Software

Packages developed by Haim Bar and collaborators, freely available on GitHub, CRAN, PyPI, and CTAN.

runcode — LaTeX Package for Reproducible Science

CTAN GitHub

A LaTeX package that executes external code (R, Python, Julia, Matlab, and any command-line tool) from within a LaTeX document and embeds the output directly in the compiled PDF. Designed for fully reproducible scientific documents. Works in server mode via the talk2stat Python package. Available through TeX Live and MiKTeX.

Version 2.4 · Co-authored with HaiYing Wang · License: LPPL 1.3c

CTAN page GitHub Paper (JDS 2021)
talk2stat — Python Package

PyPI GitHub

Opens and manages a bidirectional socket connection to R, Julia, Python, or Matlab, enabling other programs (such as the runcode LaTeX package) to send code and receive output without re-launching the interpreter.

Version 0.1.7 · Requires: pexpect

PyPI GitHub
loopmonitor — Loop Control for Long-Running Programs (Python)

PyPI GitHub

Provides on-demand status queries and graceful control of long-running Python loops without interrupting execution. Drop-in replacements for for / while loops write a JSON state file after every iteration; an ipc command-line tool lets you peek at progress, plot tracked values, set variables, or break the loop from a second terminal. Companion R package also available.

Version 0.1.2

PyPI GitHub
loopmonitor — Loop Control for Long-Running Programs (R)

GitHub R

Provides ipc_for(), ipc_while(), and ipc_repeat() as drop-in replacements for R's loop constructs, enabling on-demand inspection and control of long-running loops from a second terminal using the ipc command-line tool. Status, tracked values, and ETA are written to a JSON state file after every iteration.

Version 0.1.0 · Requires: jsonlite · Companion to the Python loopmonitor package

GitHub
edgefinder — Gene Network Inference (Python)

PyPI GitHub

Recovers gene network structure from co-expression data using a mixture-model approach based on convex geometry and beta distributions. Controls edge detection error rates without assuming network sparsity. Includes simulation code and case studies.

Version 0.1.10

PyPI Paper (PLOS ONE 2021) Paper (CSDA 2023)
QREM — Quantile Regression via EM Algorithm (R)

GitHub R

Implements mixed-effects quantile regression and variable selection via an EM algorithm. Suitable for high-dimensional settings where standard quantile regression methods may be unstable.

Version 0.2.1

GitHub Paper (Statistical Modelling 2021)
SEMMS — Scalable EMpirical Bayes Model Selection (R)

GitHub R

Variable selection for generalized linear models using a scalable empirical Bayes approach. Suitable for high-dimensional problems where the number of predictors is large relative to sample size.

Version 0.2.5 · Includes datasets and vignette

Paper (JCGS 2020) arXiv
DVX — Differential Variation and Expression (R)

GitHub R

An interactive R program for simultaneous analysis of differential variation and differential expression in genomic data.

Paper (Stat 2019)
R-CMap — Concept Mapping Software (R)

GitHub R

Open-source concept mapping software. Provides tools for data collection, multidimensional scaling, cluster analysis, and visualization. Used in social sciences, public health, and education research.

Version 0.3.4

GitHub Paper (Evaluation and Program Planning 2017)
betaMix — Beta Mixture Models for Correlation (R)

GitHub R

Identifies significant correlations in high-dimensional data using a mixture of beta distributions framework. Applications include graphical model selection and network inference. Also available in Python (betaMixPy).

Version 0.3.3

GitHub (R) GitHub (Python) Paper (CSDA 2023)
Spatial Capture-Recapture MCMC Code (R)

GitHub R

Bayesian MCMC implementation for a spatial capture-recapture model with inter-individual attraction terms. Estimates animal abundance and movement patterns.

Co-authored with Paul McLaughlin, PhD

Paper (Environmetrics 2021)