 5866: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch" 5867: */ 5868: /* Link is */ /* /OUT:"visual studio 5869: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT 5870: /PDB:"visual studio 5871: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE 5872: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib" 5873: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib" 5874: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib" 5875: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO 5876: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker' 5877: uiAccess='false'" 5878: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF 5879: /NOLOGO /TLBID:1 5880: */ 5881: #if defined __INTEL_COMPILER 5882: #if defined(__GNUC__) 5883: struct utsname sysInfo; /* For Intel on Linux and OS/X */ 5884: #endif 5885: #elif defined(__GNUC__) 5886: #ifndef __APPLE__ 5887: #include <gnu/libc-version.h> /* Only on gnu */ 5888: #endif 5889: struct utsname sysInfo; 5890: int cross = CROSS; 5891: if (cross){ 5892: printf("Cross-"); 5893: fprintf(ficlog, "Cross-"); 5894: } 5895: #endif 5896: 5897: #include <stdint.h> 5898: 5899: printf("Compiled with:");fprintf(ficlog,"Compiled with:"); 5900: #if defined(__clang__) 5901: printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */ 5902: #endif 5903: #if defined(__ICC) || defined(__INTEL_COMPILER) 5904: printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */ 5905: #endif 5906: #if defined(__GNUC__) || defined(__GNUG__) 5907: printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */ 5908: #endif 5909: #if defined(__HP_cc) || defined(__HP_aCC) 5910: printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */ 5911: #endif 5912: #if defined(__IBMC__) || defined(__IBMCPP__) 5913: printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */ 5914: #endif 5915: #if defined(_MSC_VER) 5916: printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */ 5917: #endif 5918: #if defined(__PGI) 5919: printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */ 5920: #endif 5921: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC) 5922: printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */ 5923: #endif 5924: printf(" for ");fprintf(ficlog," for "); 5925: 5926: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros 5927: #ifdef _WIN32 // note the underscore: without it, it's not msdn official! 5928: // Windows (x64 and x86) 5929: printf("Windows (x64 and x86) ");fprintf(ficlog,"Windows (x64 and x86) "); 5930: #elif __unix__ // all unices, not all compilers 5931: // Unix 5932: printf("Unix ");fprintf(ficlog,"Unix "); 5933: #elif __linux__ 5934: // linux 5935: printf("linux ");fprintf(ficlog,"linux "); 5936: #elif __APPLE__ 5937: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though.. 5938: printf("Mac OS ");fprintf(ficlog,"Mac OS "); 5939: #endif 5940: 5941: /* __MINGW32__ */ 5942: /* __CYGWIN__ */ 5943: /* __MINGW64__ */ 5944: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx 5945: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */ 5946: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */ 5947: /* _WIN64 // Defined for applications for Win64. */ 5948: /* _M_X64 // Defined for compilations that target x64 processors. */ 5949: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */ 5950: 5951: #if UINTPTR_MAX == 0xffffffff 5952: printf(" 32-bit"); fprintf(ficlog," 32-bit");/* 32-bit */ 5953: #elif UINTPTR_MAX == 0xffffffffffffffff 5954: printf(" 64-bit"); fprintf(ficlog," 64-bit");/* 64-bit */ 5955: #else 5956: printf(" wtf-bit"); fprintf(ficlog," wtf-bit");/* wtf */ 5957: #endif 5958: 5959: #if defined(__GNUC__) 5960: # if defined(__GNUC_PATCHLEVEL__) 5961: # define __GNUC_VERSION__ (__GNUC__ * 10000 \ 5962: + __GNUC_MINOR__ * 100 \ 5963: + __GNUC_PATCHLEVEL__) 5964: # else 5965: # define __GNUC_VERSION__ (__GNUC__ * 10000 \ 5966: + __GNUC_MINOR__ * 100) 5967: # endif 5968: printf(" using GNU C version %d.\n", __GNUC_VERSION__); 5969: fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__); 5970: 5971: if (uname(&sysInfo) != -1) { 5972: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine); 5973: fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine); 5974: } 5975: else 5976: perror("uname() error"); 5977: //#ifndef __INTEL_COMPILER 5978: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__) 5979: printf("GNU libc version: %s\n", gnu_get_libc_version()); 5980: fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version()); 5981: #endif 5982: #endif 5983: 5984: // void main() 5985: // { 5986: #if defined(_MSC_VER) 5987: if (IsWow64()){ 5988: printf("The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n"); 5989: fprintf(ficlog, "The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n"); 5990: } 5991: else{ 5992: printf("The process is not running under WOW64 (i.e probably on a 64bit Windows).\n"); 5993: fprintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bit Windows).\n"); 5994: } 5995: // printf("\nPress Enter to continue..."); 5996: // getchar(); 5997: // } 5998: 5999: #endif 6000: 6001: 6002: } 6003: 6004: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){ 6005: /*--------------- Prevalence limit (period or stable prevalence) --------------*/ 6006: int i, j, k, i1 ; 6007: double ftolpl = 1.e-10; 6008: double age, agebase, agelim; 6009: 6010: strcpy(filerespl,"pl"); 6011: strcat(filerespl,fileres); 6012: if((ficrespl=fopen(filerespl,"w"))==NULL) { 6013: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1; 6014: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1; 6015: } 6016: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl); 6017: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl); 6018: pstamp(ficrespl); 6019: fprintf(ficrespl,"# Period (stable) prevalence \n"); 6020: fprintf(ficrespl,"#Age "); 6021: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i); 6022: fprintf(ficrespl,"\n"); 6023: 6024: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */ 6025: 6026: agebase=ageminpar; 6027: agelim=agemaxpar; 6028: 6029: i1=pow(2,cptcoveff); 6030: if (cptcovn < 1){i1=1;} 6031: 6032: for(cptcov=1,k=0;cptcov<=i1;cptcov++){ 6033: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */ 6034: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){ 6035: k=k+1; 6036: /* to clean */ 6037: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]); 6038: fprintf(ficrespl,"\n#******"); 6039: printf("\n#******"); 6040: fprintf(ficlog,"\n#******"); 6041: for(j=1;j<=cptcoveff;j++) { 6042: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 6043: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 6044: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 6045: } 6046: fprintf(ficrespl,"******\n"); 6047: printf("******\n"); 6048: fprintf(ficlog,"******\n"); 6049: 6050: fprintf(ficrespl,"#Age "); 6051: for(j=1;j<=cptcoveff;j++) { 6052: fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 6053: } 6054: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i); 6055: fprintf(ficrespl,"\n"); 6056: 6057: for (age=agebase; age<=agelim; age++){ 6058: /* for (age=agebase; age<=agebase; age++){ */ 6059: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k); 6060: fprintf(ficrespl,"%.0f ",age ); 6061: for(j=1;j<=cptcoveff;j++) 6062: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 6063: for(i=1; i<=nlstate;i++) 6064: fprintf(ficrespl," %.5f", prlim[i][i]); 6065: fprintf(ficrespl,"\n"); 6066: } /* Age */ 6067: /* was end of cptcod */ 6068: } /* cptcov */ 6069: return 0; 6070: } 6071: 6072: int hPijx(double *p, int bage, int fage){ 6073: /*------------- h Pij x at various ages ------------*/ 6074: 6075: int stepsize; 6076: int agelim; 6077: int hstepm; 6078: int nhstepm; 6079: int h, i, i1, j, k; 6080: 6081: double agedeb; 6082: double ***p3mat; 6083: 6084: