bbsbayes2

An R Package for Hierarchical Bayesian Analysis of North American Breeding Bird Survey Data (second iteration)

https://github.com/bbsbayes/bbsbayes2

Science Score: 39.0%

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CITATION.cff file
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codemeta.json file
Found codemeta.json file
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Found .zenodo.json file
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Found 4 DOI reference(s) in README
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Committers with academic emails
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Scientific vocabulary similarity
Low similarity (16.1%) to scientific vocabulary

Last synced: 9 months ago · JSON representation

Repository

An R Package for Hierarchical Bayesian Analysis of North American Breeding Bird Survey Data (second iteration)

Basic Info

Host: GitHub
Owner: bbsBayes
License: other
Language: R
Default Branch: main
Homepage: https://bbsbayes.github.io/bbsBayes2/
Size: 185 MB

Statistics

Stars: 10
Watchers: 2
Forks: 4
Open Issues: 21
Releases: 6

Created over 3 years ago · Last pushed 10 months ago

Metadata Files

Readme Changelog Contributing License Code of conduct Codemeta

Critical News:

Error in the non-hierarchical first-difference model

In versions 1.1.0, 1.1.1, and 1.1.2.0, the non-hierarchical variant of the first-difference model included a coding error. Estimates of trends and population trajectories from this model in these versions will be biased.

The error was fixed in version 1.1.2.1. I am so sorry folks, please reach out if you would like more information or assistance in fixing/recovering from this.

bbsBayes2

bbsBayes2 is a package for performing hierarchical Bayesian analysis of North American Breeding Bird Survey (BBS) data. 'bbsBayes2' will run a full model analysis for one or more species that you choose, or you can take more control and specify how the data should be stratified, prepared for Stan, or modelled.

bbsBayes2 is the successor to bbsBayes, with a major shift in functionality. The MCMC backend is now Stan instead of JAGS, the workflow has been streamlined, the syntax has changed, and there are new functions. This vignette should help you get started with the package, and there are three others that should help explain some of the new features, choices, and more advanced uses:

Installation instructions are below.

See the documentation for an overview of how to use bbsBayes2.

In addition, there are four vignettes that will help users get familiar with the package and the new functionality.

Getting Started vignette
Stratification vignette The stratification vignette explains the built-in options for spatial stratifications as well as the workflow required to apply a custom stratification.
Models vignette The models vignette explains the four built-in models that differ in the way the temporal components are structured, and it also covers the built-in options for error distributions and the differences among the model variants (e.g., model_variant = "spatial").
Advanced vignette The advanced vignette is helpful for users wanting to take the bbsBayes2 functionality further, including alternate calculations of population trend, customizing the Stan models, adding covariates, and even some experimental functions that allow for k-fold cross-validations to compare among models.

Installation

bbsBayes2 can be installed from the bbsBayes R-Universe:

r install.packages("bbsBayes2", repos = c(bbsbayes = 'https://bbsbayes.r-universe.dev', CRAN = 'https://cloud.r-project.org'))

Alternatively you can install directly from our GitHub repository with either the pak (recommended) or remotes packages.

With pak:

{r} install.packages("pak") pak::pkg_install("bbsBayes/bbsBayes2")

With remotes:

{r} install.packages("remotes") remotes::install_github("bbsBayes/bbsBayes2")

If you want to install the developmental branch (which often includes additional options and newest updates), you can use the following. NOTE: bbsBayes2 is supported by a small team of committed researchers with limited capacity. The development branch may not be stable.

{r} pak::pkg_install("bbsBayes/bbsBayes2@dev")

Why bbsBayes2

We hope you'll agree that the BBS is a spectacular dataset. Generations of committed and expert birders have contributed their time and expertise to carefully keeping track of local bird populations. For many BBS observers, it's been a commitment that has lasted 20, 30, or even 40 years! Many federal, state, and provincial government agencies, as well as local and national conservation organizations have supported the coordination and curation of almost 60-years of data.

The BBS was started at the dawn of the modern North American conservation movement, inspired by changes in bird populations noticed by biologists, naturalists, farmers, and other stewards of the natural world. A continental-scale survey of birds, carefully designed to quantify changes in populations through time, in hopes that Rachel Carson's "Silent Spring", would never come to pass.

bbsBayes2 was created: to help researchers make use of these precious data; to better understand the spatial and temporal changes in bird populations; to make agency-derived estimates of population status more transparent; and to inspire improvements, elaborations, and critical feedback on the models provided here. We hope you enjoy the package and we hope you will contribute your ideas and code to this open software initiative.

