/adapref

R package to do adaptive preferential sampling in phylodynamics

Primary LanguageR

adapref

The goal of adapref is to allow adaptive preferential sampling in phylodynamics. It is a package to be used jointly with phylodyn and spmrf. Many of the functions of this package have been developed starting from the work done in these two packages. We acknowledge the developers for their work.

Installation

  1. Install (if necessary) package dependencies and helpers: devtools, ape, spmrf, rstan, loo and phylodyn.

  2. Load devtools using library(devtools).

  3. Install adapref using

    1. install_github("lorenzocapp/adapref"), or

    2. install_github("lorenzocapp/adapref", build_vignettes = TRUE) if you want some illustrative vignettes (note: using build_vignettes = TRUE will make the install take longer).

Vignettes

  1. Adaptive preferential sampling with simulated data: A short tutorial to describe the basics functioning of the package.

References

  1. L. Cappello, J.A. Palacios, Adaptive Preferential Sampling in Phylodynamics, soon in arxiv! 2020