Plot overlapping kernel densities of two-species activities

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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

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  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 recordTable

speciesA

Name of species 1

speciesB

Name of species 2

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?

addLegend

logical. Add a legend to the plots?

legendPosition

character. Position of the legend (keyword)

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)

add.rug

logical. add a rug to the plot?

...

additional arguments to be passed to function overlapPlot

Details

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

Value

Returns invisibly the data.frame with plot coordinates returned by overlapPlot.

Note

Please be aware that the function (like the other activity... function of this package) use clock time, not solar 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

References

Mike Meredith and Martin Ridout (2014). overlap: Estimates of coefficient of overlapping for animal activity patterns. R package version 0.2.4. https://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

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# load record table
data(recordTableSample)

# 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 (recordTable = recordTableSample,
                 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
)

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