DiagTest3Grp: Diagnostic test summary measures for three ordinal groups

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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.

Author
Jingqin Luo, Chengjie Xiong
Date of publication
2014-02-20 22:40:48
Maintainer
Jingqin Luo<rosy@wubios.wustl.edu>
License
GPL (>= 2.0)
Version
1.6

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...

Files in this package

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