Code for generating benthic photosynthetically active radiation (bPAR) and the bPAR index as reported in (NESP TWQ 5.3, AIMS, JCU and Go2Q)

This dataset contains code used to generate the daily benthic light (bPAR) data product provided at https://eatlas.org.au/data/uuid/356e7b3c-1508-432e-9d85-263ec8a67cef and the bPAR index for water quality in the Great Barrier Reef (GBR). It can also be used to calculate photosynthetically active radiation (PAR) at any specified depth in GBR waters.

The amount of light available for photosynthesis (photosynthetically active radiation, or PAR) is an important determinant of ecosystem health. PAR reaching the bottom of the water column is known as benthic PAR (bPAR). Where there is sufficient light reaching the bottom, seagrasses and corals may thrive. bPAR varies seasonally as a function of surface PAR, but also varies function of both water depth and water quality.

This dataset contains the code used to generate the bPAR data product and the derived bPAR index for water quality developed through NESP TWQ projects 2.3.1 and 5.3.

Methods:
Daily benthic light (bPAR) is derived from NASA MODIS Ocean Color data in combination with bathymetric data from Beaman (2010) using the algorithm described by Magno-Canto et al. (2019, 2020). Ocean colour observations are used to estimate inherent optical properties (total absorption and total backscattering coefficients) at each of ten MODIS wavelengths, using the SWIM algorithm of McKinna et al. (2015). These in turn are used to calculate spectrally-resolved light attenuation (Kd). The Beer-Lambert equation is then used to propagate surface PAR using the calculated Kd down to the depth of the bottom of the water column defined by the bathymetry data (i.e. depth map) obtained from Beaman (2010). This yields an estimate of instantaneous bPAR on a nominal 1 km2 grid scale across the study region.

Instantaneous bPAR is then used to calculate daily integrated benthic light by considering the path and angle of the sun over the course of each day, assuming constant atmospheric conditions within each day.

The C code for generating the bPAR product from MODIS data is in the process of being implemented in NASA’s SeaDAS processing and visualisation software package.

Daily bPAR is then is used to derive an index for water quality in the Great Barrier Reef (GBR). Daily bPAR observations at a nominal 1km2 resolution are used to calculate a cumulative seasonal and annual light stress experienced by benthic photosynthesising organisms at each pixel. This light stress is aggregated over each NRM region and waterbody of the GBR and scaled to produce an index with a value between 0 (no light penetration to benthic habitats) and 1 (excellent light penetration to benthic habitats). The R script RS_bPAR_final.R calculates the index and generates figures plotting variations in the value of the index over time as well as showing how this index varies in each region as a function of river load.

The full method used to calculate bPAR is described in the following publications:
Magno-Canto, M.M., McKinna, L.I., Robson, B.J. and Fabricius, K.E., 2019. Model for deriving benthic irradiance in the Great Barrier Reef from MODIS satellite imagery. Optics express, 27(20), pp.A1350-A1371.

Magno-Canto, M.M., McKinna, L.I., Robson, B.J., Fabricius, K.E. and Garcia, R., 2020. Model for deriving benthic irradiance in the Great Barrier Reef from MODIS satellite imagery: erratum. Optics Express, 28(19), pp.27473-27475.

The full method used to calculate the bPAR index are described in the manuscript:
Canto, M. M., Fabricius, K. E., Logan, M., Lewis, S., McKinna, L. I. W., & Robson, B. J. (2021). A benthic light index of water quality in the Great Barrier Reef, Australia. Marine Pollution Bulletin, 169, 112539. https://doi.org/10.1016/j.marpolbul.2021.112539

Format:
The functions needed to calculate benthic PAR or PAR at any specified depth is provided as c code in the file “get_bpar.c”. This is designed to be executed as part of NASA’s SeaDAS software.

The script to calculate the bPAR index, “RS_bPAR_final.R” can be executed in the R programming language (v 3.4 or later). This script calls on functions defined in a second R script, “WQI_functions.R” and spatial data and region labels provided in the R data files “Polys.rda” and “spatial.csv”, which are also provided.

References:

Magno-Canto, M.M., McKinna, L.I., Robson, B.J. and Fabricius, K.E., 2019. Model for deriving benthic irradiance in the Great Barrier Reef from MODIS satellite imagery. Optics express, 27(20), pp.A1350-A1371.

Magno-Canto, M.M., McKinna, L.I., Robson, B.J., Fabricius, K.E. and Garcia, R., 2020. Model for deriving benthic irradiance in the Great Barrier Reef from MODIS satellite imagery: erratum. Optics Express, 28(19), pp.27473-27475.

