R Observatory: Metrics for nlmixr2plot version 5.2.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

CRAN requires the check problems on this package to be fixed before Oct 22 or it will be archived. See the check details

nlmixr2plot needs nlmixr2est, which CRAN will archive unless its check problems are fixed by Oct 23.

nlmixr2plot

5.2.1

Nonlinear Mixed Effects Models in Population PK/PD, Plot Functions

2packages dependsuggested by 1

18.5Kdownloads / year

93.8%test coverage

13/13flavors OK

Overview

About

Maintained by Matthew FidlerCRAN page ↗GitHub ↗Website ↗Issues ↗

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). This package is for 'ggplot2' plotting methods for 'nlmixr2' objects.

Changes in 5.2.1

The model-diagram test of a long product no longer checks how long modelGraph() takes, and is skipped on CRAN. The timing check failed at random on loaded CRAN machines (48 s against a 30 s limit).
plot() no longer fails on a fit with more than one variance level. A model with between-occasion variability reports omega as a list holding one matrix per level rather than as a single matrix, and the between-subject-variability guard tested nrow(omega) > 0, which is NA for a list, so plot() stopped with "missing value where TRUE/FALSE needed" before drawing anything. The guard now asks whether the fit reports any between-subject eta, which is what the BSV plots need and does not depend on the number of variance levels.
The between-subject-variability plots now take their etas from the subject-level omega block (dropping any fixed at zero) rather than from every column ranef() returns, so a mixture fit no longer gets a QQ plot of its mixnum subpopulation labels or a spurious correlation panel, and an occasion-only fit is correctly treated as having no BSV.

Show all changes in 5.2.1Hide the rest of the changes in 5.2.1

plot() of a fit, vpcPlot() and plot() of an augPred() object now emit one fitResult event on the rxode2 event bus (when rxode2 has one) with the plots they made, so loggers such as nlmixr2log can store them with the fit. Simulations done inside vpcPlot() emit nothing. Without a listener nothing changes.
modelDiagram(..., engine = "ggplot2", labels = TRUE) now draws the arrow labels on a white background, so the arrow no longer runs through the label text.
plot() of an augPred() object no longer titles a single-endpoint figure with the last endpoint of an earlier multiple-endpoint plot.
The figures from plot() of a fit, traceplot() and plot() of an augPred() object no longer carry the fit, the full plotting data or the other figures in their environments, so saving them (with saveRDS() or as a 'targets' target) is far smaller. Before, each figure's aes(), facet and layer environments held the frame it was built in, and with it the whole fit or every figure built before it (the trace plot and the individual plots could each serialize to hundreds of MB). Each figure now stores its data once, in $data; the plots look the same.
The VPC figures from vpcPlot(), vpcPlotTad(), vpcCens() and vpcCensTad() no longer carry the VPC simulation, and with method = "tidyvpc" no longer carry the fit either. 'vpc' built its figure in about a dozen frames that each held the whole simulation, and the tidyvpc figure kept the frame of vpcPlot() itself, so saving a VPC of a 1500-observation fit with 50 simulations wrote 97 MB ('vpc') or up to 34 MB ('tidyvpc'). The 'vpc' figure now takes about 3 MB, and neither grows with the number of simulations. The figures look the same.
The engine = "ggplot2" diagram from modelDiagram() no longer keeps its layer data and a second copy of itself in its environments, and adds its scales last; together about 1 MB (up to 3.4 MB for large models) less for each saved diagram. The diagrams look the same.
The bootplot figure that plot() includes for a fit with bootstrap results no longer carries the frame of plot(), with the plotting data and every other figure: for theo_sd with 3 bootstrap samples it went from 152 MB to 6 MB saved. It still carries the fit, which nlmixr2extra::bootplot() keeps in its own frame.

From NEWS.md in the release

Install

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

install.packages("nlmixr2plot", 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/nlmixr2plot")

Development version from nlmixr2/nlmixr2plot. 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-nlmixr2plot

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-nlmixr2plot

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: 13.3 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-10-14
ERROR12 OK, 1 ERROR2026-10-13
OK13 OK2026-10-08
ERROR12 OK, 1 ERROR2026-09-15
OK13 OK2026-08-20

Show 6 earlier changesHide 6 earlier changes

ERROR12 OK, 1 ERROR2026-08-18
OK13 OK2026-08-12
ERROR11 OK, 2 ERROR2026-07-23
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 5.2.1

READMEYes · 303 wordsVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 5.2.1Citation fileNoWebsiteYes · pkgdown

Help pages: 7 (1 internal)
Examples that run: 0%6 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 80%
Documented parameters: 100%
Return-value docs: 80%
Help pages citing references: 0%

Vignettes (2)

Automatic model diagrams HTML
nlmixr2plot events for loggers HTML

How these are measured

Downloads

18.5K

CRAN downloads in the past year

Rank #2,983 · ~51/day · ~1.5K/mo

Releases R versions

Daily download trend is not available in this view yet.