strcpy(filerespij,"pij"); strcat(filerespij,fileres); 6085: if((ficrespij=fopen(filerespij,"w"))==NULL) { 6086: printf("Problem with Pij resultfile: %s\n", filerespij); return 1; 6087: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1; 6088: } 6089: printf("Computing pij: result on file '%s' \n", filerespij); 6090: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij); 6091: 6092: stepsize=(int) (stepm+YEARM-1)/YEARM; 6093: /*if (stepm<=24) stepsize=2;*/ 6094: 6095: agelim=AGESUP; 6096: hstepm=stepsize*YEARM; /* Every year of age */ 6097: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 6098: 6099: /* hstepm=1; aff par mois*/ 6100: pstamp(ficrespij); 6101: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x "); 6102: i1= pow(2,cptcoveff); 6103: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */ 6104: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */ 6105: /* k=k+1; */ 6106: for (k=1; k <= (int) pow(2,cptcoveff); k++){ 6107: fprintf(ficrespij,"\n#****** "); 6108: for(j=1;j<=cptcoveff;j++) 6109: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 6110: fprintf(ficrespij,"******\n"); 6111: 6112: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */ 6113: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 6114: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */ 6115: 6116: /* nhstepm=nhstepm*YEARM; aff par mois*/ 6117: 6118: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 6119: oldm=oldms;savm=savms; 6120: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); 6121: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j="); 6122: for(i=1; i<=nlstate;i++) 6123: for(j=1; j<=nlstate+ndeath;j++) 6124: fprintf(ficrespij," %1d-%1d",i,j); 6125: fprintf(ficrespij,"\n"); 6126: for (h=0; h<=nhstepm; h++){ 6127: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/ 6128: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); 6129: for(i=1; i<=nlstate;i++) 6130: for(j=1; j<=nlstate+ndeath;j++) 6131: fprintf(ficrespij," %.5f", p3mat[i][j][h]); 6132: fprintf(ficrespij,"\n"); 6133: } 6134: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 6135: fprintf(ficrespij,"\n"); 6136: } 6137: /*}*/ 6138: } 6139: return 0; 6140: } 6141: 6142: 6143: /***********************************************/ 6144: /**************** Main Program *****************/ 6145: /***********************************************/ 6146: 6147: int main(int argc, char *argv[]) 6148: { 6149: #ifdef GSL 6150: const gsl_multimin_fminimizer_type *T; 6151: size_t iteri = 0, it; 6152: int rval = GSL_CONTINUE; 6153: int status = GSL_SUCCESS; 6154: double ssval; 6155: #endif 6156: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav); 6157: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod; 6158: 6159: int jj, ll, li, lj, lk; 6160: int numlinepar=0; /* Current linenumber of parameter file */ 6161: int itimes; 6162: int NDIM=2; 6163: int vpopbased=0; 6164: 6165: char ca[32], cb[32]; 6166: /* FILE *fichtm; *//* Html File */ 6167: /* FILE *ficgp;*/ /*Gnuplot File */ 6168: struct stat info; 6169: double agedeb; 6170: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20; 6171: 6172: double fret; 6173: double dum; /* Dummy variable */ 6174: double ***p3mat; 6175: double ***mobaverage; 6176: 6177: char line[MAXLINE]; 6178: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE]; 6179: char pathr[MAXLINE], pathimach[MAXLINE]; 6180: char *tok, *val; /* pathtot */ 6181: int firstobs=1, lastobs=10; 6182: int c, h , cpt; 6183: int jl; 6184: int i1, j1, jk, stepsize; 6185: int *tab; 6186: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */ 6187: int mobilav=0,popforecast=0; 6188: int hstepm, nhstepm; 6189: int agemortsup; 6190: float sumlpop=0.; 6191: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000; 6192: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000; 6193: 6194: double bage=0, fage=110, age, agelim, agebase; 6195: double ftolpl=FTOL; 6196: double **prlim; 6197: double ***param; /* Matrix of parameters */ 6198: double *p; 6199: double **matcov; /* Matrix of covariance */ 6200: double ***delti3; /* Scale */ 6201: double *delti; /* Scale */ 6202: double ***eij, ***vareij; 6203: double **varpl; /* Variances of prevalence limits by age */ 6204: double *epj, vepp; 6205: 6206: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000; 6207: double **ximort; 6208: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234"; 6209: int *dcwave; 6210: 6211: char z[1]="c"; 6212: 6213: /*char *strt;*/ 6214: char strtend[80]; 6215: 6216: 6217: /* setlocale (LC_ALL, ""); */ 6218: /* bindtextdomain (PACKAGE, LOCALEDIR); */ 6219: /* textdomain (PACKAGE); */ 6220: /* setlocale (LC_CTYPE, ""); */ 6221: /* setlocale (LC_MESSAGES, ""); */ 6222: 6223: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */ 6224: rstart_time = time(NULL); 6225: /* (void) gettimeofday(&start_time,&tzp);*/ 6226: start_time = *localtime(&rstart_time); 6227: curr_time=start_time; 6228: /*tml = *localtime(&start_time.tm_sec);*/ 6229: /* strcpy(strstart,asctime(&tml)); */ 6230: strcpy(strstart,asctime(&start_time)); 6231: 6232: /* printf("Localtime (at start)=%s",strstart); */ 6233: /* tp.tm_sec = tp.tm_sec +86400; */ 6234: /* tm = *localtime(&start_time.tm_sec); */ 6235: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */ 6236: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */ 6237: /* tmg.tm_hour=tmg.tm_hour + 1; */ 6238: /* tp.tm_sec = mktime(&tmg); */ 6239: /* strt=asctime(&tmg); */ 6240: /* printf("Time(after) =%s",strstart); */ 6241: /* (void) time (&time_value); 6242: * printf("time=%d,t-=%d\n",time_value,time_value-86400); 6243: * tm = *localtime(&time_value); 6244: * strstart=asctime(&tm); 6245: * printf("tim_value=%d,asctime=%s\n",time_value,strstart); 6246: */ 6247: 6248: nberr=0; /* Number of errors and warnings */ 6249: nbwarn=0; 6250: #ifdef WIN32 6251: _getcwd(pathcd, size); 6252: #else 6253: getcwd(pathcd, size); 6254: #endif 6255: 6256: printf("\n%s\n%s",version,fullversion); 6257: if(argc <=1){ 6258: printf("\nEnter the parameter file name: "); 6259: fgets(pathr,FILENAMELENGTH,stdin); 6260: i=strlen(pathr); 6261: if(pathr[i-1]=='\n') 6262: pathr[i-1]='\0'; 6263: i=strlen(pathr); 6264: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */ 6265: pathr[i-1]='\0'; 6266: for (tok = pathr; tok != NULL; ){ 6267: printf("Pathr |%s|\n",pathr); 6268: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0'); 6269: printf("val= |%s| pathr=%s\n",val,pathr); 6270: strcpy (pathtot, val); 6271: if(pathr[0] == '\0') break; /* Dirty */ 6272: } 6273: } 6274: else{ 6275: strcpy(pathtot,argv[1]); 6276: } 6277: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/ 6278: /*cygwin_split_path(pathtot,path,optionfile); 6279: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/ 6280: /* cutv(path,optionfile,pathtot,'\\');*/ 6281: 6282: /* Split argv[0], imach program to get pathimach */ 6283: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]); 6284: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname); 6285: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname); 6286: /* strcpy(pathimach,argv[0]); */ 6287: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */ 6288: split(pathtot,path,optionfile,optionfilext,optionfilefiname); 6289: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname); 6290: #ifdef WIN32 6291: _chdir(path); /* Can be a relative path */ 6292: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */ 6293: #else 6294: chdir(path); /* Can be a relative path */ 6295: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */ 6296: #endif 6297: printf("Current directory %s!