plot.thres2: Threshold and density plot (two-state setting)

Description

This function provides a graph including the sample densities (diseased and non-diseased populations), the threshold and its confidence interval.

Usage

# S3 method for thres2
plot(x, bw = c("nrd0", "nrd0"), ci = TRUE,
  which.boot = c("norm", "perc"), col = c(1, 2, 3),
  lty = c(1, 1, 1, 2), lwd = c(1, 1, 1),
  legend = TRUE, leg.pos = "topleft", leg.cex = 1,
  xlim = NULL, ylim = NULL,
  main = paste0("Threshold estimate ", ifelse(ci, "and CI ", ""),
  "(method ", x$T$method, ")"),
  xlab = "", ...)

Value

Estimates of the density functions for both samples and vertical lines representing the threshold and its confidence limits are drawn.

Arguments

x

an object of class thres2.

bw

vector containing the bandwith for the non-diseased sample in the first position and the bandwith for the diseased sample in the second position (to be passed to density()). Default, c("nrd0", "nrd0").

ci

should the confidence interval be plotted? Default, TRUE. No confidence interval will be plotted if x does not contain one (that is, x$CI is NULL).

which.boot

in case x contains confidence intervals calculated by bootstrapping, which one should be printed? The user can choose between "norm" (based on normal distribution) or "perc" (based on percentiles). Default, "norm". This argument is ignored if the confidence intervals were calculated by the delta method.

col

a 3-dimensional vector containing:

col[1]: color for the density of the non-diseased sample

col[2]: color for the density of the diseased sample

col[3]: color for the threshold and its corresponding confidence interval

Default, c(1, 2, 3). If length(col) is not 3, col will be recycled.

lty

a 4-dimensional vector containing:

lty[1]: line type for the density of the non-diseased sample

lty[2]: line type for the density of the diseased sample

lty[3]: line type for the threshold

lty[4]: line type for the confidence interval

Default, c(1, 1, 1, 2). If length(lty) is not 4, lty will be recycled.

lwd

a 3-dimensional vector containing:

lwd[1]: line width for the density of the non-diseased sample

lwd[2]: line width for the density of the diseased sample

lwd[3]: line width for the threshold and its corresponding confidence interval

Default, c(1, 1, 1). If length(lwd) is not 3, lwd will be recycled.

legend

logical asking if an automatic legend should be added to the graph. Default, TRUE.

leg.pos

position of the legend. Default, "topleft". Ignored if legend=FALSE.

leg.cex

number that reescales the size of the legend. Ignored if legend=FALSE. Default, 1.

xlim

2-dimensional vector indicating the lower and upper limits for x-axis. Default value (NULL) sets those limits automatically.

ylim

2-dimensional vector indicating the lower and upper limits for y-axis. Default value (NULL) sets those limits automatically.

main, xlab, ...

further arguments to be passed to plot().

References

Skaltsa K, Jover L, Carrasco JL. (2010). Estimation of the diagnostic threshold accounting for decision costs and sampling uncertainty. Biometrical Journal 52(5):676-697.

Examples

Run this code

n1 <- 100
n2 <- 100
set.seed(1234)
par1.1 <- 0
par1.2 <- 1
par2.1 <- 2
par2.2 <- 1
rho <- 0.2
k1 <- rnorm(n1, par1.1, par1.2) # non-diseased
k2 <- rnorm(n2, par2.1, par2.2) # diseased

thres <- thres2(k1, k2, rho, method="eq", ci.method="d")
plot(thres, col=c(1, 2, 4), lwd=c(2, 2, 1), leg.pos="topright")