RConsortium/pharma-skills

If that path is not accessible, fetch from GitHub: https://github.com/RConsortium/pharma-skills/blob/main/_automation/benchmark-runner/SKILL.md

https://github.com/RConsortium/pharma-skills/blob/main/_automation/benchmark-runner/SKILL.md

Repository: `RConsortium/pharma-skills` (https://github.com/RConsortium/pharma-skills)

Create a single routine at [claude.ai/code/routines](https://claude.ai/code/routines):

<!-- BENCHMARK_PARTIAL: {"eval_id":"github-issue-27","model":"Claude Routine","skill_sha":"b5ede6a...","issue_number":27,"blinded_map":{"candidate_1":"output_B","candidate_2":"output_A"},"agent_a_asset_url":"https://github.com/RConsortium/p

# Get-or-create release, then POST to its upload_url with the zip as data-binary.   # See https://docs.github.com/en/rest/releases for the exact endpoints.

# See https://docs.github.com/en/rest/releases for the exact endpoints.

https://github.com/RConsortium/pharma-skills/releases/download/benchmark-results/benchmark_agent_a_{eval_id}.zip

# Option B — curl (release assets are public for public repos; token only needed for private):

curl -L "{agent_a_asset_url}" -o /tmp/benchmark_{id}/benchmark_agent_a_{eval_id}.zip

--- <!-- BENCHMARK_COMPLETE: {"eval_id":"{id}","model":"{model}","skill_sha":"{skill_sha}"} --> *Posted automatically by `benchmark-runner` · Repo: https://github.com/RConsortium/pharma-skills*

*Posted automatically by `benchmark-runner` · Repo: https://github.com/RConsortium/pharma-skills*

[Credential-related source omitted]

Executable file

- Score trend per eval (grouped by skill)

Executable file

[Credential-related source omitted]

[Credential-related source omitted]

while True:         url = (             f"https://api.github.com/repos/{repo}/issues/{issue_number}/comments"

url = (             f"https://api.github.com/repos/{repo}/issues/{issue_number}/comments"             f"?per_page=100&page={page}"

f"https://api.github.com/repos/{repo}/issues/{issue_number}/comments"

f"?per_page=100&page={page}"         )         request = urllib.request.Request(

)         request = urllib.request.Request(             url,

request = urllib.request.Request(

},         )         with urllib.request.urlopen(request, timeout=30) as response:

)         with urllib.request.urlopen(request, timeout=30) as response:             page_comments = json.loads(response.read().decode("utf-8"))

with urllib.request.urlopen(request, timeout=30) as response:

[Credential-related source omitted]

[Credential-related source omitted]

[Credential-related source omitted]

rm = e.get("_runs_model")

f"{'???' if rm is None else rm:>8} "

Executable file

[Credential-related source omitted]

[Credential-related source omitted]

raise RuntimeError("GH_TOKEN or GITHUB_TOKEN is not set")     data = json.dumps(payload).encode("utf-8") if payload is not None else None     request = urllib.request.Request(

data = json.dumps(payload).encode("utf-8") if payload is not None else None     request = urllib.request.Request(         url,

request = urllib.request.Request(

method=method,     )     with urllib.request.urlopen(request, timeout=30) as response:

)     with urllib.request.urlopen(request, timeout=30) as response:         return json.loads(response.read().decode("utf-8"))

with urllib.request.urlopen(request, timeout=30) as response:

while True:         url = (             f"https://api.github.com/repos/{repo}/issues/{issue_number}/comments"

url = (             f"https://api.github.com/repos/{repo}/issues/{issue_number}/comments"             f"?per_page=100&page={page}"

f"https://api.github.com/repos/{repo}/issues/{issue_number}/comments"

def post_issue_comment(repo: str, issue_number: str, body: str) -> str:     data = _api_request(         f"https://api.github.com/repos/{repo}/issues/{issue_number}/comments",

data = _api_request(         f"https://api.github.com/repos/{repo}/issues/{issue_number}/comments",         method="POST",

f"https://api.github.com/repos/{repo}/issues/{issue_number}/comments",

def update_issue_comment(repo: str, comment_id: int, body: str) -> str:     data = _api_request(         f"https://api.github.com/repos/{repo}/issues/comments/{comment_id}",

data = _api_request(         f"https://api.github.com/repos/{repo}/issues/comments/{comment_id}",         method="PATCH",

f"https://api.github.com/repos/{repo}/issues/comments/{comment_id}",

Executable file

#!/usr/bin/env bash

sudo apt-get update -qq

sudo apt-get install -y r-base

sudo apt-get install -y --no-install-recommends \

if ! grep -q "${domain}" /etc/hosts 2>/dev/null; then     local ip     ip=$(curl -s --max-time 10 -w "%{remote_ip}" -o /dev/null "https://${domain}" 2>/dev/null || true)

local ip     ip=$(curl -s --max-time 10 -w "%{remote_ip}" -o /dev/null "https://${domain}" 2>/dev/null || true)     if [ -n "${ip}" ]; then

ip=$(curl -s --max-time 10 -w "%{remote_ip}" -o /dev/null "https://${domain}" 2>/dev/null || true)

echo "${ip} ${domain}" | sudo tee -a /etc/hosts > /dev/null

'pak',     type  = 'source',     repos = 'https://cloud.r-project.org',

type  = 'source',     repos = 'https://cloud.r-project.org',     quiet = FALSE

repos = 'https://cloud.r-project.org',

message('[setup] CRAN source build failed — trying r-lib CDN binary...') cdn_url <- sprintf(   'https://r-lib.github.io/p/pak/stable/%s/%s/%s',

cdn_url <- sprintf(   'https://r-lib.github.io/p/pak/stable/%s/%s/%s',   .Platform\$pkgType, R.Version()\$os, R.Version()\$arch

'https://r-lib.github.io/p/pak/stable/%s/%s/%s',

# Always set curl + SSL-bypass as the download fallback.

# load; system curl resolves using the /etc/hosts pin we set above.

ppm_url <- if (nzchar(os_codename)) {   sprintf("https://packagemanager.posit.co/cran/__linux__/%s/latest", os_codename)

sprintf("https://packagemanager.posit.co/cran/__linux__/%s/latest", os_codename)

