R Observatory: Metrics for pmxTools version 1.6

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

pmxTools

1.6Package record

Pharmacometric and Pharmacokinetic Toolkit

0packages dependsuggested by 3

14.4Kdownloads / year

67.0%test coverage

13/13flavors OK

Overview

About

Maintained by Justin WilkinsCRAN page ↗GitHub ↗Website ↗Issues ↗

Pharmacometric tools for common data analytical tasks; closed-form solutions for calculating concentrations at given times after dosing based on compartmental PK models (1-compartment, 2-compartment and 3-compartment, covering infusions, zero- and first-order absorption, and lag times, after single doses and at steady state, per Bertrand & Mentre (2008) https://web.archive.org/web/20231002021707/https://www.facm.ucl.ac.be/cooperation/Vietnam/WBI-Vietnam-October-2011/Modelling/Monolix32_PKPD_library.pdf); parametric simulation from NONMEM-generated parameter estimates and other output; and parsing, tabulating and plotting results generated by Perl-speaks-NONMEM (PsN).

Changes in 1.6

Added cut_quantile(), which creates quantile-based bins for one or more continuous variables, with per-variable control over the number of groups.
Added datamap(), which plots individual dosing and observation records over time.
dgr_table() now takes fields as a named character vector mapping column names to display labels. The separate names argument is deprecated, but unnamed fields with names continues to work.
Added dependencies purrr and tidyr.
Fixed read_nm(), which passed the file extension to xml2::read_xml() as an encoding rather than appending it to the file name, and read the unresolved file name instead of the one located on disk. The directory argument and file names given without the .xml extension were therefore ignored, and macOS reported an Unsupported encoding: .xml warning (#36).
Removed the blanket stats and utils imports, which caused a replacing previous import 'stats::filter' by 'dplyr::filter' warning when the package was loaded (#36).
calc_derived() and the calc_derived_*() functions now return AUCtau and AUCtau_dose_normalized as plain numbers. PKNCA 0.12.1.9000 attaches a method attribute to the AUC it returns, which propagated into the derived-parameter list and broke comparisons against plain numeric values (#37).
Test snapshots are now committed, the CI workflows have been refreshed, and the documentation has been regenerated with roxygen2 8.1.0 (#36).
calc_derived() and the calc_derived_*() functions now work with vector inputs (#29).

From NEWS.md in the release

Install

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

install.packages("pmxTools", 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("kestrel99/pmxTools")

Development version from kestrel99/pmxTools. 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-pmxtools

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-pmxTools

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-pmxTools

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: 3.4 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-08
WARNING12 OK, 1 WARNING2026-06-07
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.6

READMEYes · 113 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 1.6Citation fileNoWebsiteYes · pkgdown

Help pages: 47 (1 internal)includes a package overview page
Examples that run: 41