Annotation of imach/src/imach.c, revision 1.125
1.125 ! lievre 1: /* $Id: imach.c,v 1.124 2006/03/22 17:13:53 lievre Exp $
! 2: $State: Exp $
! 3: $Log: imach.c,v $
! 4: Revision 1.124 2006/03/22 17:13:53 lievre
! 5: Parameters are printed with %lf instead of %f (more numbers after the comma).
! 6: The log-likelihood is printed in the log file
! 7:
! 8: Revision 1.123 2006/03/20 10:52:43 brouard
! 9: * imach.c (Module): <title> changed, corresponds to .htm file
! 10: name. <head> headers where missing.
! 11:
! 12: * imach.c (Module): Weights can have a decimal point as for
! 13: English (a comma might work with a correct LC_NUMERIC environment,
! 14: otherwise the weight is truncated).
! 15: Modification of warning when the covariates values are not 0 or
! 16: 1.
! 17: Version 0.98g
! 18:
! 19: Revision 1.122 2006/03/20 09:45:41 brouard
! 20: (Module): Weights can have a decimal point as for
! 21: English (a comma might work with a correct LC_NUMERIC environment,
! 22: otherwise the weight is truncated).
! 23: Modification of warning when the covariates values are not 0 or
! 24: 1.
! 25: Version 0.98g
! 26:
! 27: Revision 1.121 2006/03/16 17:45:01 lievre
! 28: * imach.c (Module): Comments concerning covariates added
! 29:
! 30: * imach.c (Module): refinements in the computation of lli if
! 31: status=-2 in order to have more reliable computation if stepm is
! 32: not 1 month. Version 0.98f
! 33:
! 34: Revision 1.120 2006/03/16 15:10:38 lievre
! 35: (Module): refinements in the computation of lli if
! 36: status=-2 in order to have more reliable computation if stepm is
! 37: not 1 month. Version 0.98f
! 38:
! 39: Revision 1.119 2006/03/15 17:42:26 brouard
! 40: (Module): Bug if status = -2, the loglikelihood was
! 41: computed as likelihood omitting the logarithm. Version O.98e
! 42:
! 43: Revision 1.118 2006/03/14 18:20:07 brouard
! 44: (Module): varevsij Comments added explaining the second
! 45: table of variances if popbased=1 .
! 46: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
! 47: (Module): Function pstamp added
! 48: (Module): Version 0.98d
! 49:
! 50: Revision 1.117 2006/03/14 17:16:22 brouard
! 51: (Module): varevsij Comments added explaining the second
! 52: table of variances if popbased=1 .
! 53: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
! 54: (Module): Function pstamp added
! 55: (Module): Version 0.98d
! 56:
! 57: Revision 1.116 2006/03/06 10:29:27 brouard
! 58: (Module): Variance-covariance wrong links and
! 59: varian-covariance of ej. is needed (Saito).
! 60:
! 61: Revision 1.115 2006/02/27 12:17:45 brouard
! 62: (Module): One freematrix added in mlikeli! 0.98c
! 63:
! 64: Revision 1.114 2006/02/26 12:57:58 brouard
! 65: (Module): Some improvements in processing parameter
! 66: filename with strsep.
! 67:
! 68: Revision 1.113 2006/02/24 14:20:24 brouard
! 69: (Module): Memory leaks checks with valgrind and:
! 70: datafile was not closed, some imatrix were not freed and on matrix
! 71: allocation too.
! 72:
! 73: Revision 1.112 2006/01/30 09:55:26 brouard
! 74: (Module): Back to gnuplot.exe instead of wgnuplot.exe
! 75:
! 76: Revision 1.111 2006/01/25 20:38:18 brouard
! 77: (Module): Lots of cleaning and bugs added (Gompertz)
! 78: (Module): Comments can be added in data file. Missing date values
! 79: can be a simple dot '.'.
! 80:
! 81: Revision 1.110 2006/01/25 00:51:50 brouard
! 82: (Module): Lots of cleaning and bugs added (Gompertz)
! 83:
! 84: Revision 1.109 2006/01/24 19:37:15 brouard
! 85: (Module): Comments (lines starting with a #) are allowed in data.
! 86:
! 87: Revision 1.108 2006/01/19 18:05:42 lievre
! 88: Gnuplot problem appeared...
! 89: To be fixed
! 90:
! 91: Revision 1.107 2006/01/19 16:20:37 brouard
! 92: Test existence of gnuplot in imach path
! 93:
! 94: Revision 1.106 2006/01/19 13:24:36 brouard
! 95: Some cleaning and links added in html output
! 96:
! 97: Revision 1.105 2006/01/05 20:23:19 lievre
! 98: *** empty log message ***
! 99:
! 100: Revision 1.104 2005/09/30 16:11:43 lievre
! 101: (Module): sump fixed, loop imx fixed, and simplifications.
! 102: (Module): If the status is missing at the last wave but we know
! 103: that the person is alive, then we can code his/her status as -2
! 104: (instead of missing=-1 in earlier versions) and his/her
! 105: contributions to the likelihood is 1 - Prob of dying from last
! 106: health status (= 1-p13= p11+p12 in the easiest case of somebody in
! 107: the healthy state at last known wave). Version is 0.98
! 108:
! 109: Revision 1.103 2005/09/30 15:54:49 lievre
! 110: (Module): sump fixed, loop imx fixed, and simplifications.
! 111:
! 112: Revision 1.102 2004/09/15 17:31:30 brouard
! 113: Add the possibility to read data file including tab characters.
! 114:
! 115: Revision 1.101 2004/09/15 10:38:38 brouard
! 116: Fix on curr_time
! 117:
! 118: Revision 1.100 2004/07/12 18:29:06 brouard
! 119: Add version for Mac OS X. Just define UNIX in Makefile
! 120:
! 121: Revision 1.99 2004/06/05 08:57:40 brouard
! 122: *** empty log message ***
! 123:
! 124: Revision 1.98 2004/05/16 15:05:56 brouard
! 125: New version 0.97 . First attempt to estimate force of mortality
! 126: directly from the data i.e. without the need of knowing the health
! 127: state at each age, but using a Gompertz model: log u =a + b*age .
! 128: This is the basic analysis of mortality and should be done before any
! 129: other analysis, in order to test if the mortality estimated from the
! 130: cross-longitudinal survey is different from the mortality estimated
! 131: from other sources like vital statistic data.
! 132:
! 133: The same imach parameter file can be used but the option for mle should be -3.
! 134:
! 135: Agnès, who wrote this part of the code, tried to keep most of the
! 136: former routines in order to include the new code within the former code.
! 137:
! 138: The output is very simple: only an estimate of the intercept and of
! 139: the slope with 95% confident intervals.
! 140:
! 141: Current limitations:
! 142: A) Even if you enter covariates, i.e. with the
! 143: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
! 144: B) There is no computation of Life Expectancy nor Life Table.
! 145:
! 146: Revision 1.97 2004/02/20 13:25:42 lievre
! 147: Version 0.96d. Population forecasting command line is (temporarily)
! 148: suppressed.
! 149:
! 150: Revision 1.96 2003/07/15 15:38:55 brouard
! 151: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
! 152: rewritten within the same printf. Workaround: many printfs.
! 153:
! 154: Revision 1.95 2003/07/08 07:54:34 brouard
! 155: * imach.c (Repository):
! 156: (Repository): Using imachwizard code to output a more meaningful covariance
! 157: matrix (cov(a12,c31) instead of numbers.
! 158:
! 159: Revision 1.94 2003/06/27 13:00:02 brouard
! 160: Just cleaning
! 161:
! 162: Revision 1.93 2003/06/25 16:33:55 brouard
! 163: (Module): On windows (cygwin) function asctime_r doesn't
! 164: exist so I changed back to asctime which exists.
! 165: (Module): Version 0.96b
! 166:
! 167: Revision 1.92 2003/06/25 16:30:45 brouard
! 168: (Module): On windows (cygwin) function asctime_r doesn't
! 169: exist so I changed back to asctime which exists.
! 170:
! 171: Revision 1.91 2003/06/25 15:30:29 brouard
! 172: * imach.c (Repository): Duplicated warning errors corrected.
! 173: (Repository): Elapsed time after each iteration is now output. It
! 174: helps to forecast when convergence will be reached. Elapsed time
! 175: is stamped in powell. We created a new html file for the graphs
! 176: concerning matrix of covariance. It has extension -cov.htm.
! 177:
! 178: Revision 1.90 2003/06/24 12:34:15 brouard
! 179: (Module): Some bugs corrected for windows. Also, when
! 180: mle=-1 a template is output in file "or"mypar.txt with the design
! 181: of the covariance matrix to be input.
! 182:
! 183: Revision 1.89 2003/06/24 12:30:52 brouard
! 184: (Module): Some bugs corrected for windows. Also, when
! 185: mle=-1 a template is output in file "or"mypar.txt with the design
! 186: of the covariance matrix to be input.
! 187:
! 188: Revision 1.88 2003/06/23 17:54:56 brouard
! 189: * 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.
! 190:
! 191: Revision 1.87 2003/06/18 12:26:01 brouard
! 192: Version 0.96
! 193:
! 194: Revision 1.86 2003/06/17 20:04:08 brouard
! 195: (Module): Change position of html and gnuplot routines and added
! 196: routine fileappend.
! 197:
! 198: Revision 1.85 2003/06/17 13:12:43 brouard
! 199: * imach.c (Repository): Check when date of death was earlier that
! 200: current date of interview. It may happen when the death was just
! 201: prior to the death. In this case, dh was negative and likelihood
! 202: was wrong (infinity). We still send an "Error" but patch by
! 203: assuming that the date of death was just one stepm after the
! 204: interview.
! 205: (Repository): Because some people have very long ID (first column)
! 206: we changed int to long in num[] and we added a new lvector for
! 207: memory allocation. But we also truncated to 8 characters (left
! 208: truncation)
! 209: (Repository): No more line truncation errors.
! 210:
! 211: Revision 1.84 2003/06/13 21:44:43 brouard
! 212: * imach.c (Repository): Replace "freqsummary" at a correct
! 213: place. It differs from routine "prevalence" which may be called
! 214: many times. Probs is memory consuming and must be used with
! 215: parcimony.
! 216: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
! 217:
! 218: Revision 1.83 2003/06/10 13:39:11 lievre
! 219: *** empty log message ***
! 220:
! 221: Revision 1.82 2003/06/05 15:57:20 brouard
! 222: Add log in imach.c and fullversion number is now printed.
! 223:
! 224: */
! 225: /*
! 226: Interpolated Markov Chain
! 227:
! 228: Short summary of the programme:
! 229:
! 230: This program computes Healthy Life Expectancies from
! 231: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
! 232: first survey ("cross") where individuals from different ages are
! 233: interviewed on their health status or degree of disability (in the
! 234: case of a health survey which is our main interest) -2- at least a
! 235: second wave of interviews ("longitudinal") which measure each change
! 236: (if any) in individual health status. Health expectancies are
! 237: computed from the time spent in each health state according to a
! 238: model. More health states you consider, more time is necessary to reach the
! 239: Maximum Likelihood of the parameters involved in the model. The
! 240: simplest model is the multinomial logistic model where pij is the
! 241: probability to be observed in state j at the second wave
! 242: conditional to be observed in state i at the first wave. Therefore
! 243: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
! 244: 'age' is age and 'sex' is a covariate. If you want to have a more
! 245: complex model than "constant and age", you should modify the program
! 246: where the markup *Covariates have to be included here again* invites
! 247: you to do it. More covariates you add, slower the
! 248: convergence.
! 249:
! 250: The advantage of this computer programme, compared to a simple
! 251: multinomial logistic model, is clear when the delay between waves is not
! 252: identical for each individual. Also, if a individual missed an
! 253: intermediate interview, the information is lost, but taken into
! 254: account using an interpolation or extrapolation.
! 255:
! 256: hPijx is the probability to be observed in state i at age x+h
! 257: conditional to the observed state i at age x. The delay 'h' can be
! 258: split into an exact number (nh*stepm) of unobserved intermediate
! 259: states. This elementary transition (by month, quarter,
! 260: semester or year) is modelled as a multinomial logistic. The hPx
! 261: matrix is simply the matrix product of nh*stepm elementary matrices
! 262: and the contribution of each individual to the likelihood is simply
! 263: hPijx.
! 264:
! 265: Also this programme outputs the covariance matrix of the parameters but also
! 266: of the life expectancies. It also computes the period (stable) prevalence.
! 267:
! 268: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
! 269: Institut national d'études démographiques, Paris.
! 270: This software have been partly granted by Euro-REVES, a concerted action
! 271: from the European Union.
! 272: It is copyrighted identically to a GNU software product, ie programme and
! 273: software can be distributed freely for non commercial use. Latest version
! 274: can be accessed at http://euroreves.ined.fr/imach .
! 275:
! 276: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
! 277: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
! 278:
! 279: **********************************************************************/
! 280: /*
! 281: main
! 282: read parameterfile
! 283: read datafile
! 284: concatwav
! 285: freqsummary
! 286: if (mle >= 1)
! 287: mlikeli
! 288: print results files
! 289: if mle==1
! 290: computes hessian
! 291: read end of parameter file: agemin, agemax, bage, fage, estepm
! 292: begin-prev-date,...
! 293: open gnuplot file
! 294: open html file
! 295: period (stable) prevalence
! 296: for age prevalim()
! 297: h Pij x
! 298: variance of p varprob
! 299: forecasting if prevfcast==1 prevforecast call prevalence()
! 300: health expectancies
! 301: Variance-covariance of DFLE
! 302: prevalence()
! 303: movingaverage()
! 304: varevsij()
! 305: if popbased==1 varevsij(,popbased)
! 306: total life expectancies
! 307: Variance of period (stable) prevalence
! 308: end
! 309: */
! 310:
! 311:
! 312:
! 313:
! 314: #include <math.h>
! 315: #include <stdio.h>
! 316: #include <stdlib.h>
! 317: #include <string.h>
! 318: #include <unistd.h>
! 319:
! 320: #include <limits.h>
! 321: #include <sys/types.h>
! 322: #include <sys/stat.h>
! 323: #include <errno.h>
! 324: extern int errno;
! 325:
! 326: /* #include <sys/time.h> */
! 327: #include <time.h>
! 328: #include "timeval.h"
! 329:
! 330: /* #include <libintl.h> */
! 331: /* #define _(String) gettext (String) */
! 332:
! 333: #define MAXLINE 256
! 334:
! 335: #define GNUPLOTPROGRAM "gnuplot"
! 336: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
! 337: #define FILENAMELENGTH 132
! 338:
! 339: #define GLOCK_ERROR_NOPATH -1 /* empty path */
! 340: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
! 341:
! 342: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
! 343: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
! 344:
! 345: #define NINTERVMAX 8
! 346: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
! 347: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
! 348: #define NCOVMAX 8 /* Maximum number of covariates */
! 349: #define MAXN 20000
! 350: #define YEARM 12. /* Number of months per year */
! 351: #define AGESUP 130
! 352: #define AGEBASE 40
! 353: #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
! 354: #ifdef UNIX
! 355: #define DIRSEPARATOR '/'
! 356: #define CHARSEPARATOR "/"
! 357: #define ODIRSEPARATOR '\\'
! 358: #else
! 359: #define DIRSEPARATOR '\\'
! 360: #define CHARSEPARATOR "\\"
! 361: #define ODIRSEPARATOR '/'
! 362: #endif
! 363:
! 364: /* $Id: imach.c,v 1.124 2006/03/22 17:13:53 lievre Exp $ */
! 365: /* $State: Exp $ */
! 366:
! 367: char version[]="Imach version 0.98g, March 2006, INED-EUROREVES-Institut de longevite ";
! 368: char fullversion[]="$Revision: 1.124 $ $Date: 2006/03/22 17:13:53 $";
! 369: char strstart[80];
! 370: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
! 371: int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
! 372: int nvar;
! 373: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
! 374: int npar=NPARMAX;
! 375: int nlstate=2; /* Number of live states */
! 376: int ndeath=1; /* Number of dead states */
! 377: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
! 378: int popbased=0;
! 379:
! 380: int *wav; /* Number of waves for this individuual 0 is possible */
! 381: int maxwav; /* Maxim number of waves */
! 382: int jmin, jmax; /* min, max spacing between 2 waves */
! 383: int ijmin, ijmax; /* Individuals having jmin and jmax */
! 384: int gipmx, gsw; /* Global variables on the number of contributions
! 385: to the likelihood and the sum of weights (done by funcone)*/
! 386: int mle, weightopt;
! 387: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
! 388: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
! 389: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
! 390: * wave mi and wave mi+1 is not an exact multiple of stepm. */
! 391: double jmean; /* Mean space between 2 waves */
! 392: double **oldm, **newm, **savm; /* Working pointers to matrices */
! 393: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
! 394: FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
! 395: FILE *ficlog, *ficrespow;
! 396: int globpr; /* Global variable for printing or not */
! 397: double fretone; /* Only one call to likelihood */
! 398: long ipmx; /* Number of contributions */
! 399: double sw; /* Sum of weights */
! 400: char filerespow[FILENAMELENGTH];
! 401: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
! 402: FILE *ficresilk;
! 403: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
! 404: FILE *ficresprobmorprev;
! 405: FILE *fichtm, *fichtmcov; /* Html File */
! 406: FILE *ficreseij;
! 407: char filerese[FILENAMELENGTH];
! 408: FILE *ficresstdeij;
! 409: char fileresstde[FILENAMELENGTH];
! 410: FILE *ficrescveij;
! 411: char filerescve[FILENAMELENGTH];
! 412: FILE *ficresvij;
! 413: char fileresv[FILENAMELENGTH];
! 414: FILE *ficresvpl;
! 415: char fileresvpl[FILENAMELENGTH];
! 416: char title[MAXLINE];
! 417: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
! 418: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
! 419: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
! 420: char command[FILENAMELENGTH];
! 421: int outcmd=0;
! 422:
! 423: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
! 424:
! 425: char filelog[FILENAMELENGTH]; /* Log file */
! 426: char filerest[FILENAMELENGTH];
! 427: char fileregp[FILENAMELENGTH];
! 428: char popfile[FILENAMELENGTH];
! 429:
! 430: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
! 431:
! 432: struct timeval start_time, end_time, curr_time, last_time, forecast_time;
! 433: struct timezone tzp;
! 434: extern int gettimeofday();
! 435: struct tm tmg, tm, tmf, *gmtime(), *localtime();
! 436: long time_value;
! 437: extern long time();
! 438: char strcurr[80], strfor[80];
! 439:
! 440: char *endptr;
! 441: long lval;
! 442: double dval;
! 443:
! 444: #define NR_END 1
! 445: #define FREE_ARG char*
! 446: #define FTOL 1.0e-10
! 447:
! 448: #define NRANSI
! 449: #define ITMAX 200
! 450:
! 451: #define TOL 2.0e-4
! 452:
! 453: #define CGOLD 0.3819660
! 454: #define ZEPS 1.0e-10
! 455: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
! 456:
! 457: #define GOLD 1.618034
! 458: #define GLIMIT 100.0
! 459: #define TINY 1.0e-20
! 460:
! 461: static double maxarg1,maxarg2;
! 462: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
! 463: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
! 464:
! 465: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
! 466: #define rint(a) floor(a+0.5)
! 467:
! 468: static double sqrarg;
! 469: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
! 470: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
! 471: int agegomp= AGEGOMP;
! 472:
! 473: int imx;
! 474: int stepm=1;
! 475: /* Stepm, step in month: minimum step interpolation*/
! 476:
! 477: int estepm;
! 478: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
! 479:
! 480: int m,nb;
! 481: long *num;
! 482: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
! 483: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
! 484: double **pmmij, ***probs;
! 485: double *ageexmed,*agecens;
! 486: double dateintmean=0;
! 487:
! 488: double *weight;
! 489: int **s; /* Status */
! 490: double *agedc, **covar, idx;
! 491: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
! 492: double *lsurv, *lpop, *tpop;
! 493:
! 494: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
! 495: double ftolhess; /* Tolerance for computing hessian */
! 496:
! 497: /**************** split *************************/
! 498: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
! 499: {
! 500: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
! 501: the name of the file (name), its extension only (ext) and its first part of the name (finame)
! 502: */
! 503: char *ss; /* pointer */
! 504: int l1, l2; /* length counters */
! 505:
! 506: l1 = strlen(path ); /* length of path */
! 507: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
! 508: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
! 509: if ( ss == NULL ) { /* no directory, so determine current directory */
! 510: strcpy( name, path ); /* we got the fullname name because no directory */
! 511: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
! 512: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
! 513: /* get current working directory */
! 514: /* extern char* getcwd ( char *buf , int len);*/
! 515: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
! 516: return( GLOCK_ERROR_GETCWD );
! 517: }
! 518: /* got dirc from getcwd*/
! 519: printf(" DIRC = %s \n",dirc);
! 520: } else { /* strip direcotry from path */
! 521: ss++; /* after this, the filename */
! 522: l2 = strlen( ss ); /* length of filename */
! 523: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
! 524: strcpy( name, ss ); /* save file name */
! 525: strncpy( dirc, path, l1 - l2 ); /* now the directory */
! 526: dirc[l1-l2] = 0; /* add zero */
! 527: printf(" DIRC2 = %s \n",dirc);
! 528: }
! 529: /* We add a separator at the end of dirc if not exists */
! 530: l1 = strlen( dirc ); /* length of directory */
! 531: if( dirc[l1-1] != DIRSEPARATOR ){
! 532: dirc[l1] = DIRSEPARATOR;
! 533: dirc[l1+1] = 0;
! 534: printf(" DIRC3 = %s \n",dirc);
! 535: }
! 536: ss = strrchr( name, '.' ); /* find last / */
! 537: if (ss >0){
! 538: ss++;
! 539: strcpy(ext,ss); /* save extension */
! 540: l1= strlen( name);
! 541: l2= strlen(ss)+1;
! 542: strncpy( finame, name, l1-l2);
! 543: finame[l1-l2]= 0;
! 544: }
! 545:
! 546: return( 0 ); /* we're done */
! 547: }
! 548:
! 549:
! 550: /******************************************/
! 551:
! 552: void replace_back_to_slash(char *s, char*t)
! 553: {
! 554: int i;
! 555: int lg=0;
! 556: i=0;
! 557: lg=strlen(t);
! 558: for(i=0; i<= lg; i++) {
! 559: (s[i] = t[i]);
! 560: if (t[i]== '\\') s[i]='/';
! 561: }
! 562: }
! 563:
! 564: int nbocc(char *s, char occ)
! 565: {
! 566: int i,j=0;
! 567: int lg=20;
! 568: i=0;
! 569: lg=strlen(s);
! 570: for(i=0; i<= lg; i++) {
! 571: if (s[i] == occ ) j++;
! 572: }
! 573: return j;
! 574: }
! 575:
! 576: void cutv(char *u,char *v, char*t, char occ)
! 577: {
! 578: /* cuts string t into u and v where u ends before first occurence of char 'occ'
! 579: and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
! 580: gives u="abcedf" and v="ghi2j" */
! 581: int i,lg,j,p=0;
! 582: i=0;
! 583: for(j=0; j<=strlen(t)-1; j++) {
! 584: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
! 585: }
! 586:
! 587: lg=strlen(t);
! 588: for(j=0; j<p; j++) {
! 589: (u[j] = t[j]);
! 590: }
! 591: u[p]='\0';
! 592:
! 593: for(j=0; j<= lg; j++) {
! 594: if (j>=(p+1))(v[j-p-1] = t[j]);
! 595: }
! 596: }
! 597:
! 598: /********************** nrerror ********************/
! 599:
! 600: void nrerror(char error_text[])
! 601: {
! 602: fprintf(stderr,"ERREUR ...\n");
! 603: fprintf(stderr,"%s\n",error_text);
! 604: exit(EXIT_FAILURE);
! 605: }
! 606: /*********************** vector *******************/
! 607: double *vector(int nl, int nh)
! 608: {
! 609: double *v;
! 610: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
! 611: if (!v) nrerror("allocation failure in vector");
! 612: return v-nl+NR_END;
! 613: }
! 614:
! 615: /************************ free vector ******************/
! 616: void free_vector(double*v, int nl, int nh)
! 617: {
! 618: free((FREE_ARG)(v+nl-NR_END));
! 619: }
! 620:
! 621: /************************ivector *******************************/
! 622: int *ivector(long nl,long nh)
! 623: {
! 624: int *v;
! 625: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
! 626: if (!v) nrerror("allocation failure in ivector");
! 627: return v-nl+NR_END;
! 628: }
! 629:
! 630: /******************free ivector **************************/
! 631: void free_ivector(int *v, long nl, long nh)
! 632: {
! 633: free((FREE_ARG)(v+nl-NR_END));
! 634: }
! 635:
! 636: /************************lvector *******************************/
! 637: long *lvector(long nl,long nh)
! 638: {
! 639: long *v;
! 640: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
! 641: if (!v) nrerror("allocation failure in ivector");
! 642: return v-nl+NR_END;
! 643: }
! 644:
! 645: /******************free lvector **************************/
! 646: void free_lvector(long *v, long nl, long nh)
! 647: {
! 648: free((FREE_ARG)(v+nl-NR_END));
! 649: }
! 650:
! 651: /******************* imatrix *******************************/
! 652: int **imatrix(long nrl, long nrh, long ncl, long nch)
! 653: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
! 654: {
! 655: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
! 656: int **m;
! 657:
! 658: /* allocate pointers to rows */
