--- imach/src/imach.c 2017/06/29 09:47:08 1.274 +++ imach/src/imach.c 2022/08/07 05:40:09 1.331 @@ -1,6 +1,217 @@ -/* $Id: imach.c,v 1.274 2017/06/29 09:47:08 brouard Exp $ +/* $Id: imach.c,v 1.331 2022/08/07 05:40:09 brouard Exp $ $State: Exp $ $Log: imach.c,v $ + Revision 1.331 2022/08/07 05:40:09 brouard + *** empty log message *** + + Revision 1.330 2022/08/06 07:18:25 brouard + Summary: last 0.99r31 + + * imach.c (Module): Version of imach using partly decoderesult to rebuild xpxij function + + Revision 1.329 2022/08/03 17:29:54 brouard + * imach.c (Module): Many errors in graphs fixed with Vn*age covariates. + + Revision 1.328 2022/07/27 17:40:48 brouard + Summary: valgrind bug fixed by initializing to zero DummyV as well as Tage + + Revision 1.327 2022/07/27 14:47:35 brouard + Summary: Still a problem for one-step probabilities in case of quantitative variables + + Revision 1.326 2022/07/26 17:33:55 brouard + Summary: some test with nres=1 + + Revision 1.325 2022/07/25 14:27:23 brouard + Summary: r30 + + * imach.c (Module): Error cptcovn instead of nsd in bmij (was + coredumped, revealed by Feiuno, thank you. + + Revision 1.324 2022/07/23 17:44:26 brouard + *** empty log message *** + + Revision 1.323 2022/07/22 12:30:08 brouard + * imach.c (Module): Output of Wald test in the htm file and not only in the log. + + Revision 1.322 2022/07/22 12:27:48 brouard + * imach.c (Module): Output of Wald test in the htm file and not only in the log. + + Revision 1.321 2022/07/22 12:04:24 brouard + Summary: r28 + + * imach.c (Module): Output of Wald test in the htm file and not only in the log. + + Revision 1.320 2022/06/02 05:10:11 brouard + *** empty log message *** + + Revision 1.319 2022/06/02 04:45:11 brouard + * imach.c (Module): Adding the Wald tests from the log to the main + htm for better display of the maximum likelihood estimators. + + Revision 1.318 2022/05/24 08:10:59 brouard + * imach.c (Module): Some attempts to find a bug of wrong estimates + of confidencce intervals with product in the equation modelC + + Revision 1.317 2022/05/15 15:06:23 brouard + * imach.c (Module): Some minor improvements + + Revision 1.316 2022/05/11 15:11:31 brouard + Summary: r27 + + Revision 1.315 2022/05/11 15:06:32 brouard + *** empty log message *** + + Revision 1.314 2022/04/13 17:43:09 brouard + * imach.c (Module): Adding link to text data files + + Revision 1.313 2022/04/11 15:57:42 brouard + * imach.c (Module): Error in rewriting the 'r' file with yearsfproj or yearsbproj fixed + + Revision 1.312 2022/04/05 21:24:39 brouard + *** empty log message *** + + Revision 1.311 2022/04/05 21:03:51 brouard + Summary: Fixed quantitative covariates + + Fixed covariates (dummy or quantitative) + with missing values have never been allowed but are ERRORS and + program quits. Standard deviations of fixed covariates were + wrongly computed. Mean and standard deviations of time varying + covariates are still not computed. + + Revision 1.310 2022/03/17 08:45:53 brouard + Summary: 99r25 + + Improving detection of errors: result lines should be compatible with + the model. + + Revision 1.309 2021/05/20 12:39:14 brouard + Summary: Version 0.99r24 + + Revision 1.308 2021/03/31 13:11:57 brouard + Summary: Version 0.99r23 + + + * imach.c (Module): Still bugs in the result loop. Thank to Holly Benett + + Revision 1.307 2021/03/08 18:11:32 brouard + Summary: 0.99r22 fixed bug on result: + + Revision 1.306 2021/02/20 15:44:02 brouard + Summary: Version 0.99r21 + + * imach.c (Module): Fix bug on quitting after result lines! + (Module): Version 0.99r21 + + Revision 1.305 2021/02/20 15:28:30 brouard + * imach.c (Module): Fix bug on quitting after result lines! + + Revision 1.304 2021/02/12 11:34:20 brouard + * imach.c (Module): The use of a Windows BOM (huge) file is now an error + + Revision 1.303 2021/02/11 19:50:15 brouard + * (Module): imach.c Someone entered 'results:' instead of 'result:'. Now it is an error which is printed. + + Revision 1.302 2020/02/22 21:00:05 brouard + * (Module): imach.c Update mle=-3 (for computing Life expectancy + and life table from the data without any state) + + Revision 1.301 2019/06/04 13:51:20 brouard + Summary: Error in 'r'parameter file backcast yearsbproj instead of yearsfproj + + Revision 1.300 2019/05/22 19:09:45 brouard + Summary: version 0.99r19 of May 2019 + + Revision 1.299 2019/05/22 18:37:08 brouard + Summary: Cleaned 0.99r19 + + Revision 1.298 2019/05/22 18:19:56 brouard + *** empty log message *** + + Revision 1.297 2019/05/22 17:56:10 brouard + Summary: Fix bug by moving date2dmy and nhstepm which gaefin=-1 + + Revision 1.296 2019/05/20 13:03:18 brouard + Summary: Projection syntax simplified + + + We can now start projections, forward or backward, from the mean date + of inteviews up to or down to a number of years of projection: + prevforecast=1 yearsfproj=15.3 mobil_average=0 + or + prevforecast=1 starting-proj-date=1/1/2007 final-proj-date=12/31/2017 mobil_average=0 + or + prevbackcast=1 yearsbproj=12.3 mobil_average=1 + or + prevbackcast=1 starting-back-date=1/10/1999 final-back-date=1/1/1985 mobil_average=1 + + Revision 1.295 2019/05/18 09:52:50 brouard + Summary: doxygen tex bug + + Revision 1.294 2019/05/16 14:54:33 brouard + Summary: There was some wrong lines added + + Revision 1.293 2019/05/09 15:17:34 brouard + *** empty log message *** + + Revision 1.292 2019/05/09 14:17:20 brouard + Summary: Some updates + + Revision 1.291 2019/05/09 13:44:18 brouard + Summary: Before ncovmax + + Revision 1.290 2019/05/09 13:39:37 brouard + Summary: 0.99r18 unlimited number of individuals + + The number n which was limited to 20,000 cases is now unlimited, from firstobs to lastobs. If the number is too for the virtual memory, probably an error will occur. + + Revision 1.289 2018/12/13 09:16:26 brouard + Summary: Bug for young ages (<-30) will be in r17 + + Revision 1.288 2018/05/02 20:58:27 brouard + Summary: Some bugs fixed + + Revision 1.287 2018/05/01 17:57:25 brouard + Summary: Bug fixed by providing frequencies only for non missing covariates + + Revision 1.286 2018/04/27 14:27:04 brouard + Summary: some minor bugs + + Revision 1.285 2018/04/21 21:02:16 brouard + Summary: Some bugs fixed, valgrind tested + + Revision 1.284 2018/04/20 05:22:13 brouard + Summary: Computing mean and stdeviation of fixed quantitative variables + + Revision 1.283 2018/04/19 14:49:16 brouard + Summary: Some minor bugs fixed + + Revision 1.282 2018/02/27 22:50:02 brouard + *** empty log message *** + + Revision 1.281 2018/02/27 19:25:23 brouard + Summary: Adding second argument for quitting + + Revision 1.280 2018/02/21 07:58:13 brouard + Summary: 0.99r15 + + New Makefile with recent VirtualBox 5.26. Bug in sqrt negatve in imach.c + + Revision 1.279 2017/07/20 13:35:01 brouard + Summary: temporary working + + Revision 1.278 2017/07/19 14:09:02 brouard + Summary: Bug for mobil_average=0 and prevforecast fixed(?) + + Revision 1.277 2017/07/17 08:53:49 brouard + Summary: BOM files can be read now + + Revision 1.276 2017/06/30 15:48:31 brouard + Summary: Graphs improvements + + Revision 1.275 2017/06/30 13:39:33 brouard + Summary: Saito's color + Revision 1.274 2017/06/29 09:47:08 brouard Summary: Version 0.99r14 @@ -687,7 +898,7 @@ The same imach parameter file can be used but the option for mle should be -3. - Agnès, who wrote this part of the code, tried to keep most of the + Agnès, who wrote this part of the code, tried to keep most of the former routines in order to include the new code within the former code. The output is very simple: only an estimate of the intercept and of @@ -866,13 +1077,13 @@ Important routines - Tricode which tests the modality of dummy variables (in order to warn with wrong or empty modalities) and returns the number of efficient covariates cptcoveff and modalities nbcode[Tvar[k]][1]= 0 and nbcode[Tvar[k]][2]= 1 usually. - printinghtml which outputs results like life expectancy in and from a state for a combination of modalities of dummy variables - o There are 2*cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if + o There are 2**cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if race White (0 0), Black vs White (1 0), Hispanic (0 1) and 1 1 being meaningless. - Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr). - Institut national d'études démographiques, Paris. + Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr). + Institut national d'études démographiques, Paris. This software have been partly granted by Euro-REVES, a concerted action from the European Union. It is copyrighted identically to a GNU software product, ie programme and @@ -936,6 +1147,7 @@ Important routines #define POWELLNOF3INFF1TEST /* Skip test */ /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */ /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */ +/* #define FLATSUP *//* Suppresses directions where likelihood is flat */ #include #include @@ -991,7 +1203,7 @@ typedef struct { #define GNUPLOTPROGRAM "gnuplot" /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/ -#define FILENAMELENGTH 132 +#define FILENAMELENGTH 256 #define GLOCK_ERROR_NOPATH -1 /* empty path */ #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */ @@ -1002,14 +1214,15 @@ typedef struct { #define NINTERVMAX 8 #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */ #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */ -#define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */ +#define NCOVMAX 30 /**< Maximum number of covariates used in the model, including generated covariates V1*V2 or V1*age */ #define codtabm(h,k) (1 & (h-1) >> (k-1))+1 /*#define decodtabm(h,k,cptcoveff)= (h <= (1<> (k-1)) & 1) +1 : -1)*/ #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1 -#define MAXN 20000 +/*#define MAXN 20000 */ /* Should by replaced by nobs, real number of observations and unlimited */ #define YEARM 12. /**< Number of months per year */ /* #define AGESUP 130 */ -#define AGESUP 150 +/* #define AGESUP 150 */ +#define AGESUP 200 #define AGEINF 0 #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */ #define AGEBASE 40 @@ -1025,24 +1238,25 @@ typedef struct { #define ODIRSEPARATOR '\\' #endif -/* $Id: imach.c,v 1.274 2017/06/29 09:47:08 brouard Exp $ */ +/* $Id: imach.c,v 1.331 2022/08/07 05:40:09 brouard Exp $ */ /* $State: Exp $ */ #include "version.h" char version[]=__IMACH_VERSION__; -char copyright[]="February 2016,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2018"; -char fullversion[]="$Revision: 1.274 $ $Date: 2017/06/29 09:47:08 $"; +char copyright[]="July 2022,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2020, Nihon University 2021-202, INED 2000-2022"; +char fullversion[]="$Revision: 1.331 $ $Date: 2022/08/07 05:40:09 $"; char strstart[80]; char optionfilext[10], optionfilefiname[FILENAMELENGTH]; int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */ int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */ -/* Number of covariates model=V2+V1+ V3*age+V2*V4 */ -int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */ -int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */ -int cptcovs=0; /**< cptcovs number of simple covariates in the model V2+V1 =2 */ +/* Number of covariates model (1)=V2+V1+ V3*age+V2*V4 */ +/* Model(2) V1 + V2 + V3 + V8 + V7*V8 + V5*V6 + V8*age + V3*age + age*age */ +int cptcovn=0; /**< cptcovn decodemodel: number of covariates k of the models excluding age*products =6 and age*age */ +int cptcovt=0; /**< cptcovt: total number of covariates of the model (2) nbocc(+)+1 = 8 excepting constant and age and age*age */ +int cptcovs=0; /**< cptcovs number of simple covariates in the model V2+V1 =2 (dummy or quantit or time varying) */ int cptcovsnq=0; /**< cptcovsnq number of simple covariates in the model but non quantitative V2+V1 =2 */ int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */ int cptcovprodnoage=0; /**< Number of covariate products without age */ -int cptcoveff=0; /* Total number of covariates to vary for printing results */ +int cptcoveff=0; /* Total number of covariates to vary for printing results (2**cptcoveff combinations of dummies)(computed in tricode as cptcov) */ int ncovf=0; /* Total number of effective fixed covariates (dummy or quantitative) in the model */ int ncovv=0; /* Total number of effective (wave) varying covariates (dummy or quantitative) in the model */ int ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (dummy of quantitative) in the model */ @@ -1053,8 +1267,9 @@ int nqfveff=0; /**< nqfveff Number of Qu int ntveff=0; /**< ntveff number of effective time varying variables */ int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */ int cptcov=0; /* Working variable */ +int nobs=10; /* Number of observations in the data lastobs-firstobs */ int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */ -int npar=NPARMAX; +int npar=NPARMAX; /* Number of parameters (nlstate+ndeath-1)*nlstate*ncovmodel; */ int nlstate=2; /* Number of live states */ int ndeath=1; /* Number of dead states */ int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */ @@ -1193,7 +1408,12 @@ double **pmmij, ***probs; /* Global poin double ***mobaverage, ***mobaverages; /* New global variable */ double *ageexmed,*agecens; double dateintmean=0; + double anprojd, mprojd, jprojd; /* For eventual projections */ + double anprojf, mprojf, jprojf; + double anbackd, mbackd, jbackd; /* For eventual backprojections */ + double anbackf, mbackf, jbackf; + double jintmean,mintmean,aintmean; double *weight; int **s; /* Status */ double *agedc; @@ -1205,40 +1425,78 @@ double ***cotvar; /* Time varying covari double ***cotqvar; /* Time varying quantitative covariate itqv */ double idx; int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */ -/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ -/*k 1 2 3 4 5 6 7 8 9 */ -/*Tvar[k]= 5 4 3 6 5 2 7 1 1 */ -/* Tndvar[k] 1 2 3 4 5 */ -/*TDvar 4 3 6 7 1 */ /* For outputs only; combination of dummies fixed or varying */ -/* Tns[k] 1 2 2 4 5 */ /* Number of single cova */ -/* TvarsD[k] 1 2 3 */ /* Number of single dummy cova */ -/* TvarsDind 2 3 9 */ /* position K of single dummy cova */ -/* TvarsQ[k] 1 2 */ /* Number of single quantitative cova */ -/* TvarsQind 1 6 */ /* position K of single quantitative cova */ -/* Tprod[i]=k 4 7 */ -/* Tage[i]=k 5 8 */ -/* */ +/* Some documentation */ + /* Design original data + * V1 V2 V3 V4 V5 V6 V7 V8 Weight ddb ddth d1st s1 V9 V10 V11 V12 s2 V9 V10 V11 V12 + * < ncovcol=6 > nqv=2 (V7 V8) dv dv dv qtv dv dv dvv qtv + * ntv=3 nqtv=1 + * cptcovn number of covariates (not including constant and age or age*age) = number of plus sign + 1 = 10+1=11 + * For time varying covariate, quanti or dummies + * cotqvar[wav][iv(1 to nqtv)][i]= [1][12][i]=(V12) quanti + * cotvar[wav][ntv+iv][i]= [3+(1 to nqtv)][i]=(V12) quanti + * cotvar[wav][iv(1 to ntv)][i]= [1][1][i]=(V9) dummies at wav 1 + * cotvar[wav][iv(1 to ntv)][i]= [1][2][i]=(V10) dummies at wav 1 + * covar[k,i], value of kth fixed covariate dummy or quanti : + * covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8) + * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 + V9 + V9*age + V10 + * k= 1 2 3 4 5 6 7 8 9 10 11 + */ +/* According to the model, more columns can be added to covar by the product of covariates */ +/* ncovcol=1(Males=0 Females=1) nqv=1(raedyrs) ntv=2(withoutiadl=0 withiadl=1, witoutadl=0 withoutadl=1) nqtv=1(bmi) nlstate=3 ndeath=1 + # States 1=Coresidence, 2 Living alone, 3 Institution + # V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi +*/ +/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ +/* k 1 2 3 4 5 6 7 8 9 */ +/*Typevar[k]= 0 0 0 2 1 0 2 1 0 *//*0 for simple covariate (dummy, quantitative,*/ + /* fixed or varying), 1 for age product, 2 for*/ + /* product */ +/*Dummy[k]= 1 0 0 1 3 1 1 2 0 *//*Dummy[k] 0=dummy (0 1), 1 quantitative */ + /*(single or product without age), 2 dummy*/ + /* with age product, 3 quant with age product*/ +/*Tvar[k]= 5 4 3 6 5 2 7 1 1 */ +/* nsd 1 2 3 */ /* Counting single dummies covar fixed or tv */ +/*TnsdVar[Tvar] 1 2 3 */ +/*TvarsD[nsd] 4 3 1 */ /* ID of single dummy cova fixed or timevary*/ +/*TvarsDind[k] 2 3 9 */ /* position K of single dummy cova */ +/* nsq 1 2 */ /* Counting single quantit tv */ +/* TvarsQ[k] 5 2 */ /* Number of single quantitative cova */ +/* TvarsQind 1 6 */ /* position K of single quantitative cova */ +/* Tprod[i]=k 1 2 */ /* Position in model of the ith prod without age */ +/* cptcovage 1 2 */ /* Counting cov*age in the model equation */ +/* Tage[cptcovage]=k 5 8 */ /* Position in the model of ith cov*age */ +/* Tvard[1][1]@4={4,3,1,2} V4*V3 V1*V2 */ /* Position in model of the ith prod without age */ +/* Tvardk[4][1]=4;Tvardk[4][2]=3;Tvardk[7][1]=1;Tvardk[7][2]=2 */ /* Variables of a prod at position in the model equation*/ +/* TvarF TvarF[1]=Tvar[6]=2, TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1 ID of fixed covariates or product V2, V1*V2, V1 */ +/* TvarFind; TvarFind[1]=6, TvarFind[2]=7, TvarFind[3]=9 *//* Inverse V2(6) is first fixed (single or prod) */ /* Type */ /* V 1 2 3 4 5 */ /* F F V V V */ /* D Q D D Q */ /* */ int *TvarsD; +int *TnsdVar; int *TvarsDind; int *TvarsQ; int *TvarsQind; -#define MAXRESULTLINES 10 +#define MAXRESULTLINESPONE 10+1 int nresult=0; int parameterline=0; /* # of the parameter (type) line */ -int TKresult[MAXRESULTLINES]; -int Tresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */ -int Tinvresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */ -int Tvresult[MAXRESULTLINES][NCOVMAX]; /* For dummy variable , variable # (output) */ -double Tqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */ -double Tqinvresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */ -int Tvqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , variable # (output) */ - +int TKresult[MAXRESULTLINESPONE]; +int resultmodel[MAXRESULTLINESPONE][NCOVMAX];/* resultmodel[k1]=k3: k1th position in the model correspond to the k3 position in the resultline */ +int Tresult[MAXRESULTLINESPONE][NCOVMAX];/* For dummy variable , value (output) */ +int Tinvresult[MAXRESULTLINESPONE][NCOVMAX];/* For dummy variable , value (output) */ +int TinvDoQresult[MAXRESULTLINESPONE][NCOVMAX];/* For dummy variable or quanti value (output) */ +int Tvresult[MAXRESULTLINESPONE][NCOVMAX]; /* For dummy variable , variable # (output) */ +double Tqresult[MAXRESULTLINESPONE][NCOVMAX]; /* For quantitative variable , value (output) */ +double Tqinvresult[MAXRESULTLINESPONE][NCOVMAX]; /* For quantitative variable , value (output) */ +int Tvqresult[MAXRESULTLINESPONE][NCOVMAX]; /* For quantitative variable , variable # (output) */ + +/* ncovcol=1(Males=0 Females=1) nqv=1(raedyrs) ntv=2(withoutiadl=0 withiadl=1, witoutadl=0 withoutadl=1) nqtv=1(bmi) nlstate=3 ndeath=1 + # States 1=Coresidence, 2 Living alone, 3 Institution + # V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi +*/ /* int *TDvar; /\**< TDvar[1]=4, TDvarF[2]=3, TDvar[3]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 *\/ */ int *TvarF; /**< TvarF[1]=Tvar[6]=2, TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ int *TvarFind; /**< TvarFind[1]=6, TvarFind[2]=7, Tvarind[3]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ @@ -1270,6 +1528,7 @@ int *TmodelInvQind; /** Tmodelqind[1]=1 int *Ndum; /** Freq of modality (tricode */ /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */ int **Tvard; +int **Tvardk; int *Tprod;/**< Gives the k position of the k1 product */ /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3 */ int *Tposprod; /**< Gives the k1 product from the k position */ @@ -1440,7 +1699,7 @@ char *cutl(char *blocc, char *alocc, cha { /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ' and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2') - gives blocc="abcdef" and alocc="ghi2j". + gives alocc="abcdef" and blocc="ghi2j". If occ is not found blocc is null and alocc is equal to in. Returns blocc */ char *s, *t; @@ -1722,7 +1981,9 @@ char *subdirf(char fileres[]) /*************** function subdirf2 ***********/ char *subdirf2(char fileres[], char *preop) { - + /* Example subdirf2(optionfilefiname,"FB_") with optionfilefiname="texte", result="texte/FB_texte" + Errors in subdirf, 2, 3 while printing tmpout is + rewritten within the same printf. Workaround: many printfs */ /* Caution optionfilefiname is hidden */ strcpy(tmpout,optionfilefiname); strcat(tmpout,"/"); @@ -2093,10 +2354,10 @@ void linmin(double p[], double xi[], int #endif #ifdef LINMINORIGINAL #else - if(fb == fx){ /* Flat function in the direction */ - xmin=xx; + if(fb == fx){ /* Flat function in the direction */ + xmin=xx; *flat=1; - }else{ + }else{ *flat=0; #endif /*Flat mnbrak2 shift (*ax=0.000000000000, *fa=51626.272983130431), (*bx=-1.618034000000, *fb=51590.149499362531), (*cx=-4.236068025156, *fc=51590.149499362531) */ @@ -2154,10 +2415,10 @@ void linmin(double p[], double xi[], int /*************** powell ************************/ /* -Minimization of a function func of n variables. Input consists of an initial starting point -p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di- -rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value -such that failure to decrease by more than this amount on one iteration signals doneness. On +Minimization of a function func of n variables. Input consists in an initial starting point +p[1..n] ; an initial matrix xi[1..n][1..n] whose columns contain the initial set of di- +rections (usually the n unit vectors); and ftol, the fractional tolerance in the function value +such that failure to decrease by more than this amount in one iteration signals doneness. On output, p is set to the best point found, xi is the then-current direction set, fret is the returned function value at p , and iter is the number of iterations taken. The routine linmin is used. */ @@ -2182,12 +2443,6 @@ void powell(double p[], double **xi, int double fp,fptt; double *xits; int niterf, itmp; -#ifdef LINMINORIGINAL -#else - - flatdir=ivector(1,n); - for (j=1;j<=n;j++) flatdir[j]=0; -#endif pt=vector(1,n); ptt=vector(1,n); @@ -2197,16 +2452,16 @@ void powell(double p[], double **xi, int for (j=1;j<=n;j++) pt[j]=p[j]; rcurr_time = time(NULL); for (*iter=1;;++(*iter)) { - fp=(*fret); /* From former iteration or initial value */ ibig=0; del=0.0; rlast_time=rcurr_time; /* (void) gettimeofday(&curr_time,&tzp); */ rcurr_time = time(NULL); curr_time = *localtime(&rcurr_time); - printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout); - fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog); + printf("\nPowell iter=%d -2*LL=%.12f gain=%.12f=%.3g %ld sec. %ld sec.",*iter,*fret, fp-*fret,fp-*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout); + fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f gain=%.12f=%.3g %ld sec. %ld sec.",*iter,*fret, fp-*fret,fp-*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog); /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */ + fp=(*fret); /* From former iteration or initial value */ for (i=1;i<=n;i++) { fprintf(ficrespow," %.12lf", p[i]); } @@ -2311,14 +2566,14 @@ void powell(double p[], double **xi, int /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */ /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */ /* New value of last point Pn is not computed, P(n-1) */ - for(j=1;j<=n;j++) { - if(flatdir[j] >0){ - printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]); - fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]); - } - /* printf("\n"); */ - /* fprintf(ficlog,"\n"); */ - } + for(j=1;j<=n;j++) { + if(flatdir[j] >0){ + printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]); + fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]); + } + /* printf("\n"); */ + /* fprintf(ficlog,"\n"); */ + } /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /\* Did we reach enough precision? *\/ */ if (2.0*fabs(fp-(*fret)) <= ftol) { /* Did we reach enough precision? */ /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */ @@ -2356,10 +2611,6 @@ void powell(double p[], double **xi, int } #endif -#ifdef LINMINORIGINAL -#else - free_ivector(flatdir,1,n); -#endif free_vector(xit,1,n); free_vector(xits,1,n); free_vector(ptt,1,n); @@ -2473,6 +2724,13 @@ void powell(double p[], double **xi, int } printf("\n"); fprintf(ficlog,"\n"); +#ifdef FLATSUP + free_vector(xit,1,n); + free_vector(xits,1,n); + free_vector(ptt,1,n); + free_vector(pt,1,n); + return; +#endif } #endif printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig); @@ -2504,15 +2762,18 @@ void powell(double p[], double **xi, int double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij, int nres) { - /* Computes the prevalence limit in each live state at age x and for covariate combination ij - (and selected quantitative values in nres) - by left multiplying the unit - matrix by transitions matrix until convergence is reached with precision ftolpl */ - /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */ - /* Wx is row vector: population in state 1, population in state 2, population dead */ - /* or prevalence in state 1, prevalence in state 2, 0 */ - /* newm is the matrix after multiplications, its rows are identical at a factor */ - /* Initial matrix pimij */ + /**< Computes the prevalence limit in each live state at age x and for covariate combination ij + * (and selected quantitative values in nres) + * by left multiplying the unit + * matrix by transitions matrix until convergence is reached with precision ftolpl + * Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I + * Wx is row vector: population in state 1, population in state 2, population dead + * or prevalence in state 1, prevalence in state 2, 0 + * newm is the matrix after multiplications, its rows are identical at a factor. + * Inputs are the parameter, age, a tolerance for the prevalence limit ftolpl. + * Output is prlim. + * Initial matrix pimij + */ /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */ /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */ /* 0, 0 , 1} */ @@ -2533,6 +2794,7 @@ void powell(double p[], double **xi, int double **newm; double agefin, delaymax=200. ; /* 100 Max number of years to converge */ int ncvloop=0; + int first=0; min=vector(1,nlstate); max=vector(1,nlstate); @@ -2553,39 +2815,48 @@ void powell(double p[], double **xi, int newm=savm; /* Covariates have to be included here again */ cov[2]=agefin; - if(nagesqr==1) - cov[3]= agefin*agefin;; + if(nagesqr==1){ + cov[3]= agefin*agefin; + } for (k=1; k<=nsd;k++) { /* For single dummy covariates only */ /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */ - cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)]; + cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,TvarsD[k])]; + /* cov[++k1]=nbcode[TvarsD[k]][codtabm(ij,k)]; */ /* printf("prevalim Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */ } for (k=1; k<=nsq;k++) { /* For single varying covariates only */ /* Here comes the value of quantitative after renumbering k with single quantitative covariates */ - cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; + cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; + /* cov[++k1]=Tqresult[nres][k]; */ /* printf("prevalim Quantitative k=%d TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */ } for (k=1; k<=cptcovage;k++){ /* For product with age */ - if(Dummy[Tvar[Tage[k]]]){ - cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; - } else{ - cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; + if(Dummy[Tage[k]]==2){ /* dummy with age */ + cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; + /* cov[++k1]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */ + } else if(Dummy[Tage[k]]==3){ /* quantitative with age */ + cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; + /* cov[++k1]=Tqresult[nres][k]; */ } /* printf("prevalim Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */ } for (k=1; k<=cptcovprod;k++){ /* For product without age */ /* printf("prevalim Prod ij=%d k=%d Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */ - if(Dummy[Tvard[k][1]==0]){ - if(Dummy[Tvard[k][2]==0]){ - cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; + if(Dummy[Tvard[k][1]]==0){ + if(Dummy[Tvard[k][2]]==0){ + cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; + /* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */ }else{ - cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k]; + cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * Tqresult[nres][k]; + /* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k]; */ } }else{ - if(Dummy[Tvard[k][2]==0]){ - cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]]; + if(Dummy[Tvard[k][2]]==0){ + cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])] * Tqinvresult[nres][Tvard[k][1]]; + /* cov[++k1]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]]; */ }else{ cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]]; + /* cov[++k1]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]]; */ } } } @@ -2594,7 +2865,7 @@ void powell(double p[], double **xi, int /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/ /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */ /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */ - /* age and covariate values of ij are in 'cov' */ + /* age and covariate values of ij are in 'cov' */ out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */ savm=oldm; @@ -2629,10 +2900,22 @@ void powell(double p[], double **xi, int free_vector(meandiff,1,nlstate); return prlim; } - } /* age loop */ + } /* agefin loop */ /* After some age loop it doesn't converge */ - printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\ -Earliest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear); + if(!first){ + first=1; + printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d). Others in log file only...