R: Plot an Adjusted Boxplot for Skew Distributions

adjbox {robustbase} | R Documentation

## Plot an Adjusted Boxplot for Skew Distributions

### Description

Produces boxplots adjusted for skewed distributions as proposed in Hubert and Vandervieren (2004).

### Usage

    adjbox(x, ...)

    ## S3 method for class 'formula'
    adjbox(formula, data = NULL, ..., subset, na.action = NULL)

    ## Default S3 method:
    adjbox(x, ..., range = 1.5, doReflect = FALSE,
            width = NULL, varwidth = FALSE,
            notch = FALSE, outline = TRUE, names, plot = TRUE,
            border = par("fg"), col = NULL, log = "",
            pars = list(boxwex = 0.8, staplewex = 0.5, outwex = 0.5),
            horizontal = FALSE, add = FALSE, at = NULL)

### Arguments

`formula` | a formula, such as `y ~ grp`, where `y` is a numeric vector of data values to be split into groups according to the grouping variable `grp` (usually a factor).
`data` | a data.frame (or list) from which the variables in `formula` should be taken.
`subset` | an optional vector specifying a subset of observations to be used for plotting.
`na.action` | a function which indicates what should happen when the data contain `NA`s. The default is to ignore missing values in either the response or the group.
`x` | for specifying data from which the boxplots are to be produced. Either a numeric vector, or a single list containing such vectors. Additional unnamed arguments specify further data as separate vectors (each corresponding to a component boxplot). `NA`s are allowed in the data.
`...` | For the `formula` method, named arguments to be passed to the default method. For the default method, unnamed arguments are additional data vectors (unless `x` is a list when they are ignored), and named arguments are arguments and graphical parameters to be passed to `bxp` in addition to the ones given by argument `pars` (and override those in `pars`).
`range` | this determines how far the plot whiskers extend out from the box, and is simply passed as argument `coef` to `adjboxStats()`. If `range` is positive, the whiskers extend to the most extreme data point which is no more than `range` times the interquartile range from the box. A value of zero causes the whiskers to extend to the data extremes.
`doReflect` | logical indicating if the MC should also be computed on the reflected sample `-x`, and be averaged, see `mc`.
`width` | a vector giving the relative widths of the boxes making up the plot.
`varwidth` | if `varwidth` is `TRUE`, the boxes are drawn with widths proportional to the square-roots of the number of observations in the groups.
`notch` | if `notch` is `TRUE`, a notch is drawn in each side of the boxes. If the notches of two plots do not overlap this is ‘strong evidence’ that the two medians differ (Chambers et al., 1983, p. 62). See `boxplot.stats` for the calculations used.
`outline` | if `outline` is not true, the outliers are not drawn (as points whereas S+ uses lines).

`names` | group labels which will be printed under each boxplot.
`boxwex` | a scale factor to be applied to all boxes. When there are only a few groups, the appearance of the plot can be improved by making the boxes narrower.
`staplewex` | staple line width expansion, proportional to box width.
`outwex` | outlier line width expansion, proportional to box width.
`plot` | if `TRUE` (the default) then a boxplot is produced. If not, the summaries which the boxplots are based on are returned.
`border` | an optional vector of colors for the outlines of the boxplots. The values in `border` are recycled if the length of `border` is less than the number of plots.
`col` | if `col` is non-null it is assumed to contain colors to be used to colour the bodies of the box plots. By default they are in the background colour.
`log` | character indicating if x or y or both coordinates should be plotted in log scale.
`pars` | a list of (potentially many) more graphical parameters, e.g., `boxwex` or `outpch`; these are passed to `bxp` (if `plot` is true); for details, see there.
`horizontal` | logical indicating if the boxplots should be horizontal; default `FALSE` means vertical boxes.
`add` | logical, if true add boxplot to current plot.
`at` | numeric vector giving the locations where the boxplots should be drawn, particularly when `add = TRUE`; defaults to `1:n` where `n` is the number of boxes.

### Details

The generic function `adjbox` currently has a default method (`adjbox.default`) and a formula interface (`adjbox.formula`).

If multiple groups are supplied either as multiple arguments or via a formula, parallel boxplots will be plotted, in the order of the arguments or the order of the levels of the factor (see `factor`).

Missing values are ignored when forming boxplots.

Extremes of the upper and whiskers of the adjusted boxplots are computed using the medcouple (`mc()`), a robust measure of skewness. For details, cf. TODO

### Value

A `list` with the following components:

`stats` | a matrix, each column contains the extreme of the lower whisker, the lower hinge, the median, the upper hinge and the extreme of the upper whisker for one group/plot. If all the inputs have the same class attribute, so will this component.
`n` | a vector with the number of observations in each group.
`coef` | a matrix where each column contains the lower and upper extremes of the notch.
`out` | the values of any data points which lie beyond the extremes of the whiskers.
`group` | a vector of the same length as out whose elements indicate to which group the outlier belongs.
`names` | a vector of names for the groups.

### Note

The code and documentation only slightly modifies the code of `boxplot.default`, `boxplot.formula` and `boxplot.stats`

### Author(s)

R Core Development Team, slightly adapted by Tobias Verbeke

### References

Hubert, M. and Vandervieren, E. (2008). An adjusted boxplot for skewed distributions, Computational Statistics and Data Analysis 52, 5186–5201.

### See Also

The medcouple, `mc`; `boxplot`.

### Examples

    if(require("boot")) {
     ### Hubert and Vandervieren (2006), p. 10, Fig. 4.
     data(coal, package = "boot")
     coaldiff <- diff(coal$date)
     op <- par(mfrow = c(1,2))
     boxplot(coaldiff, main = "Original Boxplot")
     adjbox(coaldiff, main  = "Adjusted Boxplot")
     par(op)
    }

    ### Hubert and Vandervieren (2006), p. 11, Fig. 6. -- enhanced
    op <- par(mfrow = c(2,2), mar = c(1,3,3,1), oma = c(0,0,3,0))
    with(condroz, {
     boxplot(Ca, main = "Original Boxplot")
     adjbox (Ca, main = "Adjusted Boxplot")
     boxplot(Ca, main = "Original Boxplot [log]", log = "y")
     adjbox (Ca, main = "Adjusted Boxplot [log]", log = "y")
    })
    mtext("'Ca' from data(condroz)",
          outer=TRUE, font = par("font.main"), cex = 2)
    par(op)

[Package robustbase version 0.93-6 Index]