ngstan: stan models for sequencing data

ngstan provides Stan implementations of statistical models for the analysis of Next Generation Sequencing (NGS) data. ngstan uses the cmdstanr and instantiate packages to provide pre-compiled Stan models that can be fit using a variety of sampling algorithms available with cmdstanr (e.g. ADVI and Pathfinder), in addition to the NUTS sampler.

Documentation

Installing ngstan

The ngstan package depends on the R package CmdStanR and the command line tool CmdStan, so it is important to follow these steps in order:

1. Install the R package CmdStanR. CmdStanR is not on CRAN, so the recommended way to install it is install.packages("cmdstanr", repos = c("https://mc-stan.org/r-packages/", getOption("repos"))).
2. Optional: set environment variables CMDSTAN_INSTALL and/or CMDSTAN to manage the CmdStan installation.
3. Install ngstan using the R command below.

Type	Source	Command
Development	GitHub	remotes::install_github("dcannonwalker/ngstan")