itermplot: Plot Regression Terms for Huge Datasets

Description

Plots regression terms against their predictors, optionally with standard errors and partial residuals in a density plot.

Usage

itermplot(model, data = NULL, envir = environment(formula(model)),
          partial.resid = FALSE, scale=0, pixs = 1,
          zmax=NULL, ztransf = function(x) {x}, colramp = IDPcolorRamp,
          terms = NULL, se = FALSE,
          xlabs = NULL, ylabs = NULL, main = NULL,
          col.term = "black", lwd.term = 2,
          col.se = "gray", lty.se = 2, lwd.se = 1,
          col.smth = "darkred", lty.smth = 2,
          lwd.smth = 2, span.smth = 2/3,
          ask = interactive() && nb.fig < n.tms &&
                .Device != "postscript",
          use.factor.levels = TRUE, smooth = NULL, ...)

Arguments

model

Fitted model object

data

Data frame in which variables in model can be found

envir

Environment in which variables in model can be found

partial.resid

Logical; should partial residuals be plotted?

scale

A lower limit for the number of units covered by the limits on the `y' for each plot. The default is scale = 0, in which case each plot uses the range of the functions being plotted to create their ylim. By setting scale to be

pixs

Size of pixel in x- and y-direction in [mm] on the plotting device. When x and y are numeric, pixels are square. When x and y are factors, pixels are no longer square. The pixels are enlarged in x-direction.

zmax

Maximum number of counts per pixel in the plot. When NULL, each scatter plot has its individual scale. If a number >= maximum number of counts per pixel is supplied, the scale will be identical for all scatter plots. The maximum number o

ztransf

Function to transform the number of counts per pixel. The user has to make sure that the transformed density lies in the range [0,zmax], where zmax is any positive number (>=2). For examples see ipairs<

colramp

Color ramp to encode the number of counts within a pixel by color.

terms

Numeric. Which terms to plot (default NULL means all terms)

Logical. Plot pointwise standard errors?

xlabs

Vector of labels for the x axes

ylabs

Vector of labels for the y axes

main

Logical, or vector of main titles; if TRUE, the model's call is taken as main title, NULL or FALSE mean no titles.

col.term, lwd.term

Color and line width for the term curve

col.se, lty.se, lwd.se

Color, line type and line width for the twice-standard-error curve when se = TRUE.

col.smth, lty.smth, lwd.smth

Color, line type and line width for the smoothed curve

span.smth

Smoothing parameter f for lowess.

ask

Logical. Should user be asked before each plot? cf. par.

use.factor.levels

Logical. Should x-axis ticks use factor levels or numbers for factor terms?

smooth

NULL or a function with the same arguments as ipanel.smooth to draw a smooth through the partial residuals for non-factor terms

...

Other graphical parameters

Value

Maximum number of counts per pixel found.

Details

itermplot is a modified version of termplot of R V2.3.1. Partial residuals are displayed here as a density plot and is therfore especially suited for models of huge datasets. The model object must have a predict method that accepts type=terms, eg glm in the base package, coxph and survreg in the survival package. For the partial.resid=TRUE option it must have a residuals method that accepts type="partial", which lm, glm and gam do. The data argument should rarely be needed, but in some cases termplot may be unable to reconstruct the original data frame. Using na.action=na.exclude makes these problems less likely. Nothing sensible happens for interaction terms.

Examples

Run this code

r.lm <- lm(Sepal.Length~Sepal.Width+Petal.Length+Petal.Width+Species,
           data=iris)
par(mfrow=c(2,2),pty="s")
itermplot(r.lm, se = TRUE, partial.res=TRUE, lwd.term = 3,
          lwd.se = 2, pixs = 2)

if (require(SwissAir)) {
  data(AirQual)
  r.lm <- lm(log(ad.O3)~log(ad.NOx)+ad.T+ad.Td+ad.WS, data=AirQual)
  par(mfrow=c(2,2),pty="s")
  itermplot(r.lm, se = TRUE, partial.res=TRUE, smooth=ipanel.smooth,
            lwd.smth = 3, pixs = 1, ask=FALSE)
} else print("Package SwissAir is not available")