hzar: Hybrid Zone Analysis using R

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

AuthorGraham Derryberry
Date of publication2013-09-23 18:03:53
MaintainerGraham Derryberry <asterion@alum.mit.edu>
LicenseGPL (>= 2)
Version0.2-5

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Man pages

hzar.AIC.default: Calculate the AIC score.

hzar.AIC.hzar.obsDataGroup: Generate an AIC score table.

hzar.chain.doSeq: Repeatedly run the optimizer in series to tune the optimizer.

hzar.copyModelLabels: Copy names from one hzar object to another.

hzar.cov.rect: Generate a covariance matrix for the cline optimizer.

hzar.dataGroup.add: Prepare optimizer output for analysis.

hzar.dataGroup.null: Datagroup placeholder for the null model (frequency...

hzar.dBernoulli.LL: Transformations of Scalar Data into Bernoulli Trials

hzar.doCLTData1DRaw: Create a 'hzar.obsData' object using a table of individual...

hzar.doFit: Run the optimizer.

hzar.doFit.multi: Run hzar fit commands on a list of hzar.fitRequest objects

hzar.doMolecularData1DPops: Generate a hzar.obsData object using summary data about each...

hzar.doMorphoSets: Make hzar.obsData objects from scalar observations using...

hzar.eval.clineLL: Calculate the Log Likehoods of the table of parameters...

hzar.extract.obsData: Extract the observation data used by the optimizer.

hzar.extract.old.model.gen: Extract information about the clineMetaModel used.

hzar.first.fitRequest.old.ML: Generate a ML based hzar.fitRequest using a meta model...

hzar.gen.cline: Make a 'hzar.cline' object using the given parameters and...

hzar.getCredCut: Get the minimum log likelihood of sufficient credibility.

hzar.getCredParam: Select a credible subset of a collection of parameters.

hzar.getCredParamRed: Create a 95% credibility hzar.fzCline object

hzar.getLLCutParam: Get the region of parameter space close to the maximum...

hzar.get.ML.cline: Extract the maximum likelihood cline.

hzar.make.cline: Make a 'hzar.cline' object.

hzar.makeCline1DFreq: Make a cline model with the requested attributes.

hzar.make.clineLLfunc.old.ML: Generate a Log Likelihood method for the cline model.

hzar.make.dataGroup: Make a 'hzar.dataGroup' object with given parameters.

hzar.make.fitRequest: Generate a hzar.fitRequest with the specified attributes.

hzar.make.fzCline: Create a 'hzar.fzCline' object

hzar.make.LLfunc.null: Likelihood function for the null model

hzar.make.mcmcParam: Set the parameters controling the optimizer environment.

hzar.make.obsDataGroup: Collect optimizer output from multiple models for analysis.

hzar.makeTraitObsData: Compile and transform raw scalar data

hzar.map.dms2deg: Convert degrees, minutes, seconds, direction to degrees.

hzar.map.greatCircleDistance: The distance between two points on the Earth's surface.

hzar.map.latLong.dms: Convert D-M-S C strings to degrees

hzar.map.latLongSites: Generate a table of site locations.

hzar.mcmc.bindLL: Generate a mcmc object with sampled parameters and log...

hzar.meta.init: Observe and Alter the model parameters in the clineMetaModel

hzar.model.addBoxReq: Add parameter restriction clauses to cline model

hzar.multiFitRequest: Collect hzar.fitRequest objects to simplify automation

hzar.next.fitRequest: Generate a new fitRequest using data from another fitRequest.

hzar.overPlot.fzCline: Plot a cline region for multiple models and / or loci.

hzar-package: Hybrid Zone Analysis using R

hzar.plot.cline: Generate a plot of the cline.

hzar.plot.fzCline: Plot the 95% credible cline region for the given locus model.

hzar.plot.obsData: Generate a plot of the observed data points.

hzar.profile.dataGroup: Generate a likelihood profile for a single parameter

hzar.qScores: Calculate credibility intervals.

hzar.qScores.getScores: Generate credibility scores.

hzar.sameModel: Do the hzar objects share the same model or data?

hzar.yLabel: Suggest a y axis label

manakinLocations: Distance from locality A for each locality.

