case-study-1

code/case-study-1

Contains all code used in the first case study assessing trends of 51 forest bird species across the eastern US

• bbs-data-prep.R: preps raw BBS data for analysis.
• bird-life-extract.R: extracts data from BirdLife International for determination of species ranges.
• birdlife-species-ranges.R: calculates the species ranges based on BirdLife International
• format-data-spOccupancy.R: formats the prepared data into spOccupancy format.
• get-auc.R: extracts AUC for each of the candidate models for each species in the assessment of model predictive performance.
• get-bbs-2022-data.R: script to extract BBS data from 2022 for the assessment of out-of-sample predictive performance.
• get-prediction-data.R: generates the spatial locations for prediction across the eastern US.
• get-waic.R: script to extract WAIC from all candidate models for all species.
• main-2021.R: script to run a single-season spatial occupancy model with BBS data from 2021 for use in an assessment of model predictive performance.
• main-bcr-stPGOcc.R: script to run the Strata candidate model, where the strata are Bird Conservation Regions.
• main-stPGOcc.R: script to run the constant linear candidate model, where the temporal trend is assumed constant over the entire modeled region.
• main-svcTPGOcc.R: script to run the SVC model, where the temporal trend is allowed to vary spatially.
• main-tmax-stPGOcc.R: script to run the interaction model with maximum temperature interacting with the temporal trend.
• predict-2021-auc.R: script to predict occupancy probability for each species in 2021 as an assessment of out-of-sample predictive performance.
• pred-svcTPGOcc.R: predicts species-specific occurrence and occurrence trends across the eastern US for the SVC model.
• summary.R: summarizes results from all model fits and generates all figures for this case study.
• tmax-data-prep.R: script to extract the maximum temperature data for use as an interacting variable.