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choxos/README.md

Hi, I'm Ahmad Sofi-Mahmudi

Research software · Evidence synthesis · Meta-research · Interactive science · GNU/Linux

Projects · Writing · LinkedIn · X


I build statistical and research tools that make evidence synthesis, biostatistics, and scientific publishing more reproducible, and browser tools that let people see how the science works.

My work sits mostly at the intersection of R, Python, Bayesian modeling, meta-analysis, research integrity, interactive visualization, and GNU/Linux.

Current focus

  • Population-adjusted indirect treatment comparisons and target trial emulation methods
  • Meta-research and research integrity: retractions, citation validation, transparency, FAIR metadata
  • Interactive, backend-free browser tools for teaching anatomy, statistics, and mathematics
  • Research with language models where every claim is checked against its primary source before it is published
  • R packages for biostatistics workflows and reproducible research on GNU/Linux

Featured work

Project What it does Stack
mlumr Multilevel unanchored meta-regression for disconnected evidence networks R, Stan
cpaic Component network meta-analysis extended to population-adjusted indirect comparisons R, Stan
Mathematics-of-ITC Graduate textbook on indirect treatment comparisons with every result proved and a machine-checked Coq companion Quarto, LaTeX, Coq
ITC and TTE open problems Audited catalogs of open methodological problems, each claim verified against its registry and sources Quarto, Python
NMAViz · site Reads the evidence structure of a network meta-analysis in the browser, drawn eight ways JavaScript, SVG
OMFAtlas · site Interactive 3D atlas of oral and maxillofacial anatomy for dental education JavaScript, Three.js
MetaCan · site Provenance-tracked map of Canadian meta-research with a bilingual web app R, Python, PostgreSQL
citicious Chrome extension that flags retracted articles and hallucinated citations on academic pages TypeScript
sysreqR · krt · respondeR R packages for system requirement preflight checks on GNU/Linux, Key Resources Tables, and responder analysis R, Shiny
BiostatAgent Claude Code plugin marketplace for biostatistics in R: Bayesian modeling, ITC, and trial simulation Python, R

Also in the browser: catigraphy (CT atlas of the domestic cat) · How Things Work (everyday machines as 3D lessons) · MilleViz (the Millennium Prize Problems, explained from the picture up) · FracGen (fractal studio) · Geography Words (English words that carry a place inside them) · Game of Life (a life budget from UN life tables) · The Evidence Behind (a book auditing the evidence behind UK oral health guidance).

Tools I use

R Python Stan Shiny Quarto JavaScript TypeScript Three.js GNU/Linux Git

How I think about software

Good research software should be:

  • Reproducible enough for another analyst to rerun it.
  • Transparent enough for a reviewer to audit it.
  • Documented enough for a tired user to understand it.
  • Small and boring where possible; cleverness is not a substitute for reliability.

Open science over closed claims. Reproducible code over screenshots. Useful tools over vanity metrics.

Pinned Loading

  1. mlumr mlumr Public

    An R package for fitting multilevel unanchored meta-regression (ML-UMR) models in unanchored indirect treatment comparisons (uITCs).

    HTML 12 1

  2. sysreqR sysreqR Public

    sysreqR: Preflight checks for R package system requirements on GNU/Linux.

    R 3

  3. respondeR respondeR Public

    R package, Shiny app, and browser tool for responder analysis of continuous outcomes

    R 3

  4. cochraneauthors cochraneauthors Public

    A meta-research on the Cochrane Reviews' authors

    HTML 2 1

  5. BiostatAgent BiostatAgent Public

    Claude Code plugin marketplace for biostatistics in R — 30 agents, 17 commands, and 45 skills spanning Bayesian modeling (Stan/PyMC/JAGS), indirect treatment comparisons (NMA/MAIC/STC/ML-NMR), tidy…

    Python 11 1

  6. OMFAtlas OMFAtlas Public

    Interactive 3D atlas of oral and maxillofacial anatomy for dental education. 643 BodyParts3D meshes plus 77 schematic nerve, vessel, gland, sinus and joint structures the source dataset omits, fitt…

    JavaScript 62 15