hzar-package            Hybrid Zone Analysis using R
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.dBernoulli.LL      Transformations of Scalar Data into Bernoulli
                        Trials
hzar.dataGroup.add      Prepare optimizer output for analysis.
hzar.dataGroup.null     Datagroup placeholder for the null model
                        (frequency independent of location)
hzar.doCLTData1DRaw     Create a 'hzar.obsData' object using a table of
                        individual traits.
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 locality
hzar.doMorphoSets       Make hzar.obsData objects from scalar
                        observations using reference tables
hzar.eval.clineLL       Calculate the Log Likehoods of the table of
                        parameters provided.
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 structure.
hzar.gen.cline          Make a 'hzar.cline' object using the given
                        parameters and model.
hzar.get.ML.cline       Extract the maximum likelihood cline.
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 likelihood
hzar.make.LLfunc.null   Likelihood function for the null model
hzar.make.cline         Make a 'hzar.cline' object.
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.mcmcParam     Set the parameters controling the optimizer
                        environment.
hzar.make.obsDataGroup
                        Collect optimizer output from multiple models
                        for analysis.
hzar.makeCline1DFreq    Make a cline model with the requested
                        attributes.
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 likelihoods.
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.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.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 Cline.
manakinMorphological    Manakin observed Morphological Traits
