Software

DyAEWMA

DyAEWMA (Adaptive EWMA control chart with a Dynamic Sampling Scheme) is an R package for estimating the average time to signal (ATS) of an adaptive EWMA chart with a dynamic sampling scheme or the average run length (ARL) of the adaptive EWMA chart.

The R packgage DyAEWMA is available here and a vignette that explains how to use the package can be found here.

metagenomic_data_analysis

A suite of programs for the bioinformatics pre-processing and downstream analysis of raw sequence metagenomics data. The programs are available here and the article describing the implementation of the programs and methods can be found here.

pseudoReg-ICS

R program for estimating the state occupation probability for cluster-correlated data from a multistate model. The program allows for adjusting for informative cluster size. A vignette that describes the implementation of the program, along with the application of pseudo-value regression for estimating the effects of available covariates on the SOP is available here.

mspack2

R package for estimating several temporal functions (e.g. state occupation probabilities) for current-status data from of a general multistate model. The code estimates the SOP for the setting where the current-status data is either uncorrelated or cluster-correlated. The vignette for this package is avaiable here.

GFBioNet

R package to learn a network for biological traits via Gaussian graphical modeling and maps genomic factors regulating specific edges using node-wise regression. It reports trait–trait–factor triplets with robust false-discovery control, even under strong predictor correlation.