Selection of likely foraging dives with a vertical approach (Planque et al., 2020)
• OBJECTIVES : Identify the foraging areas of diving predators (here harbour and grey seals) by analysing dive data obtained from telemetry tags (here GPS/GSM tags). The two seal species are usually considered as benthic foragers and therefore typically perform fast U-shaped dives to forage. We therefore aimed at selecting this type of dives (called 'likely foraging dives') using two dive criteria, and to spatialise these dives (i.e. likely foraging areas).
• METHOD :
(1) Calculate individual Minimum Cost of Transport Speed (MCTS). It is based on TAD index calculation, and should ideally be run at the individual level (method presented by Vincent et al., 2016). Function MCTS_ind.
(2) Determine dive shape with the Time Allocation at Depth (TAD) index (Fedak et al., 2001). Function TAD_index.
(3) Select likely foraging dives using two dive criteria: dive shape (TAD) and vertical descent speed (vertical approach by Planque et al., 2020).
(4) Spatialise foraging areas with likely foraging dives, by determining Kernel density contours at 95%, 75% and 50%. Kernels were identified here with the function Kernel_polyg_fast, based on some part of codes (cf. the function calcHR) proposed by Fieberg (2014), on the function bkde2D ("KernSmooth" package), and on new codes using several functions in "sf" package. Output: "sf" polygons. Maps can be created with "ggplot2".
• LANGUAGE : R (version 4.0.2).
• CASE STUDY : harbour seals and grey seals captured in the Baie de Somme (France), respectively in 2008 and 2012, and fitted with GPS/GSM tags. We identified here the foraging areas at both species and individual levels.
Planque Y, Spitz J, Authier M, Guillou G, Vincent C, Caurant F. Trophic niche overlap between sympatric harbour seals (Phoca vitulina) and grey seals (Halichoerus grypus) at the southern limit of their European range (Eastern English Channel). Ecol Evol. 2021;00:1– 22. https://doi.org/10.1002/ece3.7739
Planque Yann, Caurant Florence, Vincent Cécile (2021). Dive data obtained from telemetry tracking of ten harbour seals (Phoca vitulina) and twelve grey seals (Halichoerus grypus), captured in the Baie de Somme, France, in 2008 and 2012, and fitted with GPS/GSM tags. SEANOE. https://doi.org/10.17882/80016
Before running the script, please download the file repository in the ZIP file and place it on your desktop. Place the data previously dowloaded in the subfolder "Input".
First publication on GitHub : 2021-04-14
Last update : 2021-07-06 (Version 1.2)
Affiliation : (1) Centre d'Etudes Biologiques de Chizé (CEBC, UMR 7372 CNRS - La Rochelle Université), La Rochelle, France