R Weekly 2025-W27 R package quality, in the Nix of Time!

30 Jun 2025

• How to have (my) content shared by R Weekly?

This week’s release was curated by Batool Almarzouq, with help from the R Weekly team members and contributors.

Highlight

• R Package Quality: Package Popularity

• In the Nix of Time: Creating a reproducible analytical environment with Nix and {rix}

Insights

• Three major updates to the Plotnine website

• How to open files, folders, websites in R

• R Package Quality: Package Popularity

• Multilingual Publishing: Frequently Asked Questions

• A Simple Bayesian Multi-state Survival Model for a Clinical Trial

• Counting Digits Quickly

R in Organizations

• Announcing New Stats Software Peer Review Editors: Emi Tanaka and Nima Hejazi

• rOpenSci News Digest, June 2025

• Shiny in Production 2025: Lightning Talk Lineup

R in Academia

• Prompting large language models for quality ecological statistics

Resources

• mirai 2.4.0: First Class Async and High-Performance Computing

New Packages

📦 Keep up to date wtih CRANberries 📦

CRAN

• Introducing vitals, a toolkit for evaluating LLM products in R

• {MultiLCIRT} 2.12: Multidimensional Latent Class Item Response Theory Models

• {ClimaRep} 0.6: Estimating Climate Representativeness

• {scMappR} 1.0.12: Single Cell Mapper

• {notionR} 0.0.9: R Wrapper for ‘Notion’ API

• {OpenBARD} 0.0.1: Open British Arboricultural Record Dataset

• {movedesign} 0.3.1: Study Design Toolbox for Movement Ecology Studies

• {ManyIVsNets} 0.1.1: Environmental Phillips Curve Analysis with Multiple Instrumental Variables and Networks

• {slopes} 1.0.1: Calculate Slopes of Roads, Rivers and Trajectories

• {midr} 0.5.0: Learning from Black-Box Models by Maximum Interpretation Decomposition

• {letsHerp} 0.1.0: An Interface to the Reptile Database

• {clinpubr} 1.0.1: Clinical Publication

• {FLSSS} 9.2.8: Mining Rigs for Problems in the Subset Sum Family

Updated Packages

🔍 Search on R-universe 🔍

• {mirai} 2.4.0: Minimalist Async Evaluation Framework for R - diffify

• {adsoRptionCMF} 0.1.1: Classical Model Fitting of Adsorption Isotherms - diffify

• {ggpp} 0.5.9: Grammar Extensions to ‘ggplot2’ - diffify

• {httptest2} 1.2.0: Test Helpers for ‘httr2’ - diffify

• {ggpubr} 0.6.1: ‘ggplot2’ Based Publication Ready Plots - diffify

• {dataRetrieval} 2.7.19: Retrieval Functions for USGS and EPA Hydrology and Water Quality Data - diffify

• {xpose.nlmixr2} 0.4.1: Graphical Diagnostics for Pharmacometric Models: Extension to ‘nlmixr2’ - diffify

• {unhcrthemes} 0.7.0: UNHCR ‘ggplot2’ Theme and Colour Palettes - diffify

• {CooccurrenceAffinity} 1.0.2: Affinity in Co-Occurrence Data - diffify

• {ao} 1.2.1: Alternating Optimization - diffify

• {rsconnect} 1.5.0: Deploy Docs, Apps, and APIs to ‘Posit Connect’, ‘shinyapps.io’, and ‘RPubs’ - diffify

• {mapplots} 1.5.3: Data Visualisation on Maps - diffify

• {LLMR} 0.4.2: Interface for Large Language Model APIs in R - diffify

• {fabR} 2.1.1: Wrapper Functions Collection Used in Data Pipelines - diffify

• {smoothr} 1.1.0: Smooth and Tidy Spatial Features - diffify

• {groupcompare} 1.0.1: Comparing Two Groups Using Various Descriptive Statistics - diffify

