bbousuite

bbousuite: A set of R packages to facilitate analysis of boreal caribou survival and recruitment data - Published in JOSS (2025)

https://github.com/poissonconsulting/bbousuite

Keywords from Contributors

Repository

Easily install and load bbou (boreal caribou) R packages

README.Rmd

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  fig.width = 5,
  fig.height = 4
)
library(bboutools)
```

# bbousuite


[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
[![R-CMD-check](https://github.com/poissonconsulting/bbousuite/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/poissonconsulting/bbousuite/actions/workflows/R-CMD-check.yaml)
[![Codecov test coverage](https://codecov.io/gh/poissonconsulting/bbousuite/branch/main/graph/badge.svg)](https://app.codecov.io/gh/poissonconsulting/bbousuite?branch=main)


The goal of `bbousuite` is to make it easy to install and load the (`bbou`) suite of
R packages for **B**oreal cari**BOU**.

The `bbou`suite is a set of R packages to facilitate simulation and analysis of boreal caribou survival and recruitment data to estimate population growth.  

It consists of:  

- [`bboudata`](https://poissonconsulting.github.io/bboudata/), a collection of simulated and anonymized empirical survival and recruitment datasets.  
- [`bboutools`](https://poissonconsulting.github.io/bboutools/), a set of functions to estimate population growth in a Bayesian or Maximum Likelihood (ML) framework, implemented under the hood using the [Nimble](https://r-nimble.org) R package.  
- [`bboushiny`](https://poissonconsulting.github.io/bboushiny/), a Graphical User Interface (GUI) to `bboutools`.    
- [`bbouretro`](https://poissonconsulting.github.io/bbouretro/), a set of functions to estimate population growth using traditional frequentist methods.  
- [`bbousims`](https://poissonconsulting.github.io/bbousims/), a set of functions to simulate survival and recruitment data from hypothetical radio-collaring and composition surveys.  

Each R package has a website with function documentation and a 'Get Started' guide.  
If you are completely new to the `bbou` suite, we recommend taking a look at the [bboutools 'Get Started' guide](https://poissonconsulting.github.io/bboutools/articles/bboutools.html) as this demonstrates core functionality and methods.

There are also several vignettes, including `bboutools` [analytical methods](https://poissonconsulting.github.io/bboutools/articles/methods.html) and [prior selection](https://poissonconsulting.github.io/bboutools/articles/priors.html), `bbouretro` [analytical methods](https://poissonconsulting.github.io/bbouretro/articles/retro-methods.html), using [`bbousims` with `bboutools`](https://poissonconsulting.github.io/bbousims/articles/bboutools.html), and comparison of Bayesian and traditional method estimates with [empirical](https://poissonconsulting.github.io/bbousuite/articles/empirical-comparisons.html) and [simulated](https://poissonconsulting.github.io/bbousuite/articles/simulations.html) data. 


## Installation

You can install the latest version of `bbousuite` from [GitHub](https://github.com/poissonconsulting/bbousuite) with:

``` r
# install.packages("remotes")
remotes::install_github("poissonconsulting/bbousuite")
```

## Load

To load `bbousuite`

```{r}
library(bbousuite)
```

### Packages

The packages installed and loaded by `bbousuite` suite are:

- [bboudata](https://github.com/poissonconsulting/bboudata)
- [bbouretro](https://github.com/poissonconsulting/bbouretro)
- [bboutools](https://github.com/poissonconsulting/bboutools)
- [bbousims](https://github.com/poissonconsulting/bbousims)
- [bboushiny](https://github.com/poissonconsulting/bboushiny)

## Inspiration

`bbousuite` was inspired by the [`tidyverse`](https://github.com/tidyverse/tidyverse) package.

## Getting Help or Reporting an Issue

To report bugs/issues/feature requests, please file an [issue](https://github.com/poissonconsulting/bbousuite/issues/).

## How to Contribute

If you would like to contribute to the package, please see our 
[CONTRIBUTING](https://github.com/poissonconsulting/bbousuite/blob/master/.github/CONTRIBUTING.md) guidelines.

## Code of Conduct

Please note that the bbou project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.

```{r, results = "asis", echo = FALSE}
cat(licensing_md())
```

Owner

JOSS Publication

bbousuite: A set of R packages to facilitate analysis of boreal caribou survival and recruitment data

Published

May 30, 2025

DOI

10.21105/joss.07997

Volume 10, Issue 109, Page 7997

Authors

Seb Dalgarno
Poisson Consulting, Canada

John Boulanger
Integrated Ecological Research, Canada

Ayla Pearson
Poisson Consulting, Canada

Joe Thorley
Poisson Consulting, Canada

Troy Hegel
Province of Alberta, Canada

Barry Nobert
Province of Alberta, Canada

Dave Hervieux
Province of Alberta, Canada

Editor

Ethan White

Tags

boreal caribou Bayesian maximum likelihood survival recruitment population growth

View PDF Review Thread Software Archive

GitHub Events

Committers

Last synced: 6 months ago

Issues and Pull Requests

Last synced: 6 months ago