{"id":13724440,"url":"https://github.com/birdflow-science/BirdFlowR","last_synced_at":"2025-05-07T18:32:15.001Z","repository":{"id":65742488,"uuid":"566058138","full_name":"birdflow-science/BirdFlowR","owner":"birdflow-science","description":"BirdFlow R Package","archived":false,"fork":false,"pushed_at":"2025-05-01T14:57:37.000Z","size":51003,"stargazers_count":15,"open_issues_count":24,"forks_count":4,"subscribers_count":5,"default_branch":"main","last_synced_at":"2025-05-02T17:03:13.968Z","etag":null,"topics":["bird-migration","birds","ebird","ecology","r-package"],"latest_commit_sha":null,"homepage":"https://birdflow-science.github.io/BirdFlowR/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/birdflow-science.png","metadata":{"files":{"readme":"README.Rmd","changelog":"NEWS.md","contributing":".github/CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2022-11-14T22:04:42.000Z","updated_at":"2025-04-28T20:24:17.000Z","dependencies_parsed_at":"2023-02-19T19:45:22.283Z","dependency_job_id":"d7856e66-db1f-43c2-8e5d-25f66baa2c6a","html_url":"https://github.com/birdflow-science/BirdFlowR","commit_stats":{"total_commits":235,"total_committers":6,"mean_commits":"39.166666666666664","dds":0.09361702127659577,"last_synced_commit":"cef92cedda3ea92f903d3767eff183108d1384c6"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/birdflow-science%2FBirdFlowR","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/birdflow-science%2FBirdFlowR/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/birdflow-science%2FBirdFlowR/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/birdflow-science%2FBirdFlowR/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/birdflow-science","download_url":"https://codeload.github.com/birdflow-science/BirdFlowR/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":252934177,"owners_count":21827655,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bird-migration","birds","ebird","ecology","r-package"],"created_at":"2024-08-03T01:01:57.206Z","updated_at":"2025-05-07T18:32:14.907Z","avatar_url":"https://github.com/birdflow-science.png","language":"R","funding_links":[],"categories":["Biosphere"],"sub_categories":["Avian Monitoring and Analysis"],"readme":"---\noutput: github_document\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, include = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"man/figures/README-\",\n  out.width = \"100%\", \n  dev = \"ragg_png\",\n  dpi = 100\n)\n\nset.seed(1)\n```\n\n# BirdFlowR \u003ca href=\"https://birdflow-science.github.io/BirdFlowR/\"\u003e\u003cimg src=\"man/figures/logo.png\" align=\"right\" height=\"139\" /\u003e\u003c/a\u003e\n\n\u003c!-- badges: start --\u003e\n  [![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)\n[![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)\n\u003c!-- badges: end --\u003e\n\n\n\nAn R package to predict changes in bird distributions and generate synthetic \nmigration routes based on BirdFlow models.\n\nThis package is under development and not yet formally released. Function names\nand arguments may change.\n\n\n## Installation\n\nInstall just the package:\n```{r install, eval = FALSE}\nif(!require(\"remotes\"))\n  install.packages(\"remotes\") \nremotes::install_github(\"birdflow-science/BirdFlowR\")\n```\nOr to install with example data and vignette:\n\n```{r install everything, eval = FALSE}\ninstalled \u003c- rownames(installed.packages())\nif(!\"remotes\" %in% installed)\n  install.packages(\"remotes\")\nif(!\"rnaturalearthdata\" %in% installed)\n  install.packages(\"rnaturalearthdata\")\nremotes::install_github(\"birdflow-science/BirdFlowModels\")\nremotes::install_github(\"birdflow-science/BirdFlowR\", build_vignettes = TRUE)\n```\nSee `vignette(\"Installation\")` for troubleshooting and more installation \noptions.\n\n## Usage \n\nThe two primary functions are `predict()` to project distributions and \n`route()` to generate synthetic routes.  \n\n`route_migration()` is a wrapper to `route()` which automates sampling\nlocations from the a distribution for the start of the migration and setting \nthe start and end dates to route for the migration window. We can use it to \ncreate synthetic routes for a species.\n```{r examples}\nlibrary(BirdFlowR)\nlibrary(BirdFlowModels)\n\nbf \u003c- amewoo \n\nspecies(bf)\n\n# Generate routes for the prebreeding migration \nrts \u003c- route(bf, n = 10, season = \"prebreeding\")\n\n# Plot routes\nplot_routes(rts, bf)\n\n```\n\nVisualize the movement in the BirdFlow model for a timestep.\n\n```{r movement_vectors}\n\nplot_movement_vectors(bf, start = 12)\n\n```\n\n\n## Learn more\n\n- `vignette(\"BirdFlowR\")` has a longer introduction to the package, and how to\n  use `predict()` and `route()` to project bird distributions and movement. \n- `vignette(\"Installation\")` for detailed installation instructions.\n- `vignette(\"Preprocess\")` covers downloading and formatting data for model \n  fitting with `preprocess_species()`, importing fitted models with \n  `import_birdflow()`, and reducing model size with `sparsify()`.   \n- Read the paper:\n  - [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\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbirdflow-science%2FBirdFlowR","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbirdflow-science%2FBirdFlowR","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbirdflow-science%2FBirdFlowR/lists"}