\n",pathcd); 6298: strcpy(command,"mkdir "); 6299: strcat(command,optionfilefiname); 6300: if((outcmd=system(command)) != 0){ 6301: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd); 6302: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */ 6303: /* fclose(ficlog); */ 6304: /* exit(1); */ 6305: } 6306: /* if((imk=mkdir(optionfilefiname))<0){ */ 6307: /* perror("mkdir"); */ 6308: /* } */ 6309: 6310: /*-------- arguments in the command line --------*/ 6311: 6312: /* Main Log file */ 6313: strcat(filelog, optionfilefiname); 6314: strcat(filelog,".log"); /* */ 6315: if((ficlog=fopen(filelog,"w"))==NULL) { 6316: printf("Problem with logfile %s\n",filelog); 6317: goto end; 6318: } 6319: fprintf(ficlog,"Log filename:%s\n",filelog); 6320: fprintf(ficlog,"\n%s\n%s",version,fullversion); 6321: fprintf(ficlog,"\nEnter the parameter file name: \n"); 6322: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\ 6323: path=%s \n\ 6324: optionfile=%s\n\ 6325: optionfilext=%s\n\ 6326: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname); 6327: 6328: syscompilerinfo(); 6329: 6330: printf("Local time (at start):%s",strstart); 6331: fprintf(ficlog,"Local time (at start): %s",strstart); 6332: fflush(ficlog); 6333: /* (void) gettimeofday(&curr_time,&tzp); */ 6334: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */ 6335: 6336: /* */ 6337: strcpy(fileres,"r"); 6338: strcat(fileres, optionfilefiname); 6339: strcat(fileres,".txt"); /* Other files have txt extension */ 6340: 6341: /* Main ---------arguments file --------*/ 6342: 6343: if((ficpar=fopen(optionfile,"r"))==NULL) { 6344: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno)); 6345: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno)); 6346: fflush(ficlog); 6347: /* goto end; */ 6348: exit(70); 6349: } 6350: 6351: 6352: 6353: strcpy(filereso,"o"); 6354: strcat(filereso,fileres); 6355: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */ 6356: printf("Problem with Output resultfile: %s\n", filereso); 6357: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso); 6358: fflush(ficlog); 6359: goto end; 6360: } 6361: 6362: /* Reads comments: lines beginning with '#' */ 6363: numlinepar=0; 6364: while((c=getc(ficpar))=='#' && c!= EOF){ 6365: ungetc(c,ficpar); 6366: fgets(line, MAXLINE, ficpar); 6367: numlinepar++; 6368: fputs(line,stdout); 6369: fputs(line,ficparo); 6370: fputs(line,ficlog); 6371: } 6372: ungetc(c,ficpar); 6373: 6374: 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=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); 6375: numlinepar++; 6376: 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=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); 6377: if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the model */ 6378: model[strlen(model)-1]='\0'; 6379: 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=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model); 6380: 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=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model); 6381: fflush(ficlog); 6382: if(model[0]=='#'|| model[0]== '\0'){ 6383: printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \ 6384: 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \ 6385: 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \ 6386: if(mle != -1){ 6387: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n"); 6388: exit(1); 6389: } 6390: } 6391: while((c=getc(ficpar))=='#' && c!= EOF){ 6392: ungetc(c,ficpar); 6393: fgets(line, MAXLINE, ficpar); 6394: numlinepar++; 6395: fputs(line, stdout); 6396: //puts(line); 6397: fputs(line,ficparo); 6398: fputs(line,ficlog); 6399: } 6400: ungetc(c,ficpar); 6401: 6402: 6403: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */ 6404: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/ 6405: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5 6406: v1+v2*age+v2*v3 makes cptcovn = 3 6407: */ 6408: if (strlen(model)>1) 6409: 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,age*age makes 3*/ 6410: else 6411: ncovmodel=2; /* Constant and age */ 6412: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */ 6413: npar= nforce*ncovmodel; /* Number of parameters like aij*/ 6414: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){ 6415: 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); 6416: 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); 6417: fflush(stdout); 6418: fclose (ficlog); 6419: goto end; 6420: } 6421: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); 6422: delti=delti3[1][1]; 6423: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/ 6424: if(mle==-1){ /* Print a wizard for help writing covariance matrix */ 6425: prwizard(ncovmodel, nlstate, ndeath, model, ficparo); 6426: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso); 6427: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso); 6428: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 6429: fclose (ficparo); 6430: fclose (ficlog); 6431: goto end; 6432: exit(0); 6433: } 6434: else if(mle==-3) { /* Main Wizard */ 6435: prwizard(ncovmodel, nlstate, ndeath, model, ficparo); 6436: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso); 6437: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso); 6438: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); 6439: matcov=matrix(1,npar,1,npar); 6440: } 6441: else{ 6442: /* Read guessed parameters */ 6443: /* Reads comments: lines beginning with '#' */ 6444: while((c=getc(ficpar))=='#' && c!= EOF){ 6445: ungetc(c,ficpar); 6446: fgets(line, MAXLINE, ficpar); 6447: numlinepar++; 6448: fputs(line,stdout); 6449: fputs(line,ficparo); 6450: fputs(line,ficlog); 6451: } 6452: ungetc(c,ficpar); 6453: 6454: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); 6455: for(i=1; i <=nlstate; i++){ 6456: j=0; 6457: for(jj=1; jj <=nlstate+ndeath; jj++){ 6458: if(jj==i) continue; 6459: j++; 6460: fscanf(ficpar,"%1d%1d",&i1,&j1); 6461: if ((i1 != i) && (j1 != j)){ 6462: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \ 6463: It might be a problem of design; if ncovcol and the model are correct\n \ 6464: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1); 6465: exit(1); 6466: } 6467: fprintf(ficparo,"%1d%1d",i1,j1); 6468: if(mle==1) 6469: printf("%1d%1d",i,j); 6470: fprintf(ficlog,"%1d%1d",i,j); 6471: for(k=1; k<=ncovmodel;k++){ 6472: fscanf(ficpar," %lf",&param[i][j][k]); 6473: if(mle==1){ 6474: printf(" %lf",param[i][j][k]); 6475: fprintf(ficlog," %lf",param[i][j][k]); 6476: } 6477: else 6478: fprintf(ficlog," %lf",param[i][j][k]); 6479: fprintf(ficparo," %lf",param[i][j][k]); 6480: } 6481: fscanf(ficpar,"\n"); 6482: numlinepar++; 6483: if(mle==1) 6484: printf("\n"); 6485: fprintf(ficlog,"\n"); 6486: fprintf(ficparo,"\n"); 6487: } 6488: } 6489: fflush(ficlog); 6490: 6491: /* Reads scales values */ 6492: p=param[1][1]; 6493: 6494: /* Reads comments: lines beginning with '#' */ 6495: while((c=getc(ficpar))=='#' && c!= EOF){ 6496: ungetc(c,ficpar); 6497: fgets(line, MAXLINE, ficpar); 6498: numlinepar++; 6499: fputs(line,stdout); 6500: fputs(line,ficparo); 6501: fputs(line,ficlog); 6502: } 6503: ungetc(c,ficpar); 6504: 6505: for(i=1; i <=nlstate; i++){ 6506: for(j=1; j <=nlstate+ndeath-1; j++){ 6507: fscanf(ficpar,"%1d%1d",&i1,&j1); 6508: if ( (i1-i) * (j1-j) != 0){ 6509: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1); 6510: exit(1); 6511: } 6512: printf("%1d%1d",i,j); 6513: fprintf(ficparo,"%1d%1d",i1,j1); 6514: fprintf(ficlog,"%1d%1d",i1,j1); 6515: for(k=1; k<=ncovmodel;k++){ 6516: fscanf(ficpar,"%le",&delti3[i][j][k]); 6517: printf(" %le",delti3[i][j][k]); 6518: fprintf(ficparo," %le",delti3[i][j][k]); 6519: fprintf(ficlog," %le",delti3[i][j][k]); 6520: } 6521: fscanf(ficpar,"\n"); 6522: numlinepar++; 6523: printf("\n"); 6524: fprintf(ficparo,"\n"); 6525: fprintf(ficlog,"\n"); 6526: } 6527: } 6528: fflush(ficlog); 6529: 6530: /* Reads covariance matrix */ 6531: delti=delti3[1][1]; 6532: 6533: 6534: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */ 6535: 6536: /* Reads comments: lines beginning with '#' */ 6537: while((c=getc(ficpar))=='#' && c!