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 |

**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

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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