TREvoSim v3: An individual based simulation for generating trees and character data

Authors

Russell J. Garwood
Department of Earth and Environmental Sciences, University of Manchester, Manchester, M13 9PL, United Kingdom, Natural History Museum, London, SW7 5BD, United Kingdom

Alan R. t. Spencer
Natural History Museum, London, SW7 5BD, United Kingdom, Department of Earth Science and Engineering, Imperial College, London, SW7 2AZ, United Kingdom

Charles T. m. Bates
Department of Earth and Environmental Sciences, University of Manchester, Manchester, M13 9PL, United Kingdom

Leah M. Callender-Crowe
School of Biological Sciences, University of Reading, Reading, United Kingdom

Frances S. Dunn
Oxford University Museum of Natural History, University of Oxford, Oxford, OX1 3PW, United Kingdom

Thomas J.d. Halliday
School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom

Joseph N. Keating
School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, United Kingdom

Nicolás Mongiardino Koch
Scripps Institution of Oceanography, UC San Diego, La Jolla, CA 92122, United States of America

Luke A. Parry
Department of Earth Sciences, University of Oxford, Oxford, OX1 3AN, United Kingdom

Robert S. Sansom
Department of Earth and Environmental Sciences, University of Manchester, Manchester, M13 9PL, United Kingdom

Thomas J. Smith
Department of Earth Sciences, University of Oxford, Oxford, OX1 3AN, United Kingdom

Mark D. Sutton
Department of Earth Science and Engineering, Imperial College, London, SW7 2AZ, United Kingdom

Thomas Vanteghem
Erasmus Mundus Joint Master Degree PANGEA, Université de Lille, France

Editor

Frederick Boehm

cff-version: "1.2.0"
authors:
- family-names: Garwood
  given-names: Russell J.
  orcid: "https://orcid.org/0000-0002-2803-9471"
- family-names: Spencer
  given-names: Alan R. T.
  orcid: "https://orcid.org/0000-0001-6590-405X"
- family-names: Bates
  given-names: Charles T. M.
  orcid: "https://orcid.org/0009-0000-8444-6322"
- family-names: Callender-Crowe
  given-names: Leah M.
  orcid: "https://orcid.org/0000-0002-5870-1964"
- family-names: Dunn
  given-names: Frances S.
  orcid: "https://orcid.org/0000-0001-7080-5283"
- family-names: Halliday
  given-names: Thomas J. D.
  orcid: "https://orcid.org/0000-0002-4077-732X"
- family-names: Keating
  given-names: Joseph N.
  orcid: "https://orcid.org/0000-0002-2667-7795"
- family-names: Mongiardino Koch
  given-names: Nicolás
  orcid: "https://orcid.org/0000-0001-6317-5869"
- family-names: Parry
  given-names: Luke A.
  orcid: "https://orcid.org/0000-0002-3910-0346"
- family-names: Sansom
  given-names: Robert S.
  orcid: "https://orcid.org/0000-0003-1926-2556"
- family-names: Smith
  given-names: Thomas J.
  orcid: "https://orcid.org/0000-0002-2083-7452"
- family-names: Sutton
  given-names: Mark D.
  orcid: "https://orcid.org/0000-0002-7137-7572"
- family-names: Vanteghem
  given-names: Thomas
  orcid: "https://orcid.org/0009-0003-3513-8448"
contact:
- family-names: Garwood
  given-names: Russell J.
  orcid: "https://orcid.org/0000-0002-2803-9471"
doi: 10.5281/zenodo.13358420
title: "TREvoSim"
version: 3.0.0
date-released: 2024-08-22
url: "https://github.com/palaeoware/trevosim/"
message: If you use v3 of TREvoSim, please cite cite our article in the Journal of Open Source Software. See references for other relevant papers associated with previous versions of the software and related packages.
preferred-citation:
  authors:
  - family-names: Garwood
    given-names: Russell J.
    orcid: "https://orcid.org/0000-0002-2803-9471"
  - family-names: Spencer
    given-names: Alan R. T.
    orcid: "https://orcid.org/0000-0001-6590-405X"
  - family-names: Bates
    given-names: Charles T. M.
    orcid: "https://orcid.org/0009-0000-8444-6322"
  - family-names: Callender-Crowe
    given-names: Leah M.
    orcid: "https://orcid.org/0000-0002-5870-1964"
  - family-names: Dunn
    given-names: Frances S.
    orcid: "https://orcid.org/0000-0001-7080-5283"
  - family-names: Halliday
    given-names: Thomas J. D.
    orcid: "https://orcid.org/0000-0002-4077-732X"
  - family-names: Keating
    given-names: Joseph N.
    orcid: "https://orcid.org/0000-0002-2667-7795"
  - family-names: Mongiardino Koch
    given-names: Nicolás
    orcid: "https://orcid.org/0000-0001-6317-5869"
  - family-names: Parry
    given-names: Luke A.
    orcid: "https://orcid.org/0000-0002-3910-0346"
  - family-names: Sansom
    given-names: Robert S.
    orcid: "https://orcid.org/0000-0003-1926-2556"
  - family-names: Smith
    given-names: Thomas J.
    orcid: "https://orcid.org/0000-0002-2083-7452"
  - family-names: Sutton
    given-names: Mark D.
    orcid: "https://orcid.org/0000-0002-7137-7572"
  - family-names: Vanteghem
    given-names: Thomas
    orcid: "https://orcid.org/0009-0003-3513-8448"
  date-published: 2024-09-12
  doi: 10.21105/joss.06722
  issn: 2475-9066
  issue: 101
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6722
  title: "TREvoSim v3: An individual based simulation for generating
    trees and character data"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06722"
  volume: 9
title: "TREvoSim v3: An individual based simulation for generating trees
  and character data"

