Inter- and intra-annual relationships between water clarity and river loads in the Great Barrier Reef 2002-2013 (NERP TE 4.1, AIMS, sources: NASA, DEHP, DERM, BOM, UQ)

This dataset shows various statistics of photic depth across the Great Barrier Reef (GBR). Data are broken into 35 zones along and across the GBR and photic depth is derived from 11 years of MODIS Aqua data. The data included is:
1. The statistical strength of correlation between standardized photic depth and freshwater discharges the GBR.
2. The mean photic depth and the main physical environmental variables that need to be controlled for when assessing how volumes of river freshwater discharges influence photic depth.
3. Statistics of photic depth controlled to remove the effects of main physical environmental variables (wave height, tidal range) used when assessing how volumes of river freshwater discharges. Data are into dry years (2002 to 2006) or wet years (2007 – 2012).

Water clarity is a key parameter affecting the health of coastal marine systems and their tourism values. We investigated the relationship between volumes of river freshwater discharges of major rivers (from DERM) and the water clarity in 35 zones along and across the GBR waters within the Fitzroy, Whitsundays, Burdekin, Southern and Northern Wet Tropics. For Cape York, water clarity was related to rainfall as a proxy, since river data were incomplete. We used daily 11-years (2002-2013) MODIS-Aqua remote sensing data at 1 km2 resolution, to investigate time scales and processes affecting water clarity in these regions. In all coastal, inshore and lagoonal regions except for Cape York, photic depth was strongly negatively related to the freshwater discharge of the main rivers. The declines started with the onset of river floods, and water clarity typically took 150– 260 days until complete recovery. The relationship between photic depth and rivers was strongest in the Northern Wet Tropics, the initiation area of outbreaks of crown-of-thorns starfish, where effects were strong even on the outer shelf. Previous conclusions that river runoff predominantly affects the inshore of the GBR have therefore to be revised for the Central and Northern GBR. The results were used in the setting of regional ecologically relevant targets for fine sediment in the Burnett-Mary and Wet Tropics WQIPs, and will likely be used for other WQIPs.

The analyses are based on three sets of data:
1) Daily Modis Aqua satellite data from 2002 - 2013, processed as described previously (Weeks et al. 2012, Logan et al. 2013, Fabricius et al. 2014).
2) Daily data of freshwater discharge volumes of the main rivers for the same time period, provided by the State of Queensland, Department of Environment and Heritage Protection (DEHP).
3) For the Normanby River, the discharge station only came online late 2005. Therefore, most of the first four years of daily discharge data for the main river in this region are missing (Stewart and Endeavour Rivers are much smaller than the large Normanby). Also missing are any form of river discharge information for the whole northern half of the region. As an alternative to river discharge data, we used daily rainfall data from the Lockhart River rainfall gauge for Cape York, which is located relatively centrally in this ~400 km long band. Daily rainfall data were obtained from the Australian Bureau of Meteorology (http://www.bom.gov.au/oceanography/projects/abslmp/data/index.shtml).

Method:

We spatially aggregated the data into 15 zones for the Fitzroy and Whitsundays region, and 5 zones each for the Burdekin, Southern and Northern Wet Tropics, and Cape York regions. For the Whitsundays, Burdekin, Wet Tropics and Cape York, five bands were defined parallel to the coastline:
- Coastal: 0 – 0.1 fractional units across the GBR
- Inshore: 0.1 – 0.25 fractional units across the GBR
- Lagoon: 0.25 – 0.45 fractional units across the GBR
- Midshelf: 0.45 – 0.65 fractional units across the GBR
- Outer shelf: 0.65 – 1 fractional units across the GBR

The Fitzroy region cannot be partitioned up into simple coast-parallel bands, due to its geomorphology around to the Capricorn-Bunkers and Swains complex, and the estuarine Keppel Bay. Consequently, the Fitzroy region was partitioned according to a combination of geomorphological regions and boundary rules (based on distances from coastlines and bioregions) so to reflect its oceanographic and geomorphological characteristics. The Broad Sound was analyzed separately, as its high tidal range and distance from the major Whitsundays and Fitzroy Rivers make this area unrepresentative of the more intensely used and populated areas of the Whitsundays and Fitzroy NRM Regions. The boundaries were chosen to best match those of both the Whitsundays and Fitzroy areas.

