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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

    • 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