Science Score: 67.0%
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 12 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (15.1%) to scientific vocabulary
Keywords
Repository
R package for Stratigraphic Paleobiology
Basic Info
- Host: GitHub
- Owner: MindTheGap-ERC
- License: apache-2.0
- Language: R
- Default Branch: main
- Homepage: https://mindthegap-erc.github.io/StratPal/
- Size: 7.58 MB
Statistics
- Stars: 1
- Watchers: 3
- Forks: 0
- Open Issues: 0
- Releases: 8
Topics
Metadata Files
README.md
StratPal
R package for stratigraphic paleobiology modeling pipelines.
Overview
The fossil record is a joint expression of ecological, taphonomic, evolutionary, and stratigraphic processes (Holland and Patzkowsky, 2012). This package allowing to simulate biological processes in the time domain (e.g., trait evolution, fossil abundance), and examine how their expression in the rock record (stratigraphic domain) is influenced based on age-depth models, ecological niche models, and taphonomic effects. Functions simulating common processes used in modeling trait evolution, biostratigraphy or event type data such as first/last occurrences are provided and can be used standalone or as part of a pipeline. The package comes with example data sets and tutorials in several vignettes (e.g., for transforming phylogenetic trees), which can be used as a template to set up one's own simulation.
Authors
Niklas Hohmann\ Utrecht University\ email: n.h.hohmann [at] uu.nl\ Web page: uu.nl/staff/NHohmann\ Orcid: 0000-0003-1559-1838
Requirements
R version >= 4.2
Installation
To install the package from CRAN, run
r
install.packages("StratPal")
in your R console.
Github
To install the package from GitHub, first install the remotes package by running
r
install.packages("remotes")
in the R console. Then, run
r
remotes::install_github(repo = "MindTheGap-ERC/StratPal",
build_vignettes = TRUE,
ref = "HEAD",
dependencies = TRUE)
to install the latest stable version of the package.
Usage
Run
r
library(StratPal)
to load the package. Use
r
browseVignettes(package = "StratPal")
to view the available vignettes (long form documentation) with use cases or visit the package webpage (mindthegap-erc.github.io/StratPal) to get started.
Contribution
For contribution guidelines see the CONTRIBUTING.md file
License
Apache 2.0, see LICENSE file for license text.
Copyright
Copyright 2024 Netherlands eScience Center and Utrecht University
Citation
To cite the package, please use both references:
Hohmann, N. (2025). StratPal: R package for stratigraphic paleobiology modeling pipelines (v0.6.0). Zenodo. https://doi.org/10.5281/zenodo.12790994
Hohmann, N. and Jarochowska, E. (2024). StratPal: An R package for creating stratigraphic paleobiology modelling pipelines. Methods In Ecology and Evolution. https://doi.org/10.1111/2041-210X.14507
Alternatively, you can also use the CITATION.cff file at the root of the repository, or citation("StratPal").
References {#References}
- Holland, Steven M. and Patzkowsky, Mark E. "Stratigraphic Paleobiology : Understanding the Distribution of Fossil Taxa in Time and Space."" The University of Chicago Press; 2012.
This package uses data from
Hohmann, Niklas; Koelewijn, Joël R.; Burgess, Peter; Jarochowska, Emilia. 2024. "Identification of the mode of evolution in incomplete carbonate successions." BMC Ecology and Evolution, 24, 113. DOI: 10.1186/s12862-024-02287-2.
Hohmann, Niklas, Koelewijn, Joël R.; Burgess, Peter; Jarochowska, Emilia. 2023. "Identification of the Mode of Evolution in Incomplete Carbonate Successions - Supporting Data." Open Science Framework. https://doi.org/10.17605/OSF.IO/ZBPWA, published under the CC-BY 4.0 license.
Funding information
Funded by the European Union (ERC, MindTheGap, StG project no 101041077). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council. Neither the European Union nor the granting authority can be held responsible for them. 
Owner
- Name: MindTheGap-ERC
- Login: MindTheGap-ERC
- Kind: organization
- Repositories: 1
- Profile: https://github.com/MindTheGap-ERC
Citation (CITATION.cff)
# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!
cff-version: 1.2.0
title: >-
StratPal: R package for stratigraphic paleobiology
modeling pipelines
message: >-
If you use this software, please cite it using the
metadata from this file.
type: software
authors:
- given-names: Niklas
family-names: Hohmann
email: N.H.Hohmann@uu.nl
affiliation: Utrecht University
orcid: 'https://orcid.org/0000-0003-1559-1838'
identifiers:
- type: doi
value: 10.5281/zenodo.15480833
description: DOI of most recent archived version
- type: url
value: 'https://doi.org/10.5281/zenodo.15480833'
description: URL of most recent archived version
repository-code: 'https://github.com/MindTheGap-ERC/StratPal'
url: 'https://mindthegap-erc.github.io/StratPal/'
abstract: >-
The fossil record is a joint expression of ecological,
taphonomic, evolutionary, and stratigraphic processes
(Holland and Patzkowsky, 2012). This package allowing to
simulate biological processes in the time domain (e.g.,
trait evolution, fossil abundance), and examine how their
expression in the rock record (stratigraphic domain) is
influenced based on age-depth models, ecological niche
models, and taphonomic effects. Functions simulating
common processes used in modeling trait evolution or event
type data such as first/last occurrences are provided and
can be used standalone or as part of a pipeline. The
package comes with example data sets and tutorials in
several vignettes (e.g., for transforming phylogenetic
trees), which can be used as a template to set up one's
own simulation.
keywords:
- Stratigraphic Paleobiology
- Stratigraphy
- Paleontology
- Palaeontology
- Paleobiology
license: Apache-2.0
commit: 0753d6400922bab4f670e947dc571327036bcdfc
version: 0.6.0
date-released: '2025-08-29'
GitHub Events
Total
- Create event: 4
- Release event: 4
- Issues event: 11
- Watch event: 1
- Delete event: 2
- Issue comment event: 2
- Push event: 41
- Pull request event: 19
Last Year
- Create event: 4
- Release event: 4
- Issues event: 11
- Watch event: 1
- Delete event: 2
- Issue comment event: 2
- Push event: 41
- Pull request event: 19
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 5
- Total pull requests: 8
- Average time to close issues: about 14 hours
- Average time to close pull requests: 6 minutes
- Total issue authors: 2
- Total pull request authors: 1
- Average comments per issue: 0.0
- Average comments per pull request: 0.0
- Merged pull requests: 8
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 5
- Pull requests: 8
- Average time to close issues: about 14 hours
- Average time to close pull requests: 6 minutes
- Issue authors: 2
- Pull request authors: 1
- Average comments per issue: 0.0
- Average comments per pull request: 0.0
- Merged pull requests: 8
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- NiklasHohmann (6)
- annAjnsn (1)
- EmiliaJarochowska (1)
Pull Request Authors
- NiklasHohmann (24)
- EmiliaJarochowska (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- cran 464 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 7
- Total maintainers: 1
cran.r-project.org: StratPal
Stratigraphic Paleobiology Modeling Pipelines
- Homepage: https://mindthegap-erc.github.io/StratPal/
- Documentation: http://cran.r-project.org/web/packages/StratPal/StratPal.pdf
- License: Apache License (≥ 2)
-
Latest release: 0.6.0
published 7 months ago
Rankings
Maintainers (1)
Dependencies
- R >= 4.2 depends
- admtools * imports
- knitr * suggests
- rmarkdown * suggests
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- JamesIves/github-pages-deploy-action v4.5.0 composite
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- r-lib/actions/setup-r-dependencies v2 composite