Holocene reef growth R project for Macedo and van Woesik

This code was used for the analysis for "Growth rates for coral reefs peaked at 25 °C through the Holocene" by Tonya Macedo and Robert van Woesik. <br>Overview:Main dataset: "Holocene_Reef_Growth_Final.csv" is the final dataset used for modeling, containing 1,890 samples. Main goals:Use a GLMM in INLA to determine fixed effects for coral growth rates during the Holocene. Use deep learning to evaluate non-linear relationships between variables of interest and coral reef growth rates through the Holocene. Reproduce figures from the publication or generate new figures with new data. Main scripts: Holocene_INLA_GLMM.RSets up model formulasFits modelsCompares and visualizes INLA model resultsHolocene_Deep_Learning.RSets up the H2O deep learning environmentFits 30 models using 6 different deep learning configurationsCompares and visualizes model resultsHolocene_Figures.qmdReproduces the figures used in the manuscriptUsage guidance:Each script is set up so that it can be run standalone. There is no order that the scripts need to be run. The project uses the here package for reproducible file paths, no need to set working directory.The repository is organized so that it can be cloned and executed as an R project.