README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{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 <img src="man/figures/logo.png" width = 180 alt="bayesnec Logo" align="right" />

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## 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)).