= EOF){ 6538: ungetc(c,ficpar); 6539: fgets(line, MAXLINE, ficpar); 6540: numlinepar++; 6541: fputs(line,stdout); 6542: fputs(line,ficparo); 6543: fputs(line,ficlog); 6544: } 6545: ungetc(c,ficpar); 6546: 6547: matcov=matrix(1,npar,1,npar); 6548: for(i=1; i <=npar; i++) 6549: for(j=1; j <=npar; j++) matcov[i][j]=0.; 6550: 6551: for(i=1; i <=npar; i++){ 6552: fscanf(ficpar,"%s",str); 6553: if(mle==1) 6554: printf("%s",str); 6555: fprintf(ficlog,"%s",str); 6556: fprintf(ficparo,"%s",str); 6557: for(j=1; j <=i; j++){ 6558: fscanf(ficpar," %le",&matcov[i][j]); 6559: if(mle==1){ 6560: printf(" %.5le",matcov[i][j]); 6561: } 6562: fprintf(ficlog," %.5le",matcov[i][j]); 6563: fprintf(ficparo," %.5le",matcov[i][j]); 6564: } 6565: fscanf(ficpar,"\n"); 6566: numlinepar++; 6567: if(mle==1) 6568: printf("\n"); 6569: fprintf(ficlog,"\n"); 6570: fprintf(ficparo,"\n"); 6571: } 6572: for(i=1; i <=npar; i++) 6573: for(j=i+1;j<=npar;j++) 6574: matcov[i][j]=matcov[j][i]; 6575: 6576: if(mle==1) 6577: printf("\n"); 6578: fprintf(ficlog,"\n"); 6579: 6580: fflush(ficlog); 6581: 6582: /*-------- Rewriting parameter file ----------*/ 6583: strcpy(rfileres,"r"); /* "Rparameterfile */ 6584: strcat(rfileres,optionfilefiname); /* Parameter file first name*/ 6585: strcat(rfileres,"."); /* */ 6586: strcat(rfileres,optionfilext); /* Other files have txt extension */ 6587: if((ficres =fopen(rfileres,"w"))==NULL) { 6588: printf("Problem writing new parameter file: %s\n", fileres);goto end; 6589: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end; 6590: } 6591: fprintf(ficres,"#%s\n",version); 6592: } /* End of mle != -3 */ 6593: 6594: /* Main data 6595: */ 6596: n= lastobs; 6597: num=lvector(1,n); 6598: moisnais=vector(1,n); 6599: annais=vector(1,n); 6600: moisdc=vector(1,n); 6601: andc=vector(1,n); 6602: agedc=vector(1,n); 6603: cod=ivector(1,n); 6604: weight=vector(1,n); 6605: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */ 6606: mint=matrix(1,maxwav,1,n); 6607: anint=matrix(1,maxwav,1,n); 6608: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 6609: tab=ivector(1,NCOVMAX); 6610: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */ 6611: 6612: /* Reads data from file datafile */ 6613: if (readdata(datafile, firstobs, lastobs, &imx)==1) 6614: goto end; 6615: 6616: /* Calculation of the number of parameters from char model */ 6617: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 6618: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4 6619: k=3 V4 Tvar[k=3]= 4 (from V4) 6620: k=2 V1 Tvar[k=2]= 1 (from V1) 6621: k=1 Tvar[1]=2 (from V2) 6622: */ 6623: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */ 6624: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 6625: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 6626: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage. 6627: */ 6628: /* For model-covariate k tells which data-covariate to use but 6629: because this model-covariate is a construction we invent a new column 6630: ncovcol + k1 6631: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3 6632: Tvar[3=V1*V4]=4+1 etc */ 6633: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */ 6634: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3 6635: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2) 6636: */ 6637: Tvaraff=ivector(1,NCOVMAX); /* Unclear */ 6638: 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 6639: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 6640: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */ 6641: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age 6642: 4 covariates (3 plus signs) 6643: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3 6644: */ 6645: 6646: /* Main decodemodel */ 6647: 6648: 6649: if(decodemodel(model, lastobs) == 1) 6650: goto end; 6651: 6652: if((double)(lastobs-imx)/(double)imx > 1.10){ 6653: nbwarn++; 6654: 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); 6655: 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); 6656: } 6657: /* if(mle==1){*/ 6658: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/ 6659: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */ 6660: } 6661: 6662: /*-calculation of age at interview from date of interview and age at death -*/ 6663: agev=matrix(1,maxwav,1,imx); 6664: 6665: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1) 6666: goto end; 6667: 6668: 6669: agegomp=(int)agemin; 6670: free_vector(moisnais,1,n); 6671: free_vector(annais,1,n); 6672: /* free_matrix(mint,1,maxwav,1,n); 6673: free_matrix(anint,1,maxwav,1,n);*/ 6674: free_vector(moisdc,1,n); 6675: free_vector(andc,1,n); 6676: /* */ 6677: 6678: wav=ivector(1,imx); 6679: dh=imatrix(1,lastpass-firstpass+1,1,imx); 6680: bh=imatrix(1,lastpass-firstpass+1,1,imx); 6681: mw=imatrix(1,lastpass-firstpass+1,1,imx); 6682: 6683: /* Concatenates waves */ 6684: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm); 6685: /* */ 6686: 6687: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */ 6688: 6689: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 6690: ncodemax[1]=1; 6691: Ndum =ivector(-1,NCOVMAX); 6692: if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */ 6693: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */ 6694: /* Nbcode gives the value of the lth modality of jth covariate, in 6695: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/ 6696: /* 1 to ncodemax[j] is the maximum value of this jth covariate */ 6697: 6698: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */ 6699: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/ 6700: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/ 6701: h=0; 6702: 6703: 6704: /*if (cptcovn > 0) */ 6705: 6706: 6707: m=pow(2,cptcoveff); 6708: 6709: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */ 6710: 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 */ 6711: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/ 6712: for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 6713: h++; 6714: if (h>m) 6715: h=1; 6716: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1 6717: * For k=4 covariates, h goes from 1 to 2**k 6718: * codtabm(h,k)= 1 & (h-1) >> (k-1) ; 6719: * h\k 1 2 3 4 6720: *______________________________ 6721: * 1 i=1 1 i=1 1 i=1 1 i=1 1 6722: * 2 2 1 1 1 6723: * 3 i=2 1 2 1 1 6724: * 4 2 2 1 1 6725: * 5 i=3 1 i=2 1 2 1 6726: * 6 2 1 2 1 6727: * 7 i=4 1 2 2 1 6728: * 8 2 2 2 1 6729: * 9 i=5 1 i=3 1 i=2 1 1 6730: * 10 2 1 1 1 6731: * 11 i=6 1 2 1 1 6732: * 12 2 2 1 1 6733: * 13 i=7 1 i=4 1 2 1 6734: * 14 2 1 2 1 6735: * 15 i=8 1 2 2 1 6736: * 16 2 2 2 1 6737: */ 6738: codtab[h][k]=j; 6739: /* codtab[12][3]=1; */ 6740: /*codtab[h][Tvar[k]]=j;*/ 6741: 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]]); 6742: } 6743: } 6744: } 6745: } 6746: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 6747: codtab[1][2]=1;codtab[2][2]=2; */ 6748: /* for(i=1; i <=m ;i++){ 6749: for(k=1; k <=cptcovn; k++){ 6750: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); 6751: } 6752: printf("\n"); 6753: } 6754: scanf("%d",i);*/ 6755: 6756: free_ivector(Ndum,-1,NCOVMAX); 6757: 6758: 6759: 6760: /* Initialisation of ----------- gnuplot -------------*/ 6761: strcpy(optionfilegnuplot,optionfilefiname); 6762: if(mle==-3) 6763: strcat(optionfilegnuplot,"-mort"); 6764: strcat(optionfilegnuplot,".gp"); 6765: 6766: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) { 6767: printf("Problem with file %s",optionfilegnuplot); 6768: } 6769: else{ 6770: fprintf(ficgp,"\n# %s\n", version); 6771: fprintf(ficgp,"# %s\n", optionfilegnuplot); 6772: //fprintf(ficgp,"set missing 'NaNq'\n"); 6773: fprintf(ficgp,"set datafile missing 'NaNq'\n"); 6774: } 6775: /* fclose(ficgp);*/ 6776: 6777: 6778: /* Initialisation of --------- index.htm --------*/ 6779: 6780: strcpy(optionfilehtm,optionfilefiname); /* Main html file */ 6781: if(mle==-3) 6782: strcat(optionfilehtm,"-mort"); 6783: strcat(optionfilehtm,".htm"); 6784: if((fichtm=fopen(optionfilehtm,"w"))==NULL) { 6785: printf("Problem with %s \n",optionfilehtm); 6786: exit(0); 6787: } 6788: 6789: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */ 6790: strcat(optionfilehtmcov,"-cov.htm"); 6791: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) { 6792: printf("Problem with %s \n",optionfilehtmcov), exit(0); 6793: } 6794: else{ 6795: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body>%s %s \ 6796: <hr size=\"2\" color=\"#EC5E5E\"> \n\ 6797: Title=%s Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s \n",\ 6798: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model); 6799: } 6800: 6801: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body>%s %s \ 6802: <hr size=\"2\" color=\"#EC5E5E\"> \n\ 6803: Title=%s Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s \n\ 6804: \n\ 6805: <hr size=\"2\" color=\"#EC5E5E\">\ 6806: <ul><li><h4>Parameter files</h4>\n\ 6807: - Parameter file: <a href=\"%s.