software

New: The tlverse is a centralized effort to overhaul the Targeted Learning software ecosystem in R. Check it out at tlverse.org!

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


R/txshift

An R package for efficient estimation of and nonparametric inference on the effects of stochastic intervention, including in settings with multi-stage sampling designs. This provides a flexible way to perform nonparametric variable importance analysis on continuous quantities using the Targeted Learning framework.
View the package documentation and related information here.
Joint work with David Benkeser.
[GitHub]

R/sl3

An R package providing a modern re-implementation of the Super Learner algorithm for ensemble modeling and stacked regression based on machine learning pipelines.
View the package documentation and related information here.
Joint work with Jeremy Coyle, Ivana Malenica, and Oleg Sofrygin.
[GitHub]
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/hal9001

An R package providing a fast and efficient implementation of the Highly Adaptive Lasso (HAL), a nonparametric regression estimator with optimality guarantees.
Joint work with Jeremy Coyle.
[GitHub]
Now available!

R/survtmle

An R package providing facilities for estimation and inference in right-censored survival analysis settings with and without competing risks, including extensions for data-adaptive target parameters, using Targeted Learning.
View the package documentation and related information here.
Joint work with David Benkeser.
[GitHub] | [CRAN]
Now available!

R/methyvim

An R package implementing a framework for using Targeted Learning to assess evidence for differential methylation across the genome by estimating variable importance measures at the level of CpG sites and related functional units.
View the package documentation and related information here.
Joint work with Mark van der Laan and Alan Hubbard.
[GitHub] | [Bioconductor]
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 for variance stabilization in finite samples.
View the package documentation and related information here.
Joint work with Alan Hubbard.
[GitHub] | [Bioconductor] | [Publication (JOSS)]
Now available!

R/adaptest

An R package for data-adaptive hypothesis testing in high-dimensional settings. The approach allows for effects to be discovered (“mined”) from data without loss of valid statistical inference using the framework of Targeted Learning.
Joint work with Weixin Cai and Alan Hubbard.
[GitHub] | [Bioconductor]

R/nima

An R package housing Nima’s personal R toolbox, largely containing miscellaneous convenience functions written to make statistical computing for research easier.
View the package documentation and related information here.
[GitHub] | [CRAN]
Now available!


Under Development

Nothing for now. (Or, what’s brewing is still secret.)


Miscellany

(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.