car: avPlots – R documentation

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avPlots

Added-Variable Plots

Description

These functions construct added-variable, also called partial-regression, plots for linear and generalized linear models.

Usage

avPlots(model, ...)

## Default S3 method:
avPlots(model, terms=~., intercept=FALSE, 
  layout=NULL, ask, main, ...)

avp(...)

avPlot(model, ...)

## S3 method for class 'lm'
avPlot(model, variable,
	id=TRUE, col = carPalette()[1], col.lines = carPalette()[2],
	xlab, ylab, pch = 1, lwd = 2, 
	main=paste("Added-Variable Plot:", variable),
	grid=TRUE,
	ellipse=FALSE,
  marginal.scale=FALSE, ...)

## S3 method for class 'glm'
avPlot(model, variable, 
	id=TRUE,
	col = carPalette()[1], col.lines = carPalette()[2],
	xlab, ylab, pch = 1, lwd = 2,  type=c("Wang", "Weisberg"), 
	main=paste("Added-Variable Plot:", variable), grid=TRUE,
	ellipse=FALSE, ...)

Arguments

`model`	model object produced by `lm` or `glm`.
`terms`	A one-sided formula that specifies a subset of the predictors. One added-variable plot is drawn for each term. For example, the specification `terms = ~.-X3` would plot against all terms except for `X3`. If this argument is a quoted name of one of the terms, the added-variable plot is drawn for that term only.
`intercept`	Include the intercept in the plots; default is `FALSE`.
`variable`	A quoted string giving the name of a regressor in the model matrix for the horizontal axis.
`layout`	If set to a value like `c(1, 1)` or `c(4, 3)`, the layout of the graph will have this many rows and columns. If not set, the program will select an appropriate layout. If the number of graphs exceed nine, you must select the layout yourself, or you will get a maximum of nine per page. If `layout=NA`, the function does not set the layout and the user can use the `par` function to control the layout, for example to have plots from two models in the same graphics window.
`main`	The title of the plot; if missing, one will be supplied.
`ask`	If `TRUE`, ask the user before drawing the next plot; if `FALSE` don't ask.
`...`	`avPlots` passes these arguments to `avPlot`. `avPlot` passes them to `plot`.
`id`	controls point identification; if `FALSE`, no points are identified; can be a list of named arguments to the `showLabels` function; `TRUE`, the default, is equivalent to `list(method=list(abs(residuals(model, type="pearson")), "x"), n=2, cex=1, col=carPalette()[1], location="lr")`, which identifies the 2 points with the largest residuals and the 2 points with the most extreme horizontal values (i.e., largest partial leverage).
`col`	color for points; the default is the second entry in the current car palette (see `carPalette` and `par`).
`col.lines`	color for the fitted line.
`pch`	plotting character for points; default is `1` (a circle, see `par`).
`lwd`	line width; default is `2` (see `par`).
`xlab`	x-axis label. If omitted a label will be constructed.
`ylab`	y-axis label. If omitted a label will be constructed.
`type`	if `"Wang"` use the method of Wang (1985); if `"Weisberg"` use the method in the Arc software associated with Cook and Weisberg (1999).
`grid`	If `TRUE`, the default, a light-gray background grid is put on the graph.
`ellipse`	controls plotting data-concentration ellipses. If `FALSE` (the default), no ellipses are plotted. Can be a list of named values giving `levels`, a vector of one or more bivariate-normal probability-contour levels at which to plot the ellipses; and `robust`, a logical value determing whether to use the `cov.trob` function in the MASS package to calculate the center and covariance matrix for the data ellipses. `TRUE` is equivalent to `list(levels=c(.5, .95), robust=TRUE)`.
`marginal.scale`	Consider an added-variable plot of Y versus X given Z. If this argument is `FALSE` then the limits on the horizontal axis are determined by the range of the residuals from the regression of X on Z and the limits on the vertical axis are determined by the range of the residuals from the regressnio of Y on Z. If the argument is `TRUE`, then the limits on the horizontal axis are determined by the range of X minus it mean, and on the vertical axis by the range of Y minus its means; adjustment is made if necessary to include outliers. This scaling allows visualization of the correlations between Y and Z and between X and Z. For example, if the X and Z are highly correlated, then the points will be concentrated on the middle of the plot.

Details

The function intended for direct use is avPlots (for which avp is an abbreviation).

Value

These functions are used for their side effect id producing plots, but also invisibly return the coordinates of the plotted points.

Author(s)

John Fox jfox@mcmaster.ca, Sanford Weisberg sandy@umn.edu

References

Cook, R. D. and Weisberg, S. (1999) Applied Regression, Including Computing and Graphics. Wiley.

Fox, J. (2016) Applied Regression Analysis and Generalized Linear Models, Third Edition. Sage.

Fox, J. and Weisberg, S. (2019) An R Companion to Applied Regression, Third Edition, Sage.

Wang, P C. (1985) Adding a variable in generalized linear models. Technometrics 27, 273–276.

Weisberg, S. (2014) Applied Linear Regression, Fourth Edition, Wiley.

Examples

avPlots(lm(prestige ~ income + education + type, data=Duncan))

avPlots(glm(partic != "not.work" ~ hincome + children, 
  data=Womenlf, family=binomial), id=FALSE)
  
m1 <- lm(partic ~ tfr + menwage + womwage + debt + parttime, Bfox)
par(mfrow=c(1,3))
# marginal plot, ignoring other predictors:
with(Bfox, dataEllipse(womwage, partic, levels=0.5)) 
abline(lm(partic ~ womwage, Bfox), col="red", lwd=2)
# AV plot, adjusting for others:
avPlots(m1, ~ womwage, ellipse=list(levels=0.5)) 
# AV plot, adjusting and scaling as in marginal plot
avPlots(m1, ~ womwage, marginal.scale=TRUE, ellipse=list(levels=0.5))

car

Companion to Applied Regression

v3.0-10

GPL (>= 2)

Authors

John Fox [aut, cre], Sanford Weisberg [aut], Brad Price [aut], Daniel Adler [ctb], Douglas Bates [ctb], Gabriel Baud-Bovy [ctb], Ben Bolker [ctb], Steve Ellison [ctb], David Firth [ctb], Michael Friendly [ctb], Gregor Gorjanc [ctb], Spencer Graves [ctb], Richard Heiberger [ctb], Pavel Krivitsky [ctb], Rafael Laboissiere [ctb], Martin Maechler [ctb], Georges Monette [ctb], Duncan Murdoch [ctb], Henric Nilsson [ctb], Derek Ogle [ctb], Brian Ripley [ctb], William Venables [ctb], Steve Walker [ctb], David Winsemius [ctb], Achim Zeileis [ctb], R-Core [ctb]

Initial release

2020-09-23