Tools to Use and Explore the 'BioTIME' Database

The 'BioTIME' database was first published in 2018 and inspired ideas, questions, project and research article. To make it even more accessible, an R package was created. The 'BioTIMEr' package provides tools designed to interact with the 'BioTIME' database. The functions provided include the 'BioTIME' recommended methods for preparing (gridding and rarefaction) time series data, a selection of standard biodiversity metrics (including species richness, numerical abundance and exponential Shannon) alongside examples on how to display change over time. It also includes a sample subset of both the query and meta data, the full versions of which are freely available on the 'BioTIME' website < https://biotime.st-andrews.ac.uk/home.php>.

BioTIMEr

BioTIMEr is an R package which gives you functions to work with BioTIME communities and provides an subset of the BioTIME database.

BioTIME (the Global database of assemblage time series for quantifying and understanding biodiversity change) is an international network and an open access database, free to anyone, anywhere in the world to use for education, research, and conservation.

For a complete description of the database, please refer to our open access publication entitled BioTIME 2.0: Expanding and Improving a Database of Biodiversity Time Series.

Installation

install.packages("BioTIMEr") # CRAN version

remotes::github_install("bioTIMEHub/BioTIMEr", branch = "dev") # dev version

Getting Started

Most BioTIME users are interested in standardising the extent of the datasets. Here using the data subset included inside the package.

library(BioTIMEr)
gridding(BTsubset_meta, BTsubset_data)

A likely following step would be to rarefy communities to a common sampling effort.

gridding(BTsubset_meta, BTsubset_data) |>
   resampling("ABUNDANCE")

Citation

Under the terms of the BioTIME data user agreement, users who download data agree to cite all underlying DOIs.

Please also cite BioTIMEr by running citation(package = "BioTIMEr").

Meta

• Please report any issues or bugs.
• License: MIT
• Get citation information for BioTIMEr in R doing citation(package = 'BioTIMEr')