{"id":17825931,"url":"https://github.com/joshwlambert/daisiemainland","last_synced_at":"2026-02-27T05:02:56.667Z","repository":{"id":41646823,"uuid":"337202123","full_name":"joshwlambert/DAISIEmainland","owner":"joshwlambert","description":"Simulate phylogenetic data on islands with a evolving mainland pool","archived":false,"fork":false,"pushed_at":"2024-07-12T17:10:12.000Z","size":56317,"stargazers_count":1,"open_issues_count":0,"forks_count":1,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-01-12T10:45:02.562Z","etag":null,"topics":["phylogenetics","r","simulation"],"latest_commit_sha":null,"homepage":"https://joshwlambert.github.io/DAISIEmainland/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/joshwlambert.png","metadata":{"files":{"readme":"README.md","changelog":"NEWS.md","contributing":".github/CONTRIBUTING.md","funding":null,"license":"LICENSE.md","code_of_conduct":".github/CODE_OF_CONDUCT.md","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}},"created_at":"2021-02-08T20:34:07.000Z","updated_at":"2024-07-12T17:08:24.000Z","dependencies_parsed_at":"2022-08-10T07:36:30.086Z","dependency_job_id":"aeecc7be-6394-49a0-b38a-165905729966","html_url":"https://github.com/joshwlambert/DAISIEmainland","commit_stats":{"total_commits":828,"total_committers":6,"mean_commits":138.0,"dds":"0.25120772946859904","last_synced_commit":"4ed73d1a3ce4d67c504c95b3a525c0b8ce5a2849"},"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/joshwlambert%2FDAISIEmainland","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/joshwlambert%2FDAISIEmainland/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/joshwlambert%2FDAISIEmainland/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/joshwlambert%2FDAISIEmainland/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/joshwlambert","download_url":"https://codeload.github.com/joshwlambert/DAISIEmainland/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":241418124,"owners_count":19959732,"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":["phylogenetics","r","simulation"],"created_at":"2024-10-27T18:31:21.908Z","updated_at":"2025-10-31T00:46:51.178Z","avatar_url":"https://github.com/joshwlambert.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# DAISIEmainland \u003cimg src=\"man/figures/logo.png\" align=\"right\" height=\"200\" /\u003e\n\n\u003c!-- badges: start --\u003e\n[![R-CMD-check](https://github.com/joshwlambert/DAISIEmainland/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/joshwlambert/DAISIEmainland/actions/workflows/R-CMD-check.yaml)\n[![codecov.io](https://codecov.io/github/joshwlambert/DAISIEmainland/coverage.svg?branch=main)](https://codecov.io/github/joshwlambert/DAISIEmainland/branch/main)\n[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)\n[![Project Status: Active](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6502548.svg)](https://doi.org/10.5281/zenodo.6502548)\n\u003c!-- badges: end --\u003e\n\nThe goal of DAISIEmainland is to simulate data to test whether the DAISIE model\n(Dynamic Assembly of Island biota through Speciation Immigration and Extinction)\ninitially developed in Valente et al. (2015) and used in Valente et al. (2017a,\n2017b, 2019, 2020) and Hauffe et al. (2020) can reliably estimate\nmacroevolutionary parameters (cladogenesis, extinction, carrying capacity,\nimmigration and anagenesis) when the assumption of a static mainland pool of\nspecies is violated, as is the case in nature. \n\n## Installation\n\nSee [installation instructions](https://joshwlambert.github.io/DAISIEmainland/installation.html)\n\n## Usage\n\nSee [long-form documentation](https://joshwlambert.github.io/DAISIEmainland/) for details of package\nfunctionality.\n\n## Help\n\nTo report a bug please open an [issue](https://github.com/joshwlambert/DAISIEprep/issues/new) or email at j.w.l.lambert@rug.nl.\n\n## Contribute\n\nThe DAISIE team always welcomes contributions to any of its packages. If you\nwould like to contribute to this package please follow the [contributing guidelines](https://github.com/joshwlambert/DAISIEmainland/tree/main/.github/CONTRIBUTING.md)\n\n## Code of Conduct\n\nPlease note that the DAISIEmainland project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.\n\n## Cite this package\n\n``` r\ncitation(\"DAISIEmainland\")\n```\n\n## Cite the DAISIE package\n\nEtienne R. S., Valente, L., Phillimore, A. B., Haegeman, B., Lambert, J. W., Neves, P., Xie, S., Bilderbeek, R. J. C. \u0026 Hildenbrant H. (2022). DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction. R package version 4.1.1. https://github.com/rsetienne/DAISIE\n\n## References of previous DAISIE papers\n\nValente, L., Phillimore, A.B., \u0026 Etienne, R.S. (2015). Equilibrium and non-equilibrium dynamics simultaneously operate in the Galápagos islands. Ecology Letters, 18(8), 844–852. http://doi.org/10.1111/ele.12461\n\nValente, L., Etienne, R.S., \u0026 Dávalos, L.M. (2017). Recent extinctions disturb path to equilibrium diversity in Caribbean bats. Nature Ecology \u0026 Evolution, 1(2), 0026. http://doi.org/10.1038/s41559-016-0026\n\nValente, L., Illera, J.C., Havenstein, K., Pallien, T., Etienne, R.S., \u0026 Tiedemann, R. (2017). Equilibrium Bird Species Diversity in Atlantic Islands. Current Biology, 27(11), 1660-1666. https://doi.org/10.1016/j.cub.2017.04.053\n\nValente, L., Phillimore, A.B., \u0026 Etienne, R.S. (2018). Using molecular phylogenies in island biogeography: It’s about time. Ecography, 1–3. http://doi.org/10.1111/ecog.03503\n\nValente, L., Etienne, R.S., \u0026 Garcia-R., J.C. (2019). “Deep Macroevolutionary Impact of Humans on New Zealand’s Unique Avifauna.” Current Biology 29 (15): 2563-2569.e4. https://doi.org/10.1016/j.cub.2019.06.058\n\nValente, L., Phillimore, A.B., Melo, M., Warren, B.H., Clegg, S.M., Havenstein, K., Tiedemann, R., Illera, J.C.,, Thebaud, C., Aschenbach, T. \u0026 Etienne, R.S. (2020). “A Simple Dynamic Model Explains the Diversity of Island Birds Worldwide.” Nature 579 (7797): 92–96. https://doi.org/10.1038/s41586-020-2022-5\n\nHauffe, T., Delicado, D., Etienne, R.S., \u0026 Valente, L. (2020). Lake expansion elevates equilibrium diversity via increasing colonization. Journal of Biogeography 47: 1849–1860. https://doi.org/10.1111/jbi.13914\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjoshwlambert%2Fdaisiemainland","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjoshwlambert%2Fdaisiemainland","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjoshwlambert%2Fdaisiemainland/lists"}