Tools for using genetic markers, stable isotope data, and habitat suitability data to calculate posterior probabilities of breeding origin of migrating birds.
This is an R-package for performing Genetic And Isotopic Assignment using Habitat features.
Most of the package has been written by Eric C. Anderson. The methodology for assigning individuals using stable isotope was first written by Hannah Vander Zanden and colleagues. It was reimplemented here and is now efficient enough to do leave one out cross validation, etc. These parts of the code are in the file
To install the development version from GitHub with the
devtools package, you can:
In lieu of a vignette, we provide the full source code for our use of the
gaiah package for a recent paper. See below.
If you want to reproduce all the results from the paper "Genetic assignment with isotopes and habitat suitability (GAIAH), a migratory bird case study" in Methods in Ecology and Evolution you will have to get the
gaiah package and then also clone the analysis repository from https://github.com/eriqande/gaiah-wiwa and then follow the instructions in that repository's README.
This is the initial CRAN release. The paper about it has been accepted and it is time to get it up on CRAN.