DAISIE package for R: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

Rampal Etienne; Luis Lima Valente; Albert B. Phillimore; Bart Haegeman; Joshua Lambert; Pedro Neves; Shu Xie; Richèl Bilderbeek; Torsten Hauffe; Giovanni Laudanno; Nadiah Kristensen; Raphaël Scherrer

doi:10.5281/zenodo.4054059

DAISIE package for R: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

Rampal Etienne^*, Luis Lima Valente, Albert B. Phillimore, Bart Haegeman, Joshua Lambert, Pedro Neves, Shu Xie, Richèl Bilderbeek, Torsten Hauffe (Other), Giovanni Laudanno (Other), Nadiah Kristensen (Other), Raphaël Scherrer (Other)

^*Corresponding author for this work

Etienne group - Theoretical and Evolutionary Community Ecology

Research output: Non-textual form › Software › Academic

Abstract

Simulates and computes the (maximum) likelihood of a dynamical model of island biota assembly through speciation, immigration and extinction.

Original language	English
Media of output	Online
Size	1.1 MB
DOIs	https://doi.org/10.5281/zenodo.4054059 https://doi.org/10.5281/zenodo.4054058
Publication status	Published - 13-Feb-2023

Keywords

Island biogeography
R package
Phylogenetics
Maximum likelihood estimation
Birth-death model

Access to Document

10.5281/zenodo.4054059Licence: GNU LGPL
10.5281/zenodo.4054058Licence: GNU GPL

Handle.net

Persistent link

Other files and links

Comprehensive R Archive Network (CRAN) repository

8 Article

The robustness of a simple dynamic model of island biodiversity to geological and sea-level change
Santos Neves, P., Lambert, J., Lima Valente, L. & Etienne, R., Nov-2022, In: Journal of Biogeography. 49, 11, p. 2091-2104 14 p.
Research output: Contribution to journal › Article › Academic › peer-review

Open Access
File
3 Citations (Scopus)

112 Downloads (Pure)
A simple dynamic model explains the diversity of island birds worldwide
Valente, L., Phillimore, A. B., Melo, M., Warren, B. H., Clegg, S. M., Havenstein, K., Tiedemann, R., Illera, J. C., Thébaud, C., Aschenbach, T. & Etienne, R. S., 5-Mar-2020, In: Nature. 579, 7797, p. 92-96 5 p.
Research output: Contribution to journal › Article › Academic › peer-review

Open Access
File
88 Citations (Scopus)

723 Downloads (Pure)
Lake expansion elevates equilibrium diversity via increasing colonization
Hauffe, T., Delicado, D., Etienne, R. S. & Valente, L., Sept-2020, In: Journal of Biogeography. 47, 9, p. 1849-1860 12 p.
Research output: Contribution to journal › Article › Academic › peer-review

Open Access
File
6 Citations (Scopus)

116 Downloads (Pure)

4 Academic presentation
2 Attending an event

The robustness of a simple dynamic model of island biodiversity to geological and sea-level change
Santos Neves, P. (Speaker), Lambert, J. (Contributor), Lima Valente, L. (Contributor) & Etienne, R. (Contributor)
20-Sept-2022
Activity: Talk and presentation › Academic presentation › Academic

File
Unravelling a web of diversity
Santos Neves, P. M. (Speaker), Lima Valente, L. (Contributor), Lim, J. (Contributor), Patiño, J. (Contributor), Gillespie, R. (Contributor) & Etienne, R. (Contributor)
23-Jun-2021
Activity: Talk and presentation › Academic presentation › Academic
What if MacArthur & Wilson had used dated phylogenies?
Etienne, R. (Speaker)
28-May-2019
Activity: Talk and presentation › Academic presentation › Academic

Herstel vogelstand Nieuw-Zeeland duurt minstens 50 miljoen jaar
Etienne, R. & Lima Valente, L.
14/08/2019 → 20/03/2020
2 items of Media coverage
Press/Media: Research › Academic
Global relationships that determine bird diversity on islands uncovered
Etienne, R. & Lima Valente, L.
19/02/2020 → 22/02/2020
6 items of Media coverage
Press/Media: Research › Academic
Island biodiversity: Stable but vulnerable
Etienne, R.
09/01/2017 → 31/03/2017
7 items of Media coverage, 1 Media contribution
Press/Media: Research › Academic

1 Finished
1 Active

AL: Adaptive Life
Etienne, R. (Coordinator), Kas, M. (Coordinator), Olff, H. (Coordinator), Weissing, F. (Coordinator) & Groothuis, T. (Coordinator)
01/01/2016 → 01/01/2026
Project: Research
AL-II: Adaptive diversity and eco-evolutionary dynamics
Etienne, R. (PI), van Doorn, S. (PI), Fontaine, M. (PI) & Scherrer, R. (PhD student)
01/11/2017 → 01/02/2024
Project: Research

Cite this

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title = "DAISIE package for R: Dynamical Assembly of Islands by Speciation, Immigration and Extinction",

abstract = "Simulates and computes the (maximum) likelihood of a dynamical model of island biota assembly through speciation, immigration and extinction.",

keywords = "Island biogeography, R package, Phylogenetics, Maximum likelihood estimation, Birth-death model",

author = "Rampal Etienne and {Lima Valente}, Luis and Phillimore, {Albert B.} and Bart Haegeman and Joshua Lambert and Pedro Neves and Shu Xie and Rich{\`e}l Bilderbeek and Torsten Hauffe and Giovanni Laudanno and Nadiah Kristensen and Rapha{\"e}l Scherrer",

note = "03-06-2015: version 1.0.1 13-02-2023: version 4.3.1",

year = "2023",

month = feb,

day = "13",

doi = "10.5281/zenodo.4054059",

language = "English",

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T2 - Dynamical Assembly of Islands by Speciation, Immigration and Extinction

AU - Etienne, Rampal

AU - Lima Valente, Luis

AU - Phillimore, Albert B.

AU - Haegeman, Bart

AU - Lambert, Joshua

AU - Neves, Pedro

AU - Xie, Shu

AU - Bilderbeek, Richèl

A2 - Hauffe, Torsten

A2 - Laudanno, Giovanni

A2 - Kristensen, Nadiah

A2 - Scherrer, Raphaël

N1 - 03-06-2015: version 1.0.1 13-02-2023: version 4.3.1

PY - 2023/2/13

Y1 - 2023/2/13

N2 - Simulates and computes the (maximum) likelihood of a dynamical model of island biota assembly through speciation, immigration and extinction.

AB - Simulates and computes the (maximum) likelihood of a dynamical model of island biota assembly through speciation, immigration and extinction.

KW - Island biogeography

KW - R package

KW - Phylogenetics

KW - Maximum likelihood estimation

KW - Birth-death model

UR - https://cran.r-project.org/package=DAISIE

U2 - 10.5281/zenodo.4054059

DO - 10.5281/zenodo.4054059

M3 - Software

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DAISIE package for R: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

Abstract

Keywords

Access to Document

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Research output

Activities

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Cite this