void gfmUserDefd_OneStepByGlobals(void)
{
SingleSweep(gC);
IncrementValues(gC,1);
/* update the sliding Trace */
gfduIncrementSlidingTrace(gCompleteDataLogLike,gC->Lat->TheCompleteDataLogLike);
if(gNumSweepsAfterBurnIn%300==0 && gNumSweepsAfterBurnIn > 0) {
OutputHistograms(gC);
fprint_PofZ(gC);
fprint_PiAverages(gC);
fprint_AlleleAverages(gC);
fprint_UniPriPofZ(gC);
}
}
int main(void)
{
char File[100], DatFile[100], GtypFile[100];
int temp;
double temp_d;
enum prior_type PiP = JEFFREYS, ThP = JEFFREYS;
int DoAsBurnIn = 0, DoAsReps = 0,i,g;
time_t StartTime, CurrTime, LastTime, RealRepStartTime, DummyTime;
double SecondsPerSweep, SecondsRemain;
int priorchoice;
long Seed1, Seed2;
int boing;
hyb_data *D;
hyb_prior *P;
hyb_chain *C;
printf("Welcome to the program currently named \"NewHybrids\" Version 1.1 beta");
printf("\nPre-Released 2 OCTOBER 2002.");
printf("\nwritten by Eric C. Anderson ([email protected])");
printf("\nCopyright (c) by The Regents of the University of California\n");
printf("Please see user documentation for full software agreement.");
printf("\n-----------------------\nEnter a \n\t0 to load \"TestDat.txt\"");
printf("\n\t1 to load \"TestDatWithOptions.dat\"");
printf("\n\t2 to load \"TestAFLP.dat\"");
printf("\n\t3 to load \"TestAFLPWithOptions.dat\"");
printf("\nas the Data File\n");
printf("\nOr enter the name of the file you wish to use.");
printf("\n\nRemember that file must be in the directory in which\nthe program resides.\n\n->");
/* read the DATA FILE name or a 0 */
temp = erdGetNext(File,&temp_d,stdin);
if(temp == 1 && temp_d == 0.0) { /* if input was an int equal to zero set File to "TestDat.txt" */
sprintf(File,"TestDat.dat");
}
if(temp == 1 && temp_d == 1.0) {
sprintf(File,"TestDatWithOptions.dat");
}
if(temp == 1 && temp_d == 2.0) {
sprintf(File,"TestAFLP.dat");
}
if(temp == 1 && temp_d == 3.0) {
sprintf(File,"TestAFLPWithOptions.dat");
}
/* get the DATA: */
D = GetData(File);
sprintf(DatFile,"%s",File);
/* now read in the gtyp freq categories */
printf("\n\n-----------------\n");
printf("\nNow enter a 0 to read the genotype frequency classes in the file");
printf("\"TwoGensGtypFreq.txt\". Or enter the name of the file holding your");
printf("\nown definitions of genotype frequency classes.\n\n->");
/* read the GTYP FILE name or a 0 */
temp = erdGetNext(File,&temp_d,stdin);
if(temp == 1 && temp_d == 0.0) { /* if input was an int equal to zero set File to "TestDat.txt" */
sprintf(File,"TwoGensGtypFreq.txt");
}
GetGtypFreqCats(D,File);
sprintf(GtypFile,"%s",File);
/* now we can process the individual options a little bit */
ProcessIndivOptions(D);
/* put alleles from indivs known to be in Purebred categories into the
"PriorizedAllelesPile" */
PriorizeAllelesFromFixedZ(D);
AddPriorizeAllelesFromFile(D);
printf("\n\nGive me two small integers (>0) for random number seeds\n\n");
scanf("%d%d",&Seed1,&Seed2);
setall((long)Seed1,(long)Seed2);
printf("\n\nEnter the choices for prior type for pi (mixing proportion):\n\t0 for Jeffreys\n\t1 for Uniform\n->");
scanf("%d",&priorchoice);
switch(priorchoice) {
case(0):
PiP = JEFFREYS;
break;
case(1):
PiP = UNIFORM;
break;
default:
PiP = JEFFREYS;
printf("\n\nInvalid choice. Pi Prior set to Jeffreys by default.\n\n");
}
printf("\n\nEnter the choices for theta type for pi (mixing proportion):\n\t0 for Jeffreys\n\t1 for Uniform\n->");
scanf("%d",&priorchoice);
switch(priorchoice) {
case(0):
ThP = JEFFREYS;
break;
case(1):
ThP = UNIFORM;
break;
default:
ThP = JEFFREYS;
printf("\n\nInvalid choice. Theta Prior set to Jeffreys by default.\n\n");
}
P = CreatePriors(D,PiP,ThP);
C = CreateLatentChain(D,P);
C->Seed1 = Seed1;
C->Seed2 = Seed2;