\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM), (int)(age-stepm/YEARM), (int)delaymax); + fprintf(ficlog, "Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d).\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM), (int)(age-stepm/YEARM), (int)delaymax); + }else if (first >=1 && first <10){ + fprintf(ficlog, "Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d).\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM), (int)(age-stepm/YEARM), (int)delaymax); + first++; + }else if (first ==10){ + fprintf(ficlog, "Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d).\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM), (int)(age-stepm/YEARM), (int)delaymax); + printf("Warning: the stable prevalence dit not converge. This warning came too often, IMaCh will stop notifying, even in its log file. Look at the graphs to appreciate the non convergence.\n"); + fprintf(ficlog,"Warning: the stable prevalence no convergence; too many cases, giving up noticing, even in log file\n"); + first++; + } + /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */ free_vector(min,1,nlstate); free_vector(max,1,nlstate); @@ -2698,17 +2981,19 @@ Earliest age to start was %d-%d=%d, ncvl /* Even if hstepm = 1, at least one multiplication by the unit matrix */ /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */ /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */ - for(agefin=age; agefin ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. Others in log file only...\n\ Oldest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear); @@ -2859,7 +3145,7 @@ double **pmij(double **ps, double *cov, /* printf("Int ji s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */ } ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */ + /* printf("Debug pmij() i=%d j=%d nc=%d s1=%.17f, lnpijopii=%.17f\n",i,j,nc, s1,lnpijopii); */ } } @@ -2875,17 +3162,17 @@ double **pmij(double **ps, double *cov, s1=0; for(j=1; ji} pij/pii=(1-pii)/pii and thus pii is known from s1 */ ps[i][i]=1./(s1+1.); /* Computing other pijs */ for(j=1; j0.01){ /* At least some value in the prevalence */ @@ -2972,10 +3261,10 @@ double **pmij(double **ps, double *cov, } /* End doldm, At the end doldm is diag[(w_i)] */ - /* left Product of this diag matrix by pmmij=Px (dnewm=dsavm*doldm) */ - bbmij=matprod2(dnewm, doldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, pmmij); /* Bug Valgrind */ + /* Left product of this diag matrix by pmmij=Px (dnewm=dsavm*doldm): diag[(w_i)*Px */ + bbmij=matprod2(dnewm, doldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, pmmij); /* was a Bug Valgrind */ - /* Diag(Sum_i w^i_x p^ij_x */ + /* Diag(Sum_i w^i_x p^ij_x, should be the prevalence at age x+stepm */ /* w1 p11 + w2 p21 only on live states N1./N..*N11/N1. + N2./N..*N21/N2.=(N11+N21)/N..=N.1/N.. */ for (j=1;j<=nlstate+ndeath;j++){ sumnew=0.; @@ -2993,7 +3282,7 @@ double **pmij(double **ps, double *cov, } /*End ii */ } /* End j, At the end dsavm is diag[1/(w_1p1i+w_2 p2i)] for ALL states even if the sum is only for live states */ - ps=matprod2(ps, dnewm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dsavm); /* Bug Valgrind */ + ps=matprod2(ps, dnewm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dsavm); /* was a Bug Valgrind */ /* ps is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */ /* end bmij */ return ps; /*pointer is unchanged */ @@ -3065,7 +3354,7 @@ double **bpmij(double **ps, double *cov, ps[ii][ii]=1; } } - /* Added for backcast */ /* Transposed matrix too */ + /* Added for prevbcast */ /* Transposed matrix too */ for(jj=1; jj<= nlstate+ndeath; jj++){ s1=0.; for(ii=1; ii<= nlstate+ndeath; ii++){ @@ -3133,7 +3422,7 @@ double ***hpxij(double ***po, int nhstep */ - int i, j, d, h, k; + int i, j, d, h, k, k1; double **out, cov[NCOVMAX+1]; double **newm; double agexact; @@ -3153,30 +3442,95 @@ double ***hpxij(double ***po, int nhstep cov[1]=1.; agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */ cov[2]=agexact; - if(nagesqr==1) + if(nagesqr==1){ cov[3]= agexact*agexact; - for (k=1; k<=nsd;k++) { /* For single dummy covariates only */ - /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */ - cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)]; - /* printf("hpxij Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */ - } - for (k=1; k<=nsq;k++) { /* For single varying covariates only */ - /* Here comes the value of quantitative after renumbering k with single quantitative covariates */ - cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; - /* printf("hPxij Quantitative k=%d TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */ - } - for (k=1; k<=cptcovage;k++){ - if(Dummy[Tvar[Tage[k]]]){ - cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; - } else{ - cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; - } - /* printf("hPxij Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */ - } - for (k=1; k<=cptcovprod;k++){ /* */ - /* printf("hPxij Prod ij=%d k=%d Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */ - cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; } + /* Model(2) V1 + V2 + V3 + V8 + V7*V8 + V5*V6 + V8*age + V3*age + age*age */ + /* total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age */ + for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */ + if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Single dummy */ +/* V(Tvarsel)=Tvalsel=Tresult[nres][pos](value); V(Tvresult[nres][pos] (variable): V(variable)=value) */ +/* for (k=1; k<=nsd;k++) { /\* For single dummy covariates only *\/ */ +/* /\* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates *\/ */ + /* codtabm(ij,k) (1 & (ij-1) >> (k-1))+1 */ +/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ +/* k 1 2 3 4 5 6 7 8 9 */ +/*Tvar[k]= 5 4 3 6 5 2 7 1 1 */ +/* nsd 1 2 3 */ /* Counting single dummies covar fixed or tv */ +/*TvarsD[nsd] 4 3 1 */ /* ID of single dummy cova fixed or timevary*/ +/*TvarsDind[k] 2 3 9 */ /* position K of single dummy cova */ + /* cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];or [codtabm(ij,TnsdVar[TvarsD[k]] */ + cov[2+nagesqr+k1]=Tresult[nres][resultmodel[nres][k1]]; + /* printf("hpxij Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,TnsdVar[TvarsD[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,TnsdVar[TvarsD[k]])],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,TnsdVar[TvarsD[k]])); */ + printf("hpxij Dummy combi=%d k1=%d Tvar[%d]=V%d cov[2+%d+%d]=%lf resultmodel[nres][%d]=%d nres/nresult=%d/%d \n",ij,k1,k1, Tvar[k1],nagesqr,k1,cov[2+nagesqr+k1],k1,resultmodel[nres][k1],nres,nresult); + }else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Single quantitative variables */ + /* resultmodel[nres][k1]=k3: k1th position in the model correspond to the k3 position in the resultline */ + cov[2+nagesqr+k1]=Tqresult[nres][resultmodel[nres][k1]]; + /* for (k=1; k<=nsq;k++) { /\* For single varying covariates only *\/ */ + /* /\* Here comes the value of quantitative after renumbering k with single quantitative covariates *\/ */ + /* cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; */ + printf("hPxij Quantitative k1=%d resultmodel[nres][%d]=%d,Tqresult[%d][%d]=%f\n",k1,k1,resultmodel[nres][k1],nres,resultmodel[nres][k1],Tqresult[nres][resultmodel[nres][k1]]); + }else if( Dummy[k1]==2 ){ /* For dummy with age product */ + /* Tvar[k1] Variable in the age product age*V1 is 1 */ + /* [Tinvresult[nres][V1] is its value in the resultline nres */ + cov[2+nagesqr+k1]=Tinvresult[nres][Tvar[k1]]; + printf("DhPxij Dummy with age k1=%d Tvar[%d]=%d Tinvresult[nres][%d]=%d,cov[2+%d+%d]=%.3f\n",k1,k1,Tvar[k1],Tinvresult[nres][Tvar[k1]],nagesqr,k1,cov[2+nagesqr+k1]); + /* cov[2+nagesqr+k1]=Tresult[nres][resultmodel[nres][k1]]; */ + /* for (k=1; k<=cptcovage;k++){ /\* For product with age V1+V1*age +V4 +age*V3 *\/ */ + /* 1+2 Tage[1]=2 TVar[2]=1 Dummy[2]=2, Tage[2]=4 TVar[4]=3 Dummy[4]=3 quant*/ + /* */ +/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ +/* k 1 2 3 4 5 6 7 8 9 */ +/*Tvar[k]= 5 4 3 6 5 2 7 1 1 */ +/*cptcovage=2 1 2 */ +/*Tage[k]= 5 8 */ + }else if( Dummy[k1]==3 ){ /* For quant with age product */ + cov[2+nagesqr+k1]=Tresult[nres][resultmodel[nres][k1]]; + printf("QhPxij Quant with age k1=%d resultmodel[nres][%d]=%d,Tqresult[%d][%d]=%f\n",k1,k1,resultmodel[nres][k1],nres,resultmodel[nres][k1],Tqresult[nres][resultmodel[nres][k1]]); + /* if(Dummy[Tage[k]]== 2){ /\* dummy with age *\/ */ + /* /\* if(Dummy[Tvar[Tage[k]]]== 2){ /\\* dummy with age *\\/ *\/ */ + /* /\* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; *\/ */ + /* /\* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,TnsdVar[TvarsD[Tvar[Tage[k]]]])]*cov[2]; *\/ */ + /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,TnsdVar[TvarsD[Tvar[Tage[k]]]])]*cov[2]; */ + /* printf("hPxij Age combi=%d k=%d cptcovage=%d Tage[%d]=%d Tvar[Tage[%d]]=V%d nbcode[Tvar[Tage[k]]][codtabm(ij,TnsdVar[Tvar[Tage[k]]]])]=%d nres=%d\n",ij,k,cptcovage,k,Tage[k],k,Tvar[Tage[k]], nbcode[Tvar[Tage[k]]][codtabm(ij,TnsdVar[Tvar[Tage[k]]])],nres); */ + /* } else if(Dummy[Tage[k]]== 3){ /\* quantitative with age *\/ */ + /* cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; */ + /* } */ + /* printf("hPxij Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */ + }else if(Typevar[k1]==2 ){ /* For product (not with age) */ +/* for (k=1; k<=cptcovprod;k++){ /\* For product without age *\/ */ +/* /\* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 *\/ */ +/* /\* k 1 2 3 4 5 6 7 8 9 *\/ */ +/* /\*Tvar[k]= 5 4 3 6 5 2 7 1 1 *\/ */ +/* /\*cptcovprod=1 1 2 *\/ */ +/* /\*Tprod[]= 4 7 *\/ */ +/* /\*Tvard[][1] 4 1 *\/ */ +/* /\*Tvard[][2] 3 2 *\/ */ + + /* printf("hPxij Prod ij=%d k=%d Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]=%d nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][1])]=%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2],nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])],nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]); */ + /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */ + cov[2+nagesqr+k1]=TinvDoQresult[nres][Tvardk[k1][1]] * TinvDoQresult[nres][Tvardk[k1][2]]; + printf("hPxij Prod ij=%d k1=%d cov[2+%d+%d]=%.5f Tvard[%d][1]=V%d * Tvard[%d][2]=V%d ; TinvDoQresult[nres][Tvardk[k1][1]]=%.4f * TinvDoQresult[nres][Tvardk[k1][1]]=%.4f\n",ij,k1,nagesqr,k1,cov[2+nagesqr+k1],k1,Tvard[k1][1], k1,Tvard[k1][2], TinvDoQresult[nres][Tvardk[k1][1]], TinvDoQresult[nres][Tvardk[k1][2]]); + /* if(Dummy[Tvardk[k1][1]]==0){ */ + /* if(Dummy[Tvardk[k1][2]]==0){ /\* Product of dummies *\/ */ + /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */ + /* cov[2+nagesqr+k1]=Tinvresult[nres][Tvardk[k1][1]] * Tinvresult[nres][Tvardk[k1][2]]; */ + /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,TnsdVar[Tvard[k][1]])] * nbcode[Tvard[k][2]][codtabm(ij,TnsdVar[Tvard[k][2]])]; */ + /* }else{ /\* Product of dummy by quantitative *\/ */ + /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,TnsdVar[Tvard[k][1]])] * Tqresult[nres][k]; */ + /* cov[2+nagesqr+k1]=Tresult[nres][Tinvresult[nres][Tvardk[k1][1]]] * Tqresult[nres][Tinvresult[nres][Tvardk[k1][2]]]; */ + /* } */ + /* }else{ /\* Product of quantitative by...*\/ */ + /* if(Dummy[Tvard[k][2]]==0){ /\* quant by dummy *\/ */ + /* /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,TnsdVar[Tvard[k][2]])] * Tqinvresult[nres][Tvard[k][1]]; *\/ */ + /* cov[2+nagesqr+k1]=Tqresult[nres][Tinvresult[nres][Tvardk[k1][1]]] * Tresult[nres][Tinvresult[nres][Tvardk[k1][2]]] ; */ + /* }else{ /\* Product of two quant *\/ */ + /* /\* cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]]; *\/ */ + /* cov[2+nagesqr+k1]=Tqresult[nres][Tinvresult[nres][Tvardk[k1][1]]] * Tqresult[nres][Tinvresult[nres][Tvardk[k1][2]]] ; */ + /* } */ + /* }/\*end of products quantitative *\/ */ + }/*end of products */ + } /* End of loop on model equation */ /* for (k=1; k<=cptcovn;k++) */ /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */ /* for (k=1; k<=cptcovage;k++) /\* Should start at cptcovn+1 *\/ */ @@ -3187,7 +3541,7 @@ double ***hpxij(double ***po, int nhstep /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/ /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/ - /* right multiplication of oldm by the current matrix */ + /* right multiplication of oldm by the current matrix */ out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, pmij(pmmij,cov,ncovmodel,x,nlstate)); /* if((int)age == 70){ */ @@ -3257,13 +3611,15 @@ double ***hbxij(double ***po, int nhstep cov[1]=1.; agexact=age-( (h-1)*hstepm + (d) )*stepm/YEARM; /* age just before transition, d or d-1? */ /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */ + /* Debug */ + /* printf("hBxij age=%lf, agexact=%lf\n", age, agexact); */ cov[2]=agexact; if(nagesqr==1) cov[3]= agexact*agexact; - for (k=1; k<=cptcovn;k++){ + for (k=1; k<=nsd;k++){ /* For single dummy covariates only *//* cptcovn error */ /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */ /* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */ - cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)]; + cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,TvarsD[k])];/* Bug valgrind */ /* printf("hbxij Dummy agexact=%.0f combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov[%d]=%lf codtabm(%d,Tvar[%d])=%d \n",agexact,ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],2+nagesqr+TvarsDind[k],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */ } for (k=1; k<=nsq;k++) { /* For single varying covariates only */ @@ -3271,16 +3627,30 @@ double ***hbxij(double ***po, int nhstep cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; /* printf("hPxij Quantitative k=%d TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */ } - for (k=1; k<=cptcovage;k++){ /* Should start at cptcovn+1 */ - if(Dummy[Tvar[Tage[k]]]){ - cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; - } else{ + for (k=1; k<=cptcovage;k++){ /* Should start at cptcovn+1 *//* For product with age */ + /* if(Dummy[Tvar[Tage[k]]]== 2){ /\* dummy with age error!!!*\/ */ + if(Dummy[Tage[k]]== 2){ /* dummy with age */ + cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; + } else if(Dummy[Tage[k]]== 3){ /* quantitative with age */ cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; } /* printf("hBxij Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */ } for (k=1; k<=cptcovprod;k++){ /* Useless because included in cptcovn */ - cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; + cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; + if(Dummy[Tvard[k][1]]==0){ + if(Dummy[Tvard[k][2]]==0){ + cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][1])]; + }else{ + cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * Tqresult[nres][k]; + } + }else{ + if(Dummy[Tvard[k][2]]==0){ + cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])] * Tqinvresult[nres][Tvard[k][1]]; + }else{ + cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]]; + } + } } /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/ /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/ @@ -3290,7 +3660,7 @@ double ***hbxij(double ***po, int nhstep /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */ /* 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */ out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\ - 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); + 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);/* Bug valgrind */ /* if((int)age == 70){ */ /* printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */ /* for(i=1; i<=nlstate+ndeath; i++) { */ @@ -3376,11 +3746,16 @@ double func( double *x) */ ioffset=2+nagesqr ; /* Fixed */ - for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */ - cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (k=6)*/ + for (k=1; k<=ncovf;k++){ /* For each fixed covariate dummu or quant or prod */ + /* # V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi */ + /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ + /* TvarF[1]=Tvar[6]=2, TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1 ID of fixed covariates or product V2, V1*V2, V1 */ + /* TvarFind; TvarFind[1]=6, TvarFind[2]=7, TvarFind[3]=9 *//* Inverse V2(6) is first fixed (single or prod) */ + cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (TvarFind[1]=6)*/ + /* V1*V2 (7) TvarFind[2]=7, TvarFind[3]=9 */ } /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] - is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] + is 5, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]=6 has been calculated etc */ /* For an individual i, wav[i] gives the number of effective waves */ /* We compute the contribution to Likelihood of each effective transition @@ -3392,8 +3767,8 @@ double func( double *x) meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i] */ for(mi=1; mi<= wav[i]-1; mi++){ - for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/ - /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */ + for(k=1; k <= ncovv ; k++){ /* Varying covariates in the model (single and product but no age )"V5+V4+V3+V4*V3+V5*age+V1*age+V1" +TvarVind 1,2,3,4(V4*V3) Tvar[1]@7{5, 4, 3, 6, 5, 1, 1 ; 6 because the created covar is after V5 and is 6, minus 1+1, 3,2,1,4 positions in cotvar*/ + /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; but where is the crossproduct? */ cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i]; } for (ii=1;ii<=nlstate+ndeath;ii++) @@ -3408,10 +3783,10 @@ double func( double *x) if(nagesqr==1) cov[3]= agexact*agexact; /* Should be changed here */ for (kk=1; kk<=cptcovage;kk++) { - if(!FixedV[Tvar[Tage[kk]]]) - cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */ - else - cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact; + if(!FixedV[Tvar[Tage[kk]]]) + cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */ + else + cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact; } out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); @@ -3519,8 +3894,13 @@ double func( double *x) } /* end of individual */ } else if(mle==2){ for (i=1,ipmx=0, sw=0.; i<=imx; i++){ - for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; + ioffset=2+nagesqr ; + for (k=1; k<=ncovf;k++) + cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i]; for(mi=1; mi<= wav[i]-1; mi++){ + for(k=1; k <= ncovv ; k++){ + cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i]; + } for (ii=1;ii<=nlstate+ndeath;ii++) for (j=1;j<=nlstate+ndeath;j++){ oldm[ii][j]=(ii==j ? 1.0 : 0.0); @@ -3698,7 +4078,7 @@ double funcone( double *x) /* Fixed */ /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */ /* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products *\/ */ - for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */ + for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products *//* Missing values are set to -1 but should be dropped */ cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (k=6)*/ /* cov[ioffset+TvarFind[1]]=covar[Tvar[TvarFind[1]]][i]; */ /* cov[2+6]=covar[Tvar[6]][i]; */ @@ -3825,7 +4205,7 @@ return -l; /*************** function likelione ***********/ -void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double [])) +void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*func)(double [])) { /* This routine should help understanding what is done with the selection of individuals/waves and @@ -3849,7 +4229,7 @@ void likelione(FILE *ficres,double p[], fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n"); } - *fretone=(*funcone)(p); + *fretone=(*func)(p); if(*globpri !=0){ fclose(ficresilk); if (mle ==0) @@ -3877,7 +4257,7 @@ void likelione(FILE *ficres,double p[], void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double [])) { - int i,j, iter=0; + int i,j,k, jk, jkk=0, iter=0; double **xi; double fret; double fretone; /* Only one call to likelihood */ @@ -3911,8 +4291,65 @@ void mlikeli(FILE *ficres,double p[], in if(j!=i)fprintf(ficrespow," p%1d%1d",i,j); fprintf(ficrespow,"\n"); #ifdef POWELL +#ifdef LINMINORIGINAL +#else /* LINMINORIGINAL */ + + flatdir=ivector(1,npar); + for (j=1;j<=npar;j++) flatdir[j]=0; +#endif /*LINMINORIGINAL */ + +#ifdef FLATSUP + powell(p,xi,npar,ftol,&iter,&fret,flatdir,func); + /* reorganizing p by suppressing flat directions */ + for(i=1, jk=1; i <=nlstate; i++){ + for(k=1; k <=(nlstate+ndeath); k++){ + if (k != i) { + printf("%d%d flatdir[%d]=%d",i,k,jk, flatdir[jk]); + if(flatdir[jk]==1){ + printf(" To be skipped %d%d flatdir[%d]=%d ",i,k,jk, flatdir[jk]); + } + for(j=1; j <=ncovmodel; j++){ + printf("%12.7f ",p[jk]); + jk++; + } + printf("\n"); + } + } + } +/* skipping */ + /* for(i=1, jk=1, jkk=1;(flatdir[jk]==0)&& (i <=nlstate); i++){ */ + for(i=1, jk=1, jkk=1;i <=nlstate; i++){ + for(k=1; k <=(nlstate+ndeath); k++){ + if (k != i) { + printf("%d%d flatdir[%d]=%d",i,k,jk, flatdir[jk]); + if(flatdir[jk]==1){ + printf(" To be skipped %d%d flatdir[%d]=%d jk=%d p[%d] ",i,k,jk, flatdir[jk],jk, jk); + for(j=1; j <=ncovmodel; jk++,j++){ + printf(" p[%d]=%12.7f",jk, p[jk]); + /*q[jjk]=p[jk];*/ + } + }else{ + printf(" To be kept %d%d flatdir[%d]=%d jk=%d q[%d]=p[%d] ",i,k,jk, flatdir[jk],jk, jkk, jk); + for(j=1; j <=ncovmodel; jk++,jkk++,j++){ + printf(" p[%d]=%12.7f=q[%d]",jk, p[jk],jkk); + /*q[jjk]=p[jk];*/ + } + } + printf("\n"); + } + fflush(stdout); + } + } + powell(p,xi,npar,ftol,&iter,&fret,flatdir,func); +#else /* FLATSUP */ powell(p,xi,npar,ftol,&iter,&fret,func); -#endif +#endif /* FLATSUP */ + +#ifdef LINMINORIGINAL +#else + free_ivector(flatdir,1,npar); +#endif /* LINMINORIGINAL*/ +#endif /* POWELL */ #ifdef NLOPT #ifdef NEWUOA @@ -3940,6 +4377,14 @@ void mlikeli(FILE *ficres,double p[], in } nlopt_destroy(opt); #endif +#ifdef FLATSUP + /* npared = npar -flatd/ncovmodel; */ + /* xired= matrix(1,npared,1,npared); */ + /* paramred= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ + /* powell(pred,xired,npared,ftol,&iter,&fret,flatdir,func); */ + /* free_matrix(xire,1,npared,1,npared); */ +#else /* FLATSUP */ +#endif /* FLATSUP */ free_matrix(xi,1,npar,1,npar); fclose(ficrespow); printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p)); @@ -4324,6 +4769,20 @@ void pstamp(FILE *fichier) fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart); } +void date2dmy(double date,double *day, double *month, double *year){ + double yp=0., yp1=0., yp2=0.; + + yp1=modf(date,&yp);/* extracts integral of date in yp and + fractional in yp1 */ + *year=yp; + yp2=modf((yp1*12),&yp); + *month=yp; + yp1=modf((yp2*30.5),&yp); + *day=yp; + if(*day==0) *day=1; + if(*month==0) *month=1; +} + /************ Frequencies ********************/ @@ -4339,7 +4798,7 @@ void freqsummary(char fileres[], double double ***freq; /* Frequencies */ double *x, *y, a=0.,b=0.,r=1., sa=0., sb=0.; /* for regression, y=b+m*x and r is the correlation coefficient */ int no=0, linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb); - double *meanq; + double *meanq, *stdq, *idq; double **meanqt; double *pp, **prop, *posprop, *pospropt; double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0; @@ -4352,6 +4811,8 @@ void freqsummary(char fileres[], double pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */ /* prop=matrix(1,nlstate,iagemin,iagemax+3); */ meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */ + stdq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */ + idq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */ meanqt=matrix(1,lastpass,1,nqtveff); strcpy(fileresp,"P_"); strcat(fileresp,fileresu); @@ -4375,7 +4836,7 @@ void freqsummary(char fileres[], double Title=%s
Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s
\n",\ fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model); } - fprintf(ficresphtm,"Current page is file %s
\n\n

