jedgroev / rp016

Reproduction Package Eurodeer paper n. 016

Datasets and analysis scripts of Salvatori, De Groeve et al. (2022).

Directory Structure

The repository contains the following files and directories:

file(s)/directories	description
./code/0_data_preparation.sql	SQL-query extracting the raw data from the eurodeer database
./code/0_data_preparation.R	preparation of gps_data/kde_data: calculation of HRs & intersection of GPS/KDE with TCD/CLC
./code/1_mismatch_and_modelling.Rmd	CLC/TCD mismatch analysis and statistical modelling of day-night forest use in roe and red deer
./code/2_patchsize.Rmd	patch size analysis
./code/3_validation_gps.Rmd	Validation confusion matrices of mismatching GPS location
./code/fncs/	functions used in step 1, 2, 3
./data/raw/gps/	RDS; raw gps data of roe and red deer as extracted from the eurodeer database
./data/raw/rasters/	TIF; study area extracts of TCD and CLC rasters
./data/1_analysis/	CSV; absolute and proportion of forest and open habitat calculated for GPS/KDE with TCD/CLC
./data/2_patchsize/	CSV; GPS locations with patch sizes
./data/3_validation_gps/	CSV; 100 random gps locations per population, validated using a satellite layer as ground truth
./code/results/	DIR; empty directory to store outputs

Directory tree

. 
├── README.md
├── RP016.Rproj
├── code
│   ├── 0_data_preparation.R
│   ├── 0_data_preparation.sql
│   ├── 1_mismatch_and_modelling.R
│   ├── 2_patchsize.Rmd
│   ├── 2_patchsize.html
│   ├── 3_validation_gps.Rmd
│   ├── 3_validation_gps.html
│   └── fncs
│       ├── 00_basic.R
│       ├── 01_compute_kde.R
│       ├── 02_reclass_rast.R
│       ├── 03_intersect_rast_gps.R
│       ├── 04_intersect_rast_kde.R
│       ├── 11_boxplot_mismatch.R
│       ├── 11_confusion_scheme.R
│       ├── 11_forest_proportion_barboxplot.R
│       ├── 11_model_selection.R
│       ├── 11_plot_predictions.R
│       ├── 11_proportion_plot.R
│       └── 21_patch_statistics.R
├── data
│   ├── 1_mismatch_and_modelling
│   │   ├── gps_data.csv
│   │   ├── gps_for_model.csv
│   │   ├── kde_data.csv
│   │   └── kde_for_model.csv
│   ├── 2_patchsize
│   │   ├── red.csv
│   │   └── roe.csv
│   ├── 3_validation_gps
│   │   ├── red.csv
│   │   └── roe.csv
│   └── raw
│       ├── gps
│       │   ├── red_rds
│       │   └── roe_rds
│       └── rasters
│           ├── red_raster_clc_population_14.tif
│           ├── red_raster_clc_population_17.tif
│           ├── red_raster_clc_population_21.tif
│           ├── red_raster_clc_population_3.tif
│           ├── red_raster_clc_population_8.tif
│           ├── red_raster_tcd_population_14.tif
│           ├── red_raster_tcd_population_17.tif
│           ├── red_raster_tcd_population_21.tif
│           ├── red_raster_tcd_population_3.tif
│           ├── red_raster_tcd_population_8.tif
│           ├── roe_raster_clc_population_1.tif
│           ├── roe_raster_clc_population_15.tif
│           ├── roe_raster_clc_population_2.tif
│           ├── roe_raster_clc_population_25.tif
│           ├── roe_raster_clc_population_8.tif
│           ├── roe_raster_tcd_population_1.tif
│           ├── roe_raster_tcd_population_15.tif
│           ├── roe_raster_tcd_population_2.tif
│           ├── roe_raster_tcd_population_25.tif
│           └── roe_raster_tcd_population_8.tif
└── results

References

Salvatori M, De Groeve J, van Loon E, De Baets B, Morellet N, Focardi S, Bonnot NC, Gehr B, Griggio M, Heurich M, Kroeschel M, Licoppe A, Moorcroft PRM, Pedrotti L, Signer J, Van de Weghe N, & Cagnacci F (2022) Day versus night use of forest by red and roe deer as determined by Corine Land Cover and Copernicus Tree Cover Density: assessing use of geographic layers in movement ecology. Landscape Ecology, 37: 1453-1468