https://github.com/sempwn/bennu

Bayesian Estimation of Naloxone Numbers Underreporting
https://github.com/sempwn/bennu

bayesian-data-analysis naloxone r r-package rstats stan

Last synced: 2 months ago
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Bayesian Estimation of Naloxone Numbers Underreporting

• Host: GitHub
• URL: https://github.com/sempwn/bennu
• Owner: sempwn
• License: other
• Created: 2022-12-13T00:48:07.000Z (about 2 years ago)
• Default Branch: main
• Last Pushed: 2024-10-10T17:16:40.000Z (3 months ago)
• Last Synced: 2024-10-12T01:22:48.720Z (3 months ago)
• Topics: bayesian-data-analysis, naloxone, r, r-package, rstats, stan
• Language: R
• Homepage: https://sempwn.github.io/bennu/
• Size: 25.2 MB
• Stars: 1
• Watchers: 3
• Forks: 0
• Open Issues: 11
• Metadata Files:
  • Readme: README.Rmd
  • Changelog: NEWS.md
  • License: LICENSE

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README

        
---

output: github_document

---

```{r, include = FALSE}

knitr::opts_chunk$set(

  collapse = TRUE,

  comment = "#>",

  fig.path = "man/figures/README-",

  out.width = "100%"

)

```

# bennu 

**B**ayesian **E**stimation of **N**aloxone **N**umbers **U**nderreporting (**BENNU**)

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

  

  [![R-CMD-check](https://github.com/sempwn/bennu/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/sempwn/bennu/actions/workflows/R-CMD-check.yaml)

   [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)

     [![Codecov test coverage](https://codecov.io/gh/sempwn/bennu/branch/main/graph/badge.svg)](https://app.codecov.io/gh/sempwn/bennu?branch=main)

   ![GitHub](https://img.shields.io/github/license/sempwn/bennu?style=plastic)

  

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](https://CRAN.R-project.org) with:

``` r

install.packages("bennu")

```

And the development version from [GitHub](https://github.com/) with:

``` r

# install.packages("devtools")

devtools::install_github("sempwn/bennu")

```

## Example

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

```{r example, warning=FALSE}

library(bennu)

library(rstan)

library(bayesplot)

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 data frame

```{r, warning=FALSE}

kit_summary_table(fit, data = d)

```

## Getting help

If you encounter a clear bug, please file an issue with a minimal reproducible example on [GitHub](https://github.com/sempwn/bennu/issues).