This repo is a workflow that allows the user to rapidly measure colouration in Atlantic salmon parr - a species that shows complex variations in colour pigmentation. Colour extraction and analysis was conducted using packages: patternize, recolorize and brms. To begin, please see the number prefix for scripts in the 'analysis' folder which indicates the order in which the user should navigate the workflow. Note that uploaded rda and rds files allows the user to begin from any stage they wish. However, these files were calibrated using the full dataset (I only uploaded 20 images here as a sample). Therefore, please be careful not to over-write the original rda and rds files as this will undermine your model accuracy.
If you would like to access the full image dataset, please send me an email at: [email protected]
thanks