camtrapR (version 0.97.0)

activityDensity: Plot kernel density function 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,
  all.species = FALSE,
  speciesCol = "Species",
  recordDateTimeCol = "DateTimeOriginal",
  recordDateTimeFormat = "%Y-%m-%d %H:%M:%S",
  plotR = TRUE, 
  writePNG = FALSE, 
  plotDirectory, 
  createDir = FALSE, 
  pngMaxPix = 1000,
  add.rug = TRUE,
  ...
)

Arguments

recordTable

data.frame. the record table created by recordDatabase

species

Name of the single species for which to create an kernel density plot of activity

all.species

logical. If TRUE, plots are created for all species in recordTable. This overrides argument species

speciesCol

character. name of the column specifying species in recordTable

recordDateTimeCol

character. name of the column specifying date and time in recordTable

recordDateTimeFormat

format of column recordDateTimeCol in recordTable

plotR

logical. Create plots in R graphics device?

writePNG

logical. Create pngs of the plots?

plotDirectory

character. Directory to save the pngs if writePNG = TRUE

createDir

logical. Create plotDirectory if writePNG = TRUE?

pngMaxPix

integer. number of pixels in the png along the x axis

add.rug

logical. add a rug to the plot?

...

additional arguments to be passed to function densityPlot

Value

• It returns invisibly a vector of species record observation times in radians, ie. 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.

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 (2014). overlap: Estimates of coefficient of overlapping for animal activity patterns. R package version 0.2.4. http://CRAN.R-project.org/package=overlap

See Also

http://www.kent.ac.uk/smsas/personal/msr/overlap.html

Examples

# load record database
data(recordDatabaseSample)

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

activityDensity(recordTable = recordDatabaseSample,
                        species = species4activity)


# all species at once

activityDensity(recordTable = recordDatabaseSample,
                all.species = TRUE,
                writePNG = FALSE,
                plotR = TRUE,
                add.rug = TRUE)