DAISIEprep
Extracts phylogenetic island community data from phylogenetic trees
Science Score: 36.0%
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Low similarity (14.6%) to scientific vocabulary
Keywords
Repository
Extracts phylogenetic island community data from phylogenetic trees
Basic Info
- Host: GitHub
- Owner: joshwlambert
- License: gpl-3.0
- Language: R
- Default Branch: master
- Homepage: https://joshwlambert.github.io/DAISIEprep
- Size: 17.6 MB
Statistics
- Stars: 6
- Watchers: 3
- Forks: 4
- Open Issues: 4
- Releases: 11
Topics
Metadata Files
README.md
DAISIEprep 
Package description
DAISIEprep is an R package that enables the extraction and formatting of phylogenetic data on island species for the inference model DAISIE (Dynamic Assembly of Island biota through Speciation, Immigration and Extinction). The central function, DAISIEprep::extract_island_species(), uses data from phylogenetic trees and species island endemicity statuses (i.e. endemic to the island, non-endemic, or not present on the island). The phylogenetic and endemicity data are handled together using the phylo4d S4 class from the phylobase R package.
DAISIEprep fills the niche of standardised, reproducible data processing for the suite of DAISIE inference models. Unlike other phylogenetic methods implemented in R, DAISIE has yet to have a defined methodological framework to extract and format data prior to analysis. While other phylogenetic models in R commonly use the phylo S3 data structure, defined by the R package ape, DAISIE has an idiosynchratic data structure that will be unfamiliar to new users. This package provides a set of tools for those users to facilitate the application of DAISIE's models for research. The package also opens the possibility of extracting island data from ‘big data’ macrophylogenies (>5,000 species) which would have impeded researchers who would have previously had to extract this data manually.
There are two algorithms to extract the data the min algorithm or asr (ancestral state reconstruction) algorithm. The former is based on the rules/assumptions of the DAISIE inference model of colonisation of species from mainland source pool, speciation on the island through cladogenesis or anagenensis, and island extinction. Therefore, this algorithm assumes no back-colonisation from the island to the mainland or mainland evolutionary processes. If the data seems to conform to these assumptions (by visual inspection) then this is a good method to choose (DAISIEprep::extract_island_species(..., extraction_method = “min”). Alternatively, the data may violate these assumptions, by, for example having species within an island radiation migrate back to the mainland. In these, and other cases the asr algorithm provides a method to extract data based on the most probable reconstruction of the species ranges (i.e. island presence/absence) and then can extract clades that may have non-island species (DAISIEprep::extract_island_species(..., extraction_method = “asr”). The asr algorithm utilises ancestral state reconstruction methods from other packages (e.g. castor), but the package is flexible to users extending this to incorporate other models which may better suit their data set.
Installation
Install DAISIEprep from CRAN:
r
install.packages("DAISIEprep")
The development version of DAISIEprep can be installed from GitHub:
r
if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes")
remotes::install_github("joshwlambert/DAISIEprep")
Tutorial
See tutorial.
See frequently asked questions (FAQs) about DAISIE.
Help
To report a bug please open an issue or email at j.w.l.lambert\@rug.nl{.email}.
Contribute
The DAISIE team always welcomes contributions to any of its packages. If you would like to contribute to this package please follow the contributing guidelines
Code of Conduct
Please note that the DAISIEprep project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.
Owner
- Name: Joshua Lambert
- Login: joshwlambert
- Kind: user
- Location: London, UK
- Company: LSHTM
- Repositories: 42
- Profile: https://github.com/joshwlambert
Software engineer | evolutionary biologist | island biogeographer
GitHub Events
Total
- Create event: 12
- Release event: 1
- Issues event: 12
- Delete event: 7
- Issue comment event: 15
- Push event: 37
- Pull request review event: 6
- Pull request event: 18
- Fork event: 1
Last Year
- Create event: 12
- Release event: 1
- Issues event: 12
- Delete event: 7
- Issue comment event: 15
- Push event: 37
- Pull request review event: 6
- Pull request event: 18
- Fork event: 1
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 30
- Total pull requests: 28
- Average time to close issues: 3 months
- Average time to close pull requests: 6 days
- Total issue authors: 5
- Total pull request authors: 4
- Average comments per issue: 1.47
- Average comments per pull request: 0.57
- Merged pull requests: 27
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 9
- Pull requests: 13
- Average time to close issues: about 2 months
- Average time to close pull requests: 7 days
- Issue authors: 3
- Pull request authors: 3
- Average comments per issue: 1.67
- Average comments per pull request: 0.0
- Merged pull requests: 12
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- joshwlambert (12)
- TheoPannetier (10)
- luislvalente (8)
- teunbrand (1)
- pepijnhelleman (1)
Pull Request Authors
- joshwlambert (26)
- luislvalente (6)
- TheoPannetier (2)
- Neves-P (2)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- cran 229 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 3
- Total maintainers: 1
cran.r-project.org: DAISIEprep
Extracts Phylogenetic Island Community Data from Phylogenetic Trees
- Homepage: https://github.com/joshwlambert/DAISIEprep
- Documentation: http://cran.r-project.org/web/packages/DAISIEprep/DAISIEprep.pdf
- License: GPL (≥ 3)
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Latest release: 1.0.0
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
- actions/checkout v3 composite
- r-lib/actions/check-r-package v2 composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite
- r-lib/actions/setup-r-dependencies v2 composite
- JamesIves/github-pages-deploy-action v4.4.1 composite
- actions/checkout v3 composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite
- r-lib/actions/setup-r-dependencies v2 composite
- actions/checkout v3 composite
- actions/upload-artifact v3 composite
- r-lib/actions/setup-r v2 composite
- r-lib/actions/setup-r-dependencies v2 composite
- R >= 4.0 depends
- DAISIE * imports
- ape * imports
- castor * imports
- ggplot2 * imports
- ggtree * imports
- methods * imports
- phylobase * imports
- rlang * imports
- scales * imports
- tibble * imports
- BioGeoBEARS * suggests
- corHMM * suggests
- covr * suggests
- diversitree * suggests
- dplyr * suggests
- ggimage * suggests
- knitr * suggests
- rmarkdown * suggests
- testthat >= 3.0.0 suggests
- tidyr * suggests