hzar.mcmc.bindLL: Generate a mcmc object with sampled parameters and log...
In hzar: Hybrid Zone Analysis using R

Description Usage Arguments Value Author(s) See Also Examples

This function returns the mcmc data with an added a log likelihood column.

hzar.mcmc.bindLL(fitRequest,
                 dataGroup = hzar.fit2DataGroup(fitRequest),
                 mcmcData =
                   if(inherits(fitRequest,"hzar.fitRequest")){
                     mcmc(fitRequest$mcmcRaw,
                          thin=fitRequest$mcmcParam$thin,
                          start=1+fitRequest$mcmcParam$burnin);
                   }else{
                     as.mcmc(dataGroup$data.mcmc)},
                 llData = dataGroup$data.LL,
                 t0 = start(mcmcData),
                 tF = thin(mcmcData))

`fitRequest`	The `hzar.fitRequest` or `hzar.dataGroup` object to use.
`dataGroup`	The `hzar.dataGroup` object to use.
`mcmcData`	The `mcmc` object with the series parameter values.
`llData`	The series of log likelihoods of the parameter values.
`t0`	The `start.mcmc` attribute of the result.
`tF`	The `thin.mcmc` attribute of the result.

A mcmc object, with columns for each free parameter and the log likelihood of each row.

Graham Derryberry asterion@alum.mit.edu

hzar.fitRequest hzar.dataGroup mcmc

data(manakinMolecular);
mknAdaA <-
  hzar.doMolecularData1DPops(manakinMolecular$distance,
                             manakinMolecular$ada.A,
                             manakinMolecular$ada.nSamples);
mknAdaAmodel <-
  hzar.makeCline1DFreq(mknAdaA, scaling="fixed",tails="none");
mknAdaAmodelFit <-
   hzar.first.fitRequest.old.ML(model=mknAdaAmodel ,
                                mknAdaA,
                                verbose=FALSE);
mknAdaAmodelFit$mcmcParam$chainLength <- 5e3;
mknAdaAmodelFit$mcmcParam$burnin <- 5e2;
plot(hzar.mcmc.bindLL(hzar.doFit(mknAdaAmodelFit)));