biogeobears

Set up and execute phylogenetic biogeographic analyses using BioGeoBEARS in R. Use when users request biogeographic reconstruction, ancestral range estimation, or want to analyze species distributions on phylogenies. Handles input file validation, data reformatting, RMarkdown workflow generation, and result visualization.

Quality

91%

Does it follow best practices?

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Securityby

Passed

No findings from the security scan

Quality

Content

81%Weight 40%Scale 1-5

Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.

The body is highly actionable and well-sequenced with strong validation checkpoints, but it is longer than necessary due to repeated sections and inlined reference material that could be delegated to the existing bundle files.

Suggestions

Deduplicate the installation instructions and runtime estimates, which appear in both the Step 5 README template and the Step 6 user-instructions block; keep one canonical copy.

Move detailed model descriptions, ΔAIC thresholds, and output-interpretation guidance into references/biogeobears_details.md and link to it from a short summary in SKILL.md.

Trim explanations of concepts Claude already knows (e.g. what AIC weights represent) to one-line reminders, keeping the domain-specific guidance that Claude would not infer.

Dimension	Reasoning	Score
Conciseness	The ~580-line body repeats content across sections (install instructions and runtime estimates appear in both the README template and Step 6, model descriptions are duplicated) and over-explains concepts Claude already knows (AIC weights, ΔAIC thresholds, pie vs text), so it is mostly efficient but could be tightened.	3 / 5
Actionability	Provides copy-paste-ready bash and R commands (e.g. the validate_geography_file.py invocations, mkdir/cp structure setup, rmarkdown::render calls) with specific examples covering the common reformatted-PHYLIP and CSV-to-PHYLIP cases.	5 / 5
Workflow Clarity	Six steps are clearly sequenced with explicit validation checkpoints ('Always validate the reformatted file before proceeding', rootedness check, species-name mismatch handling) and troubleshooting feedback loops for error recovery.	5 / 5
Progressive Disclosure	Structure is good with one-level-deep, clearly signaled references to real bundle files (scripts/validate_geography_file.py, scripts/biogeobears_analysis_template.Rmd, references/biogeobears_details.md), but substantial reference-grade content (full README template, model descriptions, output interpretation) is inlined in SKILL.md rather than deferred.	4 / 5
	Total	17 / 20 Passed

Description

100%Weight 40%Scale 1-5

Based on the skill's description, can an agent find and select it at the right time? Clear, specific descriptions lead to better discovery.

The description is strong across all dimensions: concrete actions, natural trigger terms, explicit what-and-when coverage, and a distinct niche with minimal conflict risk. It is written in third person with no padding.

Dimension	Reasoning	Score
Specificity	Lists multiple concrete actions ('input file validation, data reformatting, RMarkdown workflow generation, and result visualization') plus setup/execution, giving comprehensive coverage of what the skill does.	5 / 5
Completeness	Explicitly answers both 'what' (set up and execute BioGeoBEARS analyses, with four named sub-actions) and 'when' (a concrete 'Use when users request...' clause listing trigger scenarios).	5 / 5
Trigger Term Quality	Includes natural specialist phrasings users would say — 'biogeographic reconstruction', 'ancestral range estimation', 'analyze species distributions on phylogenies' — with synonyms covering the trigger space.	5 / 5
Distinctiveness Conflict Risk	Targets a clear niche (BioGeoBEARS in R for phylogenetic biogeography) with distinctive triggers that are unlikely to fire for unrelated skills.	5 / 5
	Total	20 / 20 Passed

Validation

87%

Warnings & errors only

Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.

Validation — 14 / 16 Passed

Validation for skill structure

Criteria	Description	Result
skill_md_line_count	SKILL.md is long (581 lines); consider splitting into references/ and linking	Warning
referenced_paths_exist	Referenced path issues: 3 missing	Warning

	Total	14 / 16 Passed

Repository: brunoasm/my_claude_skills
Path: biogeobears/SKILL.md
Commit: 5bdff99

Reviewed: 6 days ago

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