R Works

Approximation of Geodesic

The Atlas-Learn Approach to the Manifold Hypothesis

Differential Geometry

The 2025 paper by Robinett et al., ‘Atlas-based Manifold Representations for Interpretable Riemannian Machine Learning’, provides an algorithm for fitting a low dimensional manifold from a point cloud by means of a novel algorithm for approximating an atlas of charts. This post illustrates the Atlas-Learn method by reconstructing a sphere from a 3D point cloud of naive random samples and works through some checks on accuracy.

Simulated Flames

March 2026 Top 40 New CRAN Packages

Top 40

An idiosyncratic, unabashedly biased, time-constrained attempt to capture the depth and breadth of the new packages submitted to CRAN in a single month entirely without the use of AI: clearly unsustainable, but maybe entertaining and somewhat useful.

Stage II OSCC — Health Economics Model

This post presents a proof of concept for constructing Healthcare Economics Models from a patient’s perspective. Taking oral squamous cell carcinoma as a case study, it models the health states that a patient would visit after treatment as a continuous-time Markov chain. Estimates of jump-chain train transition probabilities and sojourn times are then used to construct a synthetic data set. Calculated values for the total expected amount of time that patients will spend it each health state for two treatment arms are combined with utilities for each health state derived from the literature to compare the total quality adjusted life years for each treatment arm. It is envisioned that models of this sort, constructed under the supervision medical experts, would be useful to clinicians both in documenting the treatment decision process and in communicating with patients.

Example of an archipelago plot

February 2026 Top 40 New CRAN Packages

Top 40

An attempt to capture the depth and breadth of what’s new on CRAN.

Can I use Skills with Posit Assistant for the RStudio IDE?

Posit Assistant does indeed support Skills.

Isabella Velásquez

A Few Claude Skills for R Users

The community has come together to create some great Claude Skills that you can try out today.

Isabella Velásquez

The sad puppy from the Kuzco AI package

January 2026 Top 40 New CRAN Packages

Top 40

An attempt to capture the depth and breadth of what’s new on CRAN.

Clownfish image with superpixel segmentation boundaries overlaid

December 2025 Top 40 New CRAN Packages

Top 40

An attempt to capture the depth and breadth of what’s new on CRAN.

Color palettes based on poison frogs

November 2025 Top 40 New CRAN Packages

Top 40

One hundred eighty-three new packages made it to CRAN in November 2025. Here are my picks organized into sixteen categories: AI, Astronomy, Causal Inference, Data, Ecology, Epidemiology, Genomics, Machine Learning, Marketing, Medical Statistics, Risk Analysis, Shiny, Statistics, Time Series, Utilities, and Visualization.

Smoothed ROC Curves, Calculus and Curvature

This post proposes smoothing ROC curves to make them into objects that can be studied with calculus. It shows how taking derivatives of the ROC curve enables conducting likelihood ratio tests and explores how basic concepts from differential geometry, such as curvature and arc length, may be helpful in examining the behavior of ROC curves. Code is provided to illustrate the ideas presented, and some trouble is taken to examine the effects of smoothing.

Joseph B. Rickert

fig-alt=Population weighted greenspace exposure

October 2025 Top 40 New CRAN Packages

Top 40

Here are my picks for the best of the two hundred and four new packages that landed on CRAN in October. Packages are organized into fifteen categories: Data, Decision Analysis, Ecology, Econometrics, Finance, Genomics, Logic, Machine Learning, Mathematics, Medical Statistics, Statistics, Time Series, Utilities, and Visualization.

ROC Curve drawn by a 'turtle' walking through specificity/sensitivity plane

ROC Curves in Two Lines of Code

ROC Curves

This post explains the basics of ROC curves using simple code and intuitive explanations.

ggextenders hex showing the image of a cat stretching

An Introduction to Writing Your Own ggplot2 Geoms

The ggextenders club provides inspiration and resources for those venturing into the exciting world of creating custom ggplot2 extensions.

Isabella Velásquez

3D plot of Regression Surface

September 2025 Top 40 New CRAN Packages

Top 40

Here are my picks of the best of the two hundred forty new packages that landed on CRAN in September, organized into thirteen categories: Computational Methods, Data, Decision Analysis, Ecology, Epidemiology, Finance, Machine Learning, Mathematics, Medical Applications, Programming, Statistics, Utilities, and Visualization.

Be Mindful of the Time

In a previous post, A Simple Bayesian Multi-state Survival Model for a Clinical Trial, I described a textbook example comparing the effectiveness of asthma treatments by fitting a discrete-time Markov model to clinical trial data. In this post, I elaborate on that analysis by fitting a continuous-time Markov chain (CTMC) to the same, discretely observed state-table data. An EM algorithm reconstructs the likelihood function to estimate the generator matrix for the CTMC. I describe some of the differences between discrete-time and continuous-time Markov models and highlight the importance of understanding how the data implicitly sets time scales when modeling real world processes.

August 2025 Top 40 New CRAN Packages

Top 40

Here are my picks for the best from the ninety-seven new packages that landed on CRAN in August, organized in eighteen categories: Causal Inference, Data, Differential Privacy, Ecology, Environmental Studies, Epidemiology, Geology, Genetics, Genomics, Health Technology Assessment, Machine Learning, Medical Statistics, Statistics, Surveys, Time Series, Toxicology, Utilities, and Visualization.

Evolution of Dirichlet distribution

A Note on the Dirichlet Distribution

In this post, I explore some properties of the Dirichlet distribution and illustrate the behavior of the symmetric Dirichlet distribution as alpha, the concentration parameter, varies. Understanding this behavior may be helpful in constructing an informative prior for the multinomial distribution.

Simplex plot of per-recurrence posterior probabilities

July 2025 Top 40 New CRAN Packages

Top 40

The CRAN new package Top 40 - Here are my picks for the best new packages to land on CRAN in July, organized in thirteen categories: Causal Inference, Computational Methods, Data, Ecology, Epidemiology, Machine Learning, Mathematics, Medical Statistics, Pharma, Statistics, Time Series, Utilities, and Visualization.

ANES 2024 is Out! How to Analyze the Data with R

Explore the newly released ANES 2024 survey data in R with {survey} and {srvyr}.

Isabella Velásquez

The polarzonoid

June 2025 Top 40 New CRAN Packages

Top 40

An attempt to capture the depth and breadth of what’s new on CRAN: here are my Top 40 picks in twenty-one categories: AI, Chess, Computational Methods, Data, Decision Analysis, Ecology, Epidemiology, Finance, Genomics, Lingusitics, Machine Learning, Mathematics, Medical Statistics, Music Theory, Networks, Programming, Statistics, Time Series, Utilities, and Visualization.

Screen showing cop9poy session

Health Technology notes: Copilot tips and guidance

In this post, we walk the reader through the fundamental driver of successfully using AI agents – prompting. Prompting is the method of instructing an LLM to perform a task by carefully designing an input text.

Vidisha Vachharajani

Plot showing distribution of diagnosis upon admission

Tidyverse with GitHub Copilot for Healthcare Analytics – Part 2

In this second installment, we analyze a complex dataset of diabetes patient encounters with 100,000+ rows and over 50 columns and dive deeper to evaluate the effectiveness of healthcare delivery and the impact of patient-level variables on downstream outcomes.

Vidisha Vachharajani

GENCODE Mouse M37

May 2025 Top 40 New CRAN Packages

Top 40

An attempt to capture the depth and breadth of what’s new on CRAN. - One Hundred seventy-six new packages made it to CRAN in May. Here are my Top 40 picks in eighteen categories: Climate Science, Computational Methods, Data, Decision Analysis, Ecology, Epidemiology, Finance, Genomics, Machine Learning, Medicine, Networks, Phylogenetics, Programming, Statistics, Time Series, Topological Data Analysis, Utilities, and Visualization.

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

This post shows how to use the elementary theory of discrete time Markov Chains to construct a multi-state model of patients progressing through various health states in a randomized clinical trial comparing different treatments for asthma management under the assumption that all patients in each of the two arms of the trial will eventually experience treatment failure. The post shows how to calculate transition probabilities using a simple multinomial Bayesian model and exploit the theory of absorbing Markov chains to calculate fundamental health metrics.

