clean_rodent_data {portalr}

Do basic cleaning of Portal rodent data

Description

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

The specific steps it does are, in order: (1) add in missing weight data (2) remove records with "bad" period codes or plot numbers (3) remove records for unidentified species (4) exclude non-granivores (5) exclude incomplete trapping sessions (6) exclude the plots that aren't long-term treatments

Usage

clean_rodent_data(
  rodent_data,
  species_table,
  fillweight = FALSE,
  type = "Rodents",
  unknowns = FALSE
)

Arguments

rodent_data

the raw rodent data table

species_table

the species table

fillweight

specify whether to fill in unknown weights with other records from that individual or species, where possible

type

specify subset of species; either all "Rodents" or only "Granivores"

unknowns

either removes all individuals not identified to species (unknowns = FALSE) or sums them in an additional column (unknowns = TRUE)