About

The gaia package performs generalized parsimony analysis on the local gene trees comprising an ancestral recombination graph (ARG) to infer the geographic locations of genetic ancestors. It relies on the succinct tree sequence format.

Installation

Install from within an R session:

remotes::install_github("blueraleigh/gaia")

Install from the command line:

git clone https://github.com/blueraleigh/gaia
cd gaia
R CMD BUILD .
R CMD INSTALL <name of tarball>

Key functions

• treeseq_discrete_mpr: Discrete state space reconstruction using arbitrary costs
• treeseq_quadratic_mpr: Continuous state space reconstruction using squared distances
• treeseq_linear_mpr: Continuous state space reconstruction using absolute distances
• treeseq_discrete_mpr_edge_history: Detailed migration histories
• treeseq_discrete_mpr_ancestry: Ancestry coefficients through time
• treeseq_discrete_mpr_ancestry_flux: Migration flux between regions

Documentation

Documentation is a work in progress and is available through the R help system (e.g., ?treeseq_discrete_mpr).