phenology_demography

Code for Youngflesh et al. 2023 PNAS

This repository contains code to assess the demographic consequences of phenological dynamics in North American birds.

Associated publications:

Youngflesh, C, GA Montgomery, JF Saracco, DAW Miller, RP Guralnick, AH Hurlbert, RB Siegel, R LaFrance, MW Tingley. Demographic consequences of phenological asynchrony for North American songbirds. PNAS 120:e2221961120.

Repository structure:

• Scripts/
  • 1-process-gr/
    • 1a-landcover.R - produce forest landcover mask
    • 1b-greenup.R - calculate greenup
  • 2-pro-PC.R - productivity as a function of pheno indices
  • 3-juv-gr.R - breeding phenology sensitivity to green-up
  • 4-sens-juv-PC/
    • 4a-process-range-maps.R - calculate migration distance
    • 4-sens-juv-pc.R - calculate breeding sens as a function of species' traits
  • 5-predict.R - predict demographic impact of phenological change
  • Model_files/ - Stan files
    • 2-pro-pc.stan - Stan file for model in 2-pro-PC.R
    • 3-juv-gr-stan - Stan file for model in 3-juv-gr.R
    • 4-sens-juv-pc.stan - Stan file for model in 4-sens-juv-pc.R
• Data/ (ignored)
  • environment/
    • RAW/
      • MCD12Q1/ - MODIS-derived landcover data
      • MCD12Q2/ - MODIS-derived phenology data
    • processed/ - processed env data
    • climate/ - climate model data from climatena.ca
  • MAPS_data/ - MAPS data
  • BOTW/ - BirdLife range maps
  • bird_phylo/ - data from birdtree.org
• Results/ (ignored)