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bayesnec

Bayesian No-Effect-Concentration estimation in R

https://github.com/open-aims/bayesnec

Science Score: 39.0%

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
    Found .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (22.3%) to scientific vocabulary

Keywords

bayesian-inference concentration-response ecotoxicology no-effect-concentration non-linear-decay threshold-derivation toxicology

Keywords from Contributors

aims marine sst weather
Last synced: 6 months ago · JSON representation

Repository

Bayesian No-Effect-Concentration estimation in R

Basic Info
Statistics
  • Stars: 13
  • Watchers: 4
  • Forks: 8
  • Open Issues: 22
  • Releases: 1
Topics
bayesian-inference concentration-response ecotoxicology no-effect-concentration non-linear-decay threshold-derivation toxicology
Created almost 6 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog License

README.Rmd 

---
output: github_document
---



```{r, include = FALSE}
stopifnot(require(knitr))
options(width = 90)
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/",
  out.width = "100%"
)
```

```{r, echo = FALSE}
version <- as.vector(read.dcf("DESCRIPTION")[, "Version"])
version <- gsub("-", ".", version)
```

# bayesnec bayesnec Logo


[![Lifecycle: maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://lifecycle.r-lib.org/articles/stages.html)
[![R build status](https://github.com/open-AIMS/bayesnec/actions/workflows/R-CMD-check.yaml/badge.svg?branch=dev)](https://github.com/open-AIMS/bayesnec/actions)
[![Codecov test coverage](https://codecov.io/gh/open-aims/bayesnec/branch/master/graph/badge.svg)](https://app.codecov.io/gh/open-aims/bayesnec?branch=master)
![pkgdown](https://github.com/open-AIMS/bayesnec/workflows/pkgdown/badge.svg)
[![CRAN Version](https://www.r-pkg.org/badges/version/bayesnec)](https://cran.r-project.org/package=bayesnec)
[![Downloads](https://cranlogs.r-pkg.org/badges/bayesnec?color=brightgreen)](https://CRAN.R-project.org/package=bayesnec)
[![license](https://img.shields.io/badge/license-GPL--2-lightgrey.svg)](https://choosealicense.com/)
[![Ask Us Anything
\!](https://img.shields.io/badge/Ask%20us-anything-1abc9c.svg)](https://github.com/open-AIMS/bayesnec/issues/new)
![Open Source
Love](https://badges.frapsoft.com/os/v2/open-source.svg?v=103)


## Overview 

`bayesnec` is a toxicity estimate and No-Effect toxicity estimation package that uses
[`brms`](https://github.com/paul-buerkner/brms) to fit
concentration(dose)-response data using Bayesian methods for the purpose of
estimating both ECX values, but more particularly 'NEC' (see [Fox (2010)](doi:10.1016/j.ecoenv.2009.09.012), 
'NSEC' (see [Fisher and Fox (2023)](10.1002/etc.5610)), and 'N(S)EC (see [Fisher et al. (2023)](10.1002/ieam.4809)). Please see `?bnec` for a
more detailed help file.

## Installation

To install the latest release version from CRAN use

```{r eval=FALSE}
install.packages("bayesnec")
```

The current development version can be downloaded from GitHub via

```{r eval=FALSE}
if (!requireNamespace("remotes")) {
  install.packages("remotes")
}
remotes::install_github("open-aims/bayesnec", ref = "dev")
```

Because `bayesnec` is based on `brms` and [Stan](https://mc-stan.org/), a C++
compiler is required. The program
[Rtools](https://cran.r-project.org/bin/windows/Rtools/) comes with a C++
compiler for Windows. On Mac, you should install Xcode. See the prerequisites
section on this
[link](https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started)
for further instructions on how to get the compilers running.

## Usage

Usage and further information about `bayesnec` can be seen on the [project
page](https://open-aims.github.io/bayesnec/) and the
[vignettes](https://open-aims.github.io/bayesnec/articles/). Help files for the
individual functions can be found on the
[reference page](https://open-aims.github.io/bayesnec/reference/).

## Further Information

`bayesnec` is provided by the
[Australian Institute of Marine Science](https://www.aims.gov.au/) under the
GPL-2 License ([GPL-2](https://opensource.org/license/gpl-2-0)).

