plot.boxcoxCensored: Plot Results of Box-Cox Transformations Based on Type I Censored Data

Description

Plot the results of calling the function boxcoxCensored, which returns an object of class "boxcoxCensored". Three different kinds of plots are available. The function plot.boxcoxCensored is automatically called by plot when given an object of class "boxcoxCensored".

Usage

## S3 method for class 'boxcoxCensored':
plot(x, plot.type = "Objective vs. lambda", same.window = TRUE, 
    ask = same.window & plot.type != "Ojective vs. lambda", 
    prob.method = "michael-schucany", plot.pos.con = 0.375, estimate.params = FALSE, 
    equal.axes = qq.line.type == "0-1" || estimate.params, add.line = TRUE, 
    qq.line.type = "least squares", duplicate.points.method = "standard", 
    points.col = 1, line.col = 1, line.lwd = par("cex"), line.lty = 1, 
    digits = .Options$digits, cex.main = 1.4 * par("cex"), cex.sub = par("cex"), 
    main = NULL, sub = NULL, xlab = NULL, ylab = NULL, xlim = NULL, 
    ylim = NULL, ...)

Arguments

an object of class "boxcoxCensored". See boxcoxCensored.object for details.

plot.type

character string indicating what kind of plot to create. Only one particular plot type will be created, unless plot.type="All", in which case all plots will be created sequentially. The possible values of plot.type are:

same.window

logical scalar indicating whether to produce all plots in the same graphics window (same.window=TRUE; the default), or to create a new graphics window for each separate plot (same.window=FALSE). The argument is relev

ask

logical scalar supplied to the function devAskNewPage, indicating whether to prompt the user before creating a new plot within a single graphics window. This argument is ignored when pl

points.col

numeric scalar determining the color of the points in the plot. The default value is points.col=1. See the entry for col in the Rhelp file for par for more information.

prob.method

character string indicating what method to use to compute the plotting positions for Q-Q plots or Tukey Mean-Difference Q-Q plots. Possible values are "kaplan-meier" (product-limit method of Kaplan and Meier (1958)), "n

plot.pos.con

numeric scalar between 0 and 1 containing the value of the plotting position constant used to construct the Q-Q plots and/or Tukey Mean-Difference Q-Q plots. The default value is plot.pos.con=0.375. See the help file for <

estimate.params

logical scalar indicating whether to compute quantiles based on estimating the distribution parameters (estimate.params=TRUE) or using the distribution parameters for a standard normal distribution (i.e, mean=0,

equal.axes

logical scalar indicating whether to use the same range on the $x$- and $y$-axes when plot.type="Q-Q Plots". The default value is TRUE if qq.line.type="0-1" or estimate.params=TRUE, otherwis

add.line

logical scalar indicating whether to add a line to the plot. If add.line=TRUE and plot.type="Q-Q Plots", a line determined by the value of qq.line.type is added to the plot. If add.line=TRUE an

qq.line.type

character string determining what kind of line to add to the plot when plot.type="Q-Q Plots". Possible values are "least squares" (a least squares line; the default), "0-1" (a line with intercept 0 and s

duplicate.points.method

a character string denoting how to plot points with duplicate $(x,y)$ values. Possible values are "standard" (a single plotting symbol is plotted; the default), "jitter" (a separate plotting symbol is plotted for eac

line.col

numeric scalar determining the color of the line in the plot. The default value is line.col=1. See the entry for col in the Rhelp file for par for more information. This arg

line.lwd

numeric scalar determining the width of the line in the plot. The default value is line.lwd=par("cex"). See the entry for lwd in the Rhelp file for par for more information.

line.lty

numeric scalar determining the line type (style) of the line in the plot. The default value is line.lty=1. See the entry for lty in the Rhelp file for par for more informatio

digits

scalar indicating how many significant digits to print for the distribution parameters and the value of the objective in the sub-title. The default value is the current setting of options("digits").

cex.main, cex.sub, main, sub, xlab, ylab, xlim, ylim, ...

graphics parameters; see par for more information. The default value of cex.main is cex.main=1.4 * par("cex"). The default value of cex.sub is cex.sub=par(

Value

plot.boxcoxCensored invisibly returns the first argument, x.

Details

The function plot.boxcoxCensored is a method for the generic function plot for the class "boxcoxCensored" (see boxcoxCensored.object). It can be invoked by calling plot and giving it an object of class "boxcoxCensored" as the first argument, or by calling plot.boxcoxCensored directly, regardless of the class of the object given as the first argument to plot.boxcoxCensored. Plots associated with Box-Cox transformations are produced on the current graphics device. These can be one or all of the following:

Objective vs.$\lambda$.
Observed Quantiles vs. Normal Quantiles (Q-Q Plot) for the transformed observations for each of the values of$\lambda$.
Tukey Mean-Difference Q-Q Plots for the transformed observations for each of the values of$\lambda$.

See the help files for boxcoxCensored and qqPlotCensored for more information.

References

Chambers, J. M. and Hastie, T. J. (1992). Statistical Models in S. Wadsworth & Brooks/Cole.

Examples

Run this code

# Generate 15 observations from a lognormal distribution with 
  # mean=10 and cv=2 and censor the observations less than 2.  
  # Then generate 15 more observations from this distribution and 
  # censor the observations less than 4.  
  # Then call the function boxcoxCensored, and then plot the results.  
  # (Note: the call to set.seed simply allows you to reproduce this example.)

  set.seed(250) 

  x.1 <- rlnormAlt(15, mean = 10, cv = 2) 
  censored.1 <- x.1 < 2
  x.1[censored.1] <- 2

  x.2 <- rlnormAlt(15, mean = 10, cv = 2) 
  censored.2 <- x.2 < 4
  x.2[censored.2] <- 4

  x <- c(x.1, x.2)
  censored <- c(censored.1, censored.2)

  # Plot the results based on the PPCC objective
  #---------------------------------------------
  boxcox.list <- boxcoxCensored(x, censored)
  dev.new()
  plot(boxcox.list)

  # Look at Q-Q Plots for the candidate values of lambda
  #-----------------------------------------------------
  plot(boxcox.list, plot.type = "Q-Q Plots", same.window = FALSE) 


  # Look at Tukey Mean-Difference Q-Q Plots 
  # for the candidate values of lambda
  #----------------------------------------
  plot(boxcox.list, plot.type = "Tukey M-D Q-Q Plots", same.window = FALSE) 

  #==========

  # Clean up
  #---------
  rm(x.1, censored.1, x.2, censored.2, x, censored, boxcox.list)
  graphics.off()

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