ctmm: plot.telemetry – R documentation

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plot.telemetry

Plotting methods for telemetry objects.

Description

Produces simple plots of telemetry objects, possibly overlayed with a Gaussian ctmm movement model or a UD utilization distribution.

Usage

plot(x,y,...)

## S3 method for class 'telemetry'
plot(x,CTMM=NULL,UD=NULL,level.UD=0.95,level=0.95,DF="CDF",error=TRUE,velocity=FALSE,
     units=TRUE,col="red",col.level="black",col.DF="blue",col.grid="white",
     transparency.error=0.25,pch=1,type='p',labels=NULL,fraction=1,add=FALSE,xlim=NULL,
     ylim=NULL,ext=NULL,cex=NULL,lwd=1,lwd.level=1,...)

## S4 method for signature 'list'
zoom(x,...)

## S4 method for signature 'telemetry'
zoom(x,fraction=1,...)

## S4 method for signature 'UD'
zoom(x,fraction=1,...)

Arguments

`x`	`telemetry` or `UD` object.
`y`	Unused option.
`CTMM`	Optional Gaussian `ctmm` movement model from the output of `ctmm.fit` or list of such objects.
`UD`	Optional `UD` object such as from the output of `akde` or list of such objects.
`level.UD`	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.
`level`	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`.
`DF`	Plot the maximum likelihood probability density function `"PDF"` or cumulative distribution function `"CDF"`.
`error`	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.
`velocity`	Plot velocity vectors if present in the data.
`units`	Convert axes to natural units.
`col`	Color option for telemetry data. Can be an array or list of arrays.
`col.level`	Color option for home-range contours. Can be an array.
`col.DF`	Color option for the density function. Can be an array.
`col.grid`	Color option for the maximum likelihood `akde` bandwidth grid.
`transparency.error`	Transparency scaling for erroneous locations when `error=1:2`. `trans=0` disables transparancy. Should be no greater than `1`.
`pch`	Plotting symbol. Can be an array or list of arrays.
`type`	How plot points are connected. Can be an array.
`labels`	Labels for UD contours. Can be an array or list of arrays.
`fraction`	Quantile fraction of the data, Gaussian `ctmm`, or `UD` range to plot, whichever is larger.
`add`	Setting to `TRUE` will disable the unit conversions and base layer plot, so that `plot.telemetry` can be overlayed atop other outputs more easily.
`xlim`	The `x` limits `c(x1, x2)` of the plot (in SI units).
`ylim`	The `y` limits `c(y1, y2)` of the plot (in SI units).
`ext`	Plot extent alternative to `xlim` and `ylim` (see `extent`).
`cex`	Relative size of plotting symbols. Only used when errors are missing.
`lwd`	Line widths of `telemetry` points.
`lwd.level`	Line widths of `UD` contours.
`...`	Additional options passed to `plot`.

Details

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”.

Value

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.

Note

If xlim or ylim are provided, then the smaller or absent range will be expanded to ensure asp=1.

Author(s)

C. H. Fleming.

Examples

# Load package and data
library(ctmm)
data(buffalo)

# Plot the data
plot(buffalo,col=rainbow(length(buffalo)))

ctmm

Continuous-Time Movement Modeling

v0.6.0

GPL-3

Authors

Christen H. Fleming [aut, cre], Justin M. Calabrese [aut], Xianghui Dong [ctb], Kevin Winner [ctb], Guillaume Péron [ctb], Michael J. Noonan [ctb], Bart Kranstauber [ctb], Eliezer Gurarie [ctb], Kamran Safi [ctb], Paul C. Cross [dtc], Thomas Mueller [dtc], Rogério C. de Paula [dtc], Thomas Akre [dtc], Jonathan Drescher-Lehman [dtc], Autumn-Lynn Harrison [dtc], Ronaldo G. Morato [dtc]

Initial release

2021-01-08