summarize_rodent_data: Generate summaries of Portal rodent data

In portalr: Create Useful Summaries of the Portal Data

Generate summaries of Portal rodent data

Description

This function is a generic interface into creating summaries of the Portal rodent species data. It contains a number of arguments to specify the kind of data to summarize (at what level of aggregation) and various choices for dealing with data quality, and output format.

abundance generates a table of rodent abundance

* biomass() generates a table of rodent biomass

* energy() generates a table of rodent energy (computed as 5.69 * (biomass ^ 0.75) after White et al 2004)

* rates() generates a table of rodent growth rates (computed as r=log(N[t+1]/N[t])

Usage

summarize_rodent_data(
  path = get_default_data_path(),
  clean = TRUE,
  level = "Site",
  type = "Rodents",
  length = "all",
  plots = length,
  unknowns = FALSE,
  shape = "crosstab",
  time = "period",
  output = "abundance",
  fillweight = (output != "abundance"),
  na_drop = TRUE,
  zero_drop = switch(tolower(level), plot = FALSE, treatment = TRUE, site = TRUE),
  min_traps = 1,
  min_plots = 24,
  effort = FALSE,
  download_if_missing = TRUE,
  quiet = FALSE,
  include_unsampled = FALSE
)

abundance(...)

biomass(...)

energy(...)

rates(...)

summarise_rodent_data(
  path = get_default_data_path(),
  clean = TRUE,
  level = "Site",
  type = "Rodents",
  length = "all",
  plots = length,
  unknowns = FALSE,
  shape = "crosstab",
  time = "period",
  output = "abundance",
  fillweight = (output != "abundance"),
  na_drop = TRUE,
  zero_drop = switch(tolower(level), plot = FALSE, treatment = TRUE, site = TRUE),
  min_traps = 1,
  min_plots = 24,
  effort = FALSE,
  download_if_missing = TRUE,
  quiet = FALSE,
  include_unsampled = 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)
level	summarize by "Plot", "Treatment", or "Site"
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)
plots	specify subset of plots; can be a vector of plots, or specific sets: "all" plots or "Longterm" plots (plots that have had the same treatment for the entire time series)
unknowns	either removes all individuals not identified to species (unknowns = FALSE) or sums them in an additional column (unknowns = TRUE)
shape	return data as a "crosstab" or "flat" list
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)
output	specify whether to return "abundance", or "biomass", or "energy", or "rates"
fillweight	specify whether to fill in unknown weights with other records from that individual or species, where possible
na_drop	logical, drop NA values (representing insufficient sampling) filling missing combinations of year-month-treatment/plot-species with NA could represent one of a few slightly different meanings: 1) that combo doesn't exist 2) that combo was skipped that month, or 3) that combo was trapped, but is unusable (a negative period code))
zero_drop	logical, drop 0s (representing sufficient sampling, but no detection)
min_traps	minimum number of traps for a plot to be included
min_plots	minimum number of plots within a period for an observation to be included
effort	logical as to whether or not the effort columns should be included in the output
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
include_unsampled	logical, overrides settings for 'na_drop' and 'zero_drop', setting both to FALSE
...	arguments passed to summarize_rodent_data

Value

a data.frame in either "long" or "wide" format, depending on the value of 'shape'

portalr documentation built on Sept. 30, 2024, 9:20 a.m.