! 659: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
! 660: if (!m) nrerror("allocation failure 1 in matrix()");
! 661: m += NR_END;
! 662: m -= nrl;
! 663:
! 664:
! 665: /* allocate rows and set pointers to them */
! 666: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
! 667: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
! 668: m[nrl] += NR_END;
! 669: m[nrl] -= ncl;
! 670:
! 671: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
! 672:
! 673: /* return pointer to array of pointers to rows */
! 674: return m;
! 675: }
! 676:
! 677: /****************** free_imatrix *************************/
! 678: void free_imatrix(m,nrl,nrh,ncl,nch)
! 679: int **m;
! 680: long nch,ncl,nrh,nrl;
! 681: /* free an int matrix allocated by imatrix() */
! 682: {
! 683: free((FREE_ARG) (m[nrl]+ncl-NR_END));
! 684: free((FREE_ARG) (m+nrl-NR_END));
! 685: }
! 686:
! 687: /******************* matrix *******************************/
! 688: double **matrix(long nrl, long nrh, long ncl, long nch)
! 689: {
! 690: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
! 691: double **m;
! 692:
! 693: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
! 694: if (!m) nrerror("allocation failure 1 in matrix()");
! 695: m += NR_END;
! 696: m -= nrl;
! 697:
! 698: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
! 699: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
! 700: m[nrl] += NR_END;
! 701: m[nrl] -= ncl;
! 702:
! 703: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
! 704: return m;
! 705: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
! 706: */
! 707: }
! 708:
! 709: /*************************free matrix ************************/
! 710: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
! 711: {
! 712: free((FREE_ARG)(m[nrl]+ncl-NR_END));
! 713: free((FREE_ARG)(m+nrl-NR_END));
! 714: }
! 715:
! 716: /******************* ma3x *******************************/
! 717: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
! 718: {
! 719: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
! 720: double ***m;
! 721:
! 722: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
! 723: if (!m) nrerror("allocation failure 1 in matrix()");
! 724: m += NR_END;
! 725: m -= nrl;
! 726:
! 727: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
! 728: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
! 729: m[nrl] += NR_END;
! 730: m[nrl] -= ncl;
! 731:
! 732: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
! 733:
! 734: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
! 735: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
! 736: m[nrl][ncl] += NR_END;
! 737: m[nrl][ncl] -= nll;
! 738: for (j=ncl+1; j<=nch; j++)
! 739: m[nrl][j]=m[nrl][j-1]+nlay;
! 740:
! 741: for (i=nrl+1; i<=nrh; i++) {
! 742: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
! 743: for (j=ncl+1; j<=nch; j++)
! 744: m[i][j]=m[i][j-1]+nlay;
! 745: }
! 746: return m;
! 747: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
! 748: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
! 749: */
! 750: }
! 751:
! 752: /*************************free ma3x ************************/
! 753: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
! 754: {
! 755: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
! 756: free((FREE_ARG)(m[nrl]+ncl-NR_END));
! 757: free((FREE_ARG)(m+nrl-NR_END));
! 758: }
! 759:
! 760: /*************** function subdirf ***********/
! 761: char *subdirf(char fileres[])
! 762: {
! 763: /* Caution optionfilefiname is hidden */
! 764: strcpy(tmpout,optionfilefiname);
! 765: strcat(tmpout,"/"); /* Add to the right */
! 766: strcat(tmpout,fileres);
! 767: return tmpout;
! 768: }
! 769:
! 770: /*************** function subdirf2 ***********/
! 771: char *subdirf2(char fileres[], char *preop)
! 772: {
! 773:
! 774: /* Caution optionfilefiname is hidden */
! 775: strcpy(tmpout,optionfilefiname);
! 776: strcat(tmpout,"/");
! 777: strcat(tmpout,preop);
! 778: strcat(tmpout,fileres);
! 779: return tmpout;
! 780: }
! 781:
! 782: /*************** function subdirf3 ***********/
! 783: char *subdirf3(char fileres[], char *preop, char *preop2)
! 784: {
! 785:
! 786: /* Caution optionfilefiname is hidden */
! 787: strcpy(tmpout,optionfilefiname);
! 788: strcat(tmpout,"/");
! 789: strcat(tmpout,preop);
! 790: strcat(tmpout,preop2);
! 791: strcat(tmpout,fileres);
! 792: return tmpout;
! 793: }
! 794:
! 795: /***************** f1dim *************************/
! 796: extern int ncom;
! 797: extern double *pcom,*xicom;
! 798: extern double (*nrfunc)(double []);
! 799:
! 800: double f1dim(double x)
! 801: {
! 802: int j;
! 803: double f;
! 804: double *xt;
! 805:
! 806: xt=vector(1,ncom);
! 807: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
! 808: f=(*nrfunc)(xt);
! 809: free_vector(xt,1,ncom);
! 810: return f;
! 811: }
! 812:
! 813: /*****************brent *************************/
! 814: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
! 815: {
! 816: int iter;
! 817: double a,b,d,etemp;
! 818: double fu,fv,fw,fx;
! 819: double ftemp;
! 820: double p,q,r,tol1,tol2,u,v,w,x,xm;
! 821: double e=0.0;
! 822:
! 823: a=(ax < cx ? ax : cx);
! 824: b=(ax > cx ? ax : cx);
! 825: x=w=v=bx;
! 826: fw=fv=fx=(*f)(x);
! 827: for (iter=1;iter<=ITMAX;iter++) {
! 828: xm=0.5*(a+b);
! 829: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
! 830: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
! 831: printf(".");fflush(stdout);
! 832: fprintf(ficlog,".");fflush(ficlog);
! 833: #ifdef DEBUG
! 834: 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);
! 835: 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);
! 836: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
! 837: #endif
! 838: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
! 839: *xmin=x;
! 840: return fx;
! 841: }
! 842: ftemp=fu;
! 843: if (fabs(e) > tol1) {
! 844: r=(x-w)*(fx-fv);
! 845: q=(x-v)*(fx-fw);
! 846: p=(x-v)*q-(x-w)*r;
! 847: q=2.0*(q-r);
! 848: if (q > 0.0) p = -p;
! 849: q=fabs(q);
! 850: etemp=e;
! 851: e=d;
! 852: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
! 853: d=CGOLD*(e=(x >= xm ? a-x : b-x));
! 854: else {
! 855: d=p/q;
! 856: u=x+d;
! 857: if (u-a < tol2 || b-u < tol2)
! 858: d=SIGN(tol1,xm-x);
! 859: }
! 860: } else {
! 861: d=CGOLD*(e=(x >= xm ? a-x : b-x));
! 862: }
! 863: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
! 864: fu=(*f)(u);
! 865: if (fu <= fx) {
! 866: if (u >= x) a=x; else b=x;
! 867: SHFT(v,w,x,u)
! 868: SHFT(fv,fw,fx,fu)
! 869: } else {
! 870: if (u < x) a=u; else b=u;
! 871: if (fu <= fw || w == x) {
! 872: v=w;
! 873: w=u;
! 874: fv=fw;
! 875: fw=fu;
! 876: } else if (fu <= fv || v == x || v == w) {
! 877: v=u;
! 878: fv=fu;
! 879: }
! 880: }
! 881: }
! 882: nrerror("Too many iterations in brent");
! 883: *xmin=x;
! 884: return fx;
! 885: }
! 886:
! 887: /****************** mnbrak ***********************/
! 888:
! 889: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
! 890: double (*func)(double))
! 891: {
! 892: double ulim,u,r,q, dum;
! 893: double fu;
! 894:
! 895: *fa=(*func)(*ax);
! 896: *fb=(*func)(*bx);
! 897: if (*fb > *fa) {
! 898: SHFT(dum,*ax,*bx,dum)
! 899: SHFT(dum,*fb,*fa,dum)
! 900: }
! 901: *cx=(*bx)+GOLD*(*bx-*ax);
! 902: *fc=(*func)(*cx);
! 903: while (*fb > *fc) {
! 904: r=(*bx-*ax)*(*fb-*fc);
! 905: q=(*bx-*cx)*(*fb-*fa);
! 906: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
! 907: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
! 908: ulim=(*bx)+GLIMIT*(*cx-*bx);
! 909: if ((*bx-u)*(u-*cx) > 0.0) {
! 910: fu=(*func)(u);
! 911: } else if ((*cx-u)*(u-ulim) > 0.0) {
! 912: fu=(*func)(u);
! 913: if (fu < *fc) {
! 914: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
! 915: SHFT(*fb,*fc,fu,(*func)(u))
! 916: }
! 917: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
! 918: u=ulim;
! 919: fu=(*func)(u);
! 920: } else {
! 921: u=(*cx)+GOLD*(*cx-*bx);
! 922: fu=(*func)(u);
! 923: }
! 924: SHFT(*ax,*bx,*cx,u)
! 925: SHFT(*fa,*fb,*fc,fu)
! 926: }
! 927: }
! 928:
! 929: /*************** linmin ************************/
! 930:
! 931: int ncom;
! 932: double *pcom,*xicom;
! 933: double (*nrfunc)(double []);
! 934:
! 935: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
! 936: {
! 937: double brent(double ax, double bx, double cx,
! 938: double (*f)(double), double tol, double *xmin);
! 939: double f1dim(double x);
! 940: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
! 941: double *fc, double (*func)(double));
! 942: int j;
! 943: double xx,xmin,bx,ax;
! 944: double fx,fb,fa;
! 945:
! 946: ncom=n;
! 947: pcom=vector(1,n);
! 948: xicom=vector(1,n);
! 949: nrfunc=func;
! 950: for (j=1;j<=n;j++) {
! 951: pcom[j]=p[j];
! 952: xicom[j]=xi[j];
! 953: }
! 954: ax=0.0;
! 955: xx=1.0;
! 956: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
! 957: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
! 958: #ifdef DEBUG
! 959: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
! 960: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
! 961: #endif
! 962: for (j=1;j<=n;j++) {
! 963: xi[j] *= xmin;
! 964: p[j] += xi[j];
! 965: }
! 966: free_vector(xicom,1,n);
! 967: free_vector(pcom,1,n);
! 968: }
! 969:
! 970: char *asc_diff_time(long time_sec, char ascdiff[])
! 971: {
! 972: long sec_left, days, hours, minutes;
! 973: days = (time_sec) / (60*60*24);
! 974: sec_left = (time_sec) % (60*60*24);
! 975: hours = (sec_left) / (60*60) ;
! 976: sec_left = (sec_left) %(60*60);
! 977: minutes = (sec_left) /60;
! 978: sec_left = (sec_left) % (60);
! 979: sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
! 980: return ascdiff;
! 981: }
! 982:
! 983: /*************** powell ************************/
! 984: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
! 985: double (*func)(double []))
! 986: {
! 987: void linmin(double p[], double xi[], int n, double *fret,
! 988: double (*func)(double []));
! 989: int i,ibig,j;
! 990: double del,t,*pt,*ptt,*xit;
! 991: double fp,fptt;
! 992: double *xits;
! 993: int niterf, itmp;
! 994:
! 995: pt=vector(1,n);
! 996: ptt=vector(1,n);
! 997: xit=vector(1,n);
! 998: xits=vector(1,n);
! 999: *fret=(*func)(p);
! 1000: for (j=1;j<=n;j++) pt[j]=p[j];
! 1001: for (*iter=1;;++(*iter)) {
! 1002: fp=(*fret);
! 1003: ibig=0;
! 1004: del=0.0;
! 1005: last_time=curr_time;
! 1006: (void) gettimeofday(&curr_time,&tzp);
! 1007: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
! 1008: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog);
! 1009: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
! 1010: for (i=1;i<=n;i++) {
! 1011: printf(" %d %.12f",i, p[i]);
! 1012: fprintf(ficlog," %d %.12lf",i, p[i]);
! 1013: fprintf(ficrespow," %.12lf", p[i]);
! 1014: }
! 1015: printf("\n");
! 1016: fprintf(ficlog,"\n");
! 1017: fprintf(ficrespow,"\n");fflush(ficrespow);
! 1018: if(*iter <=3){
! 1019: tm = *localtime(&curr_time.tv_sec);
! 1020: strcpy(strcurr,asctime(&tm));
! 1021: /* asctime_r(&tm,strcurr); */
! 1022: forecast_time=curr_time;
! 1023: itmp = strlen(strcurr);
! 1024: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
! 1025: strcurr[itmp-1]='\0';
! 1026: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
! 1027: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
! 1028: for(niterf=10;niterf<=30;niterf+=10){
! 1029: forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
! 1030: tmf = *localtime(&forecast_time.tv_sec);
! 1031: /* asctime_r(&tmf,strfor); */
! 1032: strcpy(strfor,asctime(&tmf));
! 1033: itmp = strlen(strfor);
! 1034: if(strfor[itmp-1]=='\n')
! 1035: strfor[itmp-1]='\0';
! 1036: printf(" - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
! 1037: fprintf(ficlog," - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
! 1038: }
! 1039: }
! 1040: for (i=1;i<=n;i++) {
! 1041: for (j=1;j<=n;j++) xit[j]=xi[j][i];
! 1042: fptt=(*fret);
! 1043: #ifdef DEBUG
! 1044: printf("fret=%lf \n",*fret);
! 1045: fprintf(ficlog,"fret=%lf \n",*fret);
! 1046: #endif
! 1047: printf("%d",i);fflush(stdout);
! 1048: fprintf(ficlog,"%d",i);fflush(ficlog);
! 1049: linmin(p,xit,n,fret,func);
! 1050: if (fabs(fptt-(*fret)) > del) {
! 1051: del=fabs(fptt-(*fret));
! 1052: ibig=i;
! 1053: }
! 1054: #ifdef DEBUG
! 1055: printf("%d %.12e",i,(*fret));
! 1056: fprintf(ficlog,"%d %.12e",i,(*fret));
! 1057: for (j=1;j<=n;j++) {
! 1058: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
! 1059: printf(" x(%d)=%.12e",j,xit[j]);
! 1060: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
! 1061: }
! 1062: for(j=1;j<=n;j++) {
! 1063: printf(" p=%.12e",p[j]);
! 1064: fprintf(ficlog," p=%.12e",p[j]);
! 1065: }
! 1066: printf("\n");
! 1067: fprintf(ficlog,"\n");
! 1068: #endif
! 1069: }
! 1070: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
! 1071: #ifdef DEBUG
! 1072: int k[2],l;
! 1073: k[0]=1;
! 1074: k[1]=-1;
! 1075: printf("Max: %.12e",(*func)(p));
! 1076: fprintf(ficlog,"Max: %.12e",(*func)(p));
! 1077: for (j=1;j<=n;j++) {
! 1078: printf(" %.12e",p[j]);
! 1079: fprintf(ficlog," %.12e",p[j]);
! 1080: }
! 1081: printf("\n");
! 1082: fprintf(ficlog,"\n");
! 1083: for(l=0;l<=1;l++) {
! 1084: for (j=1;j<=n;j++) {
! 1085: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
! 1086: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
! 1087: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
! 1088: }
! 1089: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
! 1090: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
! 1091: }
! 1092: #endif
! 1093:
! 1094:
! 1095: free_vector(xit,1,n);
! 1096: free_vector(xits,1,n);
! 1097: free_vector(ptt,1,n);
! 1098: free_vector(pt,1,n);
! 1099: return;
! 1100: }
! 1101: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
! 1102: for (j=1;j<=n;j++) {
! 1103: ptt[j]=2.0*p[j]-pt[j];
! 1104: xit[j]=p[j]-pt[j];
! 1105: pt[j]=p[j];
! 1106: }
! 1107: fptt=(*func)(ptt);
! 1108: if (fptt < fp) {
! 1109: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
! 1110: if (t < 0.0) {
! 1111: linmin(p,xit,n,fret,func);
! 1112: for (j=1;j<=n;j++) {
! 1113: xi[j][ibig]=xi[j][n];
! 1114: xi[j][n]=xit[j];
! 1115: }
! 1116: #ifdef DEBUG
! 1117: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
! 1118: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
! 1119: for(j=1;j<=n;j++){
! 1120: printf(" %.12e",xit[j]);
! 1121: fprintf(ficlog," %.12e",xit[j]);
! 1122: }
! 1123: printf("\n");
! 1124: fprintf(ficlog,"\n");
! 1125: #endif
! 1126: }
! 1127: }
! 1128: }
! 1129: }
! 1130:
! 1131: /**** Prevalence limit (stable or period prevalence) ****************/
! 1132:
! 1133: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
! 1134: {
! 1135: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
! 1136: matrix by transitions matrix until convergence is reached */
! 1137:
! 1138: int i, ii,j,k;
! 1139: double min, max, maxmin, maxmax,sumnew=0.;
! 1140: double **matprod2();
! 1141: double **out, cov[NCOVMAX], **pmij();
! 1142: double **newm;
! 1143: double agefin, delaymax=50 ; /* Max number of years to converge */
! 1144:
! 1145: for (ii=1;ii<=nlstate+ndeath;ii++)
! 1146: for (j=1;j<=nlstate+ndeath;j++){
! 1147: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
! 1148: }
! 1149:
! 1150: cov[1]=1.;
! 1151:
! 1152: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
! 1153: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
! 1154: newm=savm;
! 1155: /* Covariates have to be included here again */
! 1156: cov[2]=agefin;
! 1157:
! 1158: for (k=1; k<=cptcovn;k++) {
! 1159: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
! 1160: /* printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
! 1161: }
! 1162: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
! 1163: for (k=1; k<=cptcovprod;k++)
! 1164: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
! 1165:
! 1166: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
! 1167: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
! 1168: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
! 1169: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
! 1170:
! 1171: savm=oldm;
! 1172: oldm=newm;
! 1173: maxmax=0.;
! 1174: for(j=1;j<=nlstate;j++){
! 1175: min=1.;
! 1176: max=0.;
! 1177: for(i=1; i<=nlstate; i++) {
! 1178: sumnew=0;
! 1179: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
! 1180: prlim[i][j]= newm[i][j]/(1-sumnew);
! 1181: max=FMAX(max,prlim[i][j]);
! 1182: min=FMIN(min,prlim[i][j]);
! 1183: }
! 1184: maxmin=max-min;
! 1185: maxmax=FMAX(maxmax,maxmin);
! 1186: }
! 1187: if(maxmax < ftolpl){
! 1188: return prlim;
! 1189: }
! 1190: }
! 1191: }
! 1192:
! 1193: /*************** transition probabilities ***************/
! 1194:
! 1195: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
! 1196: {
! 1197: double s1, s2;
! 1198: /*double t34;*/
! 1199: int i,j,j1, nc, ii, jj;
! 1200:
! 1201: for(i=1; i<= nlstate; i++){
! 1202: for(j=1; j<i;j++){
! 1203: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
! 1204: /*s2 += param[i][j][nc]*cov[nc];*/
! 1205: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
! 1206: /* printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
! 1207: }
! 1208: ps[i][j]=s2;
! 1209: /* printf("s1=%.17e, s2=%.17e\n",s1,s2); */
! 1210: }
! 1211: for(j=i+1; j<=nlstate+ndeath;j++){
! 1212: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
! 1213: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
! 1214: /* printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
! 1215: }
! 1216: ps[i][j]=s2;
! 1217: }
! 1218: }
! 1219: /*ps[3][2]=1;*/
! 1220:
! 1221: for(i=1; i<= nlstate; i++){
! 1222: s1=0;
! 1223: for(j=1; j<i; j++)
! 1224: s1+=exp(ps[i][j]);
! 1225: for(j=i+1; j<=nlstate+ndeath; j++)
! 1226: s1+=exp(ps[i][j]);
! 1227: ps[i][i]=1./(s1+1.);
! 1228: for(j=1; j<i; j++)
! 1229: ps[i][j]= exp(ps[i][j])*ps[i][i];
! 1230: for(j=i+1; j<=nlstate+ndeath; j++)
! 1231: ps[i][j]= exp(ps[i][j])*ps[i][i];
! 1232: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
! 1233: } /* end i */
! 1234:
! 1235: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
! 1236: for(jj=1; jj<= nlstate+ndeath; jj++){
! 1237: ps[ii][jj]=0;
! 1238: ps[ii][ii]=1;
! 1239: }
! 1240: }
! 1241:
! 1242:
! 1243: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
! 1244: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
! 1245: /* printf("ddd %lf ",ps[ii][jj]); */
! 1246: /* } */
! 1247: /* printf("\n "); */
! 1248: /* } */
! 1249: /* printf("\n ");printf("%lf ",cov[2]); */
! 1250: /*
! 1251: for(i=1; i<= npar; i++) printf("%f ",x[i]);
! 1252: goto end;*/
! 1253: return ps;
! 1254: }
! 1255:
! 1256: /**************** Product of 2 matrices ******************/
! 1257:
! 1258: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
! 1259: {
! 1260: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
! 1261: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
! 1262: /* in, b, out are matrice of pointers which should have been initialized
! 1263: before: only the contents of out is modified. The function returns
! 1264: a pointer to pointers identical to out */
! 1265: long i, j, k;
! 1266: for(i=nrl; i<= nrh; i++)
! 1267: for(k=ncolol; k<=ncoloh; k++)
! 1268: for(j=ncl,out[i][k]=0.; j<=nch; j++)
! 1269: out[i][k] +=in[i][j]*b[j][k];
! 1270:
! 1271: return out;
! 1272: }
! 1273:
! 1274:
! 1275: /************* Higher Matrix Product ***************/
! 1276:
! 1277: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
! 1278: {
! 1279: /* Computes the transition matrix starting at age 'age' over
! 1280: 'nhstepm*hstepm*stepm' months (i.e. until
! 1281: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
! 1282: nhstepm*hstepm matrices.
! 1283: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
! 1284: (typically every 2 years instead of every month which is too big
! 1285: for the memory).
! 1286: Model is determined by parameters x and covariates have to be
! 1287: included manually here.
! 1288:
! 1289: */
! 1290:
! 1291: int i, j, d, h, k;
! 1292: double **out, cov[NCOVMAX];
! 1293: double **newm;
! 1294:
! 1295: /* Hstepm could be zero and should return the unit matrix */
! 1296: for (i=1;i<=nlstate+ndeath;i++)
! 1297: for (j=1;j<=nlstate+ndeath;j++){
! 1298: oldm[i][j]=(i==j ? 1.0 : 0.0);
! 1299: po[i][j][0]=(i==j ? 1.0 : 0.0);
! 1300: }
! 1301: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
! 1302: for(h=1; h <=nhstepm; h++){
! 1303: for(d=1; d <=hstepm; d++){
! 1304: newm=savm;
! 1305: /* Covariates have to be included here again */
! 1306: cov[1]=1.;
! 1307: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
! 1308: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
! 1309: for (k=1; k<=cptcovage;k++)
! 1310: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
! 1311: for (k=1; k<=cptcovprod;k++)
! 1312: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
! 1313:
! 1314:
! 1315: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
! 1316: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
! 1317: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
! 1318: pmij(pmmij,cov,ncovmodel,x,nlstate));
! 1319: savm=oldm;
! 1320: oldm=newm;
! 1321: }
! 1322: for(i=1; i<=nlstate+ndeath; i++)
! 1323: for(j=1;j<=nlstate+ndeath;j++) {
! 1324: po[i][j][h]=newm[i][j];
! 1325: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
! 1326: */
! 1327: }
! 1328: } /* end h */
! 1329: return po;
! 1330: }
! 1331:
! 1332:
! 1333: /*************** log-likelihood *************/
! 1334: double func( double *x)
! 1335: {
! 1336: int i, ii, j, k, mi, d, kk;
! 1337: double l, ll[NLSTATEMAX], cov[NCOVMAX];
! 1338: double **out;
! 1339: double sw; /* Sum of weights */
! 1340: double lli; /* Individual log likelihood */
! 1341: int s1, s2;
! 1342: double bbh, survp;
! 1343: long ipmx;
! 1344: /*extern weight */
! 1345: /* We are differentiating ll according to initial status */
! 1346: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
! 1347: /*for(i=1;i<imx;i++)
! 1348: printf(" %d\n",s[4][i]);
! 1349: */
! 1350: cov[1]=1.;
! 1351:
! 1352: for(k=1; k<=nlstate; k++) ll[k]=0.;
! 1353:
! 1354: if(mle==1){
! 1355: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
! 1356: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
! 1357: for(mi=1; mi<= wav[i]-1; mi++){
! 1358: for (ii=1;ii<=nlstate+ndeath;ii++)
! 1359: for (j=1;j<=nlstate+ndeath;j++){
! 1360: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
! 1361: savm[ii][j]=(ii==j ? 1.0 : 0.0);
! 1362: }
! 1363: for(d=0; d<dh[mi][i]; d++){
! 1364: newm=savm;
! 1365: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
! 1366: for (kk=1; kk<=cptcovage;kk++) {
! 1367: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
! 1368: }
! 1369: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
! 1370: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
! 1371: savm=oldm;
! 1372: oldm=newm;
! 1373: } /* end mult */
! 1374:
! 1375: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
! 1376: /* But now since version 0.9 we anticipate for bias at large stepm.
! 1377: * If stepm is larger than one month (smallest stepm) and if the exact delay
! 1378: * (in months) between two waves is not a multiple of stepm, we rounded to
! 1379: * the nearest (and in case of equal distance, to the lowest) interval but now
! 1380: * we keep into memory the bias bh[mi][i] and also the previous matrix product
! 1381: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
! 1382: * probability in order to take into account the bias as a fraction of the way
! 1383: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
! 1384: * -stepm/2 to stepm/2 .
! 1385: * For stepm=1 the results are the same as for previous versions of Imach.
! 1386: * For stepm > 1 the results are less biased than in previous versions.
! 1387: */
! 1388: s1=s[mw[mi][i]][i];
! 1389: s2=s[mw[mi+1][i]][i];
! 1390: bbh=(double)bh[mi][i]/(double)stepm;
! 1391: /* bias bh is positive if real duration
! 1392: * is higher than the multiple of stepm and negative otherwise.
! 1393: */
! 1394: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
! 1395: if( s2 > nlstate){
! 1396: /* i.e. if s2 is a death state and if the date of death is known
! 1397: then the contribution to the likelihood is the probability to
! 1398: die between last step unit time and current step unit time,
! 1399: which is also equal to probability to die before dh
! 1400: minus probability to die before dh-stepm .
! 1401: In version up to 0.92 likelihood was computed
! 1402: as if date of death was unknown. Death was treated as any other
! 1403: health state: the date of the interview describes the actual state
! 1404: and not the date of a change in health state. The former idea was
! 1405: to consider that at each interview the state was recorded
! 1406: (healthy, disable or death) and IMaCh was corrected; but when we
! 1407: introduced the exact date of death then we should have modified
! 1408: the contribution of an exact death to the likelihood. This new
! 1409: contribution is smaller and very dependent of the step unit
! 1410: stepm. It is no more the probability to die between last interview
! 1411: and month of death but the probability to survive from last
! 1412: interview up to one month before death multiplied by the
! 1413: probability to die within a month. Thanks to Chris
! 1414: Jackson for correcting this bug. Former versions increased
! 1415: mortality artificially. The bad side is that we add another loop
! 1416: which slows down the processing. The difference can be up to 10%
! 1417: lower mortality.
