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README.Rmd
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README.Rmd
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---
title: "Physiological responses to capture, handling and tagging in flapper skate (_Dipturus intermedius_)"
author: Georgina C. Cole^1^, Edward Lavender^2,3,4\*^, Adam Naylor^1,5^, Simon J. Girling^1^, Dmitry Aleynik^6^, Steffen J. Oppel^7^, Jane Dodd^8^, James Thorburn^3,9,10^
output: github_document
---
[](https://www.repostatus.org/#inactive)
[](https://zenodo.org/doi/10.5281/zenodo.10827243)
^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 (<[email protected]>).
# Introduction
This repository contains methods, written in [R](https://www.r-project.org/) and organised as an [RStudio](https://www.rstudio.com/) [Project](https://r4ds.had.co.nz/workflow-projects.html) 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.
<img src="README.jpg"/>
_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._
# Description
## Dependencies
The project was built in [R](https://www.r-project.org/) (version `r paste0(version$major, ".", version$minor)`) in [RStudio](https://www.rstudio.com/) and implements local dependency management using [`renv`](https://rstudio.github.io/renv/articles/renv.html). This manages the installation of the [`dv`](https://github.com/edwardlavender/dv) package for project management (from [GitHub](https://github.com/)), as well as other packages from the [Comprehensive R Archive Network](https://cran.r-project.org/). The first time the project is opened, [`renv`](https://rstudio.github.io/renv/articles/renv.html) can be used to regenerate the local project library, as described in `renv.lock` (via `.Rprofile` and `renv/activate.R`).
## Directories
The project follows a standardised structure encouraged by the [`dv`](https://github.com/edwardlavender/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](https://biogeo.ucdavis.edu/data/gadm3.6/Rsp/gadm36_GBR_0_sp.rds);
- `mesh/` contains mesh files for the West Scotland Coastal Ocean Modelling System (WeStCOMS), sourced from [Dmitry Aleynik](https://www.sams.ac.uk/people/researchers/aleynik-dr-dmitry/) at the Scottish Association for Marine Science (SAMS). These files are also available from the [SAMS Thredds Server](https://www.sams.ac.uk/facilities/thredds/);
2. **`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](https://digimap.edina.ac.uk) (higher resolution data from the [Ireland, Northern Ireland and Scotland Hydrographic surveys](https://doi.org/10.1017/S1755691015000146) 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](https://www.rstudio.com/) [Project](https://r4ds.had.co.nz/workflow-projects.html)-management files generated by [`dv`](https://github.com/edwardlavender/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); <br/>
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; <br/>
5. **`dev/`** contains project-management scripts:
- `01-dev.R` and `02-clone.R` are standard [`dv`](https://github.com/edwardlavender/dv) scripts:
- `01-dev.R` records project set up and development;
- `02-clone.R` is used to clone the project (see 'Instructions'); <br/>
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.
# Instructions
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`](https://rstudio.github.io/renv/articles/renv.html) 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`.
# Citation
Cole et al. (in prep). Physiological responses to capture, handling and tagging in flapper skate (*Dipturus intermedius*).
---