R Observatory: Metrics for nlmixr2est version 7.2.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

CRAN requires the check problems on this package to be fixed before Oct 23 or it will be archived. See the check details

nlmixr2est

7.2.1

Nonlinear Mixed Effects Models in Population PK/PD, Estimation Routines

14packages dependsuggested by 4

23.4Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Matthew FidlerCRAN page ↗GitHub ↗Website ↗

Fit and compare nonlinear mixed-effects models in differential equations with flexible dosing information commonly seen in pharmacokinetics and pharmacodynamics (Almquist, Leander, and Jirstrand 2015 doi:10.1007/s10928-015-9409-1). Differential equation solving is by compiled C code provided in the 'rxode2' package (Wang, Hallow, and James 2015 doi:10.1002/psp4.12052).

Changes in 7.2.1

Bug fixes

The Gill (1983) finite-difference step search now floors its estimate of the error in the objective at gillRtol (max(|f|, 1) * gillRtol), so an objective near 0 no longer shrinks the steps to roundoff. This fixed the nlmixr2GradFun() example erroring with a zero gradient on macOS and linux-arm64. A search that accepts an interval with zero curvature (f locally linear) now keeps its starting interval instead of an infinite one, and a search that ends as "Odd/Linear Grad" reports the central difference at its starting interval rather than at its last, largest trial step.
A test compared the C++ damped-BFGS update bitwise with the former R one; it now allows for rounding differences (failed on CRAN's noLD check).

From NEWS.md in the release

Install

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

install.packages("nlmixr2est", 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/nlmixr2est")

Development version from nlmixr2/nlmixr2est. 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-nlmixr2est

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-nlmixr2est

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: 19.8 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-10-15
ERROR12 OK, 1 ERROR2026-09-15
OK13 OK2026-08-12
ERROR7 OK, 4 NOTE, 2 ERROR2026-07-23
NOTE11 OK, 2 NOTE2026-07-16

Show 4 earlier changesHide 4 earlier changes

OK12 OK2026-04-25
NOTE12 OK, 2 NOTE2026-04-22
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-18
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 7.2.1

README· In the repository, left out of the releaseVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 7.2.1Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 186 (76 internal)
Examples that run: 61%43 run in a plain check · 22 only when donttest examples are enabled (R CMD check --as-cran) · 4 never run · 2 hold no code
Exported functions with examples: 40%
Documented parameters: 97%
Return-value docs: 98%
Help pages citing references: 2%

Vignettes (2)

How these are measured

Downloads

23.4K

CRAN downloads in the past year

Rank #2,417 · ~64/day · ~2K/mo

Releases R versions

Daily download trend is not available in this view yet.

2.9K30 days

6.7K90 days

23.4K1 year

Compare downloads with other packages →

Also on1K r2u21K conda_forge71 c2d4u

How downloads are counted

Repository

nlmixr2/nlmixr2est ↗Organization: nlmixr2

15Stars

9Forks

102Open issues

5Open PRs

31Releases

8,136Commits

21Commit identities

License file reads as GPL-2.0 · 8,136 commits · Last activity 2026-10-15 · 0% stars, 30d · Discussions: 5 posts

Responsiveness

How these are sampled

PRs merged (all time): 92%
Median days to close, 50 most recently updated closed issues: 1
Median days to close, 50 most recently updated closed PRs: 2

Stars over time

2026-07-14 · 142026-08-11 · 15

How these are measured

PracticesBeta

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

Checks run against github.com/nlmixr2/nlmixr2est 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

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-10-10 · The repository has a site deploy workflow

pkgdown site last built 2026-10-10, before release 7.2.1 (2026-10-14)

Coverage (1)

Coverage reporting (Codecov)

Reproducibility and dev environment (1)

data-raw/

Show all practicesHide 3 practices

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (3)

lintrLint workflowAir

Git structural (1)

blame-ignore revs

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

AI coding toolsBeta

This repository shows signs of AI coding tools.

GitHub Copilotfirst seen 2025-12-06
Seen in the repository: .github/copilot-instructions.md
Pull request: opened by its own account
Commits: 25 by its own account · at least 4 crediting it in the message
Claude Codefirst seen 2026-03-27
Seen in the repository: CLAUDE.md
Named in .Rbuildignore: .claude, CLAUDE.md
Named in .gitignore: .claude
Pull request it wrote: opened by a project member
Commits: at least 1,630 crediting it in the message
Antigravityfirst seen 2026-05-13
Named in .Rbuildignore: .antigravity
Named in .gitignore: .antigravity
Augment Codefirst seen 2026-05-30
Named in .Rbuildignore: .augment
Named in .gitignore: .augment
Continuefirst seen 2026-05-30
Named in .Rbuildignore: .continue
Named in .gitignore: .continue
Kilo Codefirst seen 2026-05-30
Named in .Rbuildignore: .kilocode
Named in .gitignore: .kilocode
Kiro, Amazon Q's successorfirst seen 2026-05-30
Named in .Rbuildignore: .kiro
Named in .gitignore: .kiro
Windsurf, now Devin Desktopfirst seen 2026-05-30
Named in .Rbuildignore: .windsurf
Named in .gitignore: .windsurf
Cursorfirst seen 2026-07-01
Named in .gitignore: .cursor

