Circadian rhythm of preferred temperature in fish: Behavioural thermoregulation linked to daily photocycles in zebrafish and Nile tilapia
Luisa M. Vera, Gonzalo de Alba, Silvere Santos, Tim M. Szewczyk, Simon A. Mackenzie, Francisco J. Sánchez-Vázquez, Sonia Rey-Planellas. Journal of Thermal Biology, 2023
The final code and datasets associated with this manuscript are available from the journal website and data dryad. This repository hosts all files, in addition to the development history.
The R files in /code can be run from 1 to 5:
- 1_preferredTemp_runModel.R: Loads raw data, calculates observed preferred temperatures, and fits a Bayesian cosinor model with hourly preferred temperature as the response variable.
- 2_preferredTemp_processOutput.R: Reshapes, summarises, and stores model output.
- 3_chamberComp_runModel.R: Loads raw data, calculates observed preferred temperatures, and fits a Bayesian cosinor model with hourly proportional composition of fish across chambers as the response variable.
- 4_chamberComp_processOutput.R: Reshapes, summarises, and stores model output.
- 5_figuresAndSummaries.R: Loads raw data and fitted models, summarises outputs, and generates figures.
- 00_fn.R: Helper functions for processing output.
The finalised, clean data files in /data are:
- Tilapia_RawData.csv: Raw hourly counts per chamber for Nile tilapia; -1 = NA
- ZF_Data_RawData.csv: Raw hourly counts per chamber for Zebrafish; -1 = NA
- temperature_Tilapia.csv: Mean daily temperatures per chamber
- temperature_ZF.csv: Mean daily temperatures per chamber
The output files are:
- Table_preferredTemp_summary.csv: Summarised output from the model in 1_preferredTemp_runModel.R giving the posterior mean and 95% credible intervals (HPDIs) for preferred temperature and each cosinor parameter.
- Table_chamberComp_summary.csv: Summarised output from the model in 3_chamberComp_runModel.R giving the posterior mean and 95% credible intervals (HPDIs) for proportion of fish in each chamber and each cosinor parameter.