biostatUZH: Misc Tools of the Department of Biostatistics, EBPI, University of Zurich

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Various functions developed at the Department of Biostatistics, Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland. Currently implemented topics: several CI's for proportions, several CI's for diagnostic tests, Fagan-Nomogram, bootstrap CI's for the kappa coefficient, intraclass-correlation coefficients including CI's, agreement for continuous measurements (Bland-Altman plot), CI for the area under the curve (AUC), Mantel-Haenszel estimator, Mantel-Cox hazard ratio estimator, CI for the Kaplan-Meier estimate at given time points, CI for quantile of a Kaplan-Meier or cumulative incidence estimate, sample size computations for two-sample Mann-Whitney test, McNemar test, binary diagnostic test (via normal approximation and simulation), natural re-parametrization of Weibull output from survreg, hazard ratio and event time ratio interpretations, a plot to check the adequacy of the Weibull model.

Author
Sarah R. Haile [aut], Leonhard Held [aut, cre], Sebastian Meyer [aut], Sina Rueeger [aut], Kaspar Rufibach [aut], Daniel Sabanes Bove [ctb], R Core Team [cph]
Date of publication
2016-11-18 11:13:01
Maintainer
Leonhard Held <leonhard.held@uzh.ch>
License
GPL (>=2)
Version
1.7.0
URLs

View on R-Forge

Man pages

biostatUZH-package
Misc Tools of the Department of Biostatistics, EBPI,...
BlandAltman
Bland-Altman plot to assess agreement between two continuous...
computeICCrater
Compute intraclass correlation coefficients ICC(2, 1) and...
confIntAUC
Compute confidence interval for AUC
confIntAUCbinorm
Function to compute ROC curve and (bootstrap) confidence...
confIntDiagnostic
Compute confidence intervals for operating characteristics of...
confIntFisherTrafo
Confidence interval for correlation coefficient using...
confIntICC
Confidence intervals for intraclass correlation in interrater...
confIntIndependentDiagnostic
Compute confidence intervals for the comparison of two...
confIntIndependentProportion
Compute confidence interval for the risk difference of two...
confIntKappa
Confidence intervals for weighted kappa and m >= 2 raters
confIntKM_t0
Compute confidence interval for a survival curve at a fixed...
confIntMedian
Compute exact confidence interval for median of a sample...
confIntPairedDiagnostic
Compute confidence intervals for the comparison of two...
confIntPairedProportion
Compute confidence interval for the difference of paired...
confIntProportion
Compute confidence interval for a binomial proportion via...
confIntRiskDiff
Compute confidence interval for a risk difference
confIntRiskRatio
Compute confidence interval for a risk ratio
ConvertWeibull
Transformation of survreg output for the Weibull distribution
faganPlot
Fagan-Nomogram
fischdaten
Data of the 'Fischstudie'
formatCI
Format (Confidence) Intervals
formatPercent
Format a Numeric Proportion
formatPval
Format p-Values
larynx
Survival Times of Larynx Cancer Patients
logit
Logit and inverse-logit function
mantelCoxHR
Mantel-Cox estimator of the hazard ratio
mantelHaenszel
Cochran-Mantel-Haenszel Chi-Squared Test for Count Data
plotcorr
Compact Visualization of a Correlation Matrix
populationSamplePlot
Plot that shows population and sample drawn from it
quantileCumInc
Compute arbitrary quantile of a Cumulative Incidence estimate
quantileKM
Compute arbitrary quantile of a Kaplan-Meier estimate of a...
sampleSizeMcNemar
Compute sample size for McNemar test
sampleSizePhase2BinaryTest
Compute sample size for a Phase 2 study of a binary test
sampleSizeWilcoxTwoSample
Compute sample size for two sample Wilcoxon (Mann-Whitney)...
standardErrorAUC
Standard Error of AUC
summaryROC
Function to compute ROC curve and an asymptotic confidence...
survrep
Survival Analysis Results for Reports
tableRegression
Format Coefficient Tables of Regression Models
WeibullDiag
Diagnostic Plot of Adequacy of Weibull Distribution
WeibullReg
Weibull Regression for Survival Data

