phydynR v0.2.3

In this release of the package we have added vignettes to help understanding how to use the functions described in phydynR.

We have excluded the functions to compute infector probabilities which is the probability that a particular host i infected a particular host j. If you are looking for these functions, please refer to version 0.2.2 of this R package.

phydynR v0.2.2

First release of phydynR package.

It includes functions to:

• 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;

• compute infector probabilities which is the probability that a particular host i infected a particular host j.