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.

AuthorRoger Day
Date of publication2015-08-21 07:38:39
MaintainerRoger Day <day01@pitt.edu>
LicenseGPL-3
Version0.29.11

View on CRAN

Files

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

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