} else {   message("[setup] PPM unavailable — using CRAN.")   "https://cran.r-project.org"

message("[setup] PPM unavailable — using CRAN.")   "https://cran.r-project.org" }

"https://cran.r-project.org"

## 1. Create a codespace from Github  open https://github.com/codespaces and create a codespace under main from pharma-skills

open https://github.com/codespaces and create a codespace under main from pharma-skills

claude --dangerously-skip-permissions

Executable file

Executable file

Executable file

Agent skills for deriving ADaM datasets using the [{admiral}](https://pharmaverse.github.io/admiral/)

- [admiral documentation](https://pharmaverse.github.io/admiral/)

- [CDISC ADaMIG v1.3](https://www.cdisc.org/standards/foundational/adam)

- [pharmaverse examples](https://pharmaverse.github.io/examples/)

Benchmarks are tracked as GitHub issues with the `benchmark` and `eval` labels at https://github.com/RConsortium/pharma-skills/issues.

https://github.com/RConsortium/pharma-skills/issues.

An agent skill for deriving ADaM Adverse Events Analysis Datasets (ADAE) using the [{admiral}](https://pharmaverse.github.io/admiral/) R package and the

the [{admiral}](https://pharmaverse.github.io/admiral/) R package and the

Benchmarks are tracked as GitHub issues with the `benchmark` and `eval` labels at https://github.com/RConsortium/pharma-skills/issues.

https://github.com/RConsortium/pharma-skills/issues.

- [admiral documentation](https://pharmaverse.github.io/admiral/)

- [admiral ADAE vignette](https://pharmaverse.github.io/admiral/articles/adae.html)

- [CDISC ADaMIG v1.3](https://www.cdisc.org/standards/foundational/adam)

- [pharmaverse examples — ADAE](https://pharmaverse.github.io/examples/)

- [xportr documentation](https://atorus-research.github.io/xportr/)

Inputs are generated from [`{pharmaversesdtm}`](https://pharmaverse.github.io/pharmaversesdtm/)

and [`{pharmaverseadam}`](https://pharmaverse.github.io/pharmaverseadam/) — publicly available,

It is structured around **decision guidance** — which function to use in a given situation and why — not as a comprehensive API reference. For full signatures and examples see the [admiral documentation](https://pharmaverse.github.io/admira

and examples see the [admiral documentation](https://pharmaverse.github.io/admiral/).

admiral PR [#3199](https://github.com/pharmaverse/admiral/pull/3199) adds a

Benchmarks are tracked as GitHub issues with the `benchmark` label at https://github.com/RConsortium/pharma-skills/issues.

https://github.com/RConsortium/pharma-skills/issues.

Issue [#172](https://github.com/RConsortium/pharma-skills/issues/172) (NCA

An agent skill for deriving ADaM Pharmacokinetic Concentrations Analysis Datasets (ADPC, also called ADNCA) using the [{admiral}](https://pharmaverse.github.io/admiral/) R package.

[{admiral}](https://pharmaverse.github.io/admiral/) R package.

Benchmarks are tracked as GitHub issues with the `benchmark` label at https://github.com/RConsortium/pharma-skills/issues.

https://github.com/RConsortium/pharma-skills/issues.

- [admiral PK NCA and population PK vignette](https://pharmaverse.github.io/admiral/articles/pk_adnca.html)

- [CDISC ADaM Implementation Guide for NCA (ADNCA)](https://www.cdisc.org/standards/foundational/adam)

- [PKNCA](https://humanpred.github.io/pknca/)

Unsupported or unresolved allowed-tools declaration

Benchmarks for the `admiral-adpc` skill are tracked as GitHub issues with the `benchmark` label at https://github.com/RConsortium/pharma-skills/issues, and

`benchmark` label at https://github.com/RConsortium/pharma-skills/issues, and

Inputs come from [`{pharmaversesdtm}`](https://pharmaverse.github.io/pharmaversesdtm/)

(PC, EX, VS) and [`{pharmaverseadam}`](https://pharmaverse.github.io/pharmaverseadam/)

Benchmarks are tracked as GitHub issues with the `benchmark` and `eval` labels at https://github.com/RConsortium/pharma-skills/issues.

https://github.com/RConsortium/pharma-skills/issues.

An agent skill for deriving ADaM Tumor Response Analysis Datasets (ADRS) using the [{admiral}](https://pharmaverse.github.io/admiral/) and

the [{admiral}](https://pharmaverse.github.io/admiral/) and

[{admiralonco}](https://pharmaverse.github.io/admiralonco/) R packages.

Benchmarks are tracked as GitHub issues with the `benchmark` and `eval` labels at https://github.com/RConsortium/pharma-skills/issues.

https://github.com/RConsortium/pharma-skills/issues.

- [admiralonco documentation](https://pharmaverse.github.io/admiralonco/)

- [admiralonco ADRS vignette](https://pharmaverse.github.io/admiralonco/articles/adrs.html)

- [CDISC ADaMIG v1.3](https://www.cdisc.org/standards/foundational/adam)

- [RECIST 1.1 guidelines](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3107559/)

- [pharmaverse examples — ADRS](https://pharmaverse.github.io/examples/)

Issue [#167](https://github.com/RConsortium/pharma-skills/issues/167) was run

Inputs are generated from [`{pharmaversesdtm}`](https://pharmaverse.github.io/pharmaversesdtm/) using

[`{pharmaversesdtm}`](https://pharmaverse.github.io/pharmaversesdtm/) using

An agent skill for deriving ADaM Subject-Level Analysis Datasets (ADSL) using the [{admiral}](https://pharmaverse.github.io/admiral/) R package and the

the [{admiral}](https://pharmaverse.github.io/admiral/) R package and the

- [admiral documentation](https://pharmaverse.github.io/admiral/)

- [admiral ADSL vignette](https://pharmaverse.github.io/admiral/articles/adsl.html)

- [CDISC ADaMIG v1.3](https://www.cdisc.org/standards/foundational/adam)

- [pharmaverse examples — ADSL](https://pharmaverse.github.io/examples/)

- [xportr documentation](https://atorus-research.github.io/xportr/)

Inputs are generated from [`{pharmaversesdtm}`](https://pharmaverse.github.io/pharmaversesdtm/)

and [`{pharmaverseadam}`](https://pharmaverse.github.io/pharmaverseadam/) — publicly available,

It is structured around **decision guidance** — which function to use in a given situation and why — not as a comprehensive API reference. For full signatures and examples see the [admiral documentation](https://pharmaverse.github.io/admira

It is structured around **decision guidance** — which function to use in a given situation and why — not as a comprehensive API reference. For full signatures and examples see the [admiral documentation](https://pharmaverse.github.io/admira

and examples see the [admiral documentation](https://pharmaverse.github.io/admiral/).

and examples see the [admiral documentation](https://pharmaverse.github.io/admiral/).