From outside contributors

Claude Code
Pull requests: 36 from outside contributors, first on 2026-06-08, 6 from forks

Models named in its commits

Claude Opus 4.8121 commits · Jun to Jul 2026
Claude Opus 4.730 commits · Apr to Jun 2026
Claude Fable 523 commits · Jun to Jul 2026
Claude Sonnet 520 commits · Jun to Jul 2026
Claude Sonnet 4.66 commits · Mar to Jun 2026

Some of these counts are a minimum, because the search stopped before the oldest commits.

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

47 external dependencies (excludes base and recommended)

Installing nlmixr2est adds 65 packages (41 with compiled code, 68 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, ggplot2 6.0 MB.

Depends (2)

R >= 4.1.0nlmixr2data

Imports (19)

backports checkmate cligraphicsknitr L0Learn lbfgsb3c lotrimethodsminqa n1qn1nlmeRcpp RcppTrust rex rxode2statssymengineutils

LinkingTo (9)

BH n1qn1 lbfgsb3c lotri (>= 0.5.0)Rcpp RcppArmadillo RcppEigen RcppTrust rxode2

Suggests (24)

broom.mixed callr crayon data.table devtools digest dplyr generics nloptr sys testthat tibble withr xgxr sfsmisc minpack.lmMatrixremotes fastGHQuad rmarkdown rlang numDeriv rstan loo

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

14direct

0indirect

Imports 14

Suggested by 4

Show all 18 packagesHide all 18 packages

Depends, Imports or LinkingTo, most downloaded first

nlmixr2extra nlmixr2plot nlmixr2 admixr2 xpose.nlmixr2 babelmixr2 nlmixr2lib nlmixr2rpt shinyMixR nlmixr2targets nlmixr2auto nlmixr2autoinit nlmixr2scm nlmixr2utils

Suggests, most downloaded first

nlmixr2save ggPMX nonmem2rx xpose.xtras

How these are counted

Code & Tests

Datasets

People & History

People (25)

Matthew Fidler

Author, Maintainer since 2.0.6 (2022)

Author

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Author

Contributor

Contributor · added in 6.0.0

Contributor

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Show 7 more contributorsHide 7 contributors

Contributor

Contributor

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Contributor

Contributor

Contributor

Contributor · added in 7.0.2

David Ardia

Copyright holder

Dirk Eddelbuettel

Copyright holder

Katharine Mullen

Copyright holder

Releases (32)

Pick two releases to compare their code metrics.

7.2.1Latest
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2026-10-14 · current release · diff ↗
7.2.0
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2026-10-13 · diff ↗ ·
removed 1 export
.nlmixrNlsFun
7.1.0
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2026-09-20 · diff ↗ ·
removed 1 export
.nlmixr2objectNameAssign

added 17 exports
setCov<-, .nlmixr2estFoceiPtrs, .nlmixr2estLikContribPtrs, .nlmixr2estNlmPtrs, foceiLikIterPrintEnd, foceiLikIterPrintStart, impCovControl, nlmObjectiveSetup, nlmUnscalePar, registerEstInterceptor, removeEstInterceptor, rsControl, saControl, setCovAllMethods, setCovOptions, setCovValue, trustControl
7.0.2
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2026-08-04 · diff ↗ ·
added 47 exports
.absorbIterPrintControl, .loadSymengine, .nlmFamilyControlGeneric, .nlmFamilyFitGeneric, .nlmeGetNonMuRefNames, .nlmixr0preProcessNpMuExpand, .preProcessLinCmtOde, .preProcessVaeNonMuTheta, .preProcessZeroTheta, .sensEtaOrTheta, emviControl, fbviControl, foceiGradPooledDirect_, foceiGradPooledSetupLoad_, foceiLikLoad, foceiLikRun, foceiLikUnload, focepControl, formatMinWidth, iagqControl, ifoceControl, ifoceiControl, ifocepControl, ilaplaceControl, impControl, impmapControl, iterPrintControl, magqControl, mfoceControl, mfoceiControl and 17 more
6.0.1
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2026-06-03 · diff ↗
6.0.0
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2026-05-31 · diff ↗ ·
removed 1 export
%>%

