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

Last synced: about 4 hours ago
JSON representation

Repository metadata

BirdFlow R Package

• Host: GitHub
• URL: https://github.com/birdflow-science/birdflowr
• Owner: birdflow-science
• License: mit
• Created: 2022-11-14T22:04:42.000Z (over 2 years ago)
• Default Branch: main
• Last Pushed: 2025-04-17T02:22:35.000Z (11 days ago)
• Last Synced: 2025-04-17T22:59:46.570Z (10 days ago)
• Topics: bird-migration, birds, ebird, ecology, r-package
• Language: R
• Homepage: https://birdflow-science.github.io/BirdFlowR/
• Size: 48.6 MB
• Stars: 15
• Watchers: 5
• Forks: 4
• Open Issues: 23
• 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.

This package is under development and not yet formally released. Function names
and arguments may change.


## 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)
```
See `vignette("Installation")` for troubleshooting and more installation 
options.

## 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 the 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

• Issues event: 12
• Watch event: 7
• Delete event: 2
• Issue comment event: 44
• Push event: 9
• Pull request review event: 7
• Pull request review comment event: 10
• Pull request event: 5
• Fork event: 2
• Create event: 2

Last Year

• Issues event: 12
• Watch event: 7
• Delete event: 2
• Issue comment event: 44
• Push event: 9
• Pull request review event: 7
• Pull request review comment event: 10
• Pull request event: 5
• Fork event: 2
• Create event: 2

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Committers metadata

Last synced: 6 days ago

Name	Email	Commits
Ethan Plunkett	e****n@p****m	245
chenyangkang	c****4@o****m	82
Dave Slager	s****r	18
Luke Ruud	1****d	1
Daniel Sheldon	s****n@c****u	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: 1 day ago

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

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Dependencies

Score: 5.717027701406222