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

PeerJ

article

David B. Lazarus¹  Johan Renaudie¹  Dorina Lenz²  Patrick Diver³  Jens Klump⁴ 

[1] Museum für Naturkunde;Leibniz-Institut für Zoo- und Wildtierforschung;Divdat Consulting;CSIRO

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

DOI  :  10.7717/peerj.5453

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

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.

【 授权许可】

CC BY