SimonCMills / colombiaBeta

This repository contains code for analysis of bird and dung beetle data from Colombia.

The core scripts required for analysis are listed below. Bold headings organize the codebase by topic. Solid bullets correspond to code files. Hollow sub-bullets indicate each script that produces objects required for the script to run (generally objects saved to disk, except in cases of scripts called via source()). Scripts can be run in order of first appearance in this list without problems.

Baseline species lists

• species_lists.R (baseline species list for Colombia; also creates birdlife range map objects)
• nf_species_list.R (baseline species list for neotropical forests)
  • species_lists.R

Sampling point data

• GEE_setup.sh (setup for Earth Engine)
• coord_processing.R (import and process coordinates for all points)
  • GEE_setup.sh
• points_formatting.R (Add point-level covariates, including ALOS elevations from Earth Engine via reticulate; still need to do precipitation and wildlife-friendliness)
  • GEE_setup.sh
  • coord_processing.R

Survey data

• bird_import_and_cleaning.R (Import and format bird survey data)
  • species_lists.R
  • points_formatting.R

Species ranges

• hydrosheds_extraction.R (create polygons for biogeographic clipping)
• ayerbe_maps.R (read and process Ayerbe range maps)
  • species_lists.R
• combined_bird_maps.R (create properly buffered maps--originally these were combined Ayerbe-BirdLife maps, but now they are just biogeographically buffered Ayerbe maps).
  • species_lists.R
  • bird_import_and_cleaning.R
  • hydrosheds_extraction.R
  • ayerbe_maps.R

Species traits

• birdlife_scraper.R (scrape birdlife website for trait info)
  • nf_species_list.R
• parker_standardization.R (update Parker-Stotz-Fitzpatrick databases to BirdLife taxonomy still requires some additional checking by hand)
  • nf_species_list.R
  • birdlife_scraper.R
  • species_lists.R
• elevations_prep_and_exploration.R (read in elevational range limits file and explore data)
  • species_lists.R
• species_covariate_formatting.R (create file with species covariates)
  • species_lists.R
  • parker_standardization.R
  • combined_bird_maps.R
  • elevations_prep_and_exploration.R
  • birdlife_scraper.R
• migratory_dates.R (read in file of migratory dates and format)
  • species_lists.R

Format for analysis

• format_for_analysis.R (merge various covariate files, also create new covariates from certain files and range maps)
  • combined_bird_maps.R
  • bird_import_and_cleaning.R
  • elevations_prep_and_exploration.R
  • points_formatting.R
  • species_covariate_formatting.R
  • migratory_dates.R

Analysis

• occupancyMod_full.stan (stan code for biogeographically clipped multi-species occupancy model with within-chain parallelization)
• bird_occupancy_full.R (fit the occupancy model described in occupancyMod_full.R via cmdstanR on local computer)
  • format_for_analysis.R