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

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

View on R-Forge

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.