rgr (version 1.0.4)

tbplot: Plot Vertical Tukey Boxplots

Description

Plots a series of vertical Tukey boxplots where the individual boxplots represent the data subdivided by the value of some factor. Optionally the y-axis may be scaled logarithmically and the values of the Tukey fences used to identify near and far outliers may also be optionally based on the logarithmically transformed data. A variety of other plot options are available, see Details and Note below.

Usage

tbplot(x, by, log = FALSE, logx = FALSE, notch = TRUE, xlab = "", 
	ylab = deparse(substitute(x)), ylim = NULL, main = "", 
	label = NULL, plot.order = NULL, xpos = NA, width, space = 0.25, 
	las = 1, cex = 1, adj = 0.5, add = FALSE, ssll = 1, colr = 8, 
	...)

Arguments

x

name of the variable to be plotted.

by

the name of the factor variable to be used to subdivide the data. See Details below for when by is undefined.

log

if it is required to display the data with logarithmic (y-axis) scaling, set log = TRUE.

logx

if the position of the Tukey boxplot fences are to be computed on the basis of log transformed data set logx = TRUE. For general usage, if log = TRUE then set logx = TRUE.

notch

determines if the boxplots are to be notched such that the notches indicate the 95% confidence intervals for the medians. The default is to notch the boxplets, to suppress the notches set notch = FALSE. See Details below.

xlab

a title for the x-axis, by default none is provided.

ylab

a title for the y-axis. It is often desirable to replace the default y-axis title of the input variable name text string with a more informative title, e.g., ylab = "Cu (mg/kg) in <2 mm="" c-horizon="" soil"<="" code="">.

ylim

defines the limits of the y-axis if the default limits based on the range of the data are unsatisfactory. It can be used to ensure the y-axis scaling in multiple sets of boxplots are the same to facilitate visual comparison.

main

a main title may be added optionally above the display by setting main, e.g., main = "Kola Project, 1995".

label

provides an alternate set of labels for the boxplots along the x-axis. By default the character strings defining the factors are used. Thus, label = c("Alt1", "Alt2", "Alt3").

plot.order

provides an alternate order for the boxplots. Thus, plot.order = c(2, 1, 3) will plot the 2nd ordered factor in the 1st position, the 1st in the 2nd, and the 3rd in its 3rd ordered postion, see Details and Examples below.

xpos

the locations along the x-axis for the individual vertical boxplots to be plotted. By default this is set to NA, which causes default equally spaced positions to be used, i.e. boxplot 1 plots at value 1 on the x-axis, boxplot 2 at value 2, e

width

the width of the boxes, by default this is set to the minimum distance between all adjacent boxplots times the value of space. With the default values of xpos this results in a minimum difference of 1, and with the

space

the space between the individual boxplots, by default this is 0.25 x-axis units.

las

controls whether the x-axis labels are written parallel to the x-axis, the default las = 1, or are written down from the x-axis by setting las = 2. See also, Details below.

cex

controls the size of the font used for the factor labels plotted along the x-axis. By default this is 1, however, if the labels are long it is sometimes necessary to use a smaller font, for example cex = 0.8 results in a font 80

adj

controls the justification of the x-axis labels. By default they are centred, adj = 0.5, to left justify them if the labels are written downwards at an angle set adj = 0.

add

permits the user to plot additional boxplots into an existing display. It is recommended that this option is left as add = FALSE.

ssll

determines the minimum data subset size for which a subset will be plotted. By default this is set to 1, which leads to only a circle with a median bar being plotted, as the subset size increases additional features of the boxplot are displa

colr

by default the boxes are infilled in grey, colr = 8 . If no infill is required, set colr = 0. See display.lty for the range of available colours.

...

further arguments to be passed to methods.

