rcolgem: statistical inference and modeling of genealogies generated by epidemic and ecological processes
Version 0.0.5

rcolgem is a package for phylodynamic inference using population genetic models. rcolgem implements coalescent models for populations with nonlinear dynamics and potentially many demes, and other population genetic models may be supported in the future. This package is well suited for studying infectious disease epidemics and inference of epidemiological parameters from pathogen phylogenies. The package can also be used for phylogeographic analysis and estimation of demographic histories (population size through time). rcolgem is not a package for conducting phylogenetic inference, although such packages are available in R and such tools may be incorporated in the future. A time-scaled genealogy with known times of sampling is a necessary input for most functions in rcolgem. Currently, rcolgem works best for fitting deterministic demographic models (e.g. systems of ordinary differential equations). Future versions may incorporate particle filters for fitting stochastic models. rcolgem also provides methods for simulating trees conditional on a demographic process.

Author{Erik M Volz}
Date of publication2016-05-20 22:47:59
MaintainerErik M Volz <erik.volz+rcolgem@gmail.com>
LicenseGPL-3
Version0.0.5
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("rcolgem", repos="http://R-Forge.R-project.org")

Popular man pages

binaryDatedTree: Create binary dated tree. The binaryDatedTree class includes...
calculate.cluster.size.moments.from.model: Calculate cluster size moments from model
calculate.cluster.size.moments.from.tree: Calculate cluster size moments from tree
coalescent.log.likelihood: Compute the likelihood of a gene genealogy conditonal on a...
phylo.source.attribution: Compute infector probabilities between all pairs of sampled...
simulate.binary.dated.tree: Simulate a binary dated tree using a coalescent model and...
See all...

All man pages Function index File listing

Man pages

binaryDatedTree: Create binary dated tree. The binaryDatedTree class includes...
calculate.cluster.size.moments.from.model: Calculate cluster size moments from model
calculate.cluster.size.moments.from.tree: Calculate cluster size moments from tree
coalescent.log.likelihood: Compute the likelihood of a gene genealogy conditonal on a...
phylo.source.attribution: Compute infector probabilities between all pairs of sampled...
simulate.binary.dated.tree: Simulate a binary dated tree using a coalescent model and...

Functions

DatedTree Source code
binaryDatedTree Man page Source code
build.demographic.process Source code
calculate.cluster.size.distr.from.tree Source code
calculate.cluster.size.moments.from.model Man page Source code
calculate.cluster.size.moments.from.tree Man page Source code
calculate.edgemap Source code
calculate.heights Source code
calculate.internal.states Source code
calculate.internal.states.unstructuredModel Source code
coalescent.log.likelihood Man page Source code
coalescent.log.likelihood.fgy Source code
coalescent.log.likelihood.fgy2 Source code
coalescent.log.likelihood.unstructuredModel Source code
dAL Source code
end.discrete.rates Source code
extant.at.height Source code
finite_size_correction Source code
make.fgy Source code
nfer.sample.states.from.annotation Source code
nitialize.states Source code
phylo.source.attribution Man page Source code
pseudoLogLikelihood0.fgy Source code
rescale.binaryDatedTree Source code
show.demographic.process Source code
sim.co.tree Source code
sim.co.tree.fgy Source code
simulate.binary.dated.tree Man page Source code
simulate.binary.dated.tree.0 Source code
simulate.binary.dated.tree.2 Source code
simulate.binary.dated.tree.fgy Source code
simulate.binary.dated.tree.fgy.2 Source code
simulate.binary.dated.tree.unstructured Source code
simulateTreeCpp2 Source code
solve.model Source code
solve.model.unstructured Source code
start.discrete.rates Source code
updateWCpp Source code
update_mstates_arma Source code

Files

DESCRIPTION
NAMESPACE
R
R/RcppExports.R
R/phylo.source.attribution.R
R/rcolgem.R
R/treeSimulatorCpp2.R
README
build
build/vignette.rds
inst
inst/doc
inst/doc/hiv_simtree_vignette.R
inst/doc/hiv_simtree_vignette.Rnw
inst/doc/hiv_simtree_vignette.pdf
inst/doc/hiv_vignette.R
inst/doc/hiv_vignette.Rnw
inst/doc/hiv_vignette.pdf
inst/doc/sir_vignette.R
inst/doc/sir_vignette.Rnw
inst/doc/sir_vignette.pdf
inst/extdata
inst/extdata/F2.csv
inst/extdata/G2.csv
inst/extdata/Y2.csv
inst/extdata/Ys-highSampFrac-2.tsv
inst/extdata/bdtree-highSampFrac-2.nwk
inst/extdata/deaths-highSampFrac-2.csv
inst/extdata/fs-highSampFrac-2.tsv
inst/extdata/hAs2.csv
inst/extdata/hivModel0-fit.RData
inst/extdata/hivModel0-profbeta.RData
inst/extdata/hivSimulation.nwk
inst/extdata/linelist-highSampFrac-2.csv
inst/extdata/sampleStates2.csv
inst/extdata/sirModel0-fit.RData
inst/extdata/sirModel0-profbeta.RData
inst/extdata/sirModel0.json
inst/extdata/sirModel0.nwk
inst/extdata/sirModel0.xml
inst/scripts
inst/scripts/read_master.R
man
man/binaryDatedTree.Rd
man/calculate.cluster.size.moments.from.model.Rd
man/calculate.cluster.size.moments.from.tree.Rd
man/coalescent.log.likelihood.Rd
man/phylo.source.attribution.Rd
man/simulate.binary.dated.tree.Rd
src
src/Makevars
src/RcppExports.cpp
src/dAL0.cpp
src/dCA.c
src/dQAL-6.3.c
src/phylo.source.attribution.cpp
src/rcolgem_helpers.cpp
src/treeSimulatorCpp2.cpp
vignettes
vignettes/figure
vignettes/figure/Rplots.pdf
vignettes/figure/hiv_vignette-proffigure.pdf
vignettes/figure/hiv_vignette-results0.pdf
vignettes/figure/siiirs.pdf
vignettes/figure/sir_vignette-proffigure.pdf
vignettes/figure/sir_vignette-results0.pdf
vignettes/figure/sir_vignette-results0plot.pdf
vignettes/hiv_simtree_vignette.Rnw
vignettes/hiv_vignette.Rnw
vignettes/hiv_vignette.bib
vignettes/rcolgem-manual.pdf
vignettes/sir_vignette.Rnw
vignettes/sir_vignette.bib
rcolgem documentation built on May 21, 2017, 1:30 a.m.

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