Benchmarks are tracked as GitHub issues with the `benchmark` and `eval` labels at https://github.com/RConsortium/pharma-skills/issues.

https://github.com/RConsortium/pharma-skills/issues.

Issue [#166](https://github.com/RConsortium/pharma-skills/issues/166) is the

An agent skill for deriving ADaM Time-to-Event Analysis Datasets (ADTTE) using the [{admiral}](https://pharmaverse.github.io/admiral/) R package.

the [{admiral}](https://pharmaverse.github.io/admiral/) R package.

Benchmarks are tracked as GitHub issues with the `benchmark` and `eval` labels at https://github.com/RConsortium/pharma-skills/issues.

https://github.com/RConsortium/pharma-skills/issues.

The existing [#166](https://github.com/RConsortium/pharma-skills/issues/166)

- [admiral ADTTE vignette](https://pharmaverse.github.io/admiral/articles/adtte.html)

- [CDISC ADaMIG BDS-TTE v1.0](https://www.cdisc.org/standards/foundational/adam)

- [pharmaverse examples — ADTTE](https://pharmaverse.github.io/examples/)

Issue [#166](https://github.com/RConsortium/pharma-skills/issues/166) was run

Inputs use [`{pharmaversesdtm}`](https://pharmaverse.github.io/pharmaversesdtm/)

`ae` and [`{pharmaverseadam}`](https://pharmaverse.github.io/pharmaverseadam/)

An agent skill for deriving ADaM Basic Data Structure (BDS) findings datasets using the [{admiral}](https://pharmaverse.github.io/admiral/) R package and

using the [{admiral}](https://pharmaverse.github.io/admiral/) R package and

- [admiral ADVS vignette](https://pharmaverse.github.io/admiral/articles/advs.html)

- [admiral ADLB vignette](https://pharmaverse.github.io/admiral/articles/adlb.html)

- [CDISC ADaMIG v1.3 — BDS](https://www.cdisc.org/standards/foundational/adam)

- [pharmaverse examples — BDS](https://pharmaverse.github.io/examples/)

Inputs are generated from [`{pharmaversesdtm}`](https://pharmaverse.github.io/pharmaversesdtm/)

and [`{pharmaverseadam}`](https://pharmaverse.github.io/pharmaverseadam/) — publicly available,

### Step 1 · Intake from ClinicalTrials.gov + protocol acquisition 1. Fetch `https://clinicaltrials.gov/api/v2/studies/{NCT}?format=json`; extract design (arms,

1. Fetch `https://clinicaltrials.gov/api/v2/studies/{NCT}?format=json`; extract design (arms,

- **[S1]** `paperclip: PMC2686169 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686169/` — Liu et al., *PLoS ONE* 2009. Vitamin-D-receptor activation directly induces cathelicidin and β-defensin (DEFB4); the CAMP promoter carries three VDRE

- **[S2]** `paperclip: 2094036101 https://doi.org/10.1056/nejmoa021481` — Ong et al., *NEJM* 2002. AMP deficiency underlies *S. aureus* susceptibility in atopic dermatitis.

- **[S3]** `paperclip: PMC10326740 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10326740/` — Szabó et al., *Acta Derm Venereol* 2023. LL-37 (cathelicidin) is impaired in lesional and non-lesional AD.

- **[S4]** `paperclip: PMC2782163 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2782163/` — Kim et al., *J Korean Med Sci* 2005. LL-37 is negligible in normal skin but markedly increased in psoriasis.

- **[S5]** `paperclip: 1528623386 https://doi.org/10.4049/jimmunol.179.2.984` — Albanesi et al., *J Immunol* 2007. IL-4 and IL-13 (TH2) negatively regulate β-defensin expression.

- **[S6]** `paperclip: 2098825396 https://doi.org/10.1111/jdv.12176` — Hata et al., *JEADV* 2014 (this trial's own main-study RCT publication; PMID 23638978). Darker skin type and higher BMI are risk factors for vitamin D deficiency in AD.

- **[S7]** `paperclip: 2128501903 https://doi.org/10.4172/2161-1165.1000148` — Jarrett, 2014 review. Oral vitamin D3 supplementation raises serum vitamin D.

- **[S8]** `paperclip: 2151400905 https://doi.org/10.1046/j.0905-6157.2003.00106.x` — Laske et al., 2004. Serum IgE and atopic-dermatitis severity.

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"S1": {         "paperclip_id": "PMC2686169",         "url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686169/",

"paperclip_id": "PMC2686169",         "url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686169/",         "cite": "Liu et al., PLoS ONE 2009",

"url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686169/",

"S2": {         "paperclip_id": "2094036101",         "url": "https://doi.org/10.1056/nejmoa021481",

"paperclip_id": "2094036101",         "url": "https://doi.org/10.1056/nejmoa021481",         "cite": "Ong et al., NEJM 2002",

"url": "https://doi.org/10.1056/nejmoa021481",

"S3": {         "paperclip_id": "PMC10326740",         "url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10326740/",

"paperclip_id": "PMC10326740",         "url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10326740/",         "cite": "Szabo et al., Acta Derm Venereol 2023",

"url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10326740/",

"S4": {         "paperclip_id": "PMC2782163",         "url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2782163/",

"paperclip_id": "PMC2782163",         "url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2782163/",         "cite": "Kim et al., J Korean Med Sci 2005",

"url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2782163/",

"S5": {         "paperclip_id": "1528623386",         "url": "https://doi.org/10.4049/jimmunol.179.2.984",

"paperclip_id": "1528623386",         "url": "https://doi.org/10.4049/jimmunol.179.2.984",         "cite": "Albanesi et al., J Immunol 2007",

"url": "https://doi.org/10.4049/jimmunol.179.2.984",

"S6": {         "paperclip_id": "2098825396",         "url": "https://doi.org/10.1111/jdv.12176",