Frequencies and prevalence by age at begin of transition and dummy covariate value at beginning of transition

\n",fileresphtm, fileresphtm); + fprintf(ficresphtm,"Current page is file %s
\n\n

Frequencies (weight=%d) and prevalence by age at begin of transition and dummy covariate value at beginning of transition

\n",fileresphtm, fileresphtm, weightopt); strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm")); if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) { @@ -4385,11 +4846,11 @@ Title=%s
Datafile=%s Firstpass=%d La exit(70); } else{ fprintf(ficresphtmfr,"\nIMaCh PHTM_Frequency table %s\n %s
%s \ -
\n \ +,
\n \ Title=%s
Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s
\n",\ fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model); } - fprintf(ficresphtmfr,"Current page is file %s
\n\n

Frequencies of all effective transitions of the model, by age at begin of transition, and covariate value at the begin of transition (if the covariate is a varying covariate)

Unknown status is -1
\n",fileresphtmfr, fileresphtmfr); + fprintf(ficresphtmfr,"Current page is file %s
\n\n

(weight=%d) frequencies of all effective transitions of the model, by age at begin of transition, and covariate value at the begin of transition (if the covariate is a varying covariate)

Unknown status is -1
\n",fileresphtmfr, fileresphtmfr,weightopt); y= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE); x= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE); @@ -4398,6 +4859,7 @@ Title=%s
Datafile=%s Firstpass=%d La /* j=ncoveff; /\* Only fixed dummy covariates *\/ */ j=cptcoveff; /* Only dummy covariates of the model */ + /* j=cptcovn; /\* Only dummy covariates of the model *\/ */ if (cptcovn<1) {j=1;ncodemax[1]=1;} @@ -4405,7 +4867,7 @@ Title=%s
Datafile=%s Firstpass=%d La reference=low_education V1=0,V2=0 med_educ V1=1 V2=0, high_educ V1=0 V2=1 - Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff + Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcovn */ dateintsum=0; k2cpt=0; @@ -4417,7 +4879,7 @@ Title=%s
Datafile=%s Firstpass=%d La /* if a constant only model, one pass to compute frequency tables and to write it on ficresp */ /* Loop on nj=1 or 2 if dummy covariates j!=0 - * Loop on j1(1 to 2**cptcoveff) covariate combination + * Loop on j1(1 to 2**cptcovn) covariate combination * freq[s1][s2][iage] =0. * Loop on iind * ++freq[s1][s2][iage] weighted @@ -4442,12 +4904,12 @@ Title=%s
Datafile=%s Firstpass=%d La if(nj==1) j=0; /* First pass for the constant */ else{ - j=cptcoveff; /* Other passes for the covariate values */ + j=cptcovs; /* Other passes for the covariate values */ } first=1; for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on all covariates combination of the model, excluding quantitatives, V4=0, V3=0 for example, fixed or varying covariates */ posproptt=0.; - /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]); + /*printf("cptcovn=%d Tvaraff=%d", cptcovn,Tvaraff[1]); scanf("%d", i);*/ for (i=-5; i<=nlstate+ndeath; i++) for (s2=-5; s2<=nlstate+ndeath; s2++) @@ -4460,13 +4922,16 @@ Title=%s
Datafile=%s Firstpass=%d La posprop[i]=0; pospropt[i]=0; } - /* for (z1=1; z1<= nqfveff; z1++) { */ - /* meanq[z1]+=0.; */ + for (z1=1; z1<= nqfveff; z1++) { /* zeroing for each combination j1 as well as for the total */ + idq[z1]=0.; + meanq[z1]=0.; + stdq[z1]=0.; + } + /* for (z1=1; z1<= nqtveff; z1++) { */ /* for(m=1;m<=lastpass;m++){ */ - /* meanqt[m][z1]=0.; */ - /* } */ - /* } */ - + /* meanqt[m][z1]=0.; */ + /* } */ + /* } */ /* dateintsum=0; */ /* k2cpt=0; */ @@ -4475,17 +4940,14 @@ Title=%s
Datafile=%s Firstpass=%d La bool=1; if(j !=0){ if(anyvaryingduminmodel==0){ /* If All fixed covariates */ - if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */ - /* for (z1=1; z1<= nqfveff; z1++) { */ - /* meanq[z1]+=coqvar[Tvar[z1]][iind]; /\* Computes mean of quantitative with selected filter *\/ */ - /* } */ - for (z1=1; z1<=cptcoveff; z1++) { /* loops on covariates in the model */ + if (cptcovn >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */ + for (z1=1; z1<=cptcovn; z1++) { /* loops on covariates in the model */ /* if(Tvaraff[z1] ==-20){ */ /* /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */ /* }else if(Tvaraff[z1] ==-10){ */ /* /\* sumnew+=coqvar[z1][iind]; *\/ */ - /* }else */ - if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){ /* for combination j1 of covariates */ + /* }else */ /* TODO TODO codtabm(j1,z1) or codtabm(j1,Tvaraff[z1]]z1)*/ + if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,Tvaraff[z1])]){ /* for combination j1 of covariates */ /* Tests if the value of the covariate z1 for this individual iind responded to combination j1 (V4=1 V3=0) */ bool=0; /* bool should be equal to 1 to be selected, one covariate value failed */ /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n", @@ -4499,19 +4961,19 @@ Title=%s
Datafile=%s Firstpass=%d La }/* end j==0 */ if (bool==1){ /* We selected an individual iind satisfying combination j1 (V4=1 V3=0) or all fixed covariates */ /* for(m=firstpass; m<=lastpass; m++){ */ - for(mi=1; miDatafile=%s Firstpass=%d La }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop */ } /* end j==0 */ /* bool =0 we keep that guy which corresponds to the combination of dummy values */ - if(bool==1){ + if(bool==1){ /*Selected */ /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind] and mw[mi+1][iind]. dh depends on stepm. */ agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/ @@ -4537,6 +4999,14 @@ Title=%s
Datafile=%s Firstpass=%d La if(s[m][iind]==-1) printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind],agebegin, ageend, (int)((agebegin+ageend)/2.)); freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */ + for (z1=1; z1<= nqfveff; z1++) { /* Quantitative variables, calculating mean on known values only */ + if(!isnan(covar[ncovcol+z1][iind])){ + idq[z1]=idq[z1]+weight[iind]; + meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind]; /* Computes mean of quantitative with selected filter */ + /* stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; *//*error*/ + stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]; /* *weight[iind];*/ /* Computes mean of quantitative with selected filter */ + } + } /* if((int)agev[m][iind] == 55) */ /* printf("j=%d, j1=%d Age %d, iind=%d, num=%09ld m=%d\n",j,j1,(int)agev[m][iind],iind, num[iind],m); */ /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */ @@ -4552,35 +5022,40 @@ Title=%s
Datafile=%s Firstpass=%d La bool=1; }/* end bool 2 */ } /* end m */ + /* for (z1=1; z1<= nqfveff; z1++) { /\* Quantitative variables, calculating mean *\/ */ + /* idq[z1]=idq[z1]+weight[iind]; */ + /* meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind]; /\* Computes mean of quantitative with selected filter *\/ */ + /* stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; /\* *weight[iind];*\/ /\* Computes mean of quantitative with selected filter *\/ */ + /* } */ } /* end bool */ } /* end iind = 1 to imx */ - /* prop[s][age] is feeded for any initial and valid live state as well as + /* prop[s][age] is fed for any initial and valid live state as well as freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */ /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/ - if(cptcoveff==0 && nj==1) /* no covariate and first pass */ + if(cptcovn==0 && nj==1) /* no covariate and first pass */ pstamp(ficresp); - if (cptcoveff>0 && j!=0){ + if (cptcovn>0 && j!=0){ pstamp(ficresp); printf( "\n#********** Variable "); fprintf(ficresp, "\n#********** Variable "); fprintf(ficresphtm, "\n

********** Variable "); fprintf(ficresphtmfr, "\n

********** Variable "); fprintf(ficlog, "\n#********** Variable "); - for (z1=1; z1<=cptcoveff; z1++){ + for (z1=1; z1<=cptcovs; z1++){ if(!FixedV[Tvaraff[z1]]){ - printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); - fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); - fprintf(ficresphtm, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); - fprintf(ficresphtmfr, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); - fprintf(ficlog, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]); + fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]); + fprintf(ficresphtm, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]); + fprintf(ficresphtmfr, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]); + fprintf(ficlog, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]); }else{ - printf( "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); - fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); - fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); - fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); - fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + printf( "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]); + fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]); + fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]); + fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]); + fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]); } } printf( "**********\n#"); @@ -4589,15 +5064,39 @@ Title=%s
Datafile=%s Firstpass=%d La fprintf(ficresphtmfr, "**********

\n"); fprintf(ficlog, "**********\n"); } + /* + Printing means of quantitative variables if any + */ + for (z1=1; z1<= nqfveff; z1++) { + fprintf(ficlog,"Mean of fixed quantitative variable V%d on %.3g (weighted) individuals sum=%f", ncovcol+z1, idq[z1], meanq[z1]); + fprintf(ficlog,", mean=%.3g\n",meanq[z1]/idq[z1]); + if(weightopt==1){ + printf(" Weighted mean and standard deviation of"); + fprintf(ficlog," Weighted mean and standard deviation of"); + fprintf(ficresphtmfr," Weighted mean and standard deviation of"); + } + /* mu = \frac{w x}{\sum w} + var = \frac{\sum w (x-mu)^2}{\sum w} = \frac{w x^2}{\sum w} - mu^2 + */ + printf(" fixed quantitative variable V%d on %.3g (weighted) representatives of the population : %8.5g (%8.5g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt(stdq[z1]/idq[z1]-meanq[z1]*meanq[z1]/idq[z1]/idq[z1])); + fprintf(ficlog," fixed quantitative variable V%d on %.3g (weighted) representatives of the population : %8.5g (%8.5g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt(stdq[z1]/idq[z1]-meanq[z1]*meanq[z1]/idq[z1]/idq[z1])); + fprintf(ficresphtmfr," fixed quantitative variable V%d on %.3g (weighted) representatives of the population : %8.5g (%8.5g)

\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt(stdq[z1]/idq[z1]-meanq[z1]*meanq[z1]/idq[z1]/idq[z1])); + } + /* for (z1=1; z1<= nqtveff; z1++) { */ + /* for(m=1;m<=lastpass;m++){ */ + /* fprintf(ficresphtmfr,"V quantitative id %d, pass id=%d, mean=%f

\n", z1, m, meanqt[m][z1]); */ + /* } */ + /* } */ + fprintf(ficresphtm,""); - if((cptcoveff==0 && nj==1)|| nj==2 ) /* no covariate and first pass */ + if((cptcovn==0 && nj==1)|| nj==2 ) /* no covariate and first pass */ fprintf(ficresp, " Age"); - if(nj==2) for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " V%d=%d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + if(nj==2) for (z1=1; z1<=cptcovn; z1++) fprintf(ficresp, " V%d=%d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,Tvaraff[z1])]); for(i=1; i<=nlstate;i++) { - if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," Prev(%d) N(%d) N ",i,i); + if((cptcovn==0 && nj==1)|| nj==2 ) fprintf(ficresp," Prev(%d) N(%d) N ",i,i); fprintf(ficresphtm, "",i,i); } - if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp, "\n"); + if((cptcovn==0 && nj==1)|| nj==2 ) fprintf(ficresp, "\n"); fprintf(ficresphtm, "\n"); /* Header of frequency table by age */ @@ -4665,14 +5164,14 @@ Title=%s
Datafile=%s Firstpass=%d La } /* Writing ficresp */ - if(cptcoveff==0 && nj==1){ /* no covariate and first pass */ + if(cptcovn==0 && nj==1){ /* no covariate and first pass */ if( iage <= iagemax){ fprintf(ficresp," %d",iage); } }else if( nj==2){ if( iage <= iagemax){ fprintf(ficresp," %d",iage); - for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " %d %d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + for (z1=1; z1<=cptcovn; z1++) fprintf(ficresp, " %d %d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,Tvaraff[z1])]); } } for(s1=1; s1 <=nlstate ; s1++){ @@ -4687,7 +5186,7 @@ Title=%s
Datafile=%s Firstpass=%d La } if( iage <= iagemax){ if(pos>=1.e-5){ - if(cptcoveff==0 && nj==1){ /* no covariate and first pass */ + if(cptcovn==0 && nj==1){ /* no covariate and first pass */ fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta); }else if( nj==2){ fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta); @@ -4696,7 +5195,7 @@ Title=%s
Datafile=%s Firstpass=%d La /*probs[iage][s1][j1]= pp[s1]/pos;*/ /*printf("\niage=%d s1=%d j1=%d %.5f %.0f %.0f %f",iage,s1,j1,pp[s1]/pos, pp[s1],pos,probs[iage][s1][j1]);*/ } else{ - if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," NaNq %.0f %.0f",prop[s1][iage],pospropta); + if((cptcovn==0 && nj==1)|| nj==2 ) fprintf(ficresp," NaNq %.0f %.0f",prop[s1][iage],pospropta); fprintf(ficresphtm,"",iage, prop[s1][iage],pospropta); } } @@ -4722,7 +5221,7 @@ Title=%s
Datafile=%s Firstpass=%d La } fprintf(ficresphtmfr,"\n "); fprintf(ficresphtm,"\n"); - if((cptcoveff==0 && nj==1)|| nj==2 ) { + if((cptcovn==0 && nj==1)|| nj==2 ) { if(iage <= iagemax) fprintf(ficresp,"\n"); } @@ -4823,7 +5322,7 @@ Title=%s
Datafile=%s Firstpass=%d La fprintf(ficlog,"\n"); } } - } + } /* end of state i */ printf("#Freqsummary\n"); fprintf(ficlog,"\n"); for(s1=-1; s1 <=nlstate+ndeath; s1++){ @@ -4865,11 +5364,14 @@ Title=%s
Datafile=%s Firstpass=%d La } } /* end mle=-2 */ dateintmean=dateintsum/k2cpt; + date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); fclose(ficresp); fclose(ficresphtm); fclose(ficresphtmfr); + free_vector(idq,1,nqfveff); free_vector(meanq,1,nqfveff); + free_vector(stdq,1,nqfveff); free_matrix(meanqt,1,lastpass,1,nqtveff); free_vector(x, iagemin-AGEMARGE, iagemax+4+AGEMARGE); free_vector(y, iagemin-AGEMARGE, iagemax+4+AGEMARGE); @@ -4976,7 +5478,7 @@ void prevalence(double ***probs, double /*j=cptcoveff;*/ if (cptcovn<1) {j=1;ncodemax[1]=1;} - first=1; + first=0; for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */ for (i=1; i<=nlstate; i++) for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++) @@ -4995,10 +5497,10 @@ void prevalence(double ***probs, double for (z1=1; z1<=cptcoveff; z1++){ if( Fixed[Tmodelind[z1]]==1){ iv= Tvar[Tmodelind[z1]]-ncovcol-nqv; - if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */ + if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,Tvaraff[z1])]) /* iv=1 to ntv, right modality */ bool=0; }else if( Fixed[Tmodelind[z1]]== 0) /* fixed */ - if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) { + if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,Tvaraff[z1])]) { bool=0; } } @@ -5034,12 +5536,11 @@ void prevalence(double ***probs, double if(posprop>=1.e-5){ probs[i][jk][j1]= prop[jk][i]/posprop; } else{ - if(first==1){ - first=0; + if(!first){ + first=1; printf("Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]); - fprintf(ficlog,"Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]); }else{ - fprintf(ficlog,"Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]); + fprintf(ficlog,"Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases.\n",jk,i,jk, j1,probs[i][jk][j1]); } } } @@ -5057,11 +5558,11 @@ void prevalence(double ***probs, double 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) { - /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i. + /* Concatenates waves: wav[i] is the number of effective (useful waves in the sense that a non interview is useless) of individual i. Death is a valid wave (if date is known). mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i] - and mw[mi+1][i]. dh depends on stepm. + and mw[mi+1][i]. dh depends on stepm. s[m][i] exists for any wave from firstpass to lastpass */ int i=0, mi=0, m=0, mli=0; @@ -5082,33 +5583,41 @@ void concatwav(int wav[], int **dh, int for(i=1; i<=imx; i++){ /* For simple cases and if state is death */ mi=0; /* First valid wave */ mli=0; /* Last valid wave */ - m=firstpass; - while(s[m][i] <= nlstate){ /* a live state */ + m=firstpass; /* Loop on waves */ + while(s[m][i] <= nlstate){ /* a live state or unknown state */ if(m >firstpass && s[m][i]==s[m-1][i] && mint[m][i]==mint[m-1][i] && anint[m][i]==anint[m-1][i]){/* Two succesive identical information on wave m */ mli=m-1;/* mw[++mi][i]=m-1; */ }else if(s[m][i]>=1 || s[m][i]==-4 || s[m][i]==-5){ /* Since 0.98r4 if status=-2 vital status is really unknown, wave should be skipped */ - mw[++mi][i]=m; + mw[++mi][i]=m; /* Valid wave: incrementing mi and updating mi; mw[mi] is the wave number of mi_th valid transition */ mli=m; } /* else might be a useless wave -1 and mi is not incremented and mw[mi] not updated */ if(m < lastpass){ /* m < lastpass, standard case */ m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */ } - else{ /* m >= lastpass, eventual special issue with warning */ + else{ /* m = lastpass, eventual special issue with warning */ #ifdef UNKNOWNSTATUSNOTCONTRIBUTING break; #else - if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){ + if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){ /* no death date and known date of interview, case -2 (vital status unknown is warned later */ if(firsthree == 0){ - printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p%d%d .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath); + printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p_{%d%d} .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath); firsthree=1; + }else if(firsthree >=1 && firsthree < 10){ + fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p_{%d%d} .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath); + firsthree++; + }else if(firsthree == 10){ + printf("Information, too many Information flags: no more reported to log either\n"); + fprintf(ficlog,"Information, too many Information flags: no more reported to log either\n"); + firsthree++; + }else{ + firsthree++; } - fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p%d%d .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath); - mw[++mi][i]=m; + mw[++mi][i]=m; /* Valid transition with unknown status */ mli=m; } if(s[m][i]==-2){ /* Vital status is really unknown */ nbwarn++; - if((int)anint[m][i] == 9999){ /* Has the vital status really been verified? */ + if((int)anint[m][i] == 9999){ /* Has the vital status really been verified?not a transition */ printf("Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m); fprintf(ficlog,"Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m); } @@ -5133,34 +5642,35 @@ void concatwav(int wav[], int **dh, int #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE else if ((int) andc[i] != 9999) { /* Date of death is known */ if ((int)anint[m][i]!= 9999) { /* date of last interview is known */ - if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* death occured before last wave and status should have been death instead of -1 */ + if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* month of death occured before last wave month and status should have been death instead of -1 */ nbwarn++; if(firstfiv==0){ - printf("Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m ); + printf("Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d, interviewed on %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m ); firstfiv=1; }else{ - fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m ); + fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d, interviewed on %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m ); } - }else{ /* Death occured afer last wave potential bias */ + s[m][i]=nlstate+1; /* Fixing the status as death. Be careful if multiple death states */ + }else{ /* Month of Death occured afer last wave month, potential bias */ nberr++; if(firstwo==0){ - printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictive wave at the date of last vital status scan, with a dead status or alive but unknown state status (-1). See documentation\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m ); + printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d with status %d. Potential bias if other individuals are still alive on this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictitious wave at the date of last vital status scan, with a dead status. See documentation\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m ); firstwo=1; } - fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictive wave at the date of last vital status scan, with a dead status or alive but unknown state status (-1). See documentation\n\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m ); + fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d with status %d. Potential bias if other individuals are still alive on this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictitious wave at the date of last vital status scan, with a dead status. See documentation\n\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m ); } }else{ /* if date of interview is unknown */ /* death is known but not confirmed by death status at any wave */ if(firstfour==0){ - printf("Error! Death for individual %ld line=%d occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m ); + printf("Error! Death for individual %ld line=%d occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d with status %d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m ); firstfour=1; } - fprintf(ficlog,"Error! Death for individual %ld line=%d occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m ); + fprintf(ficlog,"Error! Death for individual %ld line=%d occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d with status %d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m ); } } /* end if date of death is known */ #endif - wav[i]=mi; /* mi should be the last effective wave (or mli) */ - /* wav[i]=mw[mi][i]; */ + wav[i]=mi; /* mi should be the last effective wave (or mli), */ + /* wav[i]=mw[mi][i]; */ if(mi==0){ nbwarn++; if(first==0){ @@ -5174,7 +5684,10 @@ void concatwav(int wav[], int **dh, int } /* End individuals */ /* wav and mw are no more changed */ - + printf("Information, you have to check %d informations which haven't been logged!\n",firsthree); + fprintf(ficlog,"Information, you have to check %d informations which haven't been logged!\n",firsthree); + + for(i=1; i<=imx; i++){ for(mi=1; mi NCOVMAX)){ + if (ij <0 || ij >1 ){ + printf("ERROR, IMaCh doesn't treat covariate with missing values V%d=-1, individual %d will be skipped.\n",Tvar[k],i); + fprintf(ficlog,"ERROR, currently IMaCh doesn't treat covariate with missing values V%d=-1, individual %d will be skipped.\n",Tvar[k],i); + fflush(ficlog); + exit(1); + } + if ((ij < -1) || (ij > NCOVMAX)){ printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX ); exit(1); }else @@ -5351,12 +5874,18 @@ void concatwav(int wav[], int **dh, int /* nbcode[Tvar[j]][3]=2; */ /* To be continued (not working yet). */ ij=0; /* ij is similar to i but can jump over null modalities */ - for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/ + + /* for (i=modmincovj; i<=modmaxcovj; i++) { */ /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/ + /* Skipping the case of missing values by reducing nbcode to 0 and 1 and not -1, 0, 1 */ + /* model=V1+V2+V3, if V2=-1, 0 or 1, then nbcode[2][1]=0 and nbcode[2][2]=1 instead of + * nbcode[2][1]=-1, nbcode[2][2]=0 and nbcode[2][3]=1 */ + /*, could be restored in the future */ + for (i=0; i<=1; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/ if (Ndum[i] == 0) { /* If nobody responded to this modality k */ break; } ij++; - nbcode[Tvar[k]][ij]=i; /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality. nbcode[1][1]=0 nbcode[1][2]=1*/ + nbcode[Tvar[k]][ij]=i; /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality. nbcode[1][1]=0 nbcode[1][2]=1 . Could be -1*/ cptcode = ij; /* New max modality for covar j */ } /* end of loop on modality i=-1 to 1 or more */ break; @@ -5372,21 +5901,17 @@ void concatwav(int wav[], int **dh, int break; } /* end switch */ } /* end dummy test */ - - /* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */ - /* /\*recode from 0 *\/ */ - /* 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; */ - /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */ - /* } */ - /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */ - /* if (ij > ncodemax[j]) { */ - /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */ - /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */ - /* break; */ - /* } */ - /* } /\* end of loop on modality k *\/ */ - } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/ + if(Dummy[k]==1 && Typevar[k] !=1){ /* Dummy covariate and not age product */ + for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the modality of this covariate Vj*/ + if(isnan(covar[Tvar[k]][i])){ + printf("ERROR, IMaCh doesn't treat fixed quantitative covariate with missing values V%d=., individual %d will be skipped.\n",Tvar[k],i); + fprintf(ficlog,"ERROR, currently IMaCh doesn't treat covariate with missing values V%d=., individual %d will be skipped.\n",Tvar[k],i); + fflush(ficlog); + exit(1); + } + } + } + } /* end of loop on model-covariate k. nbcode[Tvark][1]=-1, nbcode[Tvark][1]=0 and nbcode[Tvark][2]=1 sets the value of covariate k*/ for (k=-1; k< maxncov; k++) Ndum[k]=0; /* Look at fixed dummy (single or product) covariates to check empty modalities */ @@ -5421,7 +5946,7 @@ void concatwav(int wav[], int **dh, int } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */ /* ij--; */ /* cptcoveff=ij; /\*Number of total covariates*\/ */ - *cptcov=ij; /*Number of total real effective covariates: effective + *cptcov=ij; /* cptcov= Number of total real effective covariates: effective (used as cptcoveff in other functions) * because they can be excluded from the model and real * if in the model but excluded because missing values, but how to get k from ij?*/ for(j=ij+1; j<= cptcovt; j++){ @@ -5442,6 +5967,8 @@ void concatwav(int wav[], int **dh, int { /* Health expectancies, no variances */ + /* cij is the combination in the list of combination of dummy covariates */ + /* strstart is a string of time at start of computing */ int i, j, nhstepm, hstepm, h, nstepm; int nhstepma, nstepma; /* Decreasing with age */ double age, agelim, hf; @@ -5510,7 +6037,7 @@ void concatwav(int wav[], int **dh, int /* If stepm=6 months */ /* Computed by stepm unit matrices, product of hstepma matrices, stored in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */ - + /* printf("HELLO evsij Entering hpxij age=%d cij=%d hstepm=%d x[1]=%f nres=%d\n",(int) age, cij, hstepm, x[1], nres); */ hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij, nres); hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */ @@ -5699,7 +6226,9 @@ void concatwav(int wav[], int **dh, int varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf; } } - + /* if((int)age ==50){ */ + /* printf(" age=%d cij=%d nres=%d varhe[%d][%d]=%f ",(int)age, cij, nres, 1,2,varhe[1][2]); */ + /* } */ /* Computing expectancies */ hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij,nres); for(i=1; i<=nlstate;i++) @@ -5760,22 +6289,24 @@ void concatwav(int wav[], int **dh, int /************ Variance ******************/ 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 *ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[], int nres) { - /* Variance of health expectancies */ - /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/ - /* double **newm;*/ - /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/ + /** Variance of health expectancies + * double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl); + * double **newm; + * int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav) + */ /* int movingaverage(); */ double **dnewm,**doldm; double **dnewmp,**doldmp; int i, j, nhstepm, hstepm, h, nstepm ; + int first=0; int k; double *xp; - double **gp, **gm; /* for var eij */ - double ***gradg, ***trgradg; /*for var eij */ - double **gradgp, **trgradgp; /* for var p point j */ - double *gpp, *gmp; /* for var p point j */ - double **varppt; /* for var p point j nlstate to nlstate+ndeath */ + double **gp, **gm; /**< for var eij */ + double ***gradg, ***trgradg; /**< for var eij */ + double **gradgp, **trgradgp; /**< for var p point j */ + double *gpp, *gmp; /**< for var p point j */ + double **varppt; /**< for var p point j nlstate to nlstate+ndeath */ double ***p3mat; double age,agelim, hf; /* double ***mobaverage; */ @@ -5820,7 +6351,7 @@ void concatwav(int wav[], int **dh, int fprintf(ficresprobmorprev," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); } for(j=1;j<=cptcoveff;j++) - fprintf(ficresprobmorprev,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(ij,j)]); + fprintf(ficresprobmorprev,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(ij,Tvaraff[j])]); fprintf(ficresprobmorprev,"\n"); fprintf(ficresprobmorprev,"# Age cov=%-d",ij); @@ -5836,7 +6367,7 @@ void concatwav(int wav[], int **dh, int /* fprintf(fichtm, "#Local time at start: %s", strstart);*/ fprintf(fichtm,"\n

  • Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)

    • \n"); fprintf(fichtm,"\n
    %s
    \n",digitp); - /* } */ + varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); pstamp(ficresvij); fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are "); @@ -5891,9 +6422,12 @@ void concatwav(int wav[], int **dh, int for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/ xp[i] = x[i] + (i==theta ?delti[theta]:0); } - + /**< Computes the prevalence limit with parameter theta shifted of delta up to ftolpl precision and + * returns into prlim . + */ prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres); - + + /* If popbased = 1 we use crossection prevalences. Previous step is useless but prlim is created */ if (popbased==1) { if(mobilav ==0){ for(i=1; i<=nlstate;i++) @@ -5903,27 +6437,32 @@ void concatwav(int wav[], int **dh, int prlim[i][i]=mobaverage[(int)age][i][ij]; } } - - hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres); /* Returns p3mat[i][j][h] for h=1 to nhstepm */ + /**< Computes the shifted transition matrix \f$ {}{h}_p^{ij}x\f$ at horizon h. + */ + hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres); /* Returns p3mat[i][j][h] for h=0 to nhstepm */ + /**< And for each alive state j, sums over i \f$ w^i_x {}{h}_p^{ij}x\f$, which are the probability + * at horizon h in state j including mortality. + */ for(j=1; j<= nlstate; j++){ for(h=0; h<=nhstepm; h++){ for(i=1, gp[h][j]=0.;i<=nlstate;i++) gp[h][j] += prlim[i][i]*p3mat[i][j][h]; } } - /* Next for computing probability of death (h=1 means + /* Next for computing shifted+ probability of death (h=1 means computed over hstepm matrices product = hstepm*stepm months) - as a weighted average of prlim. + as a weighted average of prlim(i) * p(i,j) p.3=w1*p13 + w2*p23 . */ for(j=nlstate+1;j<=nlstate+ndeath;j++){ for(i=1,gpp[j]=0.; i<= nlstate; i++) gpp[j] += prlim[i][i]*p3mat[i][j][1]; - } - /* end probability of death */ + } + + /* Again with minus shift */ for(i=1; i<=npar; i++) /* Computes gradient x - delta */ xp[i] = x[i] - (i==theta ?delti[theta]:0); - + prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres); if (popbased==1) { @@ -5952,19 +6491,23 @@ void concatwav(int wav[], int **dh, int for(i=1,gmp[j]=0.; i<= nlstate; i++) gmp[j] += prlim[i][i]*p3mat[i][j][1]; } - /* end probability of death */ - + /* end shifting computations */ + + /**< Computing gradient matrix at horizon h + */ for(j=1; j<= nlstate; j++) /* vareij */ for(h=0; h<=nhstepm; h++){ gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta]; } - - for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */ + /**< Gradient of overall mortality p.3 (or p.j) + */ + for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu mortality from j */ gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta]; } } /* End theta */ - + + /* We got the gradient matrix for each theta and state j */ trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */ for(h=0; h<=nhstepm; h++) /* veij */ @@ -5975,13 +6518,19 @@ void concatwav(int wav[], int **dh, int for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */ for(theta=1; theta <=npar; theta++) trgradgp[j][theta]=gradgp[theta][j]; - + /**< as well as its transposed matrix + */ hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */ for(i=1;i<=nlstate;i++) for(j=1;j<=nlstate;j++) vareij[i][j][(int)age] =0.; - + + /* Computing trgradg by matcov by gradg at age and summing over h + * and k (nhstepm) formula 15 of article + * Lievre-Brouard-Heathcote + */ + for(h=0;h<=nhstepm;h++){ for(k=0;k<=nhstepm;k++){ matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov); @@ -5992,7 +6541,11 @@ void concatwav(int wav[], int **dh, int } } - /* pptj */ + /* pptj is p.3 or p.j = trgradgp by cov by gradgp, variance of + * p.j overall mortality formula 49 but computed directly because + * we compute the grad (wix pijx) instead of grad (pijx),even if + * wix is independent of theta. + */ matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov); matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp); for(j=nlstate+1;j<=nlstate+ndeath;j++) @@ -6095,7 +6648,7 @@ void concatwav(int wav[], int **dh, int int theta; pstamp(ficresvpl); - fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n"); + fprintf(ficresvpl,"# Standard deviation of period (forward stable) prevalences \n"); fprintf(ficresvpl,"# Age "); if(nresult >=1) fprintf(ficresvpl," Result# "); @@ -6124,20 +6677,20 @@ void concatwav(int wav[], int **dh, int for(i=1; i<=npar; i++){ /* Computes gradient */ xp[i] = x[i] + (i==theta ?delti[theta]:0); } - if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) - prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); - else - prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); + /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) */ + /* prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */ + /* else */ + prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); for(i=1;i<=nlstate;i++){ gp[i] = prlim[i][i]; mgp[theta][i] = prlim[i][i]; } for(i=1; i<=npar; i++) /* Computes gradient */ xp[i] = x[i] - (i==theta ?delti[theta]:0); - if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) - prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); - else - prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); + /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) */ + /* prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */ + /* else */ + prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); for(i=1;i<=nlstate;i++){ gm[i] = prlim[i][i]; mgm[theta][i] = prlim[i][i]; @@ -6186,8 +6739,11 @@ void concatwav(int wav[], int **dh, int fprintf(ficresvpl,"%.0f ",age ); if(nresult >=1) fprintf(ficresvpl,"%d ",nres ); - for(i=1; i<=nlstate;i++) + for(i=1; i<=nlstate;i++){ fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age])); + /* for(j=1;j<=nlstate;j++) */ + /* fprintf(ficresvpl," %d %.5f ",j,prlim[j][i]); */ + } fprintf(ficresvpl,"\n"); free_vector(gp,1,nlstate); free_vector(gm,1,nlstate); @@ -6335,6 +6891,7 @@ void varprob(char optionfilefiname[], do int k2, l2, j1, z1; int k=0, l; int first=1, first1, first2; + int nres=0; /* New */ double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp; double **dnewm,**doldm; double *xp; @@ -6404,7 +6961,7 @@ void varprob(char optionfilefiname[], do fprintf(fichtm,"\n

  • Computing and drawing one step probabilities with their confidence intervals

    • \n"); fprintf(fichtm,"\n"); - fprintf(fichtm,"\n

  • Matrix of variance-covariance of one-step probabilities (drawings)

    this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back. %s
    • \n",optionfilehtmcov,optionfilehtmcov); + fprintf(fichtm,"\n

  • Matrix of variance-covariance of one-step probabilities (drawings)

    this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back. File %s
    • \n",optionfilehtmcov,optionfilehtmcov); fprintf(fichtmcov,"Current page is file %s
    \n\n

    Matrix of variance-covariance of pairs of step probabilities

    \n",optionfilehtmcov, optionfilehtmcov); fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (pij, pkl) are estimated \ and drawn. It helps understanding how is the covariance between two incidences.\ @@ -6423,25 +6980,28 @@ To be simple, these graphs help to under if (cptcovn<1) {tj=1;ncodemax[1]=1;} j1=0; for(j1=1; j1<=tj;j1++){ /* For each valid combination of covariates or only once*/ + for(nres=1;nres <=1; nres++){ /* For each resultline */ + /* for(nres=1;nres <=nresult; nres++){ /\* For each resultline *\/ */ if (cptcovn>0) { fprintf(ficresprob, "\n#********** Variable "); - for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,Tvaraff[z1])]); fprintf(ficresprob, "**********\n#\n"); fprintf(ficresprobcov, "\n#********** Variable "); - for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,Tvaraff[z1])]); fprintf(ficresprobcov, "**********\n#\n"); fprintf(ficgp, "\n#********** Variable "); - for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,Tvaraff[z1])]); fprintf(ficgp, "**********\n#\n"); fprintf(fichtmcov, "\n
    ********** Variable "); - for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + /* for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); */ + for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtmcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,Tvaraff[z1])]); fprintf(fichtmcov, "**********\n
    "); fprintf(ficresprobcor, "\n#********** Variable "); - for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,Tvaraff[z1])]); fprintf(ficresprobcor, "**********\n#"); if(invalidvarcomb[j1]){ fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1); @@ -6457,8 +7017,11 @@ To be simple, these graphs help to under cov[2]=age; if(nagesqr==1) cov[3]= age*age; - for (k=1; k<=cptcovn;k++) { - cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)]; + /* for (k=1; k<=cptcovn;k++) { */ + /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)]; */ + for (k=1; k<=nsd;k++) { /* For single dummy covariates only */ + /* Here comes the value of the covariate 'j1' after renumbering k with single dummy covariates */ + cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(j1,TvarsD[k])]; /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4 * 1 1 1 1 1 * 2 2 1 1 1 @@ -6466,12 +7029,42 @@ To be simple, these graphs help to under */ /* nbcode[1][1]=0 nbcode[1][2]=1;*/ } - /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */ - for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; - for (k=1; k<=cptcovprod;k++) - cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; - - + /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1, Tage[1]=2 */ + /* ) p nbcode[Tvar[Tage[k]]][(1 & (ij-1) >> (k-1))+1] */ + /*for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */ + for (k=1; k<=cptcovage;k++){ /* For product with age */ + if(Dummy[Tage[k]]==2){ /* dummy with age */ + cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(j1,Tvar[Tage[k]])]*cov[2]; + /* cov[++k1]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */ + } else if(Dummy[Tage[k]]==3){ /* quantitative with age */ + printf("Internal IMaCh error, don't know which value for quantitative covariate with age, Tage[k]%d, k=%d, Tvar[Tage[k]]=V%d, age=%d\n",Tage[k],k ,Tvar[Tage[k]], (int)cov[2]); + exit(1); + /* cov[2+nagesqr+Tage[k]]=meanq[k]/idq[k]*cov[2];/\* Using the mean of quantitative variable Tvar[Tage[k]] /\* Tqresult[nres][k]; *\/ */ + /* cov[++k1]=Tqresult[nres][k]; */ + } + /* cov[2+Tage[k]+nagesqr]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */ + } + for (k=1; k<=cptcovprod;k++){/* For product without age */ + if(Dummy[Tvard[k][1]]==0){ + if(Dummy[Tvard[k][2]]==0){ + cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(j1,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(j1,Tvard[k][2])]; + /* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */ + }else{ /* Should we use the mean of the quantitative variables? */ + cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(j1,Tvard[k][1])] * Tqresult[nres][k]; + /* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k]; */ + } + }else{ + if(Dummy[Tvard[k][2]]==0){ + cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(j1,Tvard[k][2])] * Tqinvresult[nres][Tvard[k][1]]; + /* cov[++k1]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]]; */ + }else{ + cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]]; + /* cov[++k1]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]]; */ + } + } + /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; */ + } +/* For each age and combination of dummy covariates we slightly move the parameters of delti in order to get the gradient*/ for(theta=1; theta <=npar; theta++){ for(i=1; i<=npar; i++) xp[i] = x[i] + (i==theta ?delti[theta]:(double)0); @@ -6601,7 +7194,12 @@ To be simple, these graphs help to under } /* Eigen vectors */ - v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12)); + if(1+(v1-lc1)*(v1-lc1)/cv12/cv12 <1.e-5){ + printf(" Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12); + fprintf(ficlog," Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12); + v11=(1./sqrt(fabs(1+(v1-lc1)*(v1-lc1)/cv12/cv12))); + }else + v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12)); /*v21=sqrt(1.-v11*v11); *//* error */ v21=(lc1-v1)/cv12*v11; v12=-v21; @@ -6632,8 +7230,8 @@ To be simple, these graphs help to under fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2); fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2); 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", \ - mu1,std,v11,sqrt(lc1),v12,sqrt(fabs(lc2)), \ - mu2,std,v21,sqrt(lc1),v22,sqrt(fabs(lc2))); /* For gnuplot only */ + mu1,std,v11,sqrt(fabs(lc1)),v12,sqrt(fabs(lc2)), \ + mu2,std,v21,sqrt(fabs(lc1)),v22,sqrt(fabs(lc2))); /* For gnuplot only */ }else{ first=0; fprintf(fichtmcov," %d (%.3f),",(int) age, c12); @@ -6651,6 +7249,7 @@ To be simple, these graphs help to under } /* k12 */ } /*l1 */ }/* k1 */ + } /* loop on nres */ } /* loop on combination of covariates j1 */ free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage); free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage); @@ -6669,16 +7268,16 @@ To be simple, these graphs help to under void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \ int lastpass, int stepm, int weightopt, char model[],\ int imx,int jmin, int jmax, double jmeanint,char rfileres[],\ - int popforecast, int mobilav, int prevfcast, int mobilavproj, int backcast, int estepm , \ - double jprev1, double mprev1,double anprev1, double dateprev1, double dateproj1, double dateback1, \ - double jprev2, double mprev2,double anprev2, double dateprev2, double dateproj2, double dateback2){ + int popforecast, int mobilav, int prevfcast, int mobilavproj, int prevbcast, int estepm , \ + double jprev1, double mprev1,double anprev1, double dateprev1, double dateprojd, double dateback1, \ + double jprev2, double mprev2,double anprev2, double dateprev2, double dateprojf, double dateback2){ int jj1, k1, i1, cpt, k4, nres; - + /* In fact some results are already printed in fichtm which is open */ fprintf(fichtm,""); - fprintf(fichtm,"
    • model=1+age+%s\n \ -
    ", model); +/* fprintf(fichtm,"
    • model=1+age+%s\n \ */ +/*
    ", model); */ fprintf(fichtm,"

    • Result files (first order: no variance)

      \n"); fprintf(fichtm,"
    • - Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): %s (html file)
      \n", jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm")); @@ -6692,10 +7291,10 @@ void printinghtml(char fileresu[], char - Estimated back transition probabilities over %d (stepm) months: %s
      \n ", stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_")); fprintf(fichtm,"\ - - Period (stable) prevalence in each health state: %s
      \n", + - Period (forward) prevalence in each health state: %s
      \n", subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_")); fprintf(fichtm,"\ - - Period (stable) back prevalence in each health state: %s
      \n", + - Backward prevalence in each health state: %s
      \n", subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_")); fprintf(fichtm,"\ - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \ @@ -6711,7 +7310,7 @@ void printinghtml(char fileresu[], char m=pow(2,cptcoveff); if (cptcovn < 1) {m=1;ncodemax[1]=1;} - fprintf(fichtm," \n
      • Graphs

        • "); + fprintf(fichtm," \n

        • Graphs (first order)

          • "); jj1=0; @@ -6746,7 +7345,7 @@ void printinghtml(char fileresu[], char fprintf(fichtm,""); } /* cptcovn >0 */ } - fprintf(fichtm," \n

        "); + fprintf(fichtm," \n
      "); jj1=0; @@ -6780,7 +7379,7 @@ void printinghtml(char fileresu[], char } /* if(nqfveff+nqtveff 0) */ /* Test to be done */ - fprintf(fichtm," ************\n
      "); + fprintf(fichtm," (model=%s) ************\n
      ",model); if(invalidvarcomb[k1]){ fprintf(fichtm,"\n

      Combination (%d) ignored because no cases

      \n",k1); printf("\nCombination (%d) ignored because no cases \n",k1); @@ -6801,48 +7400,56 @@ divided by h: hPij ",stepm,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres); /* Survival functions (period) in state j */ for(cpt=1; cpt<=nlstate;cpt++){ - fprintf(fichtm,"
      \n- Survival functions in state %d. Or probability to survive in state %d being in state (1 to %d) at different ages. %s_%d-%d-%d.svg
      \ -", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres); + fprintf(fichtm,"
      \n- Survival functions in state %d. And probability to be observed in state %d being in state (1 to %d) at different ages. %s_%d-%d-%d.svg
      ", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres); + fprintf(fichtm," (data from text file %s.txt)\n
      ",subdirf2(optionfilefiname,"PIJ_"),subdirf2(optionfilefiname,"PIJ_")); + fprintf(fichtm,"",subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres); } /* State specific survival functions (period) */ for(cpt=1; cpt<=nlstate;cpt++){ - fprintf(fichtm,"
      \n- Survival functions from state %d in each live state and total.\ - Or probability to survive in various states (1 to %d) being in state %d at different ages. \ - %s_%d%d-%d.svg
      ", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres); + fprintf(fichtm,"
      \n- Survival functions in state %d and in any other live state (total).\ + And probability to be observed in various states (up to %d) being in state %d at different ages. \ + %s_%d-%d-%d.svg
      ", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres); + fprintf(fichtm," (data from text file %s.txt)\n
      ",subdirf2(optionfilefiname,"PIJ_"),subdirf2(optionfilefiname,"PIJ_")); + fprintf(fichtm,"",subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres); } - /* Period (stable) prevalence in each health state */ + /* Period (forward stable) prevalence in each health state */ for(cpt=1; cpt<=nlstate;cpt++){ - fprintf(fichtm,"
      \n- Convergence to period (stable) prevalence in state %d. Or probability for a person being in state (1 to %d) at different ages, to be in state %d some years after. %s_%d-%d-%d.svg
      \ -", cpt, nlstate, cpt, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres); + fprintf(fichtm,"
      \n- Convergence to period (stable) prevalence in state %d. Or probability for a person being in state (1 to %d) at different ages, to be in state %d some years after. %s_%d-%d-%d.svg
      ", cpt, nlstate, cpt, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres); + fprintf(fichtm," (data from text file %s.txt)\n
      ",subdirf2(optionfilefiname,"P_"),subdirf2(optionfilefiname,"P_")); + fprintf(fichtm,"" ,subdirf2(optionfilefiname,"P_"),cpt,k1,nres); } - if(backcast==1){ - /* Period (stable) back prevalence in each health state */ + if(prevbcast==1){ + /* Backward prevalence in each health state */ for(cpt=1; cpt<=nlstate;cpt++){ fprintf(fichtm,"
      \n- Convergence to mixed (stable) back prevalence in state %d. Or probability for a person to be in state %d at a younger age, knowing that she/he was in state (1 to %d) at different older ages. %s_%d-%d-%d.svg
      \ ", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres); } } if(prevfcast==1){ - /* Projection of prevalence up to period (stable) prevalence in each health state */ + /* Projection of prevalence up to period (forward stable) prevalence in each health state */ for(cpt=1; cpt<=nlstate;cpt++){ - fprintf(fichtm,"
      \n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), from year %.1f up to year %.1f tending to period (stable) prevalence in state %d. Or probability to be in state %d being in an observed weighted state (from 1 to %d). %s_%d-%d-%d.svg
      \ -", dateprev1, dateprev2, mobilavproj, dateproj1, dateproj2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres); + fprintf(fichtm,"
      \n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), from year %.1f up to year %.1f tending to period (stable) forward prevalence in state %d. Or probability to be in state %d being in an observed weighted state (from 1 to %d). %s_%d-%d-%d.svg", dateprev1, dateprev2, mobilavproj, dateprojd, dateprojf, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres); + fprintf(fichtm," (data from text file %s.txt)\n
      ",subdirf2(optionfilefiname,"F_"),subdirf2(optionfilefiname,"F_")); + fprintf(fichtm,"", + subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres); } } - if(backcast==1){ + if(prevbcast==1){ /* Back projection of prevalence up to stable (mixed) back-prevalence in each health state */ for(cpt=1; cpt<=nlstate;cpt++){ fprintf(fichtm,"
      \n- Back projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), \ from year %.1f up to year %.1f (probably close to stable [mixed] back prevalence in state %d (randomness in cross-sectional prevalence is not taken into \ account but can visually be appreciated). Or probability to have been in an state %d, knowing that the person was in either state (1 or %d) \ -with weights corresponding to observed prevalence at different ages. %s_%d-%d-%d.svg
      \ - ", dateprev1, dateprev2, mobilavproj, dateback1, dateback2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres); +with weights corresponding to observed prevalence at different ages. %s_%d-%d-%d.svg", dateprev1, dateprev2, mobilavproj, dateback1, dateback2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres); + fprintf(fichtm," (data from text file %s.txt)\n
      ",subdirf2(optionfilefiname,"FB_"),subdirf2(optionfilefiname,"FB_")); + fprintf(fichtm," ", subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres); } } for(cpt=1; cpt<=nlstate;cpt++) { - fprintf(fichtm,"\n
      - Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): %s_%d-%d-%d.svg
      \ -",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres); + fprintf(fichtm,"\n
      - Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): %s_%d-%d-%d.svg",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres); + fprintf(fichtm," (data from text file %s.txt)\n
      ",subdirf2(optionfilefiname,"E_"),subdirf2(optionfilefiname,"E_")); + fprintf(fichtm,"", subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres ); } /* } /\* end i1 *\/ */ }/* End k1 */ @@ -6878,13 +7485,13 @@ See page 'Matrix of variance-covariance %s
      \n
      • ", estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_")); fprintf(fichtm,"\ - - 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): %s
      \n", + - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), eij are weighted by the forward (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): %s
      \n", estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_")); fprintf(fichtm,"\ - Total life expectancy and total health expectancies to be spent in each health state e.j with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): %s
      \n", estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_")); fprintf(fichtm,"\ - - Standard deviation of period (stable) prevalences: %s
      \n",\ + - Standard deviation of forward (period) prevalences: %s
      \n",\ subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_")); /* if(popforecast==1) fprintf(fichtm,"\n */ @@ -6894,11 +7501,47 @@ See page 'Matrix of variance-covariance /* else */ /* fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)

      \n",popforecast, stepm, model); */ fflush(fichtm); - fprintf(fichtm,"
      • Graphs

        • "); m=pow(2,cptcoveff); if (cptcovn < 1) {m=1;ncodemax[1]=1;} + fprintf(fichtm,"

        • Graphs (second order)

          • "); + + jj1=0; + + fprintf(fichtm," \n

          "); + jj1=0; for(nres=1; nres <= nresult; nres++){ /* For each resultline */ @@ -6908,15 +7551,26 @@ See page 'Matrix of variance-covariance /* for(i1=1; i1<=ncodemax[k1];i1++){ */ jj1++; if (cptcovn > 0) { + fprintf(fichtm,"\n

          "); + fprintf(fichtm,"

          ************ Results for covariates"); - for (cpt=1; cpt<=cptcoveff;cpt++) /**< cptcoveff number of variables */ + for (cpt=1; cpt<=cptcoveff;cpt++){ /**< cptcoveff number of variables */ fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]); + printf(" V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);fflush(stdout); /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */ + } for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */ fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); } - fprintf(fichtm," ************\n
          "); + fprintf(fichtm," (model=%s) ************\n
          ",model); if(invalidvarcomb[k1]){ fprintf(fichtm,"\n

