summarize_rodent_data {portalr}

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

Value

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