camtrapR (version 0.97.0)

activityOverlap: Plot overlapping kernel densities of two-species activities

Description

This function plots kernel density estimates of two species' diel activity data by calling the function overlapPlot from package overlap. It further computes the overlap coefficient Dhat1 by calling overlapEst.

Usage

activityOverlap(recordTable, 
  speciesA,
  speciesB,
  speciesCol = "Species",
  recordDateTimeCol = "DateTimeOriginal",
  recordDateTimeFormat = "%Y-%m-%d %H:%M:%S",
  plotR = TRUE, 
  writePNG = FALSE, 
  addLegend = TRUE,
  legendPosition = "topleft",
  plotDirectory, 
  createDir = FALSE, 
  pngMaxPix = 1000,
  add.rug = TRUE,
  ...
)

Arguments

recordTable

data.frame. the record table created by recordDatabase

speciesA

Name of species 1

speciesB

Name of species 2

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?

addLegend

logical. Add a legend to the plots?

legendPosition

character. Position of the legend (keyword)

plotDirectory

character. Path of the pngs

createDir

logical. Create plotDirectory?

pngMaxPix

integer. number of pixels in pngs along x axis

add.rug

logical. add a rug to the plot?

...

additional arguments to be passed to function overlapPlot

Value

• Returns invisibly the data.frame with plot coordinates from overlapPlot.

Details

... can be graphical parameters, e.g. linetype, linewidth, linecol.

References

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 Ridout, M.S. and Linkie, M. (2009) Estimating overlap of daily activity patterns from camera trap data. Journal of Agricultural, Biological and Environmental Statistics, 14, 322-337.

See Also

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

Examples

# load record database
data(recordDatabaseSample)

# define species of interest
speciesA_for_activity <- "VTA"    # = Viverra tangalunga, Malay Civet
speciesB_for_activity <- "PBE"    # = Prionailurus bengalensis, Leopard Cat

# create activity overlap plot
activityOverlap (recordDatabaseSample,
  speciesA = speciesA_for_activity,
  speciesB = speciesB_for_activity,
  writePNG = FALSE,
  plotR = TRUE,
  createDir = FALSE,
  pngMaxPix = 1000,
  linecol = c("red", "blue"),
  linewidth = c(3,3),
  add.rug = TRUE
)