Samuel Berchuck is a Postdoctoral Associate in Duke University’s Department of Statistical Science and Forge-Duke’s Center for Actionable Health Data Science. Joshua L. Warren is an Assistant Professor of Biostatistics at Yale University. Introduction Glaucoma is a leading cause of blindness worldwide, with a prevalence of 4% in the ...

One hundred eighty-five new packages made it to CRAN in October. Here are my picks for the “Top 40” in eight categories: Computational Methods, Data, Machine Learning, Medicine, Science, Statistics, Utilities, and Visualization. Computational Methods compboost v0.1.0: Provides a C++ implementation of component-wise boosting written to obtain high run-time performance and ...

Today, we will return to the Fama French (FF) model of asset returns and use it as a proxy for fitting and evaluating multiple linear models. In a previous post, we reviewed how to run the FF three-factor model on the returns of a portfolio. That is, we ran one ...

A few years ago, when I first became aware of Topological Data Analysis (TDA), I was really excited by the possibility that the elegant theorems of Algebraic Topology could provide some new insights into the practical problems of data analysis. But time has passed, and the sober assessment of Larry ...

Moving predictive machine learning algorithms into large-scale production environments can present many challenges. For example, problems arise when attempting to calculate prediction probabilities (“scores”) for many thousands of subjects using many thousands of features located on remote databases. xgboost (docs), a popular algorithm for classification and regression, and the model ...

In my training as a consultant, I learned that long hours of analysis were typically followed by equally long hours of preparing for presentations. I had to turn my complex analyses into recommendations, and my success as a consultant depended on my ability to influence decision makers. I used a ...

I’m thrilled to announce the release of my new book Reproducible Finance with R: Code Flows and Shiny Apps for Portfolio Analysis, which originated as a series of R Views posts in this space. The first post was written way back in November of 2016 - thanks to all the ...

It is a relatively rare event, and cause for celebration, when CRAN gets a new Task View. This week the r-miss-tastic team: Julie Josse, Nicholas Tierney and Nathalie Vialaneix launched the Missing Data Task View. Even though I did some research on R packages for a post on missing values ...

Searching for R packages is a vexing problem for both new and experienced R users. With over 13,000 packages already on CRAN, and new packages arriving at a rate of almost 200 per month, it is impossible to keep up. Package names can be almost anything, and they are rarely informative, so ...

We knew we were on to something important early on in the process of organizing R / Medicine 2018. Even during our initial attempts to articulate the differences between this conference and R / Pharma 2018, it became clear that the focus on the use of R and statistics in clinical settings was going ...

September was another relatively slow month for new package activity on CRAN: “only” 126 new packages by my count. My Top 40 list is heavy on what I characterize as “utilities”: packages that either extend R in some fashion or make it easier to do things in R. This month, the packages ...

It’s no secret that there are few industries more competitive than the pharmaceutical industry. Big money placed on long-shot bets for block-buster drugs where being first makes all the difference means a constant struggle to gain a competitive edge. So, you might find it surprising that the inaugural R / ...

Package developers relaxed a bit in August.; only 160 new packages went to CRAN that month. Here are my “Top 40” picks organized into seven categories: Data, Machine Learning, Science, Statistics, Time Series, Utilities, and Visualization. Data nsapi v0.1.1: Provides an interface to the Nederlandse Spoorwegen (Dutch Railways) API, allowing users to ...

I wish this post existed when I was struggling to add interactive plots to my Shiny app. I was mainly focused on recreating functionality found in other “dashboarding” applications. When looking for options, I found that htmlwidgets were the closest to what companies usually expect. However, while they are great ...

Today, we will look at the GDP data that is released every quarter or so by the Bureau of Economic Analysis (BEA), and get familiar with the BEA API (see the documentation here). For a primer on GDP in general, BEA publishes this guide. To access the BEA API, we ...

Why is this about trucks? Last month, at the R/Pharma conference that took place on the Harvard Campus, I presented bioWARP, a large Shiny application containing more than 500,000 lines of code. Although several other Shiny apps were presented at the conference, I noticed that none of them came close ...

In the previous post, we introduced plumber as a way to expose R processes and programs to external systems via REST API endpoints. In this post, we’ll go further by building out an API that powers a Slack slash command, all from within R using plumber. A subsequent post ...

July was a big month for submitting new packages to CRAN; by my count, 251 unique and truly new packages were accepted. In addition to quantity, I was pleased to see quality and variety. For instance, tropicalSparse, a package for exploring some abstract mathematics, and eChem, a package for teaching analytical ...

It all starts with sandboxes. Development sandboxes are dedicated safe spaces for experimentation and creativity. A sandbox is a place where you can go to test and break things, without the ramifications of breaking the real, important things. If you’re an analytic administrator who doesn’t have access or ...