Butterfly_Abundance_and_Phenology

to do: Add Zenodo DOI

Code for analyzing drivers of aggregate butterfly phenology and abundance by overwintering stage

Analysis published in:

Larsen, EA, MW Belitz, GJ Di Cecco, J Glassberg, AH Hurlbert, L Ries, & RP Guralnick. Accepted 2023-12. Overwintering strategy regulates phenological sensitivity and consequences for ecological services in a clade of temperate North American insects Functional Ecology

Repository structure:

• data/ - Datasets relevant for project

  • derived/ - data that have undergone processing

  • envir/ - environmental greenup phenology data

    • MidGreenup-2021-11-30-forest.rds - input file for forest canopy greenup dates
    • MidGreenup-2021-11-30-open.rds - input file for open canopy greenup dates

  • images/ - cartoon art used in figure legends

    • boe_art.png - image file for representing butterflies overwintering as eggs
    • bol_art.png - image file for representing butterflies overwintering as larvae
    • bop_art.png - image file for representing butterflies overwintering as pupae

  • maps/ - files for spatial alignment & aggregation

    • hex_grid_crop.shp - shapefiles for hexagonal grid used for data aggregation, from [Bird Phenology repo] (https://github.com/phenomismatch/Bird_Phenology/tree/master/Data/hex_grid_crop)
    • spatial.domain.RData - R data file for spatial domain of analysis

  • naba/ - public data related to NABA circles in analysis

    • naba_circles.csv - spreadsheet of 777 NABA circles with mapping to hex cell IDs. Includes ID, Name, State, Country, Lat, Lng, hex cell
    • naba_names.csv - spreadsheet of 780 scientific name entries in NABA data mapped to Species IDs. Includes ScientificName, n (# rows in raw datasheet), heirarchy (0 = above species, 1 = species, 2 = subspeices), SpeciesID (species level name)

• code/ - Datasets relevant for project

  • abundance_analysis.R - code for analysis of drivers of abundance metrics

  • cpc.process.R - code for calculating thermal metrics from CPC data

  • figures.R - code for Figure 1 and supplemental figures

  • gather_envir_vars.R - code for preparing environmental covariates for analysis

  • gdd_variations.R - code for supplemental analysis of variations in GDD if using different thresholds, or considering within-hex-cell variation of daily tmin and tmax values

  • phenology_analysis.R - code for analyzing drivers of phenology metrics

  • phenology_metrics.R - code for estimating phenology metrics

  • src/ - reference code files from previous analysis

    • degday1.R - function for calculating single-sine estimation of degree days

• output/ - output files from analysis (figures, tables)

  • abundance.finalmodel.csv - csv spreadsheet of model parameters and statistics for final abundance model

  • onsetDeviation.finalmodel.csv - csv spreadsheet of model parameters and statistics for final model of adult onset phenology (start of flight period) deviation

  • figures/ - directory for image files of output figures

    • Fig1.2024.png - final Figure 1 (data summary)
    • Fig2.2024.png - final Figure 2 (onset deviation model)
    • Fig3.2024.png - final Figure 3 (abundance model)
    • FigS31.png - supplementary figure 3.1
    • FigS32.png - supplementary figure 3.2
    • FigS33.png - supplementary figure 3.3