shape: An EDA Graphical Summary

In rgr: Applied Geochemistry EDA

Description

Plots a simple four panel graphical distributional summary for a dataset, comprising a histogram, a horizontal Tukey boxplot or box-and-whisker plot (Garrett, 1988), an empirical cumulative distribution function (ECDF), and a cumulative normal percentage probability (CPP) plot. The plots in all four panels will have identical x-axis scaling. Optionally the EDA graphics may be plotted with logarithmic (base 10) scaling.

Usage

shape(xx, xlab = deparse(substitute(xx)), log = FALSE, 
	xlim = NULL, nclass = NULL, ifbw = FALSE, wend = 0.05, 
	ifnright = TRUE, colr = 8, cex = 0.8, ...)

Arguments

xx	name of the variable to be plotted.
xlab	by default the character string for xx is used for the x-axis plot titles. An alternate title can be displayed with xlab = "text string", see Examples.
log	to display the data with logarithmic (x-axis) scaling, set log = TRUE.
xlim	is determined by gx.hist and used to ensure all four panels in this function have the same x-axis scaling. xlim may be defined, see Note below.
nclass	the default procedure for preparing the histogram depends on sample size. Where N <= 500 the Scott (1979) rule is used, and when N > 500 the Freedman-Diaconis (1981) rule; both these rules are resistant to the presence of outliers, and usually provide informative histograms. Alternately, the user may define the histogram binning by setting nclass, i.e. nclass = "scott", nclass = "fd" or nclass = "sturges"; the latter being designed for normal distributions (Scott, 1992). See Venables and Ripley (2001) for details.
ifbw	the default is to plot a horizontal Tukey boxplot, if a box-and-whisker plot is required set ifbw = TRUE.
wend	if ifbw = TRUE the locations of the whisker-ends have 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.
colr	by default the histogram and Tukey boxplot, or box-and-whisker plot, are infilled in grey, colr = 8. If no infill is required, set colr = 0. See function display.lty for the range of available colours.
ifnright	controls where the sample size is plotted in the histogram display, by default this in the upper right corner of the plot. If the data distribution is such that the upper left corner would be preferable, set ifnright = FALSE. If ifnright = NULL there will be no display of the sample size.
cex	by default the size of the text sample size, N, is set to 80%, i.e. cex = 0.8, and may be changed if required.
...	further arguments to be passed to methods. For example, the size of the axis scale annotation can be changed by setting cex.axis, the size of the axis titles by setting cex.lab, and the size of the plot title by setting cex.main. For example, if it is required to make the plot title smaller, add cex.main = 0.9 to reduce the font size by 10%. By default individual data points in the ECDF and CPP plots are marked by a plus sign, pch = 3, if a cross or open circle is desired, then set pch = 4 or pch = 1, respectively. See display.marks for all available symbols. Adding ifqs = TRUE results in horizontal and vertical dotted lines being plotted at the three central quartiles and their values, respectively, in the ECDF and CPP plots. By default the histogram and ‘box’ are infilled in grey, colr = 8. If no infill is required, set colr = 0. See display.lty for the range of available colours.

Details

A histogram is displayed upper left, an ECDF is displayed below it (lower left). To the right of the histogram a horizontal Tukey boxplot (default) or box-and-whisker plot (option) is displayed (upper right). In the lower right quadrant a cumulative normal percentage probability (CPP) plot is displayed. The x-axis scaling is identical in all four plots.

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 minimum and maximum are plotted, only the median and box representing the span of the middle 50 percent of the data are displayed.

Note

Any less than detection limit values represented by negative values, or zeros or other numeric codes representing blanks in the data, must be removed prior to executing this function, see ltdl.fix.df.

Any NAs in the data vector are removed prior to displaying the plots.

If the default selection for xlim is inappropriate it can be set, e.g., xlim = c(0, 200) or c(2, 200), the latter being appropriate for a logarithmcally scaled plot, i.e. log = TRUE. If the defined limits lie within the observed data range truncated plots will be displayed. If this occurs the number of data points omitted is displayed below the total number of observations in the various panels.

