Indicator Framework for assessing the condition of coral reef habitats in the Great Barrier Reef

At present, there are multiple data streams available from existing coral reef monitoring programs that measure aspects of condition and recovery. However, a holistic assessment of condition and recovery requires a multidimensional approach acknowledging complex ecological processes varying across the reef. Adding to this ecological complexity is the practical complexity in applying such knowledge to define a high-level metric that informs management and evaluates the efficacy of management strategies towards proposed conservation targets. The latter requires heuristic, measurable, sensitive, and scalable indicators to facilitate conservation planning and management. A project was set in collaboration between the Australian Institute of Marine Science (AIMS), James Cook University (JCU) and the University of Queensland (UQ) funded by the partnership between the Australian Government’s Reef Trust and the Great Barrier Reef Foundation. This project developed an integrative suite of indicators towards streamlining the decision-making processes and enabling tracking progress toward achieving the objectives of the Reef 2050 Long-term Sustainability plan. A critical component of this project is making data, information, and knowledge (provided by the ongoing monitoring programs that form the core of the RIMReP) available in a relevant and integrated form that enables high-level reporting and supports decision-making at various management scales. This includes high-level reporting on Reef 2050 objectives across the GBR management scales and sea-country-focused reporting on TUMRA objectives and issues of concern to Traditional Owner co-managers.This data record includes source code, documentation and parameter files for the calculation and integrated interpretation of indicator scores derived from coral reef monitoring programs in the GBR.Parameter files V2    Coral Cover Baseline (CC__baseline.RData, CC_baseline.RData): Spatiotemporal model and posterior distributions of coral cover values per Bioregion. This serves as a baseline reference from historical observations of coral cover (Maintenance Threshold) to evaluate monitoring observations and derive the coral cover indicator scores.    Juvenile Density Baseline (JU__baseline_mod.RData, JUV_baseline.RData): Spatiotemporal model and posterior distributions of juvenile density values per Bioregion. This serves as a baseline reference from historical observations (Maintenance Threshold) to evaluate monitoring observations and derive the Juvenile density indicator scores.    Macroalgae Baseline (MA__baseline_deep.RData, MA__baseline_offshore.RData, MA__baseline_shallow.RData): Spatiotemporal model for generating posterior distributions of macroalgae proportion values per reef and survey depth. This serves as a baseline reference from historical observations (Maintenance Threshold) to evaluate monitoring observations and derive the Macroalgae indicator scores.    Juvenile Density Contextual Threshold files (IPM_juv.RData,JuvCover_Acropora_NA_Inshore_NA_ResJuv_FALSE_Morph_NA.Rdata, JuvCover_Acropora_NA_Offshore_NA_ResJuv_FALSE_Morph_NA.Rdata,JuvCover_Mound_growth_NA_Inshore_NA_ResJuv_FALSE_Morph_Merulinidae.Rdata, JuvCover_Mound_growth_NA_Inshore_NA_ResJuv_FALSE_Morph_Poritidae.Rdata, JuvCover_Mound_growth_NA_Offshore_NA_ResJuv_FALSE_Morph_Merulinidae.Rdata, JuvCover_Mound_growth_NA_Offshore_NA_ResJuv_FALSE_Morph_Poritidae.Rdata, JuvCover_Pocilloporidae_NA_Inshore_NA_ResJuv_FALSE_Morph_NA.Rdata, JuvCover_Pocilloporidae_NA_Offshore_NA_ResJuv_FALSE_Morph_NA.Rdata, newdata_grid.RData): These files contain parameters for the estimation of the minimal density of Acropora juvenile colonies required yearly to ensure rapid recovery of benthic communities following severe disturbance. Values were derived from Integral Population Models (provided here) and numerical optimisation of the density of colonies against coral cover trajectories.     