Produces simple plots of telemetry
objects, possibly overlayed with a Gaussian ctmm
movement model or a UD
utilization distribution.
plot(x,y,...)# S3 method for telemetry
plot(x,CTMM=NULL,UD=NULL,col.bg="white",cex=NULL,col="red",lwd=1,pch=1,type='p',
error=TRUE,transparency.error=0.25,velocity=FALSE,DF="CDF",col.DF="blue",
col.grid="white",labels=NULL,convex=FALSE,level=0.95,level.UD=0.95,col.level="black",
lwd.level=1,SP=NULL,border.SP=TRUE,col.SP=NA,R=NULL,col.R="green",legend=FALSE,
fraction=1,xlim=NULL,ylim=NULL,ext=NULL,units=TRUE,add=FALSE,...)
# S4 method for list
zoom(x,...)
# S4 method for telemetry
zoom(x,fraction=1,...)
# S4 method for UD
zoom(x,fraction=1,...)
Returns a plot of \(x\) vs. \(y\), and, if specified, Gaussian ctmm
distribution or UD
.
akde
UD
plots also come with a standard resolution grid.
zoom
includes a zoom slider to manipulate fraction
.
telemetry
or UD
object.
Unused option.
Optional Gaussian ctmm
movement model from the output of ctmm.fit
or list of such objects.
Optional UD
object such as from the output of akde
or list of such objects.
Background color
Relative size of plotting symbols. Only used when error=FALSE
, because error=TRUE
uses the location-error radius instead of cex
.
Color option for telemetry data. Can be an array or list of arrays.
Line widths of telemetry
points.
Plotting symbol. Can be an array or list of arrays.
How plot points are connected. Can be an array.
Plot error circles/ellipses if present in the data. error=2
will fill in the circles and error=3
will plot densities instead. error=FALSE
will disable this feature.
Transparency scaling for erroneous locations when error=1:2
. trans=0
disables transparancy. Should be no greater than 1
.
Plot velocity vectors if present in the data.
Plot the maximum likelihood probability density function "PDF"
or cumulative distribution function "CDF"
.
Color option for the density function. Can be an array.
Color option for the maximum likelihood akde
bandwidth grid. col.grid=NA
will disable the plotting of the bandwidth grid.
Labels for UD contours. Can be an array or list of arrays.
Plot convex coverage-area contours if TRUE
. By default, the highest density region (HDR) contours are plotted.
Confidence levels placed on the contour estimates themselves. I.e., the above 50% core home-range area can be estimated with 95% confidence via level=0.95
. level=NA
will disable the plotting of confidence intervals.
Coverage level of Gaussian ctmm
model or UD
estimate contours to be displayed. I.e., level.UD=0.50
can yield the 50% core home range within the rendered contours.
Color option for home-range contours. Can be an array.
Line widths of UD
contours.
SpatialPolygonsDataFrame
object for plotting a shapefile base layer.
Color option for shapefile polygon boundaries.
Color option for shapefile polygon regions.
Background raster, such as habitat suitability
.
Color option for background raster.
Plot a color legend for background raster.
Quantile fraction of the data, Gaussian ctmm
, or UD
range to plot, whichever is larger.
The x
limits c(x1, x2)
of the plot (in SI units).
The y
limits c(y1, y2)
of the plot (in SI units).
Plot extent alternative to xlim
and ylim
(see extent
).
Convert axes to natural units.
Setting to TRUE
will disable the unit conversions and base layer plot, so that plot.telemetry
can be overlayed atop other outputs more easily.
Additional options passed to plot
.
C. H. Fleming.
Confidence intervals placed on the ctmm
Gaussian home-range contour estimates only represent uncertainty in the area's magnitude and not uncertainty in the mean location, eccentricity, or orientation angle. For akde
UD
estimates, the provided contours also only represent uncertainty in the magnitude of the area. With akde
estimates, it is also important to note the scale of the bandwidth and, by default, grid cells are plotted with akde
contours such that their length and width matches that of a bandwidth kernels' standard deviation in each direction. Therefore, this grid provides a visual approximation of the kernel-density estimate's ``resolution''. Grid lines can be disabled with the argument col.grid=NA
.
akde
, ctmm.fit
, plot
, SpatialPoints.telemetry
.
# Load package and data
library(ctmm)
data(buffalo)
# Plot the data
plot(buffalo,col=rainbow(length(buffalo)))
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