itsadug (version 0.8)

plot_smooth: Visualization of smooths.

Description

Plots a smooth from a gam or bam model based on predictions. In contrast with the default plot.gam, this function plots the summed effects and optionally removes the random effects.

Usage

plot_smooth(x, view = NULL, cond = list(), rm.ranef = NULL, n.grid = 30,
  rug = TRUE, col = "black", add = FALSE, se = 1.96, shade = TRUE,
  eegAxis = FALSE, print.summary = TRUE, main = NULL, xlab = NULL,
  ylab = NULL, ylim = NULL, h0 = 0, v0 = NULL, ...)

Arguments

x

A gam object, produced by gam or bam.

view

Text string containing the name of the smooth to be displayed. Note that variables coerced to factors in the model formula won't work as view variables.

cond

A named list of the values to use for the other predictor terms (not in view). Used for choosing between smooths that share the same view predictors.

rm.ranef

Logical: whether or not to remove random effects. Default is TRUE.

n.grid

The number of grid nodes in each direction used for calculating the plotted surface.

rug

Logical: when TRUE (default) then the covariate to which the plot applies is displayed as a rug plot at the foot of each plot of a 1-d smooth. Setting to FALSE will speed up plotting for large datasets.

col

The colors for the lines and the error bars of the plot.

add

Logical: whether or not to add the lines to an existing plot, or start a new plot (default).

se

If less than or equal to zero then only the predicted surface is plotted, but if greater than zero, then the predicted values plus confidence intervals are plotted. The value of se will be multiplied with the standard error (i.e., 1.96 results in 95%CI an

shade

Logical: Set to TRUE to produce shaded regions as confidence #' bands for smooths (not avaliable for parametric terms, which are plotted using termplot).

eegAxis

Logical: whether or not to reverse the y-axis, plotting the negative amplitudes upwards as traditionally is done in EEG research. If eeg.axes is TRUE, labels for x- and y-axis are provided, when not provided by the user. Default value is FALSE.

print.summary

Logical: whether or not to print summary.

main

Changing the main title for the plot, see also title.

xlab

Changing the label for the x axis, defaults to a description of x.

ylab

Changing the label for the y axis, defaults to a description of y.

ylim

the y limits of the plot.

h0

A vector indicating where to add solid horizontal lines for reference. By default no values provided.

v0

A vector indicating where to add dotted vertical lines for reference. By default no values provided.

...

other options to pass on to lines and plot, see par

See Also

plot.gam, plot_diff

Other functions for interpreting nonlinear effects: fvisgam, vis.gam2; plotDiff2D, plot_diff2; plotDiff, plot_diff; plot_parametric; pvis.gam, pvisgam

Examples

data(simdat)

# Model with random effect and interactions:
m1 <- bam(Y ~ te(Time, Trial)+s(Time, Subject, bs='fs', m=1),
    data=simdat)

# Default plot produces only surface of Time x Trial:
plot(m1, select=1)
# Only the Time component:
plot_smooth(m1, view="Time")
# Note the summary that is printed.

# without random effects:
plot_smooth(m1, view="Time", rm.ranef=TRUE)

# Plot summed effects:
dev.new(width=8, height=4) # use x11(,8,4) on Linux
par(mfrow=c(1,2))
fvisgam(m1, view=c("Time", "Trial"),
    plot.type='contour', color='topo', main='interaction',
    rm.ranef=TRUE)
arrows(x0=0, x1=2200, y0=-5, y1=-5, col='red',
    code=2, length=.1, lwd=2, xpd=TRUE)
plot_smooth(m1, view='Time', cond=list(Trial=-5),
    main='Trial=-5', rm.ranef=TRUE)
# see the vignette for examples:
vignette("plotfunctions", package="itsadug")