# 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.

- Author
- Roger Day
- Date of publication
- 2015-08-21 07:38:39
- Maintainer
- Roger Day <day01@pitt.edu>
- License
- GPL-3
- Version
- 0.29.11

## Man pages

- achievable.se.sp
- achievable.se.sp(): target sensitivity and specificity for a...
- argmin
- argmin Argmin function for a vector.
- binom.confint
- binom.confint
- grapes-and-grapes
- %&% string concatenation
- NNTbiomarker-package
- Plan a biomarker validation study by focusing on desired...
- NNT.from.pv
- NNT.from.pv
- NNT.from.sesp
- NNT.from.sesp
- NNTintervalsProspective
- NNTintervalsProspective
- NNTintervalsRetrospective
- NNTintervalsRetrospective
- NNT.to.pv
- NNT.to.pv
- NNT.to.sesp
- NNT.to.sesp
- pv.from.sesp
- pv.from.sesp
- ROCplots
- ROCplots
- run
- run
- runCombinePlots
- runCombinePlots
- runElicit
- runElicit
- sesp.from.pv
- sesp.from.pv
- sesp.from.pv.feasible
- sesp.from.pv.feasible
- setVerboseCatOption
- setVerboseCatOption

## Files in this package

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 |