README.md

phydynR

phydynR is an R package based on the coalescent theory in which you can

• define infectious disease models or ecological process models in terms of ordinary differential equations (ODEs) or stochastic differential equations (SDEs);

• simulate genealogies conditional on a process model;

• compute likelihoods of phylogenetic trees also conditional on a process model.

Installation

# You will need to install the R package devtools 
# (https://github.com/r-lib/devtools)

install.packages("devtools")
devtools::install_github("emvolz-phylodynamics/phydynR")

Tutorials

• We recommend that you read the Get started to understand the basic functions in phydynR.

• You can later explore other tutorials:

  • Estimating transmission rates using the SIR model.
  • Estimating transmission rates using a slightly more complex model for HIV.
  • Estimating genealogies with an epidemiological coalescent model.
  • You can try a more complex example of estimating the effective number of infections and the basic reproduction number for HIV in Senegal.

Author

phydynR has been developed by Erik Volz

Related softwares

phydynR works on a fixed phylogenetic tree and therefore is not a program that will estimate the tree for you.

PhyDyn: If you would like to take into consideration the uncertainty on the tree estimates, check out our other software PhyDyn implemented in BEAST 2. For details on how to use it start here. PhyDyn is substantially slow to run.

Coalescent.jl: implements similar specification of demographic process but it is substantially faster than phydynR. Coalescent.jl is based on the Julia programming language.

References

If you would like to understand more about the models implemented in phydynR, check out Volz, 2012