R Development Page

Contributed R Packages

Below is a list of all packages provided by project Coalescent for compartmental models.

Important note for package binaries: R-Forge provides these binaries only for the most recent version of R, but not for older versions. In order to successfully install the packages provided on R-Forge, you have to switch to the most recent version of R or, alternatively, install from the package sources (.tar.gz).



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.
  Version: 0.0.5 | Last change: 2016-05-21 00:47:59+02 | Rev.: 154
  Download: linux(.tar.gz) | windows(.zip) | Build status: Current
  R install command: install.packages("rcolgem", repos="")
Package build: Source package (Linux x86_64) Windows binary (x86_64/i386)
Package check: Linux x86_64 (patched) | Linux x86_64 (devel) Windows (patched) | Windows (devel)


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