rgr (version 1.0.4)

bwplot.by.var: Plot Vertical Box-and-Whisker Plots for Variables

Description

Plots a series of vertical box-and-whisker plots where the individual boxplots represent the data subdivided by variables. Optionally the y-axis may be scaled logarithmically. A variety of other plot options are available, see Details and Note below.

Usage

bwplot.by.var(xmat, log = FALSE, wend = 0.05, notch = FALSE, 
	xlab = "Measured Variables", ylab = "Reported Values", 
	main = "", label = NULL, plot.order = NULL, xpos = NA, 
	las = 1, cex = 1, adj = 0.5, colr = 8, pch = 3, ...)

Arguments

xmat

the data matrix or data frame containing the data.

log

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

wend

the locations of the whisker-ends has to be defined. By default these are at the 5th and 95th percentiles of the data. Setting wend = 0.02 plots the whisker ends at the 2nd and 98th percentiles. See Details below.

notch

determines if the boxplots are to be notched such that the notches indicate the 95% confidence intervals for the medians. The default is not to notch the boxplots, to have notches set notch = TRUE.

xlab

a title for the x-axis, by default xlab = "Measured Variables".

ylab

a title for the y-axis, by default ylab = "Reported Values".

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 (variables) are used. Thus, label = c("Alt1", "Alt2", "Alt3").

plot.order

provides an alternate order for the boxplots. By default the boxplots are plotted in alphabetical order of the factor variables. Thus, plot.order = c(2, 1, 3) will plot the 2nd alphabetically ordered factor in the 1st position, the 1st in t

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

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 set adj = 0.

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.

pch

by default the plotting symbol for the subset maxima and minima are set to a plus, pch = 3, alternate plotting symbols may be chosen from those displayed by display.marks.

...

further arguments to be passed to methods.

Details

There are two ways to provide data to this function. Firstly, if all the variables in a data frame are to be displayed, and there are no factor variables, the data frame name can be entered for xmat. However, if there are factor variables, or only a subset of the variables are to be displayed, the data are entered via the cbind construct, see Examples below. In a box-and-whisker plot there are two special cases. When wend = 0 the whiskers extend to the observed minima and maxima that are not plotted with the plus symbol. When wend = 0.25 no whiskers or the data minima and maxima are plotted, only the medians and boxes representing the span of the middle 50% of the data are displayed. Long variable 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 "Specific Conductivity" that was supplied to replace the variable name SC to "Specific\nConductivity". 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 = "\nPhysical soil properties". In both cases the \n forces the following text to be placed on the next lower line. If there are more than 7 labels (variables) and no alternate labels are provided las is set to 2, otherwise some variable names 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 to be consistent with the use of non-parametric statistics in this display.

See Also

bwplot, var2fact, ltdl.fix.df

Examples

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

## Display a simple box-and-whisker plot for measured variables
bwplot.by.var(cbind(Co,Cu,Ni))

## Display a more appropriately labelled and scaled box-and-whisker plot
bwplot.by.var(cbind(Co,Cu,Ni), log = TRUE, 
	ylab = "Levels (mg/kg) in < 2 mm C-horizon soil")

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

## Make test data ms.data1 available
data(ms.data1)

## Display variables in a data frame extending the whiskers to the
## 2nd and 98th percentiles of the data
bwplot.by.var(ms.data1, log=TRUE, wend = 0.02)