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bennu

Bayesian Estimation of Naloxone Numbers Underreporting (BENNU)

The package name comes from the Welsh word for “to finish” (pronounced benn-y)

R-CMD-check Lifecycle: experimental Codecov test coverage GitHub

An R package 📦 for generating estimates of total naloxone kit numbers distributed and used from naloxone kit orders data.

Installation

You can install the released version of bennu from CRAN with:

install.packages("bennu")

And the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("sempwn/bennu")

Example

This example runs output for test data generated by the package:

library(bennu)
library(rstan)
#> Loading required package: StanHeaders
#> 
#> rstan version 2.26.22 (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
library(bayesplot)
#> This is bayesplot version 1.10.0
#> - Online documentation and vignettes at mc-stan.org/bayesplot
#> - bayesplot theme set to bayesplot::theme_default()
#>    * Does _not_ affect other ggplot2 plots
#>    * See ?bayesplot_theme_set for details on theme setting

rstan_options(auto_write = TRUE)
options(mc.cores = parallel::detectCores(logical = FALSE))

## basic example code
d <- generate_model_data()
# note iter should be at least 2000 to generate a reasonable posterior sample
fit <- est_naloxone(d,iter=500)
mcmc_pairs(fit, pars = c("sigma","mu0","zeta"),
           off_diag_args = list(size = 1, alpha = 0.5))

An overall summary of the model output can also be provided as a datframe

kit_summary_table(fit, data = d)
#> # A tibble: 1 × 6
#>   Probability of kit use if dist…¹ Estimated as distrib…² Proportion kits dist…³
#>   <glue>                           <glue>                 <glue>                
#> 1 65.34% (95% CrI: 18.31% - 96.36… 24,909.00 (95% CrI: 2… 58.72% (95% CrI: 58.1…
#> # ℹ abbreviated names: ¹​`Probability of kit use if distributed`,
#> #   ²​`Estimated as distributed`,
#> #   ³​`Proportion kits distributed that are reported`
#> # ℹ 3 more variables: `Estimated kits used` <glue>,
#> #   `Proportion kits used that are reported` <glue>,
#> #   `Proportion kits ordered that are used` <glue>

Getting help

If you encounter a clear bug, please file an issue with a minimal reproducible example on GitHub.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.