README — Code and Data Availability Cresswell et al. (In Review, Nature Communications) "Multi-scale collapse of coral cover under climate change"

OVERVIEW

All materials are hosted on the AIMS Data Store and comprise four GitHub release ZIP archives and one data folder.

File / Folder Version Description

C_scape-5.1.0.zip v5.1.0 C~scape model simulation code C_scape_Input-1.0.2.zip v1.0.2 Generation of input files for running C~scape for the present study C_scape_OutputAnalysis-1.0.1.zip v1.0.1 Model output analysis and figure generation scripts C_scape_demography-1.0.0.zip v1.0.0 Demography input file construction including Bayesian regressions for coral growth, survival and fecundity model_runs/ — Input data and C~scape simulation outputs for the GBR case studies

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1. C_scape-5.1.0.zip — C~scape Simulation Code (v5.1.0)

This archive contains the C~scape model simulation code, published as a versioned GitHub release. The repository is not currently public but will be made so upon publication. An R package for the C~scape simulation code is in preparation.

• Contains all source code required to execute the C~scape simulation.
• Refer to the repository's internal README for environment setup, dependency installation, and execution instructions.

==================================================================== 2. C_scape_Input-1.0.2.zip — Simulation Input File Generation (v1.0.2)

This archive contains the code used to generate the input files for running C~scape for the present study.

• Includes scripts for preparing spatial configuration files, environmental forcing data, and parameter tables.
• Processed outputs are used directly as inputs to C~scape within the model_runs data folders.

==================================================================== 3. C_scape_OutputAnalysis-1.0.1.zip — Output Analysis and Figure Generation (v1.0.1)

This archive contains all scripts used to analyse model outputs and produce the figures presented in the manuscript.

• Analysis code is organised by figure number.
• Source data are the simulation outputs contained in the model_runs folder.

==================================================================== 4. C_scape_demography-1.0.0.zip — Demography Input File Construction (v1.0.0)

This archive contains the full workflow for constructing the demographic input files used by C~scape, including Bayesian regressions for coral growth, survival and fecundity.

• Processed demographic outputs feed directly into the inputs used in the model_runs data folders.

==================================================================== 5. model_runs/ — Model Run Input and Output Data

This folder contains all input data and summarised simulation outputs for the model runs reported in the manuscript. It is organised under a single sub-folder (18_AnnaDemographyPapers) containing four reef cluster sub-folders.

Study sites: 01_MooreReefCluster 02_LizardIslandReefCluster 03_HeronIslandCluster 04_DaviesReefCluster

Each reef cluster sub-folder contains:

data/ Input files for C~scape, comprising: - 30 temporal files describing climate forcing from 3 Shared Socioeconomic Pathways (SSP126, SSP245, SSP370) and 10 Global Climate Models - 3 connectivity files providing larval transfer probability matrices (years 2015, 2016, 2017) - 6 demography files containing coral growth, survival, and fecundity parameters by coral functional group - 1 initialisation file providing starting coral cover conditions - 1 spatial file describing reef geometry and habitat characteristics

model_outputs/ C~scape simulation outputs, comprising: - Large array files summarising model output across scenarios and draws - Counterfactual coral cover files used in the manuscript analyses

ScenarioID.xlsx Scenario lookup table cross-referencing scenario identifiers to their parameter combinations.

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