Do basic cleaning of Portal plant data — clean_plant

This function does basic quality control of the Portal plant data. It is mainly called from summarize_plant_data, with several arguments passed along.

The specific steps it does are, in order: (1) correct species names according to recent vouchers, if requested (2) restrict species to annuals or non-woody (3) remove records for unidentified species (5) exclude the plots that aren't long-term treatments

Usage

clean_plant_data(
  data_tables,
  type = "All",
  unknowns = FALSE,
  correct_sp = TRUE
)

Arguments

data_tables: the list of data_tables, returned from calling load_plant_data
type: specify subset of species; If type=Annuals, removes all non-annual species. If type=Non-woody, removes shrub and subshrub species If type=Perennials, returns all perennial species (includes shrubs and subshrubs) If type=Shrubs, returns only shrubs and subshrubs If type=Winter-annual, returns all annuals found in winter IF type=Summer-annual, returns all annuals found in summer
unknowns: either removes all individuals not identified to species (unknowns = FALSE) or sums them in an additional column (unknowns = TRUE)
correct_sp: T/F whether or not to use likely corrected plant IDs, passed to rename_species_plants