maxdrohde / exnexstan Goto Github PK

The exnexstan package provides a user-friendly interface to fitting EXNEX models in R without requiring the user to directly interface with a probabilistic programming language like BUGS, JAGS, or Stan.

Stan (https://mc-stan.org/) is used to fit the models using modern Hamiltonian Markov Chain Monte Carlo (HMC) sampling.

The exnexstan package is not on CRAN, but can be installed from GitHub using the install_github() function from the devtools package.

# Skip if devtools is already installed
install.packages("devtools")

devtools::install_github(repo = "https://github.com/maxdrohde/exnexstan")

To use exnexstan, the cmdstanr R package and the cmdstan software must be installed, working and up-to-date before exnexstan is installed.

• cmdstanr can be installed via GitHub (see https://mc-stan.org/cmdstanr/articles/cmdstanr.html).
• cmdstan can be installed from within cmdstanr (see https://mc-stan.org/cmdstanr/articles/cmdstanr.html#installing-cmdstan-1).

If you already have cmdstan installed, run

cmdstanr::install_cmdstan(overwrite=TRUE)

within R to make sure it is up-to-date. There can be errors when installing exnexstan if your cmdstan installation is outdated.

We provide two vignettes that demonstrate how to fit EXNEX models for binary data and count data with exnexstan.

• Binary data: https://maxdrohde.github.io/exnexstan/vignettes/exnex_binary_vignette.html
• Count data: https://maxdrohde.github.io/exnexstan/vignettes/exnex_poisson_vignette.html

For additional details on the functions, see the package documentation within R, or at the pkgdown site: https://maxdrohde.github.io/exnexstan/.

For the mathematical details of EXNEX and more in-depth examples, see the original paper by Neuenschwander et al. (2015).

To view the Stan code used to implement these models, you can view them here: https://github.com/maxdrohde/exnexstan/tree/master/inst.

Unless otherwise stated, these programs are for research purposes only. We provide absolutely no warranty of any kind, either expressed or implied, including but not limited to the implied warranties of merchantability and fitness for a particular purpose. The entire risk as to the quality and performance of these programs is with the user. Should any of these programs prove defective, the user assumes the cost of all necessary servicing, repair, or correction. In no event shall the creators of the software and this website be liable for damages, including any lost profits or other special, incidental or consequential damages arising out of the use of or inability to use these programs (including but not limited to loss of data or its analysis being rendered inaccurate or losses sustained by third parties).