Package of the research paper: Fitting stochastic epidemic models to gene genealogies using linear noise approximation
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.
Here are some Vignettes that helps you get familiar with our work. Just download and have fun!
ConstantR0 A short example showing how to simulate SIR trajectory and genealogy based on constant reproduction number R0, illustrating methodology ...
ChangeR0 A short example showing how to simulate SIR trajectory and genealogy based time-varying reproduction number R0, illustrating methodology ...
Ebola Case studies analyzing Ebola genealogies from Sierra Leone and Liberia in the 2014 ebola outbreaks.