plot.telemetry: Plotting methods for telemetry objects.

Description Usage Arguments Details Value Note Author(s) See Also Examples

View source: R/plot.telemetry.R

Description

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

Usage

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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,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

Confidence 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.

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).

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.

See Also

akde, ctmm.fit, plot, SpatialPoints.telemetry.

Examples

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

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

ctmm-initiative/ctmm documentation built on Oct. 12, 2018, 2:55 a.m.