hzar (version 0.2-5)

hzar-package: Hybrid Zone Analysis using R

Description

A collection of tools for modeling the shape of 1 dimensional clines.

Details

Package:

hzar

Type:

Package

Version:

0.2-5

Date:

2013-09-02

License:

GPL (>= 2)

LazyLoad:

yes

References

Brumfield, R. T., R. W. Jernigan, D. B. McDonald, and M. J. Braun. 2001. Evolutionary implications of divergent clines in an avian (Manacus: Aves) hybrid zone. Evolution 55:2070-2087. Gay, L., P.-A. Crochet, D. A. Bell, and T. Lenormand. 2008. Comparing clines on molecular and phenotypic traits in hybrid zones: a window on tension zone models. Evolution 62:2789-2806. Szymura, J., and N. H. Barton. 1986. Genetic analysis of a hybrid zone between the fire-bellied toads, Bombina bombina and B. variegata, near Cracow in souhern Poland. Evolution 40:1141-1159. Szymura, J., and N. H. Barton. 1991. The genetic structure of the hybrid zone between the fire-bellied toads Bombina bombina and B. variegata: comparisons between transects and between loci. Evolution 45:237-261.

Examples

data(manakinMolecular);
mknAdaA <-
  hzar.doMolecularData1DPops(manakinMolecular$distance,
                             manakinMolecular$ada.A,
                             manakinMolecular$ada.nSamples);
hzar.plot.obsData(mknAdaA);
mknAdaAmodel <-
  hzar.makeCline1DFreq(mknAdaA, scaling="fixed",tails="none");
mknAdaAmodel <-
  hzar.model.addBoxReq(mknAdaAmodel,-30,600);
mknAdaAmodelFitR <-
   hzar.first.fitRequest.old.ML(model=mknAdaAmodel ,
                                mknAdaA,
                                verbose=FALSE);
mknAdaAmodelFitR$mcmcParam$chainLength <- 2e3;
mknAdaAmodelFitR$mcmcParam$burnin <- 5e2;
mknAdaAmodelFit <- hzar.doFit(mknAdaAmodelFitR)
plot(hzar.mcmc.bindLL(mknAdaAmodelFit))
mknAdaAmodelData <-
  hzar.dataGroup.add(mknAdaAmodelFit);
## Not run: 
# mknAdaAmodelData <-
#   hzar.dataGroup.add(
#     mknAdaAmodelData,
#     hzar.chain.doSeq(hzar.next.fitRequest(mknAdaAmodelFit)));
# hzar.plot.cline(mknAdaAmodelData);
# hzar.plot.fzCline(mknAdaAmodelData);
# ## End(Not run)
print(hzar.getLLCutParam(mknAdaAmodelData,c("center","width")));
mknAdaAmodelNull <- hzar.dataGroup.null(mknAdaA);
mknAdaAdGs <- list(clineModel = mknAdaAmodelData,
                   nullModel  = mknAdaAmodelNull);
mknAdaAoDG <- hzar.make.obsDataGroup(mknAdaAdGs);
mknAdaAoDG <- hzar.copyModelLabels(mknAdaAdGs,mknAdaAoDG);
hzar.plot.cline(mknAdaAoDG);
print(hzar.AICc.hzar.obsDataGroup(mknAdaAoDG));