          Combination (%d) ignored because no cases

          \n",k1); @@ -6925,15 +7579,17 @@ See page 'Matrix of variance-covariance } for(cpt=1; cpt<=nlstate;cpt++) { fprintf(fichtm,"\n
          - Observed (cross-sectional with mov_average=%d) and period (incidence based) \ -prevalence (with 95%% confidence interval) in state (%d):           %s_%d-%d-%d.svg\n
          \ -",mobilav,cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres); +prevalence (with 95%% confidence interval) in state (%d): %s_%d-%d-%d.svg",mobilav,cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres); + fprintf(fichtm," (data from text file %s)\n
          ",subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_")); + fprintf(fichtm,"",subdirf2(optionfilefiname,"V_"), cpt,k1,nres); } fprintf(fichtm,"\n
          - Total life expectancy by age and \ -health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \ +health expectancies in each live states (1 to %d). If popbased=1 the smooth (due to the model) \ true period expectancies (those weighted with period prevalences are also\ drawn in addition to the population based expectancies computed using\ - observed and cahotic prevalences: %s_%d-%d.svg\n
          \ -",subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres); + observed and cahotic prevalences: %s_%d-%d.svg",nlstate, subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres); + fprintf(fichtm," (data from text file %s.txt) \n
          ",subdirf2(optionfilefiname,"T_"),subdirf2(optionfilefiname,"T_")); + fprintf(fichtm,"",subdirf2(optionfilefiname,"E_"),k1,nres); /* } /\* end i1 *\/ */ }/* End k1 */ }/* End nres */ @@ -6942,7 +7598,7 @@ true period expectancies (those weighted } /******************* Gnuplot file **************/ -void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double bage, double fage , int prevfcast, int backcast, char pathc[], double p[], int offyear, int offbyear){ +void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double bage, double fage , int prevfcast, int prevbcast, char pathc[], double p[], int offyear, int offbyear){ char dirfileres[132],optfileres[132]; char gplotcondition[132], gplotlabel[132]; @@ -7020,7 +7676,7 @@ void printinggnuplot(char fileresu[], ch continue; /* We are interested in selected combination by the resultline */ /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */ - fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); + fprintf(ficgp,"\n# 1st: Forward (stable period) prevalence with CI: 'VPL_' files and live state =%d ", cpt); strcpy(gplotlabel,"("); for (k=1; k<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */ lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */ @@ -7049,7 +7705,8 @@ void printinggnuplot(char fileresu[], ch fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres); fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres); - fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); + /* fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); */ + fprintf(ficgp,"set title \"Alive state %d %s model=%s\" font \"Helvetica,12\"\n",cpt,gplotlabel,model); fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres); /* fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres); */ /* k1-1 error should be nres-1*/ @@ -7057,7 +7714,7 @@ void printinggnuplot(char fileresu[], ch if (i==cpt) fprintf(ficgp," %%lf (%%lf)"); else fprintf(ficgp," %%*lf (%%*lf)"); } - fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres); + fprintf(ficgp,"\" t\"Forward prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres); for (i=1; i<= nlstate ; i ++) { if (i==cpt) fprintf(ficgp," %%lf (%%lf)"); else fprintf(ficgp," %%*lf (%%*lf)"); @@ -7095,7 +7752,7 @@ void printinggnuplot(char fileresu[], ch } /* end covariate */ } /* end if no covariate */ - if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */ + if(prevbcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */ /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */ fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */ if(cptcoveff ==0){ @@ -7122,7 +7779,7 @@ void printinggnuplot(char fileresu[], ch } } /* end covariate */ } /* end if no covariate */ - if(backcast == 1){ + if(prevbcast == 1){ fprintf(ficgp,", \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres); /* k1-1 error should be nres-1*/ for (i=1; i<= nlstate ; i ++) { @@ -7134,15 +7791,16 @@ void printinggnuplot(char fileresu[], ch if (i==cpt) fprintf(ficgp," %%lf (%%lf)"); else fprintf(ficgp," %%*lf (%%*lf)"); } - fprintf(ficgp,"\" t\"95%% CI\" w l lt 5,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres); + fprintf(ficgp,"\" t\"95%% CI\" w l lt 4,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres); for (i=1; i<= nlstate ; i ++) { if (i==cpt) fprintf(ficgp," %%lf (%%lf)"); else fprintf(ficgp," %%*lf (%%*lf)"); } fprintf(ficgp,"\" t\"\" w l lt 4"); } /* end if backprojcast */ - } /* end if backcast */ - fprintf(ficgp,"\nset out ;unset label;\n"); + } /* end if prevbcast */ + /* fprintf(ficgp,"\nset out ;unset label;\n"); */ + fprintf(ficgp,"\nset out ;unset title;\n"); } /* nres */ } /* k1 */ } /* cpt */ @@ -7385,7 +8043,7 @@ set ter svg size 640, 480\nunset log y\n continue; for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */ strcpy(gplotlabel,"("); - fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt); + fprintf(ficgp,"\n#\n#\n#CV preval stable (forward): 'pij' files, covariatecombination#=%d state=%d",k1, cpt); for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */ lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */ /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ @@ -7428,15 +8086,15 @@ set ter svg size 640, 480\nunset log y\n /* 7eme */ - if(backcast == 1){ - /* CV back preval stable (period) for each covariate */ + if(prevbcast == 1){ + /* CV backward prevalence for each covariate */ for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */ for(nres=1; nres <= nresult; nres++){ /* For each resultline */ if(m != 1 && TKresult[nres]!= k1) continue; for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life origin state */ strcpy(gplotlabel,"("); - fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pijb' files, covariatecombination#=%d state=%d",k1, cpt); + fprintf(ficgp,"\n#\n#\n#CV Backward stable prevalence: 'pijb' files, covariatecombination#=%d state=%d",k1, cpt); for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */ lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */ /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ @@ -7469,8 +8127,8 @@ set ter svg size 640, 480\nunset log y\n fprintf(ficgp,", '' "); /* l=(nlstate+ndeath)*(i-1)+1; */ l=(nlstate+ndeath)*(cpt-1)+1; /* fixed for i; cpt=1 1, cpt=2 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */ - /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */ - /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */ + /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */ + /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */ fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+i-1); /* To be verified */ /* for (j=2; j<= nlstate ; j ++) */ /* fprintf(ficgp,"+$%d",k+l+j-1); */ @@ -7480,11 +8138,11 @@ set ter svg size 640, 480\nunset log y\n fprintf(ficgp,"\nset out; unset label;\n"); } /* end cpt state*/ } /* end covariate */ - } /* End if backcast */ + } /* End if prevbcast */ /* 8eme */ if(prevfcast==1){ - /* Projection from cross-sectional to stable (period) for each covariate */ + /* Projection from cross-sectional to forward stable (period) prevalence for each covariate */ for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */ for(nres=1; nres <= nresult; nres++){ /* For each resultline */ @@ -7492,7 +8150,7 @@ set ter svg size 640, 480\nunset log y\n continue; for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */ strcpy(gplotlabel,"("); - fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt); + fprintf(ficgp,"\n#\n#\n#Projection of prevalence to forward stable prevalence (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt); for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */ lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */ /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ @@ -7596,7 +8254,7 @@ set ter svg size 640, 480\nunset log y\n } /* end covariate */ } /* End if prevfcast */ - if(backcast==1){ + if(prevbcast==1){ /* Back projection from cross-sectional to stable (mixed) for each covariate */ for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */ @@ -7709,7 +8367,7 @@ set ter svg size 640, 480\nunset log y\n fprintf(ficgp,"\nset out; unset label;\n"); } /* end cpt state*/ } /* end covariate */ - } /* End if backcast */ + } /* End if prevbcast */ /* 9eme writing MLE parameters */ @@ -7756,7 +8414,7 @@ set ter svg size 640, 480\nunset log y\n continue; fprintf(ficgp,"\n\n# Combination of dummy k1=%d which is ",k1); strcpy(gplotlabel,"("); - sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1); + /*sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);*/ for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */ lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */ /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ @@ -7773,7 +8431,9 @@ set ter svg size 640, 480\nunset log y\n strcpy(gplotlabel+strlen(gplotlabel),")"); fprintf(ficgp,"\n#\n"); fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),k1,ng,nres); - fprintf(ficgp,"\nset label \"%s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel); + fprintf(ficgp,"\nset key outside "); + /* fprintf(ficgp,"\nset label \"%s\" at graph 1.2,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel); */ + fprintf(ficgp,"\nset title \"%s\" font \"Helvetica,12\"\n",gplotlabel); fprintf(ficgp,"\nset ter svg size 640, 480 "); if (ng==1){ fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */ @@ -7817,41 +8477,49 @@ set ter svg size 640, 480\nunset log y\n /* for(j=3; j <=ncovmodel-nagesqr; j++) { */ for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */ /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */ - if(cptcovage >0){ /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */ - if(j==Tage[ij]) { /* Product by age To be looked at!!*/ - if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */ - if(DummyV[j]==0){ - fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);; - }else{ /* quantitative */ - fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */ - /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */ + switch(Typevar[j]){ + case 1: + if(cptcovage >0){ /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */ + if(j==Tage[ij]) { /* Product by age To be looked at!!*//* Bug valgrind */ + if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */ + if(DummyV[j]==0){/* Bug valgrind */ + fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);; + }else{ /* quantitative */ + fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */ + /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */ + } + ij++; } - ij++; } - } - }else if(cptcovprod >0){ - if(j==Tprod[ijp]) { /* */ - /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */ - if(ijp <=cptcovprod) { /* Product */ - if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */ - if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */ - /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],nbcode[Tvard[ijp][2]][codtabm(k1,j)]); */ - fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]); - }else{ /* Vn is dummy and Vm is quanti */ - /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */ - fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]); - } - }else{ /* Vn*Vm Vn is quanti */ - if(DummyV[Tvard[ijp][2]]==0){ - fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]); - }else{ /* Both quanti */ - fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]); + } + break; + case 2: + if(cptcovprod >0){ + if(j==Tprod[ijp]) { /* */ + /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */ + if(ijp <=cptcovprod) { /* Product */ + if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */ + if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */ + /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],nbcode[Tvard[ijp][2]][codtabm(k1,j)]); */ + fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]); + }else{ /* Vn is dummy and Vm is quanti */ + /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */ + fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]); + } + }else{ /* Vn*Vm Vn is quanti */ + if(DummyV[Tvard[ijp][2]]==0){ + fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]); + }else{ /* Both quanti */ + fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]); + } } + ijp++; } - ijp++; - } - } /* end Tprod */ - } else{ /* simple covariate */ + } /* end Tprod */ + } + break; + case 0: + /* simple covariate */ /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\* Valgrind bug nbcode *\/ */ if(Dummy[j]==0){ fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /* */ @@ -7859,12 +8527,17 @@ set ter svg size 640, 480\nunset log y\n fprintf(ficgp,"+p%d*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* */ /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */ } - } /* end simple */ + /* end simple */ + break; + default: + break; + } /* end switch */ } /* end j */ - }else{ - i=i-ncovmodel; - if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */ - fprintf(ficgp," (1."); + }else{ /* k=k2 */ + if(ng !=1 ){ /* For logit formula of log p11 is more difficult to get */ + fprintf(ficgp," (1.");i=i-ncovmodel; + }else + i=i-ncovmodel; } if(ng != 1){ @@ -7877,28 +8550,89 @@ set ter svg size 640, 480\nunset log y\n fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(cpt-1)*ncovmodel,k3+(cpt-1)*ncovmodel+1,k3+(cpt-1)*ncovmodel+1+nagesqr); ij=1; - for(j=3; j <=ncovmodel-nagesqr; j++){ - if(cptcovage >0){ - if((j-2)==Tage[ij]) { /* Bug valgrind */ - if(ij <=cptcovage) { /* Bug valgrind */ - fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]); - /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */ - ij++; - } - } - }else - fprintf(ficgp,"+p%d*%d",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);/* Valgrind bug nbcode */ + ijp=1; + /* for(j=3; j <=ncovmodel-nagesqr; j++){ */ + for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */ + switch(Typevar[j]){ + case 1: + if(cptcovage >0){ + if(j==Tage[ij]) { /* Bug valgrind */ + if(ij <=cptcovage) { /* Bug valgrind */ + if(DummyV[j]==0){/* Bug valgrind */ + /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]); */ + /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j+nagesqr,nbcode[Tvar[j]][codtabm(k1,j)]); */ + fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvar[j]]); + /* fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);; */ + /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */ + }else{ /* quantitative */ + /* fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /\* Tqinvresult in decoderesult *\/ */ + fprintf(ficgp,"+p%d*%f*x",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */ + /* fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /\* Tqinvresult in decoderesult *\/ */ + /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */ + } + ij++; + } + } + } + break; + case 2: + if(cptcovprod >0){ + if(j==Tprod[ijp]) { /* */ + /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */ + if(ijp <=cptcovprod) { /* Product */ + if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */ + if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */ + /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],nbcode[Tvard[ijp][2]][codtabm(k1,j)]); */ + fprintf(ficgp,"+p%d*%d*%d",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]); + /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]); */ + }else{ /* Vn is dummy and Vm is quanti */ + /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */ + fprintf(ficgp,"+p%d*%d*%f",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]); + /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]); */ + } + }else{ /* Vn*Vm Vn is quanti */ + if(DummyV[Tvard[ijp][2]]==0){ + fprintf(ficgp,"+p%d*%d*%f",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]); + /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]); */ + }else{ /* Both quanti */ + fprintf(ficgp,"+p%d*%f*%f",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]); + /* fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]); */ + } + } + ijp++; + } + } /* end Tprod */ + } /* end if */ + break; + case 0: + /* simple covariate */ + /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\* Valgrind bug nbcode *\/ */ + if(Dummy[j]==0){ + /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /\* *\/ */ + fprintf(ficgp,"+p%d*%d",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvar[j]]); /* */ + /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /\* *\/ */ + }else{ /* quantitative */ + fprintf(ficgp,"+p%d*%f",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tqinvresult[nres][Tvar[j]]); /* */ + /* fprintf(ficgp,"+p%d*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /\* *\/ */ + /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */ + } + /* end simple */ + /* fprintf(ficgp,"+p%d*%d",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);/\* Valgrind bug nbcode *\/ */ + break; + default: + break; + } /* end switch */ } fprintf(ficgp,")"); } fprintf(ficgp,")"); if(ng ==2) - fprintf(ficgp," t \"p%d%d\" ", k2,k); + fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"p%d%d\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k); else /* ng= 3 */ - fprintf(ficgp," t \"i%d%d\" ", k2,k); - }else{ /* end ng <> 1 */ + fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"i%d%d\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k); + }else{ /* end ng <> 1 */ if( k !=k2) /* logit p11 is hard to draw */ - fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k); + fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"logit(p%d%d)\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k); } if ((k+k2)!= (nlstate*2+ndeath) && ng != 1) fprintf(ficgp,","); @@ -7907,7 +8641,8 @@ set ter svg size 640, 480\nunset log y\n i=i+ncovmodel; } /* end k */ } /* end k2 */ - fprintf(ficgp,"\n set out; unset label;\n"); + /* fprintf(ficgp,"\n set out; unset label;set key default;\n"); */ + fprintf(ficgp,"\n set out; unset title;set key default;\n"); } /* end k1 */ } /* end ng */ /* avoid: */ @@ -7923,6 +8658,7 @@ set ter svg size 640, 480\nunset log y\n int modcovmax =1; int mobilavrange, mob; int iage=0; + int firstA1=0, firstA2=0; double sum=0., sumr=0.; double age; @@ -7931,8 +8667,8 @@ set ter svg size 640, 480\nunset log y\n double *agemingoodr, *agemaxgoodr; - /* modcovmax=2*cptcoveff;/\* Max number of modalities. We suppose */ - /* a covariate has 2 modalities, should be equal to ncovcombmax *\/ */ + /* modcovmax=2*cptcoveff; Max number of modalities. We suppose */ + /* a covariate has 2 modalities, should be equal to ncovcombmax */ sumnewp = vector(1,ncovcombmax); sumnewm = vector(1,ncovcombmax); @@ -8020,6 +8756,7 @@ set ter svg size 640, 480\nunset log y\n } /* age */ /* Thus we have agemingood and agemaxgood as well as goodr for raw (preobs) */ /* but they will change */ + firstA1=0;firstA2=0; for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, filling up to the youngest */ sumnewm[cptcod]=0.; sumnewmr[cptcod]=0.; @@ -8052,11 +8789,19 @@ set ter svg size 640, 480\nunset log y\n sumr+=probs[(int)age][i][cptcod]; } if(fabs(sum - 1.) > 1.e-3) { /* bad */ - printf("Moving average A1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage); + if(!firstA1){ + firstA1=1; + printf("Moving average A1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you increase bage=%d. Others in log file...\n",cptcod,sumr, (int)age, (int)bage); + } + fprintf(ficlog,"Moving average A1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage); } /* end bad */ /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */ if(fabs(sumr - 1.) > 1.e-3) { /* bad */ - printf("Moving average A2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage); + if(!firstA2){ + firstA2=1; + printf("Moving average A2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase bage=%d. Others in log file...\n",cptcod,sumr, (int)age, (int)bage); + } + fprintf(ficlog,"Moving average A2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage); } /* end bad */ }/* age */ @@ -8144,16 +8889,21 @@ set ter svg size 640, 480\nunset log y\n }/* End movingaverage */ + /************** Forecasting ******************/ - void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double ***prev, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){ - /* proj1, year, month, day of starting projection +/* void prevforecast(char fileres[], double dateintmean, double anprojd, double mprojd, double jprojd, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double ***prev, double bage, double fage, int firstpass, int lastpass, double anprojf, double p[], int cptcoveff)*/ +void prevforecast(char fileres[], double dateintmean, double dateprojd, double dateprojf, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double ***prev, double bage, double fage, int firstpass, int lastpass, double p[], int cptcoveff){ + /* dateintemean, mean date of interviews + dateprojd, year, month, day of starting projection + dateprojf date of end of projection;year of end of projection (same day and month as proj1). agemin, agemax range of age dateprev1 dateprev2 range of dates during which prevalence is computed - anproj2 year of en of projection (same day and month as proj1). */ + /* double anprojd, mprojd, jprojd; */ + /* double anprojf, mprojf, jprojf; */ int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0; double agec; /* generic age */ - double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; + double agelim, ppij, yp,yp1,yp2; double *popeffectif,*popcount; double ***p3mat; /* double ***mobaverage; */ @@ -8190,22 +8940,27 @@ set ter svg size 640, 480\nunset log y\n if(estepm > stepm){ /* Yes every two year */ stepsize=2; } + hstepm=hstepm/stepm; + + + /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp and */ + /* fractional in yp1 *\/ */ + /* aintmean=yp; */ + /* yp2=modf((yp1*12),&yp); */ + /* mintmean=yp; */ + /* yp1=modf((yp2*30.5),&yp); */ + /* jintmean=yp; */ + /* if(jintmean==0) jintmean=1; */ + /* if(mintmean==0) mintmean=1; */ - hstepm=hstepm/stepm; - yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and - fractional in yp1 */ - anprojmean=yp; - yp2=modf((yp1*12),&yp); - mprojmean=yp; - yp1=modf((yp2*30.5),&yp); - jprojmean=yp; - if(jprojmean==0) jprojmean=1; - if(mprojmean==0) jprojmean=1; + /* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); */ + /* date2dmy(dateprojd,&jprojd, &mprojd, &anprojd); */ + /* date2dmy(dateprojf,&jprojf, &mprojf, &anprojf); */ i1=pow(2,cptcoveff); if (cptcovn < 1){i1=1;} - fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); + fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2); fprintf(ficresf,"#****** Routine prevforecast **\n"); @@ -8220,7 +8975,7 @@ set ter svg size 640, 480\nunset log y\n } fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#"); for(j=1;j<=cptcoveff;j++) { - fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); } for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */ fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); @@ -8231,9 +8986,9 @@ set ter svg size 640, 480\nunset log y\n fprintf(ficresf," p%d%d",i,j); fprintf(ficresf," wp.%d",j); } - for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { + for (yearp=0; yearp<=(anprojf-anprojd);yearp +=stepsize) { fprintf(ficresf,"\n"); - fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp); + fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jprojd,mprojd,anprojd+yearp); /* for (agec=fage; agec>=(ageminpar-1); agec--){ */ for (agec=fage; agec>=(bage); agec--){ nhstepm=(int) rint((agelim-agec)*YEARM/stepm); @@ -8250,17 +9005,17 @@ set ter svg size 640, 480\nunset log y\n } fprintf(ficresf,"\n"); for(j=1;j<=cptcoveff;j++) - fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); - fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm); + fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); + fprintf(ficresf,"%.f %.f ",anprojd+yearp,agec+h*hstepm/YEARM*stepm); for(j=1; j<=nlstate+ndeath;j++) { ppij=0.; for(i=1; i<=nlstate;i++) { - /* if (mobilav>=1) */ - ppij=ppij+p3mat[i][j][h]*prev[(int)agec][i][k]; - /* else { */ /* even if mobilav==-1 we use mobaverage */ - /* ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k]; */ - /* } */ + if (mobilav>=1) + ppij=ppij+p3mat[i][j][h]*prev[(int)agec][i][k]; + else { /* even if mobilav==-1 we use mobaverage, probs may not sums to 1 */ + ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k]; + } fprintf(ficresf," %.3f", p3mat[i][j][h]); } /* end i */ fprintf(ficresf," %.3f", ppij); @@ -8279,8 +9034,9 @@ set ter svg size 640, 480\nunset log y\n } /************** Back Forecasting ******************/ - void prevbackforecast(char fileres[], double ***prevacurrent, double anback1, double mback1, double jback1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anback2, double p[], int cptcoveff){ - /* back1, year, month, day of starting backection + /* void prevbackforecast(char fileres[], double ***prevacurrent, double anback1, double mback1, double jback1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anback2, double p[], int cptcoveff){ */ + void prevbackforecast(char fileres[], double ***prevacurrent, double dateintmean, double dateprojd, double dateprojf, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double p[], int cptcoveff){ + /* back1, year, month, day of starting backprojection agemin, agemax range of age dateprev1 dateprev2 range of dates during which prevalence is computed anback2 year of end of backprojection (same day and month as back1). @@ -8288,7 +9044,7 @@ set ter svg size 640, 480\nunset log y\n */ int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0; double agec; /* generic age */ - double agelim, ppij, ppi, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; + double agelim, ppij, ppi, yp,yp1,yp2; /* ,jintmean,mintmean,aintmean;*/ double *popeffectif,*popcount; double ***p3mat; /* double ***mobaverage; */ @@ -8331,21 +9087,21 @@ set ter svg size 640, 480\nunset log y\n } hstepm=hstepm/stepm; - yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and - fractional in yp1 */ - anprojmean=yp; - yp2=modf((yp1*12),&yp); - mprojmean=yp; - yp1=modf((yp2*30.5),&yp); - jprojmean=yp; - if(jprojmean==0) jprojmean=1; - if(mprojmean==0) jprojmean=1; + /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp and */ + /* fractional in yp1 *\/ */ + /* aintmean=yp; */ + /* yp2=modf((yp1*12),&yp); */ + /* mintmean=yp; */ + /* yp1=modf((yp2*30.5),&yp); */ + /* jintmean=yp; */ + /* if(jintmean==0) jintmean=1; */ + /* if(mintmean==0) jintmean=1; */ i1=pow(2,cptcoveff); if (cptcovn < 1){i1=1;} - fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); - printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); + fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2); + printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2); fprintf(ficresfb,"#****** Routine prevbackforecast **\n"); @@ -8359,7 +9115,7 @@ set ter svg size 640, 480\nunset log y\n } fprintf(ficresfb,"\n#****** hbijx=probability over h years, hb.jx is weighted by observed prev \n#"); for(j=1;j<=cptcoveff;j++) { - fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); } for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */ fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); @@ -8370,10 +9126,10 @@ set ter svg size 640, 480\nunset log y\n fprintf(ficresfb," b%d%d",i,j); fprintf(ficresfb," b.%d",j); } - for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) { + for (yearp=0; yearp>=(anbackf-anbackd);yearp -=stepsize) { /* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { */ fprintf(ficresfb,"\n"); - fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); + fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jbackd,mbackd,anbackd+yearp); /* printf("\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */ /* for (agec=bage; agec<=agemax-1; agec++){ /\* testing *\/ */ for (agec=bage; agec<=fage; agec++){ /* testing */ @@ -8395,8 +9151,8 @@ set ter svg size 640, 480\nunset log y\n } fprintf(ficresfb,"\n"); for(j=1;j<=cptcoveff;j++) - fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); - fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec-h*hstepm/YEARM*stepm); + fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); + fprintf(ficresfb,"%.f %.f ",anbackd+yearp,agec-h*hstepm/YEARM*stepm); for(i=1; i<=nlstate+ndeath;i++) { ppij=0.;ppi=0.; for(j=1; j<=nlstate;j++) { @@ -8431,7 +9187,7 @@ set ter svg size 640, 480\nunset log y\n /* Variance of prevalence limit: varprlim */ void varprlim(char fileresu[], int nresult, double ***prevacurrent, int mobilavproj, double bage, double fage, double **prlim, int *ncvyearp, double ftolpl, double p[], double **matcov, double *delti, int stepm, int cptcoveff){ - /*------- Variance of period (stable) prevalence------*/ + /*------- Variance of forward period (stable) prevalence------*/ char fileresvpl[FILENAMELENGTH]; FILE *ficresvpl; @@ -8442,11 +9198,11 @@ set ter svg size 640, 480\nunset log y\n strcpy(fileresvpl,"VPL_"); strcat(fileresvpl,fileresu); if((ficresvpl=fopen(fileresvpl,"w"))==NULL) { - printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl); + printf("Problem with variance of forward period (stable) prevalence resultfile: %s\n", fileresvpl); exit(0); } - printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout); - fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog); + printf("Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout); + fprintf(ficlog, "Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog); /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){ for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/ @@ -8462,9 +9218,9 @@ set ter svg size 640, 480\nunset log y\n printf("\n#****** "); fprintf(ficlog,"\n#****** "); for(j=1;j<=cptcoveff;j++) { - fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); - fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); - printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); + fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); + printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); } for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */ printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); @@ -8483,8 +9239,8 @@ set ter svg size 640, 480\nunset log y\n } fclose(ficresvpl); - printf("done variance-covariance of period prevalence\n");fflush(stdout); - fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog); + printf("done variance-covariance of forward period prevalence\n");fflush(stdout); + fprintf(ficlog,"done variance-covariance of forward period prevalence\n");fflush(ficlog); } /* Variance of back prevalence: varbprlim */ @@ -8519,9 +9275,9 @@ set ter svg size 640, 480\nunset log y\n printf("\n#****** "); fprintf(ficlog,"\n#****** "); for(j=1;j<=cptcoveff;j++) { - fprintf(ficresvbl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); - fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); - printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + fprintf(ficresvbl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); + fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); + printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); } for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */ printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); @@ -8844,7 +9600,7 @@ void prwizard(int ncovmodel, int nlstate /******************* Gompertz Likelihood ******************************/ double gompertz(double x[]) { - double A,B,L=0.0,sump=0.,num=0.; + double A=0.0,B=0.,L=0.0,sump=0.,num=0.; int i,n=0; /* n is the size of the sample */ for (i=1;i<=imx ; i++) { @@ -8852,28 +9608,34 @@ double gompertz(double x[]) /* sump=sump+1;*/ num=num+1; } - - + L=0.0; + /* agegomp=AGEGOMP; */ /* for (i=0; i<=imx; i++) 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]);*/ - for (i=1;i<=imx ; i++) - { - if (cens[i] == 1 && wav[i]>1) - A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp))); - - if (cens[i] == 0 && wav[i]>1) + for (i=1;i<=imx ; i++) { + /* mu(a)=mu(agecomp)*exp(teta*(age-agegomp)) + mu(a)=x[1]*exp(x[2]*(age-agegomp)); x[1] and x[2] are per year. + * L= Product mu(agedeces)exp(-\int_ageexam^agedc mu(u) du ) for a death between agedc (in month) + * and agedc +1 month, cens[i]=0: log(x[1]/YEARM) + * + + * exp(-\int_ageexam^agecens mu(u) du ) when censored, cens[i]=1 + */ + if (wav[i] > 1 || agedc[i] < AGESUP) { + if (cens[i] == 1){ + A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp))); + } else if (cens[i] == 0){ A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp))) - +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM); - + +log(x[1]/YEARM) +x[2]*(agedc[i]-agegomp)+log(YEARM); + } else + printf("Gompertz cens[%d] neither 1 nor 0\n",i); /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */ - if (wav[i] > 1 ) { /* ??? */ - L=L+A*weight[i]; + L=L+A*weight[i]; /* 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]);*/ - } - } + } + } - /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/ + /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/ return -2*L*num/sump; } @@ -8882,7 +9644,7 @@ double gompertz(double x[]) /******************* Gompertz_f Likelihood ******************************/ double gompertz_f(const gsl_vector *v, void *params) { - double A,B,LL=0.0,sump=0.,num=0.; + double A=0.,B=0.,LL=0.0,sump=0.,num=0.; double *x= (double *) v->data; int i,n=0; /* n is the size of the sample */ @@ -8975,12 +9737,17 @@ int readdata(char datafile[], int firsto int i=0, j=0, n=0, iv=0, v; int lstra; int linei, month, year,iout; + int noffset=0; /* This is the offset if BOM data file */ char line[MAXLINE], linetmp[MAXLINE]; char stra[MAXLINE], strb[MAXLINE]; char *stratrunc; DummyV=ivector(1,NCOVMAX); /* 1 to 3 */ FixedV=ivector(1,NCOVMAX); /* 1 to 3 */ + for(v=1;v= firstobs) && (i <=lastobs))) { linei=linei+1; for(j=strlen(line); j>=0;j--){ /* Untabifies line */ @@ -9076,23 +9888,23 @@ int readdata(char datafile[], int firsto } if(lval <-1 || lval >1){ printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \ - Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \ + Should be a value of %d(nth) covariate of wave %d (0 should be the value for the reference and 1\n \ for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \ For example, for multinomial values like 1, 2 and 3,\n \ build V1=0 V2=0 for the reference value (1),\n \ V1=1 V2=0 for (2) \n \ and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \ output of IMaCh is often meaningless.\n \ - Exiting.\n",lval,linei, i,line,j); + Exiting.\n",lval,linei, i,line,iv,j); fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \ - Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \ + Should be a value of %d(nth) covariate of wave %d (0 should be the value for the reference and 1\n \ for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \ For example, for multinomial values like 1, 2 and 3,\n \ build V1=0 V2=0 for the reference value (1),\n \ V1=1 V2=0 for (2) \n \ and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \ output of IMaCh is often meaningless.\n \ - Exiting.\n",lval,linei, i,line,j);fflush(ficlog); + Exiting.\n",lval,linei, i,line,iv,j);fflush(ficlog); return 1; } cotvar[j][iv][i]=(double)(lval); @@ -9130,7 +9942,11 @@ int readdata(char datafile[], int firsto return 1; } anint[j][i]= (double) year; - mint[j][i]= (double)month; + mint[j][i]= (double)month; + /* if( (int)anint[j][i]+ (int)(mint[j][i])/12. < (int) (moisnais[i]/12.+annais[i])){ */ + /* printf("Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, mint[j][i],anint[j][i], moisnais[i],annais[i]); */ + /* fprintf(ficlog,"Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, mint[j][i],anint[j][i], moisnais[i],annais[i]); */ + /* } */ strcpy(line,stra); } /* End loop on waves */ @@ -9169,7 +9985,14 @@ int readdata(char datafile[], int firsto } annais[i]=(double)(year); - moisnais[i]=(double)(month); + moisnais[i]=(double)(month); + for (j=1;j<=maxwav;j++){ + if( (int)anint[j][i]+ (int)(mint[j][i])/12. < (int) (moisnais[i]/12.+annais[i])){ + printf("Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, (int)mint[j][i],(int)anint[j][i], j,(int)moisnais[i],(int)annais[i]); + fprintf(ficlog,"Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, (int)mint[j][i],(int)anint[j][i], j, (int)moisnais[i],(int)annais[i]); + } + } + strcpy(line,stra); /* Sample weight */ @@ -9189,6 +10012,8 @@ int readdata(char datafile[], int firsto cutv(stra, strb, line, ' '); if(strb[0]=='.') { /* Missing value */ lval=-1; + coqvar[iv][i]=NAN; + covar[ncovcol+iv][i]=NAN; /* including qvar in standard covar for performance reasons */ }else{ errno=0; /* what_kind_of_number(strb); */ @@ -9282,17 +10107,16 @@ void removefirstspace(char **stri){/*, c *stri=p2; } -int decoderesult ( char resultline[], int nres) +int decoderesult( char resultline[], int nres) /**< This routine decode one result line and returns the combination # of dummy covariates only **/ { int j=0, k=0, k1=0, k2=0, k3=0, k4=0, match=0, k2q=0, k3q=0, k4q=0; char resultsav[MAXLINE]; - int resultmodel[MAXLINE]; + /* int resultmodel[MAXLINE]; */ int modelresult[MAXLINE]; char stra[80], strb[80], strc[80], strd[80],stre[80]; removefirstspace(&resultline); - printf("decoderesult:%s\n",resultline); if (strstr(resultline,"v") !=0){ printf("Error. 'v' must be in upper case 'V' result: %s ",resultline); @@ -9307,97 +10131,136 @@ int decoderesult ( char resultline[], in TKresult[nres]=0; /* Combination for the nresult and the model */ return (0); } - if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */ - printf("ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs); - fprintf(ficlog,"ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs); + printf("ERROR: the number of variables in this result line, %d, differs from the number of variables used in the model line, %d.\n",j, cptcovs); + fprintf(ficlog,"ERROR: the number of variables in the resultline, %d, differs from the number of variables used in the model line, %d.\n",j, cptcovs); } for(k=1; k<=j;k++){ /* Loop on any covariate of the result line */ if(nbocc(resultsav,'=') >1){ - cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' ' - resultsav= V4=1 V5=25.1 V3=0 strb=V3=0 stra= V4=1 V5=25.1 */ - cutl(strc,strd,strb,'='); /* strb:V4=1 strc=1 strd=V4 */ + cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' ' (stra is the rest of the resultline to be analyzed in the next loop *//* resultsav= "V4=1 V5=25.1 V3=0" stra= "V5=25.1 V3=0" strb= "V4=1" */ + cutl(strc,strd,strb,'='); /* strb:"V4=1" strc="1" strd="V4" */ }else cutl(strc,strd,resultsav,'='); - Tvalsel[k]=atof(strc); /* 1 */ + Tvalsel[k]=atof(strc); /* 1 */ /* Tvalsel of k is the float value of the kth covariate appearing in this result line */ cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */; - Tvarsel[k]=atoi(strc); + Tvarsel[k]=atoi(strc); /* 4 */ /* Tvarsel is the id of the kth covariate in the result line Tvarsel[1] in "V4=1.." is 4.