Description Usage Arguments Details Value Author(s) References See Also Examples
View source: R/activityRadial.R
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
.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | 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,
...
)
|
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 |
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 |
createDir |
logical. Create |
pngMaxPix |
integer. image size of png (pixels along x-axis) |
... |
additional arguments to be passed to function |
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
.
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.
Juergen Niedballa
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
activityDensity
, activityHistogram
, activityOverlap
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 | # 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"
)
|
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