gtonkinhill / lnaphylodyn

Package of the research: Bayesian inference on coalescent-based phylodynamics

LNAphyloDyn:

Package of the research paper: Fitting stochastic epidemic models to gene genealogies using linear noise approximation

Installation

Prerequisites

You need to install these R packages before you install LNAPhlyodyn package: abind, smfsb, Rcpp, RcppArmadillo. You can easily install these packages by running the following code in your R console.

install.packages("abind")
install.packages("smfsb")
install.packages("Rcpp")
install.packages("RcppArmadillo")

Install LNAPhylodyn package

After installing the prerequisites packages, LNAphyloDyn package can be installed by running the following code in your console

Sys.setenv("PKG_LIBS" = "-llapack")
devtools::install_github("MingweiWilliamTang/LNAPhyloDyn")

See Errors in installation?

If you see errors when installing the package on your laptop, you can simply download the package, go to the directory and run

sourceCpp('src/LNA_functional.cpp')
source('R/basic.R', echo = TRUE)
source('R/coal_simulation.R', echo=TRUE)
source('R/general_change_point.R', echo=TRUE)
source('R/LNA_chpt_slice.R', echo=TRUE)

The above files contains most of the essential functions in the packages.

Vignettes

Here are some Vignettes that helps you get familiar with our work. Just download and have fun!

1. ConstantR0 A short example showing how to simulate SIR trajectory and genealogy based on constant reproduction number R0, illustrating methodology ...

2. ChangeR0 A short example showing how to simulate SIR trajectory and genealogy based time-varying reproduction number R0, illustrating methodology ...

3. Ebola Case studies analyzing Ebola genealogies from Sierra Leone and Liberia in the 2014 ebola outbreaks.