Software

Packages and applications

• Effective reproduction number for SARS-CoV-2 in the Czech Republic

  Author

  Shiny application estimating the effective reproduction number, risk-adjusted case counts, and age-related statistics from public data. Used by advisors at the Ministry of Health and by journalists during the pandemic.

  • Application
  • ·GitHub

  Netík, J. (2020). Effective reproduction number, risk-adjusted case counts and other age-related statistics for SARS-CoV-2 in the Czech Republic [Computer software]. https://netique.shinyapps.io/R_comparison/

• {ShinyItemAnalysis}

  Co-developer

  Test and item analysis via Shiny. Co-developer of the application and its modular architecture.

  • CRAN
  • ·Website

  Martinková, P., Hladká, A., & Netík, J. (2024). ShinyItemAnalysis: Test and item analysis via Shiny (Version 1.5.1) [Computer software]. CRAN. https://doi.org/10.32614/CRAN.package.ShinyItemAnalysis

• {reschola}

  Co-author

  Templates, themes, and utilities for reproducible analysis and reporting workflows at Schola Empirica, including a LimeSurvey API client that pulls survey data and labels straight into R.

  • Documentation
  • ·GitHub

  Bouchal, P., & Netík, J. (2024). reschola: A set of templates, themes & utilities for reproducible workflows at Schola Empirica (Version 0.5.6) [Computer software]. https://scholaempirica.github.io/reschola/

• {SIAtools}

  Lead developer

  Developer toolkit for building, testing, and distributing ShinyItemAnalysis modules as R packages.

  • CRAN
  • ·Documentation
  • ·GitHub

  Netík, J., & Martinková, P. (2025). SIAtools: 'ShinyItemAnalysis' modules development toolkit (Version 0.1.4) [Computer software]. CRAN. https://doi.org/10.32614/CRAN.package.SIAtools

• {SIAmodules}

  Co-developer

  Ready-made interactive modules for ShinyItemAnalysis: item difficulty prediction from text, computerized adaptive test simulation, and more.

  • CRAN
  • ·GitHub

  Martinková, P., & Netík, J. (2026). SIAmodules: Modules for 'ShinyItemAnalysis' (Version 0.1.3) [Computer software]. CRAN. https://CRAN.R-project.org/package=SIAmodules

• {buildr}

  Author

  Organize and run build scripts comfortably from R.

  • CRAN
  • ·GitHub

  Netík, J. (2022). buildr: Organize & run build scripts comfortably (Version 0.1.1) [Computer software]. CRAN. https://doi.org/10.32614/CRAN.package.buildr

• overleaf-mcp

  Author

  Model Context Protocol server that lets AI coding agents read, edit, and compile Overleaf projects through Overleaf's real-time API, respecting tracked changes and comments. TypeScript.

  • GitHub

  Netík, J. (2026). overleaf-mcp: Model Context Protocol server for Overleaf [Computer software]. GitHub. https://github.com/netique/overleaf-mcp

• EduTest apps

  Developer

  Standalone Shiny apps from the EduTest project that let schools analyze their own results from the CZVV-run school-leaving exam (Maturita) and unified entrance exam (JPZ), plus Item Analysis and Text Analysis modules for ShinyItemAnalysis.

  • Maturita app
  • ·Entrance exam app
  • ·SIA modules
  • ·Project site

Contributions to open-source projects

• transformersAdded the ModernBertForMultipleChoice model head (2025)PR #39232
• RStudio IDEFixed scaling of inline notebook plots on high-DPI displays and removed stray margins, resolving seven long-standing issues; shipped in the 2022.12 release (2022)PR #12324
• {mirt}Analytical derivatives for the gpcmIRT item class in DerivTheta; documentation fix in 2022 (2026)PR #282PR #226
• {ggplot2}Support for lambda functions in discrete scales and facets (2021)PR #4188
• {ellmer}Fixed authentication scope and API endpoints for Google Vertex AI (2025)PR #704
• {gridtext}Compatibility fix for R 4.2.0 font handling (2022)PR #25
• {difNLR}Model formula rendering and documentation fixes (2025)PR #27
• {Brobdingnag}Fixed a missing class import from Matrix (2022)PR #21
• Mastering ShinyCorrections to the book text (2021)PR #479

I also report and help triage bugs across the R ecosystem, including RStudio, Shiny, R Markdown, renv, and the tidyverse and r-lib packages: all issues, all pull requests.