Package: NNTbiomarker 0.31

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.

Authors:Roger Day

NNTbiomarker_0.31.tar.gz
NNTbiomarker_0.31.zip(r-4.5)NNTbiomarker_0.31.zip(r-4.4)NNTbiomarker_0.31.zip(r-4.3)
NNTbiomarker_0.31.tgz(r-4.5-any)NNTbiomarker_0.31.tgz(r-4.4-any)NNTbiomarker_0.31.tgz(r-4.3-any)
NNTbiomarker_0.31.tar.gz(r-4.5-noble)NNTbiomarker_0.31.tar.gz(r-4.4-noble)
NNTbiomarker_0.31.tgz(r-4.4-emscripten)NNTbiomarker_0.31.tgz(r-4.3-emscripten)
NNTbiomarker.pdf |NNTbiomarker.html
NNTbiomarker/json (API)

# Install 'NNTbiomarker' in R:
install.packages('NNTbiomarker', repos = c('https://professorbeautiful.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/professorbeautiful/nntbiomarkerhome/issues

On CRAN:

Conda:

3.65 score 15 scripts 131 downloads 23 exports 34 dependencies

Last updated 6 years agofrom:dc7702f3e6. Checks:1 OK, 8 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKApr 01 2025
R-4.5-winWARNINGApr 01 2025
R-4.5-macWARNINGApr 01 2025
R-4.5-linuxWARNINGApr 01 2025
R-4.4-winWARNINGApr 01 2025
R-4.4-macWARNINGApr 01 2025
R-4.4-linuxWARNINGApr 01 2025
R-4.3-winWARNINGApr 01 2025
R-4.3-macWARNINGApr 01 2025

Exports:%&%achievable.se.spargminbinom.confintNNT.from.pvNNT.from.sespNNT.to.pvNNT.to.sespNNTintervalsProspectiveNNTintervalsRetrospectivepv.from.NNTpv.from.sesppv.to.NNTpv.to.sespROCplotsrunrunCombinePlotsrunElicitsesp.from.NNTsesp.from.pvsesp.from.pv.feasiblesesp.to.NNTsesp.to.pv

Dependencies:base64encbslibcachemclicommonmarkcrayondigestfastmapfontawesomefsgluehtmltoolshttpuvjquerylibjsonlitelaterlifecyclemagrittrmemoisemimemvbutilspromisesR6rappdirsRcpprlangsassshinysourcetoolsstringistringrvctrswithrxtable

The biomarker crisis

Rendered fromThe_Biomarker_Crisis.Rmdusingknitr::rmarkdownon Apr 01 2025.

Last update: 2015-05-04
Started: 2015-05-04

debugTools

Rendered fromdebugTools.Rmdusingknitr::rmarkdownon Apr 01 2025.

Last update: 2015-05-04
Started: 2015-05-03

Using the NNTbiomarker package

Rendered fromUsing_the_NNTbiomarker_package.Rmdusingknitr::rmarkdownon Apr 01 2025.

Last update: 2015-05-04
Started: 2015-05-03

Readme and manuals

Help Manual

Help pageTopics
Plan a biomarker validation study by focusing on desired clinical actionability.NNTbiomarker-package NNTbiomarker
%&% string concatenation%&%
argmin Argmin function for a vector.argmin
binom.confintbinom.confint
NNT.to.pvNNT.to.pv pv.from.NNT
NNTintervalsRetrospectiveNNTintervalsRetrospective
ROCplotsROCplots
runrun
runCombinePlotsrunCombinePlots
runElicitrunElicit
setVerboseCatOptionifVerboseCat setVerboseCatOption