R Observatory: Metrics for optimalThreshold version 1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

optimalThreshold

1.0

Bayesian Methods for Optimal Threshold Estimation

0packages depend

2.5Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Yoann BlangeroFirst published 2020-01-131 releasesCRAN page ↗

Functions to estimate the optimal threshold of diagnostic markers or treatment selection markers. The optimal threshold is the marker value that maximizes the utility of the marker based-strategy (for diagnostic or treatment selection) in a given population. The utility function depends on the type of marker (diagnostic or treatment selection), but always takes into account the preferences of the patients or the physician in the decision process. For estimating the optimal threshold, ones must specify the distributions of the marker in different groups (defined according to the type of marker, diagnostic or treatment selection) and provides data to estimate the parameters of these distributions. Ones must also provide some features of the target populations (disease prevalence or treatment efficacies) as well as the preferences of patients or physicians. The functions rely on Bayesian inference which helps producing several indicators derived from the optimal threshold. See Blangero, Y, Rabilloud, M, Ecochard, R, and Subtil, F (2019) doi:10.1177/0962280218821394 for the original article that describes the estimation method for treatment selection markers and Subtil, F, and Rabilloud, M (2019) doi:10.1002/bimj.200900242 for diagnostic markers.

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("optimalThreshold", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-optimalthreshold

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-optimalThreshold

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-optimalThreshold

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 2.1 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

10

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

2.5K

CRAN downloads in the past year

Rank #19,404 · ~7/day · ~207/mo

Releases R versions

Daily download trend is not available in this view yet.

14230 days

58290 days

2.5K1 year

Compare downloads with other packages →

Also on98 r2u5 autocran

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.1.2

Imports (10)

ars rjags HDIntervalmgcvutilscodagrDevicesmethodsstatsgraphics

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

Yoann Blangero

Author, Maintainer

Authors (1)

Yoann Blangero

Author, Maintainer

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.0Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2020-01-13
Total releases: 1 / 6 yrs
License: GPL (>= 2.0)
Minimum R: ≥ 3.1.2
Download size: 59 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("optimalThreshold")

Format

Blangero, Y. (2020). optimalThreshold: Bayesian Methods for Optimal Threshold Estimation (Version 1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.optimalThreshold

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for optimalThreshold version 1.0 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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