The Cape York and Wet Tropics NRM regions were subdivided into three long-shore bands, with the ‘Cape York’ band extending to 14.5 degrees latitude (Lizard Island), and a northern Wet Tropics region, split at Cape Grafton south of Cairns), and the southern Wet Tropics to best capture their differences in geomorphology, rainfall, agricultural use patterns, and population outbreak dynamics of crown-of-thorns starfish.
The statistical methods to relate photic depth to river discharges are described in Fabricius KE, Logan M, Weeks S, Brodie J (2014) The effects of river run-off on water clarity across the central Great Barrier Reef. Marine Pollution Bulletin 84: 191-200, and in Murray Logan, Katharina Fabricius, Scarla Weeks, Ana Rodriguez, Stephen Lewis and Jon Brodie (2014) NERP Project 4.1: Tracking coastal turbidity over time and demonstrating the effects of river discharge events on regional turbidity in the GBR. NERP Progress Report: Southern and Northern NRM Regions. 63 pp
Photic depth: The daily 1 km2 MODIS-Aqua remote sensing data were processed as described by Weeks et al. 2012, Fabricius et al. 2014. Masks were generated to excise optically shallow waters (reefs and very shallow coastal sections of the seabed), and offshore to >200 m bathymetry. As the full gridded daily data series is too large to reside in memory (153,177 grid points per day, over 11 years), it was spatially aggregated into the 35 zones. Data were aggregated to water years (1st October to 30th September) rather than calendar years. Data availability varied greatly between days and months due to cloud cover. To explore temporal differences in photic depth between wet and dry years, the analyses were also performed separately for dry (2002-2006) and wet (2007-2012) years.

Predicted daily tidal amplitudes as a proxy for tidal currents were obtained from the Australian Navy. For each zone, a single tidal location or a set of ‘representative’ tidal locations was chosen, and the mean tidal range per day was calculated across these locations, to reduce computational exhaustion.

Hourly data on wave heights and wave frequencies were obtained from the Queensland State Government, Department of Environment and Heritage Protection (DEHP), from the 4 wave rider buoys available in the study region: Emu Point Buoy for the southern zones, Mackay Buoy for the Whitsunday zones, Townsville Buoy for the Burdekin zone, and Cairns Buoy for the Northern and Southern Wet Tropics. For the Cape York zones, wind data from the Bureau of Meteorology (http://www.bom.gov.au/oceanography/projects/abslmp/data/index.shtml) from Lockhart River were considered more representative than the wave data from the Cairns buoy.

The analyses was based on daily values and performed separately for each zone. In order to explore the long-term photic depth signals, the data were seasonally detrended and smoothed. Gradient boosted model (GBM) and generalized additive mixed effects models (GAMM) were fitted to remove the effects of tides and wind/waves. The residuals from these GAMM (which thus reflect the photic depth signal after the extraction of wave, tidal and bathymetry signals) were then decomposed to derive the intra-annual trends (i.e., seasonal based on 365.25 day cyclicity) and inter-annual trends in photic depth. Seasonal decomposition was chosen which applies a smoother (typically either a moving average or locally weighted regression smoother) through a time series to separate periodic fluctuations due to cyclical reoccurring influences and long-term trends. Following temporal decomposition, seasonal cycles were re-centered around mean GAMM fitted values, and transformed back into the original photic depth scale via exponentiation.

Limitations:

The analyses only investigated the effects of river runoff on water clarity. This does not indicate that other factors (e.g. coastal developments, dredging) do not additionally affect water clarity; such relationships would have to be investigated separately.

