https://github.com/birdflow-science/BirdFlowR
BirdFlow R Package
https://github.com/birdflow-science/BirdFlowR
bird-migration birds ebird ecology r-package
Last synced: 5 months ago
JSON representation
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: 2024-10-17T15:59:34.000Z (6 months ago)
- Last Synced: 2024-10-29T22:31:23.312Z (6 months ago)
- Topics: bird-migration, birds, ebird, ecology, r-package
- Language: R
- Homepage: https://birdflow-science.github.io/BirdFlowR/
- Size: 45 MB
- Stars: 10
- Watchers: 5
- Forks: 2
- Open Issues: 16
-
Metadata Files:
- Readme: README.Rmd
- Changelog: NEWS.md
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE
Awesome Lists containing this project
- open-sustainable-technology - BirdFlowR - Predict changes in bird distributions and generate synthetic migration routes. (Biosphere / Avian Monitoring and Analysis)
README
---
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 
[](https://github.com/birdflow-science/BirdFlowR/actions/workflows/R-CMD-check.yaml)
[](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