manakinMolecular: Molecular data samples for multiple loci accross the Manakin...

manakinMorphological: Manakin observed Morphological Traits

Files in this package

hzar
hzar/NAMESPACE
hzar/data
hzar/data/manakinLocations.csv.gz
hzar/data/manakinMolecular.csv.gz
hzar/data/manakinMorphological.csv.gz
hzar/R
hzar/R/20-hzarPrep.R hzar/R/40-hzarPostProcessing.R hzar/R/35-guassianFitting.R hzar/R/27-prepBernoulliTransform.R hzar/R/29-modelModifiers.R hzar/R/21-latLongPrep.R hzar/R/10-modelEquationPrototypeGrouping.R hzar/R/45-hzarQuantiles.R hzar/R/31-hzarFittingNew.R hzar/R/23-hzarMorphoCLT.R hzar/R/43-nullModels.R hzar/R/15-modelExpressionFunctions.R hzar/R/25-guassianPrep.R hzar/R/47-profile.R hzar/R/37-multiFit.R hzar/R/30-hzarFitting.R hzar/R/60-hzarPlottingNew.R hzar/R/90-print.R
hzar/MD5
hzar/DESCRIPTION
hzar/man
hzar/man/hzar.chain.doSeq.Rd hzar/man/hzar.first.fitRequest.old.ML.Rd hzar/man/hzar.extract.obsData.Rd hzar/man/hzar.make.LLfunc.null.Rd hzar/man/hzar.doCLTData1DRaw.Rd hzar/man/hzar.map.latLongSites.Rd hzar/man/hzar.makeCline1DFreq.Rd hzar/man/hzar.plot.fzCline.Rd hzar/man/hzar.doFit.multi.Rd hzar/man/hzar.make.cline.Rd hzar/man/hzar.make.dataGroup.Rd hzar/man/hzar.getCredParamRed.Rd hzar/man/hzar.mcmc.bindLL.Rd hzar/man/hzar.eval.clineLL.Rd hzar/man/hzar.model.addBoxReq.Rd hzar/man/hzar.getLLCutParam.Rd hzar/man/hzar.cov.rect.Rd hzar/man/hzar.makeTraitObsData.Rd hzar/man/hzar.make.obsDataGroup.Rd hzar/man/hzar.next.fitRequest.Rd hzar/man/hzar.make.fitRequest.Rd hzar/man/hzar.sameModel.Rd hzar/man/hzar.gen.cline.Rd hzar/man/hzar.map.latLong.dms.Rd hzar/man/hzar.make.fzCline.Rd hzar/man/hzar-package.Rd hzar/man/hzar.dBernoulli.LL.Rd hzar/man/hzar.overPlot.fzCline.Rd hzar/man/hzar.dataGroup.null.Rd hzar/man/hzar.multiFitRequest.Rd hzar/man/hzar.AIC.default.Rd hzar/man/hzar.getCredCut.Rd hzar/man/hzar.copyModelLabels.Rd hzar/man/manakinLocations.Rd hzar/man/hzar.map.greatCircleDistance.Rd hzar/man/hzar.dataGroup.add.Rd hzar/man/hzar.extract.old.model.gen.Rd hzar/man/hzar.map.dms2deg.Rd hzar/man/hzar.yLabel.Rd hzar/man/hzar.qScores.Rd hzar/man/hzar.doMorphoSets.Rd hzar/man/hzar.doMolecularData1DPops.Rd hzar/man/hzar.profile.dataGroup.Rd hzar/man/hzar.make.clineLLfunc.old.ML.Rd hzar/man/manakinMolecular.Rd hzar/man/hzar.make.mcmcParam.Rd hzar/man/hzar.getCredParam.Rd hzar/man/hzar.plot.obsData.Rd hzar/man/hzar.meta.init.Rd hzar/man/manakinMorphological.Rd hzar/man/hzar.AIC.hzar.obsDataGroup.Rd hzar/man/hzar.qScores.getScores.Rd hzar/man/hzar.get.ML.cline.Rd hzar/man/hzar.plot.cline.Rd hzar/man/hzar.doFit.Rd

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