boxcoxROC: Box-Cox transformation on three-class ROC data

In trinROC: Statistical Tests for Assessing Trinormal ROC Data

Box-Cox transformation on three-class ROC data

Description

A transformation function for three-class ROC data in order to obtain normally distributed classes.

Usage

boxcoxROC(
  x,
  y,
  z,
  lambda = seq(-2, 2, 0.05),
  lambda2 = NULL,
  eps = 0.02,
  verbose = TRUE
)

Arguments

x, y, z	vectors containing the data of the three classes "healthy", "intermediate" and "diseased" to be transformed. In two-class ROC analysis only.
lambda	vector of possible lambdas the log-likelihood function is evaluated.
lambda2	numeric shifting parameter. For the implemented Box-Cox transformation positive measurements in x, y, z are required. lambda2 is used to shift these measurements.
eps	numeric; indicating the bandwith around zero, where lambda is treated to be zero and the data is log-transformed.
verbose	logical; indicating whether output should be displayed (default) or not.

Details

A Box-Cox transformation computing

X^{(λ)} = log(X) if λ = 0 and X^{(λ)} = (X^λ -1)/λ otherwise

with optimal λ estimated from the likelihood kernel function, as formally described in the supplementary material in Bantis et al. (2017). If the data include any nonpositive observations, a shifting parameter lambda2 can be included in the transformation given by:

X^{(λ)} = log(X+λ_2), if λ = 0 and X^{(λ)} = ((X+λ_2)^λ -1)/λ otherwise.

Value

A list with components:

xbc, ybc, zbc	The transformed vectors.
lambda	estimated optimal parameter.
shapiro.p.value	p-values obtained from shapiro.test() of the original and transformed data.

References

Bantis LE, Nakas CT, Reiser B, Myall D and Dalrymple-Alford JC (2015) Construction of joint confidence regions for the optimal true class fractions of receiver operating characteristic (roc) surfaces and manifolds. Statistical Methods in Medical Research 26(3): 1429–1442.

Box, G. E. P. and Cox, D. R. (1964). An analysis of transformations (with discussion). Journal of the Royal Statistical Society, Series B, 26, 211–252.

See Also

shapiro.test and boxcox from the package MASS.

Examples

data(cancer)
x1 <- with(cancer, cancer[trueClass=="healthy", 9])
y1 <- with(cancer, cancer[trueClass=="intermediate", 9])
z1 <- with(cancer, cancer[trueClass=="diseased", 9])

boxcoxROC(x1, y1, z1)

trinROC documentation built on Oct. 29, 2022, 1:12 a.m.