*/ /* Typevarsel[k]=1; /\* 1 for age product *\/ */ /* cptcovsel++; */ if (nbocc(stra,'=') >0) strcpy(resultsav,stra); /* and analyzes it */ } /* Checking for missing or useless values in comparison of current model needs */ - for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ - if(Typevar[k1]==0){ /* Single covariate in model */ + for(k1=1; k1<= cptcovt ;k1++){ /* Loop on model. model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ + if(Typevar[k1]==0){ /* Single covariate in model *//*0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product */ match=0; - for(k2=1; k2 <=j;k2++){/* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */ - if(Tvar[k1]==Tvarsel[k2]) {/* Tvar[1]=5 == Tvarsel[2]=5 */ + for(k2=1; k2 <=j;k2++){/* Loop on resultline. In result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */ + if(Tvar[k1]==Tvarsel[k2]) {/* Tvar is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5 */ modelresult[k2]=k1;/* modelresult[2]=1 modelresult[1]=2 modelresult[3]=3 modelresult[6]=4 modelresult[9]=5 */ - match=1; + match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */ break; } } if(match == 0){ - printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model); + printf("Error in result line: V%d is missing in result: %s according to model=%s\n",k1, resultline, model); + fprintf(ficlog,"Error in result line: V%d is missing in result: %s according to model=%s\n",k1, resultline, model); + return 1; } } } /* Checking for missing or useless values in comparison of current model needs */ - for(k2=1; k2 <=j;k2++){ /* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */ + for(k2=1; k2 <=j;k2++){ /* Loop on resultline variables: result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */ match=0; - for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ + for(k1=1; k1<= cptcovt ;k1++){ /* loop on model: model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ if(Typevar[k1]==0){ /* Single */ if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4 */ - resultmodel[k1]=k2; /* resultmodel[2]=1 resultmodel[1]=2 resultmodel[3]=3 resultmodel[6]=4 resultmodel[9]=5 */ + resultmodel[nres][k1]=k2; /* k1th position in the model equation corresponds to k2th position in the result line. resultmodel[2]=1 resultmodel[1]=2 resultmodel[3]=3 resultmodel[6]=4 resultmodel[9]=5 */ ++match; } } } if(match == 0){ printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model); + fprintf(ficlog,"Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model); + return 1; }else if(match > 1){ printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model); + fprintf(ficlog,"Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model); + return 1; } } /* We need to deduce which combination number is chosen and save quantitative values */ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ - /* result line V4=1 V5=25.1 V3=0 V2=8 V1=1 */ - /* should give a combination of dummy V4=1, V3=0, V1=1 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 5 + (1offset) = 6*/ - /* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */ + /* nres=1st result line: V4=1 V5=25.1 V3=0 V2=8 V1=1 */ + /* should correspond to the combination 6 of dummy: V4=1, V3=0, V1=1 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 1*1 + 0*2 + 1*4 = 5 + (1offset) = 6*/ + /* nres=2nd result line: V4=1 V5=24.1 V3=1 V2=8 V1=0 */ /* should give a combination of dummy V4=1, V3=1, V1=0 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 3 + (1offset) = 4*/ /* 1 0 0 0 */ /* 2 1 0 0 */ /* 3 0 1 0 */ - /* 4 1 1 0 */ /* V4=1, V3=1, V1=0 */ + /* 4 1 1 0 */ /* V4=1, V3=1, V1=0 (nres=2)*/ /* 5 0 0 1 */ - /* 6 1 0 1 */ /* V4=1, V3=0, V1=1 */ + /* 6 1 0 1 */ /* V4=1, V3=0, V1=1 (nres=1)*/ /* 7 0 1 1 */ /* 8 1 1 1 */ /* V(Tvresult)=Tresult V4=1 V3=0 V1=1 Tresult[nres=1][2]=0 */ /* V(Tvqresult)=Tqresult V5=25.1 V2=8 Tqresult[nres=1][1]=25.1 */ /* V5*age V5 known which value for nres? */ /* Tqinvresult[2]=8 Tqinvresult[1]=25.1 */ - for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* model line */ - if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Single dummy */ - k3= resultmodel[k1]; /* resultmodel[2(V4)] = 1=k3 */ - k2=(int)Tvarsel[k3]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */ - k+=Tvalsel[k3]*pow(2,k4); /* Tvalsel[1]=1 */ - Tresult[nres][k4+1]=Tvalsel[k3];/* Tresult[nres][1]=1(V4=1) Tresult[nres][2]=0(V3=0) */ + for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* loop k1 on position in the model line (excluding product) */ + /* k counting number of combination of single dummies in the equation model */ + /* k4 counting single dummies in the equation model */ + /* k4q counting single quantitatives in the equation model */ + if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Dummy and Single */ + /* k4+1= position in the resultline V(Tvarsel)=Tvalsel=Tresult[nres][pos](value); V(Tvresult[nres][pos] (variable): V(variable)=value) */ + /* modelresult[k3]=k1: k3th position in the result line correspond to the k1 position in the model line */ + /* Value in the (current nres) resultline of the variable at the k1th position in the model equation resultmodel[nres][k1]= k3 */ + /* resultmodel[nres][k1]=k3: k1th position in the model correspond to the k3 position in the resultline */ + /* k3 is the position in the nres result line of the k1th variable of the model equation */ + /* Tvarsel[k3]: Name of the variable at the k3th position in the result line. */ + /* Tvalsel[k3]: Value of the variable at the k3th position in the result line. */ + /* Tresult[nres][result_position]= value of the dummy variable at the result_position in the nres resultline */ + /* Tvresult[nres][result_position]= id of the dummy variable at the result_position in the nres resultline */ + /* Tinvresult[nres][Name of a dummy variable]= value of the variable in the result line */ + /* TinvDoQresult[nres][Name of a Dummy or Q variable]= value of the variable in the result line */ + k3= resultmodel[nres][k1]; /* nres=1 k1=2 resultmodel[2(V4)] = 1=k3 ; k1=3 resultmodel[3(V3)] = 2=k3*/ + k2=(int)Tvarsel[k3]; /* nres=1 k1=2=>k3=1 Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 (V4); k1=3=>k3=2 Tvarsel[2]=3 (V3)*/ + k+=Tvalsel[k3]*pow(2,k4); /* nres=1 k1=2 Tvalsel[1]=1 (V4=1); k1=3 k3=2 Tvalsel[2]=0 (V3=0) */ + TinvDoQresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */ + Tresult[nres][k4+1]=Tvalsel[k3];/* Tresult[nres=2][1]=1(V4=1) Tresult[nres=2][2]=0(V3=0) */ Tvresult[nres][k4+1]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */ Tinvresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */ printf("Decoderesult Dummy k=%d, V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k2, k3, (int)Tvalsel[k3], k4); k4++;; - } else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Single quantitative */ - k3q= resultmodel[k1]; /* resultmodel[2] = 1=k3 */ - k2q=(int)Tvarsel[k3q]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */ + }else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Quantitative and single */ + /* Tqresult[nres][result_position]= value of the variable at the result_position in the nres resultline */ + /* Tqvresult[nres][result_position]= id of the variable at the result_position in the nres resultline */ + /* Tqinvresult[nres][Name of a quantitative variable]= value of the variable in the result line */ + k3q= resultmodel[nres][k1]; /* resultmodel[1(V5)] = 25.1=k3q */ + k2q=(int)Tvarsel[k3q]; /* Tvarsel[resultmodel[1]]= Tvarsel[1] = 4=k2 */ Tqresult[nres][k4q+1]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */ Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */ Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */ + TinvDoQresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */ printf("Decoderesult Quantitative nres=%d, V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]); k4q++;; + }else if( Dummy[k1]==2 ){ /* For dummy with age product */ + /* Tvar[k1]; */ /* Age variable */ + k3= resultmodel[nres][Tvar[k1]]; /* nres=1 k1=2 resultmodel[2(V4)] = 1=k3 ; k1=3 resultmodel[3(V3)] = 2=k3*/ + k2=(int)Tvarsel[k3]; /* nres=1 k1=2=>k3=1 Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 (V4); k1=3=>k3=2 Tvarsel[2]=3 (V3)*/ + TinvDoQresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */ + printf("Decoderesult Dummy with age k=%d, k1=%d Tvar[%d]=V%d k2=Tvarsel[%d]=%d Tvalsel[%d]=%d\n",k, k1, k1, Tvar[k1], k3,(int)Tvarsel[k3], k3, (int)Tvalsel[k3]); + }else if( Dummy[k1]==3 ){ /* For quant with age product */ + k3q= resultmodel[nres][Tvar[k1]]; /* resultmodel[1(V5)] = 25.1=k3q */ + k2q=(int)Tvarsel[k3q]; /* Tvarsel[resultmodel[1]]= Tvarsel[1] = 4=k2 */ + TinvDoQresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */ + printf("Decoderesult Quantitative with age nres=%d, k1=%d, Tvar[%d]=V%d V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, k1, k1, Tvar[k1], k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]); + }else if(Typevar[k1]==2 ){ /* For product quant or dummy (not with age) */ + printf("Decoderesult Quantitative or Dummy (not with age) nres=%d k1=%d Tvar[%d]=%d \n",nres, k1, k1, Tvar[k1]); + }else{ + printf("Error Decodemodel probably a product Dummy[%d]==%d && Typevar[%d]==%d\n", k1, Dummy[k1], k1, Typevar[k1]); + fprintf(ficlog,"Error Decodemodel probably a product Dummy[%d]==%d && Typevar[%d]==%d\n", k1, Dummy[k1], k1, Typevar[k1]); } } @@ -9415,11 +10278,12 @@ int decodemodel( char model[], int lasto * - cptcovs number of simple covariates * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10 * which is a new column after the 9 (ncovcol) variables. - * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual + * - if k is a product Vn*Vm, covar[k][i] is filled with correct values for each individual * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6. * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 . */ +/* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1, Tage[1]=2 */ { int i, j, k, ks, v; int j1, k1, k2, k3, k4; @@ -9497,12 +10361,12 @@ int decodemodel( char model[], int lasto * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2 * k= 1 2 3 4 5 6 7 8 9 10 11 12 * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8 - * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6} + * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6} * p Tprod[1]@2={ 6, 5} *p Tvard[1][1]@4= {7, 8, 5, 6} * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8 * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; - *How to reorganize? + *How to reorganize? Tvars(orted) * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6} * {2, 1, 4, 8, 5, 6, 3, 7} @@ -9527,22 +10391,23 @@ int decodemodel( char model[], int lasto Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0; } cptcovage=0; - for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */ - cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' - modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ - if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */ + for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model line */ + cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' cutl from left to right + modelsav==V2+V1+V5*age+V4+V3*age strb=V3*age stra=V2+V1V5*age+V4 */ /* "V5+V4+V3+V4*V3+V5*age+V1*age+V1" strb="V5" stra="V4+V3+V4*V3+V5*age+V1*age+V1" */ + if (nbocc(modelsav,'+')==0) + strcpy(strb,modelsav); /* and analyzes it */ /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/ /*scanf("%d",i);*/ - if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */ - cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */ + if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V5*age+ V4+V3*age strb=V3*age */ + cutl(strc,strd,strb,'*'); /**< k=1 strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */ if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */ /* covar is not filled and then is empty */ cptcovprod--; cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */ - Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */ + Tvar[k]=atoi(stre); /* V2+V1+V5*age+V4+V3*age Tvar[5]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */ Typevar[k]=1; /* 1 for age product */ - cptcovage++; /* Sums the number of covariates which include age as a product */ - Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */ + cptcovage++; /* Counts the number of covariates which include age as a product */ + Tage[cptcovage]=k; /* V2+V1+V4+V3*age Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */ /*printf("stre=%s ", stre);*/ } else if (strcmp(strd,"age")==0) { /* or age*Vn */ cptcovprod--; @@ -9559,14 +10424,17 @@ int decodemodel( char model[], int lasto Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but because this model-covariate is a construction we invent a new column which is after existing variables ncovcol+nqv+ntv+nqtv + k1 - If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2 - Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */ + If already ncovcol=4 and model=V2 + V1 +V1*V4 +age*V3 +V3*V2 + thus after V4 we invent V5 and V6 because age*V3 will be computed in 4 + Tvar[3=V1*V4]=4+1=5 Tvar[5=V3*V2]=4 + 2= 6, Tvar[4=age*V3]=4 etc */ Typevar[k]=2; /* 2 for double fixed dummy covariates */ cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */ Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */ - Tposprod[k]=k1; /* Tpsprod[3]=1, Tposprod[2]=5 */ + Tposprod[k]=k1; /* Tposprod[3]=1, Tposprod[2]=5 */ Tvard[k1][1] =atoi(strc); /* m 1 for V1*/ + Tvardk[k][1] =atoi(strc); /* m 1 for V1*/ Tvard[k1][2] =atoi(stre); /* n 4 for V4*/ + Tvardk[k][2] =atoi(stre); /* n 4 for V4*/ k2=k2+2; /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */ /* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) *\/ */ /* Tvar[cptcovt+k2+1]=Tvard[k1][2]; /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) *\/ */ @@ -9579,7 +10447,7 @@ int decodemodel( char model[], int lasto } } /* End age is not in the model */ } /* End if model includes a product */ - else { /* no more sum */ + else { /* not a product */ /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/ /* scanf("%d",i);*/ cutl(strd,strc,strb,'V'); @@ -9610,7 +10478,7 @@ int decodemodel( char model[], int lasto model= V5 + V4 +V3 + V4*V3 + V5*age + V2 + V1*V2 + V1*age + V5*age, V1 is not used saving its place k = 1 2 3 4 5 6 7 8 9 Tvar[k]= 5 4 3 1+1+2+1+1=6 5 2 7 1 5 - Typevar[k]= 0 0 0 2 1 0 2 1 1 + Typevar[k]= 0 0 0 2 1 0 2 1 0 Fixed[k] 1 1 1 1 3 0 0 or 2 2 3 Dummy[k] 1 0 0 0 3 1 1 2 3 Tmodelind[combination of covar]=k; @@ -9619,15 +10487,15 @@ int decodemodel( char model[], int lasto /* If Tvar[k] >ncovcol it is a product */ /* Tvar[k] is the value n of Vn with n varying for 1 to nvcol, or p Vp=Vn*Vm for product */ /* Computing effective variables, ie used by the model, that is from the cptcovt variables */ - printf("Model=%s\n\ + printf("Model=1+age+%s\n\ Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\ Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\ Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model); - fprintf(ficlog,"Model=%s\n\ + fprintf(ficlog,"Model=1+age+%s\n\ Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\ Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\ Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model); - for(k=1;k<=cptcovt; k++){ Fixed[k]=0; Dummy[k]=0;} + for(k=-1;k<=cptcovt; k++){ Fixed[k]=0; Dummy[k]=0;} for(k=1, ncovf=0, nsd=0, nsq=0, ncovv=0, ncova=0, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */ if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */ Fixed[k]= 0; @@ -9638,6 +10506,7 @@ Dummy[k] 0=dummy (0 1), 1 quantitative ( modell[k].maintype= FTYPE; TvarsD[nsd]=Tvar[k]; TvarsDind[nsd]=k; + TnsdVar[Tvar[k]]=nsd; TvarF[ncovf]=Tvar[k]; TvarFind[ncovf]=k; TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ @@ -9649,6 +10518,7 @@ Dummy[k] 0=dummy (0 1), 1 quantitative ( ncovf++; modell[k].maintype= FTYPE; TvarF[ncovf]=Tvar[k]; + /* TnsdVar[Tvar[k]]=nsd; */ /* To be done */ TvarFind[ncovf]=k; TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ @@ -9675,6 +10545,7 @@ Dummy[k] 0=dummy (0 1), 1 quantitative ( nsd++; TvarsD[nsd]=Tvar[k]; TvarsDind[nsd]=k; + TnsdVar[Tvar[k]]=nsd; /* To be verified */ ncovv++; /* Only simple time varying variables */ TvarV[ncovv]=Tvar[k]; TvarVind[ncovv]=k; /* TvarVind[2]=2 TvarVind[3]=3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Any time varying singele */ @@ -9690,7 +10561,7 @@ Dummy[k] 0=dummy (0 1), 1 quantitative ( modell[k].subtype= VQ; ncovv++; /* Only simple time varying variables */ nsq++; - TvarsQ[nsq]=Tvar[k]; + TvarsQ[nsq]=Tvar[k]; /* k=1 Tvar=5 nsq=1 TvarsQ[1]=5 */ TvarsQind[nsq]=k; TvarV[ncovv]=Tvar[k]; TvarVind[ncovv]=k; /* TvarVind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Any time varying singele */ @@ -9877,11 +10748,12 @@ Dummy[k] 0=dummy (0 1), 1 quantitative ( /* Searching for doublons in the model */ for(k1=1; k1<= cptcovt;k1++){ for(k2=1; k2 + + /* #include "syscompilerinfo.h"*/ /* command line Intel compiler 32bit windows, XP compatible:*/ /* /GS /W3 /Gy /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D @@ -10089,6 +10963,8 @@ void syscompilerinfo(int logged) /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF /NOLOGO /TLBID:1 */ + + #if defined __INTEL_COMPILER #if defined(__GNUC__) struct utsname sysInfo; /* For Intel on Linux and OS/X */ @@ -10105,8 +10981,6 @@ void syscompilerinfo(int logged) } #endif -#include - printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:"); #if defined(__clang__) printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */ @@ -10192,7 +11066,7 @@ void syscompilerinfo(int logged) #endif #endif - // void main() + // void main () // { #if defined(_MSC_VER) if (IsWow64()){ @@ -10213,7 +11087,7 @@ void syscompilerinfo(int logged) } int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){ - /*--------------- Prevalence limit (period or stable prevalence) --------------*/ + /*--------------- Prevalence limit (forward period or forward stable prevalence) --------------*/ int i, j, k, i1, k4=0, nres=0 ; /* double ftolpl = 1.e-10; */ double age, agebase, agelim; @@ -10222,13 +11096,13 @@ int prevalence_limit(double *p, double * strcpy(filerespl,"PL_"); strcat(filerespl,fileresu); if((ficrespl=fopen(filerespl,"w"))==NULL) { - printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1; - fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1; + printf("Problem with forward period (stable) prevalence resultfile: %s\n", filerespl);return 1; + fprintf(ficlog,"Problem with forward period (stable) prevalence resultfile: %s\n", filerespl);return 1; } - printf("\nComputing period (stable) prevalence: result on file '%s' \n", filerespl); - fprintf(ficlog,"\nComputing period (stable) prevalence: result on file '%s' \n", filerespl); + printf("\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl); + fprintf(ficlog,"\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl); pstamp(ficrespl); - fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl); + fprintf(ficrespl,"# Forward period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl); fprintf(ficrespl,"#Age "); for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i); fprintf(ficrespl,"\n"); @@ -10257,9 +11131,9 @@ int prevalence_limit(double *p, double * printf("#******"); fprintf(ficlog,"#******"); for(j=1;j<=cptcoveff ;j++) {/* all covariates */ - fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/ - printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); - fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); /* Here problem for varying dummy*/ + printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); + fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); } for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */ printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); @@ -10278,7 +11152,7 @@ int prevalence_limit(double *p, double * fprintf(ficrespl,"#Age "); for(j=1;j<=cptcoveff;j++) { - fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); } for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i); fprintf(ficrespl,"Total Years_to_converge\n"); @@ -10288,7 +11162,7 @@ int prevalence_limit(double *p, double * prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres); fprintf(ficrespl,"%.0f ",age ); for(j=1;j<=cptcoveff;j++) - fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); tot=0.; for(i=1; i<=nlstate;i++){ tot += prlim[i][i]; @@ -10303,7 +11177,7 @@ int prevalence_limit(double *p, double * } int back_prevalence_limit(double *p, double **bprlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp, double dateprev1,double dateprev2, int firstpass, int lastpass, int mobilavproj){ - /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/ + /*--------------- Back Prevalence limit (backward stable prevalence) --------------*/ /* Computes the back prevalence limit for any combination of covariate values * at any age between ageminpar and agemaxpar @@ -10318,13 +11192,13 @@ int back_prevalence_limit(double *p, dou strcpy(fileresplb,"PLB_"); strcat(fileresplb,fileresu); if((ficresplb=fopen(fileresplb,"w"))==NULL) { - printf("Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1; - fprintf(ficlog,"Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1; + printf("Problem with backward prevalence resultfile: %s\n", fileresplb);return 1; + fprintf(ficlog,"Problem with backward prevalence resultfile: %s\n", fileresplb);return 1; } - printf("Computing period (stable) back prevalence: result on file '%s' \n", fileresplb); - fprintf(ficlog,"Computing period (stable) back prevalence: result on file '%s' \n", fileresplb); + printf("Computing backward prevalence: result on file '%s' \n", fileresplb); + fprintf(ficlog,"Computing backward prevalence: result on file '%s' \n", fileresplb); pstamp(ficresplb); - fprintf(ficresplb,"# Period (stable) back prevalence. Precision given by ftolpl=%g \n", ftolpl); + fprintf(ficresplb,"# Backward prevalence. Precision given by ftolpl=%g \n", ftolpl); fprintf(ficresplb,"#Age "); for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i); fprintf(ficresplb,"\n"); @@ -10348,9 +11222,9 @@ int back_prevalence_limit(double *p, dou printf("#******"); fprintf(ficlog,"#******"); for(j=1;j<=cptcoveff ;j++) {/* all covariates */ - fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); - printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); - fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); + printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); + fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); } for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */ printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); @@ -10369,7 +11243,7 @@ int back_prevalence_limit(double *p, dou fprintf(ficresplb,"#Age "); for(j=1;j<=cptcoveff;j++) { - fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); } for(i=1; i<=nlstate;i++) fprintf(ficresplb," %d-%d ",i,i); fprintf(ficresplb,"Total Years_to_converge\n"); @@ -10393,7 +11267,7 @@ int back_prevalence_limit(double *p, dou } fprintf(ficresplb,"%.0f ",age ); for(j=1;j<=cptcoveff;j++) - fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); tot=0.; for(i=1; i<=nlstate;i++){ tot += bprlim[i][i]; @@ -10451,7 +11325,7 @@ int hPijx(double *p, int bage, int fage) continue; fprintf(ficrespij,"\n#****** "); for(j=1;j<=cptcoveff;j++) - fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */ printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); @@ -10513,7 +11387,7 @@ int hPijx(double *p, int bage, int fage) /*if (stepm<=24) stepsize=2;*/ /* agelim=AGESUP; */ - ageminl=30; + ageminl=AGEINF; /* was 30 */ hstepm=stepsize*YEARM; /* Every year of age */ hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ @@ -10530,7 +11404,7 @@ int hPijx(double *p, int bage, int fage) continue; fprintf(ficrespijb,"\n#****** "); for(j=1;j<=cptcoveff;j++) - fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */ fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); } @@ -10543,8 +11417,8 @@ int hPijx(double *p, int bage, int fage) /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */ for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */ /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */ - nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ - nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */ + nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm+0.1)-1; /* Typically 20 years = 20*12/6=40 or 55*12/24=27.5-1.1=>27 */ + nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 or 28*/ /* nhstepm=nhstepm*YEARM; aff par mois*/ @@ -10553,7 +11427,7 @@ int hPijx(double *p, int bage, int fage) /* oldm=oldms;savm=savms; */ /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */ - hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k, nres); + hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k, nres);/* Bug valgrind */ /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */ fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j="); for(i=1; i<=nlstate;i++) @@ -10566,7 +11440,7 @@ int hPijx(double *p, int bage, int fage) /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */ for(i=1; i<=nlstate;i++) for(j=1; j<=nlstate+ndeath;j++) - fprintf(ficrespijb," %.5f", p3mat[i][j][h]); + fprintf(ficrespijb," %.5f", p3mat[i][j][h]);/* Bug valgrind */ fprintf(ficrespijb,"\n"); } free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); @@ -10592,7 +11466,8 @@ int main(int argc, char *argv[]) double ssval; #endif int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav); - int i,j, k, n=MAXN,iter=0,m,size=100, cptcod; + int i,j, k, iter=0,m,size=100, cptcod; /* Suppressing because nobs */ + /* int i,j, k, n=MAXN,iter=0,m,size=100, cptcod; */ int ncvyear=0; /* Number of years needed for the period prevalence to converge */ int jj, ll, li, lj, lk; int numlinepar=0; /* Current linenumber of parameter file */ @@ -10602,7 +11477,7 @@ int main(int argc, char *argv[]) int vpopbased=0; int nres=0; int endishere=0; - + int noffset=0; int ncurrv=0; /* Temporary variable */ char ca[32], cb[32]; @@ -10618,6 +11493,7 @@ int main(int argc, char *argv[]) double dum=0.; /* Dummy variable */ double ***p3mat; /* double ***mobaverage; */ + double wald; char line[MAXLINE]; char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE]; @@ -10627,7 +11503,7 @@ int main(int argc, char *argv[]) char pathr[MAXLINE], pathimach[MAXLINE]; char *tok, *val; /* pathtot */ - int firstobs=1, lastobs=10; + int firstobs=1, lastobs=10; /* nobs = lastobs-firstobs declared globally ;*/ int c, h , cpt, c2; int jl=0; int i1, j1, jk, stepsize=0; @@ -10635,7 +11511,14 @@ int main(int argc, char *argv[]) int *tab; int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */ - int backcast=0; + /* double anprojd, mprojd, jprojd; /\* For eventual projections *\/ */ + /* double anprojf, mprojf, jprojf; */ + /* double jintmean,mintmean,aintmean; */ + int prvforecast = 0; /* Might be 1 (date of beginning of projection is a choice or 2 is the dateintmean */ + int prvbackcast = 0; /* Might be 1 (date of beginning of projection is a choice or 2 is the dateintmean */ + double yrfproj= 10.0; /* Number of years of forward projections */ + double yrbproj= 10.0; /* Number of years of backward projections */ + int prevbcast=0; /* defined as global for mlikeli and mle, replacing backcast */ int mobilav=0,popforecast=0; int hstepm=0, nhstepm=0; int agemortsup; @@ -10647,7 +11530,8 @@ int main(int argc, char *argv[]) double ftolpl=FTOL; double **prlim; double **bprlim; - double ***param; /* Matrix of parameters */ + double ***param; /* Matrix of parameters, param[i][j][k] param=ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel) + state of origin, state of destination including death, for each covariate: constante, age, and V1 V2 etc. */ double ***paramstart; /* Matrix of starting parameter values */ double *p, *pstart; /* p=param[1][1] pstart is for starting values guessed by freqsummary */ double **matcov; /* Matrix of covariance */ @@ -10660,8 +11544,9 @@ int main(int argc, char *argv[]) double *epj, vepp; double dateprev1, dateprev2; - double jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000, dateproj1=0, dateproj2=0; - double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000, dateback1=0, dateback2=0; + double jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000, dateproj1=0, dateproj2=0, dateprojd=0, dateprojf=0; + double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000, dateback1=0, dateback2=0, datebackd=0, datebackf=0; + double **ximort; char *alph[]={"a","a","b","c","d","e"}, str[4]="1234"; @@ -10739,8 +11624,13 @@ int main(int argc, char *argv[]) if(pathr[0] == '\0') break; /* Dirty */ } } + else if (argc<=2){ + strcpy(pathtot,argv[1]); + } else{ strcpy(pathtot,argv[1]); + strcpy(z,argv[2]); + printf("\nargv[2]=%s z=%c\n",argv[2],z[0]); } /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/ /*cygwin_split_path(pathtot,path,optionfile); @@ -10818,8 +11708,6 @@ int main(int argc, char *argv[]) exit(70); } - - strcpy(filereso,"o"); strcat(filereso,fileresu); if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */ @@ -10828,17 +11716,53 @@ int main(int argc, char *argv[]) fflush(ficlog); goto end; } + /*-------- Rewriting parameter file ----------*/ + strcpy(rfileres,"r"); /* "Rparameterfile */ + strcat(rfileres,optionfilefiname); /* Parameter file first name */ + strcat(rfileres,"."); /* */ + strcat(rfileres,optionfilext); /* Other files have txt extension */ + if((ficres =fopen(rfileres,"w"))==NULL) { + printf("Problem writing new parameter file: %s\n", rfileres);goto end; + fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end; + fflush(ficlog); + goto end; + } + fprintf(ficres,"#IMaCh %s\n",version); + /* Reads comments: lines beginning with '#' */ numlinepar=0; - - /* First parameter line */ + /* Is it a BOM UTF-8 Windows file? */ + /* First parameter line */ while(fgets(line, MAXLINE, ficpar)) { + noffset=0; + if( line[0] == (char)0xEF && line[1] == (char)0xBB) /* EF BB BF */ + { + noffset=noffset+3; + printf("# File is an UTF8 Bom.\n"); // 0xBF + } +/* else if( line[0] == (char)0xFE && line[1] == (char)0xFF)*/ + else if( line[0] == (char)0xFF && line[1] == (char)0xFE) + { + noffset=noffset+2; + printf("# File is an UTF16BE BOM file\n"); + } + else if( line[0] == 0 && line[1] == 0) + { + if( line[2] == (char)0xFE && line[3] == (char)0xFF){ + noffset=noffset+4; + printf("# File is an UTF16BE BOM file\n"); + } + } else{ + ;/*printf(" Not a BOM file\n");*/ + } + /* If line starts with a # it is a comment */ - if (line[0] == '#') { + if (line[noffset] == '#') { numlinepar++; fputs(line,stdout); fputs(line,ficparo); + fputs(line,ficres); fputs(line,ficlog); continue; }else @@ -10848,18 +11772,24 @@ int main(int argc, char *argv[]) title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){ if (num_filled != 5) { printf("Should be 5 parameters\n"); + fprintf(ficlog,"Should be 5 parameters\n"); } numlinepar++; printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass); + fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass); + fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass); + fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass); } /* Second parameter line */ while(fgets(line, MAXLINE, ficpar)) { - /* If line starts with a # it is a comment */ + /* while(fscanf(ficpar,"%[^\n]", line)) { */ + /* If line starts with a # it is a comment. Strangely fgets reads the EOL and fputs doesn't */ if (line[0] == '#') { numlinepar++; - fputs(line,stdout); - fputs(line,ficparo); - fputs(line,ficlog); + printf("%s",line); + fprintf(ficres,"%s",line); + fprintf(ficparo,"%s",line); + fprintf(ficlog,"%s",line); continue; }else break; @@ -10869,8 +11799,19 @@ int main(int argc, char *argv[]) if (num_filled != 11) { printf("Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n"); printf("but line=%s\n",line); + fprintf(ficlog,"Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n"); + fprintf(ficlog,"but line=%s\n",line); + } + if( lastpass > maxwav){ + printf("Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav); + fprintf(ficlog,"Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav); + fflush(ficlog); + goto end; } - printf("ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt); + printf("ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt); + fprintf(ficparo,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt); + fprintf(ficres,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, 0, weightopt); + fprintf(ficlog,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt); } /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */ /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */ @@ -10879,22 +11820,18 @@ int main(int argc, char *argv[]) /* If line starts with a # it is a comment */ if (line[0] == '#') { numlinepar++; - fputs(line,stdout); - fputs(line,ficparo); - fputs(line,ficlog); + printf("%s",line); + fprintf(ficres,"%s",line); + fprintf(ficparo,"%s",line); + fprintf(ficlog,"%s",line); continue; }else break; } if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){ - if (num_filled == 0){ - printf("ERROR %d: Model should be at minimum 'model=1+age.' WITHOUT space:'%s'\n",num_filled, line); - fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' WITHOUT space:'%s'\n",num_filled, line); - model[0]='\0'; - goto end; - } else if (num_filled != 1){ - printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line); - fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line); + if (num_filled != 1){ + printf("ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line); + fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line); model[0]='\0'; goto end; } @@ -10907,20 +11844,23 @@ int main(int argc, char *argv[]) } /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */ printf("model=1+age+%s\n",model);fflush(stdout); + fprintf(ficparo,"model=1+age+%s\n",model);fflush(stdout); + fprintf(ficres,"model=1+age+%s\n",model);fflush(stdout); + fprintf(ficlog,"model=1+age+%s\n",model);fflush(stdout); } /* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */ /* numlinepar=numlinepar+3; /\* In general *\/ */ /* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */ - fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model); - fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model); + /* fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model); */ + /* fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model); */ fflush(ficlog); /* if(model[0]=='#'|| model[0]== '\0'){ */ if(model[0]=='#'){ - printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \ - 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \ - 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \ + printf("Error in 'model' line: model should start with 'model=1+age+' and end without space \n \ + 'model=1+age+' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age' or \n \ + 'model=1+age+V1+V2' or 'model=1+age+V1+V2+V1*V2' etc. \n"); \ if(mle != -1){ - printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n"); + printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter vectors and subdiagonal covariance matrix.\n"); exit(1); } } @@ -10940,10 +11880,10 @@ int main(int argc, char *argv[]) ungetc(c,ficpar); - covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */ - if(nqv>=1)coqvar=matrix(1,nqv,1,n); /**< Fixed quantitative covariate */ - if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,1,n); /**< Time varying quantitative covariate */ - if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,1,ntv+nqtv,1,n); /**< Time varying covariate (dummy and quantitative)*/ + covar=matrix(0,NCOVMAX,firstobs,lastobs); /**< used in readdata */ + if(nqv>=1)coqvar=matrix(1,nqv,firstobs,lastobs); /**< Fixed quantitative covariate */ + if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,firstobs,lastobs); /**< Time varying quantitative covariate */ + if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,1,ntv+nqtv,firstobs,lastobs); /**< Time varying covariate (dummy and quantitative)*/ cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/ /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5 v1+v2*age+v2*v3 makes cptcovn = 3 @@ -11006,6 +11946,15 @@ int main(int argc, char *argv[]) for(jj=1; jj <=nlstate+ndeath; jj++){ if(jj==i) continue; j++; + while((c=getc(ficpar))=='#' && c!= EOF){ + ungetc(c,ficpar); + fgets(line, MAXLINE, ficpar); + numlinepar++; + fputs(line,stdout); + fputs(line,ficparo); + fputs(line,ficlog); + } + ungetc(c,ficpar); fscanf(ficpar,"%1d%1d",&i1,&j1); if ((i1 != i) || (j1 != jj)){ printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \ @@ -11142,30 +12091,29 @@ Please run with mle=-1 to get a correct fflush(ficlog); - /*-------- Rewriting parameter file ----------*/ - strcpy(rfileres,"r"); /* "Rparameterfile */ - strcat(rfileres,optionfilefiname); /* Parameter file first name*/ - strcat(rfileres,"."); /* */ - strcat(rfileres,optionfilext); /* Other files have txt extension */ - if((ficres =fopen(rfileres,"w"))==NULL) { - printf("Problem writing new parameter file: %s\n", rfileres);goto end; - fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end; - } - fprintf(ficres,"#%s\n",version); } /* End of mle != -3 */ /* Main data */ - n= lastobs; - num=lvector(1,n); - moisnais=vector(1,n); - annais=vector(1,n); - moisdc=vector(1,n); - andc=vector(1,n); - weight=vector(1,n); - agedc=vector(1,n); - cod=ivector(1,n); - for(i=1;i<=n;i++){ + nobs=lastobs-firstobs+1; /* was = lastobs;*/ + /* num=lvector(1,n); */ + /* moisnais=vector(1,n); */ + /* annais=vector(1,n); */ + /* moisdc=vector(1,n); */ + /* andc=vector(1,n); */ + /* weight=vector(1,n); */ + /* agedc=vector(1,n); */ + /* cod=ivector(1,n); */ + /* for(i=1;i<=n;i++){ */ + num=lvector(firstobs,lastobs); + moisnais=vector(firstobs,lastobs); + annais=vector(firstobs,lastobs); + moisdc=vector(firstobs,lastobs); + andc=vector(firstobs,lastobs); + weight=vector(firstobs,lastobs); + agedc=vector(firstobs,lastobs); + cod=ivector(firstobs,lastobs); + for(i=firstobs;i<=lastobs;i++){ num[i]=0; moisnais[i]=0; annais[i]=0; @@ -11175,9 +12123,10 @@ Please run with mle=-1 to get a correct cod[i]=0; weight[i]=1.0; /* Equal weights, 1 by default */ } - mint=matrix(1,maxwav,1,n); - anint=matrix(1,maxwav,1,n); - s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ + mint=matrix(1,maxwav,firstobs,lastobs); + anint=matrix(1,maxwav,firstobs,lastobs); + s=imatrix(1,maxwav+1,firstobs,lastobs); /* s[i][j] health state for wave i and individual j */ + printf("BUG ncovmodel=%d NCOVMAX=%d 2**ncovmodel=%f BUG\n",ncovmodel,NCOVMAX,pow(2,ncovmodel)); tab=ivector(1,NCOVMAX); ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */ ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */ @@ -11196,6 +12145,7 @@ Please run with mle=-1 to get a correct Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */ TvarsDind=ivector(1,NCOVMAX); /* */ + TnsdVar=ivector(1,NCOVMAX); /* */ TvarsD=ivector(1,NCOVMAX); /* */ TvarsQind=ivector(1,NCOVMAX); /* */ TvarsQ=ivector(1,NCOVMAX); /* */ @@ -11238,10 +12188,13 @@ Please run with mle=-1 to get a correct Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1] and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */ + Tvardk=imatrix(1,NCOVMAX,1,2); Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age 4 covariates (3 plus signs) Tage[1=V3*age]= 4; Tage[2=age*V4] = 3 - */ + */ + for(i=1;i> (k-1)) + 1; * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1 - * h\k 1 2 3 4 - *______________________________ - * 1 i=1 1 i=1 1 i=1 1 i=1 1 - * 2 2 1 1 1 - * 3 i=2 1 2 1 1 - * 4 2 2 1 1 - * 5 i=3 1 i=2 1 2 1 - * 6 2 1 2 1 - * 7 i=4 1 2 2 1 - * 8 2 2 2 1 - * 9 i=5 1 i=3 1 i=2 1 2 - * 10 2 1 1 2 - * 11 i=6 1 2 1 2 - * 12 2 2 1 2 - * 13 i=7 1 i=4 1 2 2 - * 14 2 1 2 2 - * 15 i=8 1 2 2 2 - * 16 2 2 2 2 - */ + * h\k 1 2 3 4 * h-1\k-1 4 3 2 1 + *______________________________ *______________________ + * 1 i=1 1 i=1 1 i=1 1 i=1 1 * 0 0 0 0 0 + * 2 2 1 1 1 * 1 0 0 0 1 + * 3 i=2 1 2 1 1 * 2 0 0 1 0 + * 4 2 2 1 1 * 3 0 0 1 1 + * 5 i=3 1 i=2 1 2 1 * 4 0 1 0 0 + * 6 2 1 2 1 * 5 0 1 0 1 + * 7 i=4 1 2 2 1 * 6 0 1 1 0 + * 8 2 2 2 1 * 7 0 1 1 1 + * 9 i=5 1 i=3 1 i=2 1 2 * 8 1 0 0 0 + * 10 2 1 1 2 * 9 1 0 0 1 + * 11 i=6 1 2 1 2 * 10 1 0 1 0 + * 12 2 2 1 2 * 11 1 0 1 1 + * 13 i=7 1 i=4 1 2 2 * 12 1 1 0 0 + * 14 2 1 2 2 * 13 1 1 0 1 + * 15 i=8 1 2 2 2 * 14 1 1 1 0 + * 16 2 2 2 2 * 15 1 1 1 1 + */ /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */ /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4 * and the value of each covariate? @@ -11454,7 +12407,7 @@ Title=%s
          Datafile=%s Firstpass=%d La optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model); } - fprintf(fichtm,"\n\n\nIMaCh %s\n IMaCh for Interpolated Markov Chain
          \nSponsored by Copyright (C) 2002-2015 INED-EUROREVES-Institut de longévité-2013-2016-Japan Society for the Promotion of Sciences 日本学術振興会 (Grant-in-Aid for Scientific Research 25293121) - Intel Software 2015-2018
          \ + fprintf(fichtm,"\n\n\nIMaCh %s\n IMaCh for Interpolated Markov Chain
          \nSponsored by Copyright (C) 2002-2015 INED-EUROREVES-Institut de longévité-2013-2016-Japan Society for the Promotion of Sciences 日本学術振興会 (Grant-in-Aid for Scientific Research 25293121) - Intel Software 2015-2018
          \
          \n\ IMaCh-%s
          %s           \
          \n\ @@ -11489,7 +12442,7 @@ Title=%s
          Datafile=%s Firstpass=%d La firstpass, lastpass, stepm, weightopt, model); fprintf(fichtm,"\n"); - fprintf(fichtm,"

