/statewide-deer-analysis

Analysis for the estimation of abundance of deer in Victoria

Primary LanguageR

Abundance of Deer in Victoria: Statewide Analysis of Camera Trap Data

This repository contains analysis of modelling deer abundance and distribution in Victoria using camera trap distance sampling (CTDS). The core of the analysis is available in the statewide_deer_analysis.Rmd and as an html at https://justincally.github.io/statewide-deer-analysis/. The interactive map is available at https://justincally.github.io/statewide-deer-analysis/interactive-map.html. The data used in this analysis is primarily sourced from our database (private access). However, data used in the model has been pre-formatted and is available in data/multispecies_data.rds. Additional files and folders in this repository are:

  • data/: Contains various pre-prepared data files including transect counts of signs (created by the data/species_assign_wrangle.R script). It also contains data and scripts for determining ecological vegetation communities (EVCs) for the model data. The data/prediction_raster has the raster we use to predict to across Victoria (public land). And data/historic_ala_records.rds is data used in data/species_assign_wrangle.R.

  • functions/ has a suite of functions used in data preparation and then model interrogation.

  • outputs/ is where models and model outputs such as rasters and plots are located. Note that the STAN model draws are not git tracked as they are very large files. The rasters for abundance are the combined_deer_average_density.tif and combined_deer_sd.tif (standard deviation), while the combined_threshold_raster.tif provides the estimated range distributions (LCI, median and UCI).

  • stan/ is where the stan models used in the analysis are stored.

  • docs/ is where the rendered Rmarkdown html and interactive maps are stored.