Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add LeoLin990405/r-analytics-skill --skill r-bio-phylogit clone --depth 1 https://github.com/LeoLin990405/r-analytics-skillWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/leolin990405/r-analytics-skill/r-bio-phylo)<a href="https://agentmods.dev/skills/leolin990405/r-analytics-skill/r-bio-phylo"><img src="https://agentmods.dev/badge/skills/leolin990405/r-analytics-skill/r-bio-phylo/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/leolin990405/r-analytics-skill/r-bio-phylo"><img src="https://agentmods.dev/badge/skills/leolin990405/r-analytics-skill/r-bio-phylo.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00028 | $0.00411 |
| Opus 5 | $0.00014 | $0.00205 |
| Sonnet 5 | $0.00006 | $0.00082 |
| Haiku 4.5 | $0.00003 | $0.00041 |
Grade A, and why
r-bio-phylo scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 12d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
What it actually says
R Phylogenetics
Phylogenetic analysis and visualization.
ape
library(ape)
# Read tree
tree <- read.tree("tree.nwk")
tree <- read.nexus("tree.nex")
# Plot
plot(tree)
plot(tree, type = "fan")
plot(tree, type = "cladogram")
# Tree manipulation
drop.tip(tree, c("species1", "species2"))
root(tree, outgroup = "outgroup")
ladderize(tree)
# Distance
cophenetic(tree)
dist.nodes(tree)
# Bootstrap
boot.phylo(tree, data, FUN, B = 100)
ggtree
library(ggtree)
# Basic tree
ggtree(tree) + geom_tiplab()
# Circular
ggtree(tree, layout = "circular") + geom_tiplab()
# With data
ggtree(tree) %<+% metadata +
geom_tippoint(aes(color = group)) +
geom_tiplab(aes(label = name))
# Heatmap
gheatmap(ggtree(tree), data, width = 0.3)
# Annotations
ggtree(tree) +
geom_hilight(node = 10, fill = "blue", alpha = 0.3) +
geom_cladelabel(node = 10, label = "Clade A")
phangorn
library(phangorn)
# Parsimony
pars <- parsimony(tree, data)
tree_pars <- optim.parsimony(tree, data)
# Maximum likelihood
fit <- pml(tree, data)
fit <- optim.pml(fit, model = "GTR")
# Bootstrap
bs <- bootstrap.pml(fit, bs = 100)
plotBS(tree, bs)
What ships with it
2 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 12d ago First seen · 79 lines · 28 tokens per session scan A 548052515348
r-bio-phylo is a skill published in the GitHub repository LeoLin990405/r-analytics-skill (5 stars, last pushed 6mo ago), licensed MIT. It adds 28 tokens to every session and 411 once invoked, about $0.0001 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.
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