MAPS_morph_changes

Code for Youngflesh et al. 2022 Nature Ecology and Evolution

This repository contains code to characterize avian morphological change over time, latitude, elevation, and in response to temperature.

Associated publications:

Youngflesh, C, JF Saracco, RB Siegel, MW Tingley. 2022. Abiotic conditions shape spatial and temporal morphological variation in North American birds. Nature Ecology and Evolution 6:1860-1870.

Repository structure:

• Scripts/
  • 1-process-data.R
  • 2-process-elev.R
  • 3-process-daymet/
    • 3-proces-daymet.R
    • daymet_query.txt
    • daymet_spt_batch.sh
  • 4-si-tle.R
  • 5-wi-tle.R
  • 6-si-temp-space.R
  • 7-si-temp-lag.R
  • 8-temp-cov.R
  • 9-backtransform.R
  • 10-analyze-results.R
  • 11-haldanes.R
  • model_files
    • morph-temp-space.stan
    • morph-temp-ss2.stan
    • morph-tle.stan
    • temp_sp_cov.stan
• Data/
  • bird_phylo/
    • phylo_names_key-2021-05-19.csv
    • tree-pruner-XXXX/ [ignored - available here]
  • GMTED2010_mean/ [ignored - available here]
  • MAPS_data.csv [ignored - available [here](DRYAD LINK)]
  • Gen_time_Bird_et_al_2020_table_4.csv [ignored - available here]
  • Hendry_et_al_2008_Mol_Eco.csv [ignored - available here]
• Results/ [ignored]
• Figures/
  • PPO/ - prior posterior overlap