Details

There are two ways to execute this function. Firstly by defining x and by, and secondly by combining the two variables with the split function. See the first two examples below. The split function can be useful if the factors to use in the boxplot are to be generated at run-time, see the last example below. Note that when the split construct is used instead of by the whole split statement will be displayed as the default y-axis title. Also note that when using by the subsets are listed in the order that the factors are encountered in the data, but when using split the subsets are listed alphabetically. In either case they can be re-ordered using plot.order, see Examples. The width option can be used to define different widths for the individual boxplots. For example, the widths could be scaled to be proportional to the subset population sizes as some function of the square root (const * sqrt(n)) or logarithm (const * log10(n)) of those sizes (n). The constant, const, would need to be chosen so that on average the width of the individual boxes would be approximately 0.25, see Example below. It may be desirable for cosmetic purposes to adjust the positions of the boxes along the x-axis, this can be achieved by specifying xpos. Long subset (factor) names can lead to display problems, changing the las parameter from its default of las = 1 which plots subset labels parallel to the axis to las = 2, to plot perpendicular to the axis, can help. It may also help to use label and split the character string into two lines, e.g., by changing the string "Granodiorite" that was supplied to replace the coded factor variable GRDR to "Grano-\ndiorite". If this, or setting las = 2, causes a conflict with the x-axis title, if one is needed, the title can be moved down a line by using xlab = "\nLithological Units". In both cases the \n forces the following text to be placed on the next lower line. If there are more than 7 labels (subsets) and no alternate labels are provided las is set to 2, otherwise some labels may fail to be displayed. The notches in the boxplots indicate the 95% confidence intervals for the medians and can extend beyond the upper and lower limits of the boxes indicating the middle 50% of the data when subset population sizes are small. The confidence intervals are estimated using the binomial theorem. It can be argued that for small populations a normal approximation would be better. However, it was decided to remain with a non-parametric estimate despite the fact that the calculation of the Tukey fence values involves normality assumptions.

See Also

cat2list, ltdl.fix.df

Examples

## Make test data kola.c available
data(kola.c)
attach(kola.c)

## Display a simple Tukey boxplot
tbplot(Cu, by = COUNTRY)
tbplot(split(Cu,COUNTRY))

## Display a more appropriately labelled and scaled boxplot
tbplot(Cu, by = COUNTRY, log =  TRUE, logx = TRUE, xlab = "Country", 
	ylab = "Ni (mg/kg) in <2 mm C-horizon soil")

## Display a west-to-east re-ordered plot using the full country names
tbplot(split(Cu, COUNTRY), log = TRUE, logx = TRUE, 
	ylab = "Ni (mg/kg) in <2 mm C-horizon soil",
	label = c("Finland", "Norway", "Russia"), 
	plot.order = c(2, 1, 3))

## Detach test data kola.c
detach(kola.c)

## Make test data kola.o available, setting a -9999, indicating a
## missing pH measurement, to NA
data(kola.o)
kola.o.fixed <- ltdl.fix.df(kola.o, coded = -9999)
attach(kola.o.fixed)

## Display relationship between pH in one pH unit intervals and Cu in 
## O-horizon (humus) soil
tbplot(split(Cu,trunc(pH+0.5)), log=TRUE, logx = TRUE, 
	xlab = "O-horizon soil pH to the nearest pH unit",
	ylab = "Cu (mg/kg) in <2 mm O-horizon soil")

## As above, but demonstrating the use of variable box widths and the
## suppression of 95\% confidence interval notches.  The box widths are
## computed as (Log10(n)+0.1)/5, the 0.1 is added as one subset has a
## population of 1.
table(trunc(pH+0.5))
tbplot(split(Cu,trunc(pH+0.5)), log=TRUE, logx = TRUE, notch = FALSE,
	xlab = "O-horizon soil pH to the nearest pH unit,
box widths proportional to Log(subset_size)",
	ylab = "Cu (mg/kg) in <2 mm O-horizon soil",
	width = c(0.26, 0.58, 0.24, 0.02))

## Detach test data kola.o.fixed
detach(kola.o.fixed)