Data&Code_PaperCresswell_Multi-scaleCollapseOfCoralCover

README &mdash; Code and Data Availability
Cresswell et al. (In Review, Nature Communications)
&quot;Multi-scale collapse of coral cover under climate change&quot;
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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/                        &mdash;        Input data and C~scape
                                              simulation outputs for the
                                              GBR case studies

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1. C_scape-5.1.0.zip &mdash; 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&#39;s internal README for environment
    setup, dependency installation, and execution instructions.


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2. C_scape_Input-1.0.2.zip &mdash; 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.


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3. C_scape_OutputAnalysis-1.0.1.zip &mdash; 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.


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4. C_scape_demography-1.0.0.zip &mdash; 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.


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5. model_runs/ &mdash; 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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Organization: Australian Ocean Data Network