seawaveQ (version 1.0.0)

rosBoxPlot: Boxplot of water-quality data

Description

Function to create boxplots of water-quality data that include censored values.

Usage

rosBoxPlot(data, site = "", qwcols = c("R", "P"), ...)

Arguments

data

is the dataset with columns that begin with P followed by a number indicating concentration data and columns that begin with R followed by numbers that match those of the concentration data indicating qualification codes. See example data sets fo

qwcols

is a character vector with the beginning of the column headers for remarks code (default is R), and beginning of column headers for concentration data (default is P for parameter).

site

is a label for the plot title indicating the site where the water-quality samples were collected.

...

arguments to be passed to plot method.

Value

• a boxplot

Details

This function determines the columns within the data set that have concentration data, based on them having column headings that start with P (or a user-specificed indicater in the second element of the qwcols argument) followed by a number. The function determines the associated remark, or qualification columns, based on them having column headings that start with R (or a user-specificed indicater in the first element of the qwcols argument) followed by numbers that match the associated concentration data. Then it determines which values are censored, indicated by a less than symbol in the R columns, performs regression on order statistics, ros, using the NADA package, and estimates values for the censored concentrations for constituents with less than 90-percent censoring. The water-quality concentrations are then depicted by boxplots.

References

Helsel, D.R., 2005, Nondetects and data analysis: New York, John Wiley and Sons.

Lee, Lopaka, 2012, Nondetects and data analysis for environmental data: R package version 1.5-4, http://CRAN.R-project.org/package=NADA.

Oblinger Childress, C.J., Foreman, W.T., Connor, B.F., and Maloney, T.J., 1999, New reporting procedures based on long-term method detection levels and some considerations for interpretations of water-quality data provided by the U.S. Geological Survey: U.S. Geogolical Survey Open-File Report 99--193, 19 p. (Also available at http://water.usgs.gov/owq/OFR_99-193/index.html.)

Examples

data(swData)
# summary of water-quality concentrations
apply(IllRivValleyCty[, grep("P[[:digit:]]",
      dimnames(IllRivValleyCty)[[2]])], 2, summary)
# simple boxplot of water-quality concentrations
rosBoxPlot(IllRivValleyCty)
# same boxplot function with many additional plotting arguments
rosBoxPlot(IllRivValleyCty,
           site="05586100 Illinois River at Valley City, IL",
           log="y", yaxt="n", ylim=c(0.0000001, 1), qwcols=c("R", "P"),
           ylab=c("Concentration, micrograms per liter"),
           col="skyblue1", cex.axis=0.7, cex.sub=0.8,
           par(tcl=0.5, las=1, yaxs="i", mgp=c(3, 0.5, 0),
               mar=c(5, 5, 2, 2),cex.main=0.9))
axis(2,
     at=c(0.0000001, 0.000001, 0.00001, 0.0001, 0.001, 0.01, 0.1, 1),
     labels=c("0.0000001", "0.000001","0.00001", "0.0001", "0.001",
              "0.01", "0.1", "1"), cex.axis=0.7)