NNTbiomarker: Calculate Design Parameters for Biomarker Validation Studies

Helps a clinical trial team discuss the clinical goals of a well-defined biomarker with a diagnostic, staging, prognostic, or predictive purpose. From this discussion will come a statistical plan for a (non-randomized) validation trial. Both prospective and retrospective trials are supported. In a specific focused discussion, investigators should determine the range of "discomfort" for the NNT, number needed to treat. The meaning of the discomfort range, [NNTlower, NNTupper], is that within this range most physicians would feel discomfort either in treating or withholding treatment. A pair of NNT values bracketing that range, NNTpos and NNTneg, become the targets of the study's design. If the trial can demonstrate that a positive biomarker test yields an NNT less than NNTlower, and that a negative biomarker test yields an NNT less than NNTlower, then the biomarker may be useful for patients. A highlight of the package is visualization of a "contra-Bayes" theorem, which produces criteria for retrospective case-controls studies.

Install the latest version of this package by entering the following in R:
install.packages("NNTbiomarker")
AuthorRoger Day
Date of publication2015-08-21 07:38:39
MaintainerRoger Day <day01@pitt.edu>
LicenseGPL-3
Version0.29.11

View on CRAN

Files

inst
inst/ToDo.txt
inst/shinyCombinePlots
inst/shinyCombinePlots/ui.R inst/shinyCombinePlots/server.R inst/shinyCombinePlots/drawIcon.R
inst/shinyCombinePlots/www
inst/shinyCombinePlots/www/Using_the_NNTbiomarker_package.htm
inst/shinyCombinePlots/debugTools.R inst/shinyCombinePlots/contraBayesPlot.R inst/shinyCombinePlots/conveniences.R inst/shinyCombinePlots/stepsTableInitial.R inst/shinyCombinePlots/coordstring.R inst/shinyCombinePlots/plotDiscomfort.R inst/shinyCombinePlots/global.R
inst/shinyCombinePlots/shinyapps
inst/shinyCombinePlots/shinyapps/trials
inst/shinyCombinePlots/shinyapps/trials/shinyCombinePlots.dcf
inst/Janes-fit.R inst/pageOpenTest.R inst/debugTools.R
inst/NOTUSED
inst/NOTUSED/smartBoxPlot.R inst/NOTUSED/rTrapez.R inst/NOTUSED/RSdump.R
inst/shinyROC
inst/shinyROC/app.R
inst/plot_digitizer_Figure_7_example.xml
inst/temp
inst/temp/Rmarkdown-colourPicker.Rmd
inst/ROCplots-Using-ggplot2.R
inst/rasterImages
inst/rasterImages/using-colorized-png-pictograms-in-r-base-plots.R inst/rasterImages/geom-bar-pictograms-how-to.R inst/rasterImages/easy-pictograms-using-r.R inst/testing_ggplot_guides.R
inst/shinyElicit
inst/shinyElicit/ui.R inst/shinyElicit/server.R
inst/shinyElicit/www
inst/shinyElicit/www/Steps.html
inst/shinyElicit/www/Steps.Rmd
inst/shinyElicit/www/Using_the_NNTbiomarker_package.htm
inst/shinyElicit/Steps-example.docx
inst/shinyElicit/report.R inst/shinyElicit/debugTools.R
inst/shinyElicit/Steps.md
inst/shinyElicit/Steps-example.Rmd
inst/shinyElicit/contraBayesPlot.R inst/shinyElicit/conveniences.R
inst/shinyElicit/rsconnect
inst/shinyElicit/rsconnect/shinyapps.io
inst/shinyElicit/rsconnect/shinyapps.io/trials
inst/shinyElicit/rsconnect/shinyapps.io/trials/shinyElicit.dcf
inst/shinyElicit/stepsTableInitial.R inst/shinyElicit/plotDiscomfort.R inst/shinyElicit/global.R
inst/shinyElicit/shinyapps
inst/shinyElicit/shinyapps/trials
inst/shinyElicit/shinyapps/trials/shinyElicit.dcf
inst/doc
inst/doc/Using_the_NNTbiomarker_package.Rmd
inst/doc/debugTools.html
inst/doc/The_Biomarker_Crisis.html
inst/doc/The_Biomarker_Crisis.Rmd
inst/doc/Using_the_NNTbiomarker_package.html
inst/doc/debugTools.Rmd
inst/shinyAE
inst/shinyAE/ui.R inst/shinyAE/server.R
inst/shinyAE/inst
inst/shinyAE/inst/Paik2006-10yearDFS.TAM.xml
inst/shinyAE/inst/Paik2006-10yearDFS.TAM+CHEMO.xml
inst/shinyAE/AEplot.R inst/shinyAE/skislope.R inst/shinyAE/Paik-fit.R inst/shinyAE/global.R
inst/shinyAE/shinyapps
inst/shinyAE/shinyapps/trials
inst/shinyAE/shinyapps/trials/shinyAE.dcf
inst/oncotypeDX-risk-functions.jpg.xml
inst/human.html.R
NAMESPACE
R
R/aaa.R R/argmin.R R/ROCplots.R R/achievable.se.sp.R R/sesp-pv-NNT.R R/binom.confint.R R/ifVerboseCat.R R/run.R R/NNTintervals.R R/zzz.R
vignettes
vignettes/Using_the_NNTbiomarker_package.Rmd
vignettes/Screenshot-stepsTableInitial.png
vignettes/The_Biomarker_Crisis.Rmd
vignettes/Screenshot-debugTools-closed.png
vignettes/Screenshot-debugTools-open.png
vignettes/debugTools.Rmd
vignettes/Screenshot-debugTools-closed.ezdraw
MD5
build
build/vignette.rds
DESCRIPTION
man
man/run.Rd man/NNTintervalsRetrospective.Rd man/sesp.from.pv.feasible.Rd man/runCombinePlots.Rd man/pv.from.sesp.Rd man/sesp.from.pv.Rd man/NNT.to.pv.Rd man/binom.confint.Rd man/NNT.from.pv.Rd man/NNT.from.sesp.Rd man/achievable.se.sp.Rd man/setVerboseCatOption.Rd man/NNT.to.sesp.Rd man/ROCplots.Rd man/NNTintervalsProspective.Rd man/runElicit.Rd man/NNTbiomarker-package.Rd man/argmin.Rd man/grapes-and-grapes.Rd

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