This repository contains all code and data needed to reproduce the analyses reported in "A lidar-based openness index to aid conservation planning for grassland wildlife" (Allen et al. 2022). The archived repository used in the paper also lives here on OSF (doi: 10.17605/OSF.IO/VG5HU).
Potentially useful things in here: 1) instructions on how to calculate the openness index; 2) an example of using Restricted Spatial Regression (RSR) to fit an occupancy model in the presence of (lots of) spatial autocorrelation.
The two .rmd files contain the R code for creating and manipulating the openness index (openness_mapping.rmd) and performing the occupancy modeling (openness_occupancy_modeling.rmd).
The data folder contains:
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the Duke Farms Kaufman/Skeet Shoot field and treeline shapefiles required for some analyses
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a template raster used for reprojection
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the horizon raster outputs from GRASS in the "horizon_rasters" folder (i.e., calculated mean and max angle to the horizon from each cell for each scenario - baseline, no powerlines, no treelines, no SW treeline, etc).
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the 9 lidar point cloud (.laz) files. These "Northwest New Jersey 2018" lidar tiles can be downloaded here: https://njgin.nj.gov/njgin/edata/elevation/index.html#!/ They are about 750 MB total and were too big for GitHub. They can also be found in the OSF repository in the "lidar2018" folder: https://doi.org/10.17605/OSF.IO/VG5HU
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the grsp.occupancy.openness.csv file, which contains all bird and covariate data needed to conduct the occupancy analysis. Descriptions of the fields in that file are as follows:
pt: survey point unique ID site: Kaufman ("K") or Skeet Shoot ("S") field latitude: decimal degrees (WGS84) longitude: decimal degrees (WGS84) occ1-occ4: detection/non-detection measurements in survey periods 1-4 obs1-obs4: observer for each point during survey periods 1-4 ord1-ord4: ordinal date (1-365) of each point survey in periods 1-4 dtime1-dtime4: time of day (hour and decimal minutes) of each point survey in periods 1-4 mean2018: mean-angle openness measure at each point max2018: max-angle openness measure at each point No_trees_mean: mean-angle openness measure at each point based on raster with no treelines No_trees_max: max-angle openness measure at each point based on raster with no treelines No_wires_mean: mean-angle openness measure at each point based on raster with no powerlines No_wires_max: mean-angle openness measure at each point based on raster with no powerlines No_SW_mean: mean-angle openness measure at each point based on raster with no SW treeline No_SW_max: max-angle openness measure at each point based on raster with no SW treeline No_SE_mean: mean-angle openness measure at each point based on raster with no SE treeline No_SE_max: max-angle openness measure at each point based on raster with no SE treeline No_N_mean: mean-angle openness measure at each point based on raster with no N treeline No_N_max: max-angle openness measure at each point based on raster with no N treeline