Software
Featured!

litr is an R package for writing R packages via literate programming. You define a complete R package in a single R markdown document. This enables a workflow for writing R packages that is probably very different from what you are used to.
[website]
[github]


The simulator is an R package for making the code one writes for simulation studies more organized and structured, which streamlines the process, saving time and making one's code easier to understand and easier to share.
[website]
[paper]
[github]
[CRAN]

Covariance estimation

ggb is an R package for graphguided banding of the covariance matrix. This generalizes the notion of a banded covariance matrix to situations where the variables lie on a known seed graph.
[paper]
[github]


varband is an R package for learning local dependence in ordered data (such as data collected over time or along a genome). It estimates a lower triangular matrix with a variable bandwith, leading to an easily interpretable view of the extent of the local dependence in the data.
[paper]
[github]
[CRAN]
[vignette]


hierband is an R package for convex banding of the covariance matrix.
[paper]
[CRAN]
[vignette]


spcov is an R package for sparse estimation of the covariance matrix.
[paper]
[CRAN]

Prototype selection

protoclust is an R package for prototype clustering (i.e., minimax linkage hierarchical clustering). It creates dendrograms that have a prototypical example associated with each interior node.
[paper]
[CRAN]


protoclass is an R package for interpretable classification with prototypes.
[pdf]
[CRAN]

Interaction modeling

hiertest is an R package for convex hierarchical testing of interactions.
[paper]
[CRAN]


hiernet is an R package for a lasso for hierarchical interactions.
[paper]
[CRAN]

Highdimensional time series

BigVAR is an R package for highdimensional time series. It implements multiple convexregularized approaches to estimating vector autoregressive models. This includes methods for adaptively learning the lag order and for incorporating exogenous time series.
[paper on HVAR]
[paper on VARXL]
[CRAN]
[github]

Inferential tools

outference is an R package for performing valid inference that accounts for outlier removal.
[paper]
[github]

Optimizationfocused software

hsm is an R package for hierarchical sparse modeling (HSM). This includes a novel closedform solution to the proximal operator of the latent overlapping group lasso in the case of a directed path graph HSM structure and an efficient algorithm, which we call “pathbased block coordinate descent” for more general HSM structures.
[paper]
[CRAN]


TREX is Matlab code for solving the TREX, a nonconvex optimization problem that arises in highdimensional statistics. Remarkably, this code globally optimizes a nonconvex optimization problem in polynomial time.
[paper]
[github]


CVXfromR is an R package that lets you call CVX (from Matlab) within R. CVX is a tool by
Michael Grant and Stephen Boyd that makes it easy to solve general convex
problems, and the syntax to input such problems is simple and
straightforward.
[website]

