CountXVisit: CountXVisit

In NCRN/NCRNbirds: Data analysis and visualization for NPS I&M bird monitoring.

CountXVisit

Description

Produces a Count X Visit matrix for use in analyses

Usage

CountXVisit(
  object,
  parks = NA,
  points = NA,
  AOU = NA,
  years = NA,
  times = NA,
  band = NA,
  visits = NA,
  max = F,
  type = "count",
  site = NA,
  dist = NA,
  wind = NA,
  sky = NA,
  output = "dataframe",
  ...
)

Arguments

object	An NCRNbirds object or a list of such objects.
parks	A character vector of park codes. Only visits within these parks will be returned.
points	A character vector. The names of one or more points where the data was collected.
AOU	A character vector. One or more AOU (American Onothological Union) codes of bird species.
years	A vector of numbers. Will return only data from the indicated years.
times	A numeric vector of length 1 passed on to getVisits. Returns only data from points where the number of years that a point has been visited is greater or equal to the value of times. This is determined based on the data found in the Visits slot.
band	A numeric vector. Defaults to NA. Only observations whose Distance_id field matches a value in band will be returned. NA returns all bands.
visits	The visits that will be used for the matrix. Defaults to NA. See Details below.
max	Logical, defaults to FALSE. If TRUE then the matrix will also include a single column with the maximum detections seen at each point across all the visits specified in the visits argument.
type	Either "count", the default of "occupancy". Determines the type of data in the matrix. If "count" then each number will represent the number of birds observed. If "occupancy" then the data will be 1 if one or more birds is observed, and 0 otherwise.
site	Character. Select sites in "Forest" or "Grassland" habitats. Defaults to selecting both site types.
dist	Character. Filter data by disturbance code(s). See network documentation for list and meanings of codes.
wind	Numeric. Filter data by wind code(s). See network documentation for list and meanings of codes.
sky	Numeric. Filter data by sky condition code(s). See network documentation for list and meanings of codes.
output	Either "dataframe" (the default) or "list". Note that this must be in quotes. Determines the type of output from the function.
...	Additional arguments passed to getBirds

Details

This produces a Count X Visit matrix for a NCRNbirds object or a list of such objects. Each row of the matrix will correspond to a different point in a different year. The columns of the matrix will be the park code, the point name, the year visited, and a column of abundances of the indcated species at that visit. If multiple species are indicated in AOU, their abundances will be totaled. If max=T then the maximum accross all visits will be returned as well as the indvidual visit totals.

If visits is left as NA then the visits used will be 1 through the number of visits indicated in the visits slot. Otherwise a numeric vectore e.g. c(1,2) can be used to select which visits are used.

If type is set as "occupancy" the the matix will have 1 for visits where a site is occuped and 0 forvisits where it is unoccupied rather than abundances.

NCRN/NCRNbirds documentation built on Aug. 28, 2023, 12:12 p.m.