open-science-skills

In the author's own words, from each skill's SKILL.md — showing the first 30 of 85 files.

• advisor

  Consult an independent, read-only GPT-6 Astra advisor before committing to a substantive interpretation, approach, or final result. Not for routine work, implementation, or file edits. Defaults to gpt-6-astra at xhigh for demanding reviews.

  codex/advisor/SKILL.md on GitHub (opens in a new tab)

• citation-check

  Audits the citation layer of a manuscript — in-text and reference-list parity, fabricated or nonexistent sources, DOIs that resolve to a different work, style and completeness against APA 7 or a named journal style, and whether each cited work actually supports the claim attached to it. Verifies against Crossref, OpenAlex, DataCite, and Semantic Scholar, drives LaTeX audits off the keys actually…

  codex/citation-check/SKILL.md on GitHub (opens in a new tab)

• conjoint-cleaning

  Turns a raw Qualtrics conjoint export into an analysis-ready long-format dataset — export settings and metadata rows, identifying which Qualtrics implementation produced the file, reshaping wide to long by hand or with cjoint read.qualtrics and cjdata reshape_conjoint, mapping the choice variable onto profiles, ratings and secondary DVs, attribute-level translation and factor ordering, pilot data…

  codex/conjoint-cleaning/SKILL.md on GitHub (opens in a new tab)

• conjoint-design

  Designs conjoint and factorial-vignette experiments end to end — attribute architecture and randomization restrictions, effective-N power from the closed-form AMCE standard error, treatment realism, estimand choice among AMCE, marginal means, and AMIE, design variants such as forced choice versus rating, PAP tiers for conjoint flexibility, and the regression models and R packages that implement e…

  codex/conjoint-design/SKILL.md on GitHub (opens in a new tab)

• conjoint-diagnostics

  Reviews an existing conjoint study for threats to inference and returns prioritized findings across five areas — design integrity (attributes, profile restrictions, task count and satisficing, randomization, power), estimation (estimand clarity, reference levels, subgroups, clustered standard errors, multiple testing), measurement error, external validity and behavioral benchmarking, and interpre…

  codex/conjoint-diagnostics/SKILL.md on GitHub (opens in a new tab)

• cross-national-design

  Designs multi-country survey experiments — case selection with a stated comparative logic, instrument localization and TRAPD translation, origin-country and composition choices for stimuli, per-country power and error management, and a pooled-versus-per-country analytical strategy with measurement-equivalence checks. Use when the user is fielding the same experiment in several countries, asks whi…

  codex/cross-national-design/SKILL.md on GitHub (opens in a new tab)

• deliverable-intake

  Turns raw captures, dictated braindumps in a deliverable’s inbox/, or recent macwhspr dictation-log entries into proposed planning-wiki changes, shown as a unified diff for author acceptance or rejection. Classifies every capture line as a decision, evidence claim, question, task, or dropped item with a reason, and traces it to its source. Uncertain names and citations remain UNRESOLVED. Applies…

  codex/deliverable-intake/SKILL.md on GitHub (opens in a new tab)

• deliverable-lint

  Reviews a whole deliverable, such as a talk, course module, paper, chapter, or referee report, against its manifest without rewriting. Runs a deterministic gate for build, citations, numbers, facts, and leaks, then stops on failure. It assigns a cheap finder to each section, runs a strong-model whole-work pass, and adjudicates into checks/<date>/findings.json and report.md with anchors, severitie…

  codex/deliverable-lint/SKILL.md on GitHub (opens in a new tab)

• deliverable-open

  Opens a deliverable, such as a talk, course module, paper, book chapter, or referee report, for AI-assisted work across sessions. Interviews the author until the manifest is written, then scaffolds deliverable.yml, append-only HANDOFF.md, a numbered planning/ wiki with index and open questions, inbox/ for dictated braindumps, gitignored checks/, and the house deck template for talks. Use when the…

  codex/deliverable-open/SKILL.md on GitHub (opens in a new tab)