Files in this package

biostatUZH/DESCRIPTION
biostatUZH/NAMESPACE
biostatUZH/R
biostatUZH/R/AUCbinorm.R
biostatUZH/R/Aalpha.R
biostatUZH/R/BlandAltman.R
biostatUZH/R/ConvertWeibull.R
biostatUZH/R/WeibullDiag.R
biostatUZH/R/WeibullReg.R
biostatUZH/R/agresti.R
biostatUZH/R/behrensTest.R
biostatUZH/R/clopperPearson.R
biostatUZH/R/computeICCrater.R
biostatUZH/R/confIntAUC.R
biostatUZH/R/confIntAUCbinorm.R
biostatUZH/R/confIntDiagnostic.R
biostatUZH/R/confIntFisherTrafo.R
biostatUZH/R/confIntICC.R
biostatUZH/R/confIntIndependentDiagnostic.R
biostatUZH/R/confIntIndependentProportion.R
biostatUZH/R/confIntKM_t0.R
biostatUZH/R/confIntKappa.R
biostatUZH/R/confIntMedian.R
biostatUZH/R/confIntPairedDiagnostic.R
biostatUZH/R/confIntPairedProportion.R
biostatUZH/R/confIntProportion.R
biostatUZH/R/confIntRiskDiff.R
biostatUZH/R/confIntRiskRatio.R
biostatUZH/R/faganLine.R
biostatUZH/R/faganPlot.R
biostatUZH/R/formatCI.R
biostatUZH/R/formatPercent.R
biostatUZH/R/formatPval.R
biostatUZH/R/is.wholenumber.R
biostatUZH/R/jeffrey.R
biostatUZH/R/jeffreys.R
biostatUZH/R/lamAlpha.R
biostatUZH/R/logit.R
biostatUZH/R/mantelCoxHR.R
biostatUZH/R/mantelHaenszel.R
biostatUZH/R/plotcorr.R
biostatUZH/R/populationSamplePlot.R
biostatUZH/R/quantileCumInc.R
biostatUZH/R/quantileKM.R
biostatUZH/R/rootFct.R
biostatUZH/R/sampleSizeMcNemar.R
biostatUZH/R/sampleSizePhase2BinaryTest.R
biostatUZH/R/sampleSizePhase2BinaryTestSimulated.R
biostatUZH/R/sampleSizeWilcoxTwoSample.R
biostatUZH/R/standardErrorAUC.R
biostatUZH/R/summaryROC.R
biostatUZH/R/survrep.R
biostatUZH/R/tableRegression.R
biostatUZH/R/wald.R
biostatUZH/R/wilson.R
biostatUZH/build
biostatUZH/build/vignette.rds
biostatUZH/data
biostatUZH/data/fischdaten.rda
biostatUZH/data/larynx.rda
biostatUZH/inst
biostatUZH/inst/NEWS.Rd
biostatUZH/inst/doc
biostatUZH/inst/doc/aucbinormal.Rnw
biostatUZH/inst/doc/aucbinormal.pdf
biostatUZH/inst/doc/weibull.R
biostatUZH/inst/doc/weibull.Rnw
biostatUZH/inst/doc/weibull.pdf
biostatUZH/man
biostatUZH/man/BlandAltman.Rd
biostatUZH/man/ConvertWeibull.Rd
biostatUZH/man/WeibullDiag.Rd
biostatUZH/man/WeibullReg.Rd
biostatUZH/man/biostatUZH-package.Rd
biostatUZH/man/computeICCrater.Rd
biostatUZH/man/confIntAUC.Rd
biostatUZH/man/confIntAUCbinorm.Rd
biostatUZH/man/confIntDiagnostic.Rd
biostatUZH/man/confIntFisherTrafo.Rd
biostatUZH/man/confIntICC.Rd
biostatUZH/man/confIntIndependentDiagnostic.Rd
biostatUZH/man/confIntIndependentProportion.Rd
biostatUZH/man/confIntKM_t0.Rd
biostatUZH/man/confIntKappa.Rd
biostatUZH/man/confIntMedian.Rd
biostatUZH/man/confIntPairedDiagnostic.Rd
biostatUZH/man/confIntPairedProportion.Rd
biostatUZH/man/confIntProportion.Rd
biostatUZH/man/confIntRiskDiff.Rd
biostatUZH/man/confIntRiskRatio.Rd
biostatUZH/man/faganPlot.Rd
biostatUZH/man/fischdaten.Rd
biostatUZH/man/formatCI.Rd
biostatUZH/man/formatPercent.Rd
biostatUZH/man/formatPval.Rd
biostatUZH/man/larynx.Rd
biostatUZH/man/logit.Rd
biostatUZH/man/mantelCoxHR.Rd
biostatUZH/man/mantelHaenszel.Rd
biostatUZH/man/plotcorr.Rd
biostatUZH/man/populationSamplePlot.Rd
biostatUZH/man/quantileCumInc.Rd
biostatUZH/man/quantileKM.Rd
biostatUZH/man/sampleSizeMcNemar.Rd
biostatUZH/man/sampleSizePhase2BinaryTest.Rd
biostatUZH/man/sampleSizeWilcoxTwoSample.Rd
biostatUZH/man/standardErrorAUC.Rd
biostatUZH/man/summaryROC.Rd
biostatUZH/man/survrep.Rd
biostatUZH/man/tableRegression.Rd
biostatUZH/vignettes
biostatUZH/vignettes/aucbinormal.Rnw
biostatUZH/vignettes/aucbinormal.bib
biostatUZH/vignettes/ims.bst
biostatUZH/vignettes/weibull.Rnw
biostatUZH/vignettes/weibull.bib