• ggmix

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

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

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

• casebase

Implements the case-base sampling approach of Hanley and Miettinen (2009), Saarela and Arjas (2015), and Saarela (2015), for fitting flexible hazard regression models to survival data with single event type or multiple competing causes via logistic and multinomial regression. From the fitted hazard function, cumulative incidence, risk functions of time, treatment and profile can be derived. This approach accommodates any log-linear hazard function of prognostic time, treatment, and covariates, and readily allows for non-proportionality. We also provide a plot method for visualizing incidence density via population time plots. This is joint work with Maxime Turgeon, Olli Saarela and James Hanley

• 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.

• acm4r

Fragment lengths or molecular weights from pairs of lanes are compared, and a number of matching bands are calculated using the Align-and-Count Method.