itsadug (version 2.2)

plot_diff: Plot difference curve based on model predictions.

Description

Plot difference curve based on model predictions.

Usage

plot_diff(model, view, comp, cond = NULL, plotCI = TRUE, f = 1.96,
  eegAxis = FALSE, col = "black", shade = TRUE, n.grid = 100,
  add = FALSE, print.summary = getOption("itsadug_print"), plot = TRUE,
  rm.ranef = NULL, main = NULL, ylab = NULL, xlab = NULL, xlim = NULL,
  ylim = NULL, transform.view = NULL, mark.diff = TRUE,
  hide.label = FALSE, ...)

Arguments

model

A GAMM model, resulting from the functions gam or bam.

view

Name of continuous predictor that should be plotted on the x- axis.

comp

Named list with the grouping predictor (categorical variable) and the 2 levels to calculate the difference for.

cond

A named list of the values to use for the predictor terms. Variables omitted from this list will have the closest observed value to the median for continuous variables, or the reference level for factors.

plotCI

Logical: whether or not to plot confidence intervals. Default is TRUE.

f

A number to scale the standard error. Defaults to 1.96, resulting in 95% confidence intervals. For 99% confidence intervals use a value of 2.58.

eegAxis

Logical: whether or not to reverse the y-axis, plotting negative values upwards. Default is FALSE.

col

Line color. Shading color is derived from line color.

shade

Logical: plot shaded confidence interval (TRUE) or dashed lines that indicate confidence region (FALSE).

n.grid

Number of data points sampled as predictions. Defaults to 100.

add

Logical: whether or not to add the line to an existing plot. Default is FALSE. When no plot window is available and add=TRUE, the function will generate an error.

print.summary

Logical: whether or not to print the summary. Default set to the print info messages option (see infoMessages).

plot

Logical: whether or not to plot the difference. If FALSE, then the output is returned as a list, with the estimated difference (est) and the standard error over the estimate (se.est) and the x-values (x). Default is TRUE.

rm.ranef

Logical: whether or not to remove random effects. Default is FALSE. Alternatively a string (or vector of strings) with the name of the random effect(s) to remove.

main

Text string, alternative title for plot.

ylab

Text string, alternative label for y-axis.

xlab

Text string, alternative label for x-axis.

xlim

Range of x-axis. If not specified, the function automatically generates an appropriate x-axis.

ylim

Range of y-axis. If not specified, the function automatically generates an appropriate y-axis.

transform.view

Function for transforming the values on the x-axis. Defaults to NULL (no transformation). (See plot_smooth for more info.)

mark.diff

Logical: whether or not marking where the difference is significantly different from 0.

hide.label

Logical: whether or not to hide the label (i.e., "difference"). Default is FALSE.

...

Optional arguments for plot.

Value

If the result is not being plotted, a list is returned with the estimated difference (est) and the standard error over the estimate (se) and the x-values (x) is returned.

See Also

Other Testing for significance: compareML, plot_diff2, report_stats, wald_gam

Examples

# NOT RUN {
data(simdat)
# }
# NOT RUN {
m1 <- bam(Y ~ Group + te(Time, Trial, by=Group),
    data=simdat)
plot_diff(m1, view='Time', comp=list(Group=c("Children", "Adults")))
# Reversed y-axis (for EEG data):
plot_diff(m1, view='Time', comp=list(Group=c("Children", "Adults")), 
    eegAxis=TRUE)
# retrieving plot values...
out <- plot_diff(m1, view='Time', comp=list(Group=c("Children", "Adults")), 
   plot=FALSE)
#... which might be used for indicating differences:
x <- find_difference(out$est, out$se, f=1.96, xVals=out$xVals)
# add lines:
arrows(x0=x$start, x1=x$end, y0=0, y1=0,code=3, length=.1, col='red')
# }
# NOT RUN {
# }