Format:

This dataset comprises 2 shape files and a csv file:
- FabriciusAndLoganNerpDataCorrelations.* (142 kb) (dbf, shp and shx files),
- FabriciusAndLoganNerpDataSummaries.* (142 kb) (dbf, shp and shx files) and
- FabriciusAndLoganNerpSeasonalStatsDataRound.csv (3 kb).

Data Dictionary:

FabriciusAndLoganNerpDataCorrelations.shp:

The shapefile contains a set of polygon zones for 35 zones in the entire. The attributes table contains the strength of the correlation between daily river discharge and daily satellite photic depth, over 11 years.

The attributes are:
- SP_ID: shape id
- Correlatio: correlation value

FabriciusAndLoganNerpDataSummaries.shp:

The shapefile contains a set of polygon zones for 35 zones in the entire GBR. In each zone, we calculated the mean values of hourly or daily values, over 11 years.

The attributes are:
- SP_ID: shape id
- Photic_dep: photic depth (meters), means over 11 years of daily photic depth values, calculated based on an algorithm developed by Scarla Weeks (UQ) and NASA, (equivalent to Secchi depth)
- Tidal_rang: tidal range (meters), means over 11 years of tidal range values (difference between highest and lowest sea-level within each day), calculated from tidal predictions of the Australian Navy.
- Wave_heigh: wave height (meters), means over 11 years of wave height values, calculated from the nearest one of the four coastal DERM Wave Rider Buoys.
- Wind_speed: wind speed (ms-1), means over 11 years of wind speed values, from the nearest BOM station.

FabriciusAndLoganNerpSeasonalStatsDataRound.csv:

Statistics of photic depth controlled to remove the effects of main physical environmental variables (wave height, tidal range) used when assessing how volumes of river freshwater discharges. Data are broken into 35 zones along and across the GBR as well as into dry years (2002 to 2006) or wet years (2007 – 2012).

The attributes are:
- Region: geographical region
- Zone: Coastal, Inshore, Lagoon, Midshelf, Outershelf
- Period: Wet or Dry years
- Maximum: (m) the maximum smoothed photic depth over the year
- MaxDate: (calendar date) date within a year cycle corresponding to the maximum photic depth, typically middle to end of dry season
- Minimum: (m) the minimum smoothed photic depth over the year, showing the difference between dry and wet years in some of the inshore zones
- MinDate: (calendar date) date within a year cycle corresponding to the minimum photic depth, typically middle to end of wet season
- DeclineTime: (days) duration of time elapsed between the max photic depth and the NEXT minimum photic depth (in the continuous cycle)
- Decline: (m) absolute difference between max and min photic depth, showing how much photic depth is lost (in absolute terms) between seasons in wet and dry years in some of the inshore zones.
- PercentDecline: the relative decline expressed as a percentage of the max photic depth (unit: percent)
- DeclineRate: (m/day) rate of decline
- RecoveryTime: (days) duration of time elapsed between the min photic depth and the NEXT max photic depth (in the continuous cycle). Note, DeclineTime and RecoveryTime complete the 365(ish) day cycle. Showing how long it takes to re-establish clear water
- RecoveryRate: (m/day) rate of recovery (Decline/RecoveryTime)
- Recovery95Date: date within a year cycle corresponding to a recovery of 95% (up to max - decline*0.05)
- Recovery95Time: (days) duration of time elapsed between the min photic depth and the NEXT 95% recovery in photic depth (in the continuous cycle). Showing how long it takes to re-establish clear water after wet and dry wet seasons
- Recovery95Rate: (m/day) same as RecoveryRate, yet based on 95% recovery (Decline/Recovery95Time)