If it is desired to prepare a display of data falling within a defined part of the actual data range, then either a data subset can be prepared externally using the appropriate R syntax, or xx may be defined in the function call as, for example, Cu[Cu < some.value] which would remove the influence of one or more outliers having values greater than some.value. In this case the number of data values displayed will be the number that are <some.value.

In some R installations the generation of multi-panel displays and the use of function eqscplot from package MASS causes warning messages related to graphics parameters to be displayed on the current device. These may be suppressed by entering options(warn = -1) on the R command line, or that line may be included in a ‘first’ function prepared by the user that loads the ‘rgr’ package, etc.

For summary statistics displays to complement the graphics see, gx.summary1, gx.summary2 and inset.

Author(s)

Robert G. Garrett

References

Garrett, R.G., 1988. IDEAS - An Interactive Computer Graphics Tool to Assist the Exploration Geochemist. In Current Research Part F, Geological Survey of Canada Paper 88-1F, pp. 1-13. See pp. 5 for a description of box-and-whisker plots.

Venables, W.N. and Ripley, B.D., 2001. Modern Applied Statistsis with S-Plus, 3rd Edition, Springer, 501 p. See pp. 119 for a description of histogram bin selection computations.

See Also

gx.hist, bxplot, gx.ecdf, cnpplt, remove.na, display.lty, display.marks, ltdl.fix.df, inset

Examples

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

## Generates an initial display to have a first look at the data and 
## decide how best to proceed
shape(Cu)

## Provides a more appropriate initial display and indicates the 
## quartiles
shape(Cu, xlab = "Cu (mg/kg) in <2 mm O-horizon soil", log = TRUE,
	ifqs = TRUE)

## Causes the Friedman-Diaconis rule to be used to select the number of
## histogram bins and changes the ECDF and CPP plotting symbols to a
## cross/x
shape(Cu, xlab = "Cu (mg/kg) in <2 mm O-horizon soil", log = TRUE, 
	nclass = "fd", pch = 4)

## Replaces the Tukey boxplot with a box-and-whisker plot where the 
## whiskers extend to the 10th and 90th percentiles and the minimum
## and maximum observed values are marked with a plus sign.
shape(Cu, xlab = "Cu (mg/kg) in <2 mm O-horizon soil", log = TRUE, 
	ifbw =TRUE, wend = 0.1)

## Detach test data
detach(kola.o)

Example output

Loading required package: MASS
Loading required package: fastICA
Warning messages:
1: In par(old.par) : graphical parameter "cin" cannot be set
2: In par(old.par) : graphical parameter "cra" cannot be set
3: In par(old.par) : graphical parameter "csi" cannot be set
4: In par(old.par) : graphical parameter "cxy" cannot be set
5: In par(old.par) : graphical parameter "din" cannot be set
6: In par(old.par) : graphical parameter "page" cannot be set
There were 19 warnings (use warnings() to see them)
Warning messages:
1: In par(old.par) : graphical parameter "cin" cannot be set
2: In par(old.par) : graphical parameter "cra" cannot be set
3: In par(old.par) : graphical parameter "csi" cannot be set
4: In par(old.par) : graphical parameter "cxy" cannot be set
5: In par(old.par) : graphical parameter "din" cannot be set
6: In par(old.par) : graphical parameter "page" cannot be set
Warning messages:
1: In par(old.par) : graphical parameter "cin" cannot be set
2: In par(old.par) : graphical parameter "cra" cannot be set
3: In par(old.par) : graphical parameter "csi" cannot be set
4: In par(old.par) : graphical parameter "cxy" cannot be set
5: In par(old.par) : graphical parameter "din" cannot be set
6: In par(old.par) : graphical parameter "page" cannot be set

rgr documentation built on May 2, 2019, 6:09 a.m.