spiderBoxplot {GCDkit}R Documentation

Spider plot(s): Selected samples - summary boxplot

Description

Normalization of geochemical data by the given standard (optionally also one of the samples) and spiderplot plotting. No individual patterns are drawn; instead, the statistical distribution of each element is portrayed by a boxplot.

Usage

spiderBoxplot(norm = NULL, which = rep(TRUE,nrow(WR)),
    doublenorm = FALSE, norm2 = "",
    ymin = NULL, ymax = NULL, bpplot = TRUE, 
    col = "lightgray", log = TRUE)

Arguments

norm

a character string specifying the model.

which

specification of the samples to be plotted.

doublenorm

logical; should be the normalization employed? See details.

norm2

name of the variable for the second normalization.

ymin, ymax

y range of the diagram.

bpplot

logical; if FALSE, boxplot box (instead of box and percentile plot) is shown.

col

fill colour.

log

logical; should be the y axis scaled logarithmically?

Details

The parameter 'norm' is an optional search pattern to query the available normalizing model names. It can contain a substring or even a regular expression. The function fails if no matches are found or the search is ambiguous. See selectNorm for details.

The samples to be plotted can be selected based on combination of three searching mechanisms (by sample name/label, range or a Boolean condition) - see selectSamples for details.

For choosing the correct normalization values serves the auxiliary function selectNorm, which is the same as in ordinary spiderplots. If the user desires so, the data can be normalized by a sample present in the dataset. Then the elements to be plotted and their order is to be specified, as well.

Optionally, double normalization can be used. Trace-element data are first normalized by the given standard, then by the normalized content of the selected element in each analysis to eliminate effects of fractional crystallization (Thompson et al. 2003, Pearce et al. 2005, Pearce and Stern 2006). See spider2norm for details.

Distributions of individual normalized elements are plotted in the form of boxplot or box and percentile plot (Esty and Banfield 2003).

spiderbpp.png

In both cases the box denotes 50% of the population (both quartiles), the horizontal line in the middle is a median and the whiskers denote the overall range. For boxplot this is without outliers. See manual entry for 'boxplot' and 'bpplot.my' for further details.

Printed are number of observations, missing values, mean, standard deviation, minimum, 25% quartile, median (=50% quartile), 75% quartile and maximum.

Value

results

numeric matrix with statistical data for individual elements.

Warning

This function IS NOT Figaro-compatible. It means that the set of diagrams cannot be further edited in GCDkit (e.g. tools in "Plot editing" menu are inactive).

Author(s)

Vojtech Janousek, vojtech.janousek@geology.cz

References

Esty, W. W. & Banfield, J. D. (2003). The Box-Percentile Plot. Journal of Statistical Software 8 (17)

Pearce J A, Stern R J (2006) Origin of back-arc basin magmas: Trace element and isotope perspectives. Back-Arc Spreading Systems: Geological, Biological, Chemical, and Physical Interactions. Geophysical Monograph Series 166. American Geophysical Union, pp 63-86

Pearce J A, Stern R J, Bloomer S H, Fryer P (2005) Geochemical mapping of the Mariana arc-basin system: implications for the nature and distribution of subduction components. Geochem Geophys Geosyst 6: doi: 10.1029/2004GC000895

Thompson R N, Morrison M A, Dickin A P, Hendry G L (1983) Continental flood basalts... Arachnids rule OK? In: Hawkesworth C J, Norry M J (eds) Continental Basalts and Mantle Xenoliths. Shiva, Nantwich, pp 158-185

See Also

For the syntax of the setup file with normalizing values and adding new normalization schemes
see selectNorm; for further applications of 'spider' see spiderByGroupPatterns,
spider2norm and spiderByGroupFields.

Examples

 spiderBoxplot("Boynton",col="yellow",bpplot=FALSE)
 spiderBoxplot("Primordial Wood",doublenorm=TRUE,norm2="Y",
    col="khaki",ymin=0.05,ymax=1000,bpplot=TRUE)

[Package GCDkit version 4.0 Index]