R Observatory: Metrics for predictNMB version 0.2.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

predictNMB

0.2.1Package record

Evaluate Clinical Prediction Models by Net Monetary Benefit

0packages depend

3Kdownloads / year

95.4%test coverage

13/13flavors OK

Overview

About

Maintained by Rex ParsonsCRAN page ↗GitHub ↗Website ↗Issues ↗rOpenSci review: issue 566 ↗

Estimates when and where a model-guided treatment strategy may outperform a treat-all or treat-none approach by Monte Carlo simulation and evaluation of the Net Monetary Benefit. Details can be viewed in Parsons et al. (2023) doi:10.21105/joss.05328.

Changes in 0.2.1

ce_plot()
add wtp_linetype argument to ce_plot() (and default to "dashed") to

given control to user and differentiate C-E plane from main axes.

add shape argument which maps to the shape aesthetic in geom_point().

User can also specify shape = "cost-effective" to map it to whether that

point is under the WTP/cost-effectiveness plane, or shape = "method" to map

it to the cutpoint method.

add add_prop_ce argument. If TRUE, the % of points for that

cutpoint method is concatenated to the the method name in the figure legend.

outcome costs were incorrectly excluded from the costs used in the

incremental cost axis before. These are now added to the calculations in

evaluate_cutpoint_cost() and reflected in the ce_plot(). Before, the

Show all changes in 0.2.1Hide the rest of the changes in 0.2.1

incremental costs in ce_plot() were treatment costs alone.

From NEWS.md in the release

Install

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

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

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

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("ropensci/predictNMB")

Development version from ropensci/predictNMB. Installs pak first if it is not already available.

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-predictnmb

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-predictNMB

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-predictNMB

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: 8.1 min · r-release-macos-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 0.2.1

READMEYes · 854 wordsVignettesYes · 4 · dynamicNEWSYes · 100% structured · mentions 0.2.1Citation fileYes · cites a publicationWebsiteYes · pkgdown

Cites a JOSS paper

Help pages: 22 (3 internal)includes a package overview page
Examples that run: 37%7 run in a plain check · 12 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 86%
Documented parameters: 100%
Return-value docs: 92%
Help pages citing references: 0%

Vignettes (4)

predictNMB HTML
creating-nmb-functions HTML
detailed-example HTML
summarising-results-with-predictNMB HTML

How these are measured

Downloads

3K

CRAN downloads in the past year

Rank #17,364 · ~8/day · ~251/mo

Releases R versions

Daily download trend is not available in this view yet.

29430 days

74090 days

3K1 year

Compare downloads with other packages →

Also on69 r2u4 autocran678 conda_forge

How downloads are counted

Repository

ropensci/predictnmb ↗Organization: ropensci

10Stars

2Forks

0Open issues

0Open PRs

3Releases

313Commits

6Commit identities

License file reads as GPL-3.0 · 313 commits · Last activity 2024-07-21 · 0% stars, 30d · Default branch at 0.2.1.9000, ahead of CRAN 0.2.1 (checked 2026-10-21)

Responsiveness

How these are sampled

PRs merged (all time): 80%
Median days to close, 50 most recently updated closed issues: 9
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2024-06-09 · 102026-07-07 · 10

How these are measured

PracticesBeta

12 development-tooling and community-health practices detected across 7 families in the upstream repository

Checks run against github.com/ropensci/predictnmb on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Governance and community (2)

Code of conduct (inherited from ropensci)Contributing guide

Docs source (3)

README.Rmdpkgdown

GitHub Pages site last deployed 2023-03-29

Coverage (1)

Coverage reporting (Codecov)

Show all practicesHide 3 practices

CRAN release process (1)

cran-comments.md

Research and citation (2)

CITATION.cffcodemeta.json

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

19 external dependencies (excludes base and recommended)

Installing predictNMB adds 36 packages (17 with compiled code, 33 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, cutpointr 2.2 MB.

Depends (1)

R >= 3.5.0

Imports (11)

assertthat cutpointr dplyr ggplot2 magrittr pmsampsize rlang scalesstatstibble tidyr

LinkingTo (0)

none

Suggests (10)

spelling covr flextable knitrparallelpbapply rmarkdown testthat vdiffr withr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (7)

Rex Parsons

Author, Maintainer since 0.1.0 (2023)

Author

Author

Contributor

Contributor

Reviewer

Tinula Kariyawasam reviewed predictNMB for rOpenSci, see <https://github.com/ropensci/software-review/issues/566>.

Emi Tanaka

Reviewer

Emi Tanaka reviewed predictNMB for rOpenSci, see <https://github.com/ropensci/software-review/issues/566>.

Releases (3)

Pick two releases to compare their code metrics.

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
0.2.1Latest
record
2023-06-03 · current release · diff ↗
0.2.0
record
2023-05-19 · diff ↗ ·
removed 1 export
evaluate_cutpoint

added 4 exports
ce_plot, evaluate_cutpoint_cost, evaluate_cutpoint_nmb, evaluate_cutpoint_qalys
R
R 4.3.0 released · 2023-04-21
0.1.0
record
2023-04-12
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2023-04-12
Total releases: 3 / 3 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.5.0
Download size: 4.7 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("predictNMB")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.21105/joss.05328.

The repository also keeps a CITATION.cff.

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 predictNMB version 0.2.1 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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