Plot kernel density estimation of single-species activity

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

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

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.

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.

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

Author

Juergen Niedballa

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)
 }