Data and code from: Loggerhead turtle oceanic-neritic habitat shift reveals key foraging areas in the Western Indian Ocean
Creators: name: Monsinjon, Jonathan
name: Laforge, Antoine
name: Gaspar, Philippe
name: Barat, Anne
name: Bousquet, Olivier
name: Ciccione, Stéphane
name: Jean, Claire
name: Ballorain, Katia
name: Dalleau, Mayeul
name: Coelho, Rui
name: Bonhommeau, Sylvain
name: Bourjea, Jérôme
Publisher: name: figshare
Year: 2023
Subjects: Behavioural ecology

description: Data and code from: Loggerhead turtle oceanic-neritic habitat shift reveals key foraging areas in the Western Indian Ocean Authors: Jonathan R. Monsinjon, Antoine Laforge, Philippe Gaspar, Anne Barat, Olivier Bousquet, Stéphane Ciccione, Claire Jean, Katia Ballorain, Mayeul Dalleau, Rui Coelho, Sylvain Bonhommeau, Jérôme Bourjea Correspondence: jonathan.monsinjon@gmail.com <br> 1. R code (run with R version 4.1.0) used to interpolate raw locations at regular 12-h time step: <br> # Author Antoine Laforge <br> # Files 20210614_InterpoFunctions_AL.R Main_foieGras_AL.R <br> # Notes 20210614_InterpoFunctions_AL.R contains the functions used in the main script Main_foieGras_AL.R The scripts use functions of the package 'foieGras', which is now available under the name 'aniMotum': https://github.com/ianjonsen/aniMotum Interpolated tracks were then corrected for daily surface currents (from the GLORYS12 ocean reanalysis accessed from Mercator Ocean International) and a series of oceanographic data were extracted at each location using Python code (run with Python version 3.10) from 'cooloc': https://gitlab.mercator-ocean.fr/pgiffard/coloc/-/tree/master/cooloc <br> 2. R code (run with R version 4.2.2) used to infer behavioral states and compare turtle-habitat groups and oceanographic variables (same version provided in .Rmd and .html): <br> # Author Jonathan R. Monsinjon <br> # Files R-Ontogenetic shift and key foraging areas.Rmd R-Ontogenetic shift and key foraging areas.html <br> # Notes This script was used for turtle behavioral analysis, comparison of Hidden Markov Models, identification of oceanic and neritic regions, comparison of oceanographic data and time proportion allocated to each behavior, production of figures, and various exploratory tasks. <br> 3. Data: <br> # File trackingdata_movement.csv <br> # Notes This file, exported via R-Ontogenetic shift and key foraging areas.Rmd, contains turtle interpolated positions centered at 12-pm with current-corrected positions, oceanic and neritic regions, estimated behavioral states, and a series of oceanographic variables GLORYS12 and LMTL-SEAPODYM. Details on the columns are given below (label/description). <br> turtle/turtle's name lon/longitude of interpolated locations (in decimal degrees; EPSG:4326) lat/latitude of interpolated locations (in decimal degrees; EPSG:4326) id/Argos Platform Transmitters Terminal (PTT) identification number date/date in yyyy-mm-dd HH:MM:SS format (GMT0) x.se/standard error of the longitude of interpolated locations (in km) y.se/standard error of the latitude of interpolated locations (in km) us/zonal component of estimated turtle swimming velocity (in m/s) vs/meridional component of estimated turtle swimming velocity (in m/s) u.se/standard error of the zonal component of turtle displacement velocity (in m/s) v.se/standard error of the meridional component of turtle displacement velocity (in m/s) s/stochastic volatility of interpolated locations s.se/standard error of the stochastic volatility parameter x/projected longitude of interpolated locations (in km; EPSG:3857) y/projected latitude of interpolated locations (in km; EPSG:3857) dtobs/number of hours between interpolated locations and the closest observed (Argos) location uc/zonal component of surface current velocity (in m/s) vc/meridional component of surface current velocity (in m/s) thetao/sea surface temperature (in °C) zos/sea surface height above geoid (in m) mlotst/mixed layer thickness (in m) ut/zonal component of turtle displacement velocity (in m/s) vt/meridional component of turtle displacement velocity (in m/s) lat_corr_uc/latitude of current-corrected interpolated locations (in decimal degrees; EPSG:4326) lon_corr_uc/longitude of current-corrected interpolated locations (in decimal degrees; EPSG:4326) mnkc/total biomass of micronekton available in the epipelagic zone accounting for the diel migration of mesopelagic micronekton (in g m-2) mnkc_epi/biomass of epipelagic micronekton (in g m-2) zooc/biomass of zooplankton (in g m-2) npp/net primary production (in mg m-2 day-1) bathy/elevation from GEBCO Gridded Bathymetry Data (in m) speed/turtle swimming speed calculated from us and vs (in m/s) reliable/Boolean variable: set to FALSE if x.se&gt;8.333333, y.se&gt;8.333333, dtobs&gt;24, speed&gt;0.746634 segment/segments' ID (integer) if keepsegment is TRUE keepsegment/Boolean variable: set to TRUE if at least three consecutive daily locations available after unreliable data were filtered out heading/turtle main direction: Unknown, South, or North PPOW/Pelagic Province Of the World where interpolated locations were found MEOW/Marine Ecoregion Of the World where interpolated locations were found phase/Oceanic or Neritic if interpolated locations are within a PPOW or a MEOW respectively segment2/level 2 segments' ID (integer) if keepsegment2 is TRUE keepsegment2/Boolean variable: set to TRUE if keepsegment is TRUE and at least three consecutive daily locations available after locations were assigned to an Oceanic or Neritic phase tracer/row number step/daily step length calculated from lon_corr_uc and lat_corr_uc (in km) angle/daily turning angle calculated from lon_corr_uc and lat_corr_uc (in radians) state/behavioral state inferred from hidden Markov models via the Viterbi algorithm (1 is traveling, 2 is searching, 3 is foraging) state1_probs/probability of state 1 state2_probs/probability of state 2 state3_probs/probability of state 3