Lookup tables for Synoptic text (Synoptic_text_reef.csv, Synoptic_text_region.csv, taxaLookup.csv): Descriptive text is generated as part of the framework to assist in the interpretation of indicator scores. These files are lookup tables for the conditional statements to generate the synopsis.Parameter files V1    Coral Cover Baseline (CC__baseline.RData, CC_baseline.RData, CC_baseline_posteriors.RData): Spatiotemporal model and posterior distributions of coral cover values per Bioregion. This serves as a baseline reference from historical observations of coral cover (Maintenance Threshold) to evaluate monitoring observations and derive the coral cover indicator scores.    Juvenile Density Baseline (JU__baseline.RData, JU__baseline_mod.RData, JUV_baseline.RData): Spatiotemporal model and posterior distributions of juvenile density values per Bioregion. This serves as a baseline reference from historical observations (Maintenance Threshold) to evaluate monitoring observations and derive the Juvenile density indicator scores.    Macroalgae Baseline (MA__baseline_deep.RData, MA__baseline_offshore.RData, MA__baseline_shallow.RData): Spatiotemporal model and posterior distributions of macroalgae proportion values per reef and survey depth. This serves as a baseline reference from historical observations (Maintenance Threshold) to evaluate monitoring observations and derive the Macroalgae indicator scores.    Juvenile Density Contextual Threshold files (IPM_juv.RData,JuvCover_Acropora_NA_Inshore_NA_ResJuv_FALSE_Morph_NA.Rdata, JuvCover_Acropora_NA_Offshore_NA_ResJuv_FALSE_Morph_NA.Rdata,JuvCover_Mound_growth_NA_Inshore_NA_ResJuv_FALSE_Morph_Merulinidae.Rdata, JuvCover_Mound_growth_NA_Inshore_NA_ResJuv_FALSE_Morph_Poritidae.Rdata, JuvCover_Mound_growth_NA_Offshore_NA_ResJuv_FALSE_Morph_Merulinidae.Rdata, JuvCover_Mound_growth_NA_Offshore_NA_ResJuv_FALSE_Morph_Poritidae.Rdata, JuvCover_Pocilloporidae_NA_Inshore_NA_ResJuv_FALSE_Morph_NA.Rdata, JuvCover_Pocilloporidae_NA_Offshore_NA_ResJuv_FALSE_Morph_NA.Rdata, newdata_grid.RData): These files contain parameters for the estimation of the minimal density of Acropora juvenile colonies required yearly to ensure rapid recovery of benthic communities following severe disturbance. Values were derived from Integral Population Models (provided here) and numerical optimisation of the density of colonies against coral cover trajectories.     Lookup tables for Synoptic text (Synoptic_text_reef.csv, Synoptic_text_region.csv, taxaLookup.csv): Descriptive text is generated as part of the framework to assist in the interpretation of indicator scores. These files are lookup tables for the conditional statements to generate the synopsis.Source code:    Indicator_Framework_preprint_v2: R source code for generating indicator scores from monitoring data.    Indicator Framework_v1: R source code for generating indicator scores from monitoring data.    Data visualisation example_v1: A R shiny app to deploy a dashboard with functions to provide an example for visualisation of data products derived from the Indicator framework.    Singularity Container for Indicator Framework source code: While the source code repository includes instructions to generate the singularity container, this data record also includes access to a pre-generated image of this singularity container.Documentation:    Guidelines for interpretation of the framework_v1: A detailed introduction to the indicator framework and guiding points to assist in the combine interpretation of indicator scores.    Methods_v1: A detailed methodological description detailing the approach to calculate the indicator scores within the framework. For each indicator, this document also includes required data inputs, expected outputs and guidelines for interpretationAcknowledgements:The project “Indicator framework for assessing the condition and recovery capacity of coral reef habitats in the Great Barrier Reef” is funded by the partnership between the Australian Government’s Reef Trust and the Great Barrier Reef Foundation with support from the Australian Institute of Marine Science, The University of Queensland and James Cook University. The authors are grateful for the support from the Great Barrier Reef Marine Park Authority in guiding the design of the framework throughout the project.

