EXTRA PARAMS FOR THE PROGRAM structure.  THE MOST IMPORTANT PARAMS ARE
IN THE FILE mainparams.

"(int)" means that this takes an integer value.
"(d)"   means that this is a double (ie, a Real number such as 3.14).
"(B)"   means that this variable is Boolean 
        (ie insert 1 for True, and 0 for False).

PROGRAM OPTIONS

#define FREQSCORR   1 // (B) allele frequencies are correlated among pops
#define ONEFST      0 // (B) assume same value of Fst for all subpopulations.

#define INFERALPHA  1 // (B) Infer ALPHA (the admixture parameter)
#define POPALPHAS   0 // (B) Individual alpha for each population

#define INFERLAMBDA 0 // (B) Infer LAMBDA (the allele frequencies parameter)
#define POPSPECIFICLAMBDA 0 //(B) infer a separate lambda for each pop 
					(only if INFERLAMBDA=1).

#define NOADMIX     0 (B) Use no admixture model
#define LINKAGE     0 // (B) Use the linkage model model 
#define PHASED      0 // (B) Data are in correct phase (required unless data are diploid)
                      If (LINKAGE=1, PHASED=0), then PHASEINFO can be used--this is an
		      extra line in the input file that gives phase probabilities.
                      When PHASEINFO =0 each value is set to 0.5, implying no phase information.

#define LOG10RMIN     -4.0   //(d) Log10 of minimum allowed value of r under linkage model
#define LOG10RMAX      1.0   //(d) Log10 of maximum allowed value of r
#define LOG10RPROPSD   0.1   //(d) standard deviation of log r in update
#define LOG10RSTART   -2.0   //(d) initial value of log10 r

#define COMPUTEPROB 1 // (B) Estimate the probability of the Data under 
                             the model.  This is used when choosing the 
                             best number of subpopulations.

#define ADMBURNIN   500 //(int) initial period of burnin with admixture model. 
			The admixture model normally has the best mixing properties,
			and therefore should be used as the first phase of the burnin.
                        A significant burnin is highly recommended under the linkage
                        model which otherwise can perform very badly.
                         

USING PRIOR POPULATION INFO

#define USEPOPINFO  0  // (B) Use prior population information to assist 
                             clustering.  Need POPDATA=1.
#define GENSBACK    1  //(int) For use when inferring whether an indiv-
                         idual is an immigrant, or has an immigrant an-
                         cestor in the past GENSBACK generations.  eg, if 
                         GENSBACK==2, it tests for immigrant ancestry 
                         back to grandparents. 
#define MIGRPRIOR 0.001 //(d) prior prob that an individual is a migrant 
                             (used only when USEPOPINFO==1).  This should 
                             be small, eg 0.01 or 0.1.
#define PFROMPOPFLAGONLY 0 // (B) only use individuals with POPFLAG=1 to update	P.
                                  This is to enable use of a reference set of 
                                  individuals for clustering additional "test" 
                                  individuals.

OUTPUT OPTIONS

#define PRINTKLD     1 // (B) Print estimated Kullback-Leibler diver-
                              gence to screen during the run
#define PRINTLAMBDA  1 // (B) Print current value(s) of lambda to screen
#define PRINTQSUM    1 // (B) Print summary of current population membership to screen



#define SITEBYSITE   0  // (B) whether or not to print site by site results. Large!

#define PRINTQHAT    0  // (B) Q-hat printed to a separate file.  Turn this 
                           on before using STRAT.
#define UPDATEFREQ   5  // (int) frequency of printing update on the screen.
                                 Set automatically if this is 0.
#define PRINTLIKES   0  // (B) print current likelihood to screen every rep
#define INTERMEDSAVE 0  // (int) number of saves to file during run

#define ECHODATA     1  // (B) Print some of data file to screen to check
                              that the data entry is correct.
(NEXT 3 ARE FOR COLLECTING DISTRIBUTION OF Q:)
#define ANCESTDIST   0  // (B) collect data about the distribution of an-
                              cestry coefficients (Q) for each individual
#define NUMBOXES   1000 // (int) the distribution of Q values is stored as 
                              a histogram with this number of boxes. 
#define ANCESTPINT 0.90 //(d) the size of the displayed probability  
                              interval on Q (values between 0.0--1.0)

PRIORS
#define ALPHA      1.0  // (d) Dirichlet parameter for degree of admixture 
                             (this is the initial value if INFERALPHA==1).
#define FPRIORMEAN 0.01 // (d) Prior mean and SD of Fst for pops.
#define FPRIORSD   0.05  // (d) The prior is a Gamma distribution with these parameters

#define LAMBDA      1.0 // (d) Dirichlet parameter for allele frequencies 
#define UNIFPRIORALPHA 1 // (B) use a uniform prior for alpha;
                                otherwise gamma prior
#define ALPHAMAX     20.0 // (d) max value of alpha if uniform prior
#define ALPHAPRIORA  0.05 // (only if UNIFPRIORALPHA==0): alpha has a gamma 
                            prior with mean A*B, and 
#define ALPHAPRIORB  0.001 // variance A*B^2.  Suggest A=0.1, B=1.0

MISCELLANEOUS

#define ALPHAPROPSD 0.025 //(d) SD of proposal for updating alpha
#define STARTATPOPINFO 0 //Use given populations as the initial condition 
                           for population origins.  (Need POPDATA==1).  It 
                           is assumed that the PopData in the input file 
                           are between 1 and k where k<=MAXPOPS.
#define RANDOMIZE    1  //(B) use new random seed for each run 
#define METROFREQ    10  //(int) Frequency of using Metropolis step to update
                           Q under admixture model (ie use the metr. move every
                           i steps).  If this is set to 0, it is never used.
                           (Proposal for each q^(i) sampled from prior.  The 
                           goal is to improve mixing for small alpha.)
#define REPORTHITRATE 0 //(B) report hit rate if using METROFREQ