Genetic and Isotopic Assignment Accounting for Habitat Suitability

Tools for using genetic markers, stable isotope data, and habitat suitability data to calculate posterior probabilities of breeding origin of migrating birds.


Travis-CI Build Status

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 R/vander-zanden-appendix.R.

Installing

To install the development version from GitHub with the devtools package, you can:

devtools::install_github("eriqande/gaiah")

Vignettes?

In lieu of a vignette, we provide the full source code for our use of the gaiah package for a recent paper. See below.

Reproducing the results from Ruegg et al. (2017)

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.

News

gaiah 0.0.2

This is the initial CRAN release. The paper about it has been accepted and it is time to get it up on CRAN.

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("gaiah")

0.0.2 by Eric C. Anderson, a year ago


Browse source code at https://github.com/cran/gaiah


Authors: Eric C. Anderson [cre, aut]


Documentation:   PDF Manual  


CC0 license


Imports dplyr, geosphere, ggplot2, lazyeval, magrittr, maptools, raster, rgeos, sp, stringr, tidyr

Suggests knitr, rmarkdown


See at CRAN