The Agent Skills Directory

[COMMAND_EXECUTION]: The skill performs standard file system operations, including creating structured analysis directories using mkdir -p and managing data files with cp, to prepare the biogeographic analysis environment.
[DYNAMIC_EXECUTION]: The skill generates customized RMarkdown (.Rmd) scripts by populating a predefined template (scripts/biogeobears_analysis_template.Rmd) with user-supplied parameters. These scripts are designed to be executed in an R environment using rmarkdown::render to perform statistical modeling and ancestral range reconstruction.
[INDIRECT_PROMPT_INJECTION]: The skill ingests and processes external data files, including phylogenetic trees in Newick format and geographic distribution data in various tabular formats.
Ingestion points: Tree files are parsed for tip labels in the SKILL.md workflow; geography files are read and reformatted by the bundled scripts/validate_geography_file.py script.
Boundary markers: No specific boundary markers or "ignore" instructions are implemented for the content of the processed files.
Capability inventory: The skill possesses the capability to modify the local file system and generate executable R code that fits complex evolutionary models.
Sanitization: The scripts/validate_geography_file.py script performs format validation, ensuring correct delimiters (tabs), character sets (binary 0/1), and metadata consistency (species counts and area matching).

biogeobears