          Parameter line 2

          • Tolerance for the convergence of the likelihood: ftol=%f \n
          • Interval for the elementary matrix (in month): stepm=%d",\ + fprintf(fichtm,"

            Parameter line 2

            • Tolerance for the convergence of the likelihood: ftol=%g \n
            • Interval for the elementary matrix (in month): stepm=%d",\ ftol, stepm); fprintf(fichtm,"\n
            • Number of fixed dummy covariates: ncovcol=%d ", ncovcol); ncurrv=1; @@ -11497,10 +12450,10 @@ Title=%s
              Datafile=%s Firstpass=%d La fprintf(fichtm,"\n
            • Number of fixed quantitative variables: nqv=%d ", nqv); ncurrv=i; for(i=ncurrv; i <=ncurrv-1+nqv; i++) fprintf(fichtm,"V%d ", i); - fprintf(fichtm,"\n
            • Number of time varying (wave varying) covariates: ntv=%d ", ntv); + fprintf(fichtm,"\n
            • Number of time varying (wave varying) dummy covariates: ntv=%d ", ntv); ncurrv=i; for(i=ncurrv; i <=ncurrv-1+ntv; i++) fprintf(fichtm,"V%d ", i); - fprintf(fichtm,"\n
            • Number of quantitative time varying covariates: nqtv=%d ", nqtv); + fprintf(fichtm,"\n
            • Number of time varying quantitative covariates: nqtv=%d ", nqtv); ncurrv=i; for(i=ncurrv; i <=ncurrv-1+nqtv; i++) fprintf(fichtm,"V%d ", i); fprintf(fichtm,"\n
            • Weights column \n
              Number of alive states: nlstate=%d
              Number of death states (not really implemented): ndeath=%d \n
            • Number of waves: maxwav=%d \n
            • Parameter for maximization (1), using parameter values (0), for design of parameters and variance-covariance matrix: mle=%d \n
            • Does the weight column be taken into account (1), or not (0): weight=%d
            \n", \ @@ -11510,7 +12463,7 @@ Title=%s
            Datafile=%s Firstpass=%d La ", subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_")); - fprintf(fichtm,"\n

