R Observatory: Metrics for optimalThreshold version 1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

optimalThreshold

1.0Package record

Bayesian Methods for Optimal Threshold Estimation

0packages depend

2.5Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Yoann BlangeroCRAN 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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 2.0 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 41 (1 internal)includes a package overview page
Examples that run: 100%6 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

2.5K

CRAN downloads in the past year

Rank #22,578 · ~7/day · ~212/mo

Releases R versions

Daily download trend is not available in this view yet.

20130 days

58890 days

2.5K1 year

Compare downloads with other packages →

Also on68 r2u1 autocran

How downloads are counted

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Installing optimalThreshold adds 4 packages (2 with compiled code, 187 KB of source tarballs). Heaviest: rjags 75 KB, coda 73 KB, HDInterval 29 KB.

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.

How these are counted

Code & Tests

People & History

People (1)

Yoann Blangero

Author, Maintainer since 1.0 (2020)

Releases (1)

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
1.0Latest
record
2020-01-13 · current release
R
R 3.6.0 released · 2019-04-26

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

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 package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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