# palaeoverse `palaeoverse` is an R package developed by palaeobiologists, for palaeobiologists. The aim of `palaeoverse` is to generate a community-driven software package of generic functions for the palaeobiological community. The package does not provide implementations of statistical analyses, rather it provides auxiliary functions to help streamline analyses and improve code readability and reproducibility. # Installation The stable version of `palaeoverse` can be installed from CRAN using: ``` r install.packages("palaeoverse") ``` The development version of `palaeoverse` can be installed via GitHub using: ``` r # install.packages("devtools") devtools::install_github("palaeoverse/palaeoverse") ``` # How to contribute? If you are interested in contributing to the `palaeoverse` R package, you can do so by following these [guidelines](https://palaeoverse.palaeoverse.org/CONTRIBUTING.html). We have also adopted a set of [standards and structure](https://palaeoverse.palaeoverse.org/articles/structure-and-standards.html) to follow for contributing to the project. If you would like to contribute to `palaeoverse`, we strongly advise reading this document. # Code of Conduct As with any community project, society, or meeting we feel it is important to established some expectations of behaviour in the `palaeoverse` community. Please read our [code of conduct](https://palaeoverse.palaeoverse.org/CODE_OF_CONDUCT.html), and reach out if you ever face any issues. Everyone has the right to live and work in a harassment-free environment. # Citation If you use the palaeoverse R package in your work, please cite the original article describing the package: Jones, L.A., Gearty, W., Allen, B.J., Eichenseer, K., Dean, C.D., Galván S., Kouvari, M., Godoy, P.L., Nicholl, C., Buffan, L., Dillon, E.M., Flannery-Sutherland, J.T., Chiarenza, A.A. 2023. palaeoverse: A community-driven R package to support palaeobiological analysis. *Methods in Ecology and Evolution* 14(09), 2205–2215. DOI: [10.1111/2041-210X.14099](https://doi.org/10.1111/2041-210X.14099). And the package version you are using: ``` r # Get citation citation("palaeoverse") # Get citation in BibTex format toBibtex(citation("palaeoverse")) ``` # Maintainers - [Lewis A. Jones](mailto:LewisA.Jones@outlook.com), University College London - [Palaeoverse](https://palaeoverse.org) ## Contributors All contributions to this project are gratefully acknowledged using the [`allcontributors` package](https://github.com/ropensci/allcontributors) following the [allcontributors](https://allcontributors.org) specification. Contributions of any kind are welcome! [TABLE] # Package index ## Data cleaning and preparing Functions for cleaning and preparing occurrence or taxonomic data for downstream analyses. - [`tax_check()`](https://palaeoverse.palaeoverse.org/reference/tax_check.md) : Taxonomic spell check - [`phylo_check()`](https://palaeoverse.palaeoverse.org/reference/phylo_check.md) : Check phylogeny tip names - [`tax_unique()`](https://palaeoverse.palaeoverse.org/reference/tax_unique.md) : Filter occurrences to unique taxa - [`palaeorotate()`](https://palaeoverse.palaeoverse.org/reference/palaeorotate.md) : Palaeorotate fossil occurrences - [`look_up()`](https://palaeoverse.palaeoverse.org/reference/look_up.md) : Look up geological intervals and assign geological stages - [`tax_expand_lat()`](https://palaeoverse.palaeoverse.org/reference/tax_expand_lat.md) : Generate pseudo-occurrences from latitudinal range data - [`tax_expand_time()`](https://palaeoverse.palaeoverse.org/reference/tax_expand_time.md) : Generate pseudo-occurrences from temporal range data - [`tax_certainty()`](https://palaeoverse.palaeoverse.org/reference/tax_certainty.md) : Classify the certainty of taxonomic identifications ## Data binning Functions for binning occurrence data. - [`bin_lat()`](https://palaeoverse.palaeoverse.org/reference/bin_lat.md) : Assign fossil occurrences to latitudinal bins - [`bin_space()`](https://palaeoverse.palaeoverse.org/reference/bin_space.md) : Assign fossil occurrences to spatial bins - [`bin_time()`](https://palaeoverse.palaeoverse.org/reference/bin_time.md) : Assign fossil occurrences to time bins ## Data summarisation Functions to summarise occurrence-level data. - [`tax_range_space()`](https://palaeoverse.palaeoverse.org/reference/tax_range_space.md) : Calculate the geographic range of fossil taxa - [`tax_range_time()`](https://palaeoverse.palaeoverse.org/reference/tax_range_time.md) : Calculate the temporal range of fossil taxa ## Data visualization Functions to aid in the visualisation of data and analysis results. - [`axis_geo()`](https://palaeoverse.palaeoverse.org/reference/axis_geo.md) [`axis_geo_phylo()`](https://palaeoverse.palaeoverse.org/reference/axis_geo.md) : Add an axis with a geological timescale - [`tax_range_strat()`](https://palaeoverse.palaeoverse.org/reference/tax_range_strat.md) : Generate a stratigraphic section plot ## Auxiliary functions Functions to support further functionality. - [`lat_bins()`](https://palaeoverse.palaeoverse.org/reference/lat_bins.md) **\[deprecated\]** : Generate equal-width latitudinal bins - [`lat_bins_area()`](https://palaeoverse.palaeoverse.org/reference/lat_bins_area.md) : Generate equal-area latitudinal bins - [`lat_bins_degrees()`](https://palaeoverse.palaeoverse.org/reference/lat_bins_degrees.md) : Generate equal-width latitudinal bins - [`time_bins()`](https://palaeoverse.palaeoverse.org/reference/time_bins.md) : Generate time bins - [`group_apply()`](https://palaeoverse.palaeoverse.org/reference/group_apply.md) : Apply a function over grouping(s) of data ## Built-in data palaeoverse comes with a selection of built-in datasets that are used in examples to illustrate various use cases. - [`GTS2012`](https://palaeoverse.palaeoverse.org/reference/GTS2012.md) : Geological Timescale 2012 - [`GTS2020`](https://palaeoverse.palaeoverse.org/reference/GTS2020.md) : Geological Timescale 2020 - [`interval_key`](https://palaeoverse.palaeoverse.org/reference/interval_key.md) : Example dataset: Interval key for the look_up function - [`reefs`](https://palaeoverse.palaeoverse.org/reference/reefs.md) : Example dataset: Phanerozoic reefs from the PaleoReefs Database - [`tetrapods`](https://palaeoverse.palaeoverse.org/reference/tetrapods.md) : Example dataset: Early tetrapod data from the Paleobiology Database # Articles ### All vignettes - [Latitudinal trends in Phanerozoic reefs](https://palaeoverse.palaeoverse.org/articles/phanerozoic-reefs.md): - [Contributing to palaeoverse: structure and standards](https://palaeoverse.palaeoverse.org/articles/structure-and-standards.md): - [Alpha diversity and geographic range size of Carboniferous and Permian tetrapods](https://palaeoverse.palaeoverse.org/articles/tetrapod-biodiversity.md):