Files in ndukler/epiAllele
Tests for signals of variable rates of evolution between gene classes and lineages for probabalistic alleles
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/RcppExports.R
R/alleleData-class.R
R/alleleDataValidityCheck.R
R/bic.R
R/branchRateMatrix.R
R/branchTransitions.R
R/clone.R
R/disCharToProb.R
R/exportScaledTree.R
R/fit.R
R/getAlleleData.R
R/getEdgeGroupTable.R
R/getEdgeTable.R
R/getIndexLabels.R
R/getLabelIndices.R
R/getParamIndex.R
R/getParamValue.R
R/getParams.R
R/getPiIndex.R
R/getRateIndex.R
R/getSiblings.R
R/getSiteInfo.R
R/getTree.R
R/logLikelihood.R
R/lrt.R
R/nSites.R
R/package.R
R/plotTree.R
R/rateModel-class.R
R/rateModelValidityCheck.R
R/rateSE.R
R/readPAF.R
R/scaledLL.R
R/setParamValue.R
R/simData.R
R/siteTransitions.R
R/tieRates.R
README.md
Read-and-delete-me
epiAllele.Rproj
man/alleleData-class.Rd
man/alleleData.Rd
man/bic.Rd
man/branchRateMatrix.Rd
man/branchTransitions.Rd
man/clone.Rd
man/disCharToProb.Rd
man/epiAllele-package.Rd
man/epiAllele.Rd
man/exportScaledTree.Rd
man/fit.Rd
man/getAlleleData.Rd
man/getEdgeGroupTable.Rd
man/getEdgeTable.Rd
man/getIndexLabels.Rd
man/getLabelIndices.Rd
man/getParamValue.Rd
man/getParams.Rd
man/getParmIndex.Rd
man/getPiIndex.Rd
man/getRateIndex.Rd
man/getSiblings.Rd
man/getSiteInfo.Rd
man/getTree.Rd
man/logLikelihood.Rd
man/logSumExp.Rd
man/lrt.Rd
man/multiProbToStick.Rd
man/multiStickToProb.Rd
man/nSites.Rd
man/plotTree.Rd
man/probToStick.Rd
man/rateModel-class.Rd
man/rateModel.Rd
man/rateSE.Rd
man/rcpp_hello_world.Rd
man/readPAF.Rd
man/scaledLL.Rd
man/setParamValue.Rd
man/simData.Rd
man/siteTransitions.Rd
man/stickToProb.Rd
man/tieRates.Rd
src/RcppExports.cpp
src/epiAllele_types.h
src/logSumExp.cpp
src/logSumExp.h
src/marginalTransitionsCpp.cpp
src/msgPassing.h
src/multiProbToStick.cpp
src/multiStickToProb.cpp
src/postorderMessagePassing.cpp
src/preorderMessagePassing.cpp
src/probToStick.cpp
src/setValues.cpp
src/siteGainLoss.cpp
src/stickFunctions.h
src/stickToProb.cpp
src/treeLL.cpp
tests/testthat.R
tests/testthat/testAlleleData-class.R
tests/testthat/testRateModel.R
vignettes/Introduction.Rmd
vignettes/simulationPerformance.Rmd
vignettes/treeFitting.Rmd
