plot_diff  R Documentation 
Plot difference curve based on model predictions.
plot_diff( model, view, comp, cond = NULL, se = 1.96, sim.ci = FALSE, n.grid = 100, add = FALSE, rm.ranef = TRUE, mark.diff = TRUE, col.diff = "red", col = "black", eegAxis = FALSE, transform.view = NULL, print.summary = getOption("itsadug_print"), plot = TRUE, main = NULL, ylab = NULL, xlab = NULL, xlim = NULL, ylim = NULL, hide.label = FALSE, ... )
model 
A GAMM model, resulting from the functions

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. 
se 
If less than or equal to zero then only the predicted smooth is
plotted, but if greater than zero, then the predicted values plus
confidence intervals are plotted.
The value of 
sim.ci 
Logical: Using simultaneous confidence intervals or not
(default set to FALSE). The implementation of simultaneous CIs follows
Gavin Simpson's blog of December 15, 2016:
https://fromthebottomoftheheap.net/2016/12/15/simultaneousintervalrevisited/.
This interval is calculated from simulations based.
Please specify a seed (e.g., 
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 
rm.ranef 
Logical: whether or not to remove random effects. Default is TRUE. Alternatively a string (or vector of strings) with the name of the random effect(s) to remove. 
mark.diff 
Logical: whether or not marking where the difference is significantly different from 0. 
col.diff 
Color to mark differences (red by default). 
col 
Line color. Shading color is derived from line color. 
eegAxis 
Logical: whether or not to reverse the yaxis, plotting negative values upwards. Default is FALSE. 
transform.view 
Function for transforming
the values on the xaxis. Defaults to NULL (no transformation).
(See 
print.summary 
Logical: whether or not to print the summary.
Default set to the print info messages option
(see 
plot 
Logical: whether or not to plot the difference. If FALSE, then
the output is returned as a list, with the estimated difference
( 
main 
Text string, alternative title for plot. 
ylab 
Text string, alternative label for yaxis. 
xlab 
Text string, alternative label for xaxis. 
xlim 
Range of xaxis. If not specified, the function automatically generates an appropriate xaxis. 
ylim 
Range of yaxis. If not specified, the function automatically generates an appropriate yaxis. 
hide.label 
Logical: whether or not to hide the label (i.e., 'difference'). Default is FALSE. 
... 
Optional arguments for 
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 xvalues (x
) is returned.
Martijn Wieling, Jacolien van Rij
Other Testing for significance:
compareML()
,
plot_diff2()
,
report_stats()
,
wald_gam()
data(simdat) ## Not run: m1 < bam(Y ~ Group + te(Time, Trial, by=Group) + s(Time, Subject, bs='fs', m=1), data=simdat, discrete=TRUE) plot_diff(m1, view='Time', comp=list(Group=c('Children', 'Adults'))) # in this model, excluding random effects does not change the difference: plot_diff(m1, view='Time', comp=list(Group=c('Children', 'Adults')), rm.ranef=TRUE) # simultaneous CI: plot_diff(m1, view='Time', comp=list(Group=c('Children', 'Adults')), rm.ranef=TRUE, sim.ci=TRUE) # Reversed yaxis (for EEG data) and no shading: plot_diff(m1, view='Time', comp=list(Group=c('Children', 'Adults')), eegAxis=TRUE, shade=FALSE) plot_diff(m1, view='Time', comp=list(Group=c('Children', 'Adults')), density=15, angle=90, ci.lwd=3) # 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') ## End(Not run)
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