Raritas: a program for counting high diversity categorical data with highly unequal abundances

PeerJ. 2018 Oct 9:6:e5453. doi: 10.7717/peerj.5453. eCollection 2018.

Abstract

Acquiring data on the occurrences of many types of difficult to identify objects are often still made by human observation, for example, in biodiversity and paleontologic research. Existing computer counting programs used to record such data have various limitations, including inflexibility and cost. We describe a new open-source program for this purpose-Raritas. Raritas is written in Python and can be run as a standalone app for recent versions of either MacOS or Windows, or from the command line as easily customized source code. The program explicitly supports a rare category count mode which makes it easier to collect quantitative data on rare categories, for example, rare species which are important in biodiversity surveys. Lastly, we describe the file format used by Raritas and propose it as a standard for storing geologic biodiversity data. 'Stratigraphic occurrence data' file format combines extensive sample metadata and a flexible structure for recording occurrence data of species or other categories in a series of samples.

Keywords: Biodiversity; Biostratigraphy; Data standards; Ecology; Micropaleontology; Point-counting; Python; Range chart; Rarity; Software.

Grants and funding

Johan Renaudie received partial support from DFG grant RE 3470/3-1. There was no additional external funding received for this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.