! 1418: */
! 1419: lli=log(out[s1][s2] - savm[s1][s2]);
! 1420:
! 1421:
! 1422: } else if (s2==-2) {
! 1423: for (j=1,survp=0. ; j<=nlstate; j++)
! 1424: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
! 1425: /*survp += out[s1][j]; */
! 1426: lli= log(survp);
! 1427: }
! 1428:
! 1429: else if (s2==-4) {
! 1430: for (j=3,survp=0. ; j<=nlstate; j++)
! 1431: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
! 1432: lli= log(survp);
! 1433: }
! 1434:
! 1435: else if (s2==-5) {
! 1436: for (j=1,survp=0. ; j<=2; j++)
! 1437: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
! 1438: lli= log(survp);
! 1439: }
! 1440:
! 1441: else{
! 1442: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
! 1443: /* 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 */
! 1444: }
! 1445: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
! 1446: /*if(lli ==000.0)*/
! 1447: /*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); */
! 1448: ipmx +=1;
! 1449: sw += weight[i];
! 1450: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
! 1451: } /* end of wave */
! 1452: } /* end of individual */
! 1453: } else if(mle==2){
! 1454: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
! 1455: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
! 1456: for(mi=1; mi<= wav[i]-1; mi++){
! 1457: for (ii=1;ii<=nlstate+ndeath;ii++)
! 1458: for (j=1;j<=nlstate+ndeath;j++){
! 1459: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
! 1460: savm[ii][j]=(ii==j ? 1.0 : 0.0);
! 1461: }
! 1462: for(d=0; d<=dh[mi][i]; d++){
! 1463: newm=savm;
! 1464: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
! 1465: for (kk=1; kk<=cptcovage;kk++) {
! 1466: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
! 1467: }
! 1468: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
! 1469: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
! 1470: savm=oldm;
! 1471: oldm=newm;
! 1472: } /* end mult */
! 1473:
! 1474: s1=s[mw[mi][i]][i];
! 1475: s2=s[mw[mi+1][i]][i];
! 1476: bbh=(double)bh[mi][i]/(double)stepm;
! 1477: 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 */
! 1478: ipmx +=1;
! 1479: sw += weight[i];
! 1480: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
! 1481: } /* end of wave */
! 1482: } /* end of individual */
! 1483: } else if(mle==3){ /* exponential inter-extrapolation */
! 1484: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
! 1485: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
! 1486: for(mi=1; mi<= wav[i]-1; mi++){
! 1487: for (ii=1;ii<=nlstate+ndeath;ii++)
! 1488: for (j=1;j<=nlstate+ndeath;j++){
! 1489: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
! 1490: savm[ii][j]=(ii==j ? 1.0 : 0.0);
! 1491: }
! 1492: for(d=0; d<dh[mi][i]; d++){
! 1493: newm=savm;
! 1494: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
! 1495: for (kk=1; kk<=cptcovage;kk++) {
! 1496: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
! 1497: }
! 1498: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
! 1499: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
! 1500: savm=oldm;
! 1501: oldm=newm;
! 1502: } /* end mult */
! 1503:
! 1504: s1=s[mw[mi][i]][i];
! 1505: s2=s[mw[mi+1][i]][i];
! 1506: bbh=(double)bh[mi][i]/(double)stepm;
! 1507: 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 */
! 1508: ipmx +=1;
! 1509: sw += weight[i];
! 1510: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
! 1511: } /* end of wave */
! 1512: } /* end of individual */
! 1513: }else if (mle==4){ /* ml=4 no inter-extrapolation */
! 1514: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
! 1515: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
! 1516: for(mi=1; mi<= wav[i]-1; mi++){
! 1517: for (ii=1;ii<=nlstate+ndeath;ii++)
! 1518: for (j=1;j<=nlstate+ndeath;j++){
! 1519: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
! 1520: savm[ii][j]=(ii==j ? 1.0 : 0.0);
! 1521: }
! 1522: for(d=0; d<dh[mi][i]; d++){
! 1523: newm=savm;
! 1524: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
! 1525: for (kk=1; kk<=cptcovage;kk++) {
! 1526: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
! 1527: }
! 1528:
! 1529: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
! 1530: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
! 1531: savm=oldm;
! 1532: oldm=newm;
! 1533: } /* end mult */
! 1534:
! 1535: s1=s[mw[mi][i]][i];
! 1536: s2=s[mw[mi+1][i]][i];
! 1537: if( s2 > nlstate){
! 1538: lli=log(out[s1][s2] - savm[s1][s2]);
! 1539: }else{
! 1540: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
! 1541: }
! 1542: ipmx +=1;
! 1543: sw += weight[i];
! 1544: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
! 1545: /* 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]); */
! 1546: } /* end of wave */
! 1547: } /* end of individual */
! 1548: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
! 1549: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
! 1550: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
! 1551: for(mi=1; mi<= wav[i]-1; mi++){
! 1552: for (ii=1;ii<=nlstate+ndeath;ii++)
! 1553: for (j=1;j<=nlstate+ndeath;j++){
! 1554: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
! 1555: savm[ii][j]=(ii==j ? 1.0 : 0.0);
! 1556: }
! 1557: for(d=0; d<dh[mi][i]; d++){
! 1558: newm=savm;
! 1559: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
! 1560: for (kk=1; kk<=cptcovage;kk++) {
! 1561: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
! 1562: }
! 1563:
! 1564: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
! 1565: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
! 1566: savm=oldm;
! 1567: oldm=newm;
! 1568: } /* end mult */
! 1569:
! 1570: s1=s[mw[mi][i]][i];
! 1571: s2=s[mw[mi+1][i]][i];
! 1572: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
! 1573: ipmx +=1;
! 1574: sw += weight[i];
! 1575: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
! 1576: /*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]);*/
! 1577: } /* end of wave */
! 1578: } /* end of individual */
! 1579: } /* End of if */
! 1580: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
! 1581: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
! 1582: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
! 1583: return -l;
! 1584: }
! 1585:
! 1586: /*************** log-likelihood *************/
! 1587: double funcone( double *x)
! 1588: {
! 1589: /* Same as likeli but slower because of a lot of printf and if */
! 1590: int i, ii, j, k, mi, d, kk;
! 1591: double l, ll[NLSTATEMAX], cov[NCOVMAX];
! 1592: double **out;
! 1593: double lli; /* Individual log likelihood */
! 1594: double llt;
! 1595: int s1, s2;
! 1596: double bbh, survp;
! 1597: /*extern weight */
! 1598: /* We are differentiating ll according to initial status */
! 1599: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
! 1600: /*for(i=1;i<imx;i++)
! 1601: printf(" %d\n",s[4][i]);
! 1602: */
! 1603: cov[1]=1.;
! 1604:
! 1605: for(k=1; k<=nlstate; k++) ll[k]=0.;
! 1606:
! 1607: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
! 1608: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
! 1609: for(mi=1; mi<= wav[i]-1; mi++){
! 1610: for (ii=1;ii<=nlstate+ndeath;ii++)
! 1611: for (j=1;j<=nlstate+ndeath;j++){
! 1612: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
! 1613: savm[ii][j]=(ii==j ? 1.0 : 0.0);
! 1614: }
! 1615: for(d=0; d<dh[mi][i]; d++){
! 1616: newm=savm;
! 1617: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
! 1618: for (kk=1; kk<=cptcovage;kk++) {
! 1619: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
! 1620: }
! 1621: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
! 1622: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
! 1623: savm=oldm;
! 1624: oldm=newm;
! 1625: } /* end mult */
! 1626:
! 1627: s1=s[mw[mi][i]][i];
! 1628: s2=s[mw[mi+1][i]][i];
! 1629: bbh=(double)bh[mi][i]/(double)stepm;
! 1630: /* bias is positive if real duration
! 1631: * is higher than the multiple of stepm and negative otherwise.
! 1632: */
! 1633: if( s2 > nlstate && (mle <5) ){ /* Jackson */
! 1634: lli=log(out[s1][s2] - savm[s1][s2]);
! 1635: } else if (s2==-2) {
! 1636: for (j=1,survp=0. ; j<=nlstate; j++)
! 1637: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
! 1638: lli= log(survp);
! 1639: }else if (mle==1){
! 1640: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
! 1641: } else if(mle==2){
! 1642: 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 */
! 1643: } else if(mle==3){ /* exponential inter-extrapolation */
! 1644: 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 */
! 1645: } else if (mle==4){ /* mle=4 no inter-extrapolation */
! 1646: lli=log(out[s1][s2]); /* Original formula */
! 1647: } else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */
! 1648: lli=log(out[s1][s2]); /* Original formula */
! 1649: } /* End of if */
! 1650: ipmx +=1;
! 1651: sw += weight[i];
! 1652: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
! 1653: /* 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]); */
! 1654: if(globpr){
! 1655: fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
! 1656: %11.6f %11.6f %11.6f ", \
! 1657: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
! 1658: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
! 1659: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
! 1660: llt +=ll[k]*gipmx/gsw;
! 1661: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
! 1662: }
! 1663: fprintf(ficresilk," %10.6f\n", -llt);
! 1664: }
! 1665: } /* end of wave */
! 1666: } /* end of individual */
! 1667: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
! 1668: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
! 1669: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
! 1670: if(globpr==0){ /* First time we count the contributions and weights */
! 1671: gipmx=ipmx;
! 1672: gsw=sw;
! 1673: }
! 1674: return -l;
! 1675: }
! 1676:
! 1677:
! 1678: /*************** function likelione ***********/
! 1679: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
! 1680: {
! 1681: /* This routine should help understanding what is done with
! 1682: the selection of individuals/waves and
! 1683: to check the exact contribution to the likelihood.
! 1684: Plotting could be done.
! 1685: */
! 1686: int k;
! 1687:
! 1688: if(*globpri !=0){ /* Just counts and sums, no printings */
! 1689: strcpy(fileresilk,"ilk");
! 1690: strcat(fileresilk,fileres);
! 1691: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
! 1692: printf("Problem with resultfile: %s\n", fileresilk);
! 1693: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
! 1694: }
! 1695: 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");
! 1696: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
! 1697: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
! 1698: for(k=1; k<=nlstate; k++)
! 1699: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
! 1700: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
! 1701: }
! 1702:
! 1703: *fretone=(*funcone)(p);
! 1704: if(*globpri !=0){
! 1705: fclose(ficresilk);
! 1706: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
! 1707: fflush(fichtm);
! 1708: }
! 1709: return;
! 1710: }
! 1711:
! 1712:
! 1713: /*********** Maximum Likelihood Estimation ***************/
! 1714:
! 1715: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
! 1716: {
! 1717: int i,j, iter;
! 1718: double **xi;
! 1719: double fret;
! 1720: double fretone; /* Only one call to likelihood */
! 1721: /* char filerespow[FILENAMELENGTH];*/
! 1722: xi=matrix(1,npar,1,npar);
! 1723: for (i=1;i<=npar;i++)
! 1724: for (j=1;j<=npar;j++)
! 1725: xi[i][j]=(i==j ? 1.0 : 0.0);
! 1726: printf("Powell\n"); fprintf(ficlog,"Powell\n");
! 1727: strcpy(filerespow,"pow");
! 1728: strcat(filerespow,fileres);
! 1729: if((ficrespow=fopen(filerespow,"w"))==NULL) {
! 1730: printf("Problem with resultfile: %s\n", filerespow);
! 1731: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
! 1732: }
! 1733: fprintf(ficrespow,"# Powell\n# iter -2*LL");
! 1734: for (i=1;i<=nlstate;i++)
! 1735: for(j=1;j<=nlstate+ndeath;j++)
! 1736: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
! 1737: fprintf(ficrespow,"\n");
! 1738:
! 1739: powell(p,xi,npar,ftol,&iter,&fret,func);
! 1740:
! 1741: free_matrix(xi,1,npar,1,npar);
! 1742: fclose(ficrespow);
! 1743: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
! 1744: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
! 1745: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
! 1746:
! 1747: }
! 1748:
! 1749: /**** Computes Hessian and covariance matrix ***/
! 1750: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
! 1751: {
! 1752: double **a,**y,*x,pd;
! 1753: double **hess;
! 1754: int i, j,jk;
! 1755: int *indx;
! 1756:
! 1757: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
! 1758: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
! 1759: void lubksb(double **a, int npar, int *indx, double b[]) ;
! 1760: void ludcmp(double **a, int npar, int *indx, double *d) ;
! 1761: double gompertz(double p[]);
! 1762: hess=matrix(1,npar,1,npar);
! 1763:
! 1764: printf("\nCalculation of the hessian matrix. Wait...\n");
! 1765: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
! 1766: for (i=1;i<=npar;i++){
! 1767: printf("%d",i);fflush(stdout);
! 1768: fprintf(ficlog,"%d",i);fflush(ficlog);
! 1769:
! 1770: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
! 1771:
! 1772: /* printf(" %f ",p[i]);
! 1773: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
! 1774: }
! 1775:
! 1776: for (i=1;i<=npar;i++) {
! 1777: for (j=1;j<=npar;j++) {
! 1778: if (j>i) {
! 1779: printf(".%d%d",i,j);fflush(stdout);
! 1780: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
! 1781: hess[i][j]=hessij(p,delti,i,j,func,npar);
! 1782:
! 1783: hess[j][i]=hess[i][j];
! 1784: /*printf(" %lf ",hess[i][j]);*/
! 1785: }
! 1786: }
! 1787: }
! 1788: printf("\n");
! 1789: fprintf(ficlog,"\n");
! 1790:
! 1791: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
! 1792: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
! 1793:
! 1794: a=matrix(1,npar,1,npar);
! 1795: y=matrix(1,npar,1,npar);
! 1796: x=vector(1,npar);
! 1797: indx=ivector(1,npar);
! 1798: for (i=1;i<=npar;i++)
! 1799: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
! 1800: ludcmp(a,npar,indx,&pd);
! 1801:
! 1802: for (j=1;j<=npar;j++) {
! 1803: for (i=1;i<=npar;i++) x[i]=0;
! 1804: x[j]=1;
! 1805: lubksb(a,npar,indx,x);
! 1806: for (i=1;i<=npar;i++){
! 1807: matcov[i][j]=x[i];
! 1808: }
! 1809: }
! 1810:
! 1811: printf("\n#Hessian matrix#\n");
! 1812: fprintf(ficlog,"\n#Hessian matrix#\n");
! 1813: for (i=1;i<=npar;i++) {
! 1814: for (j=1;j<=npar;j++) {
! 1815: printf("%.3e ",hess[i][j]);
! 1816: fprintf(ficlog,"%.3e ",hess[i][j]);
! 1817: }
! 1818: printf("\n");
! 1819: fprintf(ficlog,"\n");
! 1820: }
! 1821:
! 1822: /* Recompute Inverse */
! 1823: for (i=1;i<=npar;i++)
! 1824: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
! 1825: ludcmp(a,npar,indx,&pd);
! 1826:
! 1827: /* printf("\n#Hessian matrix recomputed#\n");
! 1828:
! 1829: for (j=1;j<=npar;j++) {
! 1830: for (i=1;i<=npar;i++) x[i]=0;
! 1831: x[j]=1;
! 1832: lubksb(a,npar,indx,x);
! 1833: for (i=1;i<=npar;i++){
! 1834: y[i][j]=x[i];
! 1835: printf("%.3e ",y[i][j]);
! 1836: fprintf(ficlog,"%.3e ",y[i][j]);
! 1837: }
! 1838: printf("\n");
! 1839: fprintf(ficlog,"\n");
! 1840: }
! 1841: */
! 1842:
! 1843: free_matrix(a,1,npar,1,npar);
! 1844: free_matrix(y,1,npar,1,npar);
! 1845: free_vector(x,1,npar);
! 1846: free_ivector(indx,1,npar);
! 1847: free_matrix(hess,1,npar,1,npar);
! 1848:
! 1849:
! 1850: }
! 1851:
! 1852: /*************** hessian matrix ****************/
! 1853: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
! 1854: {
! 1855: int i;
! 1856: int l=1, lmax=20;
! 1857: double k1,k2;
! 1858: double p2[NPARMAX+1];
! 1859: double res;
! 1860: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
! 1861: double fx;
! 1862: int k=0,kmax=10;
! 1863: double l1;
! 1864:
! 1865: fx=func(x);
! 1866: for (i=1;i<=npar;i++) p2[i]=x[i];
! 1867: for(l=0 ; l <=lmax; l++){
! 1868: l1=pow(10,l);
! 1869: delts=delt;
! 1870: for(k=1 ; k <kmax; k=k+1){
! 1871: delt = delta*(l1*k);
! 1872: p2[theta]=x[theta] +delt;
! 1873: k1=func(p2)-fx;
! 1874: p2[theta]=x[theta]-delt;
! 1875: k2=func(p2)-fx;
! 1876: /*res= (k1-2.0*fx+k2)/delt/delt; */
! 1877: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
! 1878:
! 1879: #ifdef DEBUG
! 1880: 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);
! 1881: 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);
! 1882: #endif
! 1883: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
! 1884: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
! 1885: k=kmax;
! 1886: }
! 1887: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
! 1888: k=kmax; l=lmax*10.;
! 1889: }
! 1890: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
! 1891: delts=delt;
! 1892: }
! 1893: }
! 1894: }
! 1895: delti[theta]=delts;
! 1896: return res;
! 1897:
! 1898: }
! 1899:
! 1900: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
! 1901: {
! 1902: int i;
! 1903: int l=1, l1, lmax=20;
! 1904: double k1,k2,k3,k4,res,fx;
! 1905: double p2[NPARMAX+1];
! 1906: int k;
! 1907:
! 1908: fx=func(x);
! 1909: for (k=1; k<=2; k++) {
! 1910: for (i=1;i<=npar;i++) p2[i]=x[i];
! 1911: p2[thetai]=x[thetai]+delti[thetai]/k;
! 1912: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
! 1913: k1=func(p2)-fx;
! 1914:
! 1915: p2[thetai]=x[thetai]+delti[thetai]/k;
! 1916: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
! 1917: k2=func(p2)-fx;
! 1918:
! 1919: p2[thetai]=x[thetai]-delti[thetai]/k;
! 1920: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
! 1921: k3=func(p2)-fx;
! 1922:
! 1923: p2[thetai]=x[thetai]-delti[thetai]/k;
! 1924: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
! 1925: k4=func(p2)-fx;
! 1926: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
! 1927: #ifdef DEBUG
! 1928: 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);
! 1929: 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);
! 1930: #endif
! 1931: }
! 1932: return res;
! 1933: }
! 1934:
! 1935: /************** Inverse of matrix **************/
! 1936: void ludcmp(double **a, int n, int *indx, double *d)
! 1937: {
! 1938: int i,imax,j,k;
! 1939: double big,dum,sum,temp;
! 1940: double *vv;
! 1941:
! 1942: vv=vector(1,n);
! 1943: *d=1.0;
! 1944: for (i=1;i<=n;i++) {
! 1945: big=0.0;
! 1946: for (j=1;j<=n;j++)
! 1947: if ((temp=fabs(a[i][j])) > big) big=temp;
! 1948: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
! 1949: vv[i]=1.0/big;
! 1950: }
! 1951: for (j=1;j<=n;j++) {
! 1952: for (i=1;i<j;i++) {
! 1953: sum=a[i][j];
! 1954: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
! 1955: a[i][j]=sum;
! 1956: }
! 1957: big=0.0;
! 1958: for (i=j;i<=n;i++) {
! 1959: sum=a[i][j];
! 1960: for (k=1;k<j;k++)
! 1961: sum -= a[i][k]*a[k][j];
! 1962: a[i][j]=sum;
! 1963: if ( (dum=vv[i]*fabs(sum)) >= big) {
! 1964: big=dum;
! 1965: imax=i;
! 1966: }
! 1967: }
! 1968: if (j != imax) {
! 1969: for (k=1;k<=n;k++) {
! 1970: dum=a[imax][k];
! 1971: a[imax][k]=a[j][k];
! 1972: a[j][k]=dum;
! 1973: }
! 1974: *d = -(*d);
! 1975: vv[imax]=vv[j];
! 1976: }
! 1977: indx[j]=imax;
! 1978: if (a[j][j] == 0.0) a[j][j]=TINY;
! 1979: if (j != n) {
! 1980: dum=1.0/(a[j][j]);
! 1981: for (i=j+1;i<=n;i++) a[i][j] *= dum;
! 1982: }
! 1983: }
! 1984: free_vector(vv,1,n); /* Doesn't work */
! 1985: ;
! 1986: }
! 1987:
! 1988: void lubksb(double **a, int n, int *indx, double b[])
! 1989: {
! 1990: int i,ii=0,ip,j;
! 1991: double sum;
! 1992:
! 1993: for (i=1;i<=n;i++) {
! 1994: ip=indx[i];
! 1995: sum=b[ip];
! 1996: b[ip]=b[i];
! 1997: if (ii)
! 1998: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
! 1999: else if (sum) ii=i;
! 2000: b[i]=sum;
! 2001: }
! 2002: for (i=n;i>=1;i--) {
! 2003: sum=b[i];
! 2004: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
! 2005: b[i]=sum/a[i][i];
! 2006: }
! 2007: }
! 2008:
! 2009: void pstamp(FILE *fichier)
! 2010: {
! 2011: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
! 2012: }
! 2013:
! 2014: /************ Frequencies ********************/
! 2015: 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[])
! 2016: { /* Some frequencies */
! 2017:
! 2018: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
! 2019: int first;
! 2020: double ***freq; /* Frequencies */
! 2021: double *pp, **prop;
! 2022: double pos,posprop, k2, dateintsum=0,k2cpt=0;
! 2023: char fileresp[FILENAMELENGTH];
! 2024:
! 2025: pp=vector(1,nlstate);
! 2026: prop=matrix(1,nlstate,iagemin,iagemax+3);
! 2027: strcpy(fileresp,"p");
! 2028: strcat(fileresp,fileres);
! 2029: if((ficresp=fopen(fileresp,"w"))==NULL) {
! 2030: printf("Problem with prevalence resultfile: %s\n", fileresp);
! 2031: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
! 2032: exit(0);
! 2033: }
! 2034: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
! 2035: j1=0;
! 2036:
! 2037: j=cptcoveff;
! 2038: if (cptcovn<1) {j=1;ncodemax[1]=1;}
! 2039:
! 2040: first=1;
! 2041:
! 2042: for(k1=1; k1<=j;k1++){
! 2043: for(i1=1; i1<=ncodemax[k1];i1++){
! 2044: j1++;
! 2045: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
! 2046: scanf("%d", i);*/
! 2047: for (i=-5; i<=nlstate+ndeath; i++)
! 2048: for (jk=-5; jk<=nlstate+ndeath; jk++)
! 2049: for(m=iagemin; m <= iagemax+3; m++)
! 2050: freq[i][jk][m]=0;
! 2051:
! 2052: for (i=1; i<=nlstate; i++)
! 2053: for(m=iagemin; m <= iagemax+3; m++)
! 2054: prop[i][m]=0;
! 2055:
! 2056: dateintsum=0;
! 2057: k2cpt=0;
! 2058: for (i=1; i<=imx; i++) {
! 2059: bool=1;
! 2060: if (cptcovn>0) {
! 2061: for (z1=1; z1<=cptcoveff; z1++)
! 2062: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
! 2063: bool=0;
! 2064: }
! 2065: if (bool==1){
! 2066: for(m=firstpass; m<=lastpass; m++){
! 2067: k2=anint[m][i]+(mint[m][i]/12.);
! 2068: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
! 2069: if(agev[m][i]==0) agev[m][i]=iagemax+1;
! 2070: if(agev[m][i]==1) agev[m][i]=iagemax+2;
! 2071: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
! 2072: if (m<lastpass) {
! 2073: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
! 2074: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
! 2075: }
! 2076:
! 2077: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
! 2078: dateintsum=dateintsum+k2;
! 2079: k2cpt++;
! 2080: }
! 2081: /*}*/
! 2082: }
! 2083: }
! 2084: }
! 2085:
! 2086: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
! 2087: pstamp(ficresp);
! 2088: if (cptcovn>0) {
! 2089: fprintf(ficresp, "\n#********** Variable ");
! 2090: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
! 2091: fprintf(ficresp, "**********\n#");
! 2092: }
! 2093: for(i=1; i<=nlstate;i++)
! 2094: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
! 2095: fprintf(ficresp, "\n");
! 2096:
! 2097: for(i=iagemin; i <= iagemax+3; i++){
! 2098: if(i==iagemax+3){
! 2099: fprintf(ficlog,"Total");
! 2100: }else{
! 2101: if(first==1){
! 2102: first=0;
! 2103: printf("See log file for details...\n");
! 2104: }
! 2105: fprintf(ficlog,"Age %d", i);
! 2106: }
! 2107: for(jk=1; jk <=nlstate ; jk++){
! 2108: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
! 2109: pp[jk] += freq[jk][m][i];
! 2110: }
! 2111: for(jk=1; jk <=nlstate ; jk++){
! 2112: for(m=-1, pos=0; m <=0 ; m++)
! 2113: pos += freq[jk][m][i];
! 2114: if(pp[jk]>=1.e-10){
! 2115: if(first==1){
! 2116: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
! 2117: }
! 2118: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
! 2119: }else{
! 2120: if(first==1)
! 2121: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
! 2122: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
! 2123: }
! 2124: }
! 2125:
! 2126: for(jk=1; jk <=nlstate ; jk++){
! 2127: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
! 2128: pp[jk] += freq[jk][m][i];
! 2129: }
! 2130: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
! 2131: pos += pp[jk];
! 2132: posprop += prop[jk][i];
! 2133: }
! 2134: for(jk=1; jk <=nlstate ; jk++){
! 2135: if(pos>=1.e-5){
! 2136: if(first==1)
! 2137: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
! 2138: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
! 2139: }else{
! 2140: if(first==1)
! 2141: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
! 2142: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
! 2143: }
! 2144: if( i <= iagemax){
! 2145: if(pos>=1.e-5){
! 2146: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
! 2147: /*probs[i][jk][j1]= pp[jk]/pos;*/
! 2148: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
! 2149: }
! 2150: else
! 2151: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
! 2152: }
! 2153: }
! 2154:
! 2155: for(jk=-1; jk <=nlstate+ndeath; jk++)
! 2156: for(m=-1; m <=nlstate+ndeath; m++)
! 2157: if(freq[jk][m][i] !=0 ) {
! 2158: if(first==1)
! 2159: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
! 2160: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
! 2161: }
! 2162: if(i <= iagemax)
! 2163: fprintf(ficresp,"\n");
! 2164: if(first==1)
! 2165: printf("Others in log...\n");
! 2166: fprintf(ficlog,"\n");
! 2167: }
! 2168: }
! 2169: }
! 2170: dateintmean=dateintsum/k2cpt;
! 2171:
! 2172: fclose(ficresp);
! 2173: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
! 2174: free_vector(pp,1,nlstate);
! 2175: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
! 2176: /* End of Freq */
! 2177: }
! 2178:
! 2179: /************ Prevalence ********************/
! 2180: 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)
! 2181: {
! 2182: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
! 2183: in each health status at the date of interview (if between dateprev1 and dateprev2).
! 2184: We still use firstpass and lastpass as another selection.