Canto, M. M., Fabricius, K. E., Logan, M., Lewis, S., McKinna, L. I. W., & Robson, B. J. (2021). A benthic light index of water quality in the Great Barrier Reef, Australia. Marine Pollution Bulletin, 169, 112539. https://doi.org/10.1016/j.marpolbul.2021.112539

Data Location:

This dataset is filed in the eAtlas enduring data repository at: data\nesp5\5.3_Benthic-light

本数据集包含用于生成每日底栖光（benthic PAR, bPAR）数据产品的代码，该产品可通过https://eatlas.org.au/data/uuid/356e7b3c-1508-432e-9d85-263ec8a67cef获取，同时包含大堡礁（Great Barrier Reef, GBR）水质的bPAR指数。它还可用于计算GBR水域内任意指定深度的光合有效辐射（photosynthetically active radiation, PAR）。

光合作用可用的光量（光合有效辐射，photosynthetically active radiation, PAR）是生态系统健康的重要决定因素。到达水柱底部的PAR被称为底栖PAR（benthic PAR, bPAR）。在光线足以到达水底的区域，海草和珊瑚可能茁壮成长。bPAR具有季节性变化，其不仅是表层PAR的函数，还受水深和水质的影响。

本数据集包含生成bPAR数据产品的代码，以及通过NESP TWQ项目2.3.1和5.3开发的衍生水质bPAR指数。

方法：
每日底栖光（bPAR）通过NASA MODIS海洋颜色数据结合Beaman（2010）的水深数据（bathymetric data），使用Magno-Canto等人（2019,2020）描述的算法推导得出。海洋颜色观测数据用于估计MODIS十个波长中每个波长的固有光学特性（总吸收系数和总后向散射系数），所采用的是McKinna等人（2015）提出的SWIM算法。这些特性进而用于计算光谱解析的光衰减系数（Kd）。随后，利用比尔-朗伯方程（Beer-Lambert equation），通过计算得到的Kd将表层PAR向下传播至Beaman（2010）提供的水深数据（即深度图）所定义的水柱底部深度。这一过程可得到研究区域内名义上1平方公里网格尺度的瞬时bPAR估计值。

瞬时bPAR随后用于计算每日积分底栖光：通过考虑太阳在一天中的路径和角度，并假设每日内大气条件恒定。

从MODIS数据生成bPAR产品的C代码正处于NASA SeaDAS处理与可视化软件包的集成过程中。

每日bPAR随后用于推导大堡礁（GBR）的水质指数。名义上1平方公里分辨率的每日bPAR观测数据用于计算每个像素处底栖光合生物所经历的累积季节性和年度光应力。该光应力在GBR的每个NRM区域和水体上进行聚合，并缩放以生成取值范围在0（无光线穿透至底栖生境）到1（光线极好地穿透至底栖生境）之间的指数。R脚本RS_bPAR_final.R负责计算该指数，并生成图表以展示指数值随时间的变化，以及该指数在各区域如何随河流负荷变化。

计算bPAR所采用的完整方法详见以下出版物：
Magno-Canto, M.M., McKinna, L.I., Robson, B.J. and Fabricius, K.E., 2019. Model for deriving benthic irradiance in the Great Barrier Reef from MODIS satellite imagery. Optics express, 27(20), pp.A1350-A1371.

Magno-Canto, M.M., McKinna, L.I., Robson, B.J., Fabricius, K.E. and Garcia, R., 2020. Model for deriving benthic irradiance in the Great Barrier Reef from MODIS satellite imagery: erratum. Optics Express, 28(19), pp.27473-27475.

计算bPAR指数的完整方法详见以下手稿：
Canto, M. M., Fabricius, K. E., Logan, M., Lewis, S., McKinna, L. I. W., & Robson, B. J. (2021). A benthic light index of water quality in the Great Barrier Reef, Australia. Marine Pollution Bulletin, 169, 112539. https://doi.org/10.1016/j.marpolbul.2021.112539

格式：
计算底栖PAR或任意指定深度PAR所需的函数以C代码形式提供于文件"get_bpar.c"中，其设计为NASA SeaDAS软件的一部分执行。

计算bPAR指数的脚本"RS_bPAR_final.R"可在R编程语言（版本3.4或更高）中运行。该脚本调用第二个R脚本"WQI_functions.R"中定义的函数，以及R数据文件"Polys.rda"和"spatial.csv"中提供的空间数据与区域标签——这些文件也一并包含在本数据集中。

参考文献：

Magno-Canto, M.M., McKinna, L.I., Robson, B.J. and Fabricius, K.E., 2019. Model for deriving benthic irradiance in the Great Barrier Reef from MODIS satellite imagery. Optics express, 27(20), pp.A1350-A1371.

Magno-Canto, M.M., McKinna, L.I., Robson, B.J., Fabricius, K.E. and Garcia, R., 2020. Model for deriving benthic irradiance in the Great Barrier Reef from MODIS satellite imagery: erratum. Optics Express, 28(19), pp.27473-27475.

Canto, M. M., Fabricius, K. E., Logan, M., Lewis, S., McKinna, L. I. W., & Robson, B. J. (2021). A benthic light index of water quality in the Great Barrier Reef, Australia. Marine Pollution Bulletin, 169, 112539. https://doi.org/10.1016/j.marpolbul.2021.112539

数据位置：

本数据集存储于eAtlas持久数据仓库中，路径为：data
esp55.3_Benthic-light