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sepkoski

A data R package of Sepkoski's fossil marine animal genera compendium (Sepkoski, 2002).

https://github.com/lewisajones/sepkoski

Science Score: 36.0%

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    Low similarity (17.1%) to scientific vocabulary
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Repository

A data R package of Sepkoski's fossil marine animal genera compendium (Sepkoski, 2002).

Basic Info
Statistics
  • Stars: 2
  • Watchers: 1
  • Forks: 1
  • Open Issues: 0
  • Releases: 1
Created over 3 years ago · Last pushed almost 2 years ago
Metadata Files
Readme Changelog Contributing License Code of conduct

README.md

sepkoski

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Overview

sepkoski is a data R package of Sepkoski's fossil marine animal genera compendium (Sepkoski, 2002), ported from Shanan Peters' online database.

The aim of sepkoski is to provide a light and easily-accessible solution to working with Sepkoski's compendium to support teaching exercises. The package provides access to:

  • sepkoski_raw Sepkoski's raw fossil marine animal genera compendium (Sepkoski, 2002).
  • sepkoski Sepkoski's compendium with first and last appearance intervals updated to be consistent with stages from the International Geological Time Scale 2023.
  • interval_table A table linking intervals in Sepkoski's compendium with the International Geological Time Scale 2023.
  • A function (sepkoski_curve()) for plotting Sepkoski's evolutionary fauna with ggplot for easy reproduction in presentations, articles, etc.
  • A function (sepkoski_curve_base()) for plotting Sepkoski's evolutionary fauna with base R for easy reproduction in presentations, articles, etc.

Note: In updating interval names, some interpretation was required. The interval_table dataset documents the linked interval names. If you notice any issue, or disagree with any of these assignments, please feel free to raise a GitHub issue, and I will do my best to address them as soon as possible.

Installation

The stable version of sepkoski can be installed via the CRAN using:

```r

Install stable version of the package

install.packages("sepkoski") ```

The development version of sepkoski can be installed via GitHub using:

```r

Install development version of the package

devtools::install_github("LewisAJones/sepkoski") ```

Usage

```r

Load library

library(sepkoski) ```

The datasets in sepkoski can be easily accessed via:

```r

Raw dataset

data("sepkoski_raw")

Updated interval dataset

data("sepkoski")

Interval table

data("interval_table") ```

The only two functions in the sepkoski package at this time are sepkoski_curve() and sepkoski_curve_base(). These can be used to plot--with base R or ggplot2--Sepkoski's evolutionary fauna (Sepkoski, 1981) using the Sepkoski (2002) fossil marine animal genera compendium. Users may provide their own values to function arguments or add layers to customise the appearance, or simply use the default arguments:

Base R

r sepkoski_curve_base() Plot with default arguments Default Phanerozoic plot of Sepkoski's three great evolutionary fauna. Number of genera are counted per international geological stage bin.

r sepkoski_curve_base(plot_args = list(main = "Sepkoski's Curve", xlab = "Age (Ma)", col = c("#2171b5", "#6baed6", "#bdd7e7", "#eff3ff")), axis_args = list(intervals = list("stages", "periods"), lab = list(FALSE, TRUE), height = 0.04)) Plot with default arguments Custom Phanerozoic plot of Sepkoski's three great evolutionary fauna. Number of genera are counted per international geological stage bin.

ggplot2

r sepkoski_curve() Plot with default arguments Default Phanerozoic plot of Sepkoski's three great evolutionary fauna. Number of genera are counted per international geological stage bin.

r library(ggplot2) library(deeptime) sepkoski_curve() + scale_fill_brewer() + coord_geo( pos = as.list(rep("bottom", 2)), dat = list("stages", "periods"), height = list(unit(2, "lines"), unit(2, "line")), size = list(4, 4), lab = list(FALSE, TRUE)) Plot with default arguments Custom Phanerozoic plot of Sepkoski's three great evolutionary fauna. Number of genera are counted per international geological stage bin.

References

Sepkoski, J. J. (1981). A factor analytic description of the Phanerozoic marine fossil record. Paleobiology, 7(1), pp. 36-53.

Sepkoski, J. J. (2002). A compendium of fossil marine animal genera. Bulletins of American paleontology, 363, pp. 1-560.

Peters, S. (2022). Sepkoski's Online Genus Database.

Owner

  • Name: Lewis A. Jones
  • Login: LewisAJones
  • Kind: user
  • Location: Vigo, Spain
  • Company: Universidade de Vigo

Postdoctoral Research Fellow (Palaeobiology) at the Universidade de Vigo.

GitHub Events

Total
  • Fork event: 1
Last Year
  • Fork event: 1

Committers

Last synced: 12 months ago

All Time
  • Total Commits: 58
  • Total Committers: 1
  • Avg Commits per committer: 58.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 7
  • Committers: 1
  • Avg Commits per committer: 7.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Lewis A. Jones 4****s 58

Issues and Pull Requests

Last synced: 12 months ago

All Time
  • Total issues: 1
  • Total pull requests: 1
  • Average time to close issues: over 1 year
  • Average time to close pull requests: about 9 hours
  • Total issue authors: 1
  • Total pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: about 9 hours
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • LewisAJones (2)
Pull Request Authors
  • LewisAJones (1)
Top Labels
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Packages

  • Total packages: 1
  • Total downloads:
    • cran 232 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 1
  • Total maintainers: 1
cran.r-project.org: sepkoski

Sepkoski's Fossil Marine Animal Genera Compendium

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 232 Last month
Rankings
Forks count: 28.8%
Dependent packages count: 29.8%
Stargazers count: 35.2%
Dependent repos count: 35.5%
Average: 43.0%
Downloads: 85.7%
Maintainers (1)
LewisA.Jones@outlook.com
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.5.0 depends
  • covr * suggests
  • knitr * suggests
  • testthat >= 3.0.0 suggests
  • vdiffr >= 1.0.0 suggests
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  • actions/checkout v3 composite
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