hzar: Hybrid Zone Analysis using R

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

Author
Graham Derryberry
Date of publication
2013-09-23 18:03:53
Maintainer
Graham Derryberry <asterion@alum.mit.edu>
License
GPL (>= 2)
Version
0.2-5

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

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