R Observatory: Metrics for nlmixr2scm version 0.4.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

nlmixr2scm needs nlmixr2est, which CRAN will archive unless its check problems are fixed by Oct 23.

nlmixr2scm

0.4.1Package record

Stepwise Covariate Modeling for 'nlmixr2' Models

0packages depend

370downloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Justin WilkinsCRAN page ↗GitHub ↗Issues ↗

Stepwise covariate modeling (SCM) for nonlinear mixed-effects models fitted with 'nlmixr2'. Forward inclusion and backward elimination are driven by likelihood-ratio tests, and the covariate terms are generated inside the model body, so continuous covariates are centered and categorical covariates expanded into indicator columns without editing the model by hand. Candidate fits can be cached and resumed, fitted in parallel, and reviewed through per-step and all-candidate summary tables. The approach follows Jonsson and Karlsson (1998) doi:10.1023/A:1011970125687, and the implementation in 'Perl-speaks-NONMEM' described by Lindbom, Ribbing and Jonsson (2004) doi:10.1016/j.cmpb.2003.11.003.

Changes in 0.4.1

runSCM() results now have class "nlmixr2scm", with new summary() and print() methods. summary() reports the options used for the search, a comparison of the base, final forward and final backward models (OFV, dOFV, AIC, BIC, parameter count and SCM covariates), the step and all-candidate tables, and the location of saved models and report files on disk. print() gives a short overview. The result gains baseFit, options and outputDir elements; the existing summaryTable, resFwd and resBck elements are unchanged.
runSCM() gained a retryOnUnderflow argument (default TRUE, appended as the last parameter to preserve positional calls). The retry mechanism treats a forward candidate whose p-value underflows to zero as an unrealistic OFV; for df = 1 that is any OFV drop above about 70, so genuinely strong covariate effects were always retried. Set retryOnUnderflow = FALSE to skip that criterion and the extra fits; the OFV-increase and maxDeltaOFV criteria are unaffected.

Show all changes in 0.4.1Hide the rest of the changes in 0.4.1

Fixed a bug in the forward search mixing two dOFV sign conventions. Since 0.3, dOFV is candidate OFV - reference OFV (negative = improvement), but the profile-on-stall rescue, retry best-attempt tracking and p-value tie-break still assumed the pre-0.3 "positive = improvement" sign. As a result:
every improving forward candidate was treated as stalled and refitted (roughly tripling forward-search run time), and the rescue refit was accepted even when it reached a worse OFV than the original fit;
rescued candidates were reported with a flipped deltObjf sign, so summaryTable and the printed "Ref OFV" column were inconsistent;
when all retries were exhausted, the attempt with the highest OFV was kept instead of the lowest;
p-value underflow ties were broken in favour of the smallest OFV drop instead of the largest.

From NEWS.md in the release

Install

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

install.packages("nlmixr2scm", 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("nlmixr2/nlmixr2scm")

Development version from nlmixr2/nlmixr2scm. 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-nlmixr2scm

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-nlmixr2scm

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

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

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 1.5 min · r-release-macos-x86_64

Status changes

OK13 OK2026-10-03
ERROR5 OK, 1 ERROR2026-09-25

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.4.1

READMEYes · 926 wordsVignettesYes · 1 · staticNEWSYes · 100% structured · mentions 0.4.1Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 3 (1 internal)includes a package overview page
Examples that run: 0%2 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 94%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

Stepwise Covariate Modelling with runSCM() HTML

How these are measured

Downloads

370

CRAN downloads in the past year

Rank #25,202 · ~1/day · ~31/mo

Releases R versions

Daily download trend is not available in this view yet.

37030 days

37090 days

3701 year

Compare downloads with other packages →

Also on5 r2u

How downloads are counted

Repository

nlmixr2/nlmixr2scm ↗Organization: nlmixr2

2Stars

2Forks

2Open issues

1Open PRs

0Releases

63Commits

3Commit identities

License file reads as GPL-3.0 · 63 commits · Last activity 2026-09-29

Responsiveness

How these are sampled

PRs merged (all time): 92%
Median days to close, 50 most recently updated closed issues: 28
Median days to close, 50 most recently updated closed PRs: 4

PRs over time

2026-09-25 · 02026-10-09 · 1

How these are measured

PracticesBeta

4 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/nlmixr2/nlmixr2scm on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

AI coding toolsBeta

This repository shows signs of AI coding tools.

Claude Codefirst seen on or before 2026-04-26
Named in .Rbuildignore: .claude
Named in .gitignore: .claude
Commits: at least 18 crediting it in the message

From outside contributors

Claude Code
Pull requests: 1 from outside contributors, first on 2026-07-24, 1 from forks

Models named in its commits

Claude Sonnet 4.611 commits · May to Jun 2026
Claude Sonnet 56 commits · Aug 2026
Claude Fable 51 commit · Jul 2026

Counts are commits, not lines of code. Commits by a tool's accounts count once across all of its accounts. Commits crediting it are the largest count among its credit lines, a minimum.How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Installing nlmixr2scm adds 73 packages (44 with compiled code, 73 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, ggplot2 6.0 MB.

Depends (1)

R >= 4.1

Imports (11)

checkmate cli data.table lotrinlmenlmixr2est nlmixr2utils rxode2statstoolsutils

LinkingTo (0)

none

Suggests (7)

future knitr nlmixr2data pkgload rmarkdown testthat (>= 3.0.0)withr

Enhances (0)

none

Dependencies facing archival

CRAN will archive these unless their check problems are fixed by the date shown. This package needs each one to install.

nlmixr2estfix by Oct 23

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (7)

Author

Author

Author

Author

Author

Contributor

Releases (2)

Pick two releases to compare their code metrics.

0.4.1Latest
record
2026-09-30 · current release · diff ↗
0.4
record
2026-09-24
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-09-24
Total releases: 2 / 1 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.1
Download size: 115 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("nlmixr2scm")

Format

Wilkins, J., Bartels, C., Denney, B., Fidler, M., Liu, Y., Mann, V., & Sarsani, V. (2026). nlmixr2scm: Stepwise Covariate Modeling for 'nlmixr2' Models (Version 0.4.1) [Computer software]. https://doi.org/10.32614/CRAN.package.nlmixr2scm

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 nlmixr2scm version 0.4.1 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →