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

In EnvStats: Package for Environmental Statistics, Including US EPA Guidance

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

x	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: "Objective vs. lambda" (the default), "Q-Q Plots", "Tukey M-D Q-Q Plots", and "All".
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 relevant only when plot.type produces more than one plot (i.e., when plot.type is not equal to "Objective vs. lambda").
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 plot.type="Objective vs. lambda" (since only one plot is produced) or when same.window=FALSE, otherwise the default value is ask=TRUE.
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 R help file for par for more information.

The following arguments can be supplied when plot.type="Q-Q Plots",
plot.type="Tukey M-D Q-Q Plots", or plot.type="All" (supplied to qqPlot):

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)), "nelson" (hazard plotting method of Nelson (1972)), "michael-schucany" (generalization of the product-limit method due to Michael and Schucany (1986)), and "hirsch-stedinger" (generalization of the product-limit method due to Hirsch and Stedinger (1987)). The default value is prob.method="michael-schucany". The "nelson" method is only available for objects that are the result of calling boxcoxCensored with the argument censoring.side="right". See the help file for qqPlotCensored for more information. This argument is ignored if plot.type="Objective vs. lambda".
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 qqPlotCensored for more information.
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, sd=1). The default value is estimate.params=FALSE because a standard normal Q-Q plot will yield roughly a straight line if the observations are from any normal distribution. If you specify plot.type="Tukey M-D Q-Q Plots", then you need to set estiamte.params=TRUE unless you want to assume the transformed data come from a standard normal distribution.
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, otherwise it is FALSE.
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 and plot.type="Tukey M-D Q-Q Plots", a horizontal line at y=0 is added to the plot. The default value is add.line=TRUE.
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 slope 1), and "robust" (a line is fit through the first and third quartiles of the x and y data). This argument is ignored if add.line=FALSE.
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 each duplicate point, where the plotting symbols cluster around the true value of x and y), and "number" (a single number is plotted at (x,y) that represents how many duplicate points are at that (x,y) coordinate).
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 R help file for par for more information. This argument is ignored if add.line=FALSE.
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 R help file for par for more information. This argument is ignored if add.line=FALSE.
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 R help file for par for more information. This argument is ignored if add.line=FALSE.
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").

Graphics parameters:

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("cex").

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.

Value

plot.boxcoxCensored invisibly returns the first argument, x.

Author(s)

Steven P. Millard ([e-mail])

References

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

See Also

qqPlotCensored, boxcoxCensored, boxcoxCensored.object, print.boxcoxCensored, Data Transformations, plot.

Examples

  # 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()

EnvStats documentation built on Sept. 11, 2024, 6:03 p.m.