Return cleaned Portal rodent individual data — summarize_individual

This function cleans and subsets the data based on a number of arguments. It returns stake number and individual level data.

Usage

summarize_individual_rodents(
  path = get_default_data_path(),
  clean = TRUE,
  type = "Rodents",
  length = "all",
  unknowns = FALSE,
  time = "period",
  fillweight = FALSE,
  min_plots = 1,
  min_traps = 1,
  download_if_missing = TRUE,
  quiet = FALSE
)

summarise_individual_rodents(
  path = get_default_data_path(),
  clean = TRUE,
  type = "Rodents",
  length = "all",
  unknowns = FALSE,
  time = "period",
  fillweight = FALSE,
  min_plots = 1,
  min_traps = 1,
  download_if_missing = TRUE,
  quiet = FALSE
)

Arguments

path: either the file path that contains the PortalData folder or "repo", which then pulls data from the PortalData GitHub repository
clean: logical, load only QA/QC rodent data (TRUE) or all data (FALSE)
type: specify subset of species; either all "Rodents" or only "Granivores"
length: specify subset of plots; use "All" plots or only "Longterm" plots (to be deprecated)
unknowns: either removes all individuals not identified to species (unknowns = FALSE) or sums them in an additional column (unknowns = TRUE)
time: specify the format of the time index in the output, either "period" (sequential Portal surveys), "newmoon" (lunar cycle numbering), "date" (calendar date), or "all" (for all time indices)
fillweight: specify whether to fill in unknown weights with other records from that individual or species, where possible
min_plots: minimum number of plots within a period for an observation to be included
min_traps: minimum number of traps for a plot to be included
download_if_missing: if the specified file path doesn't have the PortalData folder, then download it
quiet: logical, whether to run without producing messages

Value

a data.frame