InitializeChain(C);
printf("\n\nData all read and ready!!!\n\n");
printf("\n\nEntering Graphics-Free version...\n\n");
printf("\nPlease enter the number of sweeps for BurnIn (must be an integer) \n->");
scanf("%d",&DoAsBurnIn);
printf("\nPlease enter the number of sweeps to be done after BurnIn (must be an integer) \n->");
scanf("%d",&DoAsReps);
StartTime = time(NULL);
LastTime = time(NULL);
printf("\nStarting execution at %s\n\n",ctime(&StartTime));
/* then start doing the burn-in reps */
for(i=0;i<DoAsBurnIn;i++) {
SingleSweep(C);
IncrementValues(C,1);
if(i%300==0 && i > 0) {
OutputHistograms(C);
fprint_PofZ(C);
}
CurrTime = time(NULL);
if(difftime(CurrTime,LastTime) > 5.0) { /* if it has been 5 seconds since a report */
LastTime = time(NULL);
printf("\n\n\n\n\n\nNewHybrids started: %s", ctime(&StartTime));
printf("\nData = %s, GtypFile = %s, PiPrior = %s, ThetaPrior = %s, Seeds = %d %d",DatFile,GtypFile, PriorType2str(PiP), PriorType2str(ThP), Seed1, Seed2);
printf("\nCurrently on BurnIn Sweep %d of %d",i,DoAsBurnIn);
SecondsPerSweep = difftime(LastTime,StartTime)/(double)i;
printf("\nSweeps per second = %f Seconds per sweep = %f ",1.0/SecondsPerSweep,SecondsPerSweep);
SecondsRemain = (SecondsPerSweep * (double)(DoAsBurnIn-i));
printf("\nShould finish BurnIn in %.0f seconds. %.2f minutes. %.4f hours. %.4f days.",
SecondsRemain,SecondsRemain/60,SecondsRemain/3600,SecondsRemain/(3600*24));
/* print out the current pi and the average pi */
printf("\n\nCurrent Pi:\n");
CYCLE_g(C->Dat)
printf(" %.4f",C->Lat->Pi[g]->v);
END1CYCLE
printf("\nAverage Pi:\n");
CYCLE_g(C->Dat)
printf(" %.4f",C->Lat->Pi[g]->Ave);
END1CYCLE
printf("\n\n\n\n\n\n");
fflush(stdout);
}
}
printf("\n\n\n************************\n\nDone with %d Burn-In Sweeps\n\n\n*********************\n\n",DoAsBurnIn);
/* then reset the averages */
ResetAllAveragesEtc(C);
printf("\n\n\n\nAverages reset...\n\nStarting data accumulation reps...\n\n");
/* then do the actual data collection reps */
for(i=0;i<DoAsReps;i++) {
SingleSweep(C);
IncrementValues(C,1);
printf("%d ",i);
if(i%300==0 && i > 0) {
OutputHistograms(C);
fprint_PofZ(C);
printf("\n\n\n\n\n\n\n\n\nNewHybrids Proceeding:");
printf("\nData = %s, GtypFile = %s, PiPrior = %s, ThetaPrior = %s, Seeds = %d %d",DatFile,GtypFile, PriorType2str(PiP), PriorType2str(ThP), Seed1, Seed2);
printf("\nCurrently on Sweep %d of %d",i,DoAsReps);
/* print out the current pi and the average pi */
printf("\n\nCurrent Pi:\n");
CYCLE_g(C->Dat)
printf(" %.4f",C->Lat->Pi[g]->v);
END1CYCLE
printf("\nAverage Pi:\n");
CYCLE_g(C->Dat)
printf(" %.4f",C->Lat->Pi[g]->Ave);
END1CYCLE
printf("\n\n\n\n\n\n");
fflush(stdout);
}
}
/* output the final bits of information */
OutputHistograms(C);
fprint_PofZ(C);
/* then let the user know it has finished */
printf("\n\nProgram New Hybrids completed. ");
printf("\nData = %s, GtypFile = %s, PiPrior = %s, ThetaPrior = %s, Seeds = %d %d",DatFile,GtypFile, PriorType2str(PiP), PriorType2str(ThP), Seed1, Seed2);
printf("\n\nOutput is in the following files:");
printf("\n\taa-LociAndAlleles.txt --- A listing of loci and alleles read");
printf("\n\taa-Pi.hist --- text file of a histogram representation for");
printf("\n\t\tthe posterior distribution of Pi");
printf("\n\taa-PofZ.txt --- for each individual in the sample, the posterior probability");
printf("\n\t\tthat it falls into each of the genotype frequency categories");
printf("\n\taa-Theta.hist ---- a histogram representation of the posterior distributions");
printf("\n\t\tof the allele frequencies in the different populations");
printf("\n\n");
printf("\n\n\nEnter any integer to exit\n->");
scanf("%d",&boing);
return(0);
}