activityDensity: Plot kernel density estimation of single-species activity

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

Plot kernel density estimation of single-species activity

Description

The function plots a kernel density estimation of species diel activity using function densityPlot from package overlap.

Usage

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

Arguments

recordTable	data.frame. the record table created by recordTable
species	Name of the species for which to create an kernel density plot 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 if writePNG = TRUE?
pngMaxPix	integer. image size of png (pixels along x-axis)
add.rug	logical. add a rug to the plot?
...	additional arguments to be passed to function densityPlot

Details

species must be in the speciesCol of recordTable.

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

Returns invisibly a vector of species record observation times in radians, i.e. scaled to [0, 2\pi]. If allSpecies == TRUE, all species' vectors are returned in an invisible named list.

Author(s)

Juergen Niedballa

References

Martin Ridout and Matthew Linkie (2009). Estimating overlap of daily activity patterns from camera trap data. Journal of Agricultural, Biological and Environmental Statistics, 14(3), 322-337
Mike Meredith and Martin Ridout (2018). overlap: Estimates of coefficient of overlapping for animal activity patterns. R package version 0.3.2. https://CRAN.R-project.org/package=overlap

See Also

activityHistogram, activityRadial, activityOverlap https://www.kent.ac.uk/smsas/personal/msr/overlap.html

Examples

if(requireNamespace("overlap")) {
# load record table
data(recordTableSample)

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

activityDensity(recordTable = recordTableSample,
                species     = species4activity)


# all species at once

activityDensity(recordTable = recordTableSample,
                allSpecies  = TRUE,
                writePNG    = FALSE,
                plotR       = TRUE,
                add.rug     = TRUE)
 }

camtrapR documentation built on May 29, 2024, 6:45 a.m.