Usage
effect(term, mod, xlevels=list(), default.levels=10, se=TRUE,
confidence.level=.95,
transformation=list(link=family(mod)$linkfun, inverse=family(mod)$linkinv),
typical=mean)
all.effects(mod, ...)
## S3 method for class 'effect':
print(x, type=c("response", "link"), ...)
## S3 method for class 'effect.list':
print(x, ...)
## S3 method for class 'effect':
summary(object, type=c("response", "link"), ...)
## S3 method for class 'effect.list':
summary(object, ...)
## S3 method for class 'effect':
plot(x, x.var=which.max(levels),
z.var=which.min(levels), multiline=is.null(x$se), rug=TRUE, xlab,
ylab=x$response, main=paste(effect, "effect plot"),
colors=palette(), symbols=1:10, lines=1:10, cex=1.5, ylim,
factor.names=TRUE, type=c("response", "link"), ticks=list(at=NULL, n=5),
alternating=TRUE, rescale.axis=TRUE, ...)
## S3 method for class 'effect.list':
plot(x, selection, ...)
## S3 method for class 'effect':
as.data.frame(x, row.names=NULL, optional=TRUE)Arguments
term
the quoted name of a term, usually, but not necessarily, a high-order
term in the model.
mod
an object of class "lm" or "glm".
xlevels
an optional list of values at which to set covariates,
with components of the form covariate.name = vector.of.values.
default.levels
number of values for covariates that are not
specified explicitly via xlevels; covariate values set by
default are evenly spaced between the minimum and maximum values in
the data.
se
if TRUE, the default, calculate standard errors and
confidence limits for the effects.
confidence.level
level at which to compute confidence limits
based on the standard-normal distribution; the default is 0.95.
transformation
a two-element list with elements link and
inverse. For a generalized linear model, these are by default
the link function and inverse-link (mean) function. For a linear model,
these default to NULL. If
typical
a function to be applied to the columns of the model matrix
over which the effect is "averaged"; the default is mean.
x, object
an object of type "effect" or "effect.list",
as appropriate.
type
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 vertical axis labelled on the scale of the linear pre
x.var
the index (number) 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
the index (number) 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 of levels or values. This argument is only
used if multi
multiline
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 other (corresponding to z.var) used to defi
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.
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 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 bands. In a mulitline plot, the successive colors correspond
to the levels of the z.var covariate or factor.
symbols, lines
corresponding to the levels of the z.var covariate
or factor on a multiline plot. These arguments are used only if multiline = TRUE;
in this case a legend is drawn at the top of the display.
cex
character expansion for plotted symbols; default is 1.
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.
factor.names
a logical value, default TRUE, that controls the inclusion of
factor names in conditioning-variable labels.
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
alternating
if TRUE (the default), the axis labels alternate by panels in
multi-panel displays from left to right and top to bottom; if FALSE, axis labels
appear at the bottom and on the left.
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).
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.
...
arguments to be passed down.
row.names, optional
not used.