hzar (version 0.2-5)

Hybrid Zone Analysis using R

Description

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

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Version

Install

install.packages('hzar')

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Version

0.2-5

License

GPL (>= 2)

Maintainer

Graham Derryberry

Last Published

September 23rd, 2013

Functions in hzar (0.2-5)

hzar.next.fitRequest

Generate a new fitRequest using data from another fitRequest.

hzar.qScores

Calculate credibility intervals.

hzar.plot.fzCline

Plot the 95% credible cline region for the given locus model.

hzar.yLabel

Suggest a y axis label

hzar.map.latLong.dms

Convert D-M-S C strings to degrees

hzar.qScores.getScores

Generate credibility scores.

hzar.plot.cline

Generate a plot of the cline.

manakinMorphological

Manakin observed Morphological Traits

hzar.chain.doSeq

Repeatedly run the optimizer in series to tune the optimizer.

hzar.profile.dataGroup

Generate a likelihood profile for a single parameter

hzar.sameModel

Do the hzar objects share the same model or data?

hzar.AIC.default

Calculate the AIC score.

hzar.dataGroup.add

Prepare optimizer output for analysis.

hzar-package

Hybrid Zone Analysis using R

hzar.eval.clineLL

Calculate the Log Likehoods of the table of parameters provided.

hzar.make.dataGroup

Make a hzar.dataGroup object with given parameters.

hzar.getCredParamRed

Create a 95% credibility hzar.fzCline object

hzar.copyModelLabels

Copy names from one hzar object to another.

hzar.AIC.hzar.obsDataGroup

Generate an AIC score table.

hzar.map.greatCircleDistance

The distance between two points on the Earth's surface.

hzar.doMolecularData1DPops

Generate a hzar.obsData object using summary data about each locality

hzar.make.cline

Make a hzar.cline object.

hzar.doFit

Run the optimizer.

hzar.make.mcmcParam

Set the parameters controling the optimizer environment.

hzar.extract.obsData

Extract the observation data used by the optimizer.

hzar.doMorphoSets

Make hzar.obsData objects from scalar observations using reference tables

hzar.make.fzCline

Create a hzar.fzCline object

hzar.first.fitRequest.old.ML

Generate a ML based hzar.fitRequest using a meta model structure.

hzar.makeTraitObsData

Compile and transform raw scalar data

hzar.multiFitRequest

Collect hzar.fitRequest objects to simplify automation

hzar.getLLCutParam

Get the region of parameter space close to the maximum likelihood

hzar.model.addBoxReq

Add parameter restriction clauses to cline model

hzar.map.latLongSites

Generate a table of site locations.

hzar.dBernoulli.LL

Transformations of Scalar Data into Bernoulli Trials

hzar.make.clineLLfunc.old.ML

Generate a Log Likelihood method for the cline model.

hzar.doFit.multi

Run hzar fit commands on a list of hzar.fitRequest objects

hzar.map.dms2deg

Convert degrees, minutes, seconds, direction to degrees.

manakinLocations

Distance from locality A for each locality.

hzar.mcmc.bindLL

Generate a mcmc object with sampled parameters and log likelihoods.

hzar.dataGroup.null

Datagroup placeholder for the null model (frequency independent of location)

hzar.make.fitRequest

Generate a hzar.fitRequest with the specified attributes.

hzar.extract.old.model.gen

Extract information about the clineMetaModel used.

hzar.getCredCut

Get the minimum log likelihood of sufficient credibility.

hzar.meta.init

Observe and Alter the model parameters in the clineMetaModel

hzar.get.ML.cline

Extract the maximum likelihood cline.

hzar.plot.obsData

Generate a plot of the observed data points.

hzar.cov.rect

Generate a covariance matrix for the cline optimizer.

hzar.makeCline1DFreq

Make a cline model with the requested attributes.

hzar.getCredParam

Select a credible subset of a collection of parameters.

hzar.overPlot.fzCline

Plot a cline region for multiple models and / or loci.

hzar.doCLTData1DRaw

Create a hzar.obsData object using a table of individual traits.

hzar.make.LLfunc.null

Likelihood function for the null model

hzar.gen.cline

Make a hzar.cline object using the given parameters and model.

hzar.make.obsDataGroup

Collect optimizer output from multiple models for analysis.

manakinMolecular

Molecular data samples for multiple loci accross the Manakin Cline.