plot.variogram: Plotting methods for variogram objects.

In ctmm-initiative/ctmm: Continuous-Time Movement Modeling

Plotting methods for variogram objects.

Description

Produces simple plots of varigram objects (semi-variance vs. time lag) and model semi-variance functions, with approximate confidence intervals around the semi-variance estimates.

Usage

## S3 method for class 'variogram'
plot(x,CTMM=NULL,level=0.95,units=TRUE,fraction=0.5,col="black",col.CTMM="red",xlim=NULL,
     ylim=NULL,ext=NULL,...)

## S4 method for signature 'variogram'
zoom(x,fraction=0.5,...)

Arguments

x	A variogram object calculated using variogram.
CTMM	A ctmm movement model object in the same format as the output of ctmm.fit or variogram.fit.
level	Confidence level of confidence bands (95% default CIs). Can be an array.
units	Convert axes to natural units.
fraction	The proportion of the variogram object, variogram, that will be plotted. By convention, half is shown. The tail end is generally garbage.
col	Color for the empirical variogram. Can be an array.
col.CTMM	Color for the model. Can be an array.
xlim	Range of lags to plot (in SI units).
ylim	Range of semi-variance to plot (in SI units).
ext	Plot extent alternative to xlim and ylim (see extent).
...	Additional plot function parameters.

Value

Returns a plot of semi-variance vs. time lag, with the empirical variogram in black and the ctmm semi-variance function in red if specified. zoom includes a log-scale zoom slider to manipulate fraction.

Note

The errors of the empirical variogram are correlated. Smooth trends are not necessarily significant.

Author(s)

J. M. Calabrese and C. H. Fleming

References

C. H. Fleming, J. M. Calabrese, T. Mueller, K.A. Olson, P. Leimgruber, W. F. Fagan. From fine-scale foraging to home ranges: A semi-variance approach to identifying movement modes across spatiotemporal scales. The American Naturalist, 183:5, E154-E167 (2014) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1086/675504")}.

See Also

correlogram, ctmm.fit, plot, variogram, variogram.fit.

Examples

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

# Extract movement data for a single animal
Cilla <- buffalo$Cilla

# Calculate variogram
SVF <- variogram(Cilla)

# Plot the variogram
plot(SVF)

ctmm-initiative/ctmm documentation built on April 18, 2024, 9:39 a.m.