本数据集展示了大堡礁（Great Barrier Reef, GBR）范围内不同分区的透光层深度（photic depth）统计数据。研究将大堡礁沿岸及跨区域划分为35个分区，透光层深度数据源自11年的MODIS Aqua卫星遥感观测结果。所包含的数据如下：
1. 标准化透光层深度与大堡礁河流淡水径流量之间的相关统计强度。
2. 平均透光层深度，以及在评估河流淡水径流量如何影响透光层深度时所需控制的主要物理环境变量。
3. 经校正以剔除主要物理环境变量（波高、潮汐差）影响后的透光层深度统计数据，该数据按枯水年（2002年至2006年）与丰水年（2007年至2012年）进行划分。

水体透明度是影响近岸海洋生态系统健康及其旅游价值的关键参数。本研究针对菲茨罗伊、圣灵群岛、伯德金、南部及北部湿热带区域内大堡礁海域的35个分区，探究了主要河流（由昆士兰州环境与遗产保护部提供）的淡水径流量与水体透明度之间的关联。对于约克角半岛区域，由于河流数据不完备，我们采用降雨量作为替代指标来表征水体透明度。我们使用了2002年至2013年共11年的每日MODIS-Aqua遥感数据（空间分辨率1 km²），以探究影响该区域水体透明度的时间尺度与过程。除约克角半岛外，所有沿岸、近岸及泻湖区域的透光层深度均与主要河流的淡水径流量呈显著负相关关系。水体透明度下降始于河流洪水暴发之时，且通常需要150~260天才能完全恢复。透光层深度与河流径流量的关联在北部湿热带区域最为显著——该区域是长棘海星暴发的初始区域，其影响甚至可延伸至陆架外缘。此前认为河流径流主要影响大堡礁近岸区域的结论，因此需要针对大堡礁中部及北部区域进行修正。本研究结果被用于制定伯内特-玛丽及湿热带区域水质改善计划（Water Quality Improvement Plans, WQIPs）中细沉积物的区域生态相关目标，且有望应用于其他水质改善计划。

本分析基于三类数据：
1) 2002年至2013年的每日MODIS Aqua卫星数据，处理流程参照此前研究（Weeks等，2012；Logan等，2013；Fabricius等，2014）。
2) 同期主要河流的每日淡水径流量数据，由昆士兰州环境与遗产保护部（Department of Environment and Heritage Protection, DEHP）提供。
3) 诺曼比河的径流量数据仅自2005年末起可获取，因此该区域主要河流（诺曼比河）前四年的每日径流量数据大多缺失（斯图尔特河与恩迪沃弗河的径流量远小于诺曼比河）。同时，该区域北部半区的任何河流径流量数据均缺失。作为河流径流量数据的替代方案，我们采用了约克角半岛区域洛克哈特河雨量站的每日降雨量数据——该雨量站位于这片约400公里长区域的相对中心位置。每日降雨量数据源自澳大利亚气象局（http://www.bom.gov.au/oceanography/projects/abslmp/data/index.shtml）。

### 研究方法
我们将数据空间聚合为35个分区：菲茨罗伊与圣灵群岛区域划分为15个分区，伯德金、南部湿热带、北部湿热带及约克角半岛区域各划分为5个分区。对于圣灵群岛、伯德金、湿热带及约克角半岛区域，我们沿平行于海岸线的方向划定了5个带宽：
- 沿岸带：占大堡礁海域范围的0~0.1比例单位
- 近岸带：占大堡礁海域范围的0.1~0.25比例单位
- 泻湖带：占大堡礁海域范围的0.25~0.45比例单位
- 陆架中带：占大堡礁海域范围的0.45~0.65比例单位
- 陆架外缘带：占大堡礁海域范围的0.65~1比例单位

