hzar: Hybrid Zone Analysis using R
Version 0.2-5

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

Browse man pages Browse package API and functions Browse package files

AuthorGraham Derryberry
Date of publication2013-09-23 18:03:53
MaintainerGraham Derryberry <asterion@alum.mit.edu>
LicenseGPL (>= 2)
Version0.2-5
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("hzar")

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

PP.fz.getCheckFunc Source code
PP.fz.oldCheckFunc Source code
PP.fzCaMnRc Source code
PP.fzCline.add Source code
PP.fzCline.addBest Source code
PP.fzCline.addMany Source code
PP.fzCline.addOne Source code
PP.fzCline.reduce Source code
alphaExpF Source code
appHScale Source code
appHessian Source code
appThetaWalker Source code
appThetaWalkerR Source code
bLLSLDSFchoice Source code
bLLSumDistSF Source code
bLLSumLocDistFreq Source code
bLLdist Source code
buildCline1D Source code
center Source code
cline.exp.lower Source code
cline.exp.pLower Source code
cline.exp.pUpper Source code
cline.exp.scale Source code
cline.exp.sigmoid Source code
cline.exp.stepBoth Source code
cline.exp.stepLow Source code
cline.exp.stepUp Source code
cline.exp.upper Source code
cline.extract.modelPrep Source code
cline.func.gen Source code
cline.pCenter Source code
cline.pLower Source code
cline.pUpper Source code
clineMetaModel Man page
compileLLfunc Source code
deltaL Source code
deltaM Source code
deltaR Source code
eval.intercept Source code
eval.kappa Source code
fitter.gen.rParam.uniform Source code
fitter.gen.samples.rect Source code
fitter.getCovWeights Source code
fitter.wedgeSlice Source code
freq.LLfunc Source code
freqCompileLLEdge Source code
freqCompileLLF Source code
freqCompilePDF Source code
g.LLfunc Source code
g.LLfuncA Source code
g.sMuVarL Source code
g.sMuVarR Source code
g.suggestAll Source code
gCenterExpF Source code
gTailExpF Source code
guassianLLExpF Source code
guassianLLSampleExpF Source code
guassianThetaLLExpF Source code
hzar Man page
hzar-package Man page
hzar.AIC.default Man page Source code
hzar.AIC.hzar.cline Man page Source code
hzar.AIC.hzar.dataGroup Man page Source code
hzar.AIC.hzar.obsDataGroup Man page Source code
hzar.AICc.default Man page Source code
hzar.AICc.hzar.cline Man page Source code
hzar.AICc.hzar.dataGroup Man page Source code
hzar.AICc.hzar.obsDataGroup Man page Source code
hzar.chain.doSeq Man page Source code
hzar.cline Man page
hzar.copyModelLabels Man page Source code
hzar.cov.mcmc Man page Source code
hzar.cov.rect Man page Source code
hzar.dBernoulli.LL Man page Source code
hzar.dataGroup Man page
hzar.dataGroup.add Man page Source code
hzar.dataGroup.null Man page Source code
hzar.doCLTData1DPops Man page Source code
hzar.doCLTData1DRaw Man page Source code
hzar.doChain.multi Man page Source code
hzar.doFit Man page Source code
hzar.doFit.multi Man page Source code
hzar.doMolecularData1DPops Man page Source code
hzar.doMorphoSets Man page Source code
hzar.doNormalData1DPops Man page
hzar.doNormalData1DRaw Man page Source code
hzar.eval.clineLL Man page Source code
hzar.extract.obsData Man page Source code
hzar.extract.old.model.gen Man page Source code
hzar.extract.old.model.req Man page Source code
hzar.first.fitRequest.gC Man page Source code
hzar.first.fitRequest.old.ML Man page Source code
hzar.fit2DataGroup Man page Source code
hzar.fitRequest Man page
hzar.fzCline Man page
hzar.gen.cline Man page Source code
hzar.get.ML.cline Man page Source code
hzar.getCredCut Man page Source code
hzar.getCredParam Man page Source code
hzar.getCredParamRed Man page Source code
hzar.getLLCutParam Man page Source code
hzar.make.LLfunc.null Man page Source code
hzar.make.cline Man page Source code
hzar.make.clineLLfunc.old.ML Man page Source code
hzar.make.clineLLfunc.old.bayes Man page Source code
hzar.make.dataGroup Man page Source code
hzar.make.fitRequest Man page Source code
hzar.make.fzCline Man page Source code
hzar.make.mcmcParam Man page Source code
hzar.make.obsDataGroup Man page Source code
hzar.makeCline1DCLT Man page Source code
hzar.makeCline1DFreq Man page Source code
hzar.makeCline1DNormal Man page Source code
hzar.makeTraitObsData Man page Source code
hzar.map.distanceFromSite Man page Source code
