--- imach/src/imach.c 2017/03/27 05:50:23 1.256 +++ imach/src/imach.c 2017/04/18 16:48:12 1.262 @@ -1,6 +1,26 @@ -/* $Id: imach.c,v 1.256 2017/03/27 05:50:23 brouard Exp $ +/* $Id: imach.c,v 1.262 2017/04/18 16:48:12 brouard Exp $ $State: Exp $ $Log: imach.c,v $ + Revision 1.262 2017/04/18 16:48:12 brouard + *** empty log message *** + + Revision 1.261 2017/04/05 10:14:09 brouard + Summary: Bug in E_ as well as in T_ fixed nres-1 vs k1-1 + + Revision 1.260 2017/04/04 17:46:59 brouard + Summary: Gnuplot indexations fixed (humm) + + Revision 1.259 2017/04/04 13:01:16 brouard + Summary: Some errors to warnings only if date of death is unknown but status is death we could set to pi3 + + Revision 1.258 2017/04/03 10:17:47 brouard + Summary: Version 0.99r12 + + Some cleanings, conformed with updated documentation. + + Revision 1.257 2017/03/29 16:53:30 brouard + Summary: Temp + Revision 1.256 2017/03/27 05:50:23 brouard Summary: Temporary @@ -968,12 +988,12 @@ typedef struct { #define ODIRSEPARATOR '\\' #endif -/* $Id: imach.c,v 1.256 2017/03/27 05:50:23 brouard Exp $ */ +/* $Id: imach.c,v 1.262 2017/04/18 16:48:12 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: 1.256 $ $Date: 2017/03/27 05:50:23 $"; +char fullversion[]="$Revision: 1.262 $ $Date: 2017/04/18 16:48:12 $"; char strstart[80]; char optionfilext[10], optionfilefiname[FILENAMELENGTH]; int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */ @@ -1174,6 +1194,7 @@ int *TvarsQind; #define MAXRESULTLINES 10 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) */ @@ -4647,7 +4668,8 @@ Title=%s
Datafile=%s Firstpass=%d La if(posproptt < 1.e-5){ fprintf(ficresphtm,"\n

This combination (%d) is not valid and no result will be produced

",j1); fprintf(ficresphtmfr,"\n

This combination (%d) is not valid and no result will be produced

",j1); - fprintf(ficres,"\n This combination (%d) is not valid and no result will be produced\n\n",j1); + fprintf(ficlog,"# This combination (%d) is not valid and no result will be produced\n",j1); + printf("# This combination (%d) is not valid and no result will be produced\n",j1); invalidvarcomb[j1]=1; }else{ fprintf(ficresphtm,"\n

This combination (%d) is valid and result will be produced.