Owner

  • Name: Australian Institute of Marine Science
  • Login: open-AIMS
  • Kind: organization
  • Email: github@aims.gov.au

GitHub Events

Total
  • Issues event: 1
  • Watch event: 3
  • Push event: 4
  • Fork event: 1
  • Create event: 1
Last Year
  • Issues event: 1
  • Watch event: 3
  • Push event: 4
  • Fork event: 1
  • Create event: 1

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 1,122
  • Total Committers: 26
  • Avg Commits per committer: 43.154
  • Development Distribution Score (DDS): 0.643
Past Year
  • Commits: 109
  • Committers: 3
  • Avg Commits per committer: 36.333
  • Development Distribution Score (DDS): 0.394
Top Committers
Name Email Commits
beckyfisher r****6@g****m 401
Diego Barneche b****r@g****m 325
Diego Barneche d****e@y****m 195
Rebecca Fisher R****r@a****u 132
HarveyWallbanger666 4****6 16
Rebecca Fisher r****r@a****u 15
Gerard Ricardo g****o@a****u 14
Diego Barneche d****e@a****u 6
Gerard Ricardo g****o@a****u 1
runner r****r@M****l 1
runner r****r@M****l 1
runner r****r@M****l 1
runner r****r@M****l 1
runner r****r@M****l 1
runner r****r@M****l 1
runner r****r@M****l 1
runner r****r@M****l 1
runner r****r@M****l 1
runner r****r@M****l 1
runner r****r@M****l 1
runner r****r@M****l 1
runner r****r@M****l 1
runner r****r@M****l 1
runner r****r@M****l 1
runner r****r@M****l 1
runner r****r@M****l 1
Committer Domains (Top 20 + Academic)
aims.gov.au: 5 ymail.com: 1

Issues and Pull Requests

Last synced: over 1 year ago

All Time
  • Total issues: 90
  • Total pull requests: 27
  • Average time to close issues: 4 months
  • Average time to close pull requests: 9 days
  • Total issue authors: 9
  • Total pull request authors: 4
  • Average comments per issue: 0.77
  • Average comments per pull request: 0.19
  • Merged pull requests: 21
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 4
  • Pull requests: 8
  • Average time to close issues: 22 days
  • Average time to close pull requests: about 8 hours
  • Issue authors: 2
  • Pull request authors: 2
  • Average comments per issue: 0.5
  • Average comments per pull request: 0.13
  • Merged pull requests: 5
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • beckyfisher (50)
  • dbarneche (28)
  • gerard-ricardo (2)
  • jsture (2)
  • MNordborg (2)
  • darrenkoppel (1)
  • padpadpadpad (1)
  • thomasp85 (1)
  • pkoaz (1)
Pull Request Authors
  • beckyfisher (17)
  • dbarneche (7)
  • paul-buerkner (4)
  • gerard-ricardo (1)
Top Labels
Issue Labels
enhancement (40) bug (16) documentation (9) question (4)
Pull Request Labels
bug (1)

Packages

  • Total packages: 1
  • Total downloads:
    • cran 389 last-month
  • Total docker downloads: 21,613
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 15
  • Total maintainers: 1
cran.r-project.org: bayesnec

A Bayesian No-Effect- Concentration (NEC) Algorithm

  • Versions: 15
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 389 Last month
  • Docker Downloads: 21,613
Rankings
Forks count: 11.3%
Stargazers count: 21.1%
Average: 24.9%
Downloads: 27.0%
Dependent packages count: 29.8%
Dependent repos count: 35.5%
Maintainers (1)
r.fisher@aims.gov.au
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.0 depends
  • brms * depends
  • ggplot2 * depends
  • dplyr * imports
  • evaluate * imports
  • extraDistr * imports
  • formula.tools * imports
  • loo * imports
  • purrr * imports
  • rlang * imports
  • tidyr * imports
  • tidyselect * imports
  • knitr * suggests
  • rmarkdown * suggests
  • rstan * suggests
  • testthat >= 3.0.0 suggests
.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2-branch composite
  • r-lib/actions/setup-r v2-branch composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action 4.1.4 composite
  • actions/checkout v2 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/readme-renderer.yaml actions
  • actions/checkout v2 composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v1 composite
.github/workflows/test-coverage.yaml actions
  • actions/checkout v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite