catRlog:a photo-identification project management system based in R

Photo-identification (photo-ID) databases can comprise versatile troves of information for well-studied animal populations and, when organized well and curated carefully, can be readily applied to a wide range of research questions, such as population abundance estimates, meta-population connectivit...

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Bibliographic Details
Published in:Mammalian Biology
Main Authors: Keen, Eric M., Wren, Julia, O'Mahony, Eadin, Wray, Janie
Format: Article in Journal/Newspaper
Language:English
Published: 2022
Subjects:
Photo-identification
R
Shiny
Mark-recapture
Social network analysis
Canada
Pacific
Balaenoptera physalus
Megaptera novaeangliae
Online Access:https://research-portal.st-andrews.ac.uk/en/researchoutput/catrlog(bd05802a-a6d9-4dd9-be7b-892ebf1b4f33).html
https://doi.org/10.1007/s42991-021-00158-7
Description
Summary:Photo-identification (photo-ID) databases can comprise versatile troves of information for well-studied animal populations and, when organized well and curated carefully, can be readily applied to a wide range of research questions, such as population abundance estimates, meta-population connectivity and social network structure. To bring the potential impact of photo-ID data within reach of a greater number of research groups, we introduce an R-based photo-ID project management system, named 'catRlog'. As a computer directory with custom apps embedded throughout, catRlog serves as a workflow organizer that simplifies, streamlines, and improves the quality of photo-ID data processing. The system can be utilized by research teams in a number of ways, ranging from automated formatting and printing of a photo-ID catalog, to photo-ID matching, thereby creating and expanding a historical catalog, to processing of identification data to generate datasets necessary for site fidelity, mark-recapture, and social association analyses. As an R-based tool, the apps are open-source, cross-platform, readily customizable, and easily updated. catRlog has been tested using photo-ID databases of humpback whales ( Megaptera novaeangliae ) and fin whales ( Balaenoptera physalus ) within a mainland fjord system of Pacific Canada, but is a generalized system useful for almost any photo-ID project of any species in any habitat. A detailed user's manual and example dataset are provided.

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