Research

Scaffold or audit an entire research project repository organized around its source library. Use when starting, structuring, organizing, or reviewing a research repo. Build sources/{og,md,unprocessed}, references.bib, a PDF-to-Markdown converter, a repo-local process-source skill, AGENTS.md, .gitignore, .venv, and the relevant analysis/manuscript/review folders; or audit an existing layout. Not for one-PDF intake or publication replication packages.

Interviews a researcher, in rounds, until a research idea, design, or draft has no silently assumed decision left — every question numbered, each with a plain-language "why this matters" and a recommended answer, facts fetched by the assistant rather than asked, and every settled decision written to a file. Three stages, idea (a topic or hunch → a falsifiable question and a contribution claim), design (a question → estimand, identification, sample and power, measurement, pre-registration, ana...

Scaffold or audit a social-science replication package, and audit the manuscript and its archived research objects against the FAIR principles. Scaffold mode writes the folder structure, README, master.R, figure/table crosswalk, codebook template, LICENSE placeholder, .gitignore, and pre-release checklist. Audit mode grades an existing package against that checklist and runs the FAIR block over data, code, materials, prompts, preregistrations, DOIs, metadata, licenses, access restrictions, an...

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 answers left for the author to write. It formats and checks the response; it never writes the scien...

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 launch (consent-before-anything gates, force-response completeness, quota and redirect checks, anti...

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-collection side of DA-RT. Use when the user asks to write or review a pre-registration or PAP, asks wh...

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.

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.

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 explicitly asks to orchestrate, delegate, fan out, parallelize, assign subagents, obtain independen...

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

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 reporting. Use when the user asks about a council, panel, ensemble, or jury of models, asks how to ...

Run one consequential, contestable decision through a deliberative committee of GPT-6 Astra and Claude Opus 5, 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-rank under a predeclared rubric.

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 reporting, the four validity types, and open-science infrastructure. Use when the user asks whether a meth...

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 each item, asks about logprobs, top-k tokens, calibration, ECE, Brier, or reliability diagrams, or...

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

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, corrections for common failures, and power planning that accounts for the large precision penalty. Use whe...

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 legal pass, with an optional confidential note to the editor. Use when the user has been asked to ref...

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 multi-experiment designs. Use when the user has a research question or theory and asks to turn it into...

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

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 as needing author verification rather than inventing them. Use when the user is preparing a submi...

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.

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 Markdown is a tracked artifact or a scratch file to delete.

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, architectural, or analytical work — and before committing to an approach; use --codex when the us...

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 which countries to include and why, asks how to translate or adapt an instrument without breaking com...