By john-harrold
Skills and agents for the nlmixr2 pharmacometric ecosystem in R: rxode2 (ODE-based PK/PD), nlmixr2 (popPK/PD modeling), nonmem2rx (NONMEM → rxode2), monolix2rx (Monolix → rxode2), and babelmixr2 (run nlmixr2 models on NONMEM/Monolix/PKNCA).
Use this skill when the user wants to fit an nlmixr2-style model using a non-nlmixr2 backend — NONMEM, Monolix, or PKNCA — through `babelmixr2`. Triggers include `nlmixr(..., est = "nonmem")`, `est = "monolix"`, `est = "pknca"`, calls to `nonmemControl()` / `monolixControl()` / `pkncaControl()`, or "run my nlmixr2 model in NONMEM/Monolix".
Use this skill when the user wants to convert a Monolix project (`.mlxtran` + results folder) into an rxode2 / nlmixr2 model object for simulation, sharing, or qualification. Triggers include calls to `monolix2rx()` or `mlxtran()`, references to `.mlxtran` files, "translate this Monolix project", or babelmixr2's Monolix back-translation step.
Use this skill when the user is fitting population PK/PD models with the R package `nlmixr2`. Triggers include writing `ini({}) / model({})` model functions, calling `nlmixr2(model, data, est = ...)`, picking between saem / focei / foce / fo / agq / laplace / nlme / posthoc, configuring `saemControl()` / `foceiControl()`, or post-processing a fit with `augPred()`, `vpcPlot()`, `$parFixed`, `$omega`.
Use this skill when the user wants to convert a NONMEM control stream + output into an rxode2 / nlmixr2 model object for simulation, VPC, or sharing in an open-source workflow. Triggers include calls to `nonmem2rx()`, references to `.ctl`/`.mod`/`.lst`/`.xml`/`.phi` files, "translate this NONMEM run", or "qualify a NONMEM model in R".
Use this skill when the user is creating, editing, or running ODE-based pharmacometric models with the R package rxode2. Triggers include writing PK/PD models with `ini({}) / model({})` blocks, building event tables with `et()` / `eventTable()`, simulating with `rxSolve()`, population/clinical trial simulation, or debugging rxode2 compilation and solver errors.
Uses power tools
Uses Bash, Write, or Edit tools
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LLM-facing documentation for the nlmixr2 pharmacometric modeling ecosystem in R, distributed as an R package and as a Claude Code plugin.
The same content — a single combined nlmixr2verse agent plus per-package skill files for rxode2, nlmixr2, nonmem2rx, monolix2rx, and babelmixr2 — is shipped two ways:
ellmer, the Anthropic SDK, the OpenAI SDK, ...) and installers that write the files into the locations expected by Claude Code, OpenAI Codex CLI, Positron Assistant, and other tools that follow the AGENTS.md convention..claude-plugin/ directory at the repo root, so users who already use the Claude Code plugin marketplace can install without touching R.A single combined nlmixr2verse agent spans the whole ecosystem (the orchestration layer), and each package ships a skill for on-demand depth:
| Package | Skill | Purpose |
|---|---|---|
rxode2 | ✓ | ODE-based PK/PD modeling and simulation |
nlmixr2 | ✓ | Population PK/PD parameter estimation (SAEM, FOCEi, ...) |
nonmem2rx | ✓ | Convert finished NONMEM runs into rxode2 / nlmixr2 objects |
monolix2rx | ✓ | Convert Monolix projects into rxode2 / nlmixr2 objects |
babelmixr2 | ✓ | Fit nlmixr2 models via NONMEM, Monolix, or PKNCA backends |
The nlmixr2verse agent covers all five packages and the end-to-end workflow that connects them (author in rxode2 → fit in nlmixr2 → run on other engines with babelmixr2 → import legacy runs with nonmem2rx / monolix2rx).
# install.packages("remotes")
remotes::install_github("john-harrold/nlmixr2llm")
library(nlmixr2llm)
prompt <- system_prompt(packages = c("rxode2", "nlmixr2"))
# Example: with ellmer
chat <- ellmer::chat_anthropic(system_prompt = prompt)
chat$chat("Write a one-compartment PK model with first-order absorption in rxode2.")
# User-level (~/.claude/agents/, ~/.claude/skills/)
install_claude_code(scope = "user")
# Or project-local (.claude/agents/, .claude/skills/) under the current project
install_claude_code(scope = "project")
# Project AGENTS.md at the repo root
install_codex(scope = "project", packages = c("rxode2", "nlmixr2"))
# Global ~/.codex/AGENTS.md
install_codex(scope = "user", mode = "append")
Codex enforces a default 32 KiB cap on combined AGENTS.md content. The full corpus (~62 KiB) exceeds that. The combined nlmixr2verse agent is ~29 KiB on its own and is included whole whenever agents are requested, so packages = ... only subsets the skills. For Codex, install include = "agents" (just the agent, ~29 KiB) or include = "skills" with a packages = ... subset.
# Project-root agents.md (also picked up by Codex, Cursor, Aider, Zed, ...)
install_positron(workspace = ".", style = "agents_md")
# Per-package .github/instructions/*.instructions.md with applyTo: "**/*.R"
install_positron(workspace = ".", style = "instructions")
AGENTS.mdinstall_agents_md(path = ".", packages = c("rxode2", "nlmixr2"))
Covered by the agents.md cross-tool spec: Codex, Cursor, Aider, GitHub Copilot, Zed, Warp, Jules, Devin, and others.
The installers write independent copies, so re-run them after upgrading the package (pass overwrite = TRUE / mode = "write" to refresh existing files). install_claude_code() and install_positron(style = "instructions") keep a manifest (.nlmixr2llm-manifest) and, by default (prune = TRUE), remove files they installed in an earlier version but no longer ship — so a renamed agent or dropped package doesn't leave an orphan behind. Only files nlmixr2llm created are ever removed.
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