summarize_rodent_data: Generate summaries of Portal rodent data
In weecology/portalr: Create Useful Summaries of the Portal Data

summarize_rodent_data

R Documentation

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 detections)
`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`