! 2185: */
! 2186:
! 2187: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
! 2188: double ***freq; /* Frequencies */
! 2189: double *pp, **prop;
! 2190: double pos,posprop;
! 2191: double y2; /* in fractional years */
! 2192: int iagemin, iagemax;
! 2193:
! 2194: iagemin= (int) agemin;
! 2195: iagemax= (int) agemax;
! 2196: /*pp=vector(1,nlstate);*/
! 2197: prop=matrix(1,nlstate,iagemin,iagemax+3);
! 2198: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
! 2199: j1=0;
! 2200:
! 2201: j=cptcoveff;
! 2202: if (cptcovn<1) {j=1;ncodemax[1]=1;}
! 2203:
! 2204: for(k1=1; k1<=j;k1++){
! 2205: for(i1=1; i1<=ncodemax[k1];i1++){
! 2206: j1++;
! 2207:
! 2208: for (i=1; i<=nlstate; i++)
! 2209: for(m=iagemin; m <= iagemax+3; m++)
! 2210: prop[i][m]=0.0;
! 2211:
! 2212: for (i=1; i<=imx; i++) { /* Each individual */
! 2213: bool=1;
! 2214: if (cptcovn>0) {
! 2215: for (z1=1; z1<=cptcoveff; z1++)
! 2216: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
! 2217: bool=0;
! 2218: }
! 2219: if (bool==1) {
! 2220: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
! 2221: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
! 2222: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
! 2223: if(agev[m][i]==0) agev[m][i]=iagemax+1;
! 2224: if(agev[m][i]==1) agev[m][i]=iagemax+2;
! 2225: 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);
! 2226: if (s[m][i]>0 && s[m][i]<=nlstate) {
! 2227: /*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]]);*/
! 2228: prop[s[m][i]][(int)agev[m][i]] += weight[i];
! 2229: prop[s[m][i]][iagemax+3] += weight[i];
! 2230: }
! 2231: }
! 2232: } /* end selection of waves */
! 2233: }
! 2234: }
! 2235: for(i=iagemin; i <= iagemax+3; i++){
! 2236:
! 2237: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
! 2238: posprop += prop[jk][i];
! 2239: }
! 2240:
! 2241: for(jk=1; jk <=nlstate ; jk++){
! 2242: if( i <= iagemax){
! 2243: if(posprop>=1.e-5){
! 2244: probs[i][jk][j1]= prop[jk][i]/posprop;
! 2245: }
! 2246: }
! 2247: }/* end jk */
! 2248: }/* end i */
! 2249: } /* end i1 */
! 2250: } /* end k1 */
! 2251:
! 2252: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
! 2253: /*free_vector(pp,1,nlstate);*/
! 2254: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
! 2255: } /* End of prevalence */
! 2256:
! 2257: /************* Waves Concatenation ***************/
! 2258:
! 2259: 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)
! 2260: {
! 2261: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
! 2262: Death is a valid wave (if date is known).
! 2263: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
! 2264: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
! 2265: and mw[mi+1][i]. dh depends on stepm.
! 2266: */
! 2267:
! 2268: int i, mi, m;
! 2269: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
! 2270: double sum=0., jmean=0.;*/
! 2271: int first;
! 2272: int j, k=0,jk, ju, jl;
! 2273: double sum=0.;
! 2274: first=0;
! 2275: jmin=1e+5;
! 2276: jmax=-1;
! 2277: jmean=0.;
! 2278: for(i=1; i<=imx; i++){
! 2279: mi=0;
! 2280: m=firstpass;
! 2281: while(s[m][i] <= nlstate){
! 2282: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
! 2283: mw[++mi][i]=m;
! 2284: if(m >=lastpass)
! 2285: break;
! 2286: else
! 2287: m++;
! 2288: }/* end while */
! 2289: if (s[m][i] > nlstate){
! 2290: mi++; /* Death is another wave */
! 2291: /* if(mi==0) never been interviewed correctly before death */
! 2292: /* Only death is a correct wave */
! 2293: mw[mi][i]=m;
! 2294: }
! 2295:
! 2296: wav[i]=mi;
! 2297: if(mi==0){
! 2298: nbwarn++;
! 2299: if(first==0){
! 2300: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
! 2301: first=1;
! 2302: }
! 2303: if(first==1){
! 2304: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
! 2305: }
! 2306: } /* end mi==0 */
! 2307: } /* End individuals */
! 2308:
! 2309: for(i=1; i<=imx; i++){
! 2310: for(mi=1; mi<wav[i];mi++){
! 2311: if (stepm <=0)
! 2312: dh[mi][i]=1;
! 2313: else{
! 2314: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
! 2315: if (agedc[i] < 2*AGESUP) {
! 2316: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
! 2317: if(j==0) j=1; /* Survives at least one month after exam */
! 2318: else if(j<0){
! 2319: nberr++;
! 2320: 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]);
! 2321: j=1; /* Temporary Dangerous patch */
! 2322: 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);
! 2323: 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]);
! 2324: 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);
! 2325: }
! 2326: k=k+1;
! 2327: if (j >= jmax){
! 2328: jmax=j;
! 2329: ijmax=i;
! 2330: }
! 2331: if (j <= jmin){
! 2332: jmin=j;
! 2333: ijmin=i;
! 2334: }
! 2335: sum=sum+j;
! 2336: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
! 2337: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
! 2338: }
! 2339: }
! 2340: else{
! 2341: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
! 2342: /* 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]); */
! 2343:
! 2344: k=k+1;
! 2345: if (j >= jmax) {
! 2346: jmax=j;
! 2347: ijmax=i;
! 2348: }
! 2349: else if (j <= jmin){
! 2350: jmin=j;
! 2351: ijmin=i;
! 2352: }
! 2353: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
! 2354: /*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]);*/
! 2355: if(j<0){
! 2356: nberr++;
! 2357: 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]);
! 2358: 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]);
! 2359: }
! 2360: sum=sum+j;
! 2361: }
! 2362: jk= j/stepm;
! 2363: jl= j -jk*stepm;
! 2364: ju= j -(jk+1)*stepm;
! 2365: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
! 2366: if(jl==0){
! 2367: dh[mi][i]=jk;
! 2368: bh[mi][i]=0;
! 2369: }else{ /* We want a negative bias in order to only have interpolation ie
! 2370: * at the price of an extra matrix product in likelihood */
! 2371: dh[mi][i]=jk+1;
! 2372: bh[mi][i]=ju;
! 2373: }
! 2374: }else{
! 2375: if(jl <= -ju){
! 2376: dh[mi][i]=jk;
! 2377: bh[mi][i]=jl; /* bias is positive if real duration
! 2378: * is higher than the multiple of stepm and negative otherwise.
! 2379: */
! 2380: }
! 2381: else{
! 2382: dh[mi][i]=jk+1;
! 2383: bh[mi][i]=ju;
! 2384: }
! 2385: if(dh[mi][i]==0){
! 2386: dh[mi][i]=1; /* At least one step */
! 2387: bh[mi][i]=ju; /* At least one step */
! 2388: /* 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);*/
! 2389: }
! 2390: } /* end if mle */
! 2391: }
! 2392: } /* end wave */
! 2393: }
! 2394: jmean=sum/k;
! 2395: 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);
! 2396: fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
! 2397: }
! 2398:
! 2399: /*********** Tricode ****************************/
! 2400: void tricode(int *Tvar, int **nbcode, int imx)
! 2401: {
! 2402:
! 2403: int Ndum[20],ij=1, k, j, i, maxncov=19;
! 2404: int cptcode=0;
! 2405: cptcoveff=0;
! 2406:
! 2407: for (k=0; k<maxncov; k++) Ndum[k]=0;
! 2408: for (k=1; k<=7; k++) ncodemax[k]=0;
! 2409:
! 2410: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
! 2411: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
! 2412: modality*/
! 2413: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
! 2414: Ndum[ij]++; /*store the modality */
! 2415: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
! 2416: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
! 2417: Tvar[j]. If V=sex and male is 0 and
! 2418: female is 1, then cptcode=1.*/
! 2419: }
! 2420:
! 2421: for (i=0; i<=cptcode; i++) {
! 2422: if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
! 2423: }
! 2424:
! 2425: ij=1;
! 2426: for (i=1; i<=ncodemax[j]; i++) {
! 2427: for (k=0; k<= maxncov; k++) {
! 2428: if (Ndum[k] != 0) {
! 2429: nbcode[Tvar[j]][ij]=k;
! 2430: /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
! 2431:
! 2432: ij++;
! 2433: }
! 2434: if (ij > ncodemax[j]) break;
! 2435: }
! 2436: }
! 2437: }
! 2438:
! 2439: for (k=0; k< maxncov; k++) Ndum[k]=0;
! 2440:
! 2441: for (i=1; i<=ncovmodel-2; i++) {
! 2442: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
! 2443: ij=Tvar[i];
! 2444: Ndum[ij]++;
! 2445: }
! 2446:
! 2447: ij=1;
! 2448: for (i=1; i<= maxncov; i++) {
! 2449: if((Ndum[i]!=0) && (i<=ncovcol)){
! 2450: Tvaraff[ij]=i; /*For printing */
! 2451: ij++;
! 2452: }
! 2453: }
! 2454:
! 2455: cptcoveff=ij-1; /*Number of simple covariates*/
! 2456: }
! 2457:
! 2458: /*********** Health Expectancies ****************/
! 2459:
! 2460: void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
! 2461:
! 2462: {
! 2463: /* Health expectancies, no variances */
! 2464: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
! 2465: double age, agelim, hf;
! 2466: double ***p3mat;
! 2467: double eip;
! 2468:
! 2469: pstamp(ficreseij);
! 2470: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
! 2471: fprintf(ficreseij,"# Age");
! 2472: for(i=1; i<=nlstate;i++){
! 2473: for(j=1; j<=nlstate;j++){
! 2474: fprintf(ficreseij," e%1d%1d ",i,j);
! 2475: }
! 2476: fprintf(ficreseij," e%1d. ",i);
! 2477: }
! 2478: fprintf(ficreseij,"\n");
! 2479:
! 2480:
! 2481: if(estepm < stepm){
! 2482: printf ("Problem %d lower than %d\n",estepm, stepm);
! 2483: }
! 2484: else hstepm=estepm;
! 2485: /* We compute the life expectancy from trapezoids spaced every estepm months
! 2486: * This is mainly to measure the difference between two models: for example
! 2487: * if stepm=24 months pijx are given only every 2 years and by summing them
! 2488: * we are calculating an estimate of the Life Expectancy assuming a linear
! 2489: * progression in between and thus overestimating or underestimating according
! 2490: * to the curvature of the survival function. If, for the same date, we
! 2491: * estimate the model with stepm=1 month, we can keep estepm to 24 months
! 2492: * to compare the new estimate of Life expectancy with the same linear
! 2493: * hypothesis. A more precise result, taking into account a more precise
! 2494: * curvature will be obtained if estepm is as small as stepm. */
! 2495:
! 2496: /* For example we decided to compute the life expectancy with the smallest unit */
! 2497: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
! 2498: nhstepm is the number of hstepm from age to agelim
! 2499: nstepm is the number of stepm from age to agelin.
! 2500: Look at hpijx to understand the reason of that which relies in memory size
! 2501: and note for a fixed period like estepm months */
! 2502: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
! 2503: survival function given by stepm (the optimization length). Unfortunately it
! 2504: means that if the survival funtion is printed only each two years of age and if
! 2505: you sum them up and add 1 year (area under the trapezoids) you won't get the same
! 2506: results. So we changed our mind and took the option of the best precision.
! 2507: */
! 2508: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
! 2509:
! 2510: agelim=AGESUP;
! 2511: /* If stepm=6 months */
! 2512: /* Computed by stepm unit matrices, product of hstepm matrices, stored
! 2513: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
! 2514:
! 2515: /* nhstepm age range expressed in number of stepm */
! 2516: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
! 2517: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
! 2518: /* if (stepm >= YEARM) hstepm=1;*/
! 2519: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
! 2520: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 2521:
! 2522: for (age=bage; age<=fage; age ++){
! 2523:
! 2524:
! 2525: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
! 2526:
! 2527: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
! 2528:
! 2529: printf("%d|",(int)age);fflush(stdout);
! 2530: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
! 2531:
! 2532:
! 2533: /* Computing expectancies */
! 2534: for(i=1; i<=nlstate;i++)
! 2535: for(j=1; j<=nlstate;j++)
! 2536: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
! 2537: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
! 2538:
! 2539: /*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]);*/
! 2540:
! 2541: }
! 2542:
! 2543: fprintf(ficreseij,"%3.0f",age );
! 2544: for(i=1; i<=nlstate;i++){
! 2545: eip=0;
! 2546: for(j=1; j<=nlstate;j++){
! 2547: eip +=eij[i][j][(int)age];
! 2548: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
! 2549: }
! 2550: fprintf(ficreseij,"%9.4f", eip );
! 2551: }
! 2552: fprintf(ficreseij,"\n");
! 2553:
! 2554: }
! 2555: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 2556: printf("\n");
! 2557: fprintf(ficlog,"\n");
! 2558:
! 2559: }
! 2560:
! 2561: void cvevsij(char fileres[], 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[] )
! 2562:
! 2563: {
! 2564: /* Covariances of health expectancies eij and of total life expectancies according
! 2565: to initial status i, ei. .
! 2566: */
! 2567: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
! 2568: double age, agelim, hf;
! 2569: double ***p3matp, ***p3matm, ***varhe;
! 2570: double **dnewm,**doldm;
! 2571: double *xp, *xm;
! 2572: double **gp, **gm;
! 2573: double ***gradg, ***trgradg;
! 2574: int theta;
! 2575:
! 2576: double eip, vip;
! 2577:
! 2578: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
! 2579: xp=vector(1,npar);
! 2580: xm=vector(1,npar);
! 2581: dnewm=matrix(1,nlstate*nlstate,1,npar);
! 2582: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
! 2583:
! 2584: pstamp(ficresstdeij);
! 2585: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
! 2586: fprintf(ficresstdeij,"# Age");
! 2587: for(i=1; i<=nlstate;i++){
! 2588: for(j=1; j<=nlstate;j++)
! 2589: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
! 2590: fprintf(ficresstdeij," e%1d. ",i);
! 2591: }
! 2592: fprintf(ficresstdeij,"\n");
! 2593:
! 2594: pstamp(ficrescveij);
! 2595: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
! 2596: fprintf(ficrescveij,"# Age");
! 2597: for(i=1; i<=nlstate;i++)
! 2598: for(j=1; j<=nlstate;j++){
! 2599: cptj= (j-1)*nlstate+i;
! 2600: for(i2=1; i2<=nlstate;i2++)
! 2601: for(j2=1; j2<=nlstate;j2++){
! 2602: cptj2= (j2-1)*nlstate+i2;
! 2603: if(cptj2 <= cptj)
! 2604: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
! 2605: }
! 2606: }
! 2607: fprintf(ficrescveij,"\n");
! 2608:
! 2609: if(estepm < stepm){
! 2610: printf ("Problem %d lower than %d\n",estepm, stepm);
! 2611: }
! 2612: else hstepm=estepm;
! 2613: /* We compute the life expectancy from trapezoids spaced every estepm months
! 2614: * This is mainly to measure the difference between two models: for example
! 2615: * if stepm=24 months pijx are given only every 2 years and by summing them
! 2616: * we are calculating an estimate of the Life Expectancy assuming a linear
! 2617: * progression in between and thus overestimating or underestimating according
! 2618: * to the curvature of the survival function. If, for the same date, we
! 2619: * estimate the model with stepm=1 month, we can keep estepm to 24 months
! 2620: * to compare the new estimate of Life expectancy with the same linear
! 2621: * hypothesis. A more precise result, taking into account a more precise
! 2622: * curvature will be obtained if estepm is as small as stepm. */
! 2623:
! 2624: /* For example we decided to compute the life expectancy with the smallest unit */
! 2625: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
! 2626: nhstepm is the number of hstepm from age to agelim
! 2627: nstepm is the number of stepm from age to agelin.
! 2628: Look at hpijx to understand the reason of that which relies in memory size
! 2629: and note for a fixed period like estepm months */
! 2630: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
! 2631: survival function given by stepm (the optimization length). Unfortunately it
! 2632: means that if the survival funtion is printed only each two years of age and if
! 2633: you sum them up and add 1 year (area under the trapezoids) you won't get the same
! 2634: results. So we changed our mind and took the option of the best precision.
! 2635: */
! 2636: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
! 2637:
! 2638: /* If stepm=6 months */
! 2639: /* nhstepm age range expressed in number of stepm */
! 2640: agelim=AGESUP;
! 2641: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
! 2642: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
! 2643: /* if (stepm >= YEARM) hstepm=1;*/
! 2644: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
! 2645:
! 2646: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 2647: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 2648: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
! 2649: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
! 2650: gp=matrix(0,nhstepm,1,nlstate*nlstate);
! 2651: gm=matrix(0,nhstepm,1,nlstate*nlstate);
! 2652:
! 2653: for (age=bage; age<=fage; age ++){
! 2654:
! 2655: /* Computed by stepm unit matrices, product of hstepm matrices, stored
! 2656: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
! 2657:
! 2658: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
! 2659:
! 2660: /* Computing Variances of health expectancies */
! 2661: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
! 2662: decrease memory allocation */
! 2663: for(theta=1; theta <=npar; theta++){
! 2664: for(i=1; i<=npar; i++){
! 2665: xp[i] = x[i] + (i==theta ?delti[theta]:0);
! 2666: xm[i] = x[i] - (i==theta ?delti[theta]:0);
! 2667: }
! 2668: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
! 2669: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
! 2670:
! 2671: for(j=1; j<= nlstate; j++){
! 2672: for(i=1; i<=nlstate; i++){
! 2673: for(h=0; h<=nhstepm-1; h++){
! 2674: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
! 2675: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
! 2676: }
! 2677: }
! 2678: }
! 2679:
! 2680: for(ij=1; ij<= nlstate*nlstate; ij++)
! 2681: for(h=0; h<=nhstepm-1; h++){
! 2682: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
! 2683: }
! 2684: }/* End theta */
! 2685:
! 2686:
! 2687: for(h=0; h<=nhstepm-1; h++)
! 2688: for(j=1; j<=nlstate*nlstate;j++)
! 2689: for(theta=1; theta <=npar; theta++)
! 2690: trgradg[h][j][theta]=gradg[h][theta][j];
! 2691:
! 2692:
! 2693: for(ij=1;ij<=nlstate*nlstate;ij++)
! 2694: for(ji=1;ji<=nlstate*nlstate;ji++)
! 2695: varhe[ij][ji][(int)age] =0.;
! 2696:
! 2697: printf("%d|",(int)age);fflush(stdout);
! 2698: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
! 2699: for(h=0;h<=nhstepm-1;h++){
! 2700: for(k=0;k<=nhstepm-1;k++){
! 2701: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
! 2702: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
! 2703: for(ij=1;ij<=nlstate*nlstate;ij++)
! 2704: for(ji=1;ji<=nlstate*nlstate;ji++)
! 2705: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
! 2706: }
! 2707: }
! 2708:
! 2709: /* Computing expectancies */
! 2710: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
! 2711: for(i=1; i<=nlstate;i++)
! 2712: for(j=1; j<=nlstate;j++)
! 2713: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
! 2714: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
! 2715:
! 2716: /* 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]);*/
! 2717:
! 2718: }
! 2719:
! 2720: fprintf(ficresstdeij,"%3.0f",age );
! 2721: for(i=1; i<=nlstate;i++){
! 2722: eip=0.;
! 2723: vip=0.;
! 2724: for(j=1; j<=nlstate;j++){
! 2725: eip += eij[i][j][(int)age];
! 2726: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
! 2727: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
! 2728: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
! 2729: }
! 2730: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
! 2731: }
! 2732: fprintf(ficresstdeij,"\n");
! 2733:
! 2734: fprintf(ficrescveij,"%3.0f",age );
! 2735: for(i=1; i<=nlstate;i++)
! 2736: for(j=1; j<=nlstate;j++){
! 2737: cptj= (j-1)*nlstate+i;
! 2738: for(i2=1; i2<=nlstate;i2++)
! 2739: for(j2=1; j2<=nlstate;j2++){
! 2740: cptj2= (j2-1)*nlstate+i2;
! 2741: if(cptj2 <= cptj)
! 2742: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
! 2743: }
! 2744: }
! 2745: fprintf(ficrescveij,"\n");
! 2746:
! 2747: }
! 2748: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
! 2749: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
! 2750: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
! 2751: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
! 2752: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 2753: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 2754: printf("\n");
! 2755: fprintf(ficlog,"\n");
! 2756:
! 2757: free_vector(xm,1,npar);
! 2758: free_vector(xp,1,npar);
! 2759: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
! 2760: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
! 2761: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
! 2762: }
! 2763:
! 2764: /************ Variance ******************/
! 2765: 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[])
! 2766: {
! 2767: /* Variance of health expectancies */
! 2768: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
! 2769: /* double **newm;*/
! 2770: double **dnewm,**doldm;
! 2771: double **dnewmp,**doldmp;
! 2772: int i, j, nhstepm, hstepm, h, nstepm ;
! 2773: int k, cptcode;
! 2774: double *xp;
! 2775: double **gp, **gm; /* for var eij */
! 2776: double ***gradg, ***trgradg; /*for var eij */
! 2777: double **gradgp, **trgradgp; /* for var p point j */
! 2778: double *gpp, *gmp; /* for var p point j */
! 2779: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
! 2780: double ***p3mat;
! 2781: double age,agelim, hf;
! 2782: double ***mobaverage;
! 2783: int theta;
! 2784: char digit[4];
! 2785: char digitp[25];
! 2786:
! 2787: char fileresprobmorprev[FILENAMELENGTH];
! 2788:
! 2789: if(popbased==1){
! 2790: if(mobilav!=0)
! 2791: strcpy(digitp,"-populbased-mobilav-");
! 2792: else strcpy(digitp,"-populbased-nomobil-");
! 2793: }
! 2794: else
! 2795: strcpy(digitp,"-stablbased-");
! 2796:
! 2797: if (mobilav!=0) {
! 2798: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 2799: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
! 2800: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
! 2801: printf(" Error in movingaverage mobilav=%d\n",mobilav);
! 2802: }
! 2803: }
! 2804:
! 2805: strcpy(fileresprobmorprev,"prmorprev");
! 2806: sprintf(digit,"%-d",ij);
! 2807: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
! 2808: strcat(fileresprobmorprev,digit); /* Tvar to be done */
! 2809: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
! 2810: strcat(fileresprobmorprev,fileres);
! 2811: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
! 2812: printf("Problem with resultfile: %s\n", fileresprobmorprev);
! 2813: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
! 2814: }
! 2815: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
! 2816:
! 2817: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
! 2818: pstamp(ficresprobmorprev);
! 2819: 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);
! 2820: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
! 2821: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
! 2822: fprintf(ficresprobmorprev," p.%-d SE",j);
! 2823: for(i=1; i<=nlstate;i++)
! 2824: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
! 2825: }
! 2826: fprintf(ficresprobmorprev,"\n");
! 2827: fprintf(ficgp,"\n# Routine varevsij");
! 2828: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
! 2829: 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");
! 2830: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
! 2831: /* } */
! 2832: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
! 2833: pstamp(ficresvij);
! 2834: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
! 2835: if(popbased==1)
! 2836: fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
! 2837: else
! 2838: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
! 2839: fprintf(ficresvij,"# Age");
! 2840: for(i=1; i<=nlstate;i++)
! 2841: for(j=1; j<=nlstate;j++)
! 2842: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
! 2843: fprintf(ficresvij,"\n");
! 2844:
! 2845: xp=vector(1,npar);
! 2846: dnewm=matrix(1,nlstate,1,npar);
! 2847: doldm=matrix(1,nlstate,1,nlstate);
! 2848: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
! 2849: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
! 2850:
! 2851: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
! 2852: gpp=vector(nlstate+1,nlstate+ndeath);
! 2853: gmp=vector(nlstate+1,nlstate+ndeath);
! 2854: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
! 2855:
! 2856: if(estepm < stepm){
! 2857: printf ("Problem %d lower than %d\n",estepm, stepm);
! 2858: }
! 2859: else hstepm=estepm;
! 2860: /* For example we decided to compute the life expectancy with the smallest unit */
! 2861: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
! 2862: nhstepm is the number of hstepm from age to agelim
! 2863: nstepm is the number of stepm from age to agelin.
! 2864: Look at hpijx to understand the reason of that which relies in memory size
! 2865: and note for a fixed period like k years */
! 2866: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
! 2867: survival function given by stepm (the optimization length). Unfortunately it
! 2868: means that if the survival funtion is printed every two years of age and if
! 2869: you sum them up and add 1 year (area under the trapezoids) you won't get the same
! 2870: results. So we changed our mind and took the option of the best precision.
! 2871: */
! 2872: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
! 2873: agelim = AGESUP;
! 2874: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
! 2875: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
! 2876: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
! 2877: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 2878: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
! 2879: gp=matrix(0,nhstepm,1,nlstate);
! 2880: gm=matrix(0,nhstepm,1,nlstate);
! 2881:
! 2882:
! 2883: for(theta=1; theta <=npar; theta++){
! 2884: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
! 2885: xp[i] = x[i] + (i==theta ?delti[theta]:0);
! 2886: }
! 2887: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
! 2888: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
! 2889:
! 2890: if (popbased==1) {
! 2891: if(mobilav ==0){
! 2892: for(i=1; i<=nlstate;i++)
! 2893: prlim[i][i]=probs[(int)age][i][ij];
! 2894: }else{ /* mobilav */
! 2895: for(i=1; i<=nlstate;i++)
! 2896: prlim[i][i]=mobaverage[(int)age][i][ij];
! 2897: }
! 2898: }
! 2899:
! 2900: for(j=1; j<= nlstate; j++){
! 2901: for(h=0; h<=nhstepm; h++){
! 2902: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
! 2903: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
! 2904: }
! 2905: }
! 2906: /* This for computing probability of death (h=1 means
! 2907: computed over hstepm matrices product = hstepm*stepm months)
! 2908: as a weighted average of prlim.
! 2909: */
! 2910: for(j=nlstate+1;j<=nlstate+ndeath;j++){
! 2911: for(i=1,gpp[j]=0.; i<= nlstate; i++)
! 2912: gpp[j] += prlim[i][i]*p3mat[i][j][1];
! 2913: }
! 2914: /* end probability of death */
! 2915:
! 2916: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
! 2917: xp[i] = x[i] - (i==theta ?delti[theta]:0);
! 2918: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
! 2919: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
! 2920:
! 2921: if (popbased==1) {
! 2922: if(mobilav ==0){
! 2923: for(i=1; i<=nlstate;i++)
! 2924: prlim[i][i]=probs[(int)age][i][ij];
! 2925: }else{ /* mobilav */
! 2926: for(i=1; i<=nlstate;i++)
! 2927: prlim[i][i]=mobaverage[(int)age][i][ij];
! 2928: }
! 2929: }
! 2930:
! 2931: for(j=1; j<= nlstate; j++){
! 2932: for(h=0; h<=nhstepm; h++){
! 2933: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
! 2934: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
! 2935: }
! 2936: }
! 2937: /* This for computing probability of death (h=1 means
! 2938: computed over hstepm matrices product = hstepm*stepm months)
! 2939: as a weighted average of prlim.
