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bennu

Bayesian Estimation of Naloxone Numbers Underreporting

https://github.com/sempwn/bennu

Science Score: 13.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
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    DOI references
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    Academic publication links
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    Committers with academic emails
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    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (17.5%) to scientific vocabulary

Keywords

bayesian-data-analysis naloxone r r-package rstats stan
Last synced: 6 months ago · JSON representation

Repository

Bayesian Estimation of Naloxone Numbers Underreporting

Basic Info
Statistics
  • Stars: 2
  • Watchers: 2
  • Forks: 0
  • Open Issues: 10
  • Releases: 1
Topics
bayesian-data-analysis naloxone r r-package rstats stan
Created about 3 years ago · Last pushed 7 months ago
Metadata Files
Readme Changelog License

README.Rmd 

---
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).

Owner

  • Name: Mike Irvine
  • Login: sempwn
  • Kind: user
  • Location: Vancouver, Canada

Math Modelling & Data science in epidemiology and public health.

GitHub Events

Total
  • Issues event: 1
  • Delete event: 1
  • Push event: 2
  • Pull request event: 1
  • Create event: 1
Last Year
  • Issues event: 1
  • Delete event: 1
  • Push event: 2
  • Pull request event: 1
  • Create event: 1

Committers

Last synced: over 1 year ago

All Time
  • Total Commits: 86
  • Total Committers: 4
  • Avg Commits per committer: 21.5
  • Development Distribution Score (DDS): 0.058
Past Year
  • Commits: 21
  • Committers: 1
  • Avg Commits per committer: 21.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
sempwn m****e@b****a 81
Andrew Johnson a****n@a****m 2
sempwn m****i@g****m 2
Mike Irvine m****i@g****m 1
Committer Domains (Top 20 + Academic)
arjohnsonau.com: 1 bccdc.ca: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 20
  • Total pull requests: 21
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 3 days
  • Total issue authors: 2
  • Total pull request authors: 2
  • Average comments per issue: 0.2
  • Average comments per pull request: 0.14
  • Merged pull requests: 20
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • sempwn (18)
  • gewliz (3)
Pull Request Authors
  • sempwn (25)
  • andrjohns (1)
Top Labels
Issue Labels
enhancement (4) High priority (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 271 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 3
  • Total maintainers: 1
cran.r-project.org: bennu

Bayesian Estimation of Naloxone Kit Number Under-Reporting

  • Versions: 3
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 271 Last month
Rankings
Forks count: 28.7%
Dependent packages count: 29.1%
Stargazers count: 31.7%
Dependent repos count: 34.9%
Average: 42.8%
Downloads: 89.6%
Maintainers (1)
mike.irvine@bccdc.ca
Last synced: 6 months ago

Dependencies

.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action v4.4.1 composite
  • actions/checkout v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/test-coverage.yaml actions
  • actions/checkout v3 composite
  • actions/upload-artifact v3 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
DESCRIPTION cran
  • R >= 3.4.0 depends
  • Rcpp >= 0.12.0 imports
  • RcppParallel >= 5.0.1 imports
  • methods * imports
  • rstan >= 2.18.1 imports
  • rstantools >= 2.1.1 imports
  • tidyr * imports
  • covr * suggests
  • testthat >= 3.0.0 suggests