R: Displaying compositions and amounts with box-plots

boxplot {compositions} | R Documentation

## Displaying compositions and amounts with box-plots

### Description

For the different interpretations of amounts or compositional data, a different type of boxplot is feasible. Thus different boxplots are drawn.

### Usage

    ## S3 method for class 'acomp'
    boxplot(x,fak=NULL,...,
                             xlim=NULL,ylim=NULL,log=TRUE,
                             panel=vp.logboxplot,dots=!boxes,boxes=TRUE,
                              notch=FALSE,
                              plotMissings=TRUE,
                              mp=~simpleMissingSubplot(missingPlotRect,
                                                    missingInfo,c("NM","TM",cn))
                              )
    ## S3 method for class 'rcomp'
    boxplot(x,fak=NULL,...,
                             xlim=NULL,ylim=NULL,log=FALSE,
                             panel=vp.boxplot,dots=!boxes,boxes=TRUE,
                              notch=FALSE,
                              plotMissings=TRUE,
                              mp=~simpleMissingSubplot(missingPlotRect,
                                                    missingInfo,c("NM","TM",cn)))
    ## S3 method for class 'aplus'
    boxplot(x,fak=NULL,...,log=TRUE,
                              plotMissings=TRUE,
                              mp=~simpleMissingSubplot(missingPlotRect,
                                                       missingInfo,
                                                       names(missingInfo)))
    ## S3 method for class 'rplus'
    boxplot(x,fak=NULL,...,ylim=NULL,log=FALSE,
                              plotMissings=TRUE,
                              mp=~simpleMissingSubplot(missingPlotRect,
                                                       missingInfo,
                                                       names(missingInfo)))
    vp.boxplot(x,y,...,dots=FALSE,boxes=TRUE,xlim=NULL,ylim=NULL,log=FALSE,
                              notch=FALSE,plotMissings=TRUE,
                              mp=~simpleMissingSubplot(missingPlotRect,
                                                       missingInfo,c("NM","TM",cn)),
                              missingness=attr(y,"missingness") )
    vp.logboxplot(x,y,...,dots=FALSE,boxes=TRUE,xlim,ylim,log=TRUE,notch=FALSE,
                              plotMissings=TRUE,
                              mp=~simpleMissingSubplot(missingPlotRect,
                                                       missingInfo,c("NM","TM",cn)),
                              missingness=attr(y,"missingness"))

### Arguments

`x` | a data set
`fak` | a factor to split the data set, not yet implemented in aplus and rplus
`xlim` | x-limits of the plot.
`ylim` | y-limits of the plot.
`log` | logical indicating whether ploting should be done on log scale
`panel` | the panel function to be used or a list of multiple panel functions
`...` | further graphical parameters
`dots` | a logical indicating whether the points should be drawn
`boxes` | a logical indicating whether the boxes should be drawn
`y` | used by pairs
`notch` | logical, should the boxes be notched?
`plotMissings` | Logical indicating that missings should be displayed.
`mp` | A formula providing a function call, which will be evaluated within each panel with missings to plot the missingness situation. The call can use the variables `missingPlotRect`, which provides a rectangle to plot the information to in a par("usr") like specification. In the r`X` is the current data
`missingness` | The missingness information as a result from `missingType` of the full data information the panels could base there missing plots on.

### Details

`boxplot.aplus` and `boxplot.rplus` are wrappers of `bxp`, which just take into account the possible logarithmic scale of the data.

`boxplot.acomp` and `boxplot.rcomp` generate a matrix of box-plots, where each cell represents the difference between the row and column variables. Such difference is respectively computed as a log-ratio and a rest.

`vp.boxplot` and `vp.logboxplot` are only used as panel functions. They should not be directly called.

### Author(s)

K.Gerald v.d. Boogaart http://www.stat.boogaart.de

### See Also

`plot.acomp`, `qqnorm.acomp`

### Examples

    data(SimulatedAmounts)
    boxplot(acomp(sa.lognormals))
    boxplot(rcomp(sa.lognormals))
    boxplot(aplus(sa.lognormals))
    boxplot(rplus(sa.lognormals))
    # And now with missing!!!
    boxplot(acomp(sa.tnormals))

[Package compositions version 2.0-0 Index]