Hybrid Zone Analysis using R
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Documentation for package ‘hzar’ version 0.2-5
Help Pages
| hzar-package | Hybrid Zone Analysis using R |
-- C --
| clineMetaModel | Make a cline model with the requested attributes. |
-- H --
| hzar | Hybrid Zone Analysis using R |
| hzar.AIC.default | Calculate the AIC score. |
| hzar.AIC.hzar.cline | Calculate the AIC score. |
| hzar.AIC.hzar.dataGroup | Calculate the AIC score. |
| hzar.AIC.hzar.obsDataGroup | Generate an AIC score table. |
| hzar.AICc.default | Calculate the AIC score. |
| hzar.AICc.hzar.cline | Calculate the AIC score. |
| hzar.AICc.hzar.dataGroup | Calculate the AIC score. |
| hzar.AICc.hzar.obsDataGroup | Generate an AIC score table. |
| hzar.chain.doSeq | Repeatedly run the optimizer in series to tune the optimizer. |
| hzar.cline | Make a 'hzar.cline' object. |
| hzar.copyModelLabels | Copy names from one hzar object to another. |
| hzar.cov.mcmc | Generate a covariance matrix for the cline optimizer. |
| hzar.cov.rect | Generate a covariance matrix for the cline optimizer. |
| hzar.dataGroup | Make a 'hzar.dataGroup' object with given parameters. |
| hzar.dataGroup.add | Prepare optimizer output for analysis. |
| hzar.dataGroup.null | Datagroup placeholder for the null model (frequency independent of location) |
| hzar.dBernoulli.LL | Transformations of Scalar Data into Bernoulli Trials |
| hzar.doChain.multi | Run hzar fit commands on a list of hzar.fitRequest objects |
| hzar.doCLTData1DPops | Generate a hzar.obsData object using summary data about each locality |
| 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.doNormalData1DPops | Generate a hzar.obsData object using summary data about each locality |
| hzar.doNormalData1DRaw | Create a 'hzar.obsData' object using a table of individual traits. |
| 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.extract.old.model.req | Extract information about the clineMetaModel used. |
| hzar.first.fitRequest.gC | Generate a ML based hzar.fitRequest using a meta model structure. |
| hzar.first.fitRequest.old.ML | Generate a ML based hzar.fitRequest using a meta model structure. |
| hzar.fit2DataGroup | Prepare optimizer output for analysis. |
| hzar.fitRequest | Generate a hzar.fitRequest with the specified attributes. |
| hzar.fzCline | Create a 'hzar.fzCline' object |
| 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.cline | Make a 'hzar.cline' object. |
| hzar.make.clineLLfunc.old.bayes | Generate a Log Likelihood method for the cline model. |
| 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.makeCline1DCLT | Make a cline model with the requested attributes. |
| hzar.makeCline1DFreq | Make a cline model with the requested attributes. |
| hzar.makeCline1DNormal | Make a cline model with the requested attributes. |
| hzar.makeTraitObsData | Compile and transform raw scalar data |
| hzar.map.distanceFromSite | Generate a table of site locations. |
| 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.map.latLongSites.dms | Generate a table of site locations. |
| hzar.mapSiteDist | Create a 'hzar.obsData' object using a table of individual traits. |
| hzar.mcmc.bindLL | Generate a mcmc object with sampled parameters and log likelihoods. |
| hzar.meta.fix | Observe and Alter the model parameters in the clineMetaModel |
| hzar.meta.fix<- | Observe and Alter the model parameters in the clineMetaModel |
| hzar.meta.init | Observe and Alter the model parameters in the clineMetaModel |
| hzar.meta.init<- | Observe and Alter the model parameters in the clineMetaModel |
| hzar.meta.lower | Observe and Alter the model parameters in the clineMetaModel |
| hzar.meta.lower<- | Observe and Alter the model parameters in the clineMetaModel |
| hzar.meta.tune | Observe and Alter the model parameters in the clineMetaModel |
| hzar.meta.tune<- | Observe and Alter the model parameters in the clineMetaModel |
| hzar.meta.upper | Observe and Alter the model parameters in the clineMetaModel |
| hzar.meta.upper<- | Observe and Alter the model parameters in the clineMetaModel |
| hzar.model.addBoxReq | Add parameter restriction clauses to cline model |
| hzar.model.addCenterRange | Add parameter restriction clauses to cline model |
| hzar.model.addMaxCenter | Add parameter restriction clauses to cline model |
| hzar.model.addMaxDelta | Add parameter restriction clauses to cline model |
| hzar.model.addMaxVariance | Add parameter restriction clauses to cline model |
| hzar.model.addMaxWidth | Add parameter restriction clauses to cline model |
| hzar.model.addMinCenter | Add parameter restriction clauses to cline model |
| hzar.model.addMuRange | Add parameter restriction clauses to cline model |
| hzar.model.addNormalBox | 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.obsData | Generate a hzar.obsData object using summary data about each locality |
| hzar.obsDataGroup | Collect optimizer output from multiple models for analysis. |
| 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.qScores.dataGroup | Calculate credibility intervals. |
| hzar.qScores.obsDataGroup | Calculate credibility intervals. |
| hzar.sameModel | Do the hzar objects share the same model or data? |
| hzar.sameObsData | Do the hzar objects share the same model or data? |
| hzar.yLabel | Suggest a y axis label |
-- M --
| manakinLocations | Distance from locality A for each locality. |
| manakinMolecular | Molecular data samples for multiple loci accross the Manakin Cline. |
| manakinMorphological | Manakin observed Morphological Traits |