Repeated marine heatwaves reorganize coral reefs for resilience at the cost of diversity -- Data & Code

README for "Repeated marine heatwaves reorganize coral reefs for resilience at the cost of diversity -- Data & Code" on ZenodoLast modified on 4/27/2026Authors: Andrew Walker & Robert van Woesik.Description: This repository contains the code and data utilized in the study of the same name. **DATA REFINING STAGE**"1 Linking Disturbances.R"Description: Script links sampling methodology to samples, cleans and filters samples for timeseries, and links marine heatwaves and cyclones to sites/samples.Input: 1_Code_Output: Input data for "1 Linking Disturbances.R". Contains updated and cleaned spreadsheet for the coral cover dataset. Sampling_Methods: CSV of the sampling methodologies employed by the numerous sources in the dataset. Cell_i_Heatwave_Events.csv: These CSV files represent NOAA's CRW SST data that has been processed through HeatwaveR functions to detect marine heatwaves at each site. Wave_Data_All_Cells: Contains the daily maximum significant wave height for each cell that a sample is within. Cell_Numbers_for_Wave_Height: Contains the raster cell numbers that each sample falls within. Used as a quick lookup table to link samples to wave data. All_Storms_post_1970_2024_Filtered: Contains data from IBTrACS on the centroids of cyclones, with their date and lat/lon.Output: "1_All_Cover_Values.csv" "2 Extracting Ambient SST Conditions.R"Description: Script links links a variety of ambient temperature metrics to the samples.Input: 1_All_Cover_Values.csv: Input data from "1 Linking Disturbances.R". Daily SST rasters from NOAA's CRW. NOAA CRW Thermal History SST Trend raster product.Output: "2_All_Cover_Values.csv" "3 Identifying Recovery and Impact.R"Description: Script identifies whether samples were impacted by a cyclone/heatwave, or if they follow a cyclone/heatwave. This code allows for easy removal of data that do not fit certain criteria later on.Input: 2_All_Cover_Values.csv: Input data from "2 Extracting Ambient SST Conditions.R". Output: "3_Series_Data.csv" "Reef Point Monthly Heatwave Extraction.R"Description: Script logs whether a coral reef cell experienced a marine heatwave at a monthly resolution from 1985-2023.Inputs: Cell_i_Heatwave_Events.csv: These CSV files represent NOAA's CRW SST data that has been processed through HeatwaveR functions to detect marine heatwaves at each site. Reef_Area_Points.csv: Filtered spatial point dataset of coral reefs at a 4km resolution.Output: "Reef_Area_Points_Monthly_Heatwave.csv" "4 Calculating Spatial Scale of Heatwaves.R"Description: Script calculates the nearby percent reef area and the percentage of coral reefs nearby that experienced a marine heatwave within the prior 3 years.Inputs: 3_Series_Data.csv: Input data from "3 Identifying Recovery and Impact.R". Reef_Area_Points.csv: Filtered spatial point dataset of coral reefs at a 4km resolution. Reef_Area_Points_Monthly_Heatwave.csv: Reef_Area_Points.csv dataset, with monthly resolution information on whether a reef cell experienced a marine heatwave. Derived from "Reef Point Monthly Heatwave Extraction.R"Output: "4_Series_Data.csv" "9 Creating Genera Dataset.R"Description: Script processes the raw taxa data, checking to ensure that taxanomic specifications are correct, and aggregating data to the genus level. Also contains code to extract heatwave frequency.Inputs: All_Species_Cover.csv: Raw data, contains percent cover data for coral taxa. Cell_i_Heatwave_Events.csv: These CSV files represent NOAA's CRW SST data that has been processed through HeatwaveR functions to detect marine heatwaves at each site.Outputs: "Genus_Morph_Data.csv" **MODELING STAGE**"5 Impact.R"Description: Script contains the creation of the R-INLA model for the impact for marine heatwaves.Inputs: 4_Series_Data.csv: Input data from "4 Calculating Spatial Scale of Heatwaves.R". Outputs: "Raw_Impact_Data.csv": Subset of input data that contains only samples that were impacted by a marine heatwave. "Impact Variance.png": Plot of the increase in the variance of the impact of marine heatwaves as more time passes between surveys. "Impact_corplot.png": Correlation plot of the predictor variables utilized in the study. "Impact_Model.rds": R-INLA model object. "Impact_Coefficients.csv": CSV of the beta coefficients of the linear predictor variables utilized in the model. This