Georgina C. Cole¹, Edward Lavender^2,3,4*, Adam Naylor^1,5, Simon J. Girling¹, Dmitry Aleynik⁶, Steffen J. Oppel⁷, Jane Dodd⁸, James Thorburn^3,9,10

¹ Royal Zoological Society of Scotland, UK
² Centre for Research into Ecological and Environmental Modelling, University of St Andrews, UK
³ Scottish Oceans Institute, University of St Andrews, UK
⁴ Department of Systems Analysis, Integrated Assessment and Modelling, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Switzerland
⁵ New Zealand Centre for Conservation Medicine, Auckland Zoo, New Zealand
⁶ Scottish Association for Marine Science, UK
⁷ Swiss Ornithological Institute, Switzerland
⁸ Nature Scot, UK
⁹ School of Applied Sciences, Edinburgh Napier University, UK
¹⁰ Centre for Conservation and Restoration Science, Edinburgh Napier University, UK

^* This repository is maintained by Edward Lavender (edward.lavender@eawag.ch).

This repository contains methods, written in R and organised as an RStudio Project for Cole et al. (in prep). Physiological responses to capture, handling and tagging in flapper skate (Dipturus intermedius).

We studied the physiological responses of flapper skate following catch-and-release angling and acoustic tagging in the Loch Sunart to the Sound of Jura Marine Protected Area on the west coast of Scotland (Figure 1). We recorded capture fight times and blood parameters following capture (blood sample one: BS1) and following handling (blood sample two: BS2). Using statistical modelling (as recorded in this repository) we investigated capture fights and relationships between blood parameters (for both BS1 and BS2) and aspects of the capture and handing process (such as fight time), individual characteristics (such as sex) and environmental conditions (such as temperature). This work was conducted as part of the Movement Ecology of Flapper Skate project.

Figure 1. A flapper skate is released following capture and handing in the Loch Sunart to the Sound of Jura Marine Protected Area on the west coast of Scotland. Photograph courtesy of the Movement Ecology of Flapper Skate project.

The project was built in R (version 4.3.1) in RStudio and implements local dependency management using renv. This manages the installation of the dv package for project management (from GitHub), as well as other packages from the Comprehensive R Archive Network. The first time the project is opened, renv can be used to regenerate the local project library, as described in renv.lock (via .Rprofile and renv/activate.R).

The project follows a standardised structure encouraged by the dv package. The high-level structure was generated via dv::use_template_proj(). The contents as follows:

1. renv/ implements local dependency management.

2. data-raw/ contains ‘raw’ data:

   • skate/ contains skate data:
     • Skate acoustic tagging data .xlsx contains raw data from capture and tagging, including the details of capture events, blood parameters and heart and respiratory rates during handling, with one individual per sheet. This file is used for the fight time, heart and respiratory rate analyses in this project.
     • Skate data analysis shared.xlsx summarises capture events and blood parameters in one place. (This document was collated by G. C. Cole.) The Data all without formulas sheet includes capture events, raw blood parameters and temperature-corrected blood parameter values. This sheet is used for the blood parameter analyses in this project.
   • spatial/ contains spatial data:
     • coast/ contains coastline data for the region, sourced from the Database of Global Administrative Areas;
     • mesh/ contains mesh files for the West Scotland Coastal Ocean Modelling System (WeStCOMS), sourced from Dmitry Aleynik at the Scottish Association for Marine Science (SAMS). These files are also available from the SAMS Thredds Server;

3. data/ contains processed data and results:

   • skate/ contains processed skate data:
     • physio.rds contains processed blood physiology data from process_bloods.R;
     • vital.rds contains processed vital signs data from process_vitals.R;
     • fights.rds contains processed capture fights data from process_fights.R;
   • spatial/ contains processed spatial data:
     • bathy/ contains one arc-second bathymetry data from Digimap (higher resolution data from the Ireland, Northern Ireland and Scotland Hydrographic surveys are not available for all sampled locations);
     • coast/ contains processed coastline data from process_spatial.R;
     • mesh/ contains processed WeStCOMS mesh files from process_spatial.R;
   • estimates/ contains model outputs from analyse_*.R scripts;
   • inst/ contains RStudio Project-management files generated by dv:
     • tree.rds is a record of the project directory tree (as generated by dv::use_template_tree() in dev/01-dev.R, see below);
       

4. R/ contains R scripts for data processing and analysis:

   • define_global_param.R defines global parameters;
   • define_helpers.R defines helper functions;
   • process_spatial.R processes raw spatial data;
   • process_bloods.R processes raw blood parameter data;
   • process_vitals.R processes raw vital signs data;
   • process_fights.R processes raw capture fights data;
   • analyse_fights.R analyses capture fights;
   • analyse_bloods.R analyses BS1 and BS2;
   • analyse_bloods_change.R analyses the change in blood parameters during handling;
   • analyse_bloods_synthesis.R synthesises results across blood parameters;
   • analyse_vitals.R analyses heart and respiratory rates during handling;
     

5. dev/ contains project-management scripts:

   • 01-dev.R and 02-clone.R are standard dv scripts:
     • 01-dev.R records project set up and development;
     • 02-clone.R is used to clone the project (see ‘Instructions’);
       

6. fig/ contains figures.

7. doc/ contains supporting documents.

Note that the data-raw/, data/ (except data/inst/), fig/ and doc directories are not currently provided in the online version of this repository.

Follow the steps described below to clone the project and reproduce the workflow.

1. Clone the project via GitHub. Follow the instructions in dev/02-clone.R to install project packages and create directories:

   • Packages. Open dev/02-clone.R to use renv to regenerate the local project library. Packages can also be manually reinstalled via 02-clone.R. (However, note that package versions may differ in this case.)
   • Directories. Rebuild the project directory tree, via dv::use_template_proj() and dv::use_template_tree().

2. Obtain raw data from the authors and/or links provided above

3. Define global parameters via define_global_param.R and define_helpers.R.

4. Process raw data via process_spatial.R, process_bloods.R, process_vitals.R and process_fights.R.

5. Implement data analysis via analyse_fights.R, analyse_bloods.R, analyse_bloods_change.R, analyse_bloods_synthesis.R and analyse_vitals.R.

Cole et al. (in prep). Physiological responses to capture, handling and tagging in flapper skate (Dipturus intermedius).