DOI: 10.5281/zenodo.4572775
title: Data accompanying Milodowski et al. (Journal of Applied Ecology, 2021): "The impact of logging on vertical canopy structure across a gradient of tropical forest degradation intensity in Borneo"

description: <b>Description: </b>LiDAR point cloud data: LiDAR point clouds for the GEM inventory plots across SAFE, Maliau Conservation Area and Danum Valley in Malaysian Borneo. The georeferenced point clouds were produced following a survey by the Natural Environment Research Council Airborne Research Facility in 2014, noise points were removed and ground points classified using Lastools. Digital terrain models (DTM) were produced from classified ground points at 10 m resolution. Point clouds were normalised (through ground subtraction) to produce point heights relative to the local ground elevation. <br><br>Crown surveys: In each plot, the positions and heights of all trees with a stem diameter at breast height (DBH) ≥ 10 cm were mapped using ground-based Field-Map technology (IFER, Ltd., Jílové u Prahy, Czech Republic) in 2016. We mapped individual tree crowns by measuring 5-30 spatial positions, representing the boundary of a crown projected onto the horizontal plane. Crown projections were smoothed using the "smooth contour line" feature of Field-Map software v.11.<br><br>Small stem inventories: At SAFE and Maliau Basin, DBH was measured for all stems &gt;2 cm for 4-5 of the subplots in each GEM plot in 2012-2013 (in the manuscript, we used the average stem size distributions to estimate canopy volume contributions for the un-surveyed subplots). At the Danum Valley sites, DBH was measured for all subplots in a stem census comprising all stems &gt;1 cm in 2011=2012 (DAN-04) and 2013-2014 (DAN-05), as part of the ForestGEO 50 ha inventory plot. Full data from Danum Valley is available, subject to conditions of usage, from the ForestGEO data portal: http://ctfs.si.edu/datarequest/.<b>Project: </b>This dataset was collected as part of the following SAFE research project: <b>Biodiversity and land-use impacts on tropical ecosystem function (BALI): Quantifying functional trait distributions across the disturbance gradient</b><b>Funding: </b>These data were collected as part of research funded by: Natural Environmental Research Council (Human Modified Tropical Forests Consortium Grant, NE/K016377/1)This dataset is released under the CC-BY 4.0 licence, requiring that you cite the dataset in any outputs, but has the additional condition that you acknowledge the contribution of these funders in any outputs.<b>Permits: </b>These data were collected under permit from the following authorities:Sabah Biodiversity Council (Research licence (Research licence Unknown))<b>XML metadata: </b>GEMINI compliant metadata for this dataset is available here<b>Files: </b>This dataset consists of 2 files: data_archive_for_JApplEcol_Milodowski_2021.xlsx, Carbon_plot_point_cloud_buffer.las<b>data_archive_for_JApplEcol_Milodowski_2021.xlsx</b>This file contains dataset metadata and 6 data tables:<b>Attribute table for GEM plot crown surveys</b> (described in worksheet GEM_crown_surveys)Description: Field inventory of GEM plots with measurement of positions, heights, DBH and individual tree crowns for trees with diameter at breast height (DBH) &gt; 10 cm.Number of fields: 15Number of data rows: 4155Fields: <b>SAFEPlotName</b>: SAFE plot name (Field type: location)<b>Plot</b>: GEM plot name (Field type: id)<b>Subplot</b>: Subplot ID (Field type: id)<b>FieldMap_census_date</b>: Date of survey (Field type: date)<b>X_m_FieldMapcensus</b>: Relative location within subplot (Field type: numeric)<b>Y_m_FieldMapcensus</b>: Relative location within subplot (Field type: numeric)<b>Z_m_FieldMapcensus</b>: Relative location within subplot (Field type: numeric)<b>DBH_cm_FieldMapcensus</b>: DBH (Field type: numeric)<b>Height_m_FieldMapcensus</b>: Tree height (Field type: numeric)<b>CrownProjection_Area_m2_FieldMapcensus</b>: Projected Area of Crown (Field type: numeric)<b>Note_FieldMapcensus</b>: Field notes (Field type: comments)<b>Standing_dead_FieldMapcensus</b>: Standing dead trees labelled with Y (other trees with N) (Field type: categorical)<b>Broken_dead_FieldMapcensus</b>: Broken dead trees labelled with Y (other trees with N) (Field type: categorical)<b>Lying_dead_FieldMapcensus</b>: Fallen dead trees labelled with Y (other trees with N) (Field type: categorical)<b>Broken_live_FieldMapcensus</b>: Broken, but alive trees labelled with a Y (other trees with N) (Field type: categorical)<b>Attribute table for small stem surveys at SAFE/Maliau GEM plots</b> (described in worksheet SAFE_small_tree_census)Description: Small stem survey data for the small tree census carried out for subplots at SAFE and Maliau GEM plotsNumber of fields: 20Number of data rows: 2181Fields: <b>SAFEPlotName</b>: SAFE plot name (Field type: location)<b>Plot</b>: GEM plot name (Field type: id)<b>SUBPLOT</b>: Subplot ID (Field type: id)<b>CensusDate</b>: Date of census (Field type: date)<b>Observers</b>: Observers (Field type: comments)<b>TreeTagNumber</b>: Tree Identification Number (Tag number) (Field type: id)<b>D.POM_NSdirection</b>: Diameter at point of measurement (POM) in north-south direction (Field type: numeric)<b>D.POM_EWdirection</b>: Diameter at point of measurement (POM) in east-west direction (Field type: numeric)<b>H.POM</b>: Height of the diameter measurement (default is 1.3 m) (Field type: numeric)<b>HEIGHT</b>: Height of tree (Field type: numeric)<b>FLAG1</b>: Census flag (status of the tree) (Field type: comments)<b>COMMENTS</b>: Comments from field survey (Field type: comments)<b>DH_Liana_NSdirection</b>: Additional diameter measurements for lianas (Field type: comments)<b>DH_Liana_EWdirection</b>: Additional diameter measurements for lianas (Field type: numeric)<b>DMax_Liana_NSdirection</b>: Additional diameter measurements for lianas (Field type: numeric)<b>DMax_Liana_EWdirection</b>: Additional diameter measurements for lianas (Field type: numeric)<b>LeafSampleCollected</b>: Flag to specify whether leaf sample taken (Y-yes; P-photo; N-not possible) (Field type: categorical)<b>Comments_DataEntry</b>: Comment on data entry (Field type: comments)<b>CombinedCode</b>: Combined tree code (plot and tree number) (Field type: id)<b>Species</b>: Species ID (Field type: comments)<b>Attribute table for stem surveys at DAN04</b> (described in worksheet Danum_census_DAN04)Description: Stem survey data for DAN04 (SAFE plot name: Car_D1)Number of fields: 19Number of data rows: 4590Fields: <b>SAFEPlotName</b>: SAFE plot name (Field type: location)<b>Plot</b>: GEM plot name (Field type: id)<b>Subplot</b>: Subplot number (Field type: id)<b>Date</b>: Date measured (Field type: date)<b>x_coord</b>: Relative x coordinate within subplot (Field type: numeric)<b>y_coord</b>: Relative y coordinate within subplot (Field type: numeric)<b>Tag_6digit</b>: Tree identification tag (Field type: id)<b>Species_6char</b>: Species code (Field type: id)<b>NumberOfStem</b>: Number of stems (Field type: numeric)<b>Diameter_MainStem_mm</b>: Diameter of main stem (Field type: numeric)<b>Codes</b>: Further flags (Field type: comments)<b>Notes</b>: Field notes (Field type: comments)<b>Diameter_Stem1_mm</b>: Additional stem diameters (for multiple stems) (Field type: numeric)<b>Diameter_Stem2_mm</b>: Additional stem diameters (for multiple stems) (Field type: numeric)<b>Diameter_Stem3_mm</b>: Additional stem diameters (for multiple stems) (Field type: numeric)<b>Diameter_Stem4_mm</b>: Additional stem diameters (for multiple stems) (Field type: numeric)<b>Diameter_Stem5_mm</b>: Additional stem diameters (for multiple stems) (Field type: numeric)<b>Diameter_Stem6_mm</b>: Additional stem diameters (for multiple stems) (Field type: numeric)<b>Diameter_Stem7_mm</b>: Additional stem diameters (for multiple stems) (Field type: numeric)<b>Attribute table for stem surveys at DAN05</b> (described in worksheet Danum_census_DAN05)Description: Stem survey data for DAN05 (SAFE plot name: Car_D2)Number of fields: 16Number of data rows: 5562Fields: <b>SAFEPlotName</b>: SAFE plot name (Field type: location)<b>Plot</b>: GEM plot name (Field type: id)<b>Subplot</b>: Subplot number (Field type: id)<b>Date</b>: Date measured (Field type: date)<b>x_coord</b>: Relative x coordinate within subplot (Field type: numeric)<b>y_coord</b>: Relative y coordinate within subplot (Field type: numeric)<b>Tag_6digit</b>: Tree identification tag (Field type: id)<b>Species_6char</b>: Species code (Field type: id)<b>NumberOfStem</b>: Number of stems (Field type: numeric)<b>Diameter_MainStem_mm</b>: Diameter of main stem (Field type: numeric)<b>Codes</b>: Further flags (Field type: comments)<b>Notes</b>: Field notes (Field type: comments)<b>Diameter_Stem1_mm</b>: Additional stem diameters (for multiple stems) (Field type: numeric)<b>Diameter_Stem2_mm</b>: Additional stem diameters (for multiple stems) (Field type: numeric)<b>Diameter_Stem3_mm</b>: Additional stem diameters (for multiple stems) (Field type: numeric)<b>Diameter_Stem4_mm</b>: Additional stem diameters (for multiple stems) (Field type: numeric)<b>GEM plot coordinates</b> (described in worksheet GEM_plot_GPS_corner_coordinates)Description: Corner coordinates for the GEM plot, measured with GPSNumber of fields: 6Number of data rows: 40Fields: <b>SAFEPlotName</b>: Location (Field type: location)<b>Plot</b>: Plot name (Field type: id)<b>x_relative</b>: x coordinate relative to plot origin (Field type: numeric)<b>y_relative</b>: y coordinate relative to plot origin (Field type: numeric)<b>x_utm</b>: x coordinate in UTM 50N (Field type: numeric)<b>y_utm</b>: y_coordinate in UTM 50N (Field type: numeric)<b>GEM plot subplot coordinates</b> (described in worksheet GEM_subplot_fitted_coordinates)Description: GEM subplot coordinates derived from corner GPS locations, using least squares affine transformationNumber of fields: 13Number of data rows: 200Fields: <b>SAFEPlotName</b>: SAFE plot name (Field type: location)<b>Plot</b>: GEM plot name (Field type: id)<b>Subplot</b>: Subplot number (Field type: id)<b>x11</b>: x coordinate in UTM 50N (Field type: numeric)<b>y11</b>: y coordinate in UTM 50N (Field type: numeric)<b>x12</b>: x coordinate in UTM 50N (Field type: numeric)<b>y12</b>: y coordinate in UTM 50N (Field type: numeric)<b>x22</b>: x coordinate in UTM 50N (Field type: numeric)<b>y22</b>: y coordinate in UTM 50N (Field type: numeric)<b>x21</b>: x coordinate in UTM 50N (Field type: numeric)<b>y21</b>: y coordinate in UTM 50N (Field type: numeric)<b>x11_close</b>: x coordinate in UTM 50N (Field type: numeric)<b>y11_close</b>: y coordinate in UTM 50N (Field type: numeric)<b>Carbon_plot_point_cloud_buffer.las</b>Description: las file containing GEM carbon plot point clouds clipped SAFE, Maliau Basin and Danum Valley monitoring sitesThis file contains 1 data tables:<b>Attribute table for lidar point cloud</b> (described in worksheet GEM_plot_lidar)Description: GEM carbon plot point clouds for SAFE, Maliau Basin and Danum Valley monitoring sitesNumber of fields: 1Number of data rows: Unavailable (table metadata description only).Fields: <b>Carbon_plot_point_cloud_buffer</b>: LiDAR point cloud data covering the GEM plots (Field type: numeric)<b>Date range: </b>2001-09-15 to 2016-10-23<b>Latitudinal extent: </b>4.6000 to 5.0000<b>Longitudinal extent: </b>116.9000 to 117.9000