R Weekly 2025-W39 Parse RMarkdown, Vibe Code, Quality Control

22 Sep 2025

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

This week’s release was curated by Jonathan Carroll, with help from the RWeekly team members and contributors.

Highlight

• All the Ways to Programmatically Edit or Parse R Markdown / Quarto Documents

• I Vibe Coded an R Package

• Quality Control for Scanned Multiple-Choice Exams

Insights

• Phoenician colonization

• Quality Control for Scanned Multiple-Choice Exams

• All the Ways to Programmatically Edit or Parse R Markdown / Quarto Documents

• Complete Guide to Applying Functions to Each Row in R Matrices and Data Frames

• Positron at posit::conf(2025) Roundup

• RStudio IDE and Posit Workbench 2025.09.0: What’s New

• What’s New in Posit Package Manager: September 2025

• Positron for Product Owners

• Deploy to Connect Cloud from Positron and VS Code

• I Vibe Coded an R Package

• Some Papua New Guinea data doodles by @ellis2013nz

• Easily clean up messy databases with fuzzy matching in R

R in Organizations

• Faster Clinical Trial Reporting: A Beginner’s Guide to Implementing CDISC SDTM and ADaM Standards with Open-Source R Packages

Tutorials

• Building DNA Sequence Alignment With Needleman-Wunsch Algorithm From Scratch - A Note To My Self

• Learning About Assemblying DNA, BLAST, and Multiple Loci Sequence Testing (MLST) - A Note To Myself

• Transfer Learning using ahead::ridge2f on synthetic stocks returns

• Reimagining Equity Solvency Capital Requirement Approximation

• Augmented Dynamic Adaptive Model (ADAM) for Daily Seasonal Data

Resources

• Goal-Driven Flexible Bayesian Design

New Packages

📦 Keep up to date wtih CRANberries 📦

CRAN

• Introducing admiralneuro!
• {admiralneuro} 0.1.0: Neuroscience Extension Package for ADaM in ‘R’ Asset Library
• {shinystate} 0.1.0: Customization of Shiny Bookmarkable State
• {isocubes} 1.0.0: Voxel Data Visualization with Isometric Cubes
• {descutils} 1.0: Utilities for Describing and Comparing Data
• {sqlq} 1.0.1: ‘SQL’ Query Builder
• {ezTrack} 0.1.0: Exploring Animal Movement Data
• {broadcast} 0.1.3: Broadcasted Array Operations Like ‘NumPy’
• {repo.data} 0.1.4: R Repository Data
• {pregnancy} 0.1.1: Calculate and Track Dates and Medications During Pregnancy
• {DUToolkit} 1.0.1: Visualizing and Quantifying Decision Uncertainty

GitHub or Bitbucket

• The ‘Tanakh’ R package

Updated Packages

🔍 Search on R-universe 🔍

• Survivor Australia vs. The World is now in {survivoR}

• RcppSimdJson 0.1.14 on CRAN: New Upstream Major

• RcppSMC 0.2.9 on CRAN: Maintenance

• RcppArmadillo 15.0.2-1 on CRAN: New Upstream, Some Changes

• {RcppArmadillo} 15.0.2-2: ‘Rcpp’ Integration for the ‘Armadillo’ Templated Linear Algebra

• {ggplotify} 0.1.3: Convert Plot to ‘grob’ or ‘ggplot’ Object - diffify
• {dbi.table} 1.0.5: Database Queries Using ‘data.table’ Syntax - diffify
• {table1} 1.5.1: Tables of Descriptive Statistics in HTML - diffify
• {vismeteor} 2.0.1: Analysis of Visual Meteor Data - diffify
• {altdoc} 0.6.0: Package Documentation Websites with ‘Quarto’, ‘Docsify’, ‘Docute’, or ‘MkDocs’ - diffify
• {vroom} 1.6.6: Read and Write Rectangular Text Data Quickly - diffify
• {inDAGO} 1.0.2: A GUI for Dual and Bulk RNA-Sequencing Analysis - diffify
• {weatherOz} 2.0.2: An API Client for Australian Weather and Climate Data Resources - diffify
• {progressr} 0.16.0: An Inclusive, Unifying API for Progress Updates - diffify Library - diffify
• {ggstar} 1.0.6: Multiple Geometric Shape Point Layer for ‘ggplot2’ - diffify
• {duckdb} 1.4.0: DBI Package for the DuckDB Database Management System - diffify
• {cartographr} 0.2.4: Crafting Print-Ready Maps and Layered Visualizations - diffify
• {kerasnip} 0.0.3: A Bridge Between ‘keras’ and ‘tidymodels’ - diffify
• {duckplyr} 1.1.2: A ‘DuckDB’-Backed Version of ‘dplyr’ - diffify
• {Rlabkey} 3.4.4: Data Exchange Between R and ‘LabKey’ Server - diffify
• {pillar} 1.11.1: Coloured Formatting for Columns - diffify
• {ggpath} 1.1.0: Robust Image Rendering Support for ‘ggplot2’ - diffify
• {noctua} 2.6.3: Connect to ‘AWS Athena’ using R ‘AWS SDK’ ‘paws’ (‘DBI’ Interface) - diffify
• {ggstats} 0.11.0: Extension to ‘ggplot2’ for Plotting Stats - diffify
• {marquee} 1.2.1: Markdown Parser and Renderer for R Graphics - diffify

Videos and Podcasts

• Listen to the R-Weekly Highlights Podcast

R Project Updates

Updates from R Core:

Upcoming Events in 3 Months

Events in 3 Months:

• R-multiverse: a new way to publish R packages

• From a slow analysis script to a fast and structured program in R workshop

• Structural Bayesian Techniques for Experimental and Behavioral Economics, With applications in R and Stan workshop

• Generative AI and R workshops in Hobart Australia

• A list of R conferences and meetings

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

• Weekly R Workshops for Ukraine

Connect

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Quotes of the Week

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