summarize_individual_rodents {portalr}

Return cleaned Portal rodent individual data

Description

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