MCResult.plotBias: Plot Estimated Systematical Bias with Confidence Bounds

In mcr: Method Comparison Regression

Plot Estimated Systematical Bias with Confidence Bounds

Description

This function plots the estimated systematical bias ( Intercept + Slope * Refrencemethod ) - Referencemethod with confidence bounds, covering the whole range of reference method X or only part of it.

Usage

MCResult.plotBias(
  x,
  xn = 100,
  alpha = 0.05,
  add = FALSE,
  prop = FALSE,
  xlim = NULL,
  ylim = NULL,
  bias = TRUE,
  bias.lty = 1,
  bias.lwd = 2,
  bias.col = NULL,
  ci.area = TRUE,
  ci.area.col = NULL,
  ci.border = FALSE,
  ci.border.col = NULL,
  ci.border.lwd = 1,
  ci.border.lty = 2,
  zeroline = TRUE,
  zeroline.col = NULL,
  zeroline.lty = 2,
  zeroline.lwd = 1,
  main = NULL,
  sub = NULL,
  add.grid = TRUE,
  xlab = NULL,
  ylab = NULL,
  cut.point = NULL,
  cut.point.col = "red",
  cut.point.lwd = 2,
  cut.point.lty = 1,
  ...
)

Arguments

x	object of class "MCResult".
xn	# number of poits for drawing of confidence bounds/area.
alpha	numeric value specifying the 100(1-alpha)% confidence level of confidence intervals (Default is 0.05).
add	logical value. If add=TRUE, the grafic will be drawn in current grafical window.
prop	a logical value. If prop=TRUE the proportional bias \%bias(Xc) = [ Intercept + (Slope-1) * Xc ] / Xc will be drawn.
xlim	limits of the x-axis. If xlim=NULL the x-limits will be calculated automatically.
ylim	limits of the y-axis. If ylim=NULL the y-limits will be calculated automatically.
bias	logical value. If identity=TRUE the bias line will be drawn. If ci.bounds=FALSE and ci.area=FALSE the bias line will be drawn always.
bias.lty	type of the bias line.
bias.lwd	width of the bias line.
bias.col	color of the bias line.
ci.area	logical value. If ci.area=TRUE (default) the confidence area will be drawn.
ci.area.col	color of the confidence area.
ci.border	logical value. If ci.border=TRUE the confidence limits will be drawn.
ci.border.col	color of the confidence limits.
ci.border.lwd	line width of confidence limits.
ci.border.lty	line type of confidence limits.
zeroline	logical value. If zeroline=TRUE the zero-line will be drawn.
zeroline.col	color of the zero-line.
zeroline.lty	type of the zero-line.
zeroline.lwd	width of the zero-line.
main	character string. The main title of plot. If main = NULL it will include regression name.
sub	character string. The subtitle of plot. If sub=NULL and ci.border=TRUE or ci.area=TRUE it will include the art of confidence bounds calculation.
add.grid	logical value. If grid=TRUE (default) the gridlines will be drawn.
xlab	label for the x-axis
ylab	label for the y-axis
cut.point	numeric value. Decision level of interest.
cut.point.col	color of the confidence bounds at the required decision level.
cut.point.lwd	line width of the confidence bounds at the required decision level.
cut.point.lty	line type of the confidence bounds at the required decision level.
...	further graphical parameters

Value

No return value, instead a plot is generated

See Also

calcBias, plot.mcr, plotResiduals, plotDifference, compareFit

Examples

#library("mcr")
data(creatinine,package="mcr")

creatinine <- creatinine[complete.cases(creatinine),]
x <- creatinine$serum.crea
y <- creatinine$plasma.crea

# Calculation of models
m1 <- mcreg(x,y,method.reg="WDeming", method.ci="jackknife",
                mref.name="serum.crea",mtest.name="plasma.crea", na.rm=TRUE)
m2 <- mcreg(x,y,method.reg="WDeming", method.ci="bootstrap",
                method.bootstrap.ci="BCa",mref.name="serum.crea",
                mtest.name="plasma.crea", na.rm=TRUE)

# Grafical comparison of systematical Bias of two models
plotBias(m1, zeroline=TRUE,zeroline.col="black",zeroline.lty=1,
                ci.area=TRUE,ci.border=FALSE, ci.area.col=grey(0.9),
                main = "Bias between serum and plasma creatinine",
                sub="Comparison of Jackknife and BCa-Bootstrap confidence bounds ")
plotBias(m2, ci.area=FALSE, ci.border=TRUE, ci.border.lwd=2,
                ci.border.col="red",bias=FALSE ,add=TRUE)
includeLegend(place="topleft",models=list(m1,m2), lwd=c(10,2),
                lty=c(2,1),colors=c(grey(0.9),"red"), bias=TRUE,
                design="1", digits=4)

# Drawing of proportional bias
plotBias(m1, ci.area=FALSE, ci.border=TRUE)
plotBias(m1, ci.area=FALSE, ci.border=TRUE, prop=TRUE)
plotBias(m1, ci.area=FALSE, ci.border=TRUE, prop=TRUE, cut.point=0.6)
plotBias(m1, ci.area=FALSE, ci.border=TRUE, prop=TRUE, cut.point=0.6,
             xlim=c(0.4,0.8),cut.point.col="orange", cut.point.lwd=3, main ="")

mcr documentation built on Sept. 23, 2024, 5:10 p.m.