activityRadial: Radial plots of single-species activity

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

Description

The function generates a radial plot of species diel activity using an adapted version of function radial.plot from package plotrix (without the need to install the package). Records are aggregated by hour. The number of independent events is used as input, which in turn is based on the argument minDeltaTime in recordTable.

Usage

  activityRadial(recordTable, 
  species,
  allSpecies = FALSE,
  speciesCol = "Species",
  recordDateTimeCol = "DateTimeOriginal",
  recordDateTimeFormat = "%Y-%m-%d %H:%M:%S",
  byNumber = FALSE,
  plotR = TRUE, 
  writePNG = FALSE, 
  plotDirectory, 
  createDir = FALSE, 
  pngMaxPix = 1000,
  ...
)

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
byNumber	logical. If FALSE, plot proportion of records. If TRUE, plot number of records
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?
pngMaxPix	integer. image size of png (pixels along x-axis)
...	additional arguments to be passed to function radial.plot

Details

radial.plot was adjusted to show a clockwise 24-hour clock face. It is recommended to set argument lwd to a value >= 2. You may also wish to add argument rp.type="p" to show a polygon instead of bars.

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 a data.frame containing all information needed to create the plot: radial position, lengths, hour (for labels). If allSpecies == TRUE, all species' data frames are returned in an invisible named list.

Author(s)

Juergen Niedballa

References

Lemon, J. (2006) Plotrix: a package in the red light district of R. R-News, 6(4): 8-12.
https://CRAN.R-project.org/package=plotrix

See Also

activityDensity, activityHistogram, activityOverlap

Examples

# load record table
data(recordTableSample)

species4activity <- "PBE"    # = Prionailurus bengalensis, Leopard Cat

activityRadial(recordTable       = recordTableSample,
               species           = species4activity,
               allSpecies        = FALSE,
               speciesCol        = "Species",
               recordDateTimeCol = "DateTimeOriginal",
               plotR             = TRUE,
               writePNG          = FALSE,
               lwd               = 5
)

# plot type = polygon

activityRadial(recordTable       = recordTableSample,
               species           = species4activity,
               allSpecies        = FALSE,
               speciesCol        = "Species",
               recordDateTimeCol = "DateTimeOriginal",
               plotR             = TRUE,
               writePNG          = FALSE,
               lwd               = 5,
               rp.type           = "p"      
)

jniedballa/camtrapR documentation built on Dec. 16, 2020, 8:05 a.m.