Reproducible Pipelines skill

Main orchestration workflow for systematic literature research - search, evaluate, traverse, synthesize

Collaboratively build and refine paper screening rubrics through brainstorming, test-driven development, and iterative feedback

Check if medicinal chemistry papers are in ChEMBL database to access curated bioactivity data

Safely remove intermediate files from completed research sessions while preserving important data

Two-stage paper screening - abstract scoring then deep dive for specific data extraction

Use Unpaywall API to find free full-text versions of paywalled papers

Classical end-to-end empirical analysis workflow in the traditional Python econometric stack — pandas + numpy + scipy + statsmodels + linearmodels + pyfixest + rdrobust + econml + causalml + matplotlib/seaborn. **Defaults to economics empirical-paper style** (AER / QJE / AEJ) — every run produces a publication-ready output set with a multi-column regression table (M1→M6 progressive controls/FE) as the centerpiece, plus Table 1 (descriptives), mechanism / heterogeneity / robustness tables, and event-study + coefficient + trend figures. Covers the full 8-step pipeline an applied economist or quantitative social scientist runs on every paper — (1) data cleaning, (2) variable construction & transformation, (3) descriptive statistics & Table 1, (4) statistical diagnostic tests, (5) baseline empirical modeling, (6) robustness battery, (7) further analysis (mechanism, heterogeneity, mediation, moderation), (8) publication-ready tables & figures. **Also covers two parallel domain modes that share the same 8-step scaffolding** — **Mode A — Epidemiology / public health** (target-trial emulation via `zepid` / hand-rolled `pandas`, IPTW + g-formula + TMLE doubly-robust triplet via `zepid` / `econml` / `lifelines`, Mendelian randomization via `pymr` / `mrtool` (or `rpy2` → `MendelianRandomization`/`TwoSampleMR`), KM / AFT / Cox survival via `lifelines`, E-value sensitivity, principal stratification — STROBE / TRIPOD reporting), and **Mode B — ML causal inference** (DML via `econml.dml` / `doubleml`, S/T/X/R/DR meta-learners via `econml.metalearners` / `causalml`, causal forest via `econml.grf` / `causalml`, Dragonnet / TARNet / CEVAE neural causal via `causalml`, BCF via `pymc-bart` / `bcf-py`, matrix completion, CATE distribution + policy tree via `econml.policy` / `policytree-py`, off-policy evaluation, conformal causal via `mapie`, fairness audit via `fairlearn`, DAG learning via `causal-learn` / `cdt` / LLM-assisted). Prescribes which library to reach for at each step, shows the canonical code, and links to deeper `references/` files for variant-specific patterns. Use when the user asks for a **complete empirical analysis** in Python, wants to replicate an applied-economics paper from scratch, needs a reproducible workflow that is NOT opinionated on any single vertical package (contrast with StatsPAI), wants explicit control over every estimator and diagnostic, or asks "how do I write a full empirical pipeline in Python?". Also triggers when the user names a specific classical step in isolation — "winsorize at 1/99%", "run Breusch-Pagan", "build a Table 1 balance table", "do a placebo test", "event study plot", "mediation analysis" — and wants it wired into the broader pipeline. Mode A triggers on "target trial emulation", "IPTW", "TMLE", "Mendelian randomization", "STROBE", "公共健康", "流行病学". Mode B triggers on "DML", "double machine learning", "causal forest", "meta-learner", "Dragonnet", "BCF", "policy tree", "conformal causal", "fairness audit", "因果机器学习".

Classical end-to-end empirical analysis workflow in the modern tidyverse + econometrics R ecosystem — dplyr + tidyr + haven + fixest + sandwich + lmtest + clubSandwich + AER + ivreg + did + bacondecomp + HonestDiD + eventstudyr + rdrobust + rddensity + Synth + gsynth + synthdid + MatchIt + WeightIt + cobalt + ebal + grf + DoubleML + mediation + marginaleffects + modelsummary + kableExtra + gt + ggplot2 + ggpubr + cowplot + binsreg. **Defaults to economics empirical-paper style** (AER / QJE / AEJ) — every run produces a publication-ready output set with a multi-column regression table (M1→M6 progressive controls/FE) as the centerpiece, plus Table 1 (descriptives), mechanism / heterogeneity / robustness tables, and event-study + coefficient + trend figures. Covers the full 8-step R pipeline an applied economist runs on every paper — (1) data import & cleaning (read_dta/read_csv, naniar, janitor, validate-merges), (2) variable construction (mutate/across/winsorize/group_by + lag/lead with dplyr), (3) descriptive statistics & Table 1 (gtsummary, modelsummary::datasummary, tableone), (4) classical diagnostic tests (shapiro/jarque.bera.test/bptest/dwtest/bgtest/vif/adf.test/kpss.test/Hausman), (5) baseline modeling (fixest::feols, ivreg, did::att_gt, eventstudyr, sun_ab, did_imputation, synthdid, rdrobust, MatchIt, WeightIt, grf::causal_forest, DoubleML, mediation), (6) robustness battery (modelsummary stack, clubSandwich CRSE, fwildclusterboot, ri2, robomit Oster, bacondecomp, HonestDiD), (7) further analysis (interactions + marginaleffects, mediation::mediate, gsem via lavaan, dose-response splines, grf CATE), (8) publication-ready tables & figures (modelsummary, kableExtra, gt, stargazer, texreg, flextable to LaTeX/Word/HTML; ggplot2 + ggpubr + cowplot + binsreg + iplot for figures). **Also covers two parallel domain modes that share the same 8-step scaffolding** — **Mode A — Epidemiology / public health** (target-trial emulation, IPTW + g-formula + TMLE doubly-robust triplet via `WeightIt` / `gfoRmula` / `tmle` / `ltmle`, Mendelian randomization via `MendelianRandomization` / `TwoSampleMR` / `MRPRESSO`, KM / Cox / AFT / RMST survival via `survival` / `survminer` / `flexsurv`, E-value sensitivity via `EValue`, principal stratification — STROBE / TRIPOD reporting), and **Mode B — ML causal inference** (DML via `DoubleML`, S/T/X/R/DR meta-learners via `causalweight` / `grf`, causal forest via `grf::causal_forest`, BART/BCF via `bartCause` / `bcf`, matrix completion via `MCPanel`, CATE distribution + policy tree via `policytree`, off-policy evaluation, conformal causal via `conformalInference` / `cfcausal`, fairness audit via `fairmodels`, DAG learning via `pcalg` / `bnlearn` / LLM-assisted). Use when the user asks for a complete R empirical analysis, wants a tidyverse-style reproducible R script / Quarto workflow, prefers fixest over reghdfe, needs the R counterpart to StatsPAI / 00.1 / 00.2, or names a specific R step in isolation ("feols with cluster", "MatchIt nearest neighbor", "bacondecomp in R", "gtsummary table 1", "modelsummary to Word"). Mode A triggers on "target trial emulation R", "tmle ltmle", "MendelianRandomization", "TwoSampleMR", "MRPRESSO", "survival cox AFT", "STROBE R", "EValue R", "公共健康 R", "流行病学 R". Mode B triggers on "DoubleML R", "grf causal forest", "policytree", "bartCause bcf", "conformal causal R", "fairmodels", "pcalg NOTEARS", "因果机器学习 R".