%s\">%s.%s</a> \n\ 6808: - Copy of the parameter file: <a href=\"o%s\">o%s</a> \n\ 6809: - Log file of the run: <a href=\"%s\">%s</a> \n\ 6810: - Gnuplot file name: <a href=\"%s\">%s</a> \n\ 6811: - Date and time at start: %s</ul>\n",\ 6812: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\ 6813: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\ 6814: fileres,fileres,\ 6815: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart); 6816: fflush(fichtm); 6817: 6818: strcpy(pathr,path); 6819: strcat(pathr,optionfilefiname); 6820: #ifdef WIN32 6821: _chdir(optionfilefiname); /* Move to directory named optionfile */ 6822: #else 6823: chdir(optionfilefiname); /* Move to directory named optionfile */ 6824: #endif 6825: 6826: 6827: /* Calculates basic frequencies. Computes observed prevalence at single age 6828: and prints on file fileres'p'. */ 6829: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart); 6830: 6831: fprintf(fichtm,"\n"); 6832: fprintf(fichtm," Total number of observations=%d \n\ 6833: Youngest age at first (selected) pass %.2f, oldest age %.2f \n\ 6834: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf \n",\ 6835: imx,agemin,agemax,jmin,jmax,jmean); 6836: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ 6837: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ 6838: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ 6839: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ 6840: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */ 6841: 6842: 6843: /* For Powell, parameters are in a vector p[] starting at p[1] 6844: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */ 6845: p=param[1][1]; /* *(*(*(param +1)+1)+0) */ 6846: 6847: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/ 6848: /* For mortality only */ 6849: if (mle==-3){ 6850: ximort=matrix(1,NDIM,1,NDIM); 6851: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */ 6852: cens=ivector(1,n); 6853: ageexmed=vector(1,n); 6854: agecens=vector(1,n); 6855: dcwave=ivector(1,n); 6856: 6857: for (i=1; i<=imx; i++){ 6858: dcwave[i]=-1; 6859: for (m=firstpass; m<=lastpass; m++) 6860: if (s[m][i]>nlstate) { 6861: dcwave[i]=m; 6862: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/ 6863: break; 6864: } 6865: } 6866: 6867: for (i=1; i<=imx; i++) { 6868: if (wav[i]>0){ 6869: ageexmed[i]=agev[mw[1][i]][i]; 6870: j=wav[i]; 6871: agecens[i]=1.; 6872: 6873: if (ageexmed[i]> 1 && wav[i] > 0){ 6874: agecens[i]=agev[mw[j][i]][i]; 6875: cens[i]= 1; 6876: }else if (ageexmed[i]< 1) 6877: cens[i]= -1; 6878: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass) 6879: cens[i]=0 ; 6880: } 6881: else cens[i]=-1; 6882: } 6883: 6884: for (i=1;i<=NDIM;i++) { 6885: for (j=1;j<=NDIM;j++) 6886: ximort[i][j]=(i == j ? 1.0 : 0.0); 6887: } 6888: 6889: /*p[1]=0.0268; p[NDIM]=0.083;*/ 6890: /*printf("%lf %lf", p[1], p[2]);*/ 6891: 6892: 6893: #ifdef GSL 6894: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n"); 6895: #else 6896: printf("Powell\n"); fprintf(ficlog,"Powell\n"); 6897: #endif 6898: strcpy(filerespow,"pow-mort"); 6899: strcat(filerespow,fileres); 6900: if((ficrespow=fopen(filerespow,"w"))==NULL) { 6901: printf("Problem with resultfile: %s\n", filerespow); 6902: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow); 6903: } 6904: #ifdef GSL 6905: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL"); 6906: #else 6907: fprintf(ficrespow,"# Powell\n# iter -2*LL"); 6908: #endif 6909: /* for (i=1;i<=nlstate;i++) 6910: for(j=1;j<=nlstate+ndeath;j++) 6911: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j); 6912: */ 6913: fprintf(ficrespow,"\n"); 6914: #ifdef GSL 6915: /* gsl starts here */ 6916: T = gsl_multimin_fminimizer_nmsimplex; 6917: gsl_multimin_fminimizer *sfm = NULL; 6918: gsl_vector *ss, *x; 6919: gsl_multimin_function minex_func; 6920: 6921: /* Initial vertex size vector */ 6922: ss = gsl_vector_alloc (NDIM); 6923: 6924: if (ss == NULL){ 6925: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0); 6926: } 6927: /* Set all step sizes to 1 */ 6928: gsl_vector_set_all (ss, 0.001); 6929: 6930: /* Starting point */ 6931: 6932: x = gsl_vector_alloc (NDIM); 6933: 6934: if (x == NULL){ 6935: gsl_vector_free(ss); 6936: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0); 6937: } 6938: 6939: /* Initialize method and iterate */ 6940: /* p[1]=0.0268; p[NDIM]=0.083; */ 6941: /* gsl_vector_set(x, 0, 0.0268); */ 6942: /* gsl_vector_set(x, 1, 0.083); */ 6943: gsl_vector_set(x, 0, p[1]); 6944: gsl_vector_set(x, 1, p[2]); 6945: 6946: minex_func.f = &gompertz_f; 6947: minex_func.n = NDIM; 6948: minex_func.params = (void *)&p; /* ??? */ 6949: 6950: sfm = gsl_multimin_fminimizer_alloc (T, NDIM); 6951: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss); 6952: 6953: printf("Iterations beginning .....\n\n"); 6954: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n"); 6955: 6956: iteri=0; 6957: while (rval == GSL_CONTINUE){ 6958: iteri++; 6959: status = gsl_multimin_fminimizer_iterate(sfm); 6960: 6961: if (status) printf("error: %s\n", gsl_strerror (status)); 6962: fflush(0); 6963: 6964: if (status) 6965: break; 6966: 6967: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6); 6968: ssval = gsl_multimin_fminimizer_size (sfm); 6969: 6970: if (rval == GSL_SUCCESS) 6971: printf ("converged to a local maximum at\n"); 6972: 6973: printf("%5d ", iteri); 6974: for (it = 0; it < NDIM; it++){ 6975: printf ("%10.5f ", gsl_vector_get (sfm->x, it)); 6976: } 6977: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval); 6978: } 6979: 6980: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n"); 6981: 6982: gsl_vector_free(x); /* initial values */ 6983: gsl_vector_free(ss); /* inital step size */ 6984: for (it=0; it<NDIM; it++){ 6985: p[it+1]=gsl_vector_get(sfm->x,it); 6986: fprintf(ficrespow," %.12lf", p[it]); 6987: } 6988: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */ 6989: #endif 6990: #ifdef POWELL 6991: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz); 6992: #endif 6993: fclose(ficrespow); 6994: 6995: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 6996: 6997: for(i=1; i <=NDIM; i++) 6998: for(j=i+1;j<=NDIM;j++) 6999: matcov[i][j]=matcov[j][i]; 7000: 7001: printf("\nCovariance matrix\n "); 7002: for(i=1; i <=NDIM; i++) { 7003: for(j=1;j<=NDIM;j++){ 7004: printf("%f ",matcov[i][j]); 7005: } 7006: printf("\n "); 7007: } 7008: 7009: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp); 7010: for (i=1;i<=NDIM;i++) 7011: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i])); 7012: 7013: lsurv=vector(1,AGESUP); 7014: lpop=vector(1,AGESUP); 7015: tpop=vector(1,AGESUP); 7016: lsurv[agegomp]=100000; 7017: 7018: for (k=agegomp;k<=AGESUP;k++) { 7019: agemortsup=k; 7020: if (p[1]*exp(p[2]*(k-agegomp))>1) break; 7021: } 7022: 7023: for (k=agegomp;k<agemortsup;k++) 7024: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp))); 7025: 7026: for (k=agegomp;k<agemortsup;k++){ 7027: lpop[k]=(lsurv[k]+lsurv[k+1])/2.; 7028: sumlpop=sumlpop+lpop[k]; 7029: } 7030: 7031: tpop[agegomp]=sumlpop; 7032: for (k=agegomp;k<(agemortsup-3);k++){ 7033: /* tpop[k+1]=2;*/ 7034: tpop[k+1]=tpop[k]-lpop[k]; 7035: } 7036: 7037: 7038: printf("\nAge lx qx dx Lx Tx e(x)\n"); 7039: for (k=agegomp;k<(agemortsup-2);k++) 7040: 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]); 7041: 7042: 7043: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */ 7044: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p); 7045: 7046: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \ 7047: stepm, weightopt,\ 7048: model,imx,p,matcov,agemortsup); 7049: 7050: free_vector(lsurv,1,AGESUP); 7051: free_vector(lpop,1,AGESUP); 7052: free_vector(tpop,1,AGESUP); 7053: #ifdef GSL 7054: free_ivector(cens,1,n); 7055: free_vector(agecens,1,n); 7056: free_ivector(dcwave,1,n); 7057: free_matrix(ximort,1,NDIM,1,NDIM); 7058: #endif 7059: } /* Endof if mle==-3 mortality only */ 7060: /* Standard maximisation */ 7061: else{ /* For mle >=1 */ 7062: globpr=0;/* debug */ 7063: /* Computes likelihood for initial parameters */ 7064: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */ 7065: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw); 7066: for (k=1; k<=npar;k++) 7067: printf(" %d %8.5f",k,p[k]); 7068: printf("\n"); 7069: globpr=1; /* again, to print the contributions */ 7070: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */ 7071: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw); 7072: for (k=1; k<=npar;k++) 7073: printf(" %d %8.5f",k,p[k]); 7074: printf("\n"); 7075: if(mle>=1){ /* Could be 1 or 2, Real Maximisation */ 7076: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func); 7077: } 7078: 7079: /*--------- results files --------------*/ 7080: 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=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model); 7081: 7082: 7083: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); 7084: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); 7085: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); 7086: for(i=1,jk=1; i <=nlstate; i++){ 7087: for(k=1; k <=(nlstate+ndeath); k++){ 7088: if (k != i) { 7089: printf("%d%d ",i,k); 7090: fprintf(ficlog,"%d%d ",i,k); 7091: fprintf(ficres,"%1d%1d ",i,k); 7092: for(j=1; j <=ncovmodel; j++){ 7093: printf("%lf ",p[jk]); 7094: fprintf(ficlog,"%lf ",p[jk]); 7095: fprintf(ficres,"%lf ",p[jk]); 7096: jk++; 7097: } 7098: printf("\n"); 7099: fprintf(ficlog,"\n"); 7100: fprintf(ficres,"\n"); 7101: } 7102: } 7103: } 7104: if(mle!=0){ 7105: /* Computing hessian and covariance matrix */ 7106: ftolhess=ftol; /* Usually correct */ 7107: hesscov(matcov, p, npar, delti, ftolhess, func); 7108: } 7109: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n"); 7110: printf("# Scales (for hessian or gradient estimation)\n"); 7111: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n"); 7112: for(i=1,jk=1; i <=nlstate; i++){ 7113: for(j=1; j <=nlstate+ndeath; j++){ 7114: if (j!=i) { 7115: fprintf(ficres,"%1d%1d",i,j); 7116: printf("%1d%1d",i,j); 7117: fprintf(ficlog,"%1d%1d",i,j); 7118: for(k=1; k<=ncovmodel;k++){ 7119: printf(" %.5e",delti[jk]); 7120: fprintf(ficlog," %.5e",delti[jk]); 7121: fprintf(ficres," %.5e",delti[jk]); 7122: jk++; 7123: } 7124: printf("\n"); 7125: fprintf(ficlog,"\n"); 7126: fprintf(ficres,"\n"); 7127: } 7128: } 7129: } 7130: 7131: 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"); 7132: if(mle>=1) 7133: 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"); 7134: 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"); 7135: /* # 121 Var(a12)\n\ */ 7136: /* # 122 Cov(b12,a12) Var(b12)\n\ */ 7137: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */ 7138: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */ 7139: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */ 7140: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */ 7141: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */ 7142: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */ 7143: 7144: 7145: /* Just to have a covariance matrix which will be more understandable 7146: even is we still don't want to manage dictionary of variables 7147: */ 7148: for(itimes=1;itimes<=2;itimes++){ 7149: jj=0; 7150: for(i=1; i <=nlstate; i++){ 7151: for(j=1; j <=nlstate+ndeath; j++){ 7152: if(j==i) continue; 7153: for(k=1; k<=ncovmodel;k++){ 7154: jj++; 7155: ca[0]= k+'a'-1;ca[1]='\0'; 7156: if(itimes==1){ 7157: if(mle>=1) 7158: printf("#%1d%1d%d",i,j,k); 7159: fprintf(ficlog,"#%1d%1d%d",i,j,k); 7160: fprintf(ficres,"#%1d%1d%d",i,j,k); 7161: }else{ 7162: if(mle>=1) 7163: printf("%1d%1d%d",i,j,k); 7164: fprintf(ficlog,"%1d%1d%d",i,j,k); 7165: fprintf(ficres,"%1d%1d%d",i,j,k); 7166: } 7167: ll=0; 7168: for(li=1;li <=nlstate; li++){ 7169: for(lj=1;lj <=nlstate+ndeath; lj++){ 7170: if(lj==li) continue; 7171: for(lk=1;lk<=ncovmodel;lk++){ 7172: ll++; 7173: if(ll<=jj){ 7174: cb[0]= lk +'a'-1;cb[1]='\0'; 7175: if(ll<jj){ 7176: if(itimes==1){ 7177: if(mle>=1) 7178: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj); 7179: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj); 7180: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj); 7181: }else{ 7182: if(mle>=1) 7183: printf(" %.5e",matcov[jj][ll]); 7184: fprintf(ficlog," %.5e",matcov[jj][ll]); 7185: fprintf(ficres," %.5e",matcov[jj][ll]); 7186: } 7187: }else{ 7188: if(itimes==1){ 7189: if(mle>=1) 7190: printf(" Var(%s%1d%1d)",ca,i,j); 7191: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j); 7192: fprintf(ficres," Var(%s%1d%1d)",ca,i,j); 7193: }else{ 7194: if(mle>=1) 7195: printf(" %.5e",matcov[jj][ll]); 7196: fprintf(ficlog," %.5e",matcov[jj][ll]); 7197: fprintf(ficres," %.5e",matcov[jj][ll]); 7198: } 7199: } 7200: } 7201: } /* end lk */ 7202: } /* end lj */ 7203: } /* end li */ 7204: if(mle>=1) 7205: printf("\n"); 7206: fprintf(ficlog,"\n"); 7207: fprintf(ficres,"\n"); 7208: numlinepar++; 7209: } /* end k*/ 7210: } /*end j */ 7211: } /* end i */ 7212: } /* end itimes */ 7213: 7214: fflush(ficlog); 7215: fflush(ficres); 7216: 7217: while((c=getc(ficpar))=='#' && c!= EOF){ 7218: ungetc(c,ficpar); 7219: fgets(line, MAXLINE, ficpar); 7220: fputs(line,stdout); 7221: fputs(line,ficparo); 7222: } 7223: ungetc(c,ficpar); 7224: 7225: estepm=0; 7226: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); 7227: if (estepm==0 || estepm < stepm) estepm=stepm; 7228: if (fage <= 2) { 7229: bage = ageminpar; 7230: fage = agemaxpar; 7231: } 7232: 7233: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n"); 7234: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm); 7235: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm); 7236: 7237: /* Other stuffs, more or less useful */ 7238: while((c=getc(ficpar))=='#' && c!= EOF){ 7239: ungetc(c,ficpar); 7240: fgets(line, MAXLINE, ficpar); 7241: fputs(line,stdout); 7242: fputs(line,ficparo); 7243: } 7244: ungetc(c,ficpar); 7245: 7246: 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); 7247: 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); 7248: 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); 7249: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav); 7250: 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); 7251: 7252: while((c=getc(ficpar))=='#' && c!= EOF){ 7253: ungetc(c,ficpar); 7254: fgets(line, MAXLINE, ficpar); 7255: fputs(line,stdout); 7256: fputs(line,ficparo); 7257: } 7258: ungetc(c,ficpar); 7259: 7260: 7261: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.; 7262: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.; 7263: 7264: fscanf(ficpar,"pop_based=%d\n",&popbased); 7265: fprintf(ficparo,"pop_based=%d\n",popbased); 7266: fprintf(ficres,"pop_based=%d\n",popbased); 7267: 7268: while((c=getc(ficpar))=='#' && c!