Summarize biovolumes for classified bins — summarize

Wraps iRfcb::ifcb_summarize_biovolumes() and joins with taxonomy.

Usage

summarize_biovolumes(
  feature_folder,
  hdr_folder,
  classifications,
  taxa_lookup,
  non_bio_classes = character(0),
  pixels_per_micron = 2.77,
  custom_classes = NULL
)

Arguments

feature_folder: Path to the feature CSV directory.
hdr_folder: Path to the raw data directory (for .hdr files).
classifications: A data.frame from read_h5_classifications().
taxa_lookup: A data.frame with columns clean_names, name, AphiaID.
non_bio_classes: Character vector of non-biological class names to exclude.
pixels_per_micron: Conversion factor from pixels to microns. Default 2.77, which is the optical calibration constant for the standard IFCB instrument. Different IFCB units may use slightly different values.
custom_classes: Optional data frame of custom classes with an is_diatom column. Used to extend diatom identification.

Value

A data.frame with per-sample, per-class biovolume data joined with taxonomy.