由于摩羯座-邦克斯与斯温兹复合体附近的地貌特征，以及河口的基普尔湾，菲茨罗伊区域无法采用简单的平行海岸线分区方式。因此，菲茨罗伊区域结合地貌区域与边界规则（基于距海岸线的距离及生物区域）进行分区，以反映其海洋学与地貌学特征。宽湾海峡单独进行分析，因其潮汐差大且距离圣灵群岛与菲茨罗伊主要河流较远，无法代表圣灵群岛与菲茨罗伊自然资源管理区域（Natural Resource Management Regions, NRM Regions）中开发与人口密集程度更高的区域。分区边界的设定尽可能匹配圣灵群岛与菲茨罗伊区域的实际边界。

约克角半岛与湿热带自然资源管理区域被划分为3个沿岸长带：‘约克角半岛’带延伸至南纬14.5度（蜥蜴岛），北部湿热带区域以凯恩斯以南的格拉夫顿角为界划分为南北两部分，以分别体现其在地貌、降雨量、农业利用模式及长棘海星种群暴发动态上的差异。

用于关联透光层深度与河流径流量的统计方法详见以下文献：Fabricius KE等（2014）《河流径流对大堡礁中部区域水体透明度的影响》，《海洋污染公报》84卷：191-200；以及Murray Logan等（2014）《NERP项目4.1：实时追踪沿岸浊度并论证河流径流事件对大堡礁区域浊度的影响》，NERP进展报告：南部与北部自然资源管理区域，共63页。

#### 透光层深度处理
每日1 km²分辨率的MODIS-Aqua遥感数据按照Weeks等（2012）、Fabricius等（2014）的方法进行处理。我们生成了掩膜图层，以剔除光学浅水区（珊瑚礁及极浅海床沿岸区域）以及水深超过200米的远海区域。由于每日完整网格化数据序列体量过大无法直接载入内存（每日153177个网格点，覆盖11年），因此将其空间聚合至上述35个分区。数据按水文年（10月1日至次年9月30日）而非日历年进行聚合。受云量影响，每日及每月的数据可用性差异极大。为探究枯水年与丰水年透光层深度的时间差异，我们分别针对枯水年（2002-2006年）与丰水年（2007-2012年）开展了分析。

每日潮汐振幅预测值作为潮汐流的替代指标源自澳大利亚海军。我们为每个分区选择单个潮汐测点或一组‘代表性’潮汐测点，并计算这些测点的每日平均潮汐差，以降低计算负荷。

波高与波频的逐小时数据源自昆士兰州环境与遗产保护部，来自研究区域内的4个波浪浮标：南部区域采用埃默角浮标，圣灵群岛区域采用麦凯浮标，伯德金区域采用汤斯维尔浮标，北部及南部湿热带区域采用凯恩斯浮标。对于约克角半岛区域，澳大利亚气象局（http://www.bom.gov.au/oceanography/projects/abslmp/data/index.shtml）提供的洛克哈特河气象站的风数据比凯恩斯浮标的波浪数据更具代表性。

本分析基于每日数据，并针对每个分区单独开展。为探究长期透光层深度信号，我们对数据进行了季节去趋势处理与平滑。我们采用梯度提升模型（Gradient Boosted Model, GBM）与广义加性混合效应模型（Generalized Additive Mixed Effects Model, GAMM）以剔除潮汐与风浪的影响。随后，我们对GAMM模型的残差（即剔除波浪、潮汐及水深信号后的透光层深度信号）进行分解，以得到年内趋势（即基于365.25天周期的季节趋势）与年际透光层深度趋势。我们选用了时间序列平滑分解法（通常采用移动平均或局部加权回归平滑器），以分离周期性重复影响带来的波动与长期趋势。时间分解完成后，季节周期将围绕GAMM模型拟合值的均值重新居中，并通过指数变换还原至原始透光层深度尺度。

