an object of class "eff", "effpoly", "efflist", "mlm.efflist", or "summary.eff", as appropriate.

an object of class "eff", "effpoly", "efflist", or "mlm.efflist", as appropriate.

for printing or summarizing linear and generalized linear models, if "response" (the default), effects are printed on the scale of the response variable; if "link", effects are printed on the scale of the linear predictor.

For plotting linear or genealized linearized models, "rescale" (the default) plots the vertical axis on the link scale (e.g., the logit scale for a logit model) but labels the axis on the response scale (e.g., the probability scale for a logit model); "response" plots and labels the vertical axis on the scale of the response (e.g., the probability scale for a logit model); and "link" plots and labels the vertical axis on the scale of the link (e.g., the logit scale for a logit model).

For polytomous logit models, this argument takes either "probability" or "logit", with the former as the default.

this argument is deprecated — use the type argument instead. Setting rescale.axis=TRUE is equivalent to type="rescale"; setting rescale.axis=FALSE is equivalent to type="response". If specified, rescale.axis will override type.

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.

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 of levels or values. This argument is only used if multiline = TRUE.

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 other (corresponding to z.var) used to define lines in the graph; defaults to TRUE if there are no standard errors in the object being plotted, and FALSE otherwise.

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.

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.

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.

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.

the title for the plot, printed at the top; the default title is constructed from the name of the effect.

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 of the z.var covariate or factor. In a stacked plot or a plot without confidence bands for a multinomial or proportional-odds logit model, the successive colors correspond to the levels of the response factor. In all but stacked plots, colors defaults to palette(). If colors is shorter than the number of levels, then it is recycled, so colors="black" will use black for all levels.

For stacked multinomial-logit plots, colors defaults to rainbow_hcl(levels), where levels is the number of levels of the response variable; for stacked proportional-odds model plots, colors defautls to sequential_hcl(levels). colors does not recycle for stacked plots.

Warning: This argument cannot be abbreviated to col, which is used for a different purpose (see below).

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 = TRUE or for polytomous logit models where the effects are plotted without confidence bands; in these cases a legend is drawn at the top of the display. If these arguments are too short they are recycled.

character expansion for plotted symbols; default is 1.5.

line width for fitted lines.

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.

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 predictor is not in the list, or if the argument is NULL (the default), then the horizontal axis limits are computed from the data.

a logical value, default TRUE, that controls the inclusion of factor names in conditioning-variable labels.

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 "lines" can also be used for either of these. For multiline plots, the default is "none" for no confidence bounds, but style "bars" or "bands" can also be used. For a variate the option "bars" displays the error bars at each of the levels points for which the horizontal variable was evaluated.

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, even if color provides no additional information in this case. If this argument is too short it is recycled.

For ci.style="bands", the alpha transparency of the fill color. Not all graphic devices support transparency.

(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 envelopes cannot be shown.

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 n (default, 5) gives the approximate number of tick marks desired; if at is non-NULL, then the value of n is ignored.

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 ticks argument. If a predictor doesn't appear in the list, or if ticks.x is NULL (the default), then the tick marks are computed by the function.

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 are numeric predictors in the model whose axes are to be transformed; the trans function is applied to the values of the predictor, and inverse is used for computing proper axis tick labels. If a numeric predictor is missing from transform.x then its axis is not transformed; if the argument is NULL (the default), then no predictor axes are transformed.

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.

rotation angles for the horizontal and vertical tick marks, respectively. Default is 0.

if TRUE, add grid lines to the plot. Default is FALSE.

the layout argument to the lattice function xyplot (or, in some cases densityplot), which is used to draw the effect display; if not specified, the plot will be formatted so that it appears on a single page.

additional arguments to be passed to the key trellis argument to xyplot or densityplot, e.g., to position the key (legend) in the plotting region; may also be used to modify the default behavior of the key.

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 argument to print.trellis. Normally these arguments are not set by the user, but by plot.efflist. Warning: Note that col is not used to specify colors; use colors instead (see above).

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.

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.

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.

if TRUE (the default), then the menu of terms to plot is presented in a dialog box rather than as a text menu.

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 used. This argument is ignored if the horizontal axis is a factor.

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; the default is "adjusted", and this argument is effective only when partial residuals are included in the effect object to be plotted — see Effect.

whether to show a loess smooth of the partial residuals, if they are present; the default is TRUE. For a non-Gaussian glm model, a non-robust loess smooth is used; for a lm model or a Gaussian glm model, a robust smooth is employed.

of the xyplot smoother to be applied to partial residuals; the default is 2/3.

if partial residuals are present in the effect object, also plot the partial fitted values (which will be shown as filled circles).

color for plotting partial residuals (default "blue").

color for plotting the smooth of the partial residuals; the default is the residuals.color.

plotting symbol for partial residuals (default 1, open circles).

if a single numeric value (the default is 3), the color of the strips at the tops of lattice panels are set to gray scale, with the number of graditions, if there is more than one conditioning variable, corresponding to the value given (which will be rounded to a whole number). This argument can also be a vector of colors, specified in any manner recognized in R (e.g, by name).

foreground color or colors for the strips at the top of lattice panels (the default is "black"); can be a single value or a vector of values of the same length as bg.

"off" or "on", determines whether or not conditioning values in the strips at the top of lattice panels are clipped on the left and right. The normal lattice default is "on"; the default in setStrip is "off", allowing the lines representing numeric conditioning values to be displayed more clearly at the extreme left and right of strips.

a set of lattice strip specifications returned by setStrip.

arguments to be passed down.

a character string to label the effect.

an array containing the estimated effect.

a character string to label the lower confidence limits.

an array containing the lower confidence limits.

a character string to label the upper confidence limits.

an array containing the upper confidence limits.