EnvStats: plot.gofGroup – R documentation

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plot.gofGroup

Plot Results of Group Goodness-of-Fit Test

Description

Plot the results of calling the function gofGroupTest, which returns an object of class "gofGroup" when performing a goodness-of-fit test to determine whether data in a set of groups appear to all come from the same probability distribution (with possibly different parameters for each group). Five different kinds of plots are available.

The function plot.gofGroup is automatically called by plot when given an object of class
"gofGroup". The names of other functions associated with goodness-of-fit test are listed under Goodness-of-Fit Tests.

Usage

## S3 method for class 'gofGroup'
plot(x, plot.type = "Summary", 
    captions = list(QQ = NULL, MDQQ = NULL, ScoresQQ = NULL, ScoresMDQQ = NULL, 
      Results = NULL), 
    x.labels = list(QQ = NULL, MDQQ = NULL, ScoresQQ = NULL, ScoresMDQQ = NULL), 
    y.labels = list(QQ = NULL, MDQQ = NULL, ScoresQQ = NULL, ScoresMDQQ = NULL), 
    same.window = FALSE, ask = same.window & plot.type == "All", add.line = TRUE, 
    digits = ifelse(plot.type == "Summary", 2, .Options$digits), test.result.font = 1, 
    test.result.cex = ifelse(plot.type == "Summary", 0.9, 1) * par("cex"), 
    test.result.mar = c(0, 0, 3, 0) + 0.1, individual.p.values = FALSE, 
    cex.main = ifelse(plot.type == "Summary", 1.2, 1.5) * par("cex"), 
    cex.axis = ifelse(plot.type == "Summary", 0.9, 1) * par("cex"), 
    cex.lab = ifelse(plot.type == "Summary", 0.9, 1) * par("cex"), 
    main = NULL, xlab = NULL, ylab = NULL, xlim = NULL, ylim = NULL, add.om.title = TRUE, 
    oma = if (plot.type == "Summary" & add.om.title) c(0, 0, 5, 0) else c(0, 0, 0, 0), 
    om.title = NULL, om.font = 2, om.cex.main = 1.5 * par("cex"), om.line = 1, ...)

Arguments

`x`	an object of class `"gofGroup"`. See `gofGroup.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: `"Summary"` (the default), `"Q-Q Plot"` `"Tukey M-D Q-Q Plot"`, `"Scores Q-Q Plot"`, `"Scores Tukey M-D Q-Q Plot"`, `"Test Results"`, and `"All"`. See the DETAILS section for more information.
`captions`	a list with 1 to 5 components with the names `"QQ"`, `"MDQQ"`, `"ScoresQQ"`, `"ScoresMDQQ"`, and/or `"Results"`. Each component either has the value `NULL` or else it is a character string containing the title for that particular kind of plot. When the component has the value `NULL` (the default), a default title is used. This argument is useful when you are creating more than one kind of plot with a single call to `plot.gofGroup` (i.e., when `plot.type="Summary"` or `plot.type="All"`) and you want to specify titles different from the default ones. If you are creating only one kind of plot, then you can just use the `main` argument to specify a title different from the default one.
`x.labels`	a list of 1 to 4 components with the names `"QQ"`, `"MDQQ"`, `"ScoresQQ"`, and/or `"ScoresMDQQ"`. Each component either has the value `NULL` or else it is a character string containing the label for the x-axis for that particular kind of plot. When the component has the value `NULL` (the default), a default x-axis label is used. This argument is useful when you are creating more than one kind of plot with a single call to `plot.gofGroup` (i.e., when `plot.type="Summary"` or `plot.type="All"`) and you want to specify x-axis labels different from the default ones. If you are creating only one plot, then you can just use the `xlab` argument to specify an x-axis label different from the default one.
`y.labels`	a list of 1 to 4 components with the names `"QQ"`, `"MDQQ"`, `"ScoresQQ"`, and/or `"ScoresMDQQ"`. Each component either has the value `NULL` or else it is a character string containing the label for the y-axis for that particular kind of plot. When the component has the value `NULL` (the default), a default y-axis label is used. This argument is useful when you are creating more than one kind of plot with a single call to `plot.gofGroup` (i.e., when `plot.type="Summary"` or `plot.type="All"`) and you want to specify y-axis labels different from the default ones. If you are creating only one plot, then you can just use the `ylab` argument to specify a y-axis label different from the default one.
`same.window`	logical scalar indicating whether to produce all plots in the same graphics window (`same.window=TRUE`), or to create a new graphics window for each separate plot (`same.window=FALSE`; the default). The argument is relevant only when `plot.type="All"`.
`ask`	logical scalar supplied to the function `devAskNewPage`, indicating whether to prompt the user before creating a new plot within a single graphics window. The default value is `FALSE` unless `same.window=TRUE` and `plot.type == "All"`.
`add.line`	logical scalar indicating whether to add a line to the plot. If `add.line=TRUE` and `plot.type="Q-Q Plot"` or `plot.type="Scores Q-Q Plot"`, a 0-1 line is added to the plot. If `add.line=TRUE` and `plot.type="Tukey M-D Q-Q Plot"` or `plot.type="Scores Tukey M-D Q-Q Plot"`, a horizontal line at y=0 is added to the plot. The default value is `add.line=TRUE`. This argument is ignored if `plot.type="Test Results"`.

