drought_CV_eBird_reproducible

A code repository to accompany the manuscript "Drought influences habitat associations and abundances of birds in California's Central Valley."

List of files the user needs to run the full workflow

• 'data/greatvalley_outline.shp' (Provided). This is a shapefile that delineates the Central Valley ecoregion

• 'data/fveg_WHRNHUM' - the Functional Vegetation LANDFIRE raster

• 'data/fveg_attributes.txt' - A .txt file describing the FVEG features

• 'data/CA_Aug2020_species_counts.csv' - One of two parts constituting eBird relational database, which contains information on species counts for all California eBird checklists as of August 2020. This csv has four columns:

  • SAMPLING.EVENT.IDENTIFIER - a unique ID indicating the eBird checklist event to which this observation corresponds

  • name_clean - The common name of the species, as given by eBird, with whitespace and punctuation removed

  • SCIENTIFIC.NAME - The scientific name of the species, as given by eBird

  • total_count - The count reported for the species (>=1, or "X" indicating no count reported. 0s are implicit)

• 'data/CA_Aug2020_checklist_info.csv' - One of two parts constituting a relational database of eBird data, this file stores metadata for each checklist event. This csv has the following columns:

  • SAMPLING.EVENT.IDENTIFIER - a unique ID indicating the eBird checklist event to which this observation corresponds. Used for joining to counts csv

  • LATITUDE

  • LONGITUDE

  • OBSERVATION.DATE

  • TIME.OBSERVATIONS.STARTED

  • OBSERVER.ID - a unique ID grouping checklists submitted by the same eBird observer

  • DURATION.MINUTES

  • EFFORT.DISTANCE.KM

  • PROTOCOL.CODE - the eBird sampling protocol category that the checklist followed

  • EFFORT.AREA.HA

  • ALL.SPECIES.REPORTED - a logical flag indicating whether the checklist is complete

  • NUMBER.OBSERVERS

• 'data/ebird_protocol_codes.csv' - Table of eBird protocol definitions. Provided

• 'data/all_CA_breeding_birds.csv' - List of birds breeding in California that were considered for this analysis. Provided

• 'data/LandUseClassification_AcrossSites_FVEG.xlsx' - Table relating land cover features to habitat groups. Provided

• 'data/spei07.nc' - The SPEI raster file. Obtained from SPEIbase.

• 'intermediate/EVI_df.csv' - A data frame giving the average EVI in each grid cell in each season. See manuscript for details on processing.

• 'intermediate/NDWI_df.csv' - A data frame giving the average NDWI in each grid cell in each season. See manuscript for details on processing.

Contact me

If you have any questions about the code in this repository, you can contact the corresponding author.