fences {rgr} | R Documentation |
Function to generate fence values to support the selection of the upper and lower bounds of background variability, i.e. threshold(s) or action levels, when an obvious graphical solution is not visually recognizable.
fences(xx, display = TRUE)
xx |
name of the variable to be processed. |
display |
the default is to display the tabular output on the current device, i.e. display = TRUE . However, when the function is used in conjunction with fences.summary then display = FALSE in order to suppress output to the current device as it will be saved to a text file for subsequent use/editing and reference. |
The fence values are computed by several procedures both with and without a logarithic data transformation, together with the 98th percentile of the data for display. These computations are based on results returned from function gx.stats
. Fences are computed following Tukey's boxplot procedure, as median +/- 2 * MAD (Median Absolute Deviation), and mean +/- 2 * SD (Standard Deviation), see Reimann et al. (2005). It is essential that these estimates are viewed in the context of the graphical distributional displays, e.g., shape
and its graphical components, gx.hist
, gx.ecdf
, cnpplt
and bxplot
, and if spatial coordinates for the sample sites are available edamap7
, edamap8
and caplot
. The final selection of a range for background or the selection of a threshold level needs to take the statistical and spatial distributions of the data into account. It is also necessary to be aware that it might be appropriate to have more than one background range/threshold in an area (Reimann and Garrett, 2005). The presence of relevant information in the data frame may permit the data to be subset on the basis of criteria using the tbplot
and bwplot
functions. If these indicate that the medians and middle 50%s of the data are visibly different, multiple background ranges may be advisable.
Any less than detection limit values represented by negative values, or zeros or other numeric codes representing blanks in the data vector, must be removed prior to executing this function, see ltdl.fix.df
.
Any NA
s in the data vector are removed prior to computing the fences.
Robert G. Garrett
Reimann, C. and Garrett, R.G., 2005. Geochemical background - Concept and reality. Science of the Total Environment, 350(1-3):12-27.
Reimann, C., Filzmoser, P. and Garrett, R.G., 2005. Background and threshold: critical comparison of methods of determination. Science of the Total Environment, 346(1-3):1-16.
gx.stats
, fences.summary
, ltdl.fix.df
, remove.na
## Make test data available data(kola.o) attach(kola.o) ## Display the fences computed for Cu fences(Cu) ## Detach test data detach(kola.o)