NNTbiomarker: Calculate Design Parameters for Biomarker Validation Studies

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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

View on CRAN

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