software

casebase

Journal Article: casebase: An Alternative Framework for Survival Analysis and Comparison of Event Rates

A method for fitting fully parametric hazard models and covariate-conditional survival curves using the familiar interface of the glm function. Our implementation includes extensions to other models such as penalized regression for variable selection and competing risk analysis. In addition, we provide functions for exploratory data analysis and visualizing the estimated quantities such as the hazard function, survival curve, and their standard errors. The ultimate goal of our package is to make fitting flexible hazards accessible to end users who favor reporting absolute risks and survival curves over hazard ratios.

ggmix

Journal Article: Simultaneous SNP selection and adjustment for population structure in high dimensional prediction models

A General Framework for Variable Selection in Linear Mixed Models with Applications to Genetic Studies with Structured Populations. This is a penalized regression method that selects and estimates predictors in a single random effects model.

sail

Journal Article: A sparse additive model for high-dimensional interactions with an exposure variable

Sparse additive interaction learning. This software package implements the sail method described in the accompanying paper. This is a penalized regression method that selects and estimates both linear and non-linear interactions with a single exposure variable.

eclust

Journal Article: An analytic approach for interpretable predictive models in high-dimensional data in the presence of interactions with exposures

A Statistical Software Tool for the Analysis of High-Dimensional Interactions. This software is written in the open source software environment R. Its main functionality is to cluster a high-dimensional dataset (e.g., genomics, brain imaging) by leveraging the environmental exposures.

manhattanly

Watch the Plotcon talk in New York City about manhattanly

Create interactive Q-Q, manhattan, and volcano plots that are usable from the R console, in the 'RStudio' viewer pane, in 'R Markdown' documents, and in 'Shiny' apps. Hover the mouse pointer over a point to show details or drag a rectangle to zoom.

gglasso

A unified algorithm, blockwise-majorization-descent (BMD), for efficiently computing the solution paths of the group-lasso penalized least squares, logistic regression, Huberized SVM, and squared SVM.