achievable.se.sp: achievable.se.sp(): target sensitivity and specificity for a...

In NNTbiomarker: Calculate Design Parameters for Biomarker Validation Studies

Description

For a retrospective study design, given a prevalence value, produce a plot displaying the achievable contours of either predictive values or NNT values. The calculation uses the "contra-Bayes" theorem, sesp.from.pv.

Usage

achievable.se.sp(the.prev = 0.5, axes = c("pv", "NNT"),
  sesp.seq = seq(0.5, 1, 0.1), drawNNTaxes = TRUE, drawPVaxes = FALSE,
  drawArrows = TRUE, drawTable = TRUE, latexTable = TRUE,
  placePointLabels = TRUE, cexText = 0.5, cexSubtitle = 0.5,
  cexTitle = 0.7, y0arrow = 0.25, lwdArrow = 1, ltyArrow = 2,
  title = FALSE, mtext = FALSE, contours = TRUE, ...)

Arguments

the.prev	Prevalence (prior probability)
axes	Should the axes be predictive values ("pv") or NNT values? Default is "pv".
sesp.seq	Sequence of values at which the sensitivity and specificity will be explored.
drawNNTaxes	(default=TRUE) Option for tweaking the plot.
drawPVaxes	(default=FALSE) Option for tweaking the plot.
drawArrows	(default=TRUE) Arrow option; deprecated.
drawTable	(default=TRUE) Option for tweaking the plot.
latexTable	(default=TRUE) Option for tweaking the plot.
placePointLabels	(default=TRUE) Write A, B, C, ... in circles where sensitivity=specificity.
cexText	(default=0.5) Option for tweaking the plot.
cexSubtitle	(default=0.5) Option for tweaking the plot.
cexTitle	(default=0.7) Option for tweaking the plot.
y0arrow	(default=0.25) Arrow option; deprecated.
lwdArrow	(default=1) Arrow option; deprecated.
ltyArrow	(default=2) Arrow option; deprecated.
title	(default=FALSE) Option for tweaking the plot.
mtext	(default=FALSE) Option for tweaking the plot.
contours	(default=TRUE) Option for tweaking the plot.
...	Options to pass to plot.default()

Value

The predictive values when sensitivity equals specificity: sesp.to.pv(cbind(sesp.seq,sesp.seq), prev=the.prev))

NNTbiomarker documentation built on May 1, 2019, 11:15 p.m.