"paperclip_id": "2098825396",         "url": "https://doi.org/10.1111/jdv.12176",         "cite": "Hata et al., JEADV 2014 (this trial's main-study RCT publication, PMID 23638978)",

"url": "https://doi.org/10.1111/jdv.12176",

"S7": {         "paperclip_id": "2128501903",         "url": "https://doi.org/10.4172/2161-1165.1000148",

"paperclip_id": "2128501903",         "url": "https://doi.org/10.4172/2161-1165.1000148",         "cite": "Jarrett et al., 2014 review",

"url": "https://doi.org/10.4172/2161-1165.1000148",

"S8": {         "paperclip_id": "2151400905",         "url": "https://doi.org/10.1046/j.0905-6157.2003.00106.x",

"paperclip_id": "2151400905",         "url": "https://doi.org/10.1046/j.0905-6157.2003.00106.x",         "cite": "Laske et al., 2004",

"url": "https://doi.org/10.1046/j.0905-6157.2003.00106.x",

"S9": {         "paperclip_id": "4405923810",         "url": "https://doi.org/10.21873/invivo.13848",

"paperclip_id": "4405923810",         "url": "https://doi.org/10.21873/invivo.13848",         "cite": "Kralova et al., In Vivo 2024 (abstract corpus) - 1000/2000/4000/8000 IU in young healthy adults",

"url": "https://doi.org/10.21873/invivo.13848",

#!/usr/bin/env Rscript

| Node | Parents | Equation | Source | Evidence | |---|---|---|---|---| | `WBC[t]` | `WBC[t−1]`, `baseline_wbc`, `cyc_active`, `rtx_infusion/is_rtx`, `aza_active`, `f_heme` | `0.5·WBC[t−1] + 0.5·base − drag + N(0, 0.7²)`; `drag = 1.7 + 0.7·

|---|---|---|---|---| | `WBC[t]` | `WBC[t−1]`, `baseline_wbc`, `cyc_active`, `rtx_infusion/is_rtx`, `aza_active`, `f_heme` | `0.5·WBC[t−1] + 0.5·base − drag + N(0, 0.7²)`; `drag = 1.7 + 0.7·f_heme` (CYC), `0.6 + 0.4·f_heme` (RTX late), `0.6

| `WBC[t]` | `WBC[t−1]`, `baseline_wbc`, `cyc_active`, `rtx_infusion/is_rtx`, `aza_active`, `f_heme` | `0.5·WBC[t−1] + 0.5·base − drag + N(0, 0.7²)`; `drag = 1.7 + 0.7·f_heme` (CYC), `0.6 + 0.4·f_heme` (RTX late), `0.6 + 0.3·f_heme` (AZA) |

| `remission_day` | `remit_ever` | `clip(exp(Normal(log 45, 0.55²)), 8, 175)` | `model: params (remit_day_median)` | Median time-to-remission ~43–57 d (calibration target) | | `bvaswg[t]` | `bvaswg[t−1]`, `baseline_bvaswg`, `remission_day`,

| `bvaswg[t]` | `bvaswg[t−1]`, `baseline_bvaswg`, `remission_day`, `day` | Linear decline to 0 by `remission_day` if remitting; else plateau at `0.45·baseline`; `=0` once in remission | `ctgov: outcomesModule` | BVAS/WG = 0 defines remissio

| `flare[t]` | `is_rtx`, `anca_type`, `new_diagnosis`, `prednisone`, `f_relapse`, `in_remission`, `day` | `Bern(min(0.6, exp(log 0.045 − 0.20·rtx + 0.62·1{PR3} + 0.35·1{relapsing} − 0.020·pred + 1.0·f_relapse)))`, post-6mo only | `paperclip

|---|---|---|---|---| | `Leukopenia / Neutropenia / Anaemia / Thrombocytopenia [t]` | `WBC/ANC/HGB/PLT[t]`, `cyc_active`, `aza_active` | Grade = CTCAE(lab); reported w.p. `{1:.20–.25, 2:.55–.85, 3:.95–.97, 4:1.0}`; serious only at Gr 4 | `c

| `Leukopenia / Neutropenia / Anaemia / Thrombocytopenia [t]` | `WBC/ANC/HGB/PLT[t]`, `cyc_active`, `aza_active` | Grade = CTCAE(lab); reported w.p. `{1:.20–.25, 2:.55–.85, 3:.95–.97, 4:1.0}`; serious only at Gr 4 | `ctgov: resultsSection (

| `Infection[t]` | `is_rtx`, `cyc/aza_active`, `prednisone`, `f_infect` | `Bern(min(0.6, exp(log 0.050 + 1.0·f_infect + 0.12·rtx + 0.004·pred)))`; serious fraction 0.30 | `paperclip: PMC5570101 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5

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dm$is_leuko <- as.integer(dm$USUBJID %in% leuko_ids)   lk <- .arm_mean(dm, "ARMCD", "is_leuko");     m$leuko_RTX <- lk$RTX %||% 0; m$leuko_CYC <- lk$CYC %||% 0   re$nc <- as.integer(re$DISPOSITION != "COMPLETED")

lk <- .arm_mean(dm, "ARMCD", "is_leuko");     m$leuko_RTX <- lk$RTX %||% 0; m$leuko_CYC <- lk$CYC %||% 0   re$nc <- as.integer(re$DISPOSITION != "COMPLETED")   nc <- .arm_mean(re, "ARMCD", "nc");           m$noncomplete_RTX <- nc$RTX %||% 0

re$nc <- as.integer(re$DISPOSITION != "COMPLETED")

nc <- .arm_mean(re, "ARMCD", "nc");           m$noncomplete_RTX <- nc$RTX %||% 0; m$noncomplete_CYC <- nc$CYC %||% 0

#!/usr/bin/env Rscript

2. **find-protocol.** Otherwise run the vendored `find_protocol.py`, which turns an NCT ID into that    trial's full protocol PDF taken **strictly** from the public HuggingFace dataset    [`trialdesignbench/source`](https://huggingface.co/d

trial's full protocol PDF taken **strictly** from the public HuggingFace dataset    [`trialdesignbench/source`](https://huggingface.co/datasets/trialdesignbench/source) — nothing from    ClinicalTrials.gov, NEJM, or anywhere else.

