Tools: scientific communication

Preregistration, environments, visualization, and publishing

The maintained version of the “Useful Tools” list closing Chapter 10. Last reviewed August 2026.

Preregistration and archiving

OSF Registries: preregistration with a timestamped, citable record; supports embargo.
AsPredicted: short-form preregistration, nine questions.
Zenodo: archive a repository snapshot and get a DOI.

Environment management

Python: venv, conda, uv (fast, increasingly the default in new projects).
R: renv.
Containers: Docker, Apptainer for HPC. Strongest guarantee, highest setup cost.

Version control

Git with GitHub or GitLab. Tag the commit that produced published results so a replicator can check out that exact state.

Static visualization

Python: matplotlib, seaborn, plotnine (grammar of graphics).
R: ggplot2.
Accessibility: viridis and ColorBrewer palettes are colorblind-safe and survive grayscale printing.

Interactive and dashboards

Streamlit, Shiny (R and Python), Dash, Observable, Tableau Public. Chapter 10 asks for a static fallback and a maintenance memo for any of these; the longevity problem is real.

Reproducible reporting

Quarto (this site is built with it), Jupyter, R Markdown, Jupyter Book.

Uncertainty visualization

matplotlib error bars and fill-between for confidence bands; small-multiple ensemble plots for seed sensitivity; ggdist (R) for distributional visualizations including hypothetical outcome plots.