Arguments associated with plot.type="Test Results"

`digits`	scalar indicating how many significant digits to print for the test results when `plot.type="Summary"` or `plot.type="Test Results"`. If `plot.type == "Summary"`, the default value is `digits=2`, otherwise it is `.Options$digits` (i.e., the current setting of `options("digits")`).
`individual.p.values`	logical scalar indicating whether to display the p-values associated with each individual group. The default value is `individual.p.values=FALSE`.
`test.result.font`	numeric scalar indicating which font to use to print out the test results. The default value is `test.result.font=1`. See the description of the `font` argument in the help file for `par` for more information. You may get better results if you use a font number that corresponds to a fixed font (e.g., courier).
`test.result.cex`	numeric scalar indicating the value of `cex` to use to print out the test results. The default value is `0.9*par("cex")` when `plot.type="Summary"`, otherwise it is `par("cex")`. See the description of the `cex` argument in the help file for `par` for more information.
`test.result.mar`	numeric vector indicating the value of `mar` to use to print out the test results. The default value is `test.result.mar=c(0, 0, 3, 0)+0.1`. See the description of the `mar` argument in the help file for `par` for more information.

Arguments associated with plot.type="Summary"

`add.om.title`	logical scalar indicating whether to add a title in the outer margin when `plot.type="Summary"`. The default value is `add.om.title=TRUE`.
`om.title`	character string containing the outer margin title. The default value is `om.title=NULL`, which will result in a default title.
`om.font`	numeric scalar indicating the font to use for the outer margin. The default value is `om.font=2`.
`om.cex.main`	numeric scalar indicating the value of `cex` for the outer margin title. The default value is `1.5 * par("cex")`.
`om.line`	numeric scalar indicating the line to place the outer margin title on. The default value is `om.line=1`.

Graphics parameters:

cex.main, cex.axis, cex.lab, main, xlab, ylab, xlim, ylim, oma, ...

additional graphics parameters. See the help file for par.

Details

The function plot.gofGroup is a method for the generic function plot for the class "gofGroup" (see gofGroup.object). It can be invoked by calling plot and giving it an object of class "gofGroup" as the first argument, or by calling plot.gofGroup directly, regardless of the class of the object given as the first argument to plot.gofGroup.

Plots associated with the goodness-of-fit test are produced on the current graphics device. These can be one or all of the following:

plot.type="Q-Q Plot". Q-Q Plot of observed p-values vs. quantiles from a Uniform [0,1] distribution. See the help file for qqPlot.
plot.type="Tukey M-D Q-Q Plot". Tukey mean-difference Q-Q plot for observed p-values and quantiles from a Uniform [0,1] distribution. See the help file for qqPlot.
plot.type="Scores Q-Q Plot". Q-Q Plot of Normal scores vs. quantiles from a Normal(0,1) distribution or Q-Q Plot of Chisquare scores vs. quantiles from a Chisquare distribution with 2 degrees of freedom. See the help file for qqPlot.
plot.type="Scores Tukey M-D Q-Q Plot". Tukey mean-difference Q-Q plot based on Normal scores or Chisquare scores. See the help file for qqPlot.
Results of the goodness-of-fit test (plot.type="Test Results"). See the help file for print.gofGroup.

See the help file for gofGroupTest for more information.

Value

plot.gofGroup 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 "gofGroup" then plot it.

  # Example 10-4 of USEPA (2009, page 10-20) gives an example of 
  # simultaneously testing the assumption of normality for nickel 
  # concentrations (ppb) in groundwater collected at 4 monitoring 
  # wells over 5 months.  The data for this example are stored in 
  # EPA.09.Ex.10.1.nickel.df.

  EPA.09.Ex.10.1.nickel.df
  #   Month   Well Nickel.ppb
  #1      1 Well.1       58.8
  #2      3 Well.1        1.0
  #3      6 Well.1      262.0
  #...
  #18     6 Well.4       85.6
  #19     8 Well.4       10.0
  #20    10 Well.4      637.0


  # Test for a normal distribution at each well:
  #--------------------------------------------

  gofGroup.obj <- gofGroupTest(Nickel.ppb ~ Well, 
    data = EPA.09.Ex.10.1.nickel.df)

  dev.new()
  plot(gofGroup.obj)

  # Make your own titles for the summary plot
  #------------------------------------------
  dev.new()
  plot(gofGroup.obj, captions = list(QQ = "Q-Q Plot", 
    ScoresQQ = "Scores Q-Q Plot", Results = "Results"),
    om.title = "Summary Plot")

  # Just the Q-Q Plot
  #------------------
  dev.new()
  plot(gofGroup.obj, plot.type="Q-Q")


  # Make your own title for the Q-Q Plot
  #-------------------------------------
  dev.new()
  plot(gofGroup.obj, plot.type="Q-Q", main = "Q-Q Plot")

  #==========

  # Clean up
  #---------
  rm(gofGroup.obj)
  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