",j1); @@ -4929,10 +4951,10 @@ void concatwav(int wav[], int **dh, int #else if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){ 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 pi. .\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); + 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; } - 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 pi. .\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); + 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; mli=m; } @@ -4959,13 +4981,9 @@ void concatwav(int wav[], int **dh, int /* if(mi==0) never been interviewed correctly before death */ /* Only death is a correct wave */ mw[mi][i]=m; - } + } /* else not in a death state */ #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE - else if ((int) andc[i] != 9999) { /* Status is negative. A death occured after lastpass, we can't take it into account because of potential bias */ - /* m++; */ - /* mi++; */ - /* s[m][i]=nlstate+1; /\* We are setting the status to the last of non live state *\/ */ - /* mw[mi][i]=m; */ + 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 */ nbwarn++; @@ -4978,12 +4996,12 @@ void concatwav(int wav[], int **dh, int }else{ /* Death occured afer last wave 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.\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. 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 ); 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.\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. 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 ); } - }else{ /* end date of interview is known */ + }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 ); @@ -5014,7 +5032,7 @@ void concatwav(int wav[], int **dh, int if (stepm <=0) dh[mi][i]=1; else{ - if (s[mw[mi+1][i]][i] > nlstate) { /* A death */ + if (s[mw[mi+1][i]][i] > nlstate) { /* A death, but what if date is unknown? */ if (agedc[i] < 2*AGESUP) { j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); if(j==0) j=1; /* Survives at least one month after exam */ @@ -6376,7 +6394,7 @@ 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 prevfcast, int backcast, int estepm , \ + int popforecast, int mobilav, int prevfcast, int mobilavproj, int backcast, int estepm , \ double jprev1, double mprev1,double anprev1, double dateprev1, \ double jprev2, double mprev2,double anprev2, double dateprev2){ int jj1, k1, i1, cpt, k4, nres; @@ -6450,7 +6468,7 @@ void printinghtml(char fileresu[], char } } /* aij, bij */ - fprintf(fichtm,"
- Logit model (yours is: 1+age+%s), for example: logit(pij)=log(pij/pii)= aij+ bij age + V1 age + etc. as a function of age: %s_%d-1-%d.svg
\ + fprintf(fichtm,"
- Logit model (yours is: logit(pij)=log(pij/pii)= aij+ bij age+%s) as a function of age: %s_%d-1-%d.svg
\ ",model,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres); /* Pij */ fprintf(fichtm,"
\n- Pij or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s_%d-2-%d.svg
\ @@ -6487,8 +6505,8 @@ divided by h: hPij if(prevfcast==1){ /* Projection of prevalence up to period (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) up to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. %s_%d-%d-%d.svg
\ -", dateprev1, dateprev2, 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) up to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. %s_%d-%d-%d.svg
\ +", dateprev1, dateprev2, mobilavproj, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres); } } @@ -6576,9 +6594,9 @@ See page 'Matrix of variance-covariance } } for(cpt=1; cpt<=nlstate;cpt++) { - fprintf(fichtm,"\n
- Observed (cross-sectional) and period (incidence based) \ + 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
\ -",cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres); +",mobilav,cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,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) \ @@ -6673,24 +6691,26 @@ void printinggnuplot(char fileresu[], ch /* printf("\n#\n"); */ fprintf(ficgp,"\n#\n"); if(invalidvarcomb[k1]){ + /*k1=k1-1;*/ /* To be checked */ fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); continue; } 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 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); - + 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*/ for (i=1; i<= nlstate ; i ++) { 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_"),k1-1,k1-1,nres); + 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); for (i=1; i<= nlstate ; i ++) { if (i==cpt) fprintf(ficgp," %%lf (%%lf)"); else fprintf(ficgp," %%*lf (%%*lf)"); } - fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres); + fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%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)"); @@ -6763,20 +6783,20 @@ void printinggnuplot(char fileresu[], ch fprintf(ficgp,"\nreplot "); for (i=1; i<= nlstate+1 ; i ++) { k=2*i; - fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1, vpopbased); + fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1, vpopbased); for (j=1; j<= nlstate+1 ; j ++) { if (j==i) fprintf(ficgp," %%lf (%%lf)"); else fprintf(ficgp," %%*lf (%%*lf)"); } if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i); else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1); - fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased); + fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1,vpopbased); for (j=1; j<= nlstate+1 ; j ++) { if (j==i) fprintf(ficgp," %%lf (%%lf)"); else fprintf(ficgp," %%*lf (%%*lf)"); } fprintf(ficgp,"\" t\"\" w l lt 0,"); - fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased); + fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1,vpopbased); for (j=1; j<= nlstate+1 ; j ++) { if (j==i) fprintf(ficgp," %%lf (%%lf)"); else fprintf(ficgp," %%*lf (%%*lf)"); @@ -6797,7 +6817,7 @@ void printinggnuplot(char fileresu[], ch continue; for (cpt=1; cpt<= nlstate ; cpt ++) { - fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files: combination=%d state=%d",k1, cpt); + fprintf(ficgp,"\n\n# 3d: Life expectancy with EXP_ files: combination=%d state=%d",k1, cpt); for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */ lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */ /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ @@ -6819,7 +6839,7 @@ void printinggnuplot(char fileresu[], ch k=2+(nlstate+1)*(cpt-1); fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres); fprintf(ficgp,"set ter svg size 640, 480\n\ -plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt); +plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),nres-1,nres-1,k,cpt); /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1); for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) "); fprintf(ficgp,"\" t \"e%d1\" w l",cpt); @@ -6829,11 +6849,11 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u */ for (i=1; i< nlstate ; i ++) { - fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+i,cpt,i+1); + fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),nres-1,nres-1,k+i,cpt,i+1); /* fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/ } - fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+nlstate,cpt); + fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),nres-1,nres-1,k+nlstate,cpt); } } /* end nres */ } /* end kl 3eme */ @@ -9103,16 +9123,16 @@ int calandcheckages(int imx, int maxwav, *nberr = *nberr + 1; if(firstone == 0){ firstone=1; - printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\nOther similar cases in log file\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m); + printf("Warning (#%d)! