Uses the output of modelEstimation in the EGRET package (results in the named list eList), and the data frame CIAnnualResults (produced by EGRETci package using scripts described in the vignette) to produce a graph of annual flux, flow normalized flux, and confidence bands for flow-normalized flux. In addition to the arguments listed below, it will accept any additional arguments that are listed for the EGRET function plotFluxHist.

plotFluxHistBoot(eList, CIAnnualResults, yearStart = NA, yearEnd = NA,
  fluxUnit = 9, fluxMax = NA, plotFlowNorm = TRUE, col.pred = "green",
  plotAnnual = TRUE, plotGenFlux = FALSE, cex = 0.8, cex.axis = 1.1,
  lwd = 2, col = "black", col.gen = "red", cex.main = 1.1,
  printTitle = TRUE, customPar = FALSE, ...)

Arguments

eList

named list with at least the Daily, Sample, and INFO dataframes. Created from the EGRET package, after running modelEstimation.

CIAnnualResults

data frame from ciBands (needs nBoot, probs, and blockLength attributes).

yearStart

numeric is the calendar year containing the first estimated annual value to be plotted, default is NA (which allows it to be set automatically by the data).

yearEnd

numeric is the calendar year just after the last estimated annual value to be plotted, default is NA (which allows it to be set automatically by the data).

fluxUnit

integer representing entry in pre-defined fluxUnit class array. printFluxUnitCheatSheet

fluxMax

numeric specifying the maximum value to be used on the vertical axis, default is NA (which allows it to be set automatically by the data), uses units specificed by fluxUnit.

plotFlowNorm

logical variable if TRUE flow normalized flux line is plotted, if FALSE not plotted, default is TRUE.

col.pred

character color of line for flow-normalized flux and for the confidence limits, default is "green".

plotAnnual

logical variable if TRUE, annual mean flux points from WRTDS output are plotted, if FALSE not plotted.

plotGenFlux

logical variable. If TRUE, annual mean flux points from WRTDS_K output are plotted, if FALSE not plotted.

cex

numeric value giving the amount by which plotting symbols should be magnified, default = 0.8.

cex.axis

numeric magnification to be used for axis annotation relative to the current setting of cex, default = 1.1.

lwd

numeric magnification of line width, default = 2.

col

color of annual mean points on plot, see ?par 'Color Specification', default = "black".

col.gen

color of annual mean points for WRTDS_K output on plot, see ?par 'Color Specification', default = "red".

cex.main

numeric title scale

printTitle

logical print title of the plot, 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.

...

graphical parameters

Examples

library(EGRET) eList <- Choptank_eList CIAnnualResults <- Choptank_CIAnnualResults plotFluxHistBoot(eList, CIAnnualResults, fluxUnit=5)
if (FALSE) { CIAnnualResults <- ciCalculations(eList, nBoot = 100, blockLength = 200) plotFluxHistBoot(eList, CIAnnualResults, fluxUnit=5) }