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

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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 publication
2016-05-20 22:47:59
Maintainer
Erik M Volz <erik.volz+rcolgem@gmail.com>
License
GPL-3
Version
0.0.5

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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...

Files in this package

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