Man pages for ndukler/epiAllele
Tests for signals of variable rates of evolution between gene classes and lineages for probabalistic alleles

alleleData-classClass alleleData
bicCompute BIC for rate models
branchRateMatrixCompute exponentiated rate matrix for all branches
branchTransitionsCompute transitions per branch
cloneCopy object
disCharToProbDiscrete characters to probabailites
epiAllele-packageA short title line describing what the package does
exportScaledTreeExports scaled tree
fitFits rate model
getAlleleDataReturns alleleData
getEdgeGroupTableGet edgeGroupTable
getEdgeTableGet edge table
getIndexLabelsGet all site labels for an index
getLabelIndicesGet all site indices for a label
getParamsReturns alleleData
getParamValueGet parameter values
getParmIndexGet parameter index
getPiIndexGet pi parameter index
getRateIndexGet rate parameter index
getSiblingsCompute transitions per branch
getSiteInfoExtract site information table
getTreeGets tree
logLikelihoodCompute log-likelihood
logSumExpVector logSumExp
lrtCompute LRT for rate models
nSitesExtract site information table
plotTreeTree visualization
rateModel-classClass rateModel
rateSEEstimates the standard error of the rate
rcpp_hello_worldSimple function using Rcpp
readPAFRead in *.paf file
scaledLLCompute scaled negative log-likelihood
setParamValueSet parameter values
simDataSimulate data
siteTransitionsCompute transitions per branch
tieRatesTie rates across siteLabels or edgeGroups
ndukler/epiAllele documentation built on May 5, 2019, 4:50 p.m.