incR: a new R package to analyse incubation behaviour

Capilla-Lasheras, P. (2018) incR: a new R package to analyse incubation behaviour. Journal of Avian Biology, 49(8), e01710. (doi: 10.1111/jav.01710)

Abstract

Incubation represents a life stage of crucial importance for the optimal development of avian embryos. For most birds, incubation poses a trade‐off between investing in self‐maintenance and offspring care. Furthermore, incubation is affected by environmental temperatures and, therefore, will be likely impacted by climate change. Despite its relevance and readily available temperature logging methods, avian incubation research is hindered by recognised limitations in available software. In this paper, a new quantitative approach to analyse incubation behaviour is presented. This new approach is embedded in a free R package, incR. The flexibility of the R environment eases the analysis, validation and visualisation of incubation temperature data. The core algorithm in incR is validated here and it is shown that the method extracts accurate metrics of incubation behaviour (e.g. number and duration of incubation bouts). This paper also presents a suggested workflow along with detailed R code to aid the practical implementation of incR.

• Item Type: Articles
• Additional Information: This work was supported by a postgraduate scholarship from Iberdrola Foundation and by the Biotechnology and Biological Sciences Research Council‐funded South West Biosciences Doctoral Training Partnership (BB/M009122/1).
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Capilla Lasheras, Dr Pablo
• Authors: Capilla-Lasheras, P.
• College/School: College of Medical Veterinary and Life Sciences > School of Biodiversity, One Health & Veterinary Medicine
• Journal Name: Journal of Avian Biology
• Publisher: Wiley
• ISSN: 0908-8857
• ISSN (Online): 1600-048X
• Published Online: 10 May 2018
• Copyright Holders: Copyright © 2018 The Author
• First Published: First published in Journal of Avian Biology 49(8): e01710
• Publisher Policy: Reproduced under a Creative Commons License