R Graphical Manual

Browse All

Last data update: 2014.03.03

R: Plot Regression Terms for Huge Datasets

itermplot

R Documentation

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 the maximum value of diff(ylim) or above for all the plots, then all subsequent plots will be produced in the same vertical units. This is essential for comparing the importance of fitted terms in additive models.
`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 of counts per pixel is delivered by the return value.
`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` and `ilagplot`.
`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)
`se`	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

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.

Value

Maximum number of counts per pixel found.

Author(s)

Rene Locher

Examples

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.resid=TRUE, smooth=ipanel.smooth,
            lwd.smth = 3, pixs = 1, ask=FALSE)
} else print("Package SwissAir is not available")

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(IDPmisc)
Loading required package: grid
Loading required package: lattice
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/IDPmisc/itermplot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: itermplot
> ### Title: Plot Regression Terms for Huge Datasets
> ### Aliases: itermplot
> ### Keywords: hplot
> 
> ### ** Examples
> 
> 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.resid=TRUE, smooth=ipanel.smooth,
+             lwd.smth = 3, pixs = 1, ask=FALSE)
+ } else print("Package SwissAir is not available")
Loading required package: SwissAir
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>