当前，现有珊瑚礁监测项目已产出多组数据流，用于监测珊瑚礁健康状态与恢复状况。然而，要对珊瑚礁健康状态及恢复情况开展全面评估，需采用多维研究方法，充分考虑珊瑚礁范围内复杂多变的生态过程。而在将此类研究成果转化为可指导管理工作、并能评估针对既定保护目标的管理策略有效性的高阶指标时，又面临着实践层面的复杂性，进一步加剧了整体工作的难度。
为此，需要开发具备启发性、可量化、敏感性强且可拓展的指标体系，以助力保护规划与管理工作的开展。

本数据集依托一项合作项目产生，该项目由澳大利亚海洋科学研究所（Australian Institute of Marine Science, AIMS）、詹姆斯·库克大学（James Cook University, JCU）与昆士兰大学（University of Queensland, UQ）联合开展，资助方为澳大利亚政府珊瑚礁信托基金（Australian Government’s Reef Trust）与大堡礁基金会（Great Barrier Reef Foundation）的合作项目。项目旨在构建一套整合式指标体系，以优化决策流程，并实现对《大堡礁2050长期可持续性计划》（Reef 2050 Long-term Sustainability Plan）目标达成进度的跟踪。

本项目的核心内容之一，是将构成RIMReP核心的长期监测项目所产出的数据、信息与知识，以适配需求且整合统一的形式进行共享，从而支撑高阶报告编制，并为不同管理尺度下的决策提供支持。此类应用场景包括：针对大堡礁（Great Barrier Reef, GBR）全管理尺度下的《大堡礁2050长期可持续性计划》目标开展高阶报告编制，以及面向原住民传统所有者共管方（Traditional Owner co-managers）所关注的TUMRA目标与相关议题，开展基于海域原住民传统领地（sea-country）的专项报告编制。

本数据记录包含用于计算与整合解读大堡礁珊瑚礁监测项目产出的指标得分的源代码、文档与参数文件。

### V2版参数文件
1. 珊瑚覆盖度基线文件（CC__baseline.RData、CC_baseline.RData）：包含各生物区域（Bioregion）珊瑚覆盖度值的时空模型与后验分布。该文件以历史珊瑚覆盖度观测数据为基础构建维护阈值（Maintenance Threshold），用于评估当前监测观测结果，并计算珊瑚覆盖度指标得分。
2. 幼体密度基线文件（JU__baseline_mod.RData、JUV_baseline.RData）：包含各生物区域幼体密度值的时空模型与后验分布。该文件以历史幼体密度观测数据为基础构建维护阈值，用于评估当前监测观测结果，并计算幼体密度指标得分。
3. 大型藻类基线文件（MA__baseline_deep.RData、MA__baseline_offshore.RData、MA__baseline_shallow.RData）：包含各珊瑚礁及调查水深下大型藻类占比的时空模型与后验分布。该文件以历史大型藻类占比观测数据为基础构建维护阈值，用于评估当前监测观测结果，并计算大型藻类指标得分。
4. 幼体密度情境阈值文件（IPM_juv.RData、JuvCover_Acropora_NA_Inshore_NA_ResJuv_FALSE_Morph_NA.Rdata、JuvCover_Acropora_NA_Offshore_NA_ResJuv_FALSE_Morph_NA.Rdata、JuvCover_Mound_growth_NA_Inshore_NA_ResJuv_FALSE_Morph_Merulinidae.Rdata、JuvCover_Mound_growth_NA_Inshore_NA_ResJuv_FALSE_Morph_Poritidae.Rdata、JuvCover_Mound_growth_NA_Offshore_NA_ResJuv_FALSE_Morph_Merulinidae.Rdata、JuvCover_Mound_growth_NA_Offshore_NA_ResJuv_FALSE_Morph_Poritidae.Rdata、JuvCover_Pocilloporidae_NA_Inshore_NA_ResJuv_FALSE_Morph_NA.Rdata、JuvCover_Pocilloporidae_NA_Offshore_NA_ResJuv_FALSE_Morph_NA.Rdata、newdata_grid.RData）：包含用于估算严重扰动后底栖群落快速恢复所需的年度鹿角珊瑚（Acropora）幼体群落最小密度的参数。该密度值通过积分种群模型（Integral Population Models, IPM）与基于珊瑚覆盖度轨迹的种群密度数值优化方法计算得到。
5. 概要文本查找表（Synoptic_text_reef.csv、Synoptic_text_region.csv、taxaLookup.csv）：用于生成辅助指标得分解读的描述性文本，本文件为生成概要文本的条件语句查找表。

