gaia temporal sampling

A set of scripts for testing the effects of various temporal sampling schemes on the accuracy of gaia ancestor location inference on the cluster.

Workflow:

Run the SLiM simulation up to 20 times to generate unique tree sequence output (using slim.sh and run-pareto.slim)
Simplify the output tree sequences to fit various sampling schemes (using simplify_trees.sh/.py)
Create sample location matrices from the simplified trees (using sample_loc_mat_from_trees.sh/.py)
Run gaia on the simplified trees with sample locations (using run_gaia.sh/.R)
Analyze the accuracy of gaia inference (using sampling_scheme_analysis.py)
Visualize the results across sampling schemes (using sampling_scheme_comparison.py)

Name		Name	Last commit message	Last commit date
Latest commit History 28 Commits
accuracy_analysis		accuracy_analysis
inferred_locations		inferred_locations
landscapes		landscapes
sample_locations		sample_locations
trees		trees
.gitignore		.gitignore
README.md		README.md
cont_unif.sh		cont_unif.sh
cont_unif.slim		cont_unif.slim
run-pareto.slim		run-pareto.slim
run_gaia.R		run_gaia.R
run_gaia.sh		run_gaia.sh
sample_loc_mat_from_trees.py		sample_loc_mat_from_trees.py
sample_loc_mat_from_trees.sh		sample_loc_mat_from_trees.sh
sampling_scheme_analysis.py		sampling_scheme_analysis.py
sampling_scheme_comparison.py		sampling_scheme_comparison.py
simplify_trees.py		simplify_trees.py
simplify_trees.sh		simplify_trees.sh
simplify_trees_cont_unif.py		simplify_trees_cont_unif.py
simplify_trees_cont_unif.sh		simplify_trees_cont_unif.sh
simplify_trees_cont_unif_test.py		simplify_trees_cont_unif_test.py
slim.sh		slim.sh