Healthcare Infographic

Tidyverse with GitHub Copilot for Healthcare Analytics – Part 1

In this post, the first in a series of two focused on healthcare applications, I will introduce a complex healthcare data set and outline the problems I propose to solve using tidyverse and GitHub Copilot to facilitate nuanced argument tuning of tidyverse functions and accelerate the data analysis process.

Vidisha Vachharajani

Coastline reconstruction

April 2025 Top 40 New CRAN Packages

Top 40

An attempt to capture the depth and breadth of what’s new on CRAN. Here are my Top 40 picks in twenty-two categories: Archaeology, Artificial Intelligence, Biology, Chemistry, Climate Science, Data, Ecology, Epidemiology, Genomics, Geoscience, Health Technology Assessment, Linguistics, Machine Learning,Mathematics, Medicine, Networks, Psychology, Statistics, Time Series, Utilities, and Visualization.

Book cover of Evidence Synthesis for Decision Making in Healthcare

Cost-Effectiveness Analysis

In a previous post, we presented an rjags version of a Bayesian model from the textbook: Evidence Synthesis for Decision Making in Healthcare by Welton et al. (2012). This post continues the work of porting key models from the text to JAGS.

Robert Horton and Joseph Rickert

VS code screen caoture

A Data Scientist’s View of Running R in Visual Studio Code

VS Code is Microsoft’s open-source software development environment that can be customized for any language. It is arguably the general purpose GUI programming tool of choice when working across multiple computer languages. As a data scientist, its R - Python integration deserves careful consideration.

John Mark Agosta

Conditional distribution of age across groups

March 2025 Top 40 New CRAN Packages

Top 40

An attempt to capture the depth and breadth of what’s new on CRAN: here are my Top 40 picks in sixteen categories: Agriculture, Archaeology, Biology, Climate Modeling, Computational Methods, Data, Ecology, Epidemiology, Genomics, Machine Learning, Medicine, Risk Forecasting, Statistics, Time Series, Utilities, and Visualization.

Down a Rabbit Hole with ARIMA Models

This post describes a chance encounter with a time series data set for which the forecast and fable packages found different ARIMA models that don’t look much alike, but produce surprisingly close forecasts. It is a reminder of the inherent identifiability problem of ARIMA models and a record of a couple of afternoons spent down this rabbit hole.

Gif of gander session

February 2025 Top 40 New CRAN Packages

Top 40

An attempt to capture the depth and breadth of what’s new on CRAN: Here are my Top 40 picks in fifteen categories: Artificial Intelligence, Computational Methods, Ecology, Genomics, Health Sciences, Mathematics, Machine Learning, Medicine, Music, Pharma, Statistics, Time Series, Utilities, Visualization, and Weather.

How Many Ways to Color This Grid: Teaching Combinatorics Using R

Puzzle Corner

A simplified version of the four color theorem: suppose you have a 2x2 grid of squares, and you need to paint each square one of four colors: red, blue, green, or yellow. The restriction is that no two adjacent squares (sharing a side) can have the same color. How many valid ways can you color the grid?

Vidisha Vachharajani

Original-Odhner-Arithmos-Typ-5 calculator, circa 1912-1928. Source: Wikipedia

Digital Difficulties

Puzzle Corner

Here’s another puzzle, from Henry Dudeney’s Perplexities column in Strand Magazine, January 1924.

Evidence Synthesis for Decision Making in Healthcare

This post presents a JAGS version of a WinBUGS model presented in the classic textbook Evidence Synthesis for Decision Making in Healthcare by Nicky J. Welton, Alexander J. Sutton, Nicola J. Cooper, Keith R. Abrams, and A.E. Ades.

Joseph Rickert and Robert Horton

January 2025 Top 40 New CRAN Packages

Top 40

An attempt to capture the depth and breadth of what’s new on CRAN.

A First Look at TimeGPT using nixtlar

TimeGPT is a pre-trained, multi-layer, encoder/decoder transformer model with self-attention mechanisms designed specifically for time series forecasting. This post, a revision of the of the post first published on 2025-02-12, corrects an error that deleteriously affected the ARIMA and exponential smoothing forecasts which are contrasted with the TimeGPT forecast.

