Data for: Horizontal viewsheds of large herbivores as a function of woodland structure
Data files
Nov 14, 2023 version files 25.54 KB
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2023-08-07-herbivore-viewshed-dataset.ods
22.25 KB
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README.md
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Abstract
This dataset contains values of tree stem density per hectare of different size classes (Sapling: > 0.3m, < 1.3m height, Small stem: >=1.3m height, < 10cm DBH, Medium stem: 10-20cm DBH, Large: 21-30cm DBH, Very large: >=31cm DBH), Viewshed Coefficient values (vc), Leaf Area Index (LAI) values for 0.75 - 1.5m above the ground and average percentage cover of bramble (Rubus frutocisus agg.). These data have come from 71 circular 15m-radius sampling plots (four-character codes in plotID column across ten woodland sites (three-character codes in site column).
The "raw_data" tab contains the untransformed, unscaled raw data. The "transformed_scaled_data" tab contains the transformed, scaled data that were used in the modelling approach in the associated manuscript.
Raw and transformed data from tree stem surveys and mobile hand-held terrestrial laser scanner surveys of temperate woodlands in North Wales for the purpose of assessing the effect of woodland structure on viewsheds for herbivores living in the woodland understory. Analysis in the associated publication found a significant negative effect of small stem density on the viewshed coefficient (vc), meaning higher densities of small stems resulted in lower visibility for herbivores.
Description of the data and file structure
This dataset contains values of tree stem density per hectare of different size classes (Sapling: > 0.3m, < 1.3m height, Small stem: >=1.3m height, < 10cm DBH, Medium stem: 10-20cm DBH, Large: 21-30cm DBH, Very large: >=31cm DBH), Viewshed Coefficient values (vc), and Leaf Area Index (LAI) values for 0.75 - 1.5m above the ground. These data have come from 71 circular 15m-radius sampling plots (four-character codes in plotID column across ten woodland sites (three-character codes in site column).
The tree stem density data were collected through manual stem counts and measurements using a Diameter at Breast Height (DBH) tape.
The units of these stem density columns are "stem density per hectare".
The Viewshed Coefficient (vc) values were produced from 3D pointcloud datasets collected with a hand-held mobile GeoSLAM (Nottingham) ZEB Revo terrestrial laser scanner. The pointclouds were processed in R version 4.0.3 (R Core Team, 2021) following methodology in the associated manuscript using the viewshed3d (Lecigne & Eitel, 2022) and lidR (Roussel et al., 2020) packages. The vc values were calculated using the h_visibility function in the viewshed3d package.
The Leaf Area Index (LAI) data were also extracted from the 3D pointcloud data following methodology in the associated manuscript by generating Leaf Area Density (LAD) profiles using the LAD function in the lidR package, then calculating LAI values from these profiles using the lai function in the leafR (de Almedia et al, 2021) package.
The "average.bramble.perc.cover" column contains values of average percentage bramble (Rubus frutocisus agg.) cover for each plot. Bramble cover was measured following methodology in the associated manuscript using randomly placed 0.25m^2 quadrats.
The "raw_data" tab contains the untransformed, unscaled raw data. The "transformed_scaled_data" tab contains the transformed, scaled data that were used in the modelling approach in the associated manuscript.
In the "transformed_scaled_data" tab, the columns containing ".log" in the title have been log transformed. In addition, all values accept those in the "vc" column have been scaled through z-scoring.
Sharing/Access information
Any questions or trouble with access, please email the corresponding author: Amy Gresham amygresham48@gmail.com
Code/Software
All pointcloud processing that generated these data was conducted in R version 4.0.3 using the lidR (Roussel et al., 2020), viewshed3d (Lecigne & Eitel, 2022) and leafR (de Almedia et al, 2021) packages.
Please email the corresponding author for any enquiries: Amy Gresham amygresham48@gmail.com
The tree stem density data were collected through manual stem counts and measurements using a Diameter at Breast Height (DBH) tape. The units of these stem density columns are "stem density per hectare".
The Viewshed Coefficient (vc) values were produced from 3D pointcloud datasets collected with a hand-held mobile terrestrial laser scanner (GeoSLAM ZEB Revo). The pointclouds were processed in R (version 4.0.3) following methodology in the associated manuscript using the viewshed3d (Lecigne & Eitel, 2022) and lidR (Roussel et al., 2020) packages. The vc values were calculated using the h_visibility function in the viewshed3d package.
The Leaf Area Index (LAI) data were also extracted from the 3D pointcloud data following methodology in the associated manuscript by generating Leaf Area Density (LAD) profiles using the LAD function in the lidR package, then calculating LAI values from these profiles using the lai function in the leafR (de Almedia et al, 2021) package.
The "average.bramble.perc.cover" column contains values of average percentage bramble (Rubus frutocisus agg.) cover for each plot. Bramble cover was measured following methodology in the associated manuscript using randomly placed 0.25m^2 quadrats.
In the "transformed.scaled.data" tab, the columns containing ".log" in the title have been log transformed. In addition, all values accept those in the "vc" column have been scaled through z-scoring.