! 2940: */
! 2941: for(j=nlstate+1;j<=nlstate+ndeath;j++){
! 2942: for(i=1,gmp[j]=0.; i<= nlstate; i++)
! 2943: gmp[j] += prlim[i][i]*p3mat[i][j][1];
! 2944: }
! 2945: /* end probability of death */
! 2946:
! 2947: for(j=1; j<= nlstate; j++) /* vareij */
! 2948: for(h=0; h<=nhstepm; h++){
! 2949: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
! 2950: }
! 2951:
! 2952: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
! 2953: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
! 2954: }
! 2955:
! 2956: } /* End theta */
! 2957:
! 2958: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
! 2959:
! 2960: for(h=0; h<=nhstepm; h++) /* veij */
! 2961: for(j=1; j<=nlstate;j++)
! 2962: for(theta=1; theta <=npar; theta++)
! 2963: trgradg[h][j][theta]=gradg[h][theta][j];
! 2964:
! 2965: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
! 2966: for(theta=1; theta <=npar; theta++)
! 2967: trgradgp[j][theta]=gradgp[theta][j];
! 2968:
! 2969:
! 2970: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
! 2971: for(i=1;i<=nlstate;i++)
! 2972: for(j=1;j<=nlstate;j++)
! 2973: vareij[i][j][(int)age] =0.;
! 2974:
! 2975: for(h=0;h<=nhstepm;h++){
! 2976: for(k=0;k<=nhstepm;k++){
! 2977: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
! 2978: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
! 2979: for(i=1;i<=nlstate;i++)
! 2980: for(j=1;j<=nlstate;j++)
! 2981: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
! 2982: }
! 2983: }
! 2984:
! 2985: /* pptj */
! 2986: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
! 2987: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
! 2988: for(j=nlstate+1;j<=nlstate+ndeath;j++)
! 2989: for(i=nlstate+1;i<=nlstate+ndeath;i++)
! 2990: varppt[j][i]=doldmp[j][i];
! 2991: /* end ppptj */
! 2992: /* x centered again */
! 2993: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
! 2994: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
! 2995:
! 2996: if (popbased==1) {
! 2997: if(mobilav ==0){
! 2998: for(i=1; i<=nlstate;i++)
! 2999: prlim[i][i]=probs[(int)age][i][ij];
! 3000: }else{ /* mobilav */
! 3001: for(i=1; i<=nlstate;i++)
! 3002: prlim[i][i]=mobaverage[(int)age][i][ij];
! 3003: }
! 3004: }
! 3005:
! 3006: /* This for computing probability of death (h=1 means
! 3007: computed over hstepm (estepm) matrices product = hstepm*stepm months)
! 3008: as a weighted average of prlim.
! 3009: */
! 3010: for(j=nlstate+1;j<=nlstate+ndeath;j++){
! 3011: for(i=1,gmp[j]=0.;i<= nlstate; i++)
! 3012: gmp[j] += prlim[i][i]*p3mat[i][j][1];
! 3013: }
! 3014: /* end probability of death */
! 3015:
! 3016: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
! 3017: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
! 3018: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
! 3019: for(i=1; i<=nlstate;i++){
! 3020: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
! 3021: }
! 3022: }
! 3023: fprintf(ficresprobmorprev,"\n");
! 3024:
! 3025: fprintf(ficresvij,"%.0f ",age );
! 3026: for(i=1; i<=nlstate;i++)
! 3027: for(j=1; j<=nlstate;j++){
! 3028: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
! 3029: }
! 3030: fprintf(ficresvij,"\n");
! 3031: free_matrix(gp,0,nhstepm,1,nlstate);
! 3032: free_matrix(gm,0,nhstepm,1,nlstate);
! 3033: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
! 3034: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
! 3035: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 3036: } /* End age */
! 3037: free_vector(gpp,nlstate+1,nlstate+ndeath);
! 3038: free_vector(gmp,nlstate+1,nlstate+ndeath);
! 3039: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
! 3040: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
! 3041: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
! 3042: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
! 3043: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
! 3044: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
! 3045: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
! 3046: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
! 3047: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
! 3048: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
! 3049: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
! 3050: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
! 3051: fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
! 3052: /* fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
! 3053: */
! 3054: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
! 3055: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
! 3056:
! 3057: free_vector(xp,1,npar);
! 3058: free_matrix(doldm,1,nlstate,1,nlstate);
! 3059: free_matrix(dnewm,1,nlstate,1,npar);
! 3060: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
! 3061: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
! 3062: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
! 3063: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 3064: fclose(ficresprobmorprev);
! 3065: fflush(ficgp);
! 3066: fflush(fichtm);
! 3067: } /* end varevsij */
! 3068:
! 3069: /************ Variance of prevlim ******************/
! 3070: 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[])
! 3071: {
! 3072: /* Variance of prevalence limit */
! 3073: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
! 3074: double **newm;
! 3075: double **dnewm,**doldm;
! 3076: int i, j, nhstepm, hstepm;
! 3077: int k, cptcode;
! 3078: double *xp;
! 3079: double *gp, *gm;
! 3080: double **gradg, **trgradg;
! 3081: double age,agelim;
! 3082: int theta;
! 3083:
! 3084: pstamp(ficresvpl);
! 3085: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
! 3086: fprintf(ficresvpl,"# Age");
! 3087: for(i=1; i<=nlstate;i++)
! 3088: fprintf(ficresvpl," %1d-%1d",i,i);
! 3089: fprintf(ficresvpl,"\n");
! 3090:
! 3091: xp=vector(1,npar);
! 3092: dnewm=matrix(1,nlstate,1,npar);
! 3093: doldm=matrix(1,nlstate,1,nlstate);
! 3094:
! 3095: hstepm=1*YEARM; /* Every year of age */
! 3096: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
! 3097: agelim = AGESUP;
! 3098: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
! 3099: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
! 3100: if (stepm >= YEARM) hstepm=1;
! 3101: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
! 3102: gradg=matrix(1,npar,1,nlstate);
! 3103: gp=vector(1,nlstate);
! 3104: gm=vector(1,nlstate);
! 3105:
! 3106: for(theta=1; theta <=npar; theta++){
! 3107: for(i=1; i<=npar; i++){ /* Computes gradient */
! 3108: xp[i] = x[i] + (i==theta ?delti[theta]:0);
! 3109: }
! 3110: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
! 3111: for(i=1;i<=nlstate;i++)
! 3112: gp[i] = prlim[i][i];
! 3113:
! 3114: for(i=1; i<=npar; i++) /* Computes gradient */
! 3115: xp[i] = x[i] - (i==theta ?delti[theta]:0);
! 3116: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
! 3117: for(i=1;i<=nlstate;i++)
! 3118: gm[i] = prlim[i][i];
! 3119:
! 3120: for(i=1;i<=nlstate;i++)
! 3121: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
! 3122: } /* End theta */
! 3123:
! 3124: trgradg =matrix(1,nlstate,1,npar);
! 3125:
! 3126: for(j=1; j<=nlstate;j++)
! 3127: for(theta=1; theta <=npar; theta++)
! 3128: trgradg[j][theta]=gradg[theta][j];
! 3129:
! 3130: for(i=1;i<=nlstate;i++)
! 3131: varpl[i][(int)age] =0.;
! 3132: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
! 3133: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
! 3134: for(i=1;i<=nlstate;i++)
! 3135: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
! 3136:
! 3137: fprintf(ficresvpl,"%.0f ",age );
! 3138: for(i=1; i<=nlstate;i++)
! 3139: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
! 3140: fprintf(ficresvpl,"\n");
! 3141: free_vector(gp,1,nlstate);
! 3142: free_vector(gm,1,nlstate);
! 3143: free_matrix(gradg,1,npar,1,nlstate);
! 3144: free_matrix(trgradg,1,nlstate,1,npar);
! 3145: } /* End age */
! 3146:
! 3147: free_vector(xp,1,npar);
! 3148: free_matrix(doldm,1,nlstate,1,npar);
! 3149: free_matrix(dnewm,1,nlstate,1,nlstate);
! 3150:
! 3151: }
! 3152:
! 3153: /************ Variance of one-step probabilities ******************/
! 3154: 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[])
! 3155: {
! 3156: int i, j=0, i1, k1, l1, t, tj;
! 3157: int k2, l2, j1, z1;
! 3158: int k=0,l, cptcode;
! 3159: int first=1, first1;
! 3160: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
! 3161: double **dnewm,**doldm;
! 3162: double *xp;
! 3163: double *gp, *gm;
! 3164: double **gradg, **trgradg;
! 3165: double **mu;
! 3166: double age,agelim, cov[NCOVMAX];
! 3167: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
! 3168: int theta;
! 3169: char fileresprob[FILENAMELENGTH];
! 3170: char fileresprobcov[FILENAMELENGTH];
! 3171: char fileresprobcor[FILENAMELENGTH];
! 3172:
! 3173: double ***varpij;
! 3174:
! 3175: strcpy(fileresprob,"prob");
! 3176: strcat(fileresprob,fileres);
! 3177: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
! 3178: printf("Problem with resultfile: %s\n", fileresprob);
! 3179: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
! 3180: }
! 3181: strcpy(fileresprobcov,"probcov");
! 3182: strcat(fileresprobcov,fileres);
! 3183: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
! 3184: printf("Problem with resultfile: %s\n", fileresprobcov);
! 3185: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
! 3186: }
! 3187: strcpy(fileresprobcor,"probcor");
! 3188: strcat(fileresprobcor,fileres);
! 3189: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
! 3190: printf("Problem with resultfile: %s\n", fileresprobcor);
! 3191: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
! 3192: }
! 3193: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
! 3194: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
! 3195: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
! 3196: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
! 3197: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
! 3198: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
! 3199: pstamp(ficresprob);
! 3200: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
! 3201: fprintf(ficresprob,"# Age");
! 3202: pstamp(ficresprobcov);
! 3203: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
! 3204: fprintf(ficresprobcov,"# Age");
! 3205: pstamp(ficresprobcor);
! 3206: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
! 3207: fprintf(ficresprobcor,"# Age");
! 3208:
! 3209:
! 3210: for(i=1; i<=nlstate;i++)
! 3211: for(j=1; j<=(nlstate+ndeath);j++){
! 3212: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
! 3213: fprintf(ficresprobcov," p%1d-%1d ",i,j);
! 3214: fprintf(ficresprobcor," p%1d-%1d ",i,j);
! 3215: }
! 3216: /* fprintf(ficresprob,"\n");
! 3217: fprintf(ficresprobcov,"\n");
! 3218: fprintf(ficresprobcor,"\n");
! 3219: */
! 3220: xp=vector(1,npar);
! 3221: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
! 3222: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
! 3223: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
! 3224: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
! 3225: first=1;
! 3226: fprintf(ficgp,"\n# Routine varprob");
! 3227: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
! 3228: fprintf(fichtm,"\n");
! 3229:
! 3230: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
! 3231: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
! 3232: file %s<br>\n",optionfilehtmcov);
! 3233: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
! 3234: and drawn. It helps understanding how is the covariance between two incidences.\
! 3235: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
! 3236: fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
! 3237: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
! 3238: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
! 3239: standard deviations wide on each axis. <br>\
! 3240: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
! 3241: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
! 3242: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
! 3243:
! 3244: cov[1]=1;
! 3245: tj=cptcoveff;
! 3246: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
! 3247: j1=0;
! 3248: for(t=1; t<=tj;t++){
! 3249: for(i1=1; i1<=ncodemax[t];i1++){
! 3250: j1++;
! 3251: if (cptcovn>0) {
! 3252: fprintf(ficresprob, "\n#********** Variable ");
! 3253: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
! 3254: fprintf(ficresprob, "**********\n#\n");
! 3255: fprintf(ficresprobcov, "\n#********** Variable ");
! 3256: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
! 3257: fprintf(ficresprobcov, "**********\n#\n");
! 3258:
! 3259: fprintf(ficgp, "\n#********** Variable ");
! 3260: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
! 3261: fprintf(ficgp, "**********\n#\n");
! 3262:
! 3263:
! 3264: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
! 3265: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
! 3266: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
! 3267:
! 3268: fprintf(ficresprobcor, "\n#********** Variable ");
! 3269: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
! 3270: fprintf(ficresprobcor, "**********\n#");
! 3271: }
! 3272:
! 3273: for (age=bage; age<=fage; age ++){
! 3274: cov[2]=age;
! 3275: for (k=1; k<=cptcovn;k++) {
! 3276: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
! 3277: }
! 3278: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
! 3279: for (k=1; k<=cptcovprod;k++)
! 3280: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
! 3281:
! 3282: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
! 3283: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
! 3284: gp=vector(1,(nlstate)*(nlstate+ndeath));
! 3285: gm=vector(1,(nlstate)*(nlstate+ndeath));
! 3286:
! 3287: for(theta=1; theta <=npar; theta++){
! 3288: for(i=1; i<=npar; i++)
! 3289: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
! 3290:
! 3291: pmij(pmmij,cov,ncovmodel,xp,nlstate);
! 3292:
! 3293: k=0;
! 3294: for(i=1; i<= (nlstate); i++){
! 3295: for(j=1; j<=(nlstate+ndeath);j++){
! 3296: k=k+1;
! 3297: gp[k]=pmmij[i][j];
! 3298: }
! 3299: }
! 3300:
! 3301: for(i=1; i<=npar; i++)
! 3302: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
! 3303:
! 3304: pmij(pmmij,cov,ncovmodel,xp,nlstate);
! 3305: k=0;
! 3306: for(i=1; i<=(nlstate); i++){
! 3307: for(j=1; j<=(nlstate+ndeath);j++){
! 3308: k=k+1;
! 3309: gm[k]=pmmij[i][j];
! 3310: }
! 3311: }
! 3312:
! 3313: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
! 3314: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
! 3315: }
! 3316:
! 3317: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
! 3318: for(theta=1; theta <=npar; theta++)
! 3319: trgradg[j][theta]=gradg[theta][j];
! 3320:
! 3321: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
! 3322: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
! 3323: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
! 3324: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
! 3325: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
! 3326: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
! 3327:
! 3328: pmij(pmmij,cov,ncovmodel,x,nlstate);
! 3329:
! 3330: k=0;
! 3331: for(i=1; i<=(nlstate); i++){
! 3332: for(j=1; j<=(nlstate+ndeath);j++){
! 3333: k=k+1;
! 3334: mu[k][(int) age]=pmmij[i][j];
! 3335: }
! 3336: }
! 3337: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
! 3338: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
! 3339: varpij[i][j][(int)age] = doldm[i][j];
! 3340:
! 3341: /*printf("\n%d ",(int)age);
! 3342: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
! 3343: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
! 3344: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
! 3345: }*/
! 3346:
! 3347: fprintf(ficresprob,"\n%d ",(int)age);
! 3348: fprintf(ficresprobcov,"\n%d ",(int)age);
! 3349: fprintf(ficresprobcor,"\n%d ",(int)age);
! 3350:
! 3351: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
! 3352: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
! 3353: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
! 3354: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
! 3355: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
! 3356: }
! 3357: i=0;
! 3358: for (k=1; k<=(nlstate);k++){
! 3359: for (l=1; l<=(nlstate+ndeath);l++){
! 3360: i=i++;
! 3361: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
! 3362: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
! 3363: for (j=1; j<=i;j++){
! 3364: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
! 3365: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
! 3366: }
! 3367: }
! 3368: }/* end of loop for state */
! 3369: } /* end of loop for age */
! 3370:
! 3371: /* Confidence intervalle of pij */
! 3372: /*
! 3373: fprintf(ficgp,"\nset noparametric;unset label");
! 3374: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
! 3375: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
! 3376: fprintf(fichtm,"\n<br>Probability with confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
! 3377: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
! 3378: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
! 3379: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
! 3380: */
! 3381:
! 3382: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
! 3383: first1=1;
! 3384: for (k2=1; k2<=(nlstate);k2++){
! 3385: for (l2=1; l2<=(nlstate+ndeath);l2++){
! 3386: if(l2==k2) continue;
! 3387: j=(k2-1)*(nlstate+ndeath)+l2;
! 3388: for (k1=1; k1<=(nlstate);k1++){
! 3389: for (l1=1; l1<=(nlstate+ndeath);l1++){
! 3390: if(l1==k1) continue;
! 3391: i=(k1-1)*(nlstate+ndeath)+l1;
! 3392: if(i<=j) continue;
! 3393: for (age=bage; age<=fage; age ++){
! 3394: if ((int)age %5==0){
! 3395: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
! 3396: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
! 3397: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
! 3398: mu1=mu[i][(int) age]/stepm*YEARM ;
! 3399: mu2=mu[j][(int) age]/stepm*YEARM;
! 3400: c12=cv12/sqrt(v1*v2);
! 3401: /* Computing eigen value of matrix of covariance */
! 3402: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
! 3403: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
! 3404: /* Eigen vectors */
! 3405: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
! 3406: /*v21=sqrt(1.-v11*v11); *//* error */
! 3407: v21=(lc1-v1)/cv12*v11;
! 3408: v12=-v21;
! 3409: v22=v11;
! 3410: tnalp=v21/v11;
! 3411: if(first1==1){
! 3412: first1=0;
! 3413: 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);
! 3414: }
! 3415: 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);
! 3416: /*printf(fignu*/
! 3417: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
! 3418: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
! 3419: if(first==1){
! 3420: first=0;
! 3421: fprintf(ficgp,"\nset parametric;unset label");
! 3422: 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);
! 3423: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
! 3424: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
! 3425: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
! 3426: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
! 3427: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
! 3428: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
! 3429: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
! 3430: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
! 3431: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
! 3432: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
! 3433: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
! 3434: 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",\
! 3435: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
! 3436: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
! 3437: }else{
! 3438: first=0;
! 3439: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
! 3440: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
! 3441: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
! 3442: 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",\
! 3443: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
! 3444: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
! 3445: }/* if first */
! 3446: } /* age mod 5 */
! 3447: } /* end loop age */
! 3448: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
! 3449: first=1;
! 3450: } /*l12 */
! 3451: } /* k12 */
! 3452: } /*l1 */
! 3453: }/* k1 */
! 3454: } /* loop covariates */
! 3455: }
! 3456: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
! 3457: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
! 3458: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
! 3459: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
! 3460: free_vector(xp,1,npar);
! 3461: fclose(ficresprob);
! 3462: fclose(ficresprobcov);
! 3463: fclose(ficresprobcor);
! 3464: fflush(ficgp);
! 3465: fflush(fichtmcov);
! 3466: }
! 3467:
! 3468:
! 3469: /******************* Printing html file ***********/
! 3470: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
! 3471: int lastpass, int stepm, int weightopt, char model[],\
! 3472: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
! 3473: int popforecast, int estepm ,\
! 3474: double jprev1, double mprev1,double anprev1, \
! 3475: double jprev2, double mprev2,double anprev2){
! 3476: int jj1, k1, i1, cpt;
! 3477:
! 3478: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
! 3479: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
! 3480: </ul>");
! 3481: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
! 3482: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
! 3483: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
! 3484: fprintf(fichtm,"\
! 3485: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
! 3486: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
! 3487: fprintf(fichtm,"\
! 3488: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
! 3489: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
! 3490: fprintf(fichtm,"\
! 3491: - (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age: ei., eij . If one or more covariate are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
! 3492: <a href=\"%s\">%s</a> <br>\n",
! 3493: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
! 3494: fprintf(fichtm,"\
! 3495: - Population projections by age and states: \
! 3496: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
! 3497:
! 3498: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
! 3499:
! 3500: m=cptcoveff;
! 3501: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
! 3502:
! 3503: jj1=0;
! 3504: for(k1=1; k1<=m;k1++){
! 3505: for(i1=1; i1<=ncodemax[k1];i1++){
! 3506: jj1++;
! 3507: if (cptcovn > 0) {
! 3508: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
! 3509: for (cpt=1; cpt<=cptcoveff;cpt++)
! 3510: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
! 3511: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
! 3512: }
! 3513: /* Pij */
! 3514: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
! 3515: <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
! 3516: /* Quasi-incidences */
! 3517: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
! 3518: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
! 3519: <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
! 3520: /* Period (stable) prevalence in each health state */
! 3521: for(cpt=1; cpt<nlstate;cpt++){
! 3522: fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
! 3523: <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
! 3524: }
! 3525: for(cpt=1; cpt<=nlstate;cpt++) {
! 3526: fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
! 3527: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
! 3528: }
! 3529: } /* end i1 */
! 3530: }/* End k1 */
! 3531: fprintf(fichtm,"</ul>");
! 3532:
! 3533:
! 3534: fprintf(fichtm,"\
! 3535: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
! 3536: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
! 3537:
! 3538: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
! 3539: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
! 3540: fprintf(fichtm,"\
! 3541: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
! 3542: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
! 3543:
! 3544: fprintf(fichtm,"\
! 3545: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
! 3546: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
! 3547: fprintf(fichtm,"\
! 3548: - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
! 3549: <a href=\"%s\">%s</a> <br>\n</li>",
! 3550: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
! 3551: fprintf(fichtm,"\
! 3552: - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
! 3553: <a href=\"%s\">%s</a> <br>\n</li>",
! 3554: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
! 3555: fprintf(fichtm,"\
! 3556: - 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><br>\n",
! 3557: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
! 3558: fprintf(fichtm,"\
! 3559: - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors: <a href=\"%s\">%s</a> <br>\n",
! 3560: subdirf2(fileres,"t"),subdirf2(fileres,"t"));
! 3561: fprintf(fichtm,"\
! 3562: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
! 3563: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
! 3564:
! 3565: /* if(popforecast==1) fprintf(fichtm,"\n */
! 3566: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
! 3567: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
! 3568: /* <br>",fileres,fileres,fileres,fileres); */
! 3569: /* else */
! 3570: /* fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
! 3571: fflush(fichtm);
! 3572: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
! 3573:
! 3574: m=cptcoveff;
! 3575: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
! 3576:
! 3577: jj1=0;
! 3578: for(k1=1; k1<=m;k1++){
! 3579: for(i1=1; i1<=ncodemax[k1];i1++){
! 3580: jj1++;
! 3581: if (cptcovn > 0) {
! 3582: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
! 3583: for (cpt=1; cpt<=cptcoveff;cpt++)
! 3584: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
! 3585: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
! 3586: }
! 3587: for(cpt=1; cpt<=nlstate;cpt++) {
! 3588: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
! 3589: prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
! 3590: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
! 3591: }
! 3592: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
! 3593: health expectancies in states (1) and (2): %s%d.png<br>\
! 3594: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
! 3595: } /* end i1 */
! 3596: }/* End k1 */
! 3597: fprintf(fichtm,"</ul>");
! 3598: fflush(fichtm);
! 3599: }
! 3600:
! 3601: /******************* Gnuplot file **************/
! 3602: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
! 3603:
! 3604: char dirfileres[132],optfileres[132];
! 3605: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
! 3606: int ng;
! 3607: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
! 3608: /* printf("Problem with file %s",optionfilegnuplot); */
! 3609: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
! 3610: /* } */
! 3611:
! 3612: /*#ifdef windows */
! 3613: fprintf(ficgp,"cd \"%s\" \n",pathc);
! 3614: /*#endif */
! 3615: m=pow(2,cptcoveff);
! 3616:
! 3617: strcpy(dirfileres,optionfilefiname);
! 3618: strcpy(optfileres,"vpl");
! 3619: /* 1eme*/
! 3620: for (cpt=1; cpt<= nlstate ; cpt ++) {
! 3621: for (k1=1; k1<= m ; k1 ++) {
! 3622: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
! 3623: fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
! 3624: fprintf(ficgp,"set xlabel \"Age\" \n\
! 3625: set ylabel \"Probability\" \n\
! 3626: set ter png small\n\
! 3627: set size 0.65,0.65\n\
! 3628: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
! 3629:
! 3630: for (i=1; i<= nlstate ; i ++) {
! 3631: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
! 3632: else fprintf(ficgp," \%%*lf (\%%*lf)");
! 3633: }
! 3634: fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
! 3635: for (i=1; i<= nlstate ; i ++) {
! 3636: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
! 3637: else fprintf(ficgp," \%%*lf (\%%*lf)");
! 3638: }
! 3639: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
! 3640: for (i=1; i<= nlstate ; i ++) {
! 3641: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
! 3642: else fprintf(ficgp," \%%*lf (\%%*lf)");
! 3643: }
! 3644: fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
! 3645: }
! 3646: }
! 3647: /*2 eme*/
! 3648:
! 3649: for (k1=1; k1<= m ; k1 ++) {
! 3650: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
! 3651: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
! 3652:
! 3653: for (i=1; i<= nlstate+1 ; i ++) {
! 3654: k=2*i;
! 3655: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
! 3656: for (j=1; j<= nlstate+1 ; j ++) {
! 3657: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
! 3658: else fprintf(ficgp," \%%*lf (\%%*lf)");
! 3659: }
! 3660: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
! 3661: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
! 3662: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
! 3663: for (j=1; j<= nlstate+1 ; j ++) {
! 3664: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
! 3665: else fprintf(ficgp," \%%*lf (\%%*lf)");
! 3666: }
! 3667: fprintf(ficgp,"\" t\"\" w l 0,");
! 3668: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
! 3669: for (j=1; j<= nlstate+1 ; j ++) {
! 3670: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
! 3671: else fprintf(ficgp," \%%*lf (\%%*lf)");
! 3672: }
! 3673: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
! 3674: else fprintf(ficgp,"\" t\"\" w l 0,");
! 3675: }
! 3676: }
! 3677:
! 3678: /*3eme*/
! 3679:
! 3680: for (k1=1; k1<= m ; k1 ++) {
! 3681: for (cpt=1; cpt<= nlstate ; cpt ++) {
! 3682: /* k=2+nlstate*(2*cpt-2); */
! 3683: k=2+(nlstate+1)*(cpt-1);
! 3684: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
! 3685: fprintf(ficgp,"set ter png small\n\
! 3686: set size 0.65,0.65\n\
! 3687: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
! 3688: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
! 3689: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
! 3690: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
! 3691: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
! 3692: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
! 3693: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
! 3694:
! 3695: */
! 3696: for (i=1; i< nlstate ; i ++) {
! 3697: 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);
! 3698: /* 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);*/
! 3699:
! 3700: }
! 3701: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
! 3702: }
! 3703: }
! 3704:
! 3705: /* CV preval stable (period) */
! 3706: for (k1=1; k1<= m ; k1 ++) {
! 3707: for (cpt=1; cpt<=nlstate ; cpt ++) {
! 3708: k=3;
! 3709: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
! 3710: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
! 3711: set ter png small\nset size 0.65,0.65\n\
! 3712: unset log y\n\
! 3713: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
! 3714:
! 3715: for (i=1; i< nlstate ; i ++)
! 3716: fprintf(ficgp,"+$%d",k+i+1);
! 3717: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
! 3718:
! 3719: l=3+(nlstate+ndeath)*cpt;
! 3720: fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
! 3721: for (i=1; i< nlstate ; i ++) {
! 3722: l=3+(nlstate+ndeath)*cpt;
! 3723: fprintf(ficgp,"+$%d",l+i+1);
! 3724: }
! 3725: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
! 3726: }
! 3727: }
! 3728:
! 3729: /* proba elementaires */
! 3730: for(i=1,jk=1; i <=nlstate; i++){
! 3731: for(k=1; k <=(nlstate+ndeath); k++){
! 3732: if (k != i) {
! 3733: for(j=1; j <=ncovmodel; j++){
! 3734: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
! 3735: jk++;
! 3736: fprintf(ficgp,"\n");
! 3737: }
! 3738: }
! 3739: }
! 3740: }
! 3741:
! 3742: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
! 3743: for(jk=1; jk <=m; jk++) {
! 3744: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
! 3745: if (ng==2)
! 3746: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
! 3747: else
! 3748: fprintf(ficgp,"\nset title \"Probability\"\n");
! 3749: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
! 3750: i=1;
! 3751: for(k2=1; k2<=nlstate; k2++) {
! 3752: k3=i;
! 3753: for(k=1; k<=(nlstate+ndeath); k++) {
! 3754: if (k != k2){
! 3755: if(ng==2)
! 3756: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
! 3757: else
! 3758: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
! 3759: ij=1;
! 3760: for(j=3; j <=ncovmodel; j++) {
! 3761: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
! 3762: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
! 3763: ij++;
! 3764: }
! 3765: else
! 3766: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
! 3767: }
! 3768: fprintf(ficgp,")/(1");
! 3769:
! 3770: for(k1=1; k1 <=nlstate; k1++){
! 3771: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
! 3772: ij=1;
! 3773: for(j=3; j <=ncovmodel; j++){
! 3774: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
! 3775: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
! 3776: ij++;
! 3777: }
! 3778: else
! 3779: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
! 3780: }
! 3781: fprintf(ficgp,")");
! 3782: }
! 3783: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
! 3784: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
! 3785: i=i+ncovmodel;
! 3786: }
! 3787: } /* end k */
! 3788: } /* end k2 */
! 3789: } /* end jk */
! 3790: } /* end ng */
! 3791: fflush(ficgp);
! 3792: } /* end gnuplot */
! 3793:
! 3794:
! 3795: /*************** Moving average **************/
! 3796: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
! 3797:
! 3798: int i, cpt, cptcod;
! 3799: int modcovmax =1;
! 3800: int mobilavrange, mob;
! 3801: double age;
! 3802:
! 3803: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
! 3804: a covariate has 2 modalities */
! 3805: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
! 3806:
! 3807: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
! 3808: if(mobilav==1) mobilavrange=5; /* default */
! 3809: else mobilavrange=mobilav;
! 3810: for (age=bage; age<=fage; age++)
! 3811: for (i=1; i<=nlstate;i++)
! 3812: for (cptcod=1;cptcod<=modcovmax;cptcod++)
! 3813: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
! 3814: /* We keep the original values on the extreme ages bage, fage and for
! 3815: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
! 3816: we use a 5 terms etc. until the borders are no more concerned.
