IncR: a new R package to analyse incubation behaviour

Pablo Capilla‐Lasheras

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.

Highlights

Incubation represents a crucial life stage for egg-laying vertebrates, of which birds are a paramount example
The current package ver. (1.1.0) allows the user to visualise the results of incRscan, calculate onset and end of daily activity, percentage of daily time spent in the nest, number and average duration of on/off-bouts per day as well as individual off-bout duration and timing and nest temperature mean and variance for a customised time window
The algorithm in incRscan was able to provide accurate off-bout information (Fig. 3B, C). incR-estimated off-bout number and mean daily off-bout duration were highly correlated with real off-bout number and duration as extracted from video footage. These results show that the method presented here can yield accurate metrics of incubation behaviour

Summary

Introduction

Incubation represents a crucial life stage for egg-laying vertebrates, of which birds are a paramount example. (1.1.0) allows the user to visualise the results of incRscan (incRplot generates a plot similar to graph 3 in Fig. 1 and Supplementary material Appendix 3 Fig. A1), calculate onset and end of daily activity (incRact), percentage of daily time spent in the nest (incRatt), number and average duration of on/off-bouts per day as well as individual off-bout duration and timing (incRbouts) and nest temperature mean and variance for a customised time window (incRt). The implementation of these functions is straightforward as they only require a variable with binary data for on and off-bouts.

Results and discussion

Limitations

Conclusions