GRaF (version 0.1-12)

plot.graf: Plot graf models

Description

plot.graf provides basic plots to visualise fitted terms in graf models. The predicted probability of presence along each covariate is plotted, along with associate credible intervals, with other covariates are held either at their average value or near the peak (point of highest probability) of the latent random field.

Usage

"plot"(x, vars = NULL, resolution = 50, CI = 0.95, prior = FALSE, data = TRUE, jitter = 1,
		peak = FALSE, ...)

Arguments

x

A graf object.

vars

A vector giving the column index of covariates for which to plot fitted terms. If NULL fitted terms are plotted for all covariates.

resolution

The resolution of the prediction line for each covariate.

CI

The level at which to calculate predictive credible intervals. The default value returns upper and lower 95% credible intervals.

prior

Whether to additionally plot the value of the prior function.

data

Whether to add rug plots of the training data.

jitter

The amount to jitter the observed data points (only applies if data = TRUE). Set to 0 for no jittering.

peak

Whether to hold other covariates at the value of the training datapoint with the highest probability of presence. If FALSE covariates are held at their mean value in the training data set.

...

Additional arguments to be passed to plot.

Value

A series of plots (one per covariate) of the marginal effect of covariates (near the peak) on the probability of species presence.

See Also

graf, plot3d