R Weekly 2025-W36 {truffle} messy datasets, 25 things with R, OpenAI Codex in Positron

02 Sep 2025

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

Highlight

• Creating messy datasets for teaching purposes with {truffle}

• 25 Things You Didn’t Know You Could Do with R - Cascadia R Conf, Keynote

• Using OpenAI Codex in Positron with a demo on developing an R package using the OpenAI Codex agent

Insights

• Measuring LLM Effectiveness - Max Kuhn & Simon Couch (slides)

• I was wrong about tidymodels and LLMs

• Using OpenAI Codex in Positron with a demo on developing an R package using the OpenAI Codex agent

• 💸 R-Consortium ISC Grant Applications Open!📦 — funding to build packages and technical infrastructure for the R community

R in the Real World

• Men’s domestic chores and fertility rates - Part II, technical notes

• A guide to actuarial techniques in R and Python

R in Organizations

• Introducing multideploy: Streamline file deployments across multiple repositories

R in Academia

• surveydown: An open-source, markdown-based platform for programmable and reproducible surveys

New Packages

📦 Keep up to date wtih CRANberries 📦

CRAN

• {WSCdata} 0.1.0: A New Four-Arm Within-Study Comparison Data on Math and Vocabulary Training

• {shinypayload} 0.1.0: Accept POST Data and URL Parameters in ‘shiny’ (Same-Port Integration)

• {ptvalue} 0.1.0: Working with Precision Teaching Values

• {tastyR} 0.1.0: Recipe Data from ‘Allrecipes.com’

• {Stype.est} 0.1.0: S-Type Estimators

• {h3o} 0.3.0: H3 Geospatial Indexing System

• {gadjid} 0.1.0: Graph Adjustment Identification Distances for Causal Graphs

• {stratcols} 1.0.0: Stratigraphic Columns and Order Metrics

• {searchAnalyzeR} 0.1.0: Advanced Analytics and Testing Framework for Systematic Review Search Strategies

• {datacommons} 0.1.0: Client for the ‘Google Data Commons API V2’

• {scPOEM} 0.1.2: Single-Cell Meta-Path Based Omic Embedding

• {rcdf} 0.1.0: A Comprehensive Toolkit for Working with Encrypted Parquet Files

• {pECV} 1.0.1: Entrywise Splitting Cross-Validation for Factor Models

• {ham} 1.0.0: Healthcare Analysis Methods

• {gridify} 0.7.4: Enrich Figures and Tables with Custom Headers and Footers and More

• {GenOU} 0.2.1: Sequential Change-Point Tests for Generalized Ornstein-Uhlenbeck Processes

• {calms} 1.0-1: Comprehensive Analysis of Latent Means

• {auxvecLASSO} 0.2.0: LASSO Auxiliary Variable Selection and Auxiliary Vector Diagnostics

• {TheseusPlot} 0.1.1: Visualizing Decomposition of Differences in Rate Metrics

• {terminalgraphics} 0.1.1: Graphical Output in Terminals

• {SMMAL} 0.0.5: Semi-Supervised Estimation of Average Treatment Effects

• {pubchem.bio} 1.0.0: Biologically Informed Metabolomic Databases from ‘PubChem’

• {kfre} 0.0.2: Kidney Failure Risk Equation (KFRE) Tools

• {caradpt} 0.1.0: Covariate-Adjusted Response-Adaptive Designs for Clinical Trials

• {BSTFA} 0.1.0: Bayesian Spatio-Temporal Factor Analysis Model

• {tidypopgen} 0.3.2: Tidy Population Genetics

• {multideploy} 0.1.0: Deploy File Changes Across Multiple ‘GitHub’ Repositories

• {spatialreg.hp} 0.0-1: Hierarchical Partitioning of R2 for Spatial Simultaneous Autoregressive Model

• {SampleSizeCalculator} 0.1.0: Sample Size Calculator under Complex Survey Design

• {rappleads} 0.1.3: Get Data from ‘Apple Ads Campaign Management API’

• {NMAforest} 0.1.0: Forest Plots for Network Meta-Analysis with Proportion for Paths and Studies

• {allocation} 0.1.0: Exact Optimal Allocation Algorithms for Stratified Sampling

• {AdapDiscom} 1.0.0: Adaptive Sparse Regression for Block Missing Multimodal Data

• {LCCkNN} 0.1.0: Adaptive k-Nearest Neighbor Classifier Based on Local Curvature Estimation

• {sidra} 0.1.7: Acesso aos Dados do ‘SIDRA’ do IBGE

• {RCaucTile} 1.0.0: Tile Grid Maps for East Caucasian Languages

• {HARr} 1.1.0: ‘HAR’ (‘GEMPACK’) File Read/Write Utility

• {firesale} 0.1.0: Datastore for ‘fiery’ Web Servers

• {flankr} 1.2.0: Implementing Computational Models of Attentional Selectivity

• {CLIC} 0.1: The LIC for Distributed Cosine Regression Analysis

• {WarnEpi} 1.0.1: A Comprehensive Tool for Early Warning in Infectious Disease

• {utest} 0.4.0: Lind/Mehlum Utest

• {unfold} 1.0.0: Mapping Hidden Geometry into Future Sequences

• {mlspatial} 0.1.0: Machine Learning and Mapping for Spatial Epidemiology

• {JapanAPIs} 0.1.0: Access Japanese Data via Public APIs and Curated Datasets

• {E2E} 0.0.3: Ensemble Learning Framework for Diagnostic and Prognostic Modeling

• {ChinAPIs} 0.1.0: Access Chinese Data via Public APIs and Curated Datasets Data

• {matrixCorr} 0.3.1: Collection of Correlation and Association Estimators

• {IndiAPIs} 0.1.0: Access Indian Data via Public APIs and Curated Datasets

• {CATAcode} 1.0.0: Explore and Code Responses to Check-All-that-Apply Survey Items

• {EQUALencrypt} 0.1.0: Encryption and Decryption of Files and Data for Researchers Without Coding Skills

• {edfinr} 0.1.1: Access Tidy Education Finance Data

• {covercorr} 1.0.0: Coverage Correlation Coefficient and Testing for Independence

• {ffaframework} 0.1.1: Flood Frequency Analysis Framework

• {tma} 0.3.0: Transmodal Analysis (TMA)

• {tailor} 0.1.0: Iterative Steps for Postprocessing Model Predictions

• {degradr} 1.0.0: Estimating Remaining Useful Life with Linear Mixed Effects Models

Updated Packages

🔍 Search on R-universe 🔍

• {pharmaverseraw} 0.1.1: Raw Data for ‘pharmaversesdtm’ Package - diffify
• {orbital} 0.3.1: Predict with ‘tidymodels’ Workflows in Databases - diffify
• {crane} 0.2.0: Supplements the ‘gtsummary’ Package for Pharmaceutical Reporting - diffify
• {geoR} 1.9-6: Analysis of Geostatistical Data - diffify
• {ggredist} 0.0.3: Scales, Geometries, and Extensions of ‘ggplot2’ for Election Mapping - diffify
• {worldbank} 0.6.1: Client for World Banks’s ‘Indicators’ and ‘Poverty and Inequality Platform (PIP)’ APIs - diffify
• {rvest} 1.0.5: Easily Harvest (Scrape) Web Pages - diffify
• {usmap} 1.0.0: US Maps Including Alaska and Hawaii - diffify
• {rsconnect} 1.5.1: Deploy Docs, Apps, and APIs to ‘Posit Connect’, ‘shinyapps.io’, and ‘RPubs’ - diffify
• {openair} 2.19.0: Tools for the Analysis of Air Pollution Data - diffify
• {mapview} 2.11.3: Interactive Viewing of Spatial Data in R - diffify
• {survey} 4.4-8: Analysis of Complex Survey Samples - diffify
• {gtsummary} 2.4.0: Presentation-Ready Data Summary and Analytic Result Tables - diffify
• {usethis} 3.2.0: Automate Package and Project Setup - diffify
• {capybara} 1.8.0: Fast and Memory Efficient Fitting of Linear Models with High-Dimensional Fixed Effects - diffify
• {tidycomm} 0.4.2: Data Modification and Analysis for Communication Research - diffify
• {setwidth} 1.1.0: Automatically Set the Width Option on Terminal Emulators - diffify
• {fingerPro} 2.0: A Comprehensive Package for Sediment Source Unmixing - diffify
• {DendroSync} 0.1.5: A Set of Tools for Calculating Spatial Synchrony Between Tree-Ring Chronologies - diffify
• {azuremapsr} 0.0.2: Interface to the ‘Azure Maps’ API - diffify
• {StratPal} 0.6.0: Stratigraphic Paleobiology Modeling Pipelines - diffify
• {tok} 0.2.0: Fast Text Tokenization - diffify
• {rtop} 0.6-17: Interpolation of Data with Variable Spatial Support - diffify
• {reflectR} 2.1.4: Automatic Scoring of the Cognitive Reflection Test - diffify
• {ggPMX} 1.3.1: ‘ggplot2’ Based Tool to Facilitate Diagnostic Plots for NLME Models - diffify
• {workflows} 1.3.0: Modeling Workflows - diffify
• {cards} 0.7.0: Analysis Results Data - diffify
• {divent} 0.5-3: Entropy Partitioning to Measure Diversity - diffify
• {ggridges} 0.5.7: Ridgeline Plots in ‘ggplot2’ - diffify
• {ggpattern} 1.2.1: ‘ggplot2’ Pattern Geoms - diffify
• {feasts} 0.4.2: Feature Extraction and Statistics for Time Series - diffify
• {screenshot} 0.9.2: Take Screenshots (Screen Capture) from R Command - diffify
• {scitb} 0.2.2: Provides Some Useful Functions for Making Statistical Tables - diffify

Videos and Podcasts

• Listen to the R-Weekly Highlights Podcast

• 25 Things You Didn’t Know You Could Do with R - Cascadia R Conf, Keynote

• Advanced R: Vectors (Chapter 3 discussion)

Tutorials

• Creating messy datasets for teaching purposes with {truffle}

• Sliding Calculations of Risks of Federal Reserve Rate Cuts

• How to Finally Fix Your Tables in Typst PDFs (using {gt} tables)

• From Macarena to Bad Bunny: Latin Music’s Billboard Evolution

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