label for X-axis (if other than the variable name in the
original model formula)
xlabs
character vector with labels for X-axes in multipanel plot (if
other than the variable names in the original model formula); if used,
xlabel should not be specified
ylabel
label for Y-axis (if other than the variable name of
the dependent variable in the original model formula)
ylimit
range for vertical axis; if not specified, this range will
be chosen such that all data points across all subplots, including HPD intervals, will be accommodated
ilabel
label for the interaction shown in the lower right-hand margin of the plot, overriding the original variable name in the model formula
fun
a function to be applied for transforming the dependent variable,
if NA, no transformation is applied; for models with family = "binomial",
fun is set to plogis by default; this can be disabled by setting
fun=function(x)return(x).
pred
character string with name of predictor;
if specified, a single plot will produced for the partial effect of this
specific predictor
control
a two-element list list(predictor, val) specifying a predictor the value of which has to be set to val in the partial effect plot(s); the predictor name should be exactly as specified in names(model@fixef). It is up to the user to make sure that name and value make sense, the code here hands full 'control' to the user.
ranefs
a four-element list Group, Level, Predictor, specifying a random-effect Group (e.g. Subject), a level (e.g., S10) and a value (e.g., LogFrequency) for which partial effects have to be calibrated.
n
integer denoting number of points for the plot, chosen at equally
spaced intervals across the empirical range of the predictor variable
intr
a list specifying an interaction to be graphed; obligatory
arguments are (1) the name of the interaction variable, followed by (2)
a vector of values for that variable, followed by (3) the position for
interaction labels ('"beg"', '"mid"', or '"end"', or 'NA' if no labels are
desired), optionally followed by (4) a list with as first element
a vector of colors and as second element a vector of line types. The number
of elements in both vectors should match the number of values specified
under (2) for the interaction predictor.
lockYlim
logical specifying whether all subplots should have the same
range of values for the vertical axis; if TRUE, this range will be
chosen to accomodate all fitted values including HDP intervals for all
predictors across all plots
addlines
if TRUE, adds line(s) between levels of same factor(s)
withList
logical, if TRUE, a list will be output with all data
frames for the subplots
cexsize
character expansion size (cex) for additional information in
the plot for interactions
linecolor
color of lines in the plot, by default set to 1 (black)
addToExistingPlot
default FALSE, if set to TRUE, plot will be added to previous plot, but only if pred is specified
verbose
if TRUE (default), effect sizes and default transformations are reported
...
further graphical parameters to be passed down; warning: col,
pch, lty and cex will often generate an error as they are
internally already fully specified for specialized subplots
Details
When no predictor is specified, a series of plots is produced for the partial
effects of each predictor. The graphs are shown for the reference level for
factors and are adjusted for the median value for the other numerical
predicors in the model. Interactions are not shown. The user should set up the
appropriate number of subplots on the graphics device before running plotLMER.fnc().
Instead of showing all predictors jointly, plotLMER.fnc() can also be used to
plot the partial effect of a specific predictor. When a specific predictor
is specified (with pred = ...), a single plot is produced for that
predictor. In this case, the intr argument can be used to specify a
single second predictor that enters into an interaction with the selected
main predictor.
Polynomials have to be fitted with poly(..., degree, raw=TRUE) and
restricted cubic splines with rcs() from the rms package.
Note that any MCMC capabilities available in the languageR version of this function are not available in this version.
Value
A plot is produced on the graphical device.
Note
This code needs much more work, including (i) extension to poly with raw=FALSE, and (ii) general clean-up of the code.
Author(s)
R. H. Baayen, tweaked by Antoine Tremblay
See Also
plotLMER3d.fnc.
Examples
# see example in LMERConvenienceFunctions help page.