• {rgl} 1.3.24: 3D Visualization Using OpenGL - diffify

• {WARDEN} 1.2.2: Workflows for Health Technology Assessments in R using Discrete EveNts - diffify

• {dogesr} 0.5.2: Work with the Doges/Dogaresse Dataset - diffify

• {robcp} 0.3.9: Robust Change-Point Tests - diffify

• {ggdemetra} 0.2.9: ‘ggplot2’ Extension for Seasonal and Trading Day Adjustment with ‘RJDemetra’ - diffify

• {MIMER} 1.0.4: Data Wrangling for Antimicrobial Resistance Studies - diffify

• {directlabels} 2025.6.24: Direct Labels for Multicolor Plots - diffify

• {bartXViz} 1.0.5: Visualization of BART and BARP using SHAP - diffify

• {ggspectra} 0.3.16: Extensions to ‘ggplot2’ for Radiation Spectra - diffify

Videos and Podcasts

• Listen to the R-Weekly Highlights Podcast

• A Framework for Cohort Building in R - Nuria Mercade-Besora and Edward Burn

• In the Nix of Time: Creating a reproducible analytical environment with Nix and {rix}

• REDCapSync and RosyREDCap for standardized data pipelines and exploratory data analysis

• The power of {targets} package for reproducible data science

• First Steps with SQL in R: Making Data Talk

• Quarto Dashboards: from zero to publish in one hour

• Supporting R learners on the job during interesting times: A panel of R educators

• Using R shiny to perform and automate decision-analytic modeling for cost-effectiveness analysis

• Visualising data for patients: create accessible charts

• Advanced Distance Metrics for High-Dimensional Clustering: introducing ‘distanceHD’ R-package

• An Accelerometry Biomarker Framework with Application in Vigilance in UK Biobank Data

• Application of attention mechanism to improve performance of llm/mllm used across R/Medicine

• Bedside to Bench - Reinventing medicine with AI

• Bootstrap inference made easy: p-values and confidence intervals in one line of code

• Co-occurrence analysis and knowledge graphs for suicide risk prediction

• Dengue Forecasting Addressing the Interrupted Effect from COVID-19 Cases

• Ethical Considerations of Contrasts in Statistical Modeling of Medical Equity

• Improving Reproducibility of Medical Research with Controlled Vocabularies

• Mix, Pour, Share: The rUM Cocktail for Biomedical Project Packaging

• Model Evaluation: From Machine Learning to Generative AI

Shiny Apps

• Host, share your Shiny, Rmarkdown & streamlit apps in 3 clicks

Tutorials

• Backpropagating quasi-randomized neural networks

• Setting Future Plans in R Functions — and Why You Probably Shouldn’t

• Future Got Better at Finding Global Variables

• Sankey plots can work, but need polishing like any other graphic by @ellis2013nz

• Understanding the Link Between Uncertainty and Imports by glmnet

• Mastering Normal Distributions in R: A Comprehensive Guide to rnorm(), TidyDensity, and Statistical Analysis

• 3MW (Safer SQL in R)

R Project Updates

Updates from R Core:

Call for Participation

Post by @[email protected]

View on Mastodon

Upcoming Events in 3 Months

Events in 3 Months:

• A list of R conferences and meetings

• This week’s local R-User and applied stats events

• Weekly R Workshops for Ukraine

Connect

Join the Data Science Learning Community

rtistry

They haven’t posted it here but @votehub.com made an incredible graphic of the NYC primary showing results with population by precinct on the Z axis designed to look like a building map of NYC. One of my favorite political maps ever.

[image or embed]

— Joel Wertheimer (@wertwhile.bsky.social) June 26, 2025 at 12:36 AM

Image of al-Mubarraz, Saudi Arabia created in #rstats using data from #OpenStreetMap. pic.twitter.com/nY7tOC3tM6

— R City Views (@rcityviews) June 29, 2025

Quotes of the Week

pic.twitter.com/pqpoMeAJfM

— Motivational Quotes (@motivational) June 30, 2025