data is what is displayed in Figure 2. "Impact_Random_Walk.csv": CSV of the random walk component of the impact model. "Impact_Model_Diagnostics.png": PNG of the posterior predictive check. "Impact_Normalized_Predictions.csv" CSV of the normalized predictions for the impact of marine heatwaves. This data is what is displayed in Figure 1. "6 Recovery Weibull.R"Description: Script contains the creation of the R-INLA model for the recovery likelihood following marine heatwaves.Inputs: 4_Series_Data.csv: Input data from "4 Calculating Spatial Scale of Heatwaves.R". Outputs: "Raw_Recovery_Likelihood_Data.csv": Subset of input data that contains only samples that followed a marine heatwave. "Rec_Likelihood_corplot.png": Correlation plot of the predictor variables utilized in the study. "Weibull_Recovery_Model.rds": R-INLA model object. "Weibull_Recovery_Coefficients.csv": CSV of the beta coefficients of the linear predictor variables utilized in the model. This data is what is displayed in Figure 2. "Weibull_Recovery_Random_Walk.csv": CSV of the random walk component of the Weibull recovery model. "Likelihood_Model_Diagnostics.png": PNG of the posterior predictive check. "Weibull_Predictions.csv": CSV of the normalized predictions for the likelihood of recovery beginning following marine heatwaves. This data is what is displayed in Figure 1. "7 Logit growth STAN.stan"Description: Script contains the Stan code for the recovery rate and upper limit model. "8 Recovery STAN.R"Description: Script contains the data preparation for the R-Stan model, as well as the actual Stan model code itself.Inputs: 4_Series_Data.csv: Input data from "4 Calculating Spatial Scale of Heatwaves.R". 7 Logit growth STAN.stan: Stan scriptOutputs: "Raw_Recovery_Data.csv": Subset of input data that contains only samples that followed a marine heatwave and had a positive change in coral cover. "Stan_Corplot.png": Correlation plot of the predictor variables utilized in the Stan model. "Stan Growth Model.rds": RDS object containing the completed R-Stan model. "Rate Coefficients.csv": CSV of the beta coefficients of the linear predictor variables utilized in the model for the recovery rate. This data is what is displayed in Figure 2. "Upper Limit Coefficients.csv": CSV of the beta coefficients of the linear predictor variables utilized in the model for the upper limit of coral cover. This data is what is displayed in Figure 2. "Stan Model Summary Stats.txt": Summary statistics of the Stan model. "Stan Model/Stan_Plotting_Data.csv": CSV of the fitted values for the recovery rate and upper limit following marine heatwaves. This data is what is displayed in Figure 1. "Rate_Model_Diagnostics.png": Posterior predictive check output. "10 Genera Model.R"Description: Script contains the INLA model for the coral genera model.Inputs: Genus_Morph_Data.csv: Derived from "9 Creating Genera Dataset.R".Outputs: "Raw_Recovery_Data.csv": Subset of input data that contains only samples that followed a marine heatwave and had a positive change in coral cover. "Genera_Citations.csv": Citations that were used to derive the genera dataset. "Samples_per_Genus.csv": Table of the sample sizes "Genera_Model.rds": RDS object that contains te completed INLA model for coral genera. "Genera_Coefficients.csv": Beta coefficients of heatwave frequency for each coral genera from model. "Taxa_Model_Diagnostics.png": Posterior predictive check of the genera model. **PLOTTING STAGE**"11 Boxplots Figure.R"Description: Script contains the code for plotting the fitted values of impact, recovery likelihood, recovery rate, and upper limit.Inputs: 4_Series_Data.csv Stan_Plotting_Data.csv Impact_Normalized_Predictions.csv Weibull_Predictions.csvOutputs: "Boxplot Figure.png" "12 Effect Size Figure.R"Description: Script contains the code for plotting the effect size of the coefficients for impact, recovery likelihood, recovery rate, and upper limit.Inputs: Impact_Coefficients.csv Weibull_Recovery_Coefficients.csv Rate Coefficients.csv Upper Limit Coefficients.csvOutputs: "Effect Size Figure.png" "13 Genus Effect Size Figure.R"Description: Script contains the code for plotting the effect size of heatwave frequency for each coral genus.Inputs: Genera_Coefficients.csvOutputs: Genus_Slopes.png EXTRANEOUS R Scripts"Basic R Functions.R"Description: Contains custom functions for plotting the effect size of INLA and Stan models.