61 Phdemotions Research Methods

Comprehensive exploratory data analysis with publication-quality descriptive tables, correlation matrices, distribution plots, and assumption testing. Generates a standalone EDA report with Table 1 (gtsummary/great_tables), correlation heatmap, distribution diagnostics, VIF for multicollinearity, and normality/homoscedasticity tests. All figures are APA-formatted and colorblind-safe. Use when the user says "exploratory analysis," "EDA," "descriptive statistics," "explore the data," "Table 1," "correlations," "distributions," or when /data-clean completes successfully. Triggers on "EDA," "descriptive," "Table 1," "explore," "correlations."

Confirmatory hypothesis testing matched to pre-registration, with full assumption testing, effect sizes, confidence intervals, and APA 7th formatted output. Supports OLS/GLM regression, panel regression (fixest), mixed models (lme4), SEM/CFA (lavaan), meta-analysis (metafor), and delegates PROCESS models to /process-model. Reads pre-registration to align planned analyses, flags deviations, and generates decision log entries for post-hoc choices. Use when the user says "test hypotheses," "run analysis," "confirmatory," "regression," "SEM," "mediation," "mixed model," "meta-analysis," or when /eda completes. Triggers on "analyze," "hypothesis," "regression," "model," "test."

Create publication-quality figures that meet journal submission standards. APA 7th defaults with journal-specific overrides. Supports interaction plots, mediation path diagrams, forest plots, marginal effects, Johnson-Neyman plots, correlation heatmaps, and coefficient plots. All figures are colorblind-safe, high DPI, and exported in multiple formats (PDF, PNG, SVG, TIFF). Use when the user says "publication figures," "journal figures," "APA figures," "visualize results," "make plots," "interaction plot," "path diagram," "forest plot," or when /analyze or /process-model or /robustness completes. Triggers on "visualize," "figure," "plot," "diagram."

Produce documented data cleaning scripts that log every transformation with N before/after each step, generate a CONSORT-style exclusion flow diagram, create decision log entries for every subjective choice, compute scale reliability and composites, and write cleaned data to data/processed/. Never modifies raw data. Use when the user says "clean data," "prepare data," "apply exclusion criteria," "handle missing data," "create composites," "data preprocessing," or when /data-validate found issues to address. Triggers on "clean," "exclusion," "missing data," "preprocessing," "composites," "reverse code."

Generate a complete, manuscript-ready data profile: demographics summary table, scale identification with reliability (alpha, omega, CFA), comprehensive codebook, sample characteristics, and measurement documentation — all following current best practices at the time of execution. Searches for the latest reporting standards (JARS, TOP, APA) before generating output. Produces everything a Methods section needs to describe the data. Use when the user says "describe my data for the manuscript," "demographics table," "what scales are in here," "codebook," "Methods section data," "sample characteristics," or any time they need data documented for publication. Triggers on "profile," "demographics," "scales," "codebook," "sample description," "Methods section."

Run declarative data quality checks and generate a codebook. Checks completeness, distributions, impossible values, duplicates, outliers, encoding issues, attention check failures, and manipulation check results. Produces a pointblank/pandera validation report and an auto-generated codebook. Use when the user says "validate data," "check data quality," "generate codebook," "what's wrong with my data," "data audit," "check my dataset," or when /research-intake identifies missing validation. Triggers on "validate," "data quality," "codebook," "check my data."

Implement Hayes PROCESS mediation and moderation models transparently via lavaan and bruceR, with bootstrap CIs, index of moderated mediation, Johnson-Neyman regions of significance, and APA-formatted output that matches familiar PROCESS tables. Maps model numbers (1-24) to inspectable lavaan syntax instead of black-box macros. Use when the user says "PROCESS model," "mediation," "moderated mediation," "conditional indirect effect," "Hayes model," "indirect effect," "moderation," or when /analyze encounters a mediation/moderation hypothesis. Triggers on "PROCESS," "mediation," "moderation," "indirect effect," "Hayes."

Scaffold a new research project with full reproducibility infrastructure in R and/or Python. Creates directory structure, pipeline stubs (targets/Snakemake), environment lockfiles (renv/uv), documentation templates (codebook, decision log, pre-registration, Cornell README), Quarto manuscript template, and proper .gitignore. Can wrap existing data in gold-standard structure. Use when the user says "new project," "scaffold," "start a study," "set up a project," "I have data and need to organize it," or when /research-intake recommends scaffolding.

Bidirectional review — THE entry point for every research engagement. Reviews everything the researcher has (data, docs, code, instruments) and produces two outputs: (1) a gap analysis showing what their project needs to meet gold standards, and (2) suite-learning findings identifying what our skill suite can learn from what they brought. Runs at the START of every engagement and in lighter form at session END. Use when the user says "I have data," "review what I have," "where do I start," "look at my project," "what am I missing," or at the beginning of any research engagement. Also triggers on "intake," "gap analysis," "audit my materials," "what should I improve."