probabilityDistributions

The goal of probabilityDistributions is to provide a library of useful probability distributions for both R and Stan.

Installation

You can install the development version of probabilityDistributions from GitHub with:

# install.packages("devtools")
devtools::install_github("PRIMER-e/probabilityDistributions")

Example

This is a basic example which shows you how to calculate a Zero-Inflated Poisson (ZIP) probability mass using both R and Stan:

library(probabilityDistributions)
library(rstan)
#> Loading required package: StanHeaders
#> 
#> rstan version 2.26.13 (Stan version 2.26.1)
#> For execution on a local, multicore CPU with excess RAM we recommend calling
#> options(mc.cores = parallel::detectCores()).
#> To avoid recompilation of unchanged Stan programs, we recommend calling
#> rstan_options(auto_write = TRUE)
#> For within-chain threading using `reduce_sum()` or `map_rect()` Stan functions,
#> change `threads_per_chain` option:
#> rstan_options(threads_per_chain = 1)
#> Do not specify '-march=native' in 'LOCAL_CPPFLAGS' or a Makevars file

stan_model_code <- paste0("functions { ", 
                          zi_poisson_lpmf_stan[["source_code"]], 
                          " }",
                          sep = "\n")

model_listing <- stanc(model_code = stan_model_code)

stan_function_names <- expose_stan_functions(model_listing)

print(stan_function_names)
#> [1] "zi_poisson_lpmf"

zi_poisson_lpmf(5, 7.5, 0.2)
#> [1] -2.43612

dzip(5, 7.5, 0.2, log = TRUE)
#> [1] -2.43612

Development

After making changes run the following command before committing to rebuild the package readme, which is also the home page.

devtools::build_readme()