BirdFlowR

Predict changes in bird distributions and generate synthetic migration routes.
https://github.com/birdflow-science/birdflowr

Category: Biosphere
Sub Category: Avian Monitoring and Analysis

Keywords

bird-migration birds ebird ecology r-package

Keywords from Contributors

movement-ecology aeroecology enram eumetnet-opera nexrad radar weather-radar wsr-88d

Last synced: about 18 hours ago
JSON representation

Repository metadata

BirdFlow R Package

• Host: GitHub
• URL: https://github.com/birdflow-science/birdflowr
• Owner: birdflow-science
• License: other
• Created: 2022-11-14T22:04:42.000Z (over 3 years ago)
• Default Branch: main
• Last Pushed: 2026-06-12T19:07:20.000Z (9 days ago)
• Last Synced: 2026-06-15T08:05:11.648Z (7 days ago)
• Topics: bird-migration, birds, ebird, ecology, r-package
• Language: R
• Homepage: https://birdflow-science.github.io/BirdFlowR/
• Size: 55.2 MB
• Stars: 21
• Watchers: 6
• Forks: 2
• Open Issues: 16
• Releases: 0
• Metadata Files:
  • Readme: README.Rmd
  • Changelog: NEWS.md
  • Contributing: .github/CONTRIBUTING.md
  • License: LICENSE

README.Rmd

          ---
output: github_document
---



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

set.seed(1)
```

# BirdFlowR 


  [![R-CMD-check](https://github.com/birdflow-science/BirdFlowR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/birdflow-science/BirdFlowR/actions/workflows/R-CMD-check.yaml)
[![Codecov test coverage](https://codecov.io/gh/birdflow-science/BirdFlowR/branch/main/graph/badge.svg)](https://app.codecov.io/gh/birdflow-science/BirdFlowR?branch=main)




An R package to predict changes in bird distributions and generate synthetic 
migration routes based on BirdFlow models.


## Installation

Install just the package:
```{r install, eval = FALSE}
if (!require("remotes"))
  install.packages("remotes")
remotes::install_github("birdflow-science/BirdFlowR")
```
Or to install with example data and vignette:

```{r install everything, eval = FALSE}
installed <- rownames(installed.packages())
if (!"remotes" %in% installed)
  install.packages("remotes")
if (!"rnaturalearthdata" %in% installed)
  install.packages("rnaturalearthdata")
remotes::install_github("birdflow-science/BirdFlowModels")
remotes::install_github("birdflow-science/BirdFlowR", build_vignettes = TRUE, dependencies = TRUE)
```
See the 
[Installation vignette](https://birdflow-science.github.io/BirdFlowR/articles/Installation.html) 
for more information and help troubleshooting.

## Usage 

The two primary functions are `predict()` to project distributions and 
`route()` to generate synthetic routes.  

`route_migration()` is a wrapper to `route()` which automates sampling
locations from a distribution for the start of the migration and setting 
the start and end dates to route for the migration window. We can use it to 
create synthetic routes for a species.
```{r examples}
library(BirdFlowR)
library(BirdFlowModels)

bf <- amewoo 

species(bf)

# Generate routes for the prebreeding migration 
rts <- route(bf, n = 10, season = "prebreeding")

# Plot routes
plot_routes(rts, bf)

```

Visualize the movement in the BirdFlow model for a timestep.

```{r movement_vectors}

plot_movement_vectors(bf, start = 12)

```


## Learn more

- `vignette("BirdFlowR")` has a longer introduction to the package, and how to
  use `predict()` and `route()` to project bird distributions and movement. 
- `vignette("Installation")` for detailed installation instructions.
- `vignette("Preprocess")` covers downloading and formatting data for model 
  fitting with `preprocess_species()`, importing fitted models with 
  `import_birdflow()`, and reducing model size with `sparsify()`.   
- Read the paper:
  - [BirdFlow: Learning Seasonal Bird Movements from Citizen Science Data](https://www.biorxiv.org/content/10.1101/2022.04.12.488057v1) Miguel Fuentes, Benjamin M. Van Doren, Daniel Fink, Daniel Sheldon bioRxiv 2022.04.12.488057; doi: https://doi.org/10.1101/2022.04.12.488057



        

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Owner metadata

• Name: birdflow-science
• Login: birdflow-science
• Email:
• Kind: organization
• Description:
• Website:
• Location:
• Twitter:
• Company:
• Icon url: https://avatars.githubusercontent.com/u/107491532?v=4
• Repositories: 2
• Last ynced at: 2023-06-14T20:23:21.944Z
• Profile URL: https://github.com/birdflow-science

---

GitHub Events

Total

• Delete event: 5
• Pull request event: 14
• Fork event: 2
• Issues event: 30
• Watch event: 12
• Issue comment event: 58
• Push event: 35
• Pull request review event: 7
• Pull request review comment event: 10
• Create event: 8

Last Year

• Delete event: 1
• Pull request event: 2
• Issues event: 7
• Watch event: 5
• Issue comment event: 3
• Push event: 14
• Create event: 3

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Committers metadata

Last synced: 3 days ago

Name	Email	Commits
Ethan Plunkett	e****n@p****m	306
chenyangkang	c****4@o****m	105
Dave Slager	s****r	18
Atharva Shahane	a****8@g****m	11
Dan Sheldon	s****n@c****u	6
Adriaan Dokter	a****r@g****m	4
Luke Ruud	1****d	1
Benjamin Van Doren	8****n	1
yc85_illinois_edu	y****u@l****u	1
plunkett_umass_edu	p****u@c****u	1

Committer domains:

• ceewater-cpu001.unity.rc.umass.edu: 1
• login2.unity.rc.umass.edu: 1
• cs.umass.edu: 1
• plunkettworks.com: 1

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Issue and Pull Request metadata

Last synced: 3 days ago

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/birdflow-science/birdflowr

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Dependencies

Score: 5.913503005638271