Data

Tools

Indexes

Applications

Experiments

Open Source Science

popbayes

:package: Bayesian Model to Estimate Animal Population Trends from Counts Series

https://github.com/frbcesab/popbayes

Science Score: 10.0%

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

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 4 committers (25.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (17.9%) to scientific vocabulary

Keywords

animal bayesian counts population precision r temporal-trend
Last synced: 6 months ago · JSON representation

Repository

:package: Bayesian Model to Estimate Animal Population Trends from Counts Series

Basic Info
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 0
  • Open Issues: 2
  • Releases: 3
Topics
animal bayesian counts population precision r temporal-trend
Created over 6 years ago · Last pushed about 2 years ago
Metadata Files
Readme License

README.Rmd 

---
output: github_document
---




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



popbayes 
=========================================================


[![CRAN status](https://www.r-pkg.org/badges/version/popbayes)](https://CRAN.R-project.org/package=popbayes/)
[![R CMD Check](https://github.com/frbcesab/popbayes/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/frbcesab/popbayes/actions/workflows/R-CMD-check.yaml)
[![Website deployment](https://github.com/frbcesab/popbayes/actions/workflows/pkgdown.yaml/badge.svg)](https://github.com/frbcesab/popbayes/actions/workflows/pkgdown.yaml)
[![License: GPL (>= 2)](https://img.shields.io/badge/License-GPL%20%28%3E%3D%202%29-blue.svg)](https://choosealicense.com/licenses/gpl-2.0/)



The goal of the R package `popbayes` is to infer trends of one or several 
populations over time from series of counts. It does so by accounting for count 
precision (provided or inferred based on expert knowledge, e.g. guesstimates), 
smoothing the population rate of increase over time, and accounting for the maximum 
demographic potential of species. Inference is carried out in a Bayesian framework.
This work is part of the FRB-CESAB working group 
[AfroBioDrivers](https://www.fondationbiodiversite.fr/en/the-frb-in-action/programs-and-projects/le-cesab/afrobiodrivers/).


## Installation

**Before using this package, users need to install the freeware 
[JAGS](https://mcmc-jags.sourceforge.io/).**

You can install the stable version of the package from the [CRAN](https://cran.r-project.org) with:

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

Alternatively you can install the development version from [GitHub](https://github.com/) with:

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

remotes::install_github("frbcesab/popbayes", build_vignettes = TRUE)
```



## Overview

![](vignettes/docs/popbayes-diagram.png)


## Get started

Please read the 
[Get started](https://frbcesab.github.io/popbayes/articles/popbayes.html) 
vignette.


## Citation

Please cite this package as: 

> Casajus N. & Pradel R. (2023) popbayes: Bayesian model to estimate population 
trends from counts series. R package version 1.2.0. URL: .

You can also run:

```{r eval = FALSE}
citation("popbayes")

## A BibTeX entry for LaTeX users is:
## 
## @Manual{,
##   title  = {{popbayes}: {B}ayesian model to estimate population trends from counts series,
##   author = {{Casajus N.}, and {Pradel R.}},
##   year   = {2023},
##   note   = {R package version 1.2.0},
##   url    = {https://frbcesab.github.io/popbayes/},
## }
```

Owner

  • Name: FRB CESAB
  • Login: FRBCesab
  • Kind: organization
  • Location: Montpellier, FRANCE

GitHub Events

Total
Last Year

Committers

Last synced: 11 months ago

All Time
  • Total Commits: 198
  • Total Committers: 4
  • Avg Commits per committer: 49.5
  • Development Distribution Score (DDS): 0.237
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Nicolas Casajus n****s@g****m 151
Roger PRADEL r****l@c****r 28
Roger PRADEL p****l@n****r 12
olivroy 5****y 7
Committer Domains (Top 20 + Academic)
newcefe.newage.fr: 1 cefe.cnrs.fr: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 30
  • Total pull requests: 4
  • Average time to close issues: 3 months
  • Average time to close pull requests: 1 day
  • Total issue authors: 2
  • Total pull request authors: 2
  • Average comments per issue: 0.4
  • Average comments per pull request: 0.75
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • ahasverus (19)
  • parguel (11)
Pull Request Authors
  • olivroy (4)
  • ahasverus (2)
Top Labels
Issue Labels
enhancement (3) documentation (2) testing (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 244 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 3
  • Total maintainers: 1
cran.r-project.org: popbayes

Bayesian Model to Estimate Population Trends from Counts Series

  • Versions: 3
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 244 Last month
Rankings
Forks count: 28.8%
Dependent packages count: 29.8%
Stargazers count: 35.2%
Dependent repos count: 35.5%
Average: 43.2%
Downloads: 86.8%
Maintainers (1)
nicolas.casajus@fondationbiodiversite.fr
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.5 depends
  • R2jags * imports
  • grDevices * imports
  • graphics * imports
  • stats * imports
  • usethis * imports
  • knitr * suggests
  • rmarkdown * suggests
.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v2 composite
  • r-lib/actions/check-r-package 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/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