The impact of isosmotic conditions on the metabolism and hypoxia tolerance of a reportedly oxyconforming teleost (gmac-mo2-24)

This work is licensed under a Creative Commons Attribution 4.0 International License. You are free to reuse, redistribute, and adapt the material, provided appropriate credit is given.

---

📄 Project Summary

• Title: The impact of isosmotic conditions on the metabolism and hypoxia tolerance of a purportedly oxyconforming teleost
• Authors: Timothy D. Clark^1^, Luis L. Kuchenmüller^1^, Elizabeth C. Hoots^1^, Maryane Gradito^1^, and Jake M. Martin^1,2^
  
• Institutions:
  ^1^ School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
  ^2^ Department of Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden\

This project tests:\

1. Whether G. maculatus exhibits oxyregulation\
2. Whether isosmotic conditions reduce resting oxygen uptake and improve hypoxia tolerance

The study compares SMR, RMR, and estimated O2crit values across salinity treatments (0 ppt vs 9 ppt), using data collected from intermittent-flow respirometry and analysed in R (v4.2.3).

📍 Browse the HTML output

---

📁 Repository Structure

📁 gmac-mo2-24/
├── 📂 input-data/                 Raw and cleaned input data
├── 📂 mod-data/                   Intermediate summaries for modelling
├── 📂 output-fig/                 Final figures used in the manuscript
├── 📂 output-mod/                 Model outputs (.rds files)
├── 📄 gmac-labchart-24.Rmd        Main analysis and figure script
├── 📄 index.html                  R script for Git page 
├── 📄 supplementary-file-1.pdf    R script as supplementary file 1
└── 📄 EXP-2024-gmac-labchart.Rproj RStudio project file

---

📦 R Dependencies

This project uses the following key R packages:

🔹 Data Visualisation\

• ggthemes\
• bayesplot\
• gt\
• gtsummary\
• plotly\
• qqplotr

🔹 Tidy Data & Wrangling\

• tidyverse\
• janitor\
• readxl\
• broom.mixed\
• data.table\
• hms\
• devtools\
• mclust

🔹 Modelling & Statistical Analysis\

• brms\
• rstan\
• marginaleffects\
• performance\
• emmeans\
• tidybayes\
• respirometry\
• future

These are installed and loaded in the .Rmd using pacman::p_load(...).

---

🔍 Key Methods

• SMR estimation: Using a custom version of the calcSMR method (Chabot et al., 2016)

• Incremental regression: Polynomial Bayesian models to describe ṀO₂--DO relationships (Urbina et al., 2012)

• Model comparison: Leave-one-out cross-validation (LOO-CV) for evaluating best-fit regressions

• O₂crit detection: Rule-based detection method (Claireaux & Chabot, 2016) paried with visual validation

---

📊 Outputs

• HTML-rendered results and figures are available at:
  📍 https://jakemartinresearch.github.io/gmac-mo2-24/

• Bayesian model outputs are saved as .rds files and stored in the /output-mod/ folder.

• For plots presented per individual fish, output figures are saved as .PDF in /output-fig/ folder.

---

📥 Download or Pull This Repository into R

To work with this project in RStudio:

1. Open RStudio → File → New Project → Version Control → Git

2. Paste this URL in the Repository URL field:

<pre>https://github.com/JakeMartinResearch/gmac-mo2-24.git</pre>

3. Choose a folder on your computer

4. Click Create Project

RStudio will now pull the GitHub repo into a new local folder.

📺 Watch this 2-min tutorial on YouTube

---

📥 Download from OSF

All data and code is also available on the Open Science Framework (OSF)

🌐 Click here for the page

This is the DOI 10.17605/OSF.IO/GFXCA

---

📘 Sharing/accessing and citing

1. Licenses/restrictions placed on the data: CC-BY 4.0

2. Link to the associated publication:
   🚧 To be added 🚧

3. Recommended citation for this data:\

Clark, T. D., Kuchenmüller, L. L., Hoots, E. C., Gradito, M., & Martin, J. M. (2025, May 28). TThe role of osmorespiratory compromise in metabolism and hypoxia tolerance of a purportedly oxyconforming teleost. https://doi.org/10.17605/OSF.IO/GFXCA

---

📩 Contact

Jake M. Martin

📧 Email: jake.martin@deakin.edu.au

📧 Alt Email: jake.martin.research@gmail.com

🌐 Web: jakemartin.org

🧪 ORCID: 0000-0001-9544-9094

---