software

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


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/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, within the framework of Targeted Learning.
View the package documentation and related information here.
Joint work with David Benkeser.
[GitHub] | [CRAN]
Now available!

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/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/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/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

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.
[GitHub]

R/shifttx

An R package for assessing the effects of continuous-valued interventions with honest statistical inference by way of a causal parameter defined with the formalism of stochastic treatment regimes and estimated using Targeted Learning.
Joint work with David Benkeser.

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, within the framework of Targeted Learning.
Joint work with Weixin Cai and Alan Hubbard.
[GitHub]


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.