software

I enjoy contributing to open-source projects and develop most of my work publicly – see my GitHub Resume.


R/methyvim

An R package implementing a framework for using targeted learning to assess differential methylation across the genome by estimating variable importance measures at the level of CpG sites and related functional units for use with data generated by DNA methylation assays.
Joint work with Mark van der Laan and Alan Hubbard.
under development.


R/hal9001

An R package providing a fast and efficient implementation of the Highly Adaptive LASSO (HAL), a nonparametric regression estimator with optimal properties for finite sample inference in problem settings employing Targeted Learning.
Joint work with Jeremy Coyle and David Benkeser.
under development.


R/sl3

An R package providing a modern and forward-looking re-implementation of the Super Learner algorithm for ensemble modeling and stacked regression.
Joint work with Jeremy Coyle, Ivana Malenica, and Oleg Sofrygin.
under development.


R/survtmle

An R package providing facilities for survival analysis in settings with competing risks, including methods for data-adaptive estimation and inference, within the framework of Targeted Learning.
View the package documentation and related information here.
Joint work with David Benkeser.
GitHub | CRAN
Now available!


R/origami

An R package providing a general framework for the application of various cross-validation schemes to arbitrary functions, facilitating the extension of cross-validation procedures to numerous applications.
View the package documentation and related information here.
Joint work with Jeremy Coyle.
GitHub | CRAN | Publication (JOSS)
Now available!


R/biotmle

An R package implementing a set of techniques for discovering biomarkers from biological sequencing data, using a combination of Targeted Learning and a generalization of moderated statistics.
View the package documentation and related information here.
Joint work with Alan Hubbard.
GitHub | Bioconductor | Publication (JOSS)
Now available!


R/nima

An R package housing my personal R toolbox, largely containing miscellaneous functions I have written over the course of statistical research and programming for scientific computing.
View the package documentation and related information here.
GitHub | CRAN
Now available!


(re)Fresh/macOS

Collection of scripts designed to make fresh installs less painful on macOS. This consists in a configuration centered around a pleasant experience for scientific programming and data analysis, plus standard convenience utilities.
GitHub


(re)Fresh/Ubuntu

Collection of scripts designed to make fresh installs less painful on Ubuntu. This includes a handful of configurations for scientific programming and data analysis, even including one for ChromeOS.
GitHub


(get) Some Style

Thematic collections of scripts to set configurations to my preferences, with setup on new machines in mind.

  • my.files - a collection of my configuration files for my most-used tools. Use the same setup everywhere!

  • vimForLife - my customizations for using the awesome Neovim and truly ubiquitous Vim text editors.

  • myPkgLib - a standardized library of packages for some of my favorite tools: R, Python, Julia, and the Atom editor.