Owner

Name: bbsBayes
Login: bbsBayes
Kind: organization

Repositories: 2
Profile: https://github.com/bbsBayes

Project for R packages conducting hierarchical Bayesian analysis of North American breeding bird survey data

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GitHub Events

Total

Create event: 3
Release event: 1
Issues event: 13
Watch event: 2
Delete event: 2
Issue comment event: 12
Push event: 6
Pull request event: 2
Fork event: 1

Last Year

Create event: 3
Release event: 1
Issues event: 13
Watch event: 2
Delete event: 2
Issue comment event: 12
Push event: 6
Pull request event: 2
Fork event: 1

Committers

Last synced: 10 months ago

All Time

Total Commits: 173
Total Committers: 5
Avg Commits per committer: 34.6
Development Distribution Score (DDS): 0.434

Past Year

Commits: 25
Committers: 2
Avg Commits per committer: 12.5
Development Distribution Score (DDS): 0.16

Top Committers

Name	Email	Commits
AdamCSmithCWS	a**s@g**m	98
steffilazerte	s**i@s**a	50
Smith	A**h@e**a	22
L-Daly	1****y	2
Brandon Edwards	b**4@g**m	1

Committer Domains (Top 20 + Academic)

ec.gc.ca: 1 steffi.ca: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time

Total issues: 56
Total pull requests: 43
Average time to close issues: 4 months
Average time to close pull requests: 5 days
Total issue authors: 7
Total pull request authors: 3
Average comments per issue: 0.95
Average comments per pull request: 0.16
Merged pull requests: 41
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 17
Pull requests: 3
Average time to close issues: 7 days
Average time to close pull requests: 4 days
Issue authors: 5
Pull request authors: 1
Average comments per issue: 0.94
Average comments per pull request: 0.0
Merged pull requests: 3
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

AdamCSmithCWS (44)
steffilazerte (8)
vawinter (1)
billspat (1)
tmeeha (1)
BrandonEdwards (1)

Pull Request Authors

AdamCSmithCWS (39)
steffilazerte (2)
L-Daly (1)

Top Labels

Issue Labels

enhancement (1)

Pull Request Labels

Packages

Total packages: 2
Total downloads: unknown

Total dependent packages: 0
(may contain duplicates)
Total dependent repositories: 0
(may contain duplicates)
Total versions: 8

proxy.golang.org: github.com/bbsBayes/bbsBayes2

Documentation: https://pkg.go.dev/github.com/bbsBayes/bbsBayes2#section-documentation
License: other
Latest release: v1.1.2
published over 1 year ago

Versions: 4
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 5.4%

Average: 5.6%

Dependent repos count: 5.8%

Last synced: 10 months ago

proxy.golang.org: github.com/bbsbayes/bbsbayes2

Documentation: https://pkg.go.dev/github.com/bbsbayes/bbsbayes2#section-documentation
License: other
Latest release: v1.1.2
published over 1 year ago

Versions: 4
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 5.4%

Average: 5.6%

Dependent repos count: 5.8%

Last synced: 10 months ago

Dependencies

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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/cache v3 composite
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 >= 3.5 depends
HDInterval * imports
backports >= 1.4.1 imports
dplyr >= 1.1.0 imports
geofacet * imports
ggplot2 >= 3.4.0 imports
ggrepel * imports
magrittr * imports
mgcv * imports
posterior >= 1.2.1 imports
purrr >= 0.3.4 imports
readr >= 2.1.2 imports
rlang >= 0.4.11 imports
sbtools * imports
sf >= 1.0.8 imports
snakecase * imports
spdep >= 1.2.7 imports
stringr * imports
tidyr >= 1.2.0 imports
units >= 0.8.0 imports
withr >= 2.5.0 imports
cmdstanr * suggests
covr * suggests
knitr * suggests
rmarkdown * suggests
rnaturalearth * suggests
rnaturalearthhires * suggests
roxygen2 * suggests
testthat >= 3.0.0 suggests