! 3817: */
! 3818: for (mob=3;mob <=mobilavrange;mob=mob+2){
! 3819: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
! 3820: for (i=1; i<=nlstate;i++){
! 3821: for (cptcod=1;cptcod<=modcovmax;cptcod++){
! 3822: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
! 3823: for (cpt=1;cpt<=(mob-1)/2;cpt++){
! 3824: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
! 3825: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
! 3826: }
! 3827: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
! 3828: }
! 3829: }
! 3830: }/* end age */
! 3831: }/* end mob */
! 3832: }else return -1;
! 3833: return 0;
! 3834: }/* End movingaverage */
! 3835:
! 3836:
! 3837: /************** Forecasting ******************/
! 3838: 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){
! 3839: /* proj1, year, month, day of starting projection
! 3840: agemin, agemax range of age
! 3841: dateprev1 dateprev2 range of dates during which prevalence is computed
! 3842: anproj2 year of en of projection (same day and month as proj1).
! 3843: */
! 3844: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
! 3845: int *popage;
! 3846: double agec; /* generic age */
! 3847: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
! 3848: double *popeffectif,*popcount;
! 3849: double ***p3mat;
! 3850: double ***mobaverage;
! 3851: char fileresf[FILENAMELENGTH];
! 3852:
! 3853: agelim=AGESUP;
! 3854: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
! 3855:
! 3856: strcpy(fileresf,"f");
! 3857: strcat(fileresf,fileres);
! 3858: if((ficresf=fopen(fileresf,"w"))==NULL) {
! 3859: printf("Problem with forecast resultfile: %s\n", fileresf);
! 3860: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
! 3861: }
! 3862: printf("Computing forecasting: result on file '%s' \n", fileresf);
! 3863: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
! 3864:
! 3865: if (cptcoveff==0) ncodemax[cptcoveff]=1;
! 3866:
! 3867: if (mobilav!=0) {
! 3868: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 3869: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
! 3870: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
! 3871: printf(" Error in movingaverage mobilav=%d\n",mobilav);
! 3872: }
! 3873: }
! 3874:
! 3875: stepsize=(int) (stepm+YEARM-1)/YEARM;
! 3876: if (stepm<=12) stepsize=1;
! 3877: if(estepm < stepm){
! 3878: printf ("Problem %d lower than %d\n",estepm, stepm);
! 3879: }
! 3880: else hstepm=estepm;
! 3881:
! 3882: hstepm=hstepm/stepm;
! 3883: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
! 3884: fractional in yp1 */
! 3885: anprojmean=yp;
! 3886: yp2=modf((yp1*12),&yp);
! 3887: mprojmean=yp;
! 3888: yp1=modf((yp2*30.5),&yp);
! 3889: jprojmean=yp;
! 3890: if(jprojmean==0) jprojmean=1;
! 3891: if(mprojmean==0) jprojmean=1;
! 3892:
! 3893: i1=cptcoveff;
! 3894: if (cptcovn < 1){i1=1;}
! 3895:
! 3896: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
! 3897:
! 3898: fprintf(ficresf,"#****** Routine prevforecast **\n");
! 3899:
! 3900: /* if (h==(int)(YEARM*yearp)){ */
! 3901: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
! 3902: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
! 3903: k=k+1;
! 3904: fprintf(ficresf,"\n#******");
! 3905: for(j=1;j<=cptcoveff;j++) {
! 3906: 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]]);
! 3907: }
! 3908: fprintf(ficresf,"******\n");
! 3909: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
! 3910: for(j=1; j<=nlstate+ndeath;j++){
! 3911: for(i=1; i<=nlstate;i++)
! 3912: fprintf(ficresf," p%d%d",i,j);
! 3913: fprintf(ficresf," p.%d",j);
! 3914: }
! 3915: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
! 3916: fprintf(ficresf,"\n");
! 3917: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
! 3918:
! 3919: for (agec=fage; agec>=(ageminpar-1); agec--){
! 3920: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
! 3921: nhstepm = nhstepm/hstepm;
! 3922: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 3923: oldm=oldms;savm=savms;
! 3924: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
! 3925:
! 3926: for (h=0; h<=nhstepm; h++){
! 3927: if (h*hstepm/YEARM*stepm ==yearp) {
! 3928: fprintf(ficresf,"\n");
! 3929: for(j=1;j<=cptcoveff;j++)
! 3930: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 3931: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
! 3932: }
! 3933: for(j=1; j<=nlstate+ndeath;j++) {
! 3934: ppij=0.;
! 3935: for(i=1; i<=nlstate;i++) {
! 3936: if (mobilav==1)
! 3937: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
! 3938: else {
! 3939: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
! 3940: }
! 3941: if (h*hstepm/YEARM*stepm== yearp) {
! 3942: fprintf(ficresf," %.3f", p3mat[i][j][h]);
! 3943: }
! 3944: } /* end i */
! 3945: if (h*hstepm/YEARM*stepm==yearp) {
! 3946: fprintf(ficresf," %.3f", ppij);
! 3947: }
! 3948: }/* end j */
! 3949: } /* end h */
! 3950: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 3951: } /* end agec */
! 3952: } /* end yearp */
! 3953: } /* end cptcod */
! 3954: } /* end cptcov */
! 3955:
! 3956: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 3957:
! 3958: fclose(ficresf);
! 3959: }
! 3960:
! 3961: /************** Forecasting *****not tested NB*************/
! 3962: 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){
! 3963:
! 3964: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
! 3965: int *popage;
! 3966: double calagedatem, agelim, kk1, kk2;
! 3967: double *popeffectif,*popcount;
! 3968: double ***p3mat,***tabpop,***tabpopprev;
! 3969: double ***mobaverage;
! 3970: char filerespop[FILENAMELENGTH];
! 3971:
! 3972: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 3973: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 3974: agelim=AGESUP;
! 3975: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
! 3976:
! 3977: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
! 3978:
! 3979:
! 3980: strcpy(filerespop,"pop");
! 3981: strcat(filerespop,fileres);
! 3982: if((ficrespop=fopen(filerespop,"w"))==NULL) {
! 3983: printf("Problem with forecast resultfile: %s\n", filerespop);
! 3984: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
! 3985: }
! 3986: printf("Computing forecasting: result on file '%s' \n", filerespop);
! 3987: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
! 3988:
! 3989: if (cptcoveff==0) ncodemax[cptcoveff]=1;
! 3990:
! 3991: if (mobilav!=0) {
! 3992: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 3993: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
! 3994: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
! 3995: printf(" Error in movingaverage mobilav=%d\n",mobilav);
! 3996: }
! 3997: }
! 3998:
! 3999: stepsize=(int) (stepm+YEARM-1)/YEARM;
! 4000: if (stepm<=12) stepsize=1;
! 4001:
! 4002: agelim=AGESUP;
! 4003:
! 4004: hstepm=1;
! 4005: hstepm=hstepm/stepm;
! 4006:
! 4007: if (popforecast==1) {
! 4008: if((ficpop=fopen(popfile,"r"))==NULL) {
! 4009: printf("Problem with population file : %s\n",popfile);exit(0);
! 4010: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
! 4011: }
! 4012: popage=ivector(0,AGESUP);
! 4013: popeffectif=vector(0,AGESUP);
! 4014: popcount=vector(0,AGESUP);
! 4015:
! 4016: i=1;
! 4017: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
! 4018:
! 4019: imx=i;
! 4020: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
! 4021: }
! 4022:
! 4023: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
! 4024: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
! 4025: k=k+1;
! 4026: fprintf(ficrespop,"\n#******");
! 4027: for(j=1;j<=cptcoveff;j++) {
! 4028: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 4029: }
! 4030: fprintf(ficrespop,"******\n");
! 4031: fprintf(ficrespop,"# Age");
! 4032: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
! 4033: if (popforecast==1) fprintf(ficrespop," [Population]");
! 4034:
! 4035: for (cpt=0; cpt<=0;cpt++) {
! 4036: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
! 4037:
! 4038: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
! 4039: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
! 4040: nhstepm = nhstepm/hstepm;
! 4041:
! 4042: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 4043: oldm=oldms;savm=savms;
! 4044: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
! 4045:
! 4046: for (h=0; h<=nhstepm; h++){
! 4047: if (h==(int) (calagedatem+YEARM*cpt)) {
! 4048: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
! 4049: }
! 4050: for(j=1; j<=nlstate+ndeath;j++) {
! 4051: kk1=0.;kk2=0;
! 4052: for(i=1; i<=nlstate;i++) {
! 4053: if (mobilav==1)
! 4054: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
! 4055: else {
! 4056: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
! 4057: }
! 4058: }
! 4059: if (h==(int)(calagedatem+12*cpt)){
! 4060: tabpop[(int)(agedeb)][j][cptcod]=kk1;
! 4061: /*fprintf(ficrespop," %.3f", kk1);
! 4062: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
! 4063: }
! 4064: }
! 4065: for(i=1; i<=nlstate;i++){
! 4066: kk1=0.;
! 4067: for(j=1; j<=nlstate;j++){
! 4068: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
! 4069: }
! 4070: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
! 4071: }
! 4072:
! 4073: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
! 4074: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
! 4075: }
! 4076: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 4077: }
! 4078: }
! 4079:
! 4080: /******/
! 4081:
! 4082: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
! 4083: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
! 4084: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
! 4085: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
! 4086: nhstepm = nhstepm/hstepm;
! 4087:
! 4088: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 4089: oldm=oldms;savm=savms;
! 4090: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
! 4091: for (h=0; h<=nhstepm; h++){
! 4092: if (h==(int) (calagedatem+YEARM*cpt)) {
! 4093: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
! 4094: }
! 4095: for(j=1; j<=nlstate+ndeath;j++) {
! 4096: kk1=0.;kk2=0;
! 4097: for(i=1; i<=nlstate;i++) {
! 4098: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
! 4099: }
! 4100: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
! 4101: }
! 4102: }
! 4103: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 4104: }
! 4105: }
! 4106: }
! 4107: }
! 4108:
! 4109: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 4110:
! 4111: if (popforecast==1) {
! 4112: free_ivector(popage,0,AGESUP);
! 4113: free_vector(popeffectif,0,AGESUP);
! 4114: free_vector(popcount,0,AGESUP);
! 4115: }
! 4116: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 4117: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 4118: fclose(ficrespop);
! 4119: } /* End of popforecast */
! 4120:
! 4121: int fileappend(FILE *fichier, char *optionfich)
! 4122: {
! 4123: if((fichier=fopen(optionfich,"a"))==NULL) {
! 4124: printf("Problem with file: %s\n", optionfich);
! 4125: fprintf(ficlog,"Problem with file: %s\n", optionfich);
! 4126: return (0);
! 4127: }
! 4128: fflush(fichier);
! 4129: return (1);
! 4130: }
! 4131:
! 4132:
! 4133: /**************** function prwizard **********************/
! 4134: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
! 4135: {
! 4136:
! 4137: /* Wizard to print covariance matrix template */
! 4138:
! 4139: char ca[32], cb[32], cc[32];
! 4140: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
! 4141: int numlinepar;
! 4142:
! 4143: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
! 4144: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
! 4145: for(i=1; i <=nlstate; i++){
! 4146: jj=0;
! 4147: for(j=1; j <=nlstate+ndeath; j++){
! 4148: if(j==i) continue;
! 4149: jj++;
! 4150: /*ca[0]= k+'a'-1;ca[1]='\0';*/
! 4151: printf("%1d%1d",i,j);
! 4152: fprintf(ficparo,"%1d%1d",i,j);
! 4153: for(k=1; k<=ncovmodel;k++){
! 4154: /* printf(" %lf",param[i][j][k]); */
! 4155: /* fprintf(ficparo," %lf",param[i][j][k]); */
! 4156: printf(" 0.");
! 4157: fprintf(ficparo," 0.");
! 4158: }
! 4159: printf("\n");
! 4160: fprintf(ficparo,"\n");
! 4161: }
! 4162: }
! 4163: printf("# Scales (for hessian or gradient estimation)\n");
! 4164: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
! 4165: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
! 4166: for(i=1; i <=nlstate; i++){
! 4167: jj=0;
! 4168: for(j=1; j <=nlstate+ndeath; j++){
! 4169: if(j==i) continue;
! 4170: jj++;
! 4171: fprintf(ficparo,"%1d%1d",i,j);
! 4172: printf("%1d%1d",i,j);
! 4173: fflush(stdout);
! 4174: for(k=1; k<=ncovmodel;k++){
! 4175: /* printf(" %le",delti3[i][j][k]); */
! 4176: /* fprintf(ficparo," %le",delti3[i][j][k]); */
! 4177: printf(" 0.");
! 4178: fprintf(ficparo," 0.");
! 4179: }
! 4180: numlinepar++;
! 4181: printf("\n");
! 4182: fprintf(ficparo,"\n");
! 4183: }
! 4184: }
! 4185: printf("# Covariance matrix\n");
! 4186: /* # 121 Var(a12)\n\ */
! 4187: /* # 122 Cov(b12,a12) Var(b12)\n\ */
! 4188: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
! 4189: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
! 4190: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
! 4191: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
! 4192: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
! 4193: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
! 4194: fflush(stdout);
! 4195: fprintf(ficparo,"# Covariance matrix\n");
! 4196: /* # 121 Var(a12)\n\ */
! 4197: /* # 122 Cov(b12,a12) Var(b12)\n\ */
! 4198: /* # ...\n\ */
! 4199: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
! 4200:
! 4201: for(itimes=1;itimes<=2;itimes++){
! 4202: jj=0;
! 4203: for(i=1; i <=nlstate; i++){
! 4204: for(j=1; j <=nlstate+ndeath; j++){
! 4205: if(j==i) continue;
! 4206: for(k=1; k<=ncovmodel;k++){
! 4207: jj++;
! 4208: ca[0]= k+'a'-1;ca[1]='\0';
! 4209: if(itimes==1){
! 4210: printf("#%1d%1d%d",i,j,k);
! 4211: fprintf(ficparo,"#%1d%1d%d",i,j,k);
! 4212: }else{
! 4213: printf("%1d%1d%d",i,j,k);
! 4214: fprintf(ficparo,"%1d%1d%d",i,j,k);
! 4215: /* printf(" %.5le",matcov[i][j]); */
! 4216: }
! 4217: ll=0;
! 4218: for(li=1;li <=nlstate; li++){
! 4219: for(lj=1;lj <=nlstate+ndeath; lj++){
! 4220: if(lj==li) continue;
! 4221: for(lk=1;lk<=ncovmodel;lk++){
! 4222: ll++;
! 4223: if(ll<=jj){
! 4224: cb[0]= lk +'a'-1;cb[1]='\0';
! 4225: if(ll<jj){
! 4226: if(itimes==1){
! 4227: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
! 4228: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
! 4229: }else{
! 4230: printf(" 0.");
! 4231: fprintf(ficparo," 0.");
! 4232: }
! 4233: }else{
! 4234: if(itimes==1){
! 4235: printf(" Var(%s%1d%1d)",ca,i,j);
! 4236: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
! 4237: }else{
! 4238: printf(" 0.");
! 4239: fprintf(ficparo," 0.");
! 4240: }
! 4241: }
! 4242: }
! 4243: } /* end lk */
! 4244: } /* end lj */
! 4245: } /* end li */
! 4246: printf("\n");
! 4247: fprintf(ficparo,"\n");
! 4248: numlinepar++;
! 4249: } /* end k*/
! 4250: } /*end j */
! 4251: } /* end i */
! 4252: } /* end itimes */
! 4253:
! 4254: } /* end of prwizard */
! 4255: /******************* Gompertz Likelihood ******************************/
! 4256: double gompertz(double x[])
! 4257: {
! 4258: double A,B,L=0.0,sump=0.,num=0.;
! 4259: int i,n=0; /* n is the size of the sample */
! 4260:
! 4261: for (i=0;i<=imx-1 ; i++) {
! 4262: sump=sump+weight[i];
! 4263: /* sump=sump+1;*/
! 4264: num=num+1;
! 4265: }
! 4266:
! 4267:
! 4268: /* for (i=0; i<=imx; i++)
! 4269: 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]);*/
! 4270:
! 4271: for (i=1;i<=imx ; i++)
! 4272: {
! 4273: if (cens[i] == 1 && wav[i]>1)
! 4274: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
! 4275:
! 4276: if (cens[i] == 0 && wav[i]>1)
! 4277: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
! 4278: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
! 4279:
! 4280: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
! 4281: if (wav[i] > 1 ) { /* ??? */
! 4282: L=L+A*weight[i];
! 4283: /* 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]);*/
! 4284: }
! 4285: }
! 4286:
! 4287: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
! 4288:
! 4289: return -2*L*num/sump;
! 4290: }
! 4291:
! 4292: /******************* Printing html file ***********/
! 4293: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
! 4294: int lastpass, int stepm, int weightopt, char model[],\
! 4295: int imx, double p[],double **matcov,double agemortsup){
! 4296: int i,k;
! 4297:
! 4298: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
! 4299: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
! 4300: for (i=1;i<=2;i++)
! 4301: fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
! 4302: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
! 4303: fprintf(fichtm,"</ul>");
! 4304:
! 4305: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
! 4306:
! 4307: fprintf(fichtm,"\nAge l<inf>x</inf> q<inf>x</inf> d(x,x+1) L<inf>x</inf> T<inf>x</inf> e<infx</inf><br>");
! 4308:
! 4309: for (k=agegomp;k<(agemortsup-2);k++)
! 4310: fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
! 4311:
! 4312:
! 4313: fflush(fichtm);
! 4314: }
! 4315:
! 4316: /******************* Gnuplot file **************/
! 4317: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
! 4318:
! 4319: char dirfileres[132],optfileres[132];
! 4320: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
! 4321: int ng;
! 4322:
! 4323:
! 4324: /*#ifdef windows */
! 4325: fprintf(ficgp,"cd \"%s\" \n",pathc);
! 4326: /*#endif */
! 4327:
! 4328:
! 4329: strcpy(dirfileres,optionfilefiname);
! 4330: strcpy(optfileres,"vpl");
! 4331: fprintf(ficgp,"set out \"graphmort.png\"\n ");
! 4332: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
! 4333: fprintf(ficgp, "set ter png small\n set log y\n");
! 4334: fprintf(ficgp, "set size 0.65,0.65\n");
! 4335: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
! 4336:
! 4337: }
! 4338:
! 4339:
! 4340:
! 4341:
! 4342:
! 4343: /***********************************************/
! 4344: /**************** Main Program *****************/
! 4345: /***********************************************/
! 4346:
! 4347: int main(int argc, char *argv[])
! 4348: {
! 4349: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
! 4350: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
! 4351: int linei, month, year,iout;
! 4352: int jj, ll, li, lj, lk, imk;
! 4353: int numlinepar=0; /* Current linenumber of parameter file */
! 4354: int itimes;
! 4355: int NDIM=2;
! 4356:
! 4357: char ca[32], cb[32], cc[32];
! 4358: char dummy[]=" ";
! 4359: /* FILE *fichtm; *//* Html File */
! 4360: /* FILE *ficgp;*/ /*Gnuplot File */
! 4361: struct stat info;
! 4362: double agedeb, agefin,hf;
! 4363: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
! 4364:
! 4365: double fret;
! 4366: double **xi,tmp,delta;
! 4367:
! 4368: double dum; /* Dummy variable */
! 4369: double ***p3mat;
! 4370: double ***mobaverage;
! 4371: int *indx;
! 4372: char line[MAXLINE], linepar[MAXLINE];
! 4373: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
! 4374: char pathr[MAXLINE], pathimach[MAXLINE];
! 4375: char **bp, *tok, *val; /* pathtot */
! 4376: int firstobs=1, lastobs=10;
! 4377: int sdeb, sfin; /* Status at beginning and end */
! 4378: int c, h , cpt,l;
! 4379: int ju,jl, mi;
! 4380: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
! 4381: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
! 4382: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
! 4383: int mobilav=0,popforecast=0;
! 4384: int hstepm, nhstepm;
! 4385: int agemortsup;
! 4386: float sumlpop=0.;
! 4387: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
! 4388: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
! 4389:
! 4390: double bage, fage, age, agelim, agebase;
! 4391: double ftolpl=FTOL;
! 4392: double **prlim;
! 4393: double *severity;
! 4394: double ***param; /* Matrix of parameters */
! 4395: double *p;
! 4396: double **matcov; /* Matrix of covariance */
! 4397: double ***delti3; /* Scale */
! 4398: double *delti; /* Scale */
! 4399: double ***eij, ***vareij;
! 4400: double **varpl; /* Variances of prevalence limits by age */
! 4401: double *epj, vepp;
! 4402: double kk1, kk2;
! 4403: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
! 4404: double **ximort;
! 4405: char *alph[]={"a","a","b","c","d","e"}, str[4];
! 4406: int *dcwave;
! 4407:
! 4408: char z[1]="c", occ;
! 4409:
! 4410: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
! 4411: char *strt, strtend[80];
! 4412: char *stratrunc;
! 4413: int lstra;
! 4414:
! 4415: long total_usecs;
! 4416:
! 4417: /* setlocale (LC_ALL, ""); */
! 4418: /* bindtextdomain (PACKAGE, LOCALEDIR); */
! 4419: /* textdomain (PACKAGE); */
! 4420: /* setlocale (LC_CTYPE, ""); */
! 4421: /* setlocale (LC_MESSAGES, ""); */
! 4422:
! 4423: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
! 4424: (void) gettimeofday(&start_time,&tzp);
! 4425: curr_time=start_time;
! 4426: tm = *localtime(&start_time.tv_sec);
! 4427: tmg = *gmtime(&start_time.tv_sec);
! 4428: strcpy(strstart,asctime(&tm));
! 4429:
! 4430: /* printf("Localtime (at start)=%s",strstart); */
! 4431: /* tp.tv_sec = tp.tv_sec +86400; */
! 4432: /* tm = *localtime(&start_time.tv_sec); */
! 4433: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
! 4434: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
! 4435: /* tmg.tm_hour=tmg.tm_hour + 1; */
! 4436: /* tp.tv_sec = mktime(&tmg); */
! 4437: /* strt=asctime(&tmg); */
! 4438: /* printf("Time(after) =%s",strstart); */
! 4439: /* (void) time (&time_value);
! 4440: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
! 4441: * tm = *localtime(&time_value);
! 4442: * strstart=asctime(&tm);
! 4443: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
! 4444: */
! 4445:
! 4446: nberr=0; /* Number of errors and warnings */
! 4447: nbwarn=0;
! 4448: getcwd(pathcd, size);
! 4449:
! 4450: printf("\n%s\n%s",version,fullversion);
! 4451: if(argc <=1){
! 4452: printf("\nEnter the parameter file name: ");
! 4453: fgets(pathr,FILENAMELENGTH,stdin);
! 4454: i=strlen(pathr);
! 4455: if(pathr[i-1]=='\n')
! 4456: pathr[i-1]='\0';
! 4457: for (tok = pathr; tok != NULL; ){
! 4458: printf("Pathr |%s|\n",pathr);
! 4459: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
! 4460: printf("val= |%s| pathr=%s\n",val,pathr);
! 4461: strcpy (pathtot, val);
! 4462: if(pathr[0] == '\0') break; /* Dirty */
! 4463: }
! 4464: }
! 4465: else{
! 4466: strcpy(pathtot,argv[1]);
! 4467: }
! 4468: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
! 4469: /*cygwin_split_path(pathtot,path,optionfile);
! 4470: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
! 4471: /* cutv(path,optionfile,pathtot,'\\');*/
! 4472:
! 4473: /* Split argv[0], imach program to get pathimach */
! 4474: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
! 4475: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
! 4476: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
! 4477: /* strcpy(pathimach,argv[0]); */
! 4478: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
! 4479: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
! 4480: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
! 4481: chdir(path); /* Can be a relative path */
! 4482: if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
! 4483: printf("Current directory %s!\n",pathcd);
! 4484: strcpy(command,"mkdir ");
! 4485: strcat(command,optionfilefiname);
! 4486: if((outcmd=system(command)) != 0){
! 4487: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
! 4488: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
! 4489: /* fclose(ficlog); */
! 4490: /* exit(1); */
! 4491: }
! 4492: /* if((imk=mkdir(optionfilefiname))<0){ */
! 4493: /* perror("mkdir"); */
! 4494: /* } */
! 4495:
! 4496: /*-------- arguments in the command line --------*/
! 4497:
! 4498: /* Log file */
! 4499: strcat(filelog, optionfilefiname);
! 4500: strcat(filelog,".log"); /* */
! 4501: if((ficlog=fopen(filelog,"w"))==NULL) {
! 4502: printf("Problem with logfile %s\n",filelog);
! 4503: goto end;
! 4504: }
! 4505: fprintf(ficlog,"Log filename:%s\n",filelog);
! 4506: fprintf(ficlog,"\n%s\n%s",version,fullversion);
! 4507: fprintf(ficlog,"\nEnter the parameter file name: \n");
! 4508: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
! 4509: path=%s \n\
! 4510: optionfile=%s\n\
! 4511: optionfilext=%s\n\
! 4512: optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
! 4513:
! 4514: printf("Local time (at start):%s",strstart);
! 4515: fprintf(ficlog,"Local time (at start): %s",strstart);
! 4516: fflush(ficlog);
! 4517: /* (void) gettimeofday(&curr_time,&tzp); */
! 4518: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
! 4519:
! 4520: /* */
! 4521: strcpy(fileres,"r");
! 4522: strcat(fileres, optionfilefiname);
! 4523: strcat(fileres,".txt"); /* Other files have txt extension */
! 4524:
! 4525: /*---------arguments file --------*/
! 4526:
! 4527: if((ficpar=fopen(optionfile,"r"))==NULL) {
! 4528: printf("Problem with optionfile %s\n",optionfile);
! 4529: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
! 4530: fflush(ficlog);
! 4531: goto end;
! 4532: }
! 4533:
! 4534:
! 4535:
! 4536: strcpy(filereso,"o");
! 4537: strcat(filereso,fileres);
! 4538: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
! 4539: printf("Problem with Output resultfile: %s\n", filereso);
! 4540: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
! 4541: fflush(ficlog);
! 4542: goto end;
! 4543: }
! 4544:
! 4545: /* Reads comments: lines beginning with '#' */
! 4546: numlinepar=0;
! 4547: while((c=getc(ficpar))=='#' && c!= EOF){
! 4548: ungetc(c,ficpar);
! 4549: fgets(line, MAXLINE, ficpar);
! 4550: numlinepar++;
! 4551: puts(line);
! 4552: fputs(line,ficparo);
! 4553: fputs(line,ficlog);
! 4554: }
! 4555: ungetc(c,ficpar);
! 4556:
! 4557: fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
! 4558: numlinepar++;
! 4559: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
! 4560: fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
! 4561: fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
! 4562: fflush(ficlog);
! 4563: while((c=getc(ficpar))=='#' && c!= EOF){
! 4564: ungetc(c,ficpar);
! 4565: fgets(line, MAXLINE, ficpar);
! 4566: numlinepar++;
! 4567: puts(line);
! 4568: fputs(line,ficparo);
! 4569: fputs(line,ficlog);
! 4570: }
! 4571: ungetc(c,ficpar);
! 4572:
! 4573:
! 4574: covar=matrix(0,NCOVMAX,1,n);
! 4575: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
! 4576: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
! 4577:
! 4578: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
! 4579: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
! 4580: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
! 4581:
! 4582: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
! 4583: delti=delti3[1][1];
! 4584: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
! 4585: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
! 4586: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
! 4587: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
! 4588: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
! 4589: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
! 4590: fclose (ficparo);
! 4591: fclose (ficlog);
! 4592: goto end;
! 4593: exit(0);
! 4594: }
! 4595: else if(mle==-3) {
! 4596: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
! 4597: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
! 4598: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
! 4599: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
! 4600: matcov=matrix(1,npar,1,npar);
! 4601: }
! 4602: else{
! 4603: /* Read guess parameters */
! 4604: /* Reads comments: lines beginning with '#' */
! 4605: while((c=getc(ficpar))=='#' && c!= EOF){
! 4606: ungetc(c,ficpar);
! 4607: fgets(line, MAXLINE, ficpar);
! 4608: numlinepar++;
! 4609: puts(line);
! 4610: fputs(line,ficparo);
! 4611: fputs(line,ficlog);
! 4612: }
! 4613: ungetc(c,ficpar);
! 4614:
! 4615: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
! 4616: for(i=1; i <=nlstate; i++){
! 4617: j=0;
! 4618: for(jj=1; jj <=nlstate+ndeath; jj++){
! 4619: if(jj==i) continue;
! 4620: j++;
! 4621: fscanf(ficpar,"%1d%1d",&i1,&j1);
! 4622: if ((i1 != i) && (j1 != j)){
! 4623: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
! 4624: It might be a problem of design; if ncovcol and the model are correct\n \
! 4625: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
! 4626: exit(1);
! 4627: }
! 4628: fprintf(ficparo,"%1d%1d",i1,j1);
! 4629: if(mle==1)
! 4630: printf("%1d%1d",i,j);
! 4631: fprintf(ficlog,"%1d%1d",i,j);
! 4632: for(k=1; k<=ncovmodel;k++){
! 4633: fscanf(ficpar," %lf",¶m[i][j][k]);
! 4634: if(mle==1){
! 4635: printf(" %lf",param[i][j][k]);
! 4636: fprintf(ficlog," %lf",param[i][j][k]);
! 4637: }
! 4638: else
! 4639: fprintf(ficlog," %lf",param[i][j][k]);
! 4640: fprintf(ficparo," %lf",param[i][j][k]);
! 4641: }
! 4642: fscanf(ficpar,"\n");
! 4643: numlinepar++;
! 4644: if(mle==1)
! 4645: printf("\n");
! 4646: fprintf(ficlog,"\n");
! 4647: fprintf(ficparo,"\n");
! 4648: }
! 4649: }
! 4650: fflush(ficlog);
! 4651:
! 4652: p=param[1][1];
! 4653:
! 4654: /* Reads comments: lines beginning with '#' */
! 4655: while((c=getc(ficpar))=='#' && c!= EOF){
! 4656: ungetc(c,ficpar);
! 4657: fgets(line, MAXLINE, ficpar);
! 4658: numlinepar++;
! 4659: puts(line);
! 4660: fputs(line,ficparo);
! 4661: fputs(line,ficlog);
! 4662: }
! 4663: ungetc(c,ficpar);
! 4664:
! 4665: for(i=1; i <=nlstate; i++){
! 4666: for(j=1; j <=nlstate+ndeath-1; j++){
! 4667: fscanf(ficpar,"%1d%1d",&i1,&j1);
! 4668: if ((i1-i)*(j1-j)!=0){
! 4669: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
! 4670: exit(1);
! 4671: }
! 4672: printf("%1d%1d",i,j);
! 4673: fprintf(ficparo,"%1d%1d",i1,j1);
! 4674: fprintf(ficlog,"%1d%1d",i1,j1);
! 4675: for(k=1; k<=ncovmodel;k++){
! 4676: fscanf(ficpar,"%le",&delti3[i][j][k]);
! 4677: printf(" %le",delti3[i][j][k]);
! 4678: fprintf(ficparo," %le",delti3[i][j][k]);
! 4679: fprintf(ficlog," %le",delti3[i][j][k]);
! 4680: }
! 4681: fscanf(ficpar,"\n");
! 4682: numlinepar++;
! 4683: printf("\n");
! 4684: fprintf(ficparo,"\n");
! 4685: fprintf(ficlog,"\n");
! 4686: }
! 4687: }
! 4688: fflush(ficlog);
! 4689:
! 4690: delti=delti3[1][1];
! 4691:
! 4692:
! 4693: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
! 4694:
! 4695: /* Reads comments: lines beginning with '#' */
! 4696: while((c=getc(ficpar))=='#' && c!= EOF){
! 4697: ungetc(c,ficpar);
! 4698: fgets(line, MAXLINE, ficpar);
! 4699: numlinepar++;
! 4700: puts(line);
! 4701: fputs(line,ficparo);
! 4702: fputs(line,ficlog);
! 4703: }
! 4704: ungetc(c,ficpar);
! 4705:
! 4706: matcov=matrix(1,npar,1,npar);
! 4707: for(i=1; i <=npar; i++){
! 4708: fscanf(ficpar,"%s",&str);
! 4709: if(mle==1)
! 4710: printf("%s",str);
! 4711: fprintf(ficlog,"%s",str);
! 4712: fprintf(ficparo,"%s",str);
! 4713: for(j=1; j <=i; j++){
! 4714: fscanf(ficpar," %le",&matcov[i][j]);
! 4715: if(mle==1){
! 4716: printf(" %.5le",matcov[i][j]);
! 4717: }
! 4718: fprintf(ficlog," %.5le",matcov[i][j]);
! 4719: fprintf(ficparo," %.5le",matcov[i][j]);
! 4720: }
! 4721: fscanf(ficpar,"\n");
! 4722: numlinepar++;
! 4723: if(mle==1)
! 4724: printf("\n");
! 4725: fprintf(ficlog,"\n");
! 4726: fprintf(ficparo,"\n");
! 4727: }
! 4728: for(i=1; i <=npar; i++)
! 4729: for(j=i+1;j<=npar;j++)
! 4730: matcov[i][j]=matcov[j][i];
! 4731:
! 4732: if(mle==1)
! 4733: printf("\n");
! 4734: fprintf(ficlog,"\n");
! 4735:
! 4736: fflush(ficlog);
! 4737:
! 4738: /*-------- Rewriting parameter file ----------*/
! 4739: strcpy(rfileres,"r"); /* "Rparameterfile */
! 4740: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
! 4741: strcat(rfileres,"."); /* */
! 4742: strcat(rfileres,optionfilext); /* Other files have txt extension */
! 4743: if((ficres =fopen(rfileres,"w"))==NULL) {
! 4744: printf("Problem writing new parameter file: %s\n", fileres);goto end;
! 4745: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
! 4746: }
! 4747: fprintf(ficres,"#%s\n",version);
! 4748: } /* End of mle != -3 */
! 4749:
! 4750: /*-------- data file ----------*/
! 4751: if((fic=fopen(datafile,"r"))==NULL) {
! 4752: printf("Problem while opening datafile: %s\n", datafile);goto end;
! 4753: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
! 4754: }
! 4755:
! 4756: n= lastobs;
! 4757: severity = vector(1,maxwav);
! 4758: outcome=imatrix(1,maxwav+1,1,n);
! 4759: num=lvector(1,n);
! 4760: moisnais=vector(1,n);
! 4761: annais=vector(1,n);
! 4762: moisdc=vector(1,n);
! 4763: andc=vector(1,n);
! 4764: agedc=vector(1,n);
! 4765: cod=ivector(1,n);
! 4766: weight=vector(1,n);
! 4767: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
! 4768: mint=matrix(1,maxwav,1,n);
! 4769: anint=matrix(1,maxwav,1,n);
! 4770: s=imatrix(1,maxwav+1,1,n);
! 4771: tab=ivector(1,NCOVMAX);
! 4772: ncodemax=ivector(1,8);
! 4773:
! 4774: i=1;
! 4775: linei=0;
! 4776: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
! 4777: linei=linei+1;
! 4778: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
! 4779: if(line[j] == '\t')
! 4780: line[j] = ' ';
! 4781: }
! 4782: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
! 4783: ;
! 4784: };
! 4785: line[j+1]=0; /* Trims blanks at end of line */
! 4786: if(line[0]=='#'){
! 4787: fprintf(ficlog,"Comment line\n%s\n",line);
! 4788: printf("Comment line\n%s\n",line);
! 4789: continue;
! 4790: }
! 4791:
! 4792: for (j=maxwav;j>=1;j--){
! 4793: cutv(stra, strb,line,' ');
! 4794: errno=0;
! 4795: lval=strtol(strb,&endptr,10);
! 4796: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
! 4797: if( strb[0]=='\0' || (*endptr != '\0')){
! 4798: printf("Error reading data around '%d' at line number %d %s 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);
! 4799: exit(1);
! 4800: }
! 4801: s[j][i]=lval;
! 4802:
! 4803: strcpy(line,stra);
! 4804: cutv(stra, strb,line,' ');
! 4805: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
! 4806: }
! 4807: else if(iout=sscanf(strb,"%s.") != 0){
! 4808: month=99;
! 4809: year=9999;
! 4810: }else{
! 4811: printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);
! 4812: exit(1);
! 4813: }
! 4814: anint[j][i]= (double) year;
! 4815: mint[j][i]= (double)month;
! 4816: strcpy(line,stra);
! 4817: } /* ENd Waves */
! 4818:
! 4819: cutv(stra, strb,line,' ');
! 4820: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
! 4821: }
! 4822: else if(iout=sscanf(strb,"%s.",dummy) != 0){
! 4823: month=99;
! 4824: year=9999;
! 4825: }else{
! 4826: printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
! 4827: exit(1);
! 4828: }
! 4829: andc[i]=(double) year;
! 4830: moisdc[i]=(double) month;
! 4831: strcpy(line,stra);
! 4832:
! 4833: cutv(stra, strb,line,' ');
! 4834: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
! 4835: }
! 4836: else if(iout=sscanf(strb,"%s.") != 0){
! 4837: month=99;
! 4838: year=9999;
! 4839: }else{
! 4840: printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line,j);
! 4841: exit(1);
! 4842: }
! 4843: annais[i]=(double)(year);
! 4844: moisnais[i]=(double)(month);
! 4845: strcpy(line,stra);
! 4846:
! 4847: cutv(stra, strb,line,' ');
! 4848: errno=0;
! 4849: dval=strtod(strb,&endptr);
! 4850: if( strb[0]=='\0' || (*endptr != '\0')){
! 4851: printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
! 4852: exit(1);
! 4853: }
! 4854: weight[i]=dval;
! 4855: strcpy(line,stra);
! 4856:
! 4857: for (j=ncovcol;j>=1;j--){
! 4858: cutv(stra, strb,line,' ');
! 4859: errno=0;
! 4860: lval=strtol(strb,&endptr,10);
! 4861: if( strb[0]=='\0' || (*endptr != '\0')){
! 4862: printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1). Exiting.\n",lval, linei,i, line);
! 4863: exit(1);
! 4864: }
! 4865: if(lval <-1 || lval >1){
! 4866: printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
! 4867: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
! 4868: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
! 4869: For example, for multinomial values like 1, 2 and 3,\n \
! 4870: build V1=0 V2=0 for the reference value (1),\n \
! 4871: V1=1 V2=0 for (2) \n \
! 4872: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
! 4873: output of IMaCh is often meaningless.\n \
! 4874: Exiting.\n",lval,linei, i,line,j);
! 4875: exit(1);
! 4876: }
! 4877: covar[j][i]=(double)(lval);
! 4878: strcpy(line,stra);
! 4879: }
! 4880: lstra=strlen(stra);
! 4881:
! 4882: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
! 4883: stratrunc = &(stra[lstra-9]);
! 4884: num[i]=atol(stratrunc);
! 4885: }
! 4886: else
! 4887: num[i]=atol(stra);
! 4888: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
! 4889: 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;}*/
! 4890:
! 4891: i=i+1;
! 4892: } /* End loop reading data */
! 4893: fclose(fic);
! 4894: /* printf("ii=%d", ij);
! 4895: scanf("%d",i);*/
! 4896: imx=i-1; /* Number of individuals */
! 4897:
! 4898: /* for (i=1; i<=imx; i++){
! 4899: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
! 4900: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
! 4901: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
! 4902: }*/
! 4903: /* for (i=1; i<=imx; i++){
! 4904: if (s[4][i]==9) s[4][i]=-1;
! 4905: 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]));}*/
! 4906:
! 4907: /* for (i=1; i<=imx; i++) */
! 4908:
! 4909: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
! 4910: else weight[i]=1;*/
! 4911:
! 4912: /* Calculation of the number of parameters from char model */
! 4913: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
! 4914: Tprod=ivector(1,15);
! 4915: Tvaraff=ivector(1,15);
! 4916: Tvard=imatrix(1,15,1,2);
! 4917: Tage=ivector(1,15);
! 4918:
! 4919: if (strlen(model) >1){ /* If there is at least 1 covariate */
! 4920: j=0, j1=0, k1=1, k2=1;
! 4921: j=nbocc(model,'+'); /* j=Number of '+' */
! 4922: j1=nbocc(model,'*'); /* j1=Number of '*' */
! 4923: cptcovn=j+1;
! 4924: cptcovprod=j1; /*Number of products */
! 4925:
! 4926: strcpy(modelsav,model);
! 4927: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
! 4928: printf("Error. Non available option model=%s ",model);
! 4929: fprintf(ficlog,"Error. Non available option model=%s ",model);
! 4930: goto end;
! 4931: }
! 4932:
! 4933: /* This loop fills the array Tvar from the string 'model'.*/
! 4934:
! 4935: for(i=(j+1); i>=1;i--){
! 4936: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
! 4937: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
! 4938: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
! 4939: /*scanf("%d",i);*/
! 4940: if (strchr(strb,'*')) { /* Model includes a product */
! 4941: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
! 4942: if (strcmp(strc,"age")==0) { /* Vn*age */
! 4943: cptcovprod--;
! 4944: cutv(strb,stre,strd,'V');
! 4945: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
! 4946: cptcovage++;
! 4947: Tage[cptcovage]=i;
! 4948: /*printf("stre=%s ", stre);*/
! 4949: }
! 4950: else if (strcmp(strd,"age")==0) { /* or age*Vn */
! 4951: cptcovprod--;
! 4952: cutv(strb,stre,strc,'V');
! 4953: Tvar[i]=atoi(stre);
! 4954: cptcovage++;
! 4955: Tage[cptcovage]=i;
! 4956: }
! 4957: else { /* Age is not in the model */
! 4958: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
! 4959: Tvar[i]=ncovcol+k1;
! 4960: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
! 4961: Tprod[k1]=i;
! 4962: Tvard[k1][1]=atoi(strc); /* m*/
! 4963: Tvard[k1][2]=atoi(stre); /* n */
! 4964: Tvar[cptcovn+k2]=Tvard[k1][1];
! 4965: Tvar[cptcovn+k2+1]=Tvard[k1][2];
! 4966: for (k=1; k<=lastobs;k++)
! 4967: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
! 4968: k1++;
! 4969: k2=k2+2;
! 4970: }
! 4971: }
! 4972: else { /* no more sum */
! 4973: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
! 4974: /* scanf("%d",i);*/
! 4975: cutv(strd,strc,strb,'V');
! 4976: Tvar[i]=atoi(strc);
! 4977: }
! 4978: strcpy(modelsav,stra);
! 4979: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
! 4980: scanf("%d",i);*/
! 4981: } /* end of loop + */
! 4982: } /* end model */
! 4983:
! 4984: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
! 4985: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
! 4986:
! 4987: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
! 4988: printf("cptcovprod=%d ", cptcovprod);
! 4989: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
! 4990:
! 4991: scanf("%d ",i);*/
! 4992:
! 4993: /* if(mle==1){*/
! 4994: if (weightopt != 1) { /* Maximisation without weights*/
! 4995: for(i=1;i<=n;i++) weight[i]=1.0;
! 4996: }
! 4997: /*-calculation of age at interview from date of interview and age at death -*/
! 4998: agev=matrix(1,maxwav,1,imx);
! 4999:
! 5000: for (i=1; i<=imx; i++) {
! 5001: for(m=2; (m<= maxwav); m++) {
! 5002: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
! 5003: anint[m][i]=9999;
! 5004: s[m][i]=-1;
! 5005: }
! 5006: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
! 5007: nberr++;
! 5008: printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
! 5009: fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
! 5010: s[m][i]=-1;
! 5011: }
! 5012: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
! 5013: nberr++;
! 5014: 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]);
! 5015: 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]);
! 5016: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
! 5017: }
! 5018: }
! 5019: }
! 5020:
! 5021: for (i=1; i<=imx; i++) {
! 5022: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
! 5023: for(m=firstpass; (m<= lastpass); m++){
! 5024: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
! 5025: if (s[m][i] >= nlstate+1) {
! 5026: if(agedc[i]>0)
! 5027: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
! 5028: agev[m][i]=agedc[i];
! 5029: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
! 5030: else {
! 5031: if ((int)andc[i]!=9999){
! 5032: nbwarn++;
! 5033: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
! 5034: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
! 5035: agev[m][i]=-1;
! 5036: }
! 5037: }
! 5038: }
! 5039: else if(s[m][i] !=9){ /* Standard case, age in fractional
! 5040: years but with the precision of a month */
! 5041: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
! 5042: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
! 5043: agev[m][i]=1;
! 5044: else if(agev[m][i] <agemin){
! 5045: agemin=agev[m][i];
! 5046: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
! 5047: }
! 5048: else if(agev[m][i] >agemax){
! 5049: agemax=agev[m][i];
! 5050: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
! 5051: }
! 5052: /*agev[m][i]=anint[m][i]-annais[i];*/
! 5053: /* agev[m][i] = age[i]+2*m;*/
! 5054: }
! 5055: else { /* =9 */
! 5056: agev[m][i]=1;
! 5057: s[m][i]=-1;
! 5058: }
! 5059: }
! 5060: else /*= 0 Unknown */
! 5061: agev[m][i]=1;
! 5062: }
! 5063:
! 5064: }
! 5065: for (i=1; i<=imx; i++) {
! 5066: for(m=firstpass; (m<=lastpass); m++){
! 5067: if (s[m][i] > (nlstate+ndeath)) {
! 5068: nberr++;
! 5069: 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);
! 5070: 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);
! 5071: goto end;
! 5072: }
! 5073: }
! 5074: }
! 5075:
! 5076: /*for (i=1; i<=imx; i++){
! 5077: for (m=firstpass; (m<lastpass); m++){
! 5078: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
! 5079: }
! 5080:
! 5081: }*/
! 5082:
! 5083:
! 5084: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
! 5085: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
! 5086:
! 5087: agegomp=(int)agemin;
! 5088: free_vector(severity,1,maxwav);
! 5089: free_imatrix(outcome,1,maxwav+1,1,n);
! 5090: free_vector(moisnais,1,n);
! 5091: free_vector(annais,1,n);
! 5092: /* free_matrix(mint,1,maxwav,1,n);
! 5093: free_matrix(anint,1,maxwav,1,n);*/
! 5094: free_vector(moisdc,1,n);
! 5095: free_vector(andc,1,n);
! 5096:
! 5097:
! 5098: wav=ivector(1,imx);
! 5099: dh=imatrix(1,lastpass-firstpass+1,1,imx);
! 5100: bh=imatrix(1,lastpass-firstpass+1,1,imx);
! 5101: mw=imatrix(1,lastpass-firstpass+1,1,imx);
! 5102:
! 5103: /* Concatenates waves */
! 5104: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
! 5105:
! 5106: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
! 5107:
! 5108: Tcode=ivector(1,100);
! 5109: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
! 5110: ncodemax[1]=1;
! 5111: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
! 5112:
! 5113: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
! 5114: the estimations*/
! 5115: h=0;
! 5116: m=pow(2,cptcoveff);
! 5117:
! 5118: for(k=1;k<=cptcoveff; k++){
! 5119: for(i=1; i <=(m/pow(2,k));i++){
! 5120: for(j=1; j <= ncodemax[k]; j++){
! 5121: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
! 5122: h++;
! 5123: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
! 5124: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
! 5125: }
! 5126: }
! 5127: }
! 5128: }
! 5129: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
! 5130: codtab[1][2]=1;codtab[2][2]=2; */
! 5131: /* for(i=1; i <=m ;i++){
! 5132: for(k=1; k <=cptcovn; k++){
! 5133: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
! 5134: }
! 5135: printf("\n");
! 5136: }
! 5137: scanf("%d",i);*/
! 5138:
! 5139: /*------------ gnuplot -------------*/
! 5140: strcpy(optionfilegnuplot,optionfilefiname);
! 5141: if(mle==-3)
! 5142: strcat(optionfilegnuplot,"-mort");
! 5143: strcat(optionfilegnuplot,".gp");
! 5144:
! 5145: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
! 5146: printf("Problem with file %s",optionfilegnuplot);
! 5147: }
! 5148: else{
! 5149: fprintf(ficgp,"\n# %s\n", version);
! 5150: fprintf(ficgp,"# %s\n", optionfilegnuplot);
! 5151: fprintf(ficgp,"set missing 'NaNq'\n");
! 5152: }
! 5153: /* fclose(ficgp);*/
! 5154: /*--------- index.htm --------*/
! 5155:
! 5156: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
! 5157: if(mle==-3)
! 5158: strcat(optionfilehtm,"-mort");
! 5159: strcat(optionfilehtm,".htm");
! 5160: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
! 5161: printf("Problem with %s \n",optionfilehtm), exit(0);
! 5162: }
! 5163:
! 5164: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
! 5165: strcat(optionfilehtmcov,"-cov.htm");
! 5166: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
! 5167: printf("Problem with %s \n",optionfilehtmcov), exit(0);
! 5168: }
! 5169: else{
! 5170: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
! 5171: <hr size=\"2\" color=\"#EC5E5E\"> \n\
! 5172: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
! 5173: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
! 5174: }
! 5175:
! 5176: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
! 5177: <hr size=\"2\" color=\"#EC5E5E\"> \n\
! 5178: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
! 5179: \n\
! 5180: <hr size=\"2\" color=\"#EC5E5E\">\
! 5181: <ul><li><h4>Parameter files</h4>\n\
! 5182: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
! 5183: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
! 5184: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
! 5185: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
! 5186: - Date and time at start: %s</ul>\n",\
! 5187: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
! 5188: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
! 5189: fileres,fileres,\
! 5190: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
! 5191: fflush(fichtm);
! 5192:
! 5193: strcpy(pathr,path);
! 5194: strcat(pathr,optionfilefiname);
! 5195: chdir(optionfilefiname); /* Move to directory named optionfile */
! 5196:
! 5197: /* Calculates basic frequencies. Computes observed prevalence at single age
! 5198: and prints on file fileres'p'. */
! 5199: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
! 5200:
! 5201: fprintf(fichtm,"\n");
! 5202: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
! 5203: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
! 5204: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
! 5205: imx,agemin,agemax,jmin,jmax,jmean);
! 5206: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
! 5207: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
! 5208: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
! 5209: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
! 5210: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
! 5211:
! 5212:
! 5213: /* For Powell, parameters are in a vector p[] starting at p[1]
! 5214: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
! 5215: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
! 5216:
! 5217: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
! 5218:
! 5219: if (mle==-3){
! 5220: ximort=matrix(1,NDIM,1,NDIM);
! 5221: cens=ivector(1,n);
! 5222: ageexmed=vector(1,n);
! 5223: agecens=vector(1,n);
! 5224: dcwave=ivector(1,n);
! 5225:
! 5226: for (i=1; i<=imx; i++){
! 5227: dcwave[i]=-1;
! 5228: for (m=firstpass; m<=lastpass; m++)
! 5229: if (s[m][i]>nlstate) {
! 5230: dcwave[i]=m;
! 5231: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
! 5232: break;
! 5233: }
! 5234: }
! 5235:
! 5236: for (i=1; i<=imx; i++) {
! 5237: if (wav[i]>0){
! 5238: ageexmed[i]=agev[mw[1][i]][i];
! 5239: j=wav[i];
! 5240: agecens[i]=1.;
! 5241:
! 5242: if (ageexmed[i]> 1 && wav[i] > 0){
! 5243: agecens[i]=agev[mw[j][i]][i];
! 5244: cens[i]= 1;
! 5245: }else if (ageexmed[i]< 1)
! 5246: cens[i]= -1;
! 5247: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
! 5248: cens[i]=0 ;
! 5249: }
! 5250: else cens[i]=-1;
! 5251: }
! 5252:
! 5253: for (i=1;i<=NDIM;i++) {
! 5254: for (j=1;j<=NDIM;j++)
! 5255: ximort[i][j]=(i == j ? 1.0 : 0.0);
! 5256: }
! 5257:
! 5258: p[1]=0.0268; p[NDIM]=0.083;
! 5259: /*printf("%lf %lf", p[1], p[2]);*/
! 5260:
! 5261:
! 5262: printf("Powell\n"); fprintf(ficlog,"Powell\n");
! 5263: strcpy(filerespow,"pow-mort");
! 5264: strcat(filerespow,fileres);
! 5265: if((ficrespow=fopen(filerespow,"w"))==NULL) {
! 5266: printf("Problem with resultfile: %s\n", filerespow);
! 5267: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
! 5268: }
! 5269: fprintf(ficrespow,"# Powell\n# iter -2*LL");
! 5270: /* for (i=1;i<=nlstate;i++)
! 5271: for(j=1;j<=nlstate+ndeath;j++)
! 5272: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
! 5273: */
! 5274: fprintf(ficrespow,"\n");
! 5275:
! 5276: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
! 5277: fclose(ficrespow);
! 5278:
! 5279: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
! 5280:
! 5281: for(i=1; i <=NDIM; i++)
! 5282: for(j=i+1;j<=NDIM;j++)
! 5283: matcov[i][j]=matcov[j][i];
! 5284:
! 5285: printf("\nCovariance matrix\n ");
! 5286: for(i=1; i <=NDIM; i++) {
! 5287: for(j=1;j<=NDIM;j++){
! 5288: printf("%f ",matcov[i][j]);
! 5289: }
! 5290: printf("\n ");
! 5291: }
! 5292:
! 5293: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
! 5294: for (i=1;i<=NDIM;i++)
! 5295: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
! 5296:
! 5297: lsurv=vector(1,AGESUP);
! 5298: lpop=vector(1,AGESUP);
! 5299: tpop=vector(1,AGESUP);
! 5300: lsurv[agegomp]=100000;
! 5301:
! 5302: for (k=agegomp;k<=AGESUP;k++) {
! 5303: agemortsup=k;
! 5304: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
! 5305: }
! 5306:
! 5307: for (k=agegomp;k<agemortsup;k++)
