activityOverlap: Plot overlapping kernel densities of two-species activities

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

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 = "ymd HMS",
  plotR = TRUE,
  writePNG = FALSE,
  addLegend = TRUE,
  legendPosition = "topleft",
  plotDirectory,
  createDir = FALSE,
  pngMaxPix = 1000,
  add.rug = TRUE,
  overlapEstimator = c("Dhat1", "Dhat4", "Dhat5"),
  ...
)

Arguments

recordTable	data.frame. the record table created by recordTable
speciesA	Name of species 1 (as found in speciesCol of recordTable)
speciesB	Name of species 2 (as found in speciesCol of recordTable)
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?
overlapEstimator	character. Which overlap estimator to return (passed on to argument type in overlapEst)
...	additional arguments to be passed to function overlapPlot

Details

... can be graphical parameters passed on to function overlapPlot, e.g. linetype, linewidth, linecol (see example below).

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 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 (2018). overlap: Estimates of coefficient of overlapping for animal activity patterns. R package version 0.3.2. 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
https://www.kent.ac.uk/smsas/personal/msr/overlap.html

Examples

if(requireNamespace("overlap")) {

# 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 (basic)
activityOverlap (recordTable = recordTableSample,
                 speciesA    = "VTA",    # = Viverra tangalunga, Malay Civet
                 speciesB    = "PBE",    # = Prionailurus bengalensis, Leopard Cat
                 writePNG    = FALSE,
                 plotR       = TRUE
)


                                     
# create activity overlap plot (prettier and with some overlapPlot arguments set)

activityOverlap (recordTable = recordTableSample,
                 speciesA    = speciesA_for_activity,
                 speciesB    = speciesB_for_activity,
                 writePNG    = FALSE,
                 plotR       = TRUE,
                 createDir   = FALSE,
                 pngMaxPix   = 1000,
                 linecol     = c("black", "blue"),
                 linewidth   = c(5,3),
                 linetype    = c(1, 2),
                 olapcol     = "darkgrey",
                 add.rug     = TRUE,
                 extend      = "lightgrey",
                 ylim        = c(0, 0.25),
                 main        = paste("Activity overlap between ", 
                                     speciesA_for_activity, "and", 
                                     speciesB_for_activity)
)
}

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