### 数据局限性
本分析仅探究了河流径流对水体透明度的影响，这并不代表其他因素（如沿岸开发、疏浚作业）不会额外影响水体透明度；此类关联需单独开展研究。

### 数据集格式
本数据集包含2个矢量文件与1个逗号分隔值（CSV）文件：
1. FabriciusAndLoganNerpDataCorrelations.*（142 kb，包含dbf、shp及shx格式文件）
2. FabriciusAndLoganNerpDataSummaries.*（142 kb，包含dbf、shp及shx格式文件）
3. FabriciusAndLoganNerpSeasonalStatsDataRound.csv（3 kb）

### 数据字典
#### FabriciusAndLoganNerpDataCorrelations.shp
该矢量文件包含覆盖整个大堡礁的35个多边形分区。其属性表记录了11年间每日河流径流量与每日卫星遥感透光层深度之间的相关强度。
属性字段包括：
- SP_ID：形状ID
- Correlatio：相关系数（原文缩写，保留原拼写）

#### FabriciusAndLoganNerpDataSummaries.shp
该矢量文件包含覆盖整个大堡礁的35个多边形分区。每个分区内计算了11年间的小时或日度数据平均值。
属性字段包括：
- SP_ID：形状ID
- Photic_dep：透光层深度（单位：米），为11年间每日透光层深度的平均值，基于斯卡拉·威克斯（昆士兰大学）与美国国家航空航天局（NASA）开发的算法计算得出，等效于赛克盘透明度（Secchi depth）
- Tidal_rang：潮汐差（单位：米），为11年间每日潮汐差的平均值（每日最高与最低潮位之差），基于澳大利亚海军的潮汐预测数据计算得出
- Wave_heigh：波高（单位：米），为11年间波高的平均值，基于研究区域内4个沿岸波浪浮标中最近的一个计算得出
- Wind_speed：风速（单位：m·s⁻¹），为11年间风速的平均值，源自最近的澳大利亚气象局气象站

#### FabriciusAndLoganNerpSeasonalStatsDataRound.csv
该文件包含经校正以剔除主要物理环境变量（波高、潮汐差）影响后的透光层深度统计数据，用于评估河流淡水径流量对透光层深度的影响。数据按大堡礁35个分区以及枯水年（2002-2006年）、丰水年（2007-2012年）进行划分。
属性字段包括：
- Region：地理区域
- Zone：分区类型，包括Coastal（沿岸带）、Inshore（近岸带）、Lagoon（泻湖带）、Midshelf（陆架中带）、Outershelf（陆架外缘带）
- Period：时期，分为Wet（丰水年）与Dry（枯水年）
- Maximum：（单位：米）年度内平滑后透光层深度的最大值
- MaxDate：（日历日期）年度周期内对应透光层深度最大值的日期，通常为旱季中后期
- Minimum：（单位：米）年度内平滑后透光层深度的最小值，部分近岸分区可体现枯水年与丰水年的差异
- MinDate：（日历日期）年度周期内对应透光层深度最小值的日期，通常为雨季中后期
- DeclineTime：（单位：天）从透光层深度最大值至下一个最小值的持续时间（连续周期内）
- Decline：（单位：米）透光层深度最大值与最小值的绝对差值，体现部分近岸分区年内干湿季间透光层深度的绝对损失量
- PercentDecline：相对下降幅度，以透光层深度最大值的百分比表示（单位：%）
- DeclineRate：（单位：米/天）下降速率
- RecoveryTime：（单位：天）从透光层深度最小值至下一个最大值的持续时间（连续周期内）。注：DeclineTime与RecoveryTime共同构成约365天的周期，体现水体恢复清澈所需的时长
- RecoveryRate：（单位：米/天）恢复速率（Decline/RecoveryTime）
- Recovery95Date：（日历日期）年度周期内对应透光层深度恢复至95%（即最大值 - 下降量×0.05）的日期
- Recovery95Time：（单位：天）从透光层深度最小值至下一个95%恢复状态的持续时间（连续周期内），体现干湿季过后水体恢复清澈所需的时长
- Recovery95Rate：（单位：米/天）基于95%恢复量计算的恢复速率（Decline/Recovery95Time）