[`trialdesignbench/source`](https://huggingface.co/datasets/trialdesignbench/source) — nothing from

That script is just: `command -v paperclip || curl -fsSL https://paperclip.gxl.ai/install.sh | bash`.

That script is just: `command -v paperclip || curl -fsSL https://paperclip.gxl.ai/install.sh | bash`.

[Credential-related source omitted]

Example row: `time_to_resistance (arm) | paperclip: pmc_8567001 https://… | "median PFS 25.5 vs 16.7 months (HR 0.62; 95% CI 0.49–0.79)"`.

#!/usr/bin/env bash

command -v paperclip >/dev/null 2>&1 && { echo "paperclip already installed: $(command -v paperclip)"; exit 0; } echo "Installing paperclip CLI..."; curl -fsSL https://paperclip.gxl.ai/install.sh | bash

echo "Installing paperclip CLI..."; curl -fsSL https://paperclip.gxl.ai/install.sh | bash

echo "Installing paperclip CLI..."; curl -fsSL https://paperclip.gxl.ai/install.sh | bash

Reference the CDISC SDTM domain model (the [SDTM model](https://www.cdisc.org/standards/foundational/sdtm) and the

[SDTM model](https://www.cdisc.org/standards/foundational/sdtm) and the

[SDTMIG](https://www.cdisc.org/standards/foundational/sdtmig)) to confirm the form set is

Executable file

BASE = "https://huggingface.co/datasets/trialdesignbench/source/resolve/main"

for attempt in range(tries):         try:             r = requests.get(url, timeout=timeout, stream=bool(dest))

try:             r = requests.get(url, timeout=timeout, stream=bool(dest))             if dest:

r = requests.get(url, timeout=timeout, stream=bool(dest))

Executable file

Executable file

Executable file

HERE = os.path.dirname(os.path.abspath(__file__)) NS = "{http://www.cdisc.org/ns/odm/v2.0}"

NS = "{http://www.cdisc.org/ns/odm/v2.0}"

SCHEMA = os.path.join(HERE, "xsd_v2", "ODM.xsd")     # the rules from official ODM repo: https://github.com/cdisc-org/DataExchange-ODM/tree/main/schema

Executable file

NS = "{http://www.cdisc.org/ns/odm/v2.0}"

Executable file

NS = "http://www.cdisc.org/ns/odm/v2.0"

XMLLANG = "{http://www.w3.org/XML/1998/namespace}lang"

Executable file

<?xml version="1.0" encoding="UTF-8"?> <xs:schema xmlns="http://www.cdisc.org/ns/odm/v2.0" xmlns:xs="http://www.w3.org/2001/XMLSchema"

<xs:schema xmlns="http://www.cdisc.org/ns/odm/v2.0" xmlns:xs="http://www.w3.org/2001/XMLSchema"

xmlns:odm="http://www.cdisc.org/ns/odm/v2.0" targetNamespace="http://www.cdisc.org/ns/odm/v2.0"

<xs:import namespace="http://www.w3.org/XML/1998/namespace" schemaLocation="xml.xsd"/>

<?xml version="1.0" encoding="UTF-8"?> <xs:schema xmlns="http://www.cdisc.org/ns/odm/v2.0" xmlns:xs="http://www.w3.org/2001/XMLSchema"

<xs:schema xmlns="http://www.cdisc.org/ns/odm/v2.0" xmlns:xs="http://www.w3.org/2001/XMLSchema"

targetNamespace="http://www.cdisc.org/ns/odm/v2.0" elementFormDefault="qualified"

<xs:import namespace="http://www.w3.org/XML/1998/namespace" schemaLocation="xml.xsd"/>

<?xml version="1.0" encoding="UTF-8"?> <xs:schema xmlns="http://www.cdisc.org/ns/odm/v2.0" xmlns:xs="http://www.w3.org/2001/XMLSchema"

<xs:schema xmlns="http://www.cdisc.org/ns/odm/v2.0" xmlns:xs="http://www.w3.org/2001/XMLSchema"

xmlns:nci="http://ncicb.nci.nih.gov/xml/odm/EVS/CDISC"

xmlns:odm="http://www.cdisc.org/ns/odm/v2.0" targetNamespace="http://www.cdisc.org/ns/odm/v2.0"

<xs:schema xmlns="http://www.cdisc.org/ns/odm/v2.0" xmlns:xs="http://www.w3.org/2001/XMLSchema"

xmlns:odm="http://www.cdisc.org/ns/odm/v2.0"

xmlns:xhtml="http://www.w3.org/1999/xhtml" targetNamespace="http://www.cdisc.org/ns/odm/v2.0"

<xs:import namespace="http://www.w3.org/XML/1998/namespace" schemaLocation="xml.xsd"/>

<xs:import namespace="http://www.w3.org/1999/xhtml" schemaLocation="ODM-xhtml.xsd"/>

<?xml version="1.0" encoding="UTF-8"?> <xs:schema xmlns="http://www.cdisc.org/ns/odm/v2.0" xmlns:xs="http://www.w3.org/2001/XMLSchema"

<xs:schema xmlns="http://www.cdisc.org/ns/odm/v2.0" xmlns:xs="http://www.w3.org/2001/XMLSchema"

xmlns:odm="http://www.cdisc.org/ns/odm/v2.0" targetNamespace="http://www.cdisc.org/ns/odm/v2.0"

<xs:import namespace="http://www.w3.org/XML/1998/namespace" schemaLocation="xml.xsd"/>

<?xml version="1.0" encoding="UTF-8"?> <xs:schema xmlns="http://www.cdisc.org/ns/odm/v2.0" xmlns:xs="http://www.w3.org/2001/XMLSchema"

<xs:schema xmlns="http://www.cdisc.org/ns/odm/v2.0" xmlns:xs="http://www.w3.org/2001/XMLSchema"

targetNamespace="http://www.cdisc.org/ns/odm/v2.0" elementFormDefault="qualified"

<xs:import namespace="http://www.w3.org/XML/1998/namespace" schemaLocation="xml.xsd"/>

<?xml version="1.0" encoding="UTF-8"?> <xs:schema xmlns="http://www.cdisc.org/ns/odm/v2.0" xmlns:xs="http://www.w3.org/2001/XMLSchema"

