coding-sop

name	Coding SOP
description	Standard operating procedure for research experiments, data analysis, and visualization. Covers Python/R script execution, statistical analysis, data wrangling (pandas/tidyverse), publication-quality figures (matplotlib/plotly/ggplot2), and experiment reproducibility.

Coding SOP — Research Experiments & Data Analysis

1. Experiment Execution SOP

1.1 Hypothesis → Code → Execute → Verify

1. Hypothesize: state what you expect and why
2. Design: define variables, controls, sample size / iteration count
3. Code: workspace_save to outputs/scripts/; include docstring (hypothesis, expected outcome, dependencies)
4. Execute: exec in workspace (safe commands — see §5); capture stdout + stderr
5. Verify: compare against hypothesis; check for NaN/Inf/warnings; save to outputs/reports/
6. Iterate: if contradicted, revise (do NOT cherry-pick); if confirmed, document

1.2 Script Template

Every script must include: shebang, docstring (experiment title, hypothesis, dependencies, date), seed setting (see §6), and four sections: loading, processing, analysis, output.

2. Data Processing SOP

2.1 Pipeline: Clean → Transform → Analyze

1. Inspect: df.info(), df.describe(), df.head() — check dtypes, nulls, duplicates
2. Clean: handle missing values (drop/impute/flag — document choice), fix dtypes, remove duplicates, detect outliers (IQR, z-score, domain rules)
3. Transform: normalize/standardize, encode categoricals, feature engineering, reshape (pivot, melt, merge)
4. Validate: assert expected shape, sanity-check stats, save cleaned data via workspace_save("sources/data/<name>_clean.csv")

2.2 Common Libraries

Python: pandas/polars (DataFrames), numpy (numerics), dask (large files), spaCy (text). R: dplyr/tidyr (wrangling), data.table/arrow (large files), stringr/tidytext (text).

Browse analysis/wrangling/ for 10 deep-dive skills (pandas, missing data, survey, text mining).

3. Statistical Analysis Guide

3.1 Test Selection Tree

What is your research question?
│
├── Comparing groups?
│   ├── 2 groups
│   │   ├── Continuous DV, normal → Independent t-test
│   │   ├── Continuous DV, non-normal → Mann-Whitney U
│   │   ├── Paired/matched → Paired t-test / Wilcoxon signed-rank
│   │   └── Categorical DV → Chi-square / Fisher's exact
│   ├── 3+ groups
│   │   ├── 1 factor, normal → One-way ANOVA → post-hoc (Tukey/Bonferroni)
│   │   ├── 1 factor, non-normal → Kruskal-Wallis → post-hoc (Dunn)
│   │   ├── 2+ factors → Two-way / N-way ANOVA (check interactions)
│   │   └── Repeated measures → Repeated-measures ANOVA / Friedman
│   └── Pre/post with control → Mixed ANOVA / DiD
│
├── Predicting an outcome?
│   ├── Continuous outcome → Linear regression (OLS)
│   │   ├── Multiple predictors → Multiple regression
│   │   ├── Non-linear → Polynomial / GAM / splines
│   │   └── Endogeneity → IV / 2SLS (see econometrics skills)
│   ├── Binary outcome → Logistic regression
│   ├── Count/ordinal → Poisson / Ordinal logistic
│   ├── Time-to-event → Cox proportional hazards
│   └── Panel data → Fixed/random effects (see econometrics skills)
│
├── Exploring relationships?
│   ├── 2 continuous vars → Pearson r (normal) / Spearman rho (non-normal)
│   ├── 2 categorical vars → Chi-square test of independence
│   ├── Latent constructs → Factor analysis / SEM
│   └── Dimensionality → PCA / t-SNE
│
└── Estimating causal effects?
    ├── Randomized experiment → t-test / ANOVA with random assignment
    ├── Natural experiment → DiD, RDD, IV
    └── Observational → Propensity score matching, synthetic control

3.2 Reporting Checklist

Every test must report: test name, statistic value (t/F/chi-sq/U/z), df, exact p-value, effect size (Cohen's d / eta-sq / Cramer's V / OR), 95% CI, assumptions checked (normality, homoscedasticity, independence), sample size per group.

3.3 Common Pitfalls

• Multiple comparisons: Bonferroni, Holm, or FDR correction
• p-hacking: pre-register hypotheses; never fish for p < 0.05
• Small samples: exact tests or bootstrap over asymptotic tests
• Normality: Shapiro-Wilk (n < 50) or Q-Q plot + KS test
• Confounders: include as covariates or stratify

Deep-dive skills: browse analysis/statistics/ (10 skills: Bayesian, meta-analysis, SEM, survival, power analysis, nonparametric) and analysis/econometrics/ (12 skills: causal inference, panel data, IV, time series).