{
  "@context": "https://w3id.org/codemeta/3.0",
  "type": "SoftwareSourceCode",
  "applicationCategory": "Evolutionary simulation",
  "author": [
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      "id": "https://orcid.org/0000-0002-2803-9471",
      "type": "Person",
      "affiliation": {
        "type": "Organization",
        "name": "Department of Earth and Environmental Sciences, University of Manchester, Manchester, M13 9PL, United Kingdom; Natural History Museum, London, SW7 5BD, United Kingdom"
      },
      "email": "russell.garwood@gmail.com",
      "familyName": "Garwood",
      "givenName": "Russell J."
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      "type": "Person",
      "affiliation": {
        "type": "Organization",
        "name": "Department of Earth Science and Engineering, Imperial College, London, SW7 2AZ, United Kingdom; Natural History Museum, London, SW7 5BD, United Kingdom"
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      "familyName": "Spencer",
      "givenName": "Alan R.T. "
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  "codeRepository": "git+https://github.com/palaeoware/trevosim",
  "dateModified": "2024-08-22",
  "datePublished": "2021-01-21",
  "description": "TREvoSim is an individual-based evolutionary simulation. It creates evolutionary trees and associated character data using a model that with a fitness algorithm and replication that incorporates mutation.",
  "downloadUrl": "https://github.com/palaeoware/trevosim/releases/tag/v3.0.0",
  "identifier": "10.5281/zenodo.13358420",
  "keywords": [
    "Phylogenetics",
    "evolution",
    "modelling"
  ],
  "license": "https://spdx.org/licenses/GPL-3.0",
  "name": "TREvoSim",
  "operatingSystem": [
    "Windows",
    "MacOS",
    "Linux"
  ],
  "programmingLanguage": "C++",
  "releaseNotes": "The changes in v3.0.0 are described and discussed fully in the associated paper. In brief, these include:\n\n-- New character options\n-- New default simulation parameters\n-- Ecosystem engineering functionality\n-- An expanding playing field mode\n-- New logging capabilities\n-- The option to match fitness peaks across environments\n-- A no selection mode\n-- Mixing of organisms between playing fields\n-- Perturbations (periods of accelerated environmental change)\n-- The ability to run the simulation for a user-defined number of iterations, as opposed to for set number of species\n-- Abstraction of the fitness algorithm from the genome via many-to-one mapping (stochastic layer)\n-- A test suite integrated into the software build",
  "review": {
    "type": "Review",
    "reviewAspect": "TREvoSim v3: An individual based simulation for generating trees and character data",
    "reviewBody": "Paper accompanying release of v3.0.0"
  },
  "version": "3.0.0",
  "developmentStatus": "active",
  "funding": " BBSRC - BB/N015827/1, NERC - NE/T000813/1, Leverhulme Trust -  RPG-2023-234, the Alexander von Humboldt Foundation",
  "issueTracker": "https://github.com/palaeoware/trevosim/issues",
  "referencePublication": "https://doi.org/10.21105/joss.06722"
}