• diverge

  Generate 3-5 conceptually distinct approaches labeled by creativity dimension (Novel, Surprising, Diverse, Conventional) and hold for selection instead of implementing the first idea; the --codex mode delegates the brainstorm to a fresh Codex subagent for a clean, unanchored context and hands it the selected approach to implement. Use when a task has more than one non-obvious solution — creative,…

  codex/diverge/SKILL.md on GitHub (opens in a new tab)

• doc-to-markdown

  Read or convert any document a research workflow hands you — PDF, Word, PowerPoint, Excel, OpenDocument, RTF, EPUB, or CSV. Use whenever a document has to be read, opened, quoted, summarized, searched, extracted, or added to a source library. Decides whether to read the file directly or convert it, picks the converter from the document's actual structure, and decides whether the resulting Markdow…

  codex/doc-to-markdown/SKILL.md on GitHub (opens in a new tab)

• fact-check

  Fact-check manuscript claims against cited sources in a per-source Markdown knowledge base. Use to audit claim support, overclaiming, direction, scope, and misattribution after source intake is complete.

  codex/fact-check/SKILL.md on GitHub (opens in a new tab)

• figure-table-audit

  End-stage QA on a finished figure and table set — an inventory with in-text callouts and producing scripts, cross-reference and numbering checks, text-to-evidence consistency between claims and plotted or tabulated values, captions and statistical notes that stand alone, accessibility and production quality, and SI and replication-package linkage. Marks anything requiring values read off an image…

  codex/figure-table-audit/SKILL.md on GitHub (opens in a new tab)

• figures

  Design and format publication-quality figures. Use for chart choice, color, scales, legends, captions, accessibility, and reproducible figure workflows.

  codex/figures/SKILL.md on GitHub (opens in a new tab)

• finished

  End-of-session closure for a research or code repository. Records what actually changed into the project's own handoff and log files, distinguishing verified work from work merely attempted, and reports what was left uncommitted. Use when wrapping up a work session so the next one can resume without re-deriving state. Its start-of-session twin is sitrep.

  codex/finished/SKILL.md on GitHub (opens in a new tab)

• hypothesis-building

  Turns a theory into falsifiable, pre-registerable hypotheses — DAGs and backdoor closure, how the design resolves the FPCI, SATE versus PATE, counterfactual and directional framing, a named theoretical and empirical estimand, a justified SESOI, the choice among NHST, interval, equivalence (TOST), and minimum-effect tests, scope conditions, and primary, secondary, and exploratory tiers across mult…

  codex/hypothesis-building/SKILL.md on GitHub (opens in a new tab)

• journal-review

  Drafts a referee report on someone else's manuscript for a journal editor — a recommendation, a summary of the claim and design, three to six major concerns that drive the decision, additional concerns, and a coherent revision plan, produced by five parallel adversarial finders (Breaker, Butcher, Shredder, Void, Situator), a Blue Team error filter, a Chief Reviewer synthesis, and a Tone Guard leg…

  codex/journal-review/SKILL.md on GitHub (opens in a new tab)

• list-experiment

  Designs and diagnoses list experiments (the item count technique) — whether indirect measurement is warranted at all, control-list construction against ceiling and floor effects, design variants such as double list and direct-question pairing, difference-in-means and maximum-likelihood estimators via ictreg, the no-design-effect and no-liar assumptions with ict.test and ict.hausman.test, correcti…

  codex/list-experiment/SKILL.md on GitHub (opens in a new tab)

• literature-review

  Build or audit a literature review. Use for evidence maps, gap analysis, contribution checks, source verification, and synthesis planning.

  codex/literature-review/SKILL.md on GitHub (opens in a new tab)

• llm-calibration-logprobs

  Reads a model's own uncertainty off its token log-probabilities — collecting logprobs and aggregating multi-token labels, confidence tiers and margins for triage, calibration assessment with ECE, Brier scores, and reliability diagrams, using confidence downstream without laundering it into evidence, and what to archive for reproducibility. Use when the user asks how confident a classifier was on…

  codex/llm-calibration-logprobs/SKILL.md on GitHub (opens in a new tab)