            Some descriptive statistics

            \n
            Total number of observations=%d
            \n\ + fprintf(fichtm,"\n

            Some descriptive statistics

            \n
            Number of (used) observations=%d
            \n\ Youngest age at first (selected) pass %.2f, oldest age %.2f
            \n\ Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf
            \n",\ imx,agemin,agemax,jmin,jmax,jmean); @@ -11532,10 +12485,10 @@ Interval (in months) between two waves: for(j=1;j<=NDIM;j++) ximort[i][j]=0.; /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */ - cens=ivector(1,n); - ageexmed=vector(1,n); - agecens=vector(1,n); - dcwave=ivector(1,n); + cens=ivector(firstobs,lastobs); + ageexmed=vector(firstobs,lastobs); + agecens=vector(firstobs,lastobs); + dcwave=ivector(firstobs,lastobs); for (i=1; i<=imx; i++){ dcwave[i]=-1; @@ -11569,8 +12522,8 @@ Interval (in months) between two waves: ximort[i][j]=(i == j ? 1.0 : 0.0); } - /*p[1]=0.0268; p[NDIM]=0.083;*/ - /*printf("%lf %lf", p[1], p[2]);*/ + p[1]=0.0268; p[NDIM]=0.083; + /* printf("%lf %lf", p[1], p[2]); */ #ifdef GSL @@ -11696,9 +12649,9 @@ Interval (in months) between two waves: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i])); fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i])); } - lsurv=vector(1,AGESUP); - lpop=vector(1,AGESUP); - tpop=vector(1,AGESUP); + lsurv=vector(agegomp,AGESUP); + lpop=vector(agegomp,AGESUP); + tpop=vector(agegomp,AGESUP); lsurv[agegomp]=100000; for (k=agegomp;k<=AGESUP;k++) { @@ -11745,13 +12698,14 @@ Please run with mle=-1 to get a correct stepm, weightopt,\ model,imx,p,matcov,agemortsup); - free_vector(lsurv,1,AGESUP); - free_vector(lpop,1,AGESUP); - free_vector(tpop,1,AGESUP); + free_vector(lsurv,agegomp,AGESUP); + free_vector(lpop,agegomp,AGESUP); + free_vector(tpop,agegomp,AGESUP); free_matrix(ximort,1,NDIM,1,NDIM); - free_ivector(cens,1,n); - free_vector(agecens,1,n); - free_ivector(dcwave,1,n); + free_ivector(dcwave,firstobs,lastobs); + free_vector(agecens,firstobs,lastobs); + free_vector(ageexmed,firstobs,lastobs); + free_ivector(cens,firstobs,lastobs); #ifdef GSL #endif } /* Endof if mle==-3 mortality only */ @@ -11785,52 +12739,134 @@ Please run with mle=-1 to get a correct printf("\n"); /*--------- results files --------------*/ - fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, weightopt,model); + /* fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, weightopt,model); */ fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); - printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); + printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); /* Printing model equation */ fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); + + printf("#model= 1 + age "); + fprintf(ficres,"#model= 1 + age "); + fprintf(ficlog,"#model= 1 + age "); + fprintf(fichtm,"\n
            • model=1+age+%s\n \ +
            ", model); + + fprintf(fichtm,"\n
    AgePrev(%d)N(%d)N%dNaNq%.0f%.0f
    \n"); + fprintf(fichtm, ""); + if(nagesqr==1){ + printf(" + age*age "); + fprintf(ficres," + age*age "); + fprintf(ficlog," + age*age "); + fprintf(fichtm, ""); + } + for(j=1;j <=ncovmodel-2;j++){ + if(Typevar[j]==0) { + printf(" + V%d ",Tvar[j]); + fprintf(ficres," + V%d ",Tvar[j]); + fprintf(ficlog," + V%d ",Tvar[j]); + fprintf(fichtm, "",Tvar[j]); + }else if(Typevar[j]==1) { + printf(" + V%d*age ",Tvar[j]); + fprintf(ficres," + V%d*age ",Tvar[j]); + fprintf(ficlog," + V%d*age ",Tvar[j]); + fprintf(fichtm, "",Tvar[j]); + }else if(Typevar[j]==2) { + printf(" + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]); + fprintf(ficres," + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]); + fprintf(ficlog," + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]); + fprintf(fichtm, "",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]); + } + } + printf("\n"); + fprintf(ficres,"\n"); + fprintf(ficlog,"\n"); + fprintf(fichtm, ""); + fprintf(fichtm, "\n"); + + for(i=1,jk=1; i <=nlstate; i++){ for(k=1; k <=(nlstate+ndeath); k++){ if (k != i) { + fprintf(fichtm, ""); printf("%d%d ",i,k); fprintf(ficlog,"%d%d ",i,k); fprintf(ficres,"%1d%1d ",i,k); + fprintf(fichtm, "",i,k); for(j=1; j <=ncovmodel; j++){ printf("%12.7f ",p[jk]); fprintf(ficlog,"%12.7f ",p[jk]); fprintf(ficres,"%12.7f ",p[jk]); + fprintf(fichtm, "",p[jk]); jk++; } printf("\n"); fprintf(ficlog,"\n"); fprintf(ficres,"\n"); + fprintf(fichtm, "\n"); } } } + /* fprintf(fichtm,"\n"); */ + fprintf(fichtm,"
    Model=1+ age+ age*age+ V%d+ V%d*age+ V%d*V%d
    %1d%1d%12.7f
    \n"); + fprintf(fichtm, "\n"); + if(mle != 0){ /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */ ftolhess=ftol; /* Usually correct */ hesscov(matcov, hess, p, npar, delti, ftolhess, func); printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n"); fprintf(ficlog, "Parameters, Wald tests and Wald-based confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W \n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n"); + fprintf(fichtm, "\n

    The Wald test results are output only if the maximimzation of the Likelihood is performed (mle=1)\n
    Parameters, Wald tests and Wald-based confidence intervals\n
    W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n
    And Wald-based confidence intervals plus and minus 1.96 * W \n
    It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities and its graphs'.\n
    ",optionfilehtmcov); + fprintf(fichtm,"\n"); + fprintf(fichtm, "\n"); + if(nagesqr==1){ + printf(" + age*age "); + fprintf(ficres," + age*age "); + fprintf(ficlog," + age*age "); + fprintf(fichtm, ""); + } + for(j=1;j <=ncovmodel-2;j++){ + if(Typevar[j]==0) { + printf(" + V%d ",Tvar[j]); + fprintf(fichtm, "",Tvar[j]); + }else if(Typevar[j]==1) { + printf(" + V%d*age ",Tvar[j]); + fprintf(fichtm, "",Tvar[j]); + }else if(Typevar[j]==2) { + fprintf(fichtm, "",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]); + } + } + fprintf(fichtm, "\n"); + for(i=1,jk=1; i <=nlstate; i++){ for(k=1; k <=(nlstate+ndeath); k++){ if (k != i) { + fprintf(fichtm, ""); printf("%d%d ",i,k); fprintf(ficlog,"%d%d ",i,k); + fprintf(fichtm, "",i,k); for(j=1; j <=ncovmodel; j++){ - printf("%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk])); - fprintf(ficlog,"%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk])); + wald=p[jk]/sqrt(matcov[jk][jk]); + printf("%12.7f(%12.7f) W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk],sqrt(matcov[jk][jk]), p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk])); + fprintf(ficlog,"%12.7f(%12.7f) W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk],sqrt(matcov[jk][jk]), p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk])); + if(fabs(wald) > 1.96){ + fprintf(fichtm, "", p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk])); jk++; } printf("\n"); fprintf(ficlog,"\n"); + fprintf(fichtm, "\n"); } } } } /* end of hesscov and Wald tests */ + fprintf(fichtm,"
    Model=1+ age+ age*age+ V%d+ V%d*age+ V%d*V%d
    %1d%1d%12.7f
    (%12.7f)
    ",p[jk],sqrt(matcov[jk][jk])); + }else{ + fprintf(fichtm, "    		%12.7f (%12.7f)
    ",p[jk],sqrt(matcov[jk][jk])); + } + fprintf(fichtm,"W=%8.3f
    ",wald); + fprintf(fichtm,"[%12.7f;%12.7f]
    \n"); /* */ fprintf(ficres,"# Scales (for hessian or gradient estimation)\n"); @@ -11947,6 +12983,7 @@ Please run with mle=-1 to get a correct fputs(line,stdout); fputs(line,ficparo); fputs(line,ficlog); + fputs(line,ficres); continue; }else break; @@ -11992,6 +13029,7 @@ Please run with mle=-1 to get a correct fputs(line,stdout); fputs(line,ficparo); fputs(line,ficlog); + fputs(line,ficres); continue; }else break; @@ -12017,6 +13055,7 @@ Please run with mle=-1 to get a correct fputs(line,stdout); fputs(line,ficparo); fputs(line,ficlog); + fputs(line,ficres); continue; }else break; @@ -12039,95 +13078,114 @@ Please run with mle=-1 to get a correct } /* Results */ + endishere=0; nresult=0; + parameterline=0; do{ if(!fgets(line, MAXLINE, ficpar)){ endishere=1; - parameterline=14; + parameterline=15; }else if (line[0] == '#') { /* If line starts with a # it is a comment */ numlinepar++; fputs(line,stdout); fputs(line,ficparo); fputs(line,ficlog); + fputs(line,ficres); continue; }else if(sscanf(line,"prevforecast=%[^\n]\n",modeltemp)) parameterline=11; - else if(sscanf(line,"backcast=%[^\n]\n",modeltemp)) + else if(sscanf(line,"prevbackcast=%[^\n]\n",modeltemp)) parameterline=12; - else if(sscanf(line,"result:%[^\n]\n",modeltemp)) + else if(sscanf(line,"result:%[^\n]\n",modeltemp)){ parameterline=13; + } else{ parameterline=14; } - switch (parameterline){ + switch (parameterline){ /* =0 only if only comments */ case 11: - if((num_filled=sscanf(line,"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)) !=EOF){ - if (num_filled != 8) { - printf("Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mobil_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line); - fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line); - goto end; - } - 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); + if((num_filled=sscanf(line,"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)) !=EOF && (num_filled == 8)){ + 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); 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); 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); 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); /* day and month of proj2 are not used but only year anproj2.*/ dateproj1=anproj1+(mproj1-1)/12.+(jproj1-1)/365.; dateproj2=anproj2+(mproj2-1)/12.+(jproj2-1)/365.; - + prvforecast = 1; + } + else if((num_filled=sscanf(line,"prevforecast=%d yearsfproj=%lf mobil_average=%d\n",&prevfcast,&yrfproj,&mobilavproj)) !=EOF){/* && (num_filled == 3))*/ + printf("prevforecast=%d yearsfproj=%.2lf mobil_average=%d\n",prevfcast,yrfproj,mobilavproj); + fprintf(ficlog,"prevforecast=%d yearsfproj=%.2lf mobil_average=%d\n",prevfcast,yrfproj,mobilavproj); + fprintf(ficres,"prevforecast=%d yearsfproj=%.2lf mobil_average=%d\n",prevfcast,yrfproj,mobilavproj); + prvforecast = 2; + } + else { + printf("Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevforecast=1 yearsfproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line); + fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevforecast=1 yearproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line); + goto end; } break; case 12: - /*fscanf(ficpar,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);*/ - if((num_filled=sscanf(line,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj)) !=EOF){ - if (num_filled != 8) { - printf("Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 final-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line); - fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 final-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line); - goto end; - } - printf("backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj); - fprintf(ficparo,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj); - fprintf(ficlog,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj); - fprintf(ficres,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj); - /* day and month of proj2 are not used but only year anproj2.*/ + if((num_filled=sscanf(line,"prevbackcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&prevbcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj)) !=EOF && (num_filled == 8)){ + fprintf(ficparo,"prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj); + printf("prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj); + fprintf(ficlog,"prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj); + fprintf(ficres,"prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj); + /* day and month of back2 are not used but only year anback2.*/ dateback1=anback1+(mback1-1)/12.+(jback1-1)/365.; dateback2=anback2+(mback2-1)/12.+(jback2-1)/365.; + prvbackcast = 1; + } + else if((num_filled=sscanf(line,"prevbackcast=%d yearsbproj=%lf mobil_average=%d\n",&prevbcast,&yrbproj,&mobilavproj)) ==3){/* && (num_filled == 3))*/ + printf("prevbackcast=%d yearsbproj=%.2lf mobil_average=%d\n",prevbcast,yrbproj,mobilavproj); + fprintf(ficlog,"prevbackcast=%d yearsbproj=%.2lf mobil_average=%d\n",prevbcast,yrbproj,mobilavproj); + fprintf(ficres,"prevbackcast=%d yearsbproj=%.2lf mobil_average=%d\n",prevbcast,yrbproj,mobilavproj); + prvbackcast = 2; + } + else { + printf("Error: Not 8 (data)parameters in line but %d, for example:prevbackcast=1 starting-back-date=1/1/1990 final-back-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevbackcast=1 yearsbproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line); + fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:prevbackcast=1 starting-back-date=1/1/1990 final-back-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevbackcast=1 yearbproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line); + goto end; } break; case 13: - if((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){ - if (num_filled == 0){ - resultline[0]='\0'; - printf("Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line); - fprintf(ficlog,"Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line); - break; - } else if (num_filled != 1){ - printf("ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line); - fprintf(ficlog,"ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line); - } - nresult++; /* Sum of resultlines */ - printf("Result %d: result=%s\n",nresult, resultline); - if(nresult > MAXRESULTLINES){ - printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult); - fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult); - goto end; - } - decoderesult(resultline, nresult); /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */ + num_filled=sscanf(line,"result:%[^\n]\n",resultline); + nresult++; /* Sum of resultlines */ + printf("Result %d: result:%s\n",nresult, resultline); + if(nresult > MAXRESULTLINESPONE-1){ + printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\nYou can use the 'r' parameter file '%s' which uses option mle=0 to get other results. ",MAXRESULTLINESPONE-1,nresult,rfileres); + fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\nYou can use the 'r' parameter file '%s' which uses option mle=0 to get other results. ",MAXRESULTLINESPONE-1,nresult,rfileres); + goto end; + } + if(!decoderesult(resultline, nresult)){ /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */ fprintf(ficparo,"result: %s\n",resultline); fprintf(ficres,"result: %s\n",resultline); fprintf(ficlog,"result: %s\n",resultline); - break; - case 14: - if(ncovmodel >2 && nresult==0 ){ - printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line); - goto end; - } - break; - default: - nresult=1; - decoderesult(".",nresult ); /* No covariate */ + } else + goto end; + break; + case 14: + printf("Error: Unknown command '%s'\n",line); + fprintf(ficlog,"Error: Unknown command '%s'\n",line); + if(line[0] == ' ' || line[0] == '\n'){ + printf("It should not be an empty line '%s'\n",line); + fprintf(ficlog,"It should not be an empty line '%s'\n",line); + } + if(ncovmodel >=2 && nresult==0 ){ + printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line); + fprintf(ficlog,"ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line); } + /* goto end; */ + break; + case 15: + printf("End of resultlines.\n"); + fprintf(ficlog,"End of resultlines.\n"); + break; + default: /* parameterline =0 */ + nresult=1; + decoderesult(".",nresult ); /* No covariate */ } /* End switch parameterline */ }while(endishere==0); /* End do */ @@ -12144,11 +13202,44 @@ This is probably because your parameter Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar); }else{ /* printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p, (int)anproj1-(int)agemin, (int)anback1-(int)agemax+1); */ - printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,bage, fage, prevfcast, backcast, pathc,p, (int)anproj1-bage, (int)anback1-fage); + /* It seems that anprojd which is computed from the mean year at interview which is known yet because of freqsummary */ + /* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); */ /* Done in freqsummary */ + if(prvforecast==1){ + dateprojd=(jproj1+12*mproj1+365*anproj1)/365; + jprojd=jproj1; + mprojd=mproj1; + anprojd=anproj1; + dateprojf=(jproj2+12*mproj2+365*anproj2)/365; + jprojf=jproj2; + mprojf=mproj2; + anprojf=anproj2; + } else if(prvforecast == 2){ + dateprojd=dateintmean; + date2dmy(dateprojd,&jprojd, &mprojd, &anprojd); + dateprojf=dateintmean+yrfproj; + date2dmy(dateprojf,&jprojf, &mprojf, &anprojf); + } + if(prvbackcast==1){ + datebackd=(jback1+12*mback1+365*anback1)/365; + jbackd=jback1; + mbackd=mback1; + anbackd=anback1; + datebackf=(jback2+12*mback2+365*anback2)/365; + jbackf=jback2; + mbackf=mback2; + anbackf=anback2; + } else if(prvbackcast == 2){ + datebackd=dateintmean; + date2dmy(datebackd,&jbackd, &mbackd, &anbackd); + datebackf=dateintmean-yrbproj; + date2dmy(datebackf,&jbackf, &mbackf, &anbackf); + } + + printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,bage, fage, prevfcast, prevbcast, pathc,p, (int)anprojd-bage, (int)anbackd-fage); } printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \ - model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,backcast, estepm, \ - jprev1,mprev1,anprev1,dateprev1, dateproj1, dateback1,jprev2,mprev2,anprev2,dateprev2,dateproj2, dateback2); + model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,prevbcast, estepm, \ + jprev1,mprev1,anprev1,dateprev1, dateprojd, datebackd,jprev2,mprev2,anprev2,dateprev2,dateprojf, datebackf); /*------------ free_vector -------------*/ /* chdir(path); */ @@ -12157,8 +13248,8 @@ Please run with mle=-1 to get a correct /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */ /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */ /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx); */ - free_lvector(num,1,n); - free_vector(agedc,1,n); + free_lvector(num,firstobs,lastobs); + free_vector(agedc,firstobs,lastobs); /*free_matrix(covar,0,NCOVMAX,1,n);*/ /*free_matrix(covar,1,NCOVMAX,1,n);*/ fclose(ficparo); @@ -12221,13 +13312,23 @@ Please run with mle=-1 to get a correct }/* end if moving average */ /*---------- Forecasting ------------------*/ - if(prevfcast==1){ - /* if(stepm ==1){*/ - prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff); + if(prevfcast==1){ + /* /\* if(stepm ==1){*\/ */ + /* /\* anproj1, mproj1, jproj1 either read explicitly or yrfproj *\/ */ + /*This done previously after freqsummary.*/ + /* dateprojd=(jproj1+12*mproj1+365*anproj1)/365; */ + /* dateprojf=(jproj2+12*mproj2+365*anproj2)/365; */ + + /* } else if (prvforecast==2){ */ + /* /\* if(stepm ==1){*\/ */ + /* /\* anproj1, mproj1, jproj1 either read explicitly or yrfproj *\/ */ + /* } */ + /*prevforecast(fileresu, dateintmean, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);*/ + prevforecast(fileresu,dateintmean, dateprojd, dateprojf, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, p, cptcoveff); } - /* Backcasting */ - if(backcast==1){ + /* Prevbcasting */ + if(prevbcast==1){ ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath); ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath); ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath); @@ -12242,8 +13343,14 @@ Please run with mle=-1 to get a correct hBijx(p, bage, fage, mobaverage); fclose(ficrespijb); - prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, - mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff); + /* /\* prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, *\/ */ + /* /\* mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff); *\/ */ + /* prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, */ + /* mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */ + prevbackforecast(fileresu, mobaverage, dateintmean, dateprojd, dateprojf, agemin, agemax, dateprev1, dateprev2, + mobilavproj, bage, fage, firstpass, lastpass, p, cptcoveff); + + varbprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, bprlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff); @@ -12251,7 +13358,7 @@ Please run with mle=-1 to get a correct free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath); free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath); free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath); - } /* end Backcasting */ + } /* end Prevbcasting */ /* ------ Other prevalence ratios------------ */ @@ -12285,8 +13392,8 @@ Please run with mle=-1 to get a correct fprintf(ficreseij,"\n#****** "); printf("\n#****** "); for(j=1;j<=cptcoveff;j++) { - fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); - printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); + printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); } for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */ printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); @@ -12297,6 +13404,7 @@ Please run with mle=-1 to get a correct eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); oldm=oldms;savm=savms; + /* printf("HELLO Entering evsij bage=%d fage=%d k=%d estepm=%d nres=%d\n",(int) bage, (int)fage, k, estepm, nres); */ evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart, nres); free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage); @@ -12350,13 +13458,13 @@ Please run with mle=-1 to get a correct for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */ if(i1 != 1 && TKresult[nres]!= k) continue; - printf("\n#****** Result for:"); - fprintf(ficrest,"\n#****** Result for:"); - fprintf(ficlog,"\n#****** Result for:"); + printf("\n# model %s \n#****** Result for:", model); + fprintf(ficrest,"\n# model %s \n#****** Result for:", model); + fprintf(ficlog,"\n# model %s \n#****** Result for:", model); for(j=1;j<=cptcoveff;j++){ - printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); - fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); - fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); + fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); + fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); } for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */ printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); @@ -12370,8 +13478,8 @@ Please run with mle=-1 to get a correct fprintf(ficresstdeij,"\n#****** "); fprintf(ficrescveij,"\n#****** "); for(j=1;j<=cptcoveff;j++) { - fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); - fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); + fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); } for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */ fprintf(ficresstdeij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); @@ -12383,7 +13491,7 @@ Please run with mle=-1 to get a correct fprintf(ficresvij,"\n#****** "); /* pstamp(ficresvij); */ for(j=1;j<=cptcoveff;j++) - fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */ fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); } @@ -12415,13 +13523,13 @@ Please run with mle=-1 to get a correct if(vpopbased==1) fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav); else - fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n"); + fprintf(ficrest,"the age specific forward period (stable) prevalences in each health state \n"); fprintf(ficrest,"# Age popbased mobilav e.. (std) "); for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i); fprintf(ficrest,"\n"); /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */ - printf("Computing age specific period (stable) prevalences in each health state \n"); - fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n"); + printf("Computing age specific forward period (stable) prevalences in each health state \n"); + fprintf(ficlog,"Computing age specific forward period (stable) prevalences in each health state \n"); for(age=bage; age <=fage ;age++){ prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k, nres); /*ZZ Is it the correct prevalim */ if (vpopbased==1) { @@ -12468,16 +13576,17 @@ Please run with mle=-1 to get a correct printf("done State-specific expectancies\n");fflush(stdout); fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog); - /* variance-covariance of period prevalence*/ + /* variance-covariance of forward period prevalence*/ varprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, prlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff); - free_vector(weight,1,n); + free_vector(weight,firstobs,lastobs); + free_imatrix(Tvardk,1,NCOVMAX,1,2); free_imatrix(Tvard,1,NCOVMAX,1,2); - free_imatrix(s,1,maxwav+1,1,n); - free_matrix(anint,1,maxwav,1,n); - free_matrix(mint,1,maxwav,1,n); - free_ivector(cod,1,n); + free_imatrix(s,1,maxwav+1,firstobs,lastobs); + free_matrix(anint,1,maxwav,firstobs,lastobs); + free_matrix(mint,1,maxwav,firstobs,lastobs); + free_ivector(cod,firstobs,lastobs); free_ivector(tab,1,NCOVMAX); fclose(ficresstdeij); fclose(ficrescveij); @@ -12497,10 +13606,10 @@ Please run with mle=-1 to get a correct free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath); free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath); free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath); - if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,1,n); - if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n); - if(nqv>=1)free_matrix(coqvar,1,nqv,1,n); - free_matrix(covar,0,NCOVMAX,1,n); + if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,firstobs,lastobs); + if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,firstobs,lastobs); + if(nqv>=1)free_matrix(coqvar,1,nqv,firstobs,lastobs); + free_matrix(covar,0,NCOVMAX,firstobs,lastobs); free_matrix(matcov,1,npar,1,npar); free_matrix(hess,1,npar,1,npar); /*free_vector(delti,1,npar);*/ @@ -12520,6 +13629,7 @@ Please run with mle=-1 to get a correct free_ivector(TvarsQ,1,NCOVMAX); free_ivector(TvarsQind,1,NCOVMAX); free_ivector(TvarsD,1,NCOVMAX); + free_ivector(TnsdVar,1,NCOVMAX); free_ivector(TvarsDind,1,NCOVMAX); free_ivector(TvarFD,1,NCOVMAX); free_ivector(TvarFDind,1,NCOVMAX); @@ -12583,6 +13693,8 @@ Please run with mle=-1 to get a correct fclose(ficlog); /*------ End -----------*/ + +/* Executes gnuplot */ printf("Before Current directory %s!\n",pathcd); #ifdef WIN32 @@ -12618,13 +13730,16 @@ Please run with mle=-1 to get a correct sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot); printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout); + strcpy(pplotcmd,plotcmd); if((outcmd=system(plotcmd)) != 0){ - printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd); + printf("Error in gnuplot, command might not be in your path: '%s', err=%d\n", plotcmd, outcmd); printf("\n Trying if gnuplot resides on the same directory that IMaCh\n"); sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot); - if((outcmd=system(plotcmd)) != 0) + if((outcmd=system(plotcmd)) != 0){ printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd); + strcpy(plotcmd,pplotcmd); + } } printf(" Successful, please wait..."); while (z[0] != 'q') { @@ -12651,4 +13766,6 @@ end: printf("\nType q for exiting: "); fflush(stdout); scanf("%s",z); } + printf("End\n"); + exit(0); }