# sepkoski

## Overview

`sepkoski` is a data R package of Sepkoski’s fossil marine animal genera
compendium (Sepkoski, 2002), ported from Shanan Peters’ [online
database](http://strata.geology.wisc.edu/jack/).

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](https://stratigraphy.org/ICSchart/ChronostratChart2023-09.pdf).
- `interval_table` A table linking intervals in Sepkoski’s compendium
  with the [International Geological Time Scale
  2023](https://stratigraphy.org/ICSchart/ChronostratChart2023-09.pdf).
- A function
  ([`sepkoski_curve()`](https://sepkoski.palaeoverse.org/reference/sepkoski_curve.md))
  for plotting Sepkoski’s evolutionary fauna with ggplot for easy
  reproduction in presentations, articles, etc.
- A function
  ([`sepkoski_curve_base()`](https://sepkoski.palaeoverse.org/reference/sepkoski_curve_base.md))
  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("palaeoverse/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()`](https://sepkoski.palaeoverse.org/reference/sepkoski_curve.md)
and
[`sepkoski_curve_base()`](https://sepkoski.palaeoverse.org/reference/sepkoski_curve_base.md).
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](reference/figures/sepkoski_curve_base.png) 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](reference/figures/sepkoski_curve_base_custom.png) 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](reference/figures/sepkoski_curve.png)
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](reference/figures/sepkoski_curve_custom.png) 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](http://strata.geology.wisc.edu/jack/).

# Package index

## All functions

- [`interval_table`](https://sepkoski.palaeoverse.org/reference/interval_table.md)
  : Interval table for linking and standardising intervals
- [`sepkoski`](https://sepkoski.palaeoverse.org/reference/sepkoski.md) :
  Sepkoski's marine animal genera compendium
- [`sepkoski_curve()`](https://sepkoski.palaeoverse.org/reference/sepkoski_curve.md)
  : Plot Sepkoski's evolutionary fauna using ggplot
- [`sepkoski_curve_base()`](https://sepkoski.palaeoverse.org/reference/sepkoski_curve_base.md)
  : Plot Sepkoski's evolutionary fauna using base R
- [`sepkoski_raw`](https://sepkoski.palaeoverse.org/reference/sepkoski_raw.md)
  : Sepkoski's marine animal genera compendium (raw)