! 5308: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
! 5309:
! 5310: for (k=agegomp;k<agemortsup;k++){
! 5311: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
! 5312: sumlpop=sumlpop+lpop[k];
! 5313: }
! 5314:
! 5315: tpop[agegomp]=sumlpop;
! 5316: for (k=agegomp;k<(agemortsup-3);k++){
! 5317: /* tpop[k+1]=2;*/
! 5318: tpop[k+1]=tpop[k]-lpop[k];
! 5319: }
! 5320:
! 5321:
! 5322: printf("\nAge lx qx dx Lx Tx e(x)\n");
! 5323: for (k=agegomp;k<(agemortsup-2);k++)
! 5324: 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]);
! 5325:
! 5326:
! 5327: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
! 5328: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
! 5329:
! 5330: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
! 5331: stepm, weightopt,\
! 5332: model,imx,p,matcov,agemortsup);
! 5333:
! 5334: free_vector(lsurv,1,AGESUP);
! 5335: free_vector(lpop,1,AGESUP);
! 5336: free_vector(tpop,1,AGESUP);
! 5337: } /* Endof if mle==-3 */
! 5338:
! 5339: else{ /* For mle >=1 */
! 5340:
! 5341: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
! 5342: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
! 5343: for (k=1; k<=npar;k++)
! 5344: printf(" %d %8.5f",k,p[k]);
! 5345: printf("\n");
! 5346: globpr=1; /* to print the contributions */
! 5347: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
! 5348: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
! 5349: for (k=1; k<=npar;k++)
! 5350: printf(" %d %8.5f",k,p[k]);
! 5351: printf("\n");
! 5352: if(mle>=1){ /* Could be 1 or 2 */
! 5353: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
! 5354: }
! 5355:
! 5356: /*--------- results files --------------*/
! 5357: fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
! 5358:
! 5359:
! 5360: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
! 5361: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
! 5362: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
! 5363: for(i=1,jk=1; i <=nlstate; i++){
! 5364: for(k=1; k <=(nlstate+ndeath); k++){
! 5365: if (k != i) {
! 5366: printf("%d%d ",i,k);
! 5367: fprintf(ficlog,"%d%d ",i,k);
! 5368: fprintf(ficres,"%1d%1d ",i,k);
! 5369: for(j=1; j <=ncovmodel; j++){
! 5370: printf("%lf ",p[jk]);
! 5371: fprintf(ficlog,"%lf ",p[jk]);
! 5372: fprintf(ficres,"%lf ",p[jk]);
! 5373: jk++;
! 5374: }
! 5375: printf("\n");
! 5376: fprintf(ficlog,"\n");
! 5377: fprintf(ficres,"\n");
! 5378: }
! 5379: }
! 5380: }
! 5381: if(mle!=0){
! 5382: /* Computing hessian and covariance matrix */
! 5383: ftolhess=ftol; /* Usually correct */
! 5384: hesscov(matcov, p, npar, delti, ftolhess, func);
! 5385: }
! 5386: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
! 5387: printf("# Scales (for hessian or gradient estimation)\n");
! 5388: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
! 5389: for(i=1,jk=1; i <=nlstate; i++){
! 5390: for(j=1; j <=nlstate+ndeath; j++){
! 5391: if (j!=i) {
! 5392: fprintf(ficres,"%1d%1d",i,j);
! 5393: printf("%1d%1d",i,j);
! 5394: fprintf(ficlog,"%1d%1d",i,j);
! 5395: for(k=1; k<=ncovmodel;k++){
! 5396: printf(" %.5e",delti[jk]);
! 5397: fprintf(ficlog," %.5e",delti[jk]);
! 5398: fprintf(ficres," %.5e",delti[jk]);
! 5399: jk++;
! 5400: }
! 5401: printf("\n");
! 5402: fprintf(ficlog,"\n");
! 5403: fprintf(ficres,"\n");
! 5404: }
! 5405: }
! 5406: }
! 5407:
! 5408: 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");
! 5409: if(mle>=1)
! 5410: 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");
! 5411: 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");
! 5412: /* # 121 Var(a12)\n\ */
! 5413: /* # 122 Cov(b12,a12) Var(b12)\n\ */
! 5414: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
! 5415: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
! 5416: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
! 5417: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
! 5418: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
! 5419: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
! 5420:
! 5421:
! 5422: /* Just to have a covariance matrix which will be more understandable
! 5423: even is we still don't want to manage dictionary of variables
! 5424: */
! 5425: for(itimes=1;itimes<=2;itimes++){
! 5426: jj=0;
! 5427: for(i=1; i <=nlstate; i++){
! 5428: for(j=1; j <=nlstate+ndeath; j++){
! 5429: if(j==i) continue;
! 5430: for(k=1; k<=ncovmodel;k++){
! 5431: jj++;
! 5432: ca[0]= k+'a'-1;ca[1]='\0';
! 5433: if(itimes==1){
! 5434: if(mle>=1)
! 5435: printf("#%1d%1d%d",i,j,k);
! 5436: fprintf(ficlog,"#%1d%1d%d",i,j,k);
! 5437: fprintf(ficres,"#%1d%1d%d",i,j,k);
! 5438: }else{
! 5439: if(mle>=1)
! 5440: printf("%1d%1d%d",i,j,k);
! 5441: fprintf(ficlog,"%1d%1d%d",i,j,k);
! 5442: fprintf(ficres,"%1d%1d%d",i,j,k);
! 5443: }
! 5444: ll=0;
! 5445: for(li=1;li <=nlstate; li++){
! 5446: for(lj=1;lj <=nlstate+ndeath; lj++){
! 5447: if(lj==li) continue;
! 5448: for(lk=1;lk<=ncovmodel;lk++){
! 5449: ll++;
! 5450: if(ll<=jj){
! 5451: cb[0]= lk +'a'-1;cb[1]='\0';
! 5452: if(ll<jj){
! 5453: if(itimes==1){
! 5454: if(mle>=1)
! 5455: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
! 5456: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
! 5457: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
! 5458: }else{
! 5459: if(mle>=1)
! 5460: printf(" %.5e",matcov[jj][ll]);
! 5461: fprintf(ficlog," %.5e",matcov[jj][ll]);
! 5462: fprintf(ficres," %.5e",matcov[jj][ll]);
! 5463: }
! 5464: }else{
! 5465: if(itimes==1){
! 5466: if(mle>=1)
! 5467: printf(" Var(%s%1d%1d)",ca,i,j);
! 5468: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
! 5469: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
! 5470: }else{
! 5471: if(mle>=1)
! 5472: printf(" %.5e",matcov[jj][ll]);
! 5473: fprintf(ficlog," %.5e",matcov[jj][ll]);
! 5474: fprintf(ficres," %.5e",matcov[jj][ll]);
! 5475: }
! 5476: }
! 5477: }
! 5478: } /* end lk */
! 5479: } /* end lj */
! 5480: } /* end li */
! 5481: if(mle>=1)
! 5482: printf("\n");
! 5483: fprintf(ficlog,"\n");
! 5484: fprintf(ficres,"\n");
! 5485: numlinepar++;
! 5486: } /* end k*/
! 5487: } /*end j */
! 5488: } /* end i */
! 5489: } /* end itimes */
! 5490:
! 5491: fflush(ficlog);
! 5492: fflush(ficres);
! 5493:
! 5494: while((c=getc(ficpar))=='#' && c!= EOF){
! 5495: ungetc(c,ficpar);
! 5496: fgets(line, MAXLINE, ficpar);
! 5497: puts(line);
! 5498: fputs(line,ficparo);
! 5499: }
! 5500: ungetc(c,ficpar);
! 5501:
! 5502: estepm=0;
! 5503: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
! 5504: if (estepm==0 || estepm < stepm) estepm=stepm;
! 5505: if (fage <= 2) {
! 5506: bage = ageminpar;
! 5507: fage = agemaxpar;
! 5508: }
! 5509:
! 5510: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
! 5511: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
! 5512: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
! 5513:
! 5514: while((c=getc(ficpar))=='#' && c!= EOF){
! 5515: ungetc(c,ficpar);
! 5516: fgets(line, MAXLINE, ficpar);
! 5517: puts(line);
! 5518: fputs(line,ficparo);
! 5519: }
! 5520: ungetc(c,ficpar);
! 5521:
! 5522: 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);
! 5523: 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);
! 5524: 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);
! 5525: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
! 5526: 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);
! 5527:
! 5528: while((c=getc(ficpar))=='#' && c!= EOF){
! 5529: ungetc(c,ficpar);
! 5530: fgets(line, MAXLINE, ficpar);
! 5531: puts(line);
! 5532: fputs(line,ficparo);
! 5533: }
! 5534: ungetc(c,ficpar);
! 5535:
! 5536:
! 5537: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
! 5538: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
! 5539:
! 5540: fscanf(ficpar,"pop_based=%d\n",&popbased);
! 5541: fprintf(ficparo,"pop_based=%d\n",popbased);
! 5542: fprintf(ficres,"pop_based=%d\n",popbased);
! 5543:
! 5544: while((c=getc(ficpar))=='#' && c!= EOF){
! 5545: ungetc(c,ficpar);
! 5546: fgets(line, MAXLINE, ficpar);
! 5547: puts(line);
! 5548: fputs(line,ficparo);
! 5549: }
! 5550: ungetc(c,ficpar);
! 5551:
! 5552: 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);
! 5553: 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);
! 5554: 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);
! 5555: 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);
! 5556: 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);
! 5557: /* day and month of proj2 are not used but only year anproj2.*/
! 5558:
! 5559:
! 5560:
! 5561: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
! 5562: /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
! 5563:
! 5564: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
! 5565: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
! 5566:
! 5567: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
! 5568: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
! 5569: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
! 5570:
! 5571: /*------------ free_vector -------------*/
! 5572: /* chdir(path); */
! 5573:
! 5574: free_ivector(wav,1,imx);
! 5575: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
! 5576: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
! 5577: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
! 5578: free_lvector(num,1,n);
! 5579: free_vector(agedc,1,n);
! 5580: /*free_matrix(covar,0,NCOVMAX,1,n);*/
! 5581: /*free_matrix(covar,1,NCOVMAX,1,n);*/
! 5582: fclose(ficparo);
! 5583: fclose(ficres);
! 5584:
! 5585:
! 5586: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
! 5587:
! 5588: strcpy(filerespl,"pl");
! 5589: strcat(filerespl,fileres);
! 5590: if((ficrespl=fopen(filerespl,"w"))==NULL) {
! 5591: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
! 5592: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
! 5593: }
! 5594: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
! 5595: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
! 5596: pstamp(ficrespl);
! 5597: fprintf(ficrespl,"# Period (stable) prevalence \n");
! 5598: fprintf(ficrespl,"#Age ");
! 5599: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
! 5600: fprintf(ficrespl,"\n");
! 5601:
! 5602: prlim=matrix(1,nlstate,1,nlstate);
! 5603:
! 5604: agebase=ageminpar;
! 5605: agelim=agemaxpar;
! 5606: ftolpl=1.e-10;
! 5607: i1=cptcoveff;
! 5608: if (cptcovn < 1){i1=1;}
! 5609:
! 5610: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
! 5611: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
! 5612: k=k+1;
! 5613: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
! 5614: fprintf(ficrespl,"\n#******");
! 5615: printf("\n#******");
! 5616: fprintf(ficlog,"\n#******");
! 5617: for(j=1;j<=cptcoveff;j++) {
! 5618: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 5619: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 5620: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 5621: }
! 5622: fprintf(ficrespl,"******\n");
! 5623: printf("******\n");
! 5624: fprintf(ficlog,"******\n");
! 5625:
! 5626: for (age=agebase; age<=agelim; age++){
! 5627: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
! 5628: fprintf(ficrespl,"%.0f ",age );
! 5629: for(j=1;j<=cptcoveff;j++)
! 5630: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 5631: for(i=1; i<=nlstate;i++)
! 5632: fprintf(ficrespl," %.5f", prlim[i][i]);
! 5633: fprintf(ficrespl,"\n");
! 5634: }
! 5635: }
! 5636: }
! 5637: fclose(ficrespl);
! 5638:
! 5639: /*------------- h Pij x at various ages ------------*/
! 5640:
! 5641: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
! 5642: if((ficrespij=fopen(filerespij,"w"))==NULL) {
! 5643: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
! 5644: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
! 5645: }
! 5646: printf("Computing pij: result on file '%s' \n", filerespij);
! 5647: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
! 5648:
! 5649: stepsize=(int) (stepm+YEARM-1)/YEARM;
! 5650: /*if (stepm<=24) stepsize=2;*/
! 5651:
! 5652: agelim=AGESUP;
! 5653: hstepm=stepsize*YEARM; /* Every year of age */
! 5654: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
! 5655:
! 5656: /* hstepm=1; aff par mois*/
! 5657: pstamp(ficrespij);
! 5658: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
! 5659: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
! 5660: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
! 5661: k=k+1;
! 5662: fprintf(ficrespij,"\n#****** ");
! 5663: for(j=1;j<=cptcoveff;j++)
! 5664: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 5665: fprintf(ficrespij,"******\n");
! 5666:
! 5667: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
! 5668: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
! 5669: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
! 5670:
! 5671: /* nhstepm=nhstepm*YEARM; aff par mois*/
! 5672:
! 5673: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 5674: oldm=oldms;savm=savms;
! 5675: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
! 5676: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
! 5677: for(i=1; i<=nlstate;i++)
! 5678: for(j=1; j<=nlstate+ndeath;j++)
! 5679: fprintf(ficrespij," %1d-%1d",i,j);
! 5680: fprintf(ficrespij,"\n");
! 5681: for (h=0; h<=nhstepm; h++){
! 5682: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
! 5683: for(i=1; i<=nlstate;i++)
! 5684: for(j=1; j<=nlstate+ndeath;j++)
! 5685: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
! 5686: fprintf(ficrespij,"\n");
! 5687: }
! 5688: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 5689: fprintf(ficrespij,"\n");
! 5690: }
! 5691: }
! 5692: }
! 5693:
! 5694: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
! 5695:
! 5696: fclose(ficrespij);
! 5697:
! 5698: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 5699: for(i=1;i<=AGESUP;i++)
! 5700: for(j=1;j<=NCOVMAX;j++)
! 5701: for(k=1;k<=NCOVMAX;k++)
! 5702: probs[i][j][k]=0.;
! 5703:
! 5704: /*---------- Forecasting ------------------*/
! 5705: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
! 5706: if(prevfcast==1){
! 5707: /* if(stepm ==1){*/
! 5708: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
! 5709: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
! 5710: /* } */
! 5711: /* else{ */
! 5712: /* erreur=108; */
! 5713: /* 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); */
! 5714: /* 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); */
! 5715: /* } */
! 5716: }
! 5717:
! 5718:
! 5719: /*---------- Health expectancies and variances ------------*/
! 5720:
! 5721: strcpy(filerest,"t");
! 5722: strcat(filerest,fileres);
! 5723: if((ficrest=fopen(filerest,"w"))==NULL) {
! 5724: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
! 5725: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
! 5726: }
! 5727: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
! 5728: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
! 5729:
! 5730:
! 5731: strcpy(filerese,"e");
! 5732: strcat(filerese,fileres);
! 5733: if((ficreseij=fopen(filerese,"w"))==NULL) {
! 5734: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
! 5735: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
! 5736: }
! 5737: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
! 5738: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
! 5739:
! 5740: strcpy(fileresstde,"stde");
! 5741: strcat(fileresstde,fileres);
! 5742: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
! 5743: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
! 5744: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
! 5745: }
! 5746: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
! 5747: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
! 5748:
! 5749: strcpy(filerescve,"cve");
! 5750: strcat(filerescve,fileres);
! 5751: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
! 5752: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
! 5753: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
! 5754: }
! 5755: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
! 5756: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
! 5757:
! 5758: strcpy(fileresv,"v");
! 5759: strcat(fileresv,fileres);
! 5760: if((ficresvij=fopen(fileresv,"w"))==NULL) {
! 5761: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
! 5762: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
! 5763: }
! 5764: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
! 5765: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
! 5766:
! 5767: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
! 5768: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
! 5769: /* 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",\
! 5770: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
! 5771: */
! 5772:
! 5773: if (mobilav!=0) {
! 5774: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 5775: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
! 5776: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
! 5777: printf(" Error in movingaverage mobilav=%d\n",mobilav);
! 5778: }
! 5779: }
! 5780:
! 5781: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
! 5782: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
! 5783: k=k+1;
! 5784: fprintf(ficrest,"\n#****** ");
! 5785: for(j=1;j<=cptcoveff;j++)
! 5786: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 5787: fprintf(ficrest,"******\n");
! 5788:
! 5789: fprintf(ficreseij,"\n#****** ");
! 5790: fprintf(ficresstdeij,"\n#****** ");
! 5791: fprintf(ficrescveij,"\n#****** ");
! 5792: for(j=1;j<=cptcoveff;j++) {
! 5793: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 5794: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 5795: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 5796: }
! 5797: fprintf(ficreseij,"******\n");
! 5798: fprintf(ficresstdeij,"******\n");
! 5799: fprintf(ficrescveij,"******\n");
! 5800:
! 5801: fprintf(ficresvij,"\n#****** ");
! 5802: for(j=1;j<=cptcoveff;j++)
! 5803: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 5804: fprintf(ficresvij,"******\n");
! 5805:
! 5806: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
! 5807: oldm=oldms;savm=savms;
! 5808: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
! 5809: cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
! 5810:
! 5811: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
! 5812: oldm=oldms;savm=savms;
! 5813: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
! 5814: if(popbased==1){
! 5815: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
! 5816: }
! 5817:
! 5818: pstamp(ficrest);
! 5819: fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) ");
! 5820: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
! 5821: fprintf(ficrest,"\n");
! 5822:
! 5823: epj=vector(1,nlstate+1);
! 5824: for(age=bage; age <=fage ;age++){
! 5825: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
! 5826: if (popbased==1) {
! 5827: if(mobilav ==0){
! 5828: for(i=1; i<=nlstate;i++)
! 5829: prlim[i][i]=probs[(int)age][i][k];
! 5830: }else{ /* mobilav */
! 5831: for(i=1; i<=nlstate;i++)
! 5832: prlim[i][i]=mobaverage[(int)age][i][k];
! 5833: }
! 5834: }
! 5835:
! 5836: fprintf(ficrest," %4.0f",age);
! 5837: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
! 5838: for(i=1, epj[j]=0.;i <=nlstate;i++) {
! 5839: epj[j] += prlim[i][i]*eij[i][j][(int)age];
! 5840: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
! 5841: }
! 5842: epj[nlstate+1] +=epj[j];
! 5843: }
! 5844:
! 5845: for(i=1, vepp=0.;i <=nlstate;i++)
! 5846: for(j=1;j <=nlstate;j++)
! 5847: vepp += vareij[i][j][(int)age];
! 5848: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
! 5849: for(j=1;j <=nlstate;j++){
! 5850: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
! 5851: }
! 5852: fprintf(ficrest,"\n");
! 5853: }
! 5854: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
! 5855: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
! 5856: free_vector(epj,1,nlstate+1);
! 5857: }
! 5858: }
! 5859: free_vector(weight,1,n);
! 5860: free_imatrix(Tvard,1,15,1,2);
! 5861: free_imatrix(s,1,maxwav+1,1,n);
! 5862: free_matrix(anint,1,maxwav,1,n);
! 5863: free_matrix(mint,1,maxwav,1,n);
! 5864: free_ivector(cod,1,n);
! 5865: free_ivector(tab,1,NCOVMAX);
! 5866: fclose(ficreseij);
! 5867: fclose(ficresstdeij);
! 5868: fclose(ficrescveij);
! 5869: fclose(ficresvij);
! 5870: fclose(ficrest);
! 5871: fclose(ficpar);
! 5872:
! 5873: /*------- Variance of period (stable) prevalence------*/
! 5874:
! 5875: strcpy(fileresvpl,"vpl");
! 5876: strcat(fileresvpl,fileres);
! 5877: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
! 5878: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
! 5879: exit(0);
! 5880: }
! 5881: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
! 5882:
! 5883: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
! 5884: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
! 5885: k=k+1;
! 5886: fprintf(ficresvpl,"\n#****** ");
! 5887: for(j=1;j<=cptcoveff;j++)
! 5888: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 5889: fprintf(ficresvpl,"******\n");
! 5890:
! 5891: varpl=matrix(1,nlstate,(int) bage, (int) fage);
! 5892: oldm=oldms;savm=savms;
! 5893: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
! 5894: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
! 5895: }
! 5896: }
! 5897:
! 5898: fclose(ficresvpl);
! 5899:
! 5900: /*---------- End : free ----------------*/
! 5901: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 5902: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 5903:
! 5904: } /* mle==-3 arrives here for freeing */
! 5905: free_matrix(prlim,1,nlstate,1,nlstate);
! 5906: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
! 5907: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
! 5908: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
! 5909: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
! 5910: free_matrix(covar,0,NCOVMAX,1,n);
! 5911: free_matrix(matcov,1,npar,1,npar);
! 5912: /*free_vector(delti,1,npar);*/
! 5913: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
! 5914: free_matrix(agev,1,maxwav,1,imx);
! 5915: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
! 5916:
! 5917: free_ivector(ncodemax,1,8);
! 5918: free_ivector(Tvar,1,15);
! 5919: free_ivector(Tprod,1,15);
! 5920: free_ivector(Tvaraff,1,15);
! 5921: free_ivector(Tage,1,15);
! 5922: free_ivector(Tcode,1,100);
! 5923:
! 5924: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
! 5925: free_imatrix(codtab,1,100,1,10);
! 5926: fflush(fichtm);
! 5927: fflush(ficgp);
! 5928:
! 5929:
! 5930: if((nberr >0) || (nbwarn>0)){
! 5931: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
! 5932: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
! 5933: }else{
! 5934: printf("End of Imach\n");
! 5935: fprintf(ficlog,"End of Imach\n");
! 5936: }
! 5937: printf("See log file on %s\n",filelog);
! 5938: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
! 5939: (void) gettimeofday(&end_time,&tzp);
! 5940: tm = *localtime(&end_time.tv_sec);
! 5941: tmg = *gmtime(&end_time.tv_sec);
! 5942: strcpy(strtend,asctime(&tm));
! 5943: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
! 5944: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
! 5945: printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
! 5946:
! 5947: printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
! 5948: fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
! 5949: fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
! 5950: /* printf("Total time was %d uSec.\n", total_usecs);*/
! 5951: /* if(fileappend(fichtm,optionfilehtm)){ */
! 5952: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
! 5953: fclose(fichtm);
! 5954: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
! 5955: fclose(fichtmcov);
! 5956: fclose(ficgp);
! 5957: fclose(ficlog);
! 5958: /*------ End -----------*/
! 5959:
! 5960:
! 5961: printf("Before Current directory %s!\n",pathcd);
! 5962: if(chdir(pathcd) != 0)
! 5963: printf("Can't move to directory %s!\n",path);
! 5964: if(getcwd(pathcd,MAXLINE) > 0)
! 5965: printf("Current directory %s!\n",pathcd);
! 5966: /*strcat(plotcmd,CHARSEPARATOR);*/
! 5967: sprintf(plotcmd,"gnuplot");
! 5968: #ifndef UNIX
! 5969: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
! 5970: #endif
! 5971: if(!stat(plotcmd,&info)){
! 5972: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
! 5973: if(!stat(getenv("GNUPLOTBIN"),&info)){
! 5974: printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
! 5975: }else
! 5976: strcpy(pplotcmd,plotcmd);
! 5977: #ifdef UNIX
! 5978: strcpy(plotcmd,GNUPLOTPROGRAM);
! 5979: if(!stat(plotcmd,&info)){
! 5980: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
! 5981: }else
! 5982: strcpy(pplotcmd,plotcmd);
! 5983: #endif
! 5984: }else
! 5985: strcpy(pplotcmd,plotcmd);
! 5986:
! 5987: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
! 5988: printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
! 5989:
! 5990: if((outcmd=system(plotcmd)) != 0){
! 5991: printf("\n Problem with gnuplot\n");
! 5992: }
! 5993: printf(" Wait...");
! 5994: while (z[0] != 'q') {
! 5995: /* chdir(path); */
! 5996: printf("\nType e to edit output files, g to graph again and q for exiting: ");
! 5997: scanf("%s",z);
! 5998: /* if (z[0] == 'c') system("./imach"); */
! 5999: if (z[0] == 'e') {
! 6000: printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
! 6001: system(optionfilehtm);
! 6002: }
! 6003: else if (z[0] == 'g') system(plotcmd);
! 6004: else if (z[0] == 'q') exit(0);
! 6005: }
! 6006: end:
! 6007: while (z[0] != 'q') {
! 6008: printf("\nType q for exiting: ");
! 6009: scanf("%s",z);
! 6010: }
! 6011: }
! 6012:
! 6013:
! 6014:
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