Agent Skills
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jama-statistics
GitHub用于准备或审计JAMA稿件的统计分析，确保通过专门统计审查。强制要求报告效应量及95%置信区间、控制多重比较、预先指定分析方案，并遵循ITT原则及缺失数据处理规范。不选择研究设计或撰写正文。
Trigger Scenarios
结果仅报告P值而无效应量或置信区间
存在多次比较但无多重性控制计划
分析未预先指定或结果偏离方案
准备接受待审稿件的JAMA专门统计审查
Install
npx skills add brycewang-stanford/Awesome-Journal-Skills --skill jama-statistics -g -y
SKILL.md
Frontmatter
{
"name": "jama-statistics",
"description": "Use when preparing or auditing the statistical analysis and reporting of a JAMA manuscript so it survives JAMA's dedicated statistical review. Enforces effect sizes with 95% CIs, multiplicity control, and pre-specification; it does NOT choose the study design or write prose."
}
Statistics & Statistical Review (jama-statistics)
When to trigger
- Results report p-values without effect sizes or confidence intervals
- Many comparisons but no multiplicity plan
- The analysis was not pre-specified, or outcomes drifted from the protocol
- Preparing for JAMA's dedicated statistical review of accepted-pending manuscripts
Core reporting rules at JAMA
- Effect sizes with 95% CIs, not p-values alone. Report the estimate (mean difference, risk/hazard/odds ratio, absolute risk difference) with its 95% CI. P-values supplement; they do not substitute. Treat "significance" as a statement about the interval, not a 0.05 threshold ritual.
- Pre-specified outcomes. State the single primary outcome and the secondary outcomes exactly as registered/protocoled. Flag any post hoc analysis as exploratory.
- Intention-to-treat for RCTs. Primary analysis is ITT; per-protocol and as-treated are secondary/sensitivity.
- Multiplicity. With multiple outcomes, subgroups, or time points, pre-specify the testing hierarchy and the correction (e.g., hierarchical testing, Bonferroni/Holm, gatekeeping). Subgroups without a multiplicity plan are hypothesis-generating only.
- Missing data. State the mechanism assumed and the method (e.g., multiple imputation); report a sensitivity analysis. Complete-case-only needs justification.
- Model assumptions. Justify the model (proportional hazards, linearity, clustering, repeated measures) and report how assumptions were checked.
- Absolute and relative effects. Pair relative measures (RR, OR, HR) with absolute measures (risk difference, NNT) so clinicians grasp magnitude.
Reporting conventions to follow
- Report exact p-values (e.g., P = .03), not "P < .05"; very small as "P < .001"
- Round sensibly; do not imply false precision
- Give denominators with every percentage; report n/N
- Pre-register and report the analysis population for each estimate
- Describe software and key procedures so the analysis is reproducible
- For meta-analysis: report heterogeneity (e.g., I²), the model (fixed/random), and sensitivity analyses
Audit table
| Symptom | Fix |
|---|---|
| "P < 0.05" with no estimate | Add point estimate + 95% CI |
| Five "key" secondary outcomes, all "significant" | Pre-specify hierarchy; correct for multiplicity |
| Subgroup result drives the conclusion | Label exploratory; report interaction test |
| RCT analyzed per-protocol as primary | Re-run ITT as primary |
| 20% dropout, complete-case only | Multiple imputation + sensitivity analysis |
| Only relative risk reported | Add absolute risk difference / NNT |
Surviving JAMA's independent statistical review
The Journal of the American Medical Association applies a dedicated statistical review to manuscripts under serious consideration — distinguishing it among general medical journals. Independent statisticians re-interrogate the analysis, so pre-empt the standard queries: a pre-specified primary outcome matching the registry; intention-to-treat as primary; pre-specified multiplicity control; missing data handled by imputation with sensitivity analysis; and an absolute effect (risk difference / NNT) beside every relative measure.
Worked example: a primary-outcome readout (illustrative)
Vignette (illustrative): a multicenter, double-blind randomized clinical trial, N = 5,000 adults with type 2 diabetes and cardiovascular disease, new agent vs placebo; pre-specified primary outcome major adverse cardiovascular events (MACE) over a median 3.1 years.
- ITT result: 11.2% vs 13.6%; absolute risk difference -2.4 percentage points (95% CI, -4.3 to -0.5); hazard ratio 0.82 (95% CI, 0.70-0.96); P = .01.
- Correct readout: relative (HR with CI) and absolute (risk difference, ~42 NNT) effects both given, ITT, primary matches the registry; a "significant" secondary subgroup stays labeled exploratory with its interaction test.
Reviewer pushback and the JAMA fix
- "Primary outcome changed post hoc." Fix: restore the registered primary; demote the swap to labeled exploratory.
- "Subgroup result drives the conclusion." Fix: report the interaction test, label it hypothesis-generating, re-anchor on the primary.
Calibration anchors (hedge where uncertain): estimate-plus-95%-CI over bare p-values, ITT-as-primary, pre-specification, and absolute-with-relative reporting are durable; notation rules track the AMA Manual of Style — confirm against current author guidelines.
Checklist
- Every primary/secondary estimate has a 95% CI
- Single pre-specified primary outcome; secondaries labeled
- Multiplicity handled with a pre-specified plan
- ITT is the primary analysis for the RCT
- Missing-data method stated + sensitivity analysis
- Absolute and relative effects both reported
- Model assumptions justified and checked
- Analysis is reproducible (software, code/procedures described)
Anti-patterns
- Reporting p-values without effect sizes or CIs
- Switching or under-reporting pre-specified outcomes
- Mining subgroups and reporting only the "significant" one
- Claiming "no difference" from an underpowered study (absence of evidence ≠ evidence of absence)
- Per-protocol-as-primary to make an RCT look better
- Conclusions built on a secondary outcome while the primary was null
Output format
【Primary outcome estimate + 95% CI】...
【All estimates have CIs】yes / no
【Multiplicity plan】...
【ITT primary (RCT)】yes / no / n.a.
【Missing-data handling】...
【Absolute + relative effects reported】yes / no
【Stat-review risks remaining】...
【Next skill】jama-figures-tables
Version History
- 1839142 Current 2026-07-05 13:24
