Usage
## S3 method for class 'eff':
print(x, type=c("response", "link"), ...)
## S3 method for class 'effpoly':
print(x, type=c("probability", "logits"), ...)
## S3 method for class 'efflatent':
print(x, ...)
## S3 method for class 'efflist':
print(x, ...)
## S3 method for class 'mlm.efflist':
print(x, ...)
## S3 method for class 'summary.eff':
print(x, ...)
## S3 method for class 'eff':
summary(object, type=c("response", "link"), ...)
## S3 method for class 'effpoly':
summary(object, type=c("probability", "logits"), ...)
## S3 method for class 'efflatent':
summary(object, ...)
## S3 method for class 'efflist':
summary(object, ...)
## S3 method for class 'mlm.efflist':
summary(object, ...)
## S3 method for class 'eff':
plot(x, x.var,
z.var=which.min(levels), multiline=is.null(x$se), rug=TRUE,
xlab, ylab, main=paste(effect, "effect plot"),
colors=palette(), symbols=1:length(colors), lines=1:length(colors),
cex=1.5, lwd=2, ylim, xlim=NULL,
factor.names=TRUE, ci.style, band.transparency=0.15, band.colors=colors,
type=c("response", "link"), ticks=list(at=NULL, n=5),
alternating=TRUE, rotx=0, roty=0, grid=FALSE, layout, rescale.axis=TRUE,
transform.x=NULL, ticks.x=NULL,
key.args=NULL,
row=1, col=1, nrow=1, ncol=1, more=FALSE,
use.splines=TRUE, partial.residuals=c("adjusted", "raw"), show.fitted=FALSE,
residuals.color="blue", residuals.pch=1, span=2/3, ...)
## S3 method for class 'effpoly':
plot(x,
type=c("probability", "logit"),
x.var=which.max(levels),
rug=TRUE,
xlab,
ylab=paste(x$response, " (", type, ")", sep=""),
main=paste(effect, "effect plot"),
colors, symbols, lines, cex=1.5, lwd=2,
factor.names=TRUE, ci.style, band.colors, band.transparency=0.3,
style=c("lines", "stacked"),
confint=(style == "lines" && !is.null(x$confidence.level)),
transform.x=NULL, ticks.x=NULL, xlim=NULL,
ylim, rotx=0, alternating=TRUE, roty=0, grid=FALSE,
layout, key.args=NULL,
row=1, col=1, nrow=1, ncol=1, more=FALSE, use.splines=TRUE, ...)
## S3 method for class 'efflist':
plot(x, selection, rows, cols, ask=FALSE, graphics=TRUE, ...)
## S3 method for class 'mlm.efflist':
plot(x, ...)
## S3 method for class 'efflist':
[(x, ...)Arguments
x
an object of class "eff", "effpoly", "efflist", "mlm.efflist",
or "summary.eff", as appropriate.
object
an object of class "eff", "effpoly", "efflist", or "mlm.efflist",
as appropriate.
type
for linear and generalized linear models,
if "response" (the default), effects are printed
or the vertical axis is labelled on the scale of the response
variable; if "link", effects are printed
or the vertic
x.var
the index (number) or quoted name of the covariate or factor to place on the
horizontal axis of each panel of the effect plot. The default is the
predictor with the largest number of levels or values.
z.var
for linear, generalized linear or mixed models,
the index (number) or quoted name of the covariate or factor for which
individual lines are to be drawn in each panel of the effect plot. The default is the
predictor with the smallest number
multiline
for linear, generalized linear or mixed models,
if TRUE, each panel of the display represents combinations
of values of two predictors, with one predictor (corresponding to x.var)
on the horzontal axis, and the othe
confint
plot point-wise confidence bands around fitted effects (for
multinomial and proportional-odds logit models); defaults to TRUE,
in which case separate panels are used for different response levels.
rug
if TRUE, the default, a rug plot is shown giving the marginal
distribution of the predictor on the horizontal axis, if this predictor is
a covariate. The rug plot is suppressed if partial residuals are plotted.
xlab
the label for the horizontal axis of the effect plot; if missing, the
function will use the name of the predictor on the horizontal axis.
ylab
the label for the vertical axis of the effect plot; the default is
constructed from the name of the
response variable for the model from which the effect was computed.
main
the title for the plot, printed at the top; the default title is constructed from the
name of the effect.
colors
colors[1] is used to plot effects, colors[2] to plot
confidence limits when ci.style is not equal to "bands". In a mulitline plot, the successive colors correspond
to the levels o
symbols, lines
corresponding to the levels of the z.var covariate
or factor on a multiline plot, or to the successive levels of the response factor
in a line plot for a polytomous logit model.