<xs:schema xmlns="http://www.cdisc.org/ns/odm/v2.0" xmlns:xs="http://www.w3.org/2001/XMLSchema"

xmlns:odm="http://www.cdisc.org/ns/odm/v2.0" targetNamespace="http://www.cdisc.org/ns/odm/v2.0"

xmlns:xhtml="http://www.w3.org/1999/xhtml" xmlns:xlink="http://www.w3.org/1999/xlink"

<xs:import namespace="http://www.w3.org/XML/1998/namespace" schemaLocation="xml.xsd"/>

<xs:import namespace="http://www.w3.org/1999/xlink" schemaLocation="xlink.xsd"/>

<xs:import namespace="http://www.w3.org/1999/xhtml" schemaLocation="ODM-xhtml.xsd"/>

<!--              Added type to support expansion of TranslatedText.             Type is a Media Type as described in https://www.iana.org/assignments/media-types/media-types.xhtml

Added type to support expansion of TranslatedText.             Type is a Media Type as described in https://www.iana.org/assignments/media-types/media-types.xhtml             A TranslatedText element with Type="text/plain" must be present.

Type is a Media Type as described in https://www.iana.org/assignments/media-types/media-types.xhtml

<?xml version="1.0" encoding="UTF-8"?> <xs:schema xmlns="http://www.cdisc.org/ns/odm/v2.0" xmlns:xs="http://www.w3.org/2001/XMLSchema"

<xs:schema xmlns="http://www.cdisc.org/ns/odm/v2.0" xmlns:xs="http://www.w3.org/2001/XMLSchema"

targetNamespace="http://www.cdisc.org/ns/odm/v2.0" elementFormDefault="qualified"

as the IBM Mainframe format currently used in the submission V5 Transport standard as described in            SAS Technical Support document "TS-140 The Record Layout of a Data set in SAS Transport (XPORT) Format"            http://ftp.sas.

SAS Technical Support document "TS-140 The Record Layout of a Data set in SAS Transport (XPORT) Format"            http://ftp.sas.com/techsup/download/technote/ts140.html         with the appropriate direct translation of the converted valu

http://ftp.sas.com/techsup/download/technote/ts140.html

<U+FEFF><?xml version="1.0" encoding="UTF-8"?> <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns="http://www.w3.org/1999/xhtml" targetNamespace="http://www.w3.org/1999/xhtml" elementFormDefault="qualified" version="1.0" xml:lang="en">

<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns="http://www.w3.org/1999/xhtml" targetNamespace="http://www.w3.org/1999/xhtml" elementFormDefault="qualified" version="1.0" xml:lang="en">

- forms, objects, and inserted and deleted text   -->   <!-- Note: When using this schema with some tools, it may also be necessary to declare xmlns:xml="http://www.w3.org/XML/1998/namespace", however this causes performance issues with oth

-->   <!-- Note: When using this schema with some tools, it may also be necessary to declare xmlns:xml="http://www.w3.org/XML/1998/namespace", however this causes performance issues with other tools and thus is not in the base schemas. --> 

<!-- Note: When using this schema with some tools, it may also be necessary to declare xmlns:xml="http://www.w3.org/XML/1998/namespace", however this causes performance issues with other tools and thus is not in the base schemas. -->

Namespace = http://www.w3.org/1999/xhtml

For further information, see: http://www.w3.org/TR/xhtml1

PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"     SYSTEM "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"

SYSTEM "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"

</xs:documentation>   </xs:annotation>   <xs:import namespace="http://www.w3.org/XML/1998/namespace" schemaLocation="xml.xsd"/>

</xs:annotation>   <xs:import namespace="http://www.w3.org/XML/1998/namespace" schemaLocation="xml.xsd"/>   <xs:annotation>

<xs:import namespace="http://www.w3.org/XML/1998/namespace" schemaLocation="xml.xsd"/>

PUBLIC "-//W3C//ENTITIES Latin 1 for XHTML//EN"     SYSTEM "http://www.w3.org/TR/xhtml1/DTD/xhtml-lat1.ent"

SYSTEM "http://www.w3.org/TR/xhtml1/DTD/xhtml-lat1.ent"

PUBLIC "-//W3C//ENTITIES Special for XHTML//EN"     SYSTEM "http://www.w3.org/TR/xhtml1/DTD/xhtml-special.ent"

SYSTEM "http://www.w3.org/TR/xhtml1/DTD/xhtml-special.ent"

PUBLIC "-//W3C//ENTITIES Symbols for XHTML//EN"     SYSTEM "http://www.w3.org/TR/xhtml1/DTD/xhtml-symbol.ent"

SYSTEM "http://www.w3.org/TR/xhtml1/DTD/xhtml-symbol.ent"

<?xml version="1.0" encoding="UTF-8"?> <xs:schema xmlns="http://www.cdisc.org/ns/odm/v2.0" xmlns:xs="http://www.w3.org/2001/XMLSchema"

<xs:schema xmlns="http://www.cdisc.org/ns/odm/v2.0" xmlns:xs="http://www.w3.org/2001/XMLSchema"

targetNamespace="http://www.cdisc.org/ns/odm/v2.0"

<xs:import namespace="http://www.w3.org/XML/1998/namespace" schemaLocation="xml.xsd"/>

<?xml version="1.0" encoding="UTF-8"?> <!-- Example Demographics form with "check all that apply" and "other, specify" for "Race".  Implemented as: Use Case D - CodeList repeat with "other" field - see https://wiki.cdisc.org/display/XMLT/De

<!-- Example Demographics form with "check all that apply" and "other, specify" for "Race".  Implemented as: Use Case D - CodeList repeat with "other" field - see https://wiki.cdisc.org/display/XMLT/Details+of+Repeating+IG+Use+Cases+A-E -->

Implemented as: Use Case D - CodeList repeat with "other" field - see https://wiki.cdisc.org/display/XMLT/Details+of+Repeating+IG+Use+Cases+A-E -->

<ODM xmlns="http://www.cdisc.org/ns/odm/v2.0"

xmlns:xs="http://www.w3.org/2001/XMLSchema"

xmlns:xlink="http://www.w3.org/1999/xlink"

</ItemGroupDef>          <!-- ItemGroup that repeats over all allowed values for "Race" (IT.RACE_CODE) from a codelist, with "Other, specifiy".          This corresponds to "Repeating Item Groups Use Case D" - see https://wiki.cdisc.org/dis

