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case-study-2

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code/case-study-2

Contains all code used in the second case study assessing the impacts of land use change on Grasshopper Sparrow from 1970-2019.

  • data-prep.R: prepares the raw BBS data for analysis.
  • extract-estimates.R: script to extract the complete coefficient effects across all prediction locations for each of the candidate models.
  • format-prediction-data.R: script to format all prediction data together for use with predict functions in spOccupancy.
  • format-spOccupancy-data.R: script to format all data into the list format required for fitting models in spOccupancy.
  • get-prediction-coords.R: extracts the prediction coordinates across the US.
  • get-WAIC.R: script to calculate the WAIC values for all candidate models.
  • lulc-data-prep.R: script to prepare and extract the land cover data from USGS EROS at the BBS routes.
  • lulc-pred-data-prep.R: script to prepare and extract the land cover data from USGS EROS across all prediction locations.
  • main-constant-GRSP.R: script to fit the constant linear model that assumes constant effects of grassland and cropland cover change on Grasshopper Sparrow occurrence.
  • main-full-GRSP.R: script to fit the Full model that includes SVCs and interactive effects of grassland and cropland cover change on Grasshopper Sparrow occurrence.
  • main-int-lulc-GRSP.R: script that fits the interaction model that allows the effects of cropland and grassland cover to interact with the average amount of habitat over the 50 year period.
  • main-int-tmax-GRSP.R: script that fits the interaction model that allows the effects of cropland and grassland cover to interact with maximum temperature over the 50 year period.
  • main-svc-GRSP.R: script that fits the SVC model for the Grasshopper Sparrow case study.
  • pred-full.R: script to predict occurrence probability and the spatially-varying effects of land cover change on Grasshopper sparrow across the continental US using the full model.
  • pred-svc.R: script to predict occurrence probability and the spatially-varying effects of land cover change on Grasshopper sparrow across the continental US using the SVC model.
  • summary.R: summarizes results from all model fits and generates all figures for this case study.