• methods-reporting

  Audits a methods section against a 45-item checklist synthesized from the APSA Experimental Section rubric, JARS-Quant, CONSORT, and DA-RT — pre-registration and design documentation, subjects and recruitment, randomization and treatment detail, CONSORT-style sample flow with attrition, statistical analysis with sample-size justification and three-tier results labeling, conjoint-specific reportin…

  codex/methods-reporting/SKILL.md on GitHub (opens in a new tab)

• model-committee

  Run one consequential, contestable decision through a deliberative committee of GPT-6 Astra and Claude Opus, chaired by fable (default), astra, opus, or sol. Not for factual lookups, brainstorming, routine implementation, independent-coder reliability, or final professional judgment. Use when several options are defensible and the two model families should propose, critique, revise, and cross-ran…

  codex/model-committee/SKILL.md on GitHub (opens in a new tab)

• model-council-voting

  Runs several language models as independent coders on the same labeling or discovery task and reads their disagreement as data — panel assembly for model diversity, keeping votes independent, consensus rules, agreement statistics (Cohen's and Fleiss kappa, Krippendorff's alpha), the correlated-errors caveat that stops agreement being mistaken for validity, human validation beyond the panel, and r…

  codex/model-council-voting/SKILL.md on GitHub (opens in a new tab)

• narrative-building

  Draft or audit scientific introductions. Use for argument logic, framing, contribution structure, and coherence across multiple studies or experiments.

  codex/narrative-building/SKILL.md on GitHub (opens in a new tab)

• orchestrate

  Orchestrate complex work from an active gpt-6-astra or gpt-5.6-sol Codex session. The detected lead owns decomposition, integration, and verification; Astra keeps the hardest reasoning in the lead, while Sol escalates unusually difficult units to Astra. Both route bounded work to cheaper GPT-5.6 tiers and can use a cross-vendor Claude peer. Not for routine single-context work. Use when the user e…

  codex/orchestrate/SKILL.md on GitHub (opens in a new tab)

• paper-review-lite

  Run a pre-submission manuscript audit covering argument, numerics, references, writing, figures, methods, preregistration, and replication readiness. Add --codex for a cross-model pass in which Codex and Claude review independently and verify each other's findings.

  codex/paper-review-lite/SKILL.md on GitHub (opens in a new tab)

• paper-tex

  Typeset a working paper or journal submission in house-style LaTeX from Markdown, Word, TeX, ODT, RTF, or HTML. Use to convert drafts, build PDFs, or prepare journal-specific spacing, limits, anonymization, disclosures, and citations.

  codex/paper-tex/SKILL.md on GitHub (opens in a new tab)

• pre-registration-writing

  Writes a pre-analysis plan before data collection — registry selection (OSF, AsPredicted, AEA, EGAP), PAP document structure, an analytical strategy specified down to the model and the decision rule, analysis code pre-registered against simulated data, contingency planning for attrition, failed manipulations, and exclusions, deviation documentation, and timeline. Operationalizes the pre-data-coll…

  codex/pre-registration-writing/SKILL.md on GitHub (opens in a new tab)

• qualtrics-ops

  Operate or audit a live Qualtrics survey via the v3 APIs without breaking fielding — publish gating, quotas, flow routing, embedded data, panel-vendor redirects, read-back verification, and a read-only pre-fielding audit. Use when publishing or patching a fielding instrument, when a quota counts but never blocks, when wiring panel-vendor redirects or flow gates, or when auditing a survey before l…

  codex/qualtrics-ops/SKILL.md on GitHub (opens in a new tab)

• referee-response

  Organizes and formats an author's response to peer review — extracts every distinct point from the referee reports and the editor's letter, tags severity and type, maps the dependencies so the revision runs in the right order, flags which points the author may want to push back on, and builds the response-to-reviewers letter as a numbered comment → response → location table with the substantive a…

  codex/referee-response/SKILL.md on GitHub (opens in a new tab)

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