musseco stands for [Mu]lti-[S]tate [S]peciation and [E]xtinction [Co]alescent and is an R package to estimate parameters for a speciation and extinction coalescent process.
We have implemented the BiSSECo ([Bi]nary-[S]tate [S]peciation and [E]xtinction [Co]alescent) model in which we can estimate the within-host and between-host replicative fitness using a fixed time-scaled tree.
Installation
# You will need to install the R package devtools
# (https://github.com/r-lib/devtools)
install.packages("devtools")
devtools::install_github("emvolz-phylodynamics/musseco")Tutorials
- We recommend that you read the Get started to understand the implementation of BiSSECo.
Author
musseco has been developed by Erik Volz