Repository of code used in Embark publications.

• analyze_data_and_make_figures_and_tables.py - A python (3) (we used 3.7.4 at runtime) script to aggregate and analyze raw data from simulation outputs.
• requirements.txt - List of versions of non-standard library python packages used in analyze_data_and_make_figures_and_tables.py
• diversity_matechoice_template_for_manuscript.slim - A template for SLIM 3 used to generate all simulations in this manuscript.

To generate summary stats and build figures and tables (replicate data in manuscript)...

python analyze_data_and_make_figures_and_tables.py 
    --output-root-directory {path_to_output_directory} 
    --simulation-results-root-directory {path_to_unzipped_raw_data} 
    --get-data-from-results-files

Supplementary materials are available with the online version of this manuscript # will add when final version is available Raw simulation data is available on DRYAD

• postprocess_germline.py - A python script with post-processing algorithm for filling gaps and filtering on marker counts in merged homozygosity tracts from germline (1.5.1) using --bits 1.

All other supplementary materials are available at figshare