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

View on CRAN

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

Functions

clineMetaModel Man page
hzar Man page
hzar.AICc.default Man page
hzar.AICc.hzar.cline Man page
hzar.AICc.hzar.dataGroup Man page
hzar.AICc.hzar.obsDataGroup Man page
hzar.AIC.default Man page
hzar.AIC.hzar.cline Man page
hzar.AIC.hzar.dataGroup Man page
hzar.AIC.hzar.obsDataGroup Man page
hzar.chain.doSeq Man page
hzar.cline Man page
hzar.copyModelLabels Man page
hzar.cov.mcmc Man page
hzar.cov.rect Man page
hzar.dataGroup Man page
hzar.dataGroup.add Man page
hzar.dataGroup.null Man page
hzar.dBernoulli.LL Man page
hzar.doChain.multi Man page
hzar.doCLTData1DPops Man page
hzar.doCLTData1DRaw Man page
hzar.doFit Man page
hzar.doFit.multi Man page
hzar.doMolecularData1DPops Man page
hzar.doMorphoSets Man page
hzar.doNormalData1DPops Man page
hzar.doNormalData1DRaw Man page
hzar.eval.clineLL Man page
hzar.extract.obsData Man page
hzar.extract.old.model.gen Man page
hzar.extract.old.model.req Man page
hzar.first.fitRequest.gC Man page
hzar.first.fitRequest.old.ML Man page
hzar.fit2DataGroup Man page
hzar.fitRequest Man page
hzar.fzCline Man page
hzar.gen.cline Man page
hzar.getCredCut Man page
hzar.getCredParam Man page
hzar.getCredParamRed Man page
hzar.getLLCutParam Man page
hzar.get.ML.cline Man page
hzar.make.cline Man page
hzar.makeCline1DCLT Man page
hzar.makeCline1DFreq Man page
hzar.makeCline1DNormal Man page
hzar.make.clineLLfunc.old.bayes Man page
hzar.make.clineLLfunc.old.ML Man page
hzar.make.dataGroup Man page
hzar.make.fitRequest Man page
hzar.make.fzCline Man page
hzar.make.LLfunc.null Man page
hzar.make.mcmcParam Man page
hzar.make.obsDataGroup Man page
hzar.makeTraitObsData Man page
hzar.map.distanceFromSite Man page
hzar.map.dms2deg Man page
hzar.map.greatCircleDistance Man page
hzar.map.latLong.dms Man page
hzar.map.latLongSites Man page
hzar.map.latLongSites.dms Man page
hzar.mapSiteDist Man page
hzar.mcmc.bindLL Man page
hzar.meta.fix Man page
hzar.meta.fix<- Man page
hzar.meta.init Man page
hzar.meta.init<- Man page
hzar.meta.lower Man page
hzar.meta.lower<- Man page
hzar.meta.tune Man page
hzar.meta.tune<- Man page
hzar.meta.upper Man page
hzar.meta.upper<- Man page
hzar.model.addBoxReq Man page
hzar.model.addCenterRange Man page
hzar.model.addMaxCenter Man page
hzar.model.addMaxDelta Man page
hzar.model.addMaxVariance Man page
hzar.model.addMaxWidth Man page
hzar.model.addMinCenter Man page
hzar.model.addMuRange Man page
hzar.model.addNormalBox Man page
hzar.multiFitRequest Man page
hzar.next.fitRequest Man page
hzar.obsData Man page
hzar.obsDataGroup Man page
hzar.overPlot.fzCline Man page
hzar-package Man page
hzar.plot.cline Man page
hzar.plot.fzCline Man page
hzar.plot.obsData Man page
hzar.profile.dataGroup Man page
hzar.qScores Man page
hzar.qScores.dataGroup Man page
hzar.qScores.getScores Man page
hzar.qScores.obsDataGroup Man page
hzar.sameModel Man page
hzar.sameObsData Man page
hzar.yLabel Man page
manakinLocations Man page
manakinMolecular Man page
manakinMorphological Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.