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown but status is a death state %d at wave %d. If you don't know the vital status, please enter -2. If he/she is still alive but don't know the state, please code with '-1 or '.'. Here, we do not believe in a death, skipped.\nOther similar cases in log file\n", *nberr,(int)moisdc[i],(int)andc[i],num[i],i,s[m][i],m); } - fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m); - s[m][i]=-1; + fprintf(ficlog,"Warning (#%d)! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown but status is a death state %d at wave %d. If you don't know the vital status, please enter -2. If he/she is still alive but don't know the state, please code with '-1 or '.'. Here, we do not believe in a death, skipped.\n", *nberr,(int)moisdc[i],(int)andc[i],num[i],i,s[m][i],m); + s[m][i]=-1; /* Droping the death status */ } if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){ (*nberr)++; - printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); - fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); - s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */ + printf("Error (#%d)! Month of death of individual %ld on line %d was unknown (%2d) (year of death is %4d) and status is a death state %d at wave %d. Please impute an arbitrary (or not) month and rerun. Currently this transition to death will be skipped (status is set to -2).\nOther similar cases in log file\n", *nberr, num[i],i,(int)moisdc[i],(int)andc[i],s[m][i],m); + fprintf(ficlog,"Error (#%d)! Month of death of individual %ld on line %d was unknown (%2d) (year of death is %4d) and status is a death state %d at wave %d. Please impute an arbitrary (or not) month and rerun. Currently this transition to death will be skipped (status is set to -2).\n", *nberr, num[i],i,(int)moisdc[i],(int)andc[i],s[m][i],m); + s[m][i]=-2; /* We prefer to skip it (and to skip it in version 0.8a1 too */ } } } @@ -9778,6 +9798,7 @@ int main(int argc, char *argv[]) int NDIM=2; int vpopbased=0; int nres=0; + int endishere=0; char ca[32], cb[32]; /* FILE *fichtm; *//* Html File */ @@ -11152,11 +11173,9 @@ Please run with mle=-1 to get a correct fprintf(ficlog,"Error: Not 7 (data)parameters in line but %d, for example:begin-prev-date=1/1/1990 end-prev-date=1/6/2004 mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line); goto end; } - /* fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav); */ printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav); fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav); fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav); - printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav); fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav); } @@ -11188,125 +11207,93 @@ Please run with mle=-1 to get a correct fprintf(ficres,"pop_based=%d\n",popbased); } - while(fgets(line, MAXLINE, ficpar)) { - /* If line starts with a # it is a comment */ - if (line[0] == '#') { - numlinepar++; - fputs(line,stdout); - fputs(line,ficparo); - fputs(line,ficlog); - continue; - }else - break; - } - /* while((c=getc(ficpar))=='#' && c!= EOF){ */ - /* ungetc(c,ficpar); */ - /* fgets(line, MAXLINE, ficpar); */ - /* fputs(line,stdout); */ - /* fputs(line,ficres); */ - /* fputs(line,ficparo); */ - /* } */ - /* ungetc(c,ficpar); */ - - /* fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj); */ - 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); - 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.*/ - } - while(fgets(line, MAXLINE, ficpar)) { - /* If line starts with a # it is a comment */ - if (line[0] == '#') { - numlinepar++; - fputs(line,stdout); - fputs(line,ficparo); - fputs(line,ficlog); - continue; - }else - break; - } - /* while((c=getc(ficpar))=='#' && c!= EOF){ */ - /* ungetc(c,ficpar); */ - /* fgets(line, MAXLINE, ficpar); */ - /* fputs(line,stdout); */ - /* fputs(line,ficparo); */ - /* fputs(line,ficres); */ - /* } */ - /* ungetc(c,ficpar); */ - - 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 finloal-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 finloal-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.*/ - } /* Results */ nresult=0; - while(fgets(line, MAXLINE, ficpar)) { - /* If line starts with a # it is a comment */ - if (line[0] == '#') { + do{ + if(!fgets(line, MAXLINE, ficpar)){ + endishere=1; + parameterline=14; + }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 - break; - } - if (!feof(ficpar)) - while((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){ - if (num_filled == 0){ - resultline[0]='\0'; - printf("Warning %d: no result line 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 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 */ - fprintf(ficparo,"result: %s\n",resultline); - fprintf(ficres,"result: %s\n",resultline); - fprintf(ficlog,"result: %s\n",resultline); - while(fgets(line, MAXLINE, ficpar)) { - /* If line starts with a # it is a comment */ - if (line[0] == '#') { - numlinepar++; - fputs(line,stdout); - fputs(line,ficparo); - fputs(line,ficres); - fputs(line,ficlog); - continue; - }else - break; + }else if(sscanf(line,"prevforecast=%[^\n]\n",modeltemp)) + parameterline=11; + else if(sscanf(line,"backcast=%[^\n]\n",modeltemp)) + parameterline=12; + else if(sscanf(line,"result:%[^\n]\n",modeltemp)) + parameterline=13; + else{ + parameterline=14; } - if (feof(ficpar)) + switch (parameterline){ + 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); + 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.*/ + } break; - else{ /* Processess output results for this combination of covariate values */ - } - } /* end while */ - - + 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.*/ + } + 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 */ + 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 */ + } + } /* End switch parameterline */ + }while(endishere==0); /* End do */ /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */ /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */ @@ -11323,7 +11310,7 @@ Please run with mle=-1 to get a correct printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p); } printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \ - model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,backcast, estepm, \ + model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,backcast, estepm, \ jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2); /*------------ free_vector -------------*/ @@ -11376,6 +11363,7 @@ Please run with mle=-1 to get a correct mobaverage=mobaverages; if (mobilav!=0) { printf("Movingaveraging observed prevalence\n"); + fprintf(ficlog,"Movingaveraging observed prevalence\n"); if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){ fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); printf(" Error in movingaverage mobilav=%d\n",mobilav); @@ -11385,6 +11373,7 @@ Please run with mle=-1 to get a correct /* prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */ else if (mobilavproj !=0) { printf("Movingaveraging projected observed prevalence\n"); + fprintf(ficlog,"Movingaveraging projected observed prevalence\n"); if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){ fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj); printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);