= EOF){ 7269: ungetc(c,ficpar); 7270: fgets(line, MAXLINE, ficpar); 7271: fputs(line,stdout); 7272: fputs(line,ficparo); 7273: } 7274: ungetc(c,ficpar); 7275: 7276: 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); 7277: 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); 7278: 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); 7279: 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); 7280: 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); 7281: /* day and month of proj2 are not used but only year anproj2.*/ 7282: 7283: 7284: 7285: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */ 7286: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */ 7287: 7288: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */ 7289: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p); 7290: 7291: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\ 7292: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\ 7293: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2); 7294: 7295: /*------------ free_vector -------------*/ 7296: /* chdir(path); */ 7297: 7298: free_ivector(wav,1,imx); 7299: free_imatrix(dh,1,lastpass-firstpass+1,1,imx); 7300: free_imatrix(bh,1,lastpass-firstpass+1,1,imx); 7301: free_imatrix(mw,1,lastpass-firstpass+1,1,imx); 7302: free_lvector(num,1,n); 7303: free_vector(agedc,1,n); 7304: /*free_matrix(covar,0,NCOVMAX,1,n);*/ 7305: /*free_matrix(covar,1,NCOVMAX,1,n);*/ 7306: fclose(ficparo); 7307: fclose(ficres); 7308: 7309: 7310: /* Other results (useful)*/ 7311: 7312: 7313: /*--------------- Prevalence limit (period or stable prevalence) --------------*/ 7314: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */ 7315: prlim=matrix(1,nlstate,1,nlstate); 7316: prevalence_limit(p, prlim, ageminpar, agemaxpar); 7317: fclose(ficrespl); 7318: 7319: #ifdef FREEEXIT2 7320: #include "freeexit2.h" 7321: #endif 7322: 7323: /*------------- h Pij x at various ages ------------*/ 7324: /*#include "hpijx.h"*/ 7325: hPijx(p, bage, fage); 7326: fclose(ficrespij); 7327: 7328: /*-------------- Variance of one-step probabilities---*/ 7329: k=1; 7330: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart); 7331: 7332: 7333: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX); 7334: for(i=1;i<=AGESUP;i++) 7335: for(j=1;j<=NCOVMAX;j++) 7336: for(k=1;k<=NCOVMAX;k++) 7337: probs[i][j][k]=0.; 7338: 7339: /*---------- Forecasting ------------------*/ 7340: /*if((stepm == 1) && (strcmp(model,".")==0)){*/ 7341: if(prevfcast==1){ 7342: /* if(stepm ==1){*/ 7343: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff); 7344: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/ 7345: /* } */ 7346: /* else{ */ 7347: /* erreur=108; */ 7348: /* 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); */ 7349: /* 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); */ 7350: /* } */ 7351: } 7352: 7353: /* ------ Other prevalence ratios------------ */ 7354: 7355: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */ 7356: 7357: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); 7358: /* 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",\ 7359: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass); 7360: */ 7361: 7362: if (mobilav!=0) { 7363: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 7364: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ 7365: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); 7366: printf(" Error in movingaverage mobilav=%d\n",mobilav); 7367: } 7368: } 7369: 7370: 7371: /*---------- Health expectancies, no variances ------------*/ 7372: 7373: strcpy(filerese,"e"); 7374: strcat(filerese,fileres); 7375: if((ficreseij=fopen(filerese,"w"))==NULL) { 7376: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0); 7377: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0); 7378: } 7379: printf("Computing Health Expectancies: result on file '%s' \n", filerese); 7380: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese); 7381: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){ 7382: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/ 7383: 7384: for (k=1; k <= (int) pow(2,cptcoveff); k++){ 7385: fprintf(ficreseij,"\n#****** "); 7386: for(j=1;j<=cptcoveff;j++) { 7387: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 7388: } 7389: fprintf(ficreseij,"******\n"); 7390: 7391: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); 7392: oldm=oldms;savm=savms; 7393: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart); 7394: 7395: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage); 7396: /*}*/ 7397: } 7398: fclose(ficreseij); 7399: 7400: 7401: /*---------- Health expectancies and variances ------------*/ 7402: 7403: 7404: strcpy(filerest,"t"); 7405: strcat(filerest,fileres); 7406: if((ficrest=fopen(filerest,"w"))==NULL) { 7407: printf("Problem with total LE resultfile: %s\n", filerest);goto end; 7408: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end; 7409: } 7410: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 7411: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 7412: 7413: 7414: strcpy(fileresstde,"stde"); 7415: strcat(fileresstde,fileres); 7416: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) { 7417: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0); 7418: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0); 7419: } 7420: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde); 7421: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde); 7422: 7423: strcpy(filerescve,"cve"); 7424: strcat(filerescve,fileres); 7425: if((ficrescveij=fopen(filerescve,"w"))==NULL) { 7426: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0); 7427: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0); 7428: } 7429: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve); 7430: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve); 7431: 7432: strcpy(fileresv,"v"); 7433: strcat(fileresv,fileres); 7434: if((ficresvij=fopen(fileresv,"w"))==NULL) { 7435: printf("Problem with variance resultfile: %s\n", fileresv);exit(0); 7436: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0); 7437: } 7438: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv); 7439: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv); 7440: 7441: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){ 7442: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/ 7443: 7444: for (k=1; k <= (int) pow(2,cptcoveff); k++){ 7445: fprintf(ficrest,"\n#****** "); 7446: for(j=1;j<=cptcoveff;j++) 7447: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 7448: fprintf(ficrest,"******\n"); 7449: 7450: fprintf(ficresstdeij,"\n#****** "); 7451: fprintf(ficrescveij,"\n#****** "); 7452: for(j=1;j<=cptcoveff;j++) { 7453: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 7454: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 7455: } 7456: fprintf(ficresstdeij,"******\n"); 7457: fprintf(ficrescveij,"******\n"); 7458: 7459: fprintf(ficresvij,"\n#****** "); 7460: for(j=1;j<=cptcoveff;j++) 7461: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 7462: fprintf(ficresvij,"******\n"); 7463: 7464: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); 7465: oldm=oldms;savm=savms; 7466: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart); 7467: /* 7468: */ 7469: /* goto endfree; */ 7470: 7471: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); 7472: pstamp(ficrest); 7473: 7474: 7475: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/ 7476: oldm=oldms;savm=savms; /* Segmentation fault */ 7477: cptcod= 0; /* To be deleted */ 7478: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */ 7479: 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 "); 7480: if(vpopbased==1) 