4. Visualization SOP

4.1 Chart Type Selection

Data pattern	Chart type
Distribution (1 var)	Histogram, KDE, box/violin plot
Comparison (categories)	Bar chart, grouped bar, dot plot
Trend over time	Line chart, area chart
Relationship (2 vars)	Scatter plot, regression plot
Correlation matrix	Heatmap
Composition	Stacked bar, treemap
Geographic	Choropleth, point map
Network / graph	Force-directed, adjacency matrix
High-dimensional	PCA biplot, t-SNE, UMAP

4.2 Publication-Quality Standards

Set plt.rcParams for journal figures: figure.dpi: 300, font.family: serif, font.size: 10, savefig.bbox: tight. Key rules:

1. Resolution: 300 DPI minimum (600 DPI for line art)
2. Format: PDF/SVG for vector; PNG/TIFF for raster (avoid JPEG)
3. Color: colorblind-safe palettes (viridis, cividis, Set2)
4. Labels: every axis labeled with units; legend outside if crowded
5. Font: 8-12pt, match journal spec (serif or sans-serif)
6. Size: single column ~3.5in, double column ~7in width
7. Save: workspace_save("outputs/figures/fig-<desc>.pdf", content)

Deep-dive skills: browse analysis/dataviz/ (14 skills: matplotlib, plotly, D3, publication figures, color accessibility, geospatial, network viz).

5. exec Safety & Patterns

Safe (no approval): python3, Rscript, xelatex, pandoc, jq, wc, grep, find. Requires approval_card: pip install, brew install, curl, wget, anything outside workspace. Full safety rules in Workspace SOP.

Common patterns:

• exec("python3 outputs/scripts/experiment.py") — run analysis
• exec("Rscript outputs/scripts/analysis.R") — R script
• exec("python3 -c \"import pandas; ...\"") — quick inspection

Output paths: All script outputs (figures, data, reports) MUST use workspace-relative paths. Set the working directory to workspace root before execution, and use paths like outputs/figures/, outputs/reports/. Template for Python:

import os
os.chdir(os.environ.get('WORKSPACE_ROOT', '.'))

6. Reproducibility Protocol

6.1 Environment Recording

At analysis start, capture Python version, platform, and key package versions (numpy, pandas, scipy, matplotlib, sklearn). Save via workspace_save("outputs/reports/env-snapshot-<date>.json").

6.2 Reproducibility Checklist

• Random seeds: Set at script top for numpy, random, torch, tensorflow
• Version locking: Record exact versions (pip freeze / conda list)
• Data provenance: Source URL, download date, SHA-256 for raw data
• Execution order: Scripts must run independently (no notebook-state dependency)
• Relative paths: Use workspace-relative paths, not absolute
• For ML: log hyperparams, track metrics per step, save checkpoints, record hardware

7. Coding Complexity Delegation

Before writing code, assess complexity:

Simple task (single file, stdlib only, no iteration)
  → RC handles directly via exec
Complex task (multi-file, dependencies, iterative debugging)
  → Check MEMORY.md Environment for installed CLIs (codex, claude, opencode)
    → CLI found → inform user, suggest delegating via exec
      → User agrees → exec the CLI (read claude-code / codex-cli / opencode-cli skill)
      → User wants RC → proceed with RC's own capabilities
    → No CLI → recommend installation, wait for user decision
      → User insists → RC proceeds via repeated workspace_save + exec (slower)

Boundary: "complex coding" = multi-file projects, dependency management, iterative debugging, beamer/multi-chapter LaTeX, interactive visualizations. For these, the Claude Code, Codex CLI, and OpenCode CLI skills provide delegation guidance.

8. RC Local Tools Reference

• workspace_save: persist code to outputs/scripts/ (or outputs/notebooks/), figures to outputs/figures/, processed data to sources/data/. Commit message prefix: Add: / Update:.
• workspace_append: add results to an existing report or data file without overwriting. Preferred over read + save for incremental updates.
• workspace_download: save binary outputs (plots, exports) from URLs.
• exec: run scripts from workspace root. Default timeout 120s (increase for long-running). Always inspect both stdout and stderr. On failure: fix code, workspace_save again, re-run.

Related Research-Plugins Skills

For detailed methodology beyond this SOP, browse these RP skill indexes:

Index path	Skills	Covers
tools/code-exec/	7	Jupyter, Colab, Kaggle, reproducibility (Python/R)
analysis/statistics/	10	Hypothesis testing, Bayesian, meta-analysis, SEM, survival
analysis/econometrics/	12	Causal inference, panel data, IV, DiD, time series, Stata
analysis/wrangling/	10	pandas, data cleaning, missing data, survey, text mining
analysis/dataviz/	14	matplotlib, plotly, D3, publication figures, geospatial, networks
domains/ai-ml/	27	PyTorch, TensorFlow, LLM eval, experiment tracking, ML pipelines
tools/diagram/	9	Mermaid, PlantUML, GraphViz, flowcharts, scientific diagrams
domains/	147	16 disciplines — browse domains/{field}/ for domain-specific analysis methods