hzar.doMorphoSets: Make hzar.obsData objects from scalar observations using...
In GrahamDB/hzar: Hybrid Zone Analysis using R

Description Usage Arguments Value Author(s) See Also Examples

View source: R/27-prepBernoulliTransform.R

Perform a Bernoulli transform on a table of scalar traits of sampled individuals while using a separate table of localities.

1	hzar.doMorphoSets(traitNames, tDist, tDLocCol, tDDistCol, tValues, tVLocCol)

`traitNames`	The columns of `tValues` to transform.
`tDist`	A data.frame with a column of locality identifiers and a column of locality distances. See `manakinLocations` for an example.
`tDLocCol`	The name of the column of `tDist` with locality identifiers.
`tDDistCol`	The name of the column of `tDist` with locality distances.
`tValues`	A data.frame of observed scalar traits of individuals. See `manakinMorphological` for an example.
`tVLocCol`	The name of the column of `tValues` with locality identifiers where the sample was taken.

A list of hzar.obsData objects. The values of traitNames are used as names. The Bernoulli likelihood function is for each hzar.obsData object.

Graham Derryberry asterion@alum.mit.edu

manakinLocations manakinMorphological hzar.plot.obsData

data(manakinMorphological);
data(manakinLocations);
mkn <-
  hzar.doMorphoSets("beard.length",
                    tDist=manakinLocations,
                    tDLocCol="LocalityID",
                    tDDistCol="distance",
                    tValues=manakinMorphological,
                    tVLocCol="Locality")
print(str(mkn));
hzar.plot.obsData(mkn$beard.length);
mknBLModel <-
  hzar.makeCline1DFreq(mkn$beard.length, scaling="fixed",tails="none");
mknBLModel <-
  hzar.model.addBoxReq(mknBLModel,-30,600);
## Not run: 
mknBLFitR <-
   hzar.first.fitRequest.old.ML(model=mknBLModel ,
                                mkn$beard.length,
                                verbose=FALSE);
mknBLFit <- hzar.doFit(mknBLFitR)
plot(hzar.mcmc.bindLL(mknBLFit))
mknBLData <-
  hzar.dataGroup.add(mknBLFit);
print(hzar.getLLCutParam(mknBLData,c("center","width")));


## End(Not run)