activityHistogram: Plot histogram of single-species activity

In jniedballa/camtrapR: Camera Trap Data Management and Preparation of Occupancy and Spatial Capture-Recapture Analyses

Plot histogram of single-species activity

Description

The function generates a histogram of species diel activity in 1-hour intervals.

Usage

activityHistogram(
  recordTable,
  species,
  allSpecies = FALSE,
  speciesCol = "Species",
  recordDateTimeCol = "DateTimeOriginal",
  recordDateTimeFormat = "ymd HMS",
  plotR = TRUE,
  writePNG = FALSE,
  plotDirectory,
  createDir = FALSE,
  pngMaxPix = 1000,
  ...
)

Arguments

recordTable	data.frame. the record table created by recordTable
species	Name of the single species for which to create a histogram of activity
allSpecies	logical. Create plots for all species in speciesCol of recordTable? Overrides argument species
speciesCol	character. name of the column specifying species names in recordTable
recordDateTimeCol	character. name of the column specifying date and time in recordTable
recordDateTimeFormat	character. format of column recordDateTimeCol in recordTable
plotR	logical. Show plots in R graphics device?
writePNG	logical. Create pngs of the plots?
plotDirectory	character. Directory in which to create png plots if writePNG = TRUE
createDir	logical. Create plotDirectory?
pngMaxPix	integer. image size of png (pixels along x-axis)
...	additional arguments to be passed to function hist

Details

Activity is calculated from the time of day of records. The date is ignored.

recordDateTimeFormat defaults to the "YYYY-MM-DD HH:MM:SS" convention, e.g. "2014-09-30 22:59:59". recordDateTimeFormat can be interpreted either by base-R via strptime or in lubridate via parse_date_time (argument "orders"). lubridate will be used if there are no "%" characters in recordDateTimeFormat.

For "YYYY-MM-DD HH:MM:SS", recordDateTimeFormat would be either "%Y-%m-%d %H:%M:%S" or "ymd HMS". For details on how to specify date and time formats in R see strptime or parse_date_time.

Value

It returns invisibly a vector of species record date and time in POSIXlt format. If allSpecies == TRUE, all species' vectors are returned in an invisible named list.

Note

If you have a sufficiently large number of records you may wish to consider using activityDensity instead. Please be aware that this function (like the other activity... function of this package) use clock time. If your survey was long enough to see changes in sunrise and sunset times, this may result in biased representations of species activity.

Author(s)

Juergen Niedballa

See Also

activityDensity, activityRadial, activityOverlap

Examples

# load record table
data(recordTableSample)

# generate activity histogram
species4activity <- "VTA"    # = Viverra tangalunga, Malay Civet

activityHistogram (recordTable = recordTableSample,
                   species     = species4activity,
                   allSpecies = FALSE)

jniedballa/camtrapR documentation built on April 7, 2024, 9:08 p.m.