EnvStats: plot.boxcoxLm – R documentation

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plot.boxcoxLm

Plot Results of Box-Cox Transformations for a Linear Model

Description

Plot the results of calling the function boxcox when the argument x supplied to boxcox is an object of class "lm". Three different kinds of plots are available.

The function plot.boxcoxLm is automatically called by plot when given an object of class
"boxcoxLm". The names of other functions associated with Box-Cox transformations are listed under Data Transformations.

Usage

## S3 method for class 'boxcoxLm'
plot(x, plot.type = "Objective vs. lambda", same.window = TRUE, 
    ask = same.window & plot.type != "Ojective vs. lambda", 
    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 `"boxcoxLm"`. See `boxcoxLm.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):

`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 files for `qqPlot` for more information and the motivation for this choice.
`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.boxcoxLm is a method for the generic function plot for the class "boxcoxLm" (see boxcoxLm.object). It can be invoked by calling plot and giving it an object of class "boxcoxLm" as the first argument, or by calling plot.boxcoxLm directly, regardless of the class of the object given as the first argument to plot.boxcoxLm.

Plots associated with Box-Cox transformations are produced on the current graphics device. These can be one or all of the following:

Objective vs. λ.
Observed Quantiles vs. Normal Quantiles (Q-Q Plot) for the residuals of the linear model based on transformed values of the response variable for each of the values of λ.
Tukey Mean-Difference Q-Q Plots for the residuals of the linear model based on transformed values of the response variable for each of the values of λ.

See the help files for boxcox and qqPlot for more information.

Value

plot.boxcoxLm invisibly returns the first argument, x.

Author(s)

Steven P. Millard (EnvStats@ProbStatInfo.com)

References

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

Examples

# Create an object of class "boxcoxLm", then plot the results.

  # The data frame Environmental.df contains daily measurements of 
  # ozone concentration, wind speed, temperature, and solar radiation
  # in New York City for 153 consecutive days between May 1 and 
  # September 30, 1973.  In this example, we'll model ozone as a 
  # function of temperature.

  # Fit the model with the raw Ozone data
  #--------------------------------------
  ozone.fit <- lm(ozone ~ temperature, data = Environmental.df) 

  boxcox.list <- boxcox(ozone.fit)

  # Plot PPCC vs. lambda based on Q-Q plots of residuals 
  #-----------------------------------------------------
  dev.new()
  plot(boxcox.list) 

  # Look at Q-Q plots of residuals for the various transformation 
  #--------------------------------------------------------------
  plot(boxcox.list, plot.type = "Q-Q Plots", same.window = FALSE)


  # Look at Tukey Mean-Difference Q-Q plots of residuals 
  # for the various transformation 
  #-----------------------------------------------------
  plot(boxcox.list, plot.type = "Tukey M-D Q-Q Plots", same.window = FALSE)

  #==========

  # Clean up
  #---------
  rm(ozone.fit, boxcox.list)
  graphics.off()

EnvStats

Package for Environmental Statistics, Including US EPA Guidance

v2.4.0

GPL (>= 3)

Authors

Steven P. Millard [aut], Alexander Kowarik [ctb, cre] (<https://orcid.org/0000-0001-8598-4130>)

Initial release

2020-10-20