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-nlp-topicgit 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-nlp-topic)<a href="https://agentmods.dev/skills/leolin990405/r-analytics-skill/r-nlp-topic"><img src="https://agentmods.dev/badge/skills/leolin990405/r-analytics-skill/r-nlp-topic/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-nlp-topic"><img src="https://agentmods.dev/badge/skills/leolin990405/r-analytics-skill/r-nlp-topic.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 | $0.00030 | $0.00665 |
| Opus 5 | $0.00015 | $0.00332 |
| Sonnet 5 | $0.00006 | $0.00133 |
| Haiku 4.5 | $0.00003 | $0.00067 |
Grade A, and why
r-nlp-topic scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 9d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 113 lines — stays where its author put it; the contents beside it link to each section on GitHub.
R Topic Modeling
Latent topic discovery.
topicmodels (LDA)
library(topicmodels)
# Prepare DTM
dtm <- cast_dtm(df, document, word, n)
# Fit LDA
lda <- LDA(dtm, k = 10, control = list(seed = 1234))
# Topics
topics(lda) # Top topic per document
terms(lda, 10) # Top 10 terms per topic
# Tidy output
library(tidytext)
topics_beta <- tidy(lda, matrix = "beta") # Word-topic probabilities
topics_gamma <- tidy(lda, matrix = "gamma") # Document-topic probabilities
# Top terms per topic
topics_beta %>%
group_by(topic) %>%
slice_max(beta, n = 10) %>%
ungroup()
# Find optimal k
library(ldatuning)
result <- FindTopicsNumber(
dtm,
topics = seq(2, 20, by = 2),
metrics = c("Griffiths2004", "CaoJuan2009", "Arun2010", "Deveaud2014"),
method = "Gibbs",
control = list(seed = 1234)
)
FindTopicsNumber_plot(result)
LDAvis (Visualization)
library(LDAvis)
# Prepare data for visualization
phi <- posterior(lda)$terms
theta <- posterior(lda)$topics
vocab <- colnames(phi)
doc_length <- rowSums(as.matrix(dtm))
term_freq <- colSums(as.matrix(dtm))
json <- createJSON(
phi = phi,
theta = theta,
vocab = vocab,
doc.length = doc_length,
term.frequency = term_freq
)
serVis(json)
stm (Structural Topic Model)
library(stm)
# Prepare data
processed <- textProcessor(texts, metadata = df)
out <- prepDocuments(processed$documents, processed$vocab, processed$meta)
# Fit STM with covariates
model <- stm(
documents = out$documents,
vocab = out$vocab,
K = 10,
prevalence = ~ category + s(date),
data = out$meta
)
# Results
labelTopics(model)
plot(model, type = "summary")
# Topic correlations
topicCorr(model)
# Effect of covariates
effect <- estimateEffect(1:10 ~ category, model, meta = out$meta)
plot(effect, covariate = "category", topics = 1:5)
# Find optimal K
search_k <- searchK(out$documents, out$vocab, K = c(5, 10, 15, 20))
plot(search_k)
CTM (Correlated Topic Model)
library(topicmodels)
ctm <- CTM(dtm, k = 10, control = list(seed = 1234))
terms(ctm, 10)
What ships with it
3 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.
- 9d ago First seen · 113 lines · 30 tokens per session scan A 83f8ae992a7b
r-nlp-topic is a skill published in the GitHub repository LeoLin990405/r-analytics-skill (5 stars, last pushed 6mo ago), licensed MIT. It adds 30 tokens to every session and 665 once invoked, about $0.0002 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 2026-09-03.
Other skills, from other repositories
bio-applied-molecular-evolution
Test Hardy-Weinberg equilibrium, simulate Wright-Fisher drift/selection, and compute dN/dS, Tajima's D, and Fst with NumPy/SciPy. Use for neutral theory, molecular clock divergence time, selection scans, or effective population size (Ne) questions.
advanced-string-structures
Build tries, Aho-Corasick, and suffix arrays with Kasai LCP to index DNA/text and match many patterns in one pass. Use for genome motif scanning, k-mer indexing, longest-repeat search, or BWA/FM-index groundwork.
ai-science-esm2-embeddings
Generate ESM2 protein embeddings (fair-esm/transformers) and predict structure with ESMFold. Use when embedding sequences, scoring mutations zero-shot, annotating protein function, or doing fast MSA-free structure prediction.
ai-science-geneformer-scgpt
Tokenize scRNA-seq via Geneformer gene-rank or scGPT expression-bin encoding; annotate cell types, simulate in-silico knockouts. Use for foundation-model cell annotation, Geneformer/scGPT tokenization, or perturbation prediction.
ai-science-zero-shot-mutation
Score protein point mutations zero-shot with ESM-1v/ESM-2 masked-LM log-odds, ensembled, benchmarked on ProteinGym DMS. Use when predicting mutation effects, ranking missense variants, scoring VUS fitness with no labels.
bio-applied-advanced-ngs
Assemble genomes de novo: greedy OLC, de Bruijn graph/Eulerian path, N50/L50/NG50 stats, SPAdes/Flye/hifiasm CLI usage. Use when choosing k-mer size, picking an assembler for Illumina/ONT/HiFi reads, or scoring contiguity.