2K30 days

4.5K90 days

18.5K1 year

Compare downloads with other packages →

Also on561 r2u19.6K conda_forge69 c2d4u

How downloads are counted

Repository

nlmixr2/nlmixr2plot ↗Organization: nlmixr2

3Stars

0Forks

1Open issues

0Open PRs

12Releases

353Commits

3Commit identities

License file reads as GPL-3.0 · 353 commits · Last activity 2026-10-16

Responsiveness

How these are sampled

PRs merged (all time): 96%
Median days to close, 50 most recently updated closed issues: 22
Median days to close, 50 most recently updated closed PRs: 1

Releases over time

2026-07-14 · 92026-10-17 · 12

How these are measured

PracticesBeta

13 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/nlmixr2/nlmixr2plot 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 2026-10-08 · The repository has a site deploy workflow

pkgdown site last built 2026-10-08, before release 5.2.1 (2026-10-16)

Coverage (1)

Coverage reporting (Codecov)

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Show all practicesHide 2 practices

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 2026-02-27
Pull request: opened by its own account
Commits: 2 by its own account
Claude Codefirst seen 2026-05-27
Pull request it wrote: opened by a project member
Commits: at least 33 crediting it in the message

Models named in its commits

Claude Opus 4.811 commits · Jun to Jul 2026
Claude Opus 5.511 commits · Sep 2026
Claude Opus 59 commits · Jul to Aug 2026
Claude Fable 51 commit · Jul 2026
Claude Opus 4.71 commit · May 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

18 external dependencies (excludes base and recommended)

Installing nlmixr2plot adds 136 packages (87 with compiled code, 110 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, ggplot2 6.0 MB.

Depends (1)

R >= 4.3.0

Imports (10)

ggforce ggplot2 ggtibble nlmixr2est nlmixr2extra rxode2statstidyrutilsxgxr

LinkingTo (0)

none

Suggests (10)

DiagrammeR knitr rmarkdown testthat data.table dplyr withr vpc tidyvpc nlmixr2data

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

2direct

2indirect

Imports 2

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

nlmixr2 babelmixr2

Suggests, most downloaded first

shinyMixR

How these are counted

Code & Tests

People & History

People (4)

Matthew Fidler

Author, Maintainer since 2.0.6 (2022)

Vipul Mann

Author

Wenping Wang

Author

Bill Denney

Contributor

Releases (14)

Pick two releases to compare their code metrics.

5.2.1Latest
record
2026-10-16 · current release · diff ↗ ·
listed once in CRAN's queue
Seen in one reading of CRAN's incoming queue, at 2026-10-16 17:07 UTC, so it stayed less than the time between readings. It was also listed earlier, first on 2026-10-15 12:21 UTC, and left the queue for more than a day before this stay.
5.2.0
record
2026-08-05 · diff ↗ ·
added 2 exports
modelDiagram, modelGraph
5.1.0
record
2026-08-05 · diff ↗
5.0.2
record
2026-06-11 · diff ↗
R
R 4.6.0 released · 2026-04-24
5.0.1
record
2026-02-28 · diff ↗
5.0.0
record
2025-11-29 · diff ↗
3.0.3
record
2025-08-23 · diff ↗
3.0.2
record
2025-06-25 · diff ↗
R
R 4.5.0 released · 2025-04-11
3.0.1
record
2025-02-14 · diff ↗
3.0.0
record
2024-09-18 · diff ↗
2.0.9
record
2024-05-29 · diff ↗
R
R 4.4.0 released · 2024-04-24
2.0.8
record
2024-01-31 · diff ↗
R
R 4.3.0 released · 2023-04-21

Show 3 earlier eventsHide 3 earlier events

2.0.7
record
2022-10-20 · diff ↗ ·
added 3 exports
vpcCens, vpcCensTad, vpcPlotTad
2.0.6
record
2022-05-23
R
R 4.2.0 released · 2022-04-22

Across CRAN, the median accepted release of the past year spent 19 hours in the queue, 90% under 11 days.How queue time is measured

Package metadata

First published: 2022-05-23
Total releases: 14 / 4 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.3.0
Download size: 1.7 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("nlmixr2plot")

Format

Fidler, M., Denney, B., Mann, V., & Wang, W. (2026). nlmixr2plot: Nonlinear Mixed Effects Models in Population PK/PD, Plot Functions (Version 5.2.1) [Computer software]. https://doi.org/10.32614/CRAN.package.nlmixr2plot

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 nlmixr2plot version 5.2.1 [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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