Data and Code for: Marine heatwaves overwhelm the buffering benefits of marine protected areas: two decades of collapse in a Mediterranean gorgonian

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This repository contains the data and code used to analyse long-term demographic trends of the gorgonian coral Paramuricea clavata across 49 populations in the north-western Mediterranean Sea. The study investigates how repeated marine heatwave (MHW) events have driven population-level declines in mortality, height, density, recruitment, and biomass, and whether marine protected areas (MPAs) buffer these impacts. Each script contains detailed header describing its objective, model structure and validation workflow.CodeScripts are organised into 5 groups:Demographic trend models (one per response variable)Temperature, MHW detection, exposure and protection modelsFigure-generation scripts Supplementary material1. Demographic trend modelsFive scripts, one per response variable, all sharing the same hierarchical GAMM structure and five-step validation workflow (see script headers).MMortalityTrend.R — Injured surface (%) — BetaMHeightTrend.R — Max colony height (cm) — Gaussian MDensityTrend.R — Colony density (N per m²) — Gamma MRecruitsTrend.R — Recruits (% colonies < 5 cm) — Beta MBiomassTrend.R — Biomass (g per m²) — Gamma2. Temperature, MHW detection, exposure and protection modelsTempMHWDetection.R: Matches in-situ logger data to colony sampling depths and detects MHW events. MBioTempProt.R:Fits three hierarchical Bayesian linear models testing the effects of time, MHW exposure, and protection status on biomass 3. Figure-generation scriptsFigure1.R: Sampling timeline per population coloured by impact category, and SST JJASON anomaly for the Mediterranean (panels L–M of Figure 1).Figure2.R: Shared regional demographic trends for all five variables, plus posterior distribution of regional biomass loss (Figure 2). Reads model objects from the five trend scripts.Figure3_4_5_6.R: Population-level biomass decline probabilities, exposure and protection characterisation per population, and effects of MHW exposure and protection on biomass trends (Figures 3–6). Reads model objects from MBioTempProt.R.4. SupplementaryAll supplementary analyses are contained in a separate Supplementary/ folder and rendered through a Quarto script.Data Colonies_Pclavata.csv: Colony-level survey dataIn_situ_Temp.rds: In-situ daily mean temperature logger dataMHWDecadeClimat.rda: Pre-computed MHW events (output of TempMHWDetection.R)MBioTempProtData.rda: Pre-compiled modelling dataset (output of MBioTempProt.R)Map.csv: Site coordinates and zone metadatamedsea_omi_tempsal_...nc: Monthly SST anomalies (Copernicus Marine Service, 10.48670/moi-00268)Execution order MMortalityTrend.R MHeightTrend.R MDensityTrend.R MRecruitsTrend.R MBiomassTrend.RTempMHWDetection.RMBioTempProt.RFigure1.RFigure2.RFigure3_4_5_6.RSupplementary.qmdNote: Fitted model objects are saved to Stats/ and loaded directly by the figure scripts, so models do not need to be re-run each time. Given the computational cost of model fitting, it is recommended to load the pre-computed outputs.