Plot showing unbalanced treatment group sizes

Simpson’s Paradox in a Logistic Regression

In this post, I show an example of Simpson’s paradox in a logistic regression model of synthetic clinical trial data.

December 2024 Top 40 New CRAN Packages

Top 40

An attempt to capture the depth and breadth of what’s new on CRAN.

Old-School Golden scale in balance with a hand putting a coin on it

Dyson’s Algorithm: The General Case

Puzzle Corner

In a previous post, I described The Twelve Coins Problem, a notoriously hard problem that comes in many flavors and was popular on both sides of the Atlantic during World War II. In this post, I show how to build on Freeman Dyson’s solution to solve a generalization of the problem.

Some R Conferences for 2025

R Community

We share a list of upcoming conferences that either focus on the R programming language or showcase its use in the field.

Isabella Velásquez

Bayesian Meta-Analysis with brms

In our previous post, Examining Meta Analysis, we contrasted a frequentist version of a meta analysis conducted with R’s meta package with a Bayesian meta analysis done mostly in stan using therstan package as a front end. In this post, we repeat the analysis using the brms package, which also depends on stan but allows the user to formulate complex Bayesian models without writing any stan code.

Joseph Rickert, John Mount

Old-School Golden scale in balance with a hand putting a coin on it

Dyson’s Algorithm for the Twelve Coins Problem

Puzzle Corner

The Twelve Coins Problem, a notoriously hard problem that comes in many flavors, was popular on both sides of the Atlantic during World War II; it was even suggested that it should be dropped over Germany in an attempt to sabotage their war effort.

The Perplexed Banker Problem

The Perplexed Banker

Puzzle Corner

A man went into a bank with 1,000 silver dollars and 10 bags. He said, ‘Place this money, please, in the bags in such a way that if I call and ask for a certain number of dollars you can hand me over one or more bags, giving me the exact amount called for without opening any of the bags.’

Animation of Wolfram rule 193

November 2024 Top 40 New CRAN Packages

Top 40

An attempt to capture the depth and breadth of what’s new on CRAN.

A balance scale and four weights. Source: Internet Archive

Writing Signed Trinary: or, Back To the Four Weights Problem

Puzzle Corner

Let’s run some modular arithmetic using R.

A balance scale and four weights. Source: Internet Archive

Bachet’s Four Weights Problem

Puzzle Corner

Learn how to solve Bachet’s Four Weights Problem using R, with code and explanations to measure weights from 1 to 40 efficiently.

Examining Meta-Analysis

In this post we would like to review the idea of meta-analysis and compare a traditional, frequentist style, random effects meta-analysis to Bayesian methods.

John Mount, Joseph Rickert

October 2024: Top 40 New CRAN Packages

Top 40

One hundred eighty-one new packages made CRAN’s final cut in October.

Rulers of different fonts and shapes lined up

100 Bushels of Corn, Revisited

Puzzle Corner

We find more solutions to the 100 Bushels of Corn puzzle using the numbers R package.

John Mount, Nina Zumel

The Mathematicians, de Chirico (1917) source: WikiArt

100 Bushels of Corn

Puzzle Corner

100 bushes of corn are distributed to 100 people such that every man receives 3 bushels, every woman 2 bushels, and every child 1/2 a bushel. How many men, women, and children are there? (Solved with R).

Manifold Learning

Manifold Learning reduces data dimensions to discover patterns for analysis and visualization. This post provides an overview of Manifold Learning and its algorithms, the tsne package, and other R tools and resources.

R Work Opportunities

R Community

Explore new job opportunities that highlight R skills.

Isabella Velásquez

September 2024: Top 40 New CRAN Packages

Top 40

Two hundred thirty new packages made it to CRAN in September. Here are my “Top 40” selections in 17 categories.

August 2024: Top 40 New CRAN Packages

Top 40

“Top 40” is back, broadcasting on the new R Works blog.

Welcome to R Works!

R Community

We hope that the R Works blog informs and inspires R users everywhere.