DiagTest3Grp: Diagnostic test summary measures for three ordinal groups

The R package provides utilities to estimate and make inference on two summary measures for diagnostic tests when there are three ordinal groups ----volume under ROC surface (VUS) and the extended Youden index, assuming that diagnostic markers increase monotonically and stochastically with disease severity. Point estimates, variance, confidence interval and optimal cut-points both under the normal assumption and also the non-parametric method(s) will be provided for the summary measures. Statistical tests are implemented to compare multiple diagnostic tests and two diagnostic test. Sample size is calculated to estimate the summary measures within a user-specified margin of error for future study planning.

AuthorJingqin Luo, Chengjie Xiong
Date of publication2014-02-20 22:40:48
MaintainerJingqin Luo<rosy@wubios.wustl.edu>
LicenseGPL (>= 2.0)
Version1.6

View on CRAN

Man pages

AL: Alzheimer's disease neuropsychometric marker dataset

bootSample: Draw a bootstrap sample from a given vector of data values

BW.ref: Calculate the bandwidth (normal reference rule and...

CI.normal: Provide the lower and upper limit of a normal confidence...

DiagTest3Grp-internal: Internal DiagTest3Grp functions

DiagTest3Grp-package: Diagnostic test summary measures for three ordinal groups

DiagTest3Grp.Test: Statistical test on the summary measure (VUS or Youden)...

empirical.cdf: Empirical cumulative density function estimation

FisherZ: Fisher's Z transformation

FisherZ.Var: Calculate the variance of an estimator after Fisher's Z...

KernelSmoothing.cdf: Kernel smoothing cumulative density function (CDF)

NonParametric.VUS: Nonparametric estimate of volumn under ROC surface (VUS)

NonParametric.VUS.var: Boostrap variance of the nonparametric estimate on volumn...

Normal.VUS: Volume under ROC surface (VUS) and partial VUS estimate and...

Pairwise.DiagTest3Grp.Test: Do pairwise statistical test on the summary measure (VUS or...

plot.DiagTest3Grp: Scatter plot and boxplot on an object of class DiagTest3Grp

print.DiagTest3Grp: Print an object of class DiagTest3Grp

SampleSize.VUS: Sample size for volume under surface (VUS)

SampleSize.Youden3Grp: Sample size for the extended Youden index for three ordinal...

Sp.Sm.Se: Obtain empirical estimation of the three correct...

var.mu: Variance estimate of the sample estimate for a normal mean...

var.sigma: Variance of a sample estimate for a normal standard deviation...

VUS: A wrapper function for Volume under Surface (VUS) estimate,...

VUS.CutPoint: Find the optimal cut-points in volumn under ROC surface (VUS)...

Youden3Grp: The wrapper function for Youden index analysis

Youden3Grp.OptimalCutoff.Normal.trueMeanSD: The Youden index and optimal cut point estimation under...

Youden3Grp.PointEst: Provide point estimates for the extended Youden index, the...

Youden3Grp.Variance.Bootstrap: Obtain bootstrap variance and confidence itnerval on the...

Youden3Grp.Variance.Normal: Variance estimations for the extended Youden index and...

Functions

AL Man page
bootSample Man page
Bootstrap.Youden.Cutoff.1run Man page
BW.ref Man page
BW.ref Man page
CI.normal Man page
CI.normal Man page
DiagTest3Grp Man page
DiagTest3Grp-package Man page
DiagTest3Grp.Test Man page
empirical.cdf Man page
empirical.cdf Man page
FisherZ Man page
FisherZ Man page
FisherZ.Var Man page
FisherZ.Var Man page
KernelSmoothing.cdf Man page
KernelSmoothing.cdf Man page
negloglik.boxcox.3Grp Man page
NonParametric.VUS Man page
NonParametric.VUS Man page
NonParametric.VUS.var Man page
Normal.VUS Man page
Normal.VUS Man page
Normal.Youden.Cutoff.CI Man page
Pairwise.DiagTest3Grp.Test Man page
PartialDeriv.optimalCutoff Man page
PartialDeriv.Youden Man page
plot.DiagTest3Grp Man page
print.DiagTest3Grp Man page
SampleSize.VUS Man page
SampleSize.VUS Man page
SampleSize.Youden3Grp Man page
SampleSize.Youden3Grp Man page
Sp.Sm.Se Man page
var.mu Man page
var.mu Man page
var.sigma Man page
var.sigma Man page
Var.t.minus Man page
Var.Youden Man page
VUS Man page
VUS.CutPoint Man page
Youden3Grp Man page
Youden3Grp.boxcox.fit Man page
Youden3Grp.BoxCox.lambda Man page
Youden3Grp.Normal Man page
Youden3Grp.OptimalCutoff.Normal.trueMeanSD Man page
Youden3Grp.PointEst Man page
Youden3Grp.Variance.Bootstrap Man page
Youden3Grp.Variance.Bootstrap Man page
Youden3Grp.Variance.Normal Man page

