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https://github.com/neves-p/daisierobustness

Test the Robustness of DAISIE to Geodynamics and Traits
https://github.com/neves-p/daisierobustness

birth-death-process island-biogeography maximum-likelihood-estimation pipeline r r-package robustness-assessment

Last synced: 2 months ago
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Test the Robustness of DAISIE to Geodynamics and Traits

Host: GitHub
URL: https://github.com/neves-p/daisierobustness
Owner: Neves-P
License: gpl-3.0
Created: 2020-02-13T14:46:31.000Z (almost 5 years ago)
Default Branch: master
Last Pushed: 2024-06-11T15:24:52.000Z (7 months ago)
Last Synced: 2024-06-11T22:35:26.604Z (7 months ago)
Topics: birth-death-process, island-biogeography, maximum-likelihood-estimation, pipeline, r, r-package, robustness-assessment
Language: R
Homepage:
Size: 1.07 GB
Stars: 2
Watchers: 2
Forks: 3
Open Issues: 0
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE.md

Awesome Lists containing this project

README

        # DAISIErobustness

[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)

![GitHub R package version](https://img.shields.io/github/r-package/v/Neves-P/DAISIErobustness)

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3897237.svg)](https://doi.org/10.5281/zenodo.3897237)

Branch|[![GitHub Actions logo](pics/github_actions_logo.png)](https://github.com/features/actions)|[![Codecov logo](pics/Codecov.png)](https://www.codecov.io)

--------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------

`master`|[![R-CMD-check](https://github.com/Neves-P/DAISIErobustness/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/Neves-P/DAISIErobustness/actions/workflows/R-CMD-check.yaml)|[![codecov.io](https://codecov.io/github/Neves-P/DAISIErobustness/coverage.svg?branch=master)](https://codecov.io/github/Neves-P/DAISIErobustness/branch/master)

`develop`|[![R-CMD-check](https://github.com/Neves-P/DAISIErobustness/actions/workflows/R-CMD-check.yaml/badge.svg?branch=develop)](https://github.com/Neves-P/DAISIErobustness/actions/workflows/R-CMD-check.yaml)|[![codecov.io](https://codecov.io/github/Neves-P/DAISIErobustness/coverage.svg?branch=develop)](https://codecov.io/github/Neves-P/DAISIErobustness/branch/develop)

The goal of DAISIErobustness is to run robustness studies using the island biogeography model DAISIE. For the development of the geodynamical and traits models currently in use by DAISIErobustness, see the [DAISIE package v4.2.1](https://github.com/rsetienne/DAISIE/releases/tag/v4.2.1).

# Installation

DAISIErobustness can easily be installed from GitHub by running the following code:

``` r

install.packages("remotes")

remotes::install_github("Neves-P/DAISIErobustness")

```

# Pipeline usage

`DAISIErobustness` consists of a pipeline that relies on DAISIE simulations and inference code. For an extended description of the pipeline and its usage, see [here](https://github.com/Neves-P/DAISIErobustness/wiki).

# Support/Questions

For feature requests or bug-reports, please submit an [issue](https://github.com/Neves-P/DAISIErobustness/issues/new).

For other matters, contact the authors: [@Neves-P](https://github.com/Neves-P), [@joshwlambert](https://github.com/joshwlambert) or [@xieshu95](https://github.com/xieshu95).

# References

Santos Neves, P.\*, Lambert, J. W.\*, Valente, L., & Etienne, R. S. (2021). The robustness of a simple dynamic model of island biodiversity to geological and eustatic change. bioRxiv. https://doi.org/10.1101/2021.07.26.453064