These arguments are used only if multiline
cex
character expansion for plotted symbols; default is 1.5.
lwd
line width for fitted lines
ylim
2-element vector containing the lower and upper limits of the vertical axes;
if NULL, the default, then the vertical axes are scaled from the data.
xlim
a named list of 2-element vectors, with the names corresponding to numeric
predictors; if a numeric predictor is in the list, then when it appears on the horizontal
axis, the axis limits will be taken from the corresponding vector; if a predicto
factor.names
a logical value, default TRUE, that controls the inclusion of
factor names in conditioning-variable labels.
ci.style
confidence bounds can be indicated using error bars, using lines or confidence bands,
depending on the plot type.
For single line plots the default is "bars" for factors and "bands"
for variates. Style "line
band.colors
A vector of colors for the color of the confidence band with ci.style="bands".
The default is band.colors=colors. For plots with one line, the choice, setting
band.colors="red" produces a pleasing result,
band.transparency
For ci.style="bands", the alpha transparency of the fill color. Not all
graphic devices support transparency.
style
(for multinomial or proportional-odds logit models) "lines" (the default
for a line plot, or "stacked" for a stacked-bar or stacked-area plot. In the latter
case only fitted probabilities may be plotted and confidence e
ticks
a two-item list controlling the placement of tick marks on the vertical axis,
with elements at and n. If at=NULL (the default), the program
attempts to find `nice' locations for the ticks, and the value of
ticks.x
a named list of two-item lists controlling the placement of tick marks
on the horizontal axis. Each list element is named for a numeric predictor in the model,
and each sublist has elements at or n are for the tic
transform.x
transformations to be applied to the horizontal axis, in the form of a named list,
each of whose elements is itself a list of two functions, with sublist element names trans and inverse.
The names of the list elements a
alternating
if TRUE (the default), the tick labels alternate by panels in
multi-panel displays from left to right and top to bottom; if FALSE, tick labels
appear at the bottom and on the left.
rotx, roty
rotation angles for the horizontal and vertical tick marks,
respectively. Default is 0.
grid
if TRUE, add grid lines to the plot. Default is FALSE.
layout
the layout argument to the lattice function xyplot
(or, in some cases densityplot), which
is used to draw the effect displ rescale.axis
if TRUE (the default), the tick marks on the vertical axis
are labelled on the response scale (e.g., the probability scale for effects computed on
the logit scale for a binomial GLM).
key.args
additional arguments to be passed to the key trellis argument to
xyplot or densityplot,
e.g., to position the key (legend) in the row, col, nrow, ncol, more
These arguments are used to graph an effect as part of an
array of plots; row, col, nrow, and ncol are used to compose
the split argument and more the more
selection
the optional index (number) or quoted name of the effect in an effect
list to be plotted; if not supplied, a menu of high-order terms is presented or all effects
are plotted.
rows, cols
Number of rows and columns in the ``meta-array'' of plots produced for an efflist object;
if either argument is missing, then the meta-layout will be computed by the plot method.
ask
if selection is not supplied and ask is TRUE,
a menu of high-order terms is presented; if ask is FALSE (the default), effects for all
high-order terms are plotted in an array.
graphics
if TRUE (the default), then the menu of terms to plot is presented
in a dialog box rather than as a text menu.
use.splines
If TRUE, the default, then any lines drawn when the horizontal
axis is not a factor use interpolating splines computed by the spline
function. If FALSE, then linear interpoliation is partial.residuals
use "adjusted" partial residuals, computed at the panel-rounded
values of the focal predictors not on the horizontal axis of each panel, or "raw"
partial residuals, computed at the actual values of all focal predictors;
span
of the loess smoother to be applied to partial residuals, if present;
the default is 2/3.
show.fitted
if partial residuals are present in the effect object, also plot the partial
fitted values (which will be shown as filled circles).
residuals.color
color for plotting partial residuals (default "blue").
residuals.pch
plotting symbol for partial residuals (default 1, open circles).
...
arguments to be passed down.