EnvStats: plot.gofTwoSample – R documentation

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plot.gofTwoSample

Plot Results of Goodness-of-Fit Test to Compare Two Samples

Description

Plot the results of calling the function gofTest to compare two samples. gofTest returns an object of class "gofTwoSample" when supplied with both the arguments y and x. plot.gofTwoSample provides five different kinds of plots.

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

Usage

## S3 method for class 'gofTwoSample'
plot(x, plot.type = "Summary", 
    captions = list(PDFs = NULL, CDFs = NULL, QQ = NULL, MDQQ = NULL, Results = NULL), 
    x.labels = list(PDFs = NULL, CDFs = NULL, QQ = NULL, MDQQ = NULL), 
    y.labels = list(PDFs = NULL, CDFs = NULL, QQ = NULL, MDQQ = NULL), 
    same.window = FALSE, ask = same.window & plot.type == "All", x.points.col = "blue", 
    y.points.col = "black", points.pch = 1, jitter.points = TRUE, discrete = FALSE, 
    plot.pos.con = 0.375, x.ecdf.col = "blue", y.ecdf.col = "black", 
    x.ecdf.lwd = 3 * par("cex"), y.ecdf.lwd = 3 * par("cex"), x.ecdf.lty = 1, 
    y.ecdf.lty = 4, 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, 
    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, 4, 0) else c(0, 0, 0, 0), 
    om.title = NULL, om.font = 2, om.cex.main = 1.5 * par("cex"), om.line = 0, ...)

Arguments

`x`	an object of class `"gof"`. See `gof.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), `"PDFs: Observed"`, `"CDFs: Observed"`, `"Q-Q Plot"`, `"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 `"PDFs"`, `"CDFs"`, `"QQ"`, `"MDQQ"`, 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.gofTwoSample` (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 `"PDFs"`, `"CDFs"`, `"QQ"`, and/or `"MDQQ"`. 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.gofTwoSample` (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 `"PDFs"`, `"CDFs"`, `"QQ"`, and/or `"MDQQ"`. 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.gofTwoSample` (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"`.

Arguments associated with plot.type="PDFs: Observed":

`x.points.col`	a character string or numeric scalar determining the color of the plotting symbol used to display the distribution of the observed `x` values that were supplied to `gofTest`. The default value is `x.points.col="blue"`. See the entry for `col` in the R help file for `par` for more information.
`y.points.col`	a character string or numeric scalar determining the color of the plotting symbol used to display the distribution of the observed `y` values that were supplied to `gofTest`. The default value is `y.points.col="black"`. See the entry for `col` in the R help file for `par` for more information.
`points.pch`	a character string or numeric scalar determining the plotting symbol used to display the distribution of the observed `x` and `y` values that were supplied to `gofTest`. The default value is `points.pch=1`. See the entry for `pch` in the R help file for `par` for more information.
`jitter.points`	logical scalar indicating whether to jitter the points in the strip chart. The default value is `jitter.points=TRUE`.

Arguments associated with plot.type="CDFs: Observed":

`discrete`	logical scalar indicating whether the two distributions are considered to be discrete (`discrete=TRUE`) or not(`discrete=FALSE`; the default). When `discrete=TRUE`, the empirical CDFs are plotted as step functions.
`plot.pos.con`	numeric scalar between 0 and 1 containing the value of the plotting position constant used to construct the observed (empirical) CDFs. The default value is `plot.pos.con=0.375`. See the help files for `ecdfPlot` and `qqPlot` for more information and the motivation for this choice of values. NOTE: This argument is also used to determine the value of the plotting position constant for the Q-Q plot (`plot.type="Q-Q Plot"`), or the Tukey Mean-Difference Q-Q plot (`plot.type="Tukey M-D Q-Q Plot"`).
`x.ecdf.col`	a character string or numeric scalar determining the color of the line used to display the empirical CDF for the `x` values that were supplied to `gofTest`. The default value is `x.ecdf.col="blue"`. See the entry for `col` in the R help file for `par` for more information.
`y.ecdf.col`	a character string or numeric scalar determining the color of the line used to display the empirical CDF for the `y` values that were supplied to `gofTest`. The default value is `y.ecdf.col="black"`. See the entry for `col` in the R help file for `par` for more information.
`x.ecdf.lwd`	numeric scalar determining the width of the line used to display the empirical CDF for the `x` values that were supplied to `gofTest`. The default value is `x.ecdf.lwd=3*par("cex")`. See the entry for `lwd` in the R help file for `par` for more information.
`y.ecdf.lwd`	numeric scalar determining the width of the line used to display the empirical CDF for the `y` values that were supplied to `gofTest`. The default value is `y.ecdf.lwd=3*par("cex")`. See the entry for `lwd` in the R help file for `par` for more information.
`x.ecdf.lty`	numeric scalar determining the line type used to display the empirical CDF for the `x` values that were supplied to `gofTest`. The default value is `x.ecdf.lty=1`. See the entry for `lty` in the R help file for `par` for more information.
`y.ecdf.lty`	numeric scalar determining the line type used to display the empirical CDF for the `y` values that were supplied to `gofTest`. The default value is `y.ecdf.lty=4`. See the entry for `lty` in the R help file for `par` for more information.

Arguments associated with plot.type="Q-Q Plot" or
plot.type="Tukey M-D Q-Q Plot":

As explained above, plot.pos.con is used for these plot types. Also:

add.line

logical scalar indicating whether to add a line to the plot. If add.line=TRUE and plot.type="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", a horizontal line at y=0 is added to the plot. The default value is add.line=TRUE.

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")`).
`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 `1.75 * par("cex")`.
`om.line`	numeric scalar indicating the line to place the outer margin title on. The default value is `om.line=0.5`.

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

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

Observed distributions (plot.type="PDFs: Observed").
Observed CDFs (plot.type="CDFs: Observed"). See the help file for cdfCompare.
Q-Q Plot (plot.type="Q-Q Plot"). See the help file for qqPlot.
Tukey mean-difference Q-Q plot (plot.type="Tukey M-D Q-Q Plot"). See the help file for qqPlot.
Results of the goodness-of-fit test (plot.type="Test Results"). See the help file for print.gofTwoSample.

See the help file for gofTest for more information.

Value

plot.gofTwoSample 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 "gofTwoSample" then plot the results.
  # (Note: the call to set.seed simply allows you to reproduce 
  # this example.)

  set.seed(300) 
  dat1 <- rnorm(20, mean = 3, sd = 2) 
  dat2 <- rnorm(10, mean = 1, sd = 2) 
  gof.obj <- gofTest(x = dat1, y = dat2) 

  # Summary plot (the default)
  #---------------------------
  dev.new()
  plot(gof.obj)


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


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


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

  #==========

  # Clean up
  #---------
  rm(dat1, dat2, gof.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