summarize_individual_rodents: Return cleaned Portal rodent individual data

In portalr: Create Useful Summaries of the Portal 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

portalr documentation built on Dec. 11, 2021, 10:02 a.m.