7481: 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); 7482: else 7483: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n"); 7484: fprintf(ficrest,"# Age e.. (std) "); 7485: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i); 7486: fprintf(ficrest,"\n"); 7487: 7488: epj=vector(1,nlstate+1); 7489: for(age=bage; age <=fage ;age++){ 7490: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k); 7491: if (vpopbased==1) { 7492: if(mobilav ==0){ 7493: for(i=1; i<=nlstate;i++) 7494: prlim[i][i]=probs[(int)age][i][k]; 7495: }else{ /* mobilav */ 7496: for(i=1; i<=nlstate;i++) 7497: prlim[i][i]=mobaverage[(int)age][i][k]; 7498: } 7499: } 7500: 7501: fprintf(ficrest," %4.0f",age); 7502: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){ 7503: for(i=1, epj[j]=0.;i <=nlstate;i++) { 7504: epj[j] += prlim[i][i]*eij[i][j][(int)age]; 7505: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/ 7506: } 7507: epj[nlstate+1] +=epj[j]; 7508: } 7509: 7510: for(i=1, vepp=0.;i <=nlstate;i++) 7511: for(j=1;j <=nlstate;j++) 7512: vepp += vareij[i][j][(int)age]; 7513: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp)); 7514: for(j=1;j <=nlstate;j++){ 7515: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age])); 7516: } 7517: fprintf(ficrest,"\n"); 7518: } 7519: } 7520: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage); 7521: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage); 7522: free_vector(epj,1,nlstate+1); 7523: /*}*/ 7524: } 7525: free_vector(weight,1,n); 7526: free_imatrix(Tvard,1,NCOVMAX,1,2); 7527: free_imatrix(s,1,maxwav+1,1,n); 7528: free_matrix(anint,1,maxwav,1,n); 7529: free_matrix(mint,1,maxwav,1,n); 7530: free_ivector(cod,1,n); 7531: free_ivector(tab,1,NCOVMAX); 7532: fclose(ficresstdeij); 7533: fclose(ficrescveij); 7534: fclose(ficresvij); 7535: fclose(ficrest); 7536: fclose(ficpar); 7537: 7538: /*------- Variance of period (stable) prevalence------*/ 7539: 7540: strcpy(fileresvpl,"vpl"); 7541: strcat(fileresvpl,fileres); 7542: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) { 7543: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl); 7544: exit(0); 7545: } 7546: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl); 7547: 7548: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){ 7549: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/ 7550: 7551: for (k=1; k <= (int) pow(2,cptcoveff); k++){ 7552: fprintf(ficresvpl,"\n#****** "); 7553: for(j=1;j<=cptcoveff;j++) 7554: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 7555: fprintf(ficresvpl,"******\n"); 7556: 7557: varpl=matrix(1,nlstate,(int) bage, (int) fage); 7558: oldm=oldms;savm=savms; 7559: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart); 7560: free_matrix(varpl,1,nlstate,(int) bage, (int)fage); 7561: /*}*/ 7562: } 7563: 7564: fclose(ficresvpl); 7565: 7566: /*---------- End : free ----------------*/ 7567: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 7568: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX); 7569: } /* mle==-3 arrives here for freeing */ 7570: /* endfree:*/ 7571: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */ 7572: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath); 7573: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath); 7574: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath); 7575: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath); 7576: free_matrix(covar,0,NCOVMAX,1,n); 7577: free_matrix(matcov,1,npar,1,npar); 7578: /*free_vector(delti,1,npar);*/ 7579: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 7580: free_matrix(agev,1,maxwav,1,imx); 7581: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 7582: 7583: free_ivector(ncodemax,1,NCOVMAX); 7584: free_ivector(Tvar,1,NCOVMAX); 7585: free_ivector(Tprod,1,NCOVMAX); 7586: free_ivector(Tvaraff,1,NCOVMAX); 7587: free_ivector(Tage,1,NCOVMAX); 7588: 7589: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX); 7590: free_imatrix(codtab,1,100,1,10); 7591: fflush(fichtm); 7592: fflush(ficgp); 7593: 7594: 7595: if((nberr >0) || (nbwarn>0)){ 7596: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn); 7597: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn); 7598: }else{ 7599: printf("End of Imach\n"); 7600: fprintf(ficlog,"End of Imach\n"); 7601: } 7602: printf("See log file on %s\n",filelog); 7603: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */ 7604: /*(void) gettimeofday(&end_time,&tzp);*/ 7605: rend_time = time(NULL); 7606: end_time = *localtime(&rend_time); 7607: /* tml = *localtime(&end_time.tm_sec); */ 7608: strcpy(strtend,asctime(&end_time)); 7609: printf("Local time at start %s\nLocal time at end %s",strstart, strtend); 7610: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend); 7611: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout)); 7612: 7613: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time)); 7614: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout)); 7615: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time)); 7616: /* printf("Total time was %d uSec.\n", total_usecs);*/ 7617: /* if(fileappend(fichtm,optionfilehtm)){ */ 7618: fprintf(fichtm," Local time at start %s Local time at end %s \n</body></html>",strstart, strtend); 7619: fclose(fichtm); 7620: fprintf(fichtmcov," Local time at start %s Local time at end %s \n</body></html>",strstart, strtend); 7621: fclose(fichtmcov); 7622: fclose(ficgp); 7623: fclose(ficlog); 7624: /*------ End -----------*/ 7625: 7626: 7627: printf("Before Current directory %s!\n",pathcd); 7628: #ifdef WIN32 7629: if (_chdir(pathcd) != 0) 7630: printf("Can't move to directory %s!\n",path); 7631: if(_getcwd(pathcd,MAXLINE) > 0) 7632: #else 7633: if(chdir(pathcd) != 0) 7634: printf("Can't move to directory %s!\n", path); 7635: if (getcwd(pathcd, MAXLINE) > 0) 7636: #endif 7637: printf("Current directory %s!\n",pathcd); 7638: /*strcat(plotcmd,CHARSEPARATOR);*/ 7639: sprintf(plotcmd,"gnuplot"); 7640: #ifdef _WIN32 7641: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach); 7642: #endif 7643: if(!stat(plotcmd,&info)){ 7644: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout); 7645: if(!stat(getenv("GNUPLOTBIN"),&info)){ 7646: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout); 7647: }else 7648: strcpy(pplotcmd,plotcmd); 7649: #ifdef __unix 7650: strcpy(plotcmd,GNUPLOTPROGRAM); 7651: if(!stat(plotcmd,&info)){ 7652: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout); 7653: }else 7654: strcpy(pplotcmd,plotcmd); 7655: #endif 7656: }else 7657: strcpy(pplotcmd,plotcmd); 7658: 7659: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot); 7660: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout); 7661: 7662: if((outcmd=system(plotcmd)) != 0){ 7663: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd); 7664: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n"); 7665: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot); 7666: if((outcmd=system(plotcmd)) != 0) 7667: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd); 7668: } 7669: printf(" Successful, please wait..."); 7670: while (z[0] != 'q') { 7671: /* chdir(path); */ 7672: printf("\nType e to edit results with your browser, g to graph again and q for exit: "); 7673: scanf("%s",z); 7674: /* if (z[0] == 'c') system("./imach"); */ 7675: if (z[0] == 'e') { 7676: #ifdef __APPLE__ 7677: sprintf(pplotcmd, "open %s", optionfilehtm); 7678: #elif __linux 7679: sprintf(pplotcmd, "xdg-open %s", optionfilehtm); 7680: #else 7681: sprintf(pplotcmd, "%s", optionfilehtm); 7682: #endif 7683: printf("Starting browser with: %s",pplotcmd);fflush(stdout); 7684: system(pplotcmd); 7685: } 7686: else if (z[0] == 'g') system(plotcmd); 7687: else if (z[0] == 'q') exit(0); 7688: } 7689: end: 7690: while (z[0] != 'q') { 7691: printf("\nType q for exiting: "); 7692: scanf("%s",z); 7693: } 7694: }