Files

DiagTest3Grp
DiagTest3Grp/inst
DiagTest3Grp/inst/CITATION
DiagTest3Grp/NAMESPACE
DiagTest3Grp/data
DiagTest3Grp/data/AL.rda
DiagTest3Grp/R
DiagTest3Grp/R/CI.normal.R DiagTest3Grp/R/negloglik.boxcox.3Grp.R DiagTest3Grp/R/SampleSize.Youden3Grp.R DiagTest3Grp/R/print.DiagTest3Grp.R DiagTest3Grp/R/Youden3Grp.PointEst.R DiagTest3Grp/R/empirical.cdf.R DiagTest3Grp/R/PartialDeriv.optimalCutoff.R DiagTest3Grp/R/plot.DiagTest3Grp.R DiagTest3Grp/R/var.sigma.R DiagTest3Grp/R/NonParametric.VUS.R DiagTest3Grp/R/Normal.VUS.R DiagTest3Grp/R/Youden3Grp.R DiagTest3Grp/R/VUS.CutPoint.R DiagTest3Grp/R/BW.ref.R DiagTest3Grp/R/FisherZ.Var.R DiagTest3Grp/R/NonParametric.VUS.var.R DiagTest3Grp/R/KernelSmoothing.cdf.R DiagTest3Grp/R/Var.t.minus.R DiagTest3Grp/R/var.mu.R DiagTest3Grp/R/SampleSize.VUS.R DiagTest3Grp/R/Youden3Grp.Variance.Normal.R DiagTest3Grp/R/PartialDeriv.Youden.R DiagTest3Grp/R/DiagTest3Grp.Test.R DiagTest3Grp/R/VUS.R DiagTest3Grp/R/FisherZ.R DiagTest3Grp/R/Var.Youden.R DiagTest3Grp/R/Youden3Grp.BoxCox.lambda.R DiagTest3Grp/R/Youden3Grp.Variance.Bootstrap.R DiagTest3Grp/R/Sp.Sm.Se.R DiagTest3Grp/R/Pairwise.DiagTest3Grp.Test.R DiagTest3Grp/R/Youden3Grp.OptimalCutoff.Normal.trueMeanSD.R DiagTest3Grp/R/bootSample.R DiagTest3Grp/R/Youden3Grp.Normal.R DiagTest3Grp/R/Youden3Grp.boxcox.fit.R DiagTest3Grp/R/Bootstrap.Youden.Cutoff.1run.R
DiagTest3Grp/vignettes
DiagTest3Grp/vignettes/Rvignette_DiagTest3Grp.pdf
DiagTest3Grp/MD5
DiagTest3Grp/DESCRIPTION
DiagTest3Grp/man
DiagTest3Grp/man/NonParametric.VUS.var.Rd DiagTest3Grp/man/var.sigma.Rd DiagTest3Grp/man/var.mu.Rd DiagTest3Grp/man/Youden3Grp.PointEst.Rd DiagTest3Grp/man/Youden3Grp.Variance.Normal.Rd DiagTest3Grp/man/DiagTest3Grp.Test.Rd DiagTest3Grp/man/Youden3Grp.Rd DiagTest3Grp/man/Youden3Grp.OptimalCutoff.Normal.trueMeanSD.Rd DiagTest3Grp/man/BW.ref.Rd DiagTest3Grp/man/VUS.Rd DiagTest3Grp/man/DiagTest3Grp-internal.Rd DiagTest3Grp/man/print.DiagTest3Grp.Rd DiagTest3Grp/man/bootSample.Rd DiagTest3Grp/man/Pairwise.DiagTest3Grp.Test.Rd DiagTest3Grp/man/NonParametric.VUS.Rd DiagTest3Grp/man/FisherZ.Rd DiagTest3Grp/man/Youden3Grp.Variance.Bootstrap.Rd DiagTest3Grp/man/plot.DiagTest3Grp.Rd DiagTest3Grp/man/SampleSize.VUS.Rd DiagTest3Grp/man/DiagTest3Grp-package.Rd DiagTest3Grp/man/empirical.cdf.Rd DiagTest3Grp/man/CI.normal.Rd DiagTest3Grp/man/Sp.Sm.Se.Rd DiagTest3Grp/man/SampleSize.Youden3Grp.Rd DiagTest3Grp/man/Normal.VUS.Rd DiagTest3Grp/man/VUS.CutPoint.Rd DiagTest3Grp/man/KernelSmoothing.cdf.Rd DiagTest3Grp/man/AL.Rd DiagTest3Grp/man/FisherZ.Var.Rd

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