hzar.map.dms2deg Man page Source code
hzar.map.greatCircleDistance Man page Source code
hzar.map.latLong.dms Man page Source code
hzar.map.latLongSites Man page Source code
hzar.map.latLongSites.dms Man page Source code
hzar.mapSiteDist Man page Source code
hzar.mcmc.bindLL Man page Source code
hzar.meta.fix Man page Source code
hzar.meta.fix<- Man page
hzar.meta.init Man page Source code
hzar.meta.init<- Man page
hzar.meta.lower Man page Source code
hzar.meta.lower<- Man page
hzar.meta.tune Man page Source code
hzar.meta.tune<- Man page
hzar.meta.upper Man page Source code
hzar.meta.upper<- Man page
hzar.model.addBoxReq Man page Source code
hzar.model.addCenterRange Man page Source code
hzar.model.addMaxCenter Man page Source code
hzar.model.addMaxDelta Man page Source code
hzar.model.addMaxVariance Man page Source code
hzar.model.addMaxWidth Man page Source code
hzar.model.addMinCenter Man page Source code
hzar.model.addMuRange Man page Source code
hzar.model.addNormalBox Man page Source code
hzar.multiFitRequest Man page Source code
hzar.next.fitRequest Man page Source code
hzar.obsData Man page
hzar.obsDataGroup Man page
hzar.overPlot.fzCline Man page Source code
hzar.plot.cline Man page Source code
hzar.plot.fzCline Man page Source code
hzar.plot.obsData Man page Source code
hzar.profile.dataGroup Man page Source code
hzar.qScores Man page Source code
hzar.qScores.dataGroup Man page Source code
hzar.qScores.getScores Man page Source code
hzar.qScores.obsDataGroup Man page Source code
hzar.sameModel Man page Source code
hzar.sameObsData Man page Source code
hzar.yLabel Man page Source code
latLong.d Source code
latLong.p Source code
ll.compile.theta Source code
logLikeCLTEstPopMean Source code
makeGExp Source code
manakinLocations Man page
manakinMolecular Man page
manakinMorphological Man page
meta.check Source code
meta.check.names Source code
meta.cline.func.lowStep Source code
meta.cline.func.noStep Source code
meta.cline.func.pScale Source code
meta.cline.func.stepBoth Source code
meta.cline.func.upStep Source code
meta.fix Source code
meta.fixValue Source code
meta.init Source code
meta.lower Source code
meta.param.m Source code
meta.param.names Source code
meta.tail.lower Source code
meta.tail.mirror Source code
meta.tail.upper Source code
meta.tune Source code
meta.upper Source code
midpoints Source code
mkParam Source code
mkn.fixFactor Source code
model.addMaxParam Source code
model.addMinParam Source code
model.addParamRange Source code
model.addReqClause Source code
mu2fExp Source code
muExpF Source code
muL Source code
muR Source code
mvGExpF Source code
naiveHessian Source code
obs.g.summary Source code
old.dBernoulli.LL Source code
old.doMorphoSets Source code
optMuPExpF Source code
optMuPExpF.fit Source code
optimizeTrace Source code
optimizeTraceF Source code
pTailExpF Source code
param.check Source code
param.fix Source code
param.init Source code
param.lower Source code
param.name Source code
param.tune Source code
param.upper Source code
pdms2deg Source code
print.clineMetaModel Source code
print.clineParameter Source code
print.hzar.fitRequest Source code
profile.fitRequest Source code
profile.model Source code
pullMinScore Source code
qTailExpF Source code
rA.exp.LIB.add Source code
rA.exp2Arg Source code
rB.exp.LIB.add Source code
rB.exp2Arg Source code
req.Collapse.exp Source code
req.Expand.exp Source code
req.edge.exp Source code
s.exp.LIB.add Source code
s.exp1LangArg Source code
s.exp1NumArg Source code
s.exp1boolArg Source code
s.exp2NumArg Source code
s.exp2boolArg Source code
s.expBoolSimpA Source code
s.expBoolSimpB Source code
s.expNumSimpA Source code
s.expNumSimpB Source code
sampleLikelihoodMolecularPop Source code
setupCLTCenterClineParameters Source code
setupMoleCenterClineParameters Source code
sigmoidExpF Source code
simplify.exp Source code
splitParameters Source code
step1VGExpF Source code
step1VectorExpF Source code
tVec.dBernoulli.LL Source code
tVec.make Source code
tVec.makeTraitObsData Source code
tauL Source code
tauM Source code
tauR Source code
thEvalFExp Source code
vCenterExpF Source code
vTailExpF Source code
varExpF Source code
varH Source code
varL Source code
varR Source code
wMax Source code
width Source code