added 9 exports
.nlmFamilyAdjustOutput, .uiApplyMu2hook, aaaCranNlmixrThreads, postFinalObjectHooks, postFinalObjectHooksAdd, postFinalObjectHooksRm, preFinalParTableHooks, preFinalParTableHooksAdd, preFinalParTableHooksRm
R
R 4.6.0 released · 2026-04-24
5.0.2
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2025-11-28 · diff ↗
4.1.1
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2025-10-09 · diff ↗ ·
added 11 exports
.downgradeEtas, .iniS3, nlmixr2iovLogsdCv, nlmixr2iovLogsdSd, nlmixr2iovLogvarCv, nlmixr2iovLogvarSd, nlmixr2iovSdCv, nlmixr2iovSdSd, nlmixr2iovVarCv, nlmixr2iovVarSd, rmEta
4.1.0
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2025-08-29 · diff ↗ ·
added 10 exports
.agq, .collectWarn, .nlmAdjustCov, .nlmixr2FitUpdateParams, agqControl, foControl, foceControl, foiControl, laplaceControl, posthocControl
4.0.2
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2025-07-25 · diff ↗ ·
added 1 export
nlmixr2fix
4.0.1
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2025-07-20 · diff ↗
4.0.0
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2025-07-16 · diff ↗ ·
added 1 export
.nlmixr0preProcessCovariatesPresent
R
R 4.5.0 released · 2025-04-11
3.0.4
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2025-02-19 · diff ↗
3.0.3
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2025-01-18 · diff ↗

Show 21 earlier eventsHide 21 earlier events

3.0.2
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2024-11-23 · diff ↗ ·
added 6 exports
.nlmixrPreprocessLiteralFix, .preProcessDataUi, .preProcessZeroOmega, preProcessHooks, preProcessHooksAdd, preProcessHooksRm
3.0.1
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2024-10-23 · diff ↗
3.0.0
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2024-09-18 · diff ↗ ·
removed 6 exports
.popedFree, .popedSetup, .popedSolveIdME, .popedSolveIdME2, .popedSolveIdN, .popedSolveIdN2

added 4 exports
.addPkgNlmixr2, .deparseDifferent, .deparseFinal, rxUiDeparse
2.2.2
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2024-05-28 · diff ↗ ·
added 6 exports
.popedFree, .popedSetup, .popedSolveIdME, .popedSolveIdME2, .popedSolveIdN, .popedSolveIdN2
R
R 4.4.0 released · 2024-04-24
2.2.1
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2024-01-31 · diff ↗
2.2.0
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2023-12-12 · diff ↗ ·
added 27 exports
.nlmFinalizeList, .nlmFreeEnv, .nlmSetupEnv, .nlmixrNlmFunC, .nlmixrNlminbFunC, .nlmixrNlminbGradC, .nlmixrNlminbHessC, .nlmixrNlsData, .nlmixrNlsFun, .nlmixrNlsFunGrad, .nlmixrNlsFunVal, .nlmixrNlsFunValGrad, .nlmixrOptimFunC, .nlmixrOptimGradC, .uiApplyMu2, .uiFinalizeMu2, as.rxUi, bobyqaControl, lbfgsb3cControl, n1qn1Control, newuoaControl, nlmControl, nlminbControl, nlsControl, optimControl, rxGetDistributionNlsLines, uobyqaControl
2.1.8
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2023-10-08 · diff ↗
2.1.7
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2023-09-19 · diff ↗
2.1.6
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2023-05-26 · diff ↗
2.1.5
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2023-04-22 · diff ↗
R
R 4.3.0 released · 2023-04-21
2.1.4
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2023-04-02 · diff ↗ ·
added 1 export
getBaseSimModelFit
2.1.3
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2022-11-10 · diff ↗
2.1.2
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2022-11-02 · diff ↗
2.1.1
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2022-10-22 · diff ↗
2.1.0
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2022-10-19 · diff ↗ ·
added 3 exports
.nlmixr2objectNameAssign, nmNearPD, nmObjUiSetCompressed
2.0.8
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2022-06-22 · diff ↗
2.0.7
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2022-05-23 · diff ↗ ·
added 1 export
nmObjHandleControlObject
2.0.6
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2022-05-12
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-05-12
Total releases: 32 / 4 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.1.0
Bundled data: 2.3 KB / 1 file
Download size: 3.3 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("nlmixr2est")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

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 nlmixr2est version 7.2.1 [Data set]. HJJB, LLC. Data release v2026-10-17. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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