### V1版参数文件
1. 珊瑚覆盖度基线文件（CC__baseline.RData、CC_baseline.RData、CC_baseline_posteriors.RData）：包含各生物区域珊瑚覆盖度值的时空模型与后验分布。该文件以历史珊瑚覆盖度观测数据为基础构建维护阈值，用于评估当前监测观测结果，并计算珊瑚覆盖度指标得分。
2. 幼体密度基线文件（JU__baseline.RData、JU__baseline_mod.RData、JUV_baseline.RData）：包含各生物区域幼体密度值的时空模型与后验分布。该文件以历史幼体密度观测数据为基础构建维护阈值，用于评估当前监测观测结果，并计算幼体密度指标得分。
3. 大型藻类基线文件（MA__baseline_deep.RData、MA__baseline_offshore.RData、MA__baseline_shallow.RData）：包含各珊瑚礁及调查水深下大型藻类占比的时空模型与后验分布。该文件以历史大型藻类占比观测数据为基础构建维护阈值，用于评估当前监测观测结果，并计算大型藻类指标得分。
4. 幼体密度情境阈值文件（IPM_juv.RData、JuvCover_Acropora_NA_Inshore_NA_ResJuv_FALSE_Morph_NA.Rdata、JuvCover_Acropora_NA_Offshore_NA_ResJuv_FALSE_Morph_NA.Rdata、JuvCover_Mound_growth_NA_Inshore_NA_ResJuv_FALSE_Morph_Merulinidae.Rdata、JuvCover_Mound_growth_NA_Inshore_NA_ResJuv_FALSE_Morph_Poritidae.Rdata、JuvCover_Mound_growth_NA_Offshore_NA_ResJuv_FALSE_Morph_Merulinidae.Rdata、JuvCover_Mound_growth_NA_Offshore_NA_ResJuv_FALSE_Morph_Poritidae.Rdata、JuvCover_Pocilloporidae_NA_Inshore_NA_ResJuv_FALSE_Morph_NA.Rdata、JuvCover_Pocilloporidae_NA_Offshore_NA_ResJuv_FALSE_Morph_NA.Rdata、newdata_grid.RData）：包含用于估算严重扰动后底栖群落快速恢复所需的年度鹿角珊瑚幼体群落最小密度的参数。该密度值通过积分种群模型与基于珊瑚覆盖度轨迹的种群密度数值优化方法计算得到。
5. 概要文本查找表（Synoptic_text_reef.csv、Synoptic_text_region.csv、taxaLookup.csv）：用于生成辅助指标得分解读的描述性文本，本文件为生成概要文本的条件语句查找表。

### 源代码
1. `Indicator_Framework_preprint_v2`：用于从监测数据生成指标得分的R语言源代码。
2. `Indicator Framework_v1`：用于从监测数据生成指标得分的R语言源代码。
3. `Data visualisation example_v1`：用于部署可视化仪表盘的R Shiny应用程序，可展示基于本指标框架产出的数据产品的可视化示例。
4. 指标框架源代码Singularity容器：本源代码仓库已包含构建Singularity容器的说明，本数据记录同时提供预生成的Singularity容器镜像访问入口。

### 文档
1. 《指标框架解读指南_v1》：对本指标框架的详细介绍，以及用于辅助综合解读各项指标得分的指导原则。
2. 《方法说明_v1》：对本框架内指标得分计算方法的详细阐述，同时包含每项指标所需的数据输入、预期输出与解读指南。

### 致谢
本项目“大堡礁珊瑚礁生境健康状态与恢复能力评估指标框架”由澳大利亚政府珊瑚礁信托基金与大堡礁基金会合作资助，并得到澳大利亚海洋科学研究所、昆士兰大学与詹姆斯·库克大学的支持。项目组衷心感谢大堡礁海洋公园管理局在项目全程中为框架设计提供的指导。