Raritas and RaritasVox: Programs for counting high diversity categorical data with highly unequal abundances
- Published
- Accepted
- Subject Areas
- Biodiversity, Bioinformatics, Ecology, Paleontology
- Keywords
- software, point-counting, rarity, data standards, micropaleontology, biostratigraphy, biodiversity, ecology, python, range chart
- Copyright
- © 2018 Lazarus et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2018. Raritas and RaritasVox: Programs for counting high diversity categorical data with highly unequal abundances. PeerJ Preprints 6:e26836v1 https://doi.org/10.7287/peerj.preprints.26836v1
Abstract
Acquiring data on the occurrences of many types of difficult to identify objects are often still made by human observation, e.g. in biodiversity and paleontologic research. Existing computer counting programs used to record such data have various limitations, including inflexibility and cost. We describe a pair of new open-source programs for this purpose - Raritas and RaritasVox, which share a similar graphical user interface for mouse based counting, and file output format. 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. RaritasVox in addition supports voice based counting but is written in Java and is more complex to install or modify. Both programs explicitly support a rare category count mode which makes it easier to collect quantitative data on rare categories, e.g. rare species which are important in biodiversity surveys. Lastly, as to our knowledge no standards exist yet, we describe a new stratigraphic occurrence data (SOD) unitary file format which combines extensive metadata and a flexible structure for recording occurrence data of species or other categories in a series of samples.
Author Comment
This is a submission to PeerJ for review.
Supplemental Information
Appendices 1-3 for Raritas and RaritasVox programs by Lazarus et al
Contents:
Appendix 1 - User Guides: Install instructions for Raritas python script.txt; User Guide for Raritas app.pdf; User Guide for Raritas VOX.pdf
Appendix 2 - Sample files: cmudict.0.6d_myX1_X3 (Sample vocabulary definition file for VOX).txt; Sample configuration file for Raritas and Raritas VOX.txt; Sample output file - SOD v2.1 file Ocean drilling section.ods; Sample output file - SODv2.1 Land section.ods;
Appendix 3 - SOD definitions: SOD definitions full.ods; SOD readme.txt