Files

NAMESPACE
data
data/manakinLocations.csv.gz
data/manakinMolecular.csv.gz
data/manakinMorphological.csv.gz
R
R/20-hzarPrep.R
R/40-hzarPostProcessing.R
R/35-guassianFitting.R
R/27-prepBernoulliTransform.R
R/29-modelModifiers.R
R/21-latLongPrep.R
R/10-modelEquationPrototypeGrouping.R
R/45-hzarQuantiles.R
R/31-hzarFittingNew.R
R/23-hzarMorphoCLT.R
R/43-nullModels.R
R/15-modelExpressionFunctions.R
R/25-guassianPrep.R
R/47-profile.R
R/37-multiFit.R
R/30-hzarFitting.R
R/60-hzarPlottingNew.R
R/90-print.R
MD5
DESCRIPTION
man
man/hzar.chain.doSeq.Rd
man/hzar.first.fitRequest.old.ML.Rd
man/hzar.extract.obsData.Rd
man/hzar.make.LLfunc.null.Rd
man/hzar.doCLTData1DRaw.Rd
man/hzar.map.latLongSites.Rd
man/hzar.makeCline1DFreq.Rd
man/hzar.plot.fzCline.Rd
man/hzar.doFit.multi.Rd
man/hzar.make.cline.Rd
man/hzar.make.dataGroup.Rd
man/hzar.getCredParamRed.Rd
man/hzar.mcmc.bindLL.Rd
man/hzar.eval.clineLL.Rd
man/hzar.model.addBoxReq.Rd
man/hzar.getLLCutParam.Rd
man/hzar.cov.rect.Rd
man/hzar.makeTraitObsData.Rd
man/hzar.make.obsDataGroup.Rd
man/hzar.next.fitRequest.Rd
man/hzar.make.fitRequest.Rd
man/hzar.sameModel.Rd
man/hzar.gen.cline.Rd
man/hzar.map.latLong.dms.Rd
man/hzar.make.fzCline.Rd
man/hzar-package.Rd
man/hzar.dBernoulli.LL.Rd
man/hzar.overPlot.fzCline.Rd
man/hzar.dataGroup.null.Rd
man/hzar.multiFitRequest.Rd
man/hzar.AIC.default.Rd
man/hzar.getCredCut.Rd
man/hzar.copyModelLabels.Rd
man/manakinLocations.Rd
man/hzar.map.greatCircleDistance.Rd
man/hzar.dataGroup.add.Rd
man/hzar.extract.old.model.gen.Rd
man/hzar.map.dms2deg.Rd
man/hzar.yLabel.Rd
man/hzar.qScores.Rd
man/hzar.doMorphoSets.Rd
man/hzar.doMolecularData1DPops.Rd
man/hzar.profile.dataGroup.Rd
man/hzar.make.clineLLfunc.old.ML.Rd
man/manakinMolecular.Rd
man/hzar.make.mcmcParam.Rd
man/hzar.getCredParam.Rd
man/hzar.plot.obsData.Rd
man/hzar.meta.init.Rd
man/manakinMorphological.Rd
man/hzar.AIC.hzar.obsDataGroup.Rd
man/hzar.qScores.getScores.Rd
man/hzar.get.ML.cline.Rd
man/hzar.plot.cline.Rd
man/hzar.doFit.Rd
hzar documentation built on May 19, 2017, 7:03 p.m.