R: Interactive Interpretation of Linear Mixed-Effects Models
fxInteractive.lme
R Documentation
Interactive Interpretation of Linear Mixed-Effects Models
Description
This method facilitates the interpretation of linear mixed-effects models and is a byproduct of the method fxInteractive.glm for generalized linear models.
Level of grouping to be displayed, passed to predict.lme. Only one level can be displayed, default to 0.
initial.values
Initial values for the metric covariates in a named list, default to the means. See section 4 of the vignette and examples below.
preselect.var
Name of continuous variable to be displayed as character or NA (default) for menu selection.
preselect.type
The type of the initial plot to be displayed. Must be one of the values "effect" (default) or "marginal".
preselect.groups
Numeric vector with the index of the groups which are displayed in the initial plot. If NULL (the default) all groups are displayed.
dev.height
Height of graphic device in cm, default to 18.
dev.width
Width of plot area in graphic device in cm, default to 18.
dev.width.legend
Width of legend area in graphic device in cm, default to 8.
dev.pointsize
Character pointsize of graphic device, default to 10.
dev.defined
Graphic device predefined? Default to FALSE, see section 6.3 of the vignette for usage.
ylim
With a numeric vector of length 2 the plot limits in y-direction can be set. If NA (the default) these are determined automatically.
col
Vector of color specifications to represent different groups. Passed to the line commands and the legend. Actual palette and consecutive sequence if NA (default).
lty
Vector of line type specifications to represent different groups. Passed to the line commands and the legend, default to solid lines.
lwd
Vector of line width specifications to represent different groups. Passed to the line commands and the legend, default to 1.
main
Title for the plot, default to NA.
main.line
Height for plot title in lines which is passed to title(), default to 1.5.
xlab
Label for the x-axis. Name of the selected covariate, if NA (the default).
ylab
Label for the y-axis. Name of the selected plot type (see argument label.types), if NA (the default).
legend.add
Should a legend be added to the plot? Default to TRUE.
legend.space
Should the space for the legend be reserved? Default to the value of legend.add. Setting legend.add to FALSE and legend.space to TRUE plots white space instead of the legend. This can be useful when different plots are arranged in a document to ensure exact alignments and sizes, see section 6.2 of the vignette for details.
legend.only
Should just the legend be plotted? Default to FALSE. A plot with the legend alone can be useful when different plots are arranged in a document, see section 6.2 of the vignette for details.
legend.pos
Position of the legend as character, see legend for details. Default to "center".
legend.cex
Relative size of legend text. Can be reduced if the model contains many groups. Default to 1.
legend.width.factor
Factor by which the width of the legend is increased. Default to 1. Increasing this can solve the problem that the legend annotations do not fit in the surrounding box when the plots are saved as PDF or EPS files, see section 5 of the vignette for details.
rug.ticksize
Length of rugplot tickmarks, dafault to 0.02. Set to 0 or NA, if no rugplot should be drawn. For many observations the rug considerably slows down the rebuild of the plot.
rug.col
Color of rugplot tickmarks, default to "black".
vline.actual
Add vertical line at actual position of selected metric covariate? Default to TRUE.
pos.hlines
Positions of the horizontal lines for [1] the plot of the effects and [2] the plot of marginal effects. NA for no lines, default to c(0,0).
n.effects
Number of equally spaced points over the span of the selected metric covariate to calculate the effects for plotting, default to 100. Increase, if lines are not smooth.
autosave.plot
Directly save the initial plot? Default to FALSE. If set to TRUE the GUI-panel is immediately closed after initialization.
snapshot.plot
Save plot when snapshot button is pressed? Default to FALSE, see section 5 of the vignette for details.
graphics.filename
Filename (optionally including a path) as character for graphic file.
graphics.numbering
If TRUE (the default) a 3 digits number is automatically appended to the filenname to avoid that existing graphic files are overwritten.
graphics.type
Graphics file type argument, default to "pdf". On Windows systems all file types accepted by savePlot work. Under non Windows systems allowed values are "pdf", "eps", "png", "jpeg", "jpg", "tiff" and "bmp".
factor.sep
Character separating the factor-factor level combinations in the group names (default to "|").
level.sep
Character separating the factor name and the corresponding factor levels in the group names (default to ".").
latex2console
Should the textoutput triggered by the snapshot button be printed as LaTeX-code? Default to FALSE.
xtable.big.mark
Bigmark character for LaTeX output passed to print.xtable, default to ",".
xtable.decimal.mark
Decimal character for LaTeX output passed to print.xtable, default to ".".
xtable.digits
Number of digits for LaTeX output passed to xtable, default to NULL.
xtable.display
Display style for LaTeX output passed to xtable, default to NULL.
xtable.booktabs
Use the LaTeX package booktabs for horizontal lines in LaTeX tables, default to FALSE. Passed to print.xtable.
panel.title
Title used in the title bar of the GUI-panel of type character.
label.button
Label for the snapshot-button of type character.
label.slider.act
Additional label for the slider of the selected metric covariate of type character.
label.box.type
Title for the radiogroup box of type character.
label.types
Labels for radiogroup buttons (character vector of length 2). By default these are also used as corresponding annotations for the y-axis.
label.box.groups
Title for the checkbox of type character.
slider.width
Width of each slider in points (default to 200).
slider.height
Height of each slider in points (default to 60).
button.height
Height of snapshot button in points (default to 30).
box.type.height
Height of radiobox for type selection in points (default to 90).
box.group.character.width
The width of the boxes is basically a this value times the number of characters in points (default to 7).
box.group.line.height
The height of the checkbox is this value times the number of groups in points (default to 28).
dist.obj.width
Vertical distance between sliders and boxes and vertical margins in points (default to 20).
dist.obj.height
Horizontal distance between panel objects in points (default to 10).
...
Other graphical parameters passed to par.
Details
The only mandatory argument of the function is a fitted-model object of class lme (package nlme). For this object the following prerequisites must be met:
The model must contain at least one metric covariate.
The model must be specified with the formula interface and the data frame containing the variables must be passed with the data argument.
The categorical variables must be factors (ordered or unordered).
In this method the additional argument predict.lme.level is responsible for the level of grouping to be displayed, see the documentation of predict.lme.
Please refer to the documentation of fxInteractive or the vignette for more details.
Value
No object is returned, please refer to the documentation of fxInteractive or the vignette for more details.
The examples in fxInteractive.glm and fxInteractive.lm are more elaborated and show different aspects of usage and customization which are valid for this method, too.
Examples
require("nlme")
data("Orthodont")
LMEmod <- lme(distance ~ age + Sex, data = Orthodont, random = ~ age | Subject)
## Not run:
## RStudio users may need to change the graphic device, see details.
options(device = "x11")
## Grouping level 0 is used by default.
fxInteractive(LMEmod, legend.cex=0.6)
## Display grouping level 1
fxInteractive(LMEmod, predict.lme.level=1, legend.cex=0.6)
## For individual specific factors only observable factor combinations are meaningful
# the grouping variable must be the last column
combs.count <- factorCombinations(Orthodont[,c(4,3)])$counts
combs.observed <- combs.count > 0
fxInteractive(LMEmod, predict.lme.level=1, preselect.groups=combs.observed)
## End(Not run)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(LinRegInteractive)
Error in library(LinRegInteractive) :
there is no package called 'LinRegInteractive'
Execution halted