baumlab / Magel_etal_2019_SciRep

Data and R code for: Effects of bleaching-associated mass coral mortality on reef structural complexity across a gradient of local disturbance

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Data and R code accompanying:

Effects of bleaching-associated mass coral mortality on reef structural complexity across a gradient of local disturbance

Authors: Jennifer M.T. Magel, John H.R. Burns, Ruth D. Gates, Julia K. Baum

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In the data folder, KI_complexity_data.csv contains the structural complexity, local human disturbance, and benthic composition data for each permanent photoquadrat (PPQ) surveyed in our study. Variables are defined as follows:

• Year = Year that the data was collected
• heat_stress = Indicates whether the data was collected before (2015) or after (2017) the 2015-2016 El Niño
• Month = Month that the data was collected
• hum_dist = Local human disturbance level, based on fishing pressure and proximity to local villages
• 2D_Area = Two-dimensional area of the PPQ
• 3D_Area = Three-dimensional surface area of the PPQ
• rugosity = Surface rugosity of the PPQ (3D_Area/2D_Area)
• terrain_rug = Mean terrain ruggedness of the PPQ
• curvature = Mean curvature of the PPQ
• abs_curv = Absolute value of curvature for the PPQ
• nbranching = Total abundance of branching corals within the PPQ
• nplating = Total abundance of plating corals within the PPQ
• nmassive = Total abundance of massive corals within the PPQ
• dbranching = Density of branching corals within the PPQ (nbranching/2D_Area)
• dplating = Density of plating corals within the PPQ (nplating/2D_Area)
• dmassive = Density of massive corals within the PPQ (nmassive/2D_Area)

KI_habitat_volume_data.csv contains parameter settings for the ICP registration and 2.5D volume computation processes in CloudCompare, and resulting data from our 3D point cloud comparison. Variables are defined as follows:

• ICP_Overlap = Estimated amount of overlap between 2015 and 2017 point clouds (set to 95% to account for slightly different placement of GCPs between years)
• ICP_RSL = Random sampling limit (i.e. maximum number of sub-sampled points) for the ICP registration
• ICP_RMS_Final = Square root of mean square errors resulting from the ICP registration
• Vol_Step = Grid cell size for the 2.5D volume computation (set to 1 cm to match the DEM cell size)
• Vol_Cell_Height = Specifies how the height of cells containing multiple points should be computed during the 2.5D volume computation
• Vol_Match_Cells = Percentage of cells present in both the 2015 and 2017 point clouds
• Vol_Surface = Two-dimensional area of the PPQ
• Vol_Change_Total = Net change in habitat volume within the PPQ from 2015 to 2017 (Vol_Change_Loss + Vol_Change_Gain)
• Vol_Change_Gain = Total gain in habitat volume within the PPQ from 2015 to 2017
• Vol_Change_Loss = Total loss in habitat volume within the PPQ from 2015 to 2017