plotContours: Color contour plot of the estimated surfaces as a function of...

In USGS-R/EGRET: Exploration and Graphics for RivEr Trends

Color contour plot of the estimated surfaces as a function of discharge and time (surfaces include log concentration, standard error, and concentration)

Description

These plots are normally used for plotting the estimated concentration surface (whatSurface = 3) but can be used to explore the estimated surfaces for the log of concentration or for the standard error (in log space) which is what determines the bias correction. The plots are often more interpretable when the time limits for the plot are less than a decade. To explore changes over a long time period it is best to do this multiple times, for various time slices of 2 years (for example) or to use the function plotDiffContours.

Although there are a lot of optional arguments to this function, most are set to a logical default.

Obtaining a plot that provides good insight it is useful to experiment with several of the arguments such as yearStart, yearEnd, qBottom, qTop, and contourLevels.

Data come from named list, which contains a Sample dataframe with the sample data, a Daily dataframe with the daily flow data, and an INFO dataframe with metadata.

Usage

plotContours(eList, yearStart, yearEnd, qBottom = NA, qTop = NA,
  whatSurface = 3, qUnit = 2, contourLevels = NA, span = 60,
  pval = 0.05, printTitle = TRUE, vert1 = NA, vert2 = NA, horiz = NA,
  tcl = 0.03, flowDuration = TRUE, customPar = FALSE, yTicks = NA,
  tick.lwd = 1, usgsStyle = FALSE, lwd = 2, cex.main = 1,
  cex.axis = 1, concLab = 1,
  color.palette = grDevices::colorRampPalette(c("white", "gray", "blue",
  "red")), ...)

Arguments

eList	named list with at least the Daily and INFO dataframes, and surfaces matrix
yearStart	numeric value for the starting date for the graph, expressed as decimal year (typically whole number such as 1989.0)
yearEnd	numeric value for the ending date for the graph, expressed as decimal year, (for example 1993.0)
qBottom	numeric value for the bottom edge of the graph, expressed in the units of discharge that are being used (as specified in qUnit). NA will choose a "pretty" lower limit nearest to the 5% of discharge. If yTicks are specified, then the first value of yTicks becomes the lowest discharge shown on the figure.
qTop	numeric value for the top edge of the graph, expressed in the units of discharge that are being used (as specified in qUnit). NA will choose a "pretty" upper limit nearest to the 95% of discharge. If yTicks are specified, then the last value of yTicks becomes the highest discharge shown on the figure.
whatSurface	numeric value, can only accept 1, 2, or 3; whatSurface=1 is yHat (log concentration), whatSurface=2 is SE (standard error of log concentration), and whatSurface=3 is ConcHat (unbiased estimate of concentration), default = 3.
qUnit	object of qUnit class. printqUnitCheatSheet, or numeric represented the short code, or character representing the descriptive name.
contourLevels	numeric vector containing the contour levels for the contour plot, arranged in ascending order, default is NA (which causes the contour levels to be set automatically, based on the data)
span	numeric, it is the half-width (in days) of the smoothing window for computing the flow duration information, default = 60
pval	numeric, the probability value for the lower flow frequency line on the graph
printTitle	logical variable if TRUE title is printed, if FALSE not printed
vert1	numeric, the location in time for a black vertical line on the figure, yearStart<vert1<yearEnd, default is NA (vertical line is not drawn)
vert2	numeric, the location in time for a black vertical line on the figure, yearStart<vert2<yearEnd, default is NA (vertical line is not drawn)
horiz	numeric, the location in discharge for a black horizontal line on the figure, qBottom<vert1<qTop, default is NA (no horizontal line is drawn)
tcl	numeric, length of tick marks in inches, default is 0.03
flowDuration	logical variable if TRUE plot the flow duration lines (5 and 95 flow percentiles), if FALSE do not plot them, default = TRUE
customPar	logical defaults to FALSE. If TRUE, par() should be set by user before calling this function (for example, adjusting margins with par(mar=c(5,5,5,5))). If customPar FALSE, EGRET chooses the best margins.
yTicks	vector of yTick labels and marks that will be plotted in log space. (for example yTicks = c(3, 5, 10, 20, 50, 100, 200, 400). The first and last values determine the range of the y axis. If NA, the tick marks will be automatically generated.
tick.lwd	line width for axis ticks, default is 1
usgsStyle	logical option to use USGS style guidelines. Setting this option to TRUE does NOT guarantee USGS compliance. It will only change automatically generated labels.
lwd	numeric, line width of flowDuration curve, default is 2
cex.main	magnification to be used for main titles relative to the current setting of cex
cex.axis	magnification to be used for axis annotation relative to the current setting of cex
concLab	object of concUnit class, or numeric represented the short code, or character representing the descriptive name. By default, this argument sets concentration labels to use either Concentration or Conc (for tiny plots). Units are taken from the eList$INFO$param.units. To use any other words than "Concentration" see vignette(topic = "units", package = "EGRET").
color.palette	a function that creates a color palette for the contour plot. Default goes from white to gray to blue to red using the function colorRampPalette(c("white","gray","blue","red")). A few preset options are heat.colors, topo.colors, and terrain.colors.
...	arbitrary functions sent to the generic plotting function. See ?par for details on possible parameters

Examples

yearStart <- 2002
yearEnd <- 2010
qBottom <- 0.5
qTop<- 20
clevel <- seq(0,2,0.25)
eList <- Choptank_eList
plotContours(eList, yearStart, yearEnd, qBottom, qTop, 
             contourLevels = clevel)  
plotContours(eList, yearStart, yearEnd, qBottom, qTop = 50, 
             contourLevels = clevel, flowDuration = FALSE) 
colors <- grDevices::colorRampPalette(c("white","black"))
plotContours(eList, yearStart, yearEnd, qBottom, qTop = 50, 
             contourLevels = clevel, color.palette = colors, 
             flowDuration = FALSE)

USGS-R/EGRET documentation built on Nov. 20, 2024, 7:45 p.m.