Bird_Phenology

Code for characterizing bird arrival and breeding phenology.

Associated publications:

Youngflesh, C., Socolar, J., Amaral, B.R., Arab, A., Guralnick, R.P., Hurlbert, A.H., LaFrance, R., Mayor, S.J., Miller, D.A.W., Tingley, M.W. 2021. Migratory strategy drives species-level variation in bird sensitivity to vegetation green-up. Nature Ecology and Evolution

Repository structure:

• Data/ - Datasets relevant for project

  • eBird_species_list.txt - initial list of species to be queried
  • IAR_species_list.txt - list of species to be modeled using IAR
  • arr_species_list.txt - list of species to quantify breeding phenology
  • species_reference.csv - table of taxonomic information for species of interest
  • db_pass.txt (ignored) - database password
  • hex_grid_crop - .shp files for cells over study area
  • BirdLife_range_maps/ (ignored) - range maps for birds from BirdLife International
  • Processed/ (ignored) - data that have undergone processing
    • arrival_GAM_<DATE> - model output from 2-arr-GAM.R
    • arrival_master_<DATE> - output from 5-extract-arr-dates.R
    • breeding_GAM_<DATE> - model output from 8-br-GAM.R
    • breeding_master_<DATE> - output from 9-process-br-output.R
    • eBird_arrival_query_<DATE> - output from 1-query-ebird.R
    • eBird_breeding_query_<DATE> - output from 6-query-nesting-data.R
    • IAR_input_<DATE> - output from 3-process-arr-output.R
    • IAR_output_<DATE> - output from 4-arr-IAR_hm.R
    • juv_GAM_<DATE> - model output from 7-juv-GAM.R
    • juv_master_<DATE> - output from 9-process-juv-output.R

• Scripts/ - scripts to run analyses

  • 1-query-ebird.R - query eBird database for arrival
  • 2-arr-GAM/
    • 2-arr-GAM.R - R script to fit GAM models to estimate bird arrival for each species/cell/year. Takes species argument (run from 2-<Genus_species>.sh scripts)
    • 2-create-batch-scripts.sh - script to create scripts (2-<Genus_species>.sh) for HPC job submission
    • 2-master-submit.sh - script to be run (./2-master-submit.sh) on HPC cluster to submit all halfmax arr jobs
    • species/ - contains job scripts for each species
      • 2-<Genus_species>.sh - scripts to submit jobs for each species; run with 2-master-submit.sh
  • 3-process-arr-output.R - process model output from 2-arr-GAM.R, in prep for 4-IAR-arr-hm.R
  • 4-IAR-arr-hm/ - [run time: up to 3 weeks?]
    • 4-IAR-arr-hm.R - fit arrival dates using IAR model to derive arrival date estimates (one model per species)
    • 4-create-batch-scripts.sh - script to create scripts (4-<Genus_species>.sh) for HPC job submission
    • 4-master-submit.sh - script to be run (./4-master-submit.sh) on HPC cluster to submit all jobs
    • species/ - contains job scripts for each species
      • 4-<Genus_species>.sh - scripts to submit jobs for each species; run with 4-master-submit.sh
  • 5-extract-arr-dates.R - extract arrival dates for each species-cell-year from 4-IAR-arr-hm.R output
  • 6-query-nesting-data.R - query nesting data
  • 7-juv-GAM/ - halfmax model for fledging dates (derived from MAPS data)
    • 7-juv-GAM.R - R script to fit GAM models to estimate bird fledging date (from MAPS data) for each species/cell/year. Takes species argument (run from 7-<Genus_species>.sh scripts)
    • 7-create-batch-scripts.sh - script to create scripts (7-<Genus_species>.sh) for HPC job submission
    • 7-master-submit.sh - script to be run (./7-master-submit.sh) on HPC cluster to submit all halfmax juv jobs
    • species/ - contains job scripts for each species
      • 7-<Genus_species>.sh - scripts to submit jobs for each species; run with 7-master-submit.sh
  • 8-br-GAM/ - halfmax model for breeding dates (derived from eBird breeding codes)
    • 8a-query-Nestwatch.R - script to query Nestwatch data for breeding phenology
    • 8b-analyze-Nestwatch.R - script to analyze Nestwatch data and imput breeding windows
    • 8-halfmax-br.R - R script to fit GAM models to estimate bird breeding date (from eBird breeding codes) for each species/cell/year. Takes species argument (run from 8-<Genus_species>.sh scripts)
    • 8-create-batch-scripts.sh - script to create scripts (8-<Genus_species>.sh) for HPC job submission
    • 8-master-submit.sh - script to be run (./8-master-submit.sh) on HPC cluster to submit all jobs
    • species/ - contains job scripts for each species
      • 8-<Genus_species>.sh - scripts to submit jobs for each species; run with 8-master-submit.sh
  • 9-process-juv-br-output/ - process br and juv halfmax results
    • 9-process-juv-output.R - process model output from 7-juv-GAM.R
    • 9-process-br-output.R - process model output from 8-br-GAM.R
  • Other/
  • 10-bj-IAR-hm
    • 10-bj-IAR-hm.R - fit breeding dates using IAR model (both eBird- and MAPS-derived dates)
    • 10-create-batch-scripts.sh - script to create scripts (10-<Genus_species>.sh) for HPC job submission
    • 10-master-submit.sh - script to be run (./10-master-submit.sh) on HPC cluster to submit all jobs
    • species/ - contains job scripts for each species
      • 10-<Genus_species>.sh - scripts to submit jobs for each species; run with 10-master-submit.sh
  • 10-br-IAR-hm
    • 10-br-IAR-hm.R - fit breeding dates using IAR model (just eBird-derived dates)
    • 10-create-batch-scripts.sh - script to create scripts (10-<Genus_species>.sh) for HPC job submission
    • 10-master-submit.sh - script to be run (./10-master-submit.sh) on HPC cluster to submit all jobs
    • species/ - contains job scripts for each species
      • 10-<Genus_species>.sh - scripts to submit jobs for each species; run with 10-master-submit.sh
  • 11-process-bj-output.R - processing output from 10-bj-IAR-hm.R
  • 11-process-br-output.R - processing output from 10-br-IAR-hm.R
  • 12-master-pheno-process.R - produce master phenology data object

• Figures/ (ignored)