View source: R/activityDensity.R
activityDensity | R Documentation |
The function plots a kernel density estimation of species diel activity using function densityPlot
from package overlap.
activityDensity(recordTable,
species,
allSpecies = FALSE,
speciesCol = "Species",
recordDateTimeCol = "DateTimeOriginal",
recordDateTimeFormat = "%Y-%m-%d %H:%M:%S",
plotR = TRUE,
writePNG = FALSE,
plotDirectory,
createDir = FALSE,
pngMaxPix = 1000,
add.rug = TRUE,
...
)
recordTable |
data.frame. the record table created by |
species |
Name of the species for which to create an kernel density plot of activity |
allSpecies |
logical. Create plots for all species in |
speciesCol |
character. name of the column specifying species names in |
recordDateTimeCol |
character. name of the column specifying date and time in |
recordDateTimeFormat |
character. format of column |
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 |
createDir |
logical. Create |
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 |
species
must be in the speciesCol
of recordTable
.
Returns invisibly a vector of species record observation times in radians, i.e. scaled to [0, 2\pi
].
If allSpecies == TRUE
, all species' vectors are returned in an invisible named list.
Juergen Niedballa
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 (2018). overlap: Estimates of coefficient of overlapping for animal activity patterns. R package version 0.3.2. https://CRAN.R-project.org/package=overlap
activityHistogram
, activityRadial
, activityOverlap
http://www.kent.ac.uk/smsas/personal/msr/overlap.html
# load record table
data(recordTableSample)
species4activity <- "VTA" # = Viverra tangalunga, Malay Civet
activityDensity(recordTable = recordTableSample,
species = species4activity)
# all species at once
activityDensity(recordTable = recordTableSample,
allSpecies = TRUE,
writePNG = FALSE,
plotR = TRUE,
add.rug = TRUE)
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