<!-- ItemGroup that repeats over all allowed values for "Race" (IT.RACE_CODE) from a codelist, with "Other, specifiy".          This corresponds to "Repeating Item Groups Use Case D" - see https://wiki.cdisc.org/display/XMLT/Details+of+Repe

This corresponds to "Repeating Item Groups Use Case D" - see https://wiki.cdisc.org/display/XMLT/Details+of+Repeating+IG+Use+Cases+A-E -->

<?xml version="1.0" encoding="UTF-8" ?>  <xsd:schema targetNamespace="http://www.w3.org/1999/xlink"

<xsd:schema targetNamespace="http://www.w3.org/1999/xlink"

xmlns:xsd="http://www.w3.org/2001/XMLSchema"

xmlns:xlink="http://www.w3.org/1999/xlink"

<?xml version='1.0'?> <xs:schema targetNamespace="http://www.w3.org/XML/1998/namespace"

<xs:schema targetNamespace="http://www.w3.org/XML/1998/namespace"

xmlns:xs="http://www.w3.org/2001/XMLSchema"

<xs:annotation>   <xs:documentation>    See http://www.w3.org/XML/1998/namespace.html and

<xs:documentation>    See http://www.w3.org/XML/1998/namespace.html and    http://www.w3.org/TR/REC-xml for information about this namespace.

See http://www.w3.org/XML/1998/namespace.html and

http://www.w3.org/TR/REC-xml for information about this namespace.

<schema . . .>          . . .          <import namespace="http://www.w3.org/XML/1998/namespace"

. . .          <import namespace="http://www.w3.org/XML/1998/namespace"                     schemaLocation="http://www.w3.org/2001/03/xml.xsd"/>

<import namespace="http://www.w3.org/XML/1998/namespace"

schemaLocation="http://www.w3.org/2001/03/xml.xsd"/>

<xs:documentation>In keeping with the XML Schema WG's standard versioning    policy, this schema document will persist at    http://www.w3.org/2001/03/xml.xsd.

policy, this schema document will persist at    http://www.w3.org/2001/03/xml.xsd.    At the date of issue it can also be found at

http://www.w3.org/2001/03/xml.xsd.

At the date of issue it can also be found at    http://www.w3.org/2001/xml.xsd.    The schema document at that URI may however change in the future,

http://www.w3.org/2001/xml.xsd.

itself.  In other words, if the XML Schema namespace changes, the version    of this document at    http://www.w3.org/2001/xml.xsd will change

of this document at    http://www.w3.org/2001/xml.xsd will change    accordingly; the version at

http://www.w3.org/2001/xml.xsd will change

accordingly; the version at    http://www.w3.org/2001/03/xml.xsd will not change.   </xs:documentation>

http://www.w3.org/2001/03/xml.xsd will not change.

<xs:attribute name="base" type="xs:anyURI">   <xs:annotation>    <xs:documentation>See http://www.w3.org/TR/xmlbase/ for

<xs:annotation>    <xs:documentation>See http://www.w3.org/TR/xmlbase/ for                      information about this attribute.

<xs:documentation>See http://www.w3.org/TR/xmlbase/ for

Executable file

<meta name="viewport" content="width=device-width, initial-scale=1"> <title>__TITLE__</title> <script src="https://cdn.jsdelivr.net/npm/marked@12/marked.min.js"></script>

<title>__TITLE__</title> <script src="https://cdn.jsdelivr.net/npm/marked@12/marked.min.js"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/cytoscape/3.33.2/cytoscape.min.js"></script>

<script src="https://cdn.jsdelivr.net/npm/marked@12/marked.min.js"></script>

<script src="https://cdnjs.cloudflare.com/ajax/libs/cytoscape/3.33.2/cytoscape.min.js"></script>

<script src="https://cdn.jsdelivr.net/npm/dagre@0.8.5/dist/dagre.min.js"></script>

<script src="https://cdn.jsdelivr.net/npm/cytoscape-dagre@2.5.0/cytoscape-dagre.min.js"></script>

<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css">

<script src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js"></script>

<script src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js"></script>

const dec = (b64) => new TextDecoder('utf-8').decode(Uint8Array.from(atob(b64), c => c.charCodeAt(0)));

An agent skill for designing and simulating clinical trials using the [TrialSimulator](https://github.com/zhangh12/TrialSimulator) R package.

[TrialSimulator](https://github.com/zhangh12/TrialSimulator) R package.

- **R** ≥ 4.1 - **R packages** (CRAN unless noted):   - [TrialSimulator](https://github.com/zhangh12/TrialSimulator)

- **R packages** (CRAN unless noted):   - [TrialSimulator](https://github.com/zhangh12/TrialSimulator)     (the simulation engine; install from GitHub for the latest)

- [TrialSimulator](https://github.com/zhangh12/TrialSimulator)

- `DoseFinding` (only if MCPMod-style dose ranging is used) - **Agent** capable of executing the   [Agent Skills Specification](https://github.com/anthropics/skills)

- **Agent** capable of executing the   [Agent Skills Specification](https://github.com/anthropics/skills)   (Claude Code, or any compatible agent).

[Agent Skills Specification](https://github.com/anthropics/skills)

or when behavior contradicts these notes, consult `?<function>` in R or the package's pkgdown site at https://zhangh12.github.io/TrialSimulator/. Don't guess — the manual

or the package's pkgdown site at https://zhangh12.github.io/TrialSimulator/. Don't guess — the manual is the source of truth.

https://zhangh12.github.io/TrialSimulator/. Don't guess — the manual

appear in tab-completion. The author flags this in the help docs (see the user-method list at the top of https://zhangh12.github.io/TrialSimulator/reference/Trials.html).

https://zhangh12.github.io/TrialSimulator/reference/Trials.html).

machinery but an endpoint generator that simulates the outcome   accounting for the changing treatment over time.   https://zhangh12.github.io/TrialSimulator/articles/crossoverWashout.html

accounting for the changing treatment over time.   https://zhangh12.github.io/TrialSimulator/articles/crossoverWashout.html - **Dynamic treatment switching** — per-patient switching driven by each

https://zhangh12.github.io/TrialSimulator/articles/crossoverWashout.html

onward (e.g. switch at progression, rescue after non-response, dose   changes, and other outcome-driven changes).   https://zhangh12.github.io/TrialSimulator/articles/dynamicTreatmentSwitching.html

changes, and other outcome-driven changes).   https://zhangh12.github.io/TrialSimulator/articles/dynamicTreatmentSwitching.html - **Crossover at a milestone** — crossover anchored to a trial-level time:

https://zhangh12.github.io/TrialSimulator/articles/dynamicTreatmentSwitching.html

(e.g. an interim efficacy signal opens crossover for control patients   still on study).   https://zhangh12.github.io/TrialSimulator/articles/crossoverAtMilestone.html

https://zhangh12.github.io/TrialSimulator/articles/crossoverAtMilestone.html

`Controllers`, use `?Trials` / `?Controllers` (method-level `?` does not work) or the pkgdown reference page. Vignettes live at https://zhangh12.github.io/TrialSimulator/articles/. Don't disable a

not work) or the pkgdown reference page. Vignettes live at https://zhangh12.github.io/TrialSimulator/articles/. Don't disable a check to make an error go away.

https://zhangh12.github.io/TrialSimulator/articles/. Don't disable a

| Recipe | Vignette | |---|---| | §4, §19, §16 | https://zhangh12.github.io/TrialSimulator/articles/enrichmentDesign.html |

|---|---| | §4, §19, §16 | https://zhangh12.github.io/TrialSimulator/articles/enrichmentDesign.html | | §5 | https://zhangh12.github.io/TrialSimulator/articles/conditionalPower.html |

| §4, §19, §16 | https://zhangh12.github.io/TrialSimulator/articles/enrichmentDesign.html |

| §5 | https://zhangh12.github.io/TrialSimulator/articles/conditionalPower.html |

| §12, §14 | https://zhangh12.github.io/TrialSimulator/articles/adaptiveDesign.html |

| §15 | https://zhangh12.github.io/TrialSimulator/articles/responseAdaptive.html |

| §18 | https://zhangh12.github.io/TrialSimulator/articles/doseRanging.html |

| §20 | https://zhangh12.github.io/TrialSimulator/articles/crossoverAtMilestone.html |

| adaptation overview | https://zhangh12.github.io/TrialSimulator/articles/actionFunctions.html |

For full argument lists, consult `?<function>` in R or https://zhangh12.github.io/TrialSimulator/reference/.

https://zhangh12.github.io/TrialSimulator/reference/.

Canonical reference: the "Automatically Saved Results At Triggered Milestones" table in https://zhangh12.github.io/TrialSimulator/articles/actionFunctions.html.

https://zhangh12.github.io/TrialSimulator/articles/actionFunctions.html.

#!/usr/bin/env Rscript

A [Claude Code](https://claude.ai/code) skill that designs group sequential clinical trials for survival endpoints (OS, PFS, DFS). It collects trial parameters through a structured conversation, computes boundaries and sample sizes in R, ve

https://drive.google.com/file/d/1O9-SCJEoXGJv6J3YXuZZ1eiVB4Jk6Gao/view

### R (>= 4.0) - [`gsDesign`](https://cran.r-project.org/package=gsDesign) — group sequential boundaries and sample size

- [`gsDesign`](https://cran.r-project.org/package=gsDesign) — group sequential boundaries and sample size

- [`gsDesign2`](https://cran.r-project.org/package=gsDesign2) — non-proportional hazards (AHR, analytical power)

- [`lrstat`](https://cran.r-project.org/package=lrstat) — log-rank simulation for verification

- [`graphicalMCP`](https://cran.r-project.org/package=graphicalMCP) — multiplicity diagrams

- [`jsonlite`](https://cran.r-project.org/package=jsonlite) — JSON I/O

### Python (>= 3.8) - [`python-docx`](https://pypi.org/project/python-docx/) — Word report generation

- [`python-docx`](https://pypi.org/project/python-docx/) — Word report generation

#!/usr/bin/env python3

- NEJM: look for image URLs containing `/full/` or `/figure/`    - Lancet/JCO: look for high-res figure links, often ending in `.jpg` or `.png`    - PubMed Central: figures are usually at predictable URLs like `https://www.ncbi.nlm.nih.gov/

- Lancet/JCO: look for high-res figure links, often ending in `.jpg` or `.png`    - PubMed Central: figures are usually at predictable URLs like `https://www.ncbi.nlm.nih.gov/pmc/articles/PMC.../figure/...` 3. Download the KM plot image and

- PubMed Central: figures are usually at predictable URLs like `https://www.ncbi.nlm.nih.gov/pmc/articles/PMC.../figure/...` 3. Download the KM plot image and save to `reference/KMPlot/<study_name>.png` 4. If the page is paywalled or the im

Executable file

Executable file

[Credential-related source omitted]

[Credential-related source omitted]

#!/usr/bin/env Rscript

#!/usr/bin/env Rscript

#!/usr/bin/env python3

#!/usr/bin/env Rscript

#!/usr/bin/env Rscript

> "Audit rounding compliance of https://github.com/Merck/metalite.ae/tree/bdb23d472b16bc9dadbc774e64c5ca40321e9c6b against precision-spec.yml. Entry points are the `tlf_*()` functions; I'm the rule owner."

Test cases for the `rounding` skill, per `LIFECYCLE.md` phase 3 and the criteria in [`RConsortium/pharma-skills` issue #208](https://github.com/RConsortium/pharma-skills/issues/208).

#208](https://github.com/RConsortium/pharma-skills/issues/208).

#!/usr/bin/env bash

rm -f myanalysis-fixture.zip

#!/usr/bin/env Rscript

#!/usr/bin/env Rscript

An agent skill for deriving CDISC SDTM domains from raw EDC/eCRF data using the [{sdtm.oak}](https://pharmaverse.github.io/sdtm.oak/) pharmaverse R package.

the [{sdtm.oak}](https://pharmaverse.github.io/sdtm.oak/) pharmaverse R package.

- [sdtm.oak documentation](https://pharmaverse.github.io/sdtm.oak/)

- [CDISC SDTM Implementation Guide](https://www.cdisc.org/standards/foundational/sdtm)

- [pharmaverse](https://pharmaverse.org/)

Unsupported or unresolved allowed-tools declaration