Man pages for hzar
Hybrid Zone Analysis using R

hzar.AIC.defaultCalculate the AIC score.
hzar.AIC.hzar.obsDataGroupGenerate an AIC score table.
hzar.chain.doSeqRepeatedly run the optimizer in series to tune the optimizer.
hzar.copyModelLabelsCopy names from one hzar object to another.
hzar.cov.rectGenerate a covariance matrix for the cline optimizer.
hzar.dataGroup.addPrepare optimizer output for analysis.
hzar.dataGroup.nullDatagroup placeholder for the null model (frequency...
hzar.dBernoulli.LLTransformations of Scalar Data into Bernoulli Trials
hzar.doCLTData1DRawCreate a 'hzar.obsData' object using a table of individual...
hzar.doFitRun the optimizer.
hzar.doFit.multiRun hzar fit commands on a list of hzar.fitRequest objects
hzar.doMolecularData1DPopsGenerate a hzar.obsData object using summary data about each...
hzar.doMorphoSetsMake hzar.obsData objects from scalar observations using...
hzar.eval.clineLLCalculate the Log Likehoods of the table of parameters...
hzar.extract.obsDataExtract the observation data used by the optimizer.
hzar.extract.old.model.genExtract information about the clineMetaModel used.
hzar.first.fitRequest.old.MLGenerate a ML based hzar.fitRequest using a meta model...
hzar.gen.clineMake a 'hzar.cline' object using the given parameters and...
hzar.getCredCutGet the minimum log likelihood of sufficient credibility.
hzar.getCredParamSelect a credible subset of a collection of parameters.
hzar.getCredParamRedCreate a 95% credibility hzar.fzCline object
hzar.getLLCutParamGet the region of parameter space close to the maximum...
hzar.get.ML.clineExtract the maximum likelihood cline.
hzar.make.clineMake a 'hzar.cline' object.
hzar.makeCline1DFreqMake a cline model with the requested attributes.
hzar.make.clineLLfunc.old.MLGenerate a Log Likelihood method for the cline model.
hzar.make.dataGroupMake a 'hzar.dataGroup' object with given parameters.
hzar.make.fitRequestGenerate a hzar.fitRequest with the specified attributes.
hzar.make.fzClineCreate a 'hzar.fzCline' object
hzar.make.LLfunc.nullLikelihood function for the null model
hzar.make.mcmcParamSet the parameters controling the optimizer environment.
hzar.make.obsDataGroupCollect optimizer output from multiple models for analysis.
hzar.makeTraitObsDataCompile and transform raw scalar data
hzar.map.dms2degConvert degrees, minutes, seconds, direction to degrees.
hzar.map.greatCircleDistanceThe distance between two points on the Earth's surface.
hzar.map.latLong.dmsConvert D-M-S C strings to degrees
hzar.map.latLongSitesGenerate a table of site locations.
hzar.mcmc.bindLLGenerate a mcmc object with sampled parameters and log...
hzar.meta.initObserve and Alter the model parameters in the clineMetaModel
hzar.model.addBoxReqAdd parameter restriction clauses to cline model
hzar.multiFitRequestCollect hzar.fitRequest objects to simplify automation
hzar.next.fitRequestGenerate a new fitRequest using data from another fitRequest.
hzar.overPlot.fzClinePlot a cline region for multiple models and / or loci.
hzar-packageHybrid Zone Analysis using R
hzar.plot.clineGenerate a plot of the cline.
hzar.plot.fzClinePlot the 95% credible cline region for the given locus model.
hzar.plot.obsDataGenerate a plot of the observed data points.
hzar.profile.dataGroupGenerate a likelihood profile for a single parameter
hzar.qScoresCalculate credibility intervals.
hzar.qScores.getScoresGenerate credibility scores.
hzar.sameModelDo the hzar objects share the same model or data?
hzar.yLabelSuggest a y axis label
manakinLocationsDistance from locality A for each locality.
manakinMolecularMolecular data samples for multiple loci accross the Manakin...
manakinMorphologicalManakin observed Morphological Traits
hzar documentation built on May 29, 2017, 8:45 p.m.