Files in ndukler/phyloGLM
Tests for signals of variable rates of evolution between gene classes and lineages for probabalistic alleles
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/RcppExports.R
R/alleleData-class.R
R/alleleDataValidityCheck.R
R/bic.R
R/copy.R
R/disCharToProb.R
R/fit.R
R/forceParameterZero.R
R/getAlleleData.R
R/getEdgeTable.R
R/getParams.R
R/getSiblings.R
R/getSiteInfo.R
R/getTree.R
R/lrt.R
R/marginal.R
R/pack.R
R/package.R
R/phyloGrad.R
R/phyloHess.R
R/pi.R
R/plotElementTransitions.R
R/plotParams.R
R/plotTree.R
R/predict.R
R/rateBounds.R
R/rateModel-class.R
R/rateModelValidityCheck.R
R/rates.R
R/rcppModules.R
R/readPAF.R
R/scaledLL.R
R/se.R
R/setFixed.R
R/setParams.R
R/show.R
R/simulateSites.R
R/siteLL.R
R/stlMatrix-class.R
R/updateFormula.R
README.md
inst/extdata/generateSampleData.R
inst/extdata/rateMod.Rds
inst/extdata/samplePAF.txt
inst/extdata/sampleTree.nh
inst/extdata/siteCovariates.txt
man/alleleData-class.Rd
man/alleleData.Rd
man/bic.Rd
man/copy.Rd
man/disCharToProb.Rd
man/fit.Rd
man/forceParameterZero.Rd
man/getAlleleData.Rd
man/getEdgeTable.Rd
man/getParams.Rd
man/getRateBounds.Rd
man/getSiblings.Rd
man/getSiteInfo-methods.Rd
man/getTree.Rd
man/ll.Rd
man/logSumExp.Rd
man/lrt.Rd
man/marginal.Rd
man/marginalTransitions.Rd
man/matrixToStlXptr.Rd
man/pack.Rd
man/packedModel-class.Rd
man/phyloGLM.Rd
man/phyloGrad.Rd
man/phyloHess.Rd
man/pi.Rd
man/plotElementTransitions.Rd
man/plotParams.Rd
man/plotTree.Rd
man/predict.Rd
man/rateModel-class.Rd
man/rateModel.Rd
man/rates.Rd
man/readPAF.Rd
man/scaledLL.Rd
man/se.Rd
man/setFixed.Rd
man/setParams.Rd
man/setRateBounds.Rd
man/show.Rd
man/simulateSites.Rd
man/siteLL.Rd
man/stlMatrix-class.Rd
man/stlMatrix.Rd
man/unpack.Rd
man/updateFixed.Rd
man/updateFormula.Rd
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/blas_mod.f
src/expokit.h
src/expokit_dgpadm.cpp
src/lapack.f
src/logSumExp.cpp
src/logSumExp.h
src/mataid.f
src/my_expokit.f
src/my_matexp.f
src/paramIndex.cpp
src/paramIndex.h
src/phyloGLM_types.h
src/phylogeny.cpp
src/phylogeny.h
src/stlXptr.cpp
src/stlXptr.h
src/updateFixed.cpp
tests/testthat.R
tests/testthat/testAlleleData.R
tests/testthat/testParamIndex.R
tests/testthat/testRateModel.R
vignettes/.gitignore
vignettes/introduction.Rmd
vignettes/introduction.log
vignettes/rsconnect/documents/introduction.Rmd/rpubs.com/rpubs/Document.dcf
vignettes/rsconnect/documents/introduction.Rmd/rpubs.com/rpubs/Publish Document.dcf
