Description Usage Arguments Details Value Note Author(s) References See Also Examples
Given the diagnostic test measurements x, y, z in the three ordinal groups D^, D^0, D^+ separately, the function repeatedly draws a bootstrap sample each of x, y, z to estimate the extended Youden index for three ordinal groups and the associated optimal cut point and obtain the final bootstrap average estimate on the Youden index and optimal cutoff point and the confidence interval.
1 2 3  Youden3Grp.Variance.Bootstrap(x, y, z, method = "Normal", seed.seq =NULL,
randomStart.N = 5, NBOOT=10,alpha=0.05,t.minus.start = NULL,
t.plus.start = NULL, ...)

x 
A numeric vector, a diagnostic test's measurements for subjects in D (usually a healthy group). 
y 
A numeric vector, a diagnostic test's measurements for subjects in D0 (usually a mildly diseased group). 
z 
A numeric vector, a diagnostic test's measurements for subjects in D+ (usually a severly diseased group). 
method 
A character argument. Specify a method to be used for estimating the extended Youden index Choices include ‘Normal’—Estimate the extended Youden index under the assumption of normal distributions of a diagnostic test in the three groups. ‘TN’—Transformed normal. Implement Boxcox transformation to approximate normality and then estimate the extended Youden index under normality. ‘EMP’—Estimate the extended Youden index by using empirical cumulative density function. ‘KS’—Estimate the extended Youden index by using Kernel density estimation with a normal reference rule for bandwidth selection. ‘KSSJ’—Estimate the extended Youden index by using Kernel density estimation with the SheatherJones Plugin method for bandwidth selection. 
seed.seq 
A numeric vector. Users can specify a sequence of random seeds for bootstrap sampling of x. Boostrapping of y and z will use seed0+1 and seed0+2. Default will be the sequence of 1:10. 
randomStart.N 
A numeric value. An argument need to be specified when the method
“EMP”, “KS” or “KSSJ” is used to estimate the
optimal cutpoint and the extended Youden index J. Default,
randomStart.N=1. See 
NBOOT 
A numeric value. Total number of bootstrapping, default=10. 
t.minus.start 
The starting points of the lower optimal
cutpoint (t) which separate the D and D0 group. Default
t.minus.start=NULL will randomly generate starting value. See

t.plus.start 
A numeric value. The starting points of the upper optimal cutpoint (t+) which separate the
D0 and D+ group. Default t.plus.start=NULL will randomly generate
starting value. See 
alpha 
A numeric value. the significance level, will provide the basic quantile confidence interval (alpha/2*100%,1alpha/2*100%). 
... 
Other arguments to be passed to the R function 
This function is carried to get bootstrap estimates of the extended
Youden index and associated cutpoints to provide confidence interval.
See details in Youden3Grp
Return a list, including the following components
var.youden 
The normalmethod based variance on the optimal Youden index. 
var.t.minus 
A numeric value.The variance on the lower optimal cutpoint t.minus. 
var.t.plus 
A numeric value.The variance on the upper optimal cutpoint t.plus. 
var.youden.z 
A numeric value. The variance on the Fisher's Z transformed optimal Youden index. 
youden.CI 
A named numeric of length 2. CI for the estimate of youden with the lower and the upper CI limit (under the names alpha/2*100% and (1alpha/2)*100%). 
t.minus.CI 
A named numeric of length 2. CI for the estimate of t.minus (the lower optimal cutpoint) with the lower and the upper CI limit (under the names alpha/2*100% and (1alpha/2)*100%) CI 
t.plus.CI 
A named numeric of length 2. CI for the estimate of t.plus (the upper optimal cutpoint) with the lower and the upper CI limit (under the names alpha/2*100% and (1alpha/2)*100%). 
youden.z.CI 
A named numeric of length 2. CI for the estimate of FisherZ transformed youden with the lower and the upper CI limit (under the names alpha/2*100% and (1alpha/2)*100%). 
Bug reports, malfunctioning, or suggestions for further improvements or contributions can be sent to Jingqin Luo <[email protected]>.
Jingqin Luo
Luo, J and Xiong, C. (2012) Youden Index and Associated Optimal Cutpoint for Three Ordinal Groups. Communications In StatisticsSimulation and Computation (in press).
1 2 3 4 5 6 7 8  x < rnorm(50,6,1)
y < rnorm(60,8,1.2)
z < rnorm(40,10,1.4)
temp.res < Youden3Grp.Variance.Bootstrap(x=x, y=y, z=z,
method="Normal",seed.seq=1:10,randomStart.N=3,NBOOT=10)

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