fences.summary {rgr} | R Documentation |
Function to generate fences and save the values in the R working directory for subsets of the data for a variable when the data can be subdivided by some criterion (factor) such as EcoRegion, Province, physical sample parent material, etc. The function supports the selection of the upper and lower bounds of background variability, and threshold(s) or action levels, when obvious graphical solutions are not visually recognizable.
fences.summary(group, x, file = NULL)
group |
the name of the factor variable by which the data are to be subset. |
x |
name of the variable to be processed. |
file |
the first part of the file name identifying the data source for saving the function output in the R working directory, see Details below. |
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.
file
contains the first part of the file name identifying the data source for the output file to be saved in the R working directory, see Note below. The function concatenates the working directory name with file
, _
, group
as a character string, _
, x
as a character string, and _fences.txt
to be used as the file name.
Output to the current device is suppressed. The output file can be inspected with a text viewer, and column spacings edited for cosmetic purposes with an ASCII editor of the user's choice.
To set the R working directory, use at the R command line, for example, setwd("C:\\R\\WDn")
which will result in all saved output being placed in that folder.
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.
The function fences
is employed to compute the statistical fence estimates.
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.
fences
, ltdl.fix.df
, remove.na
## Make test data available data(kola.c) attach(kola.c) ## Saves the file kola_c_COUNTRY_Cu_fences.txt for later use ## in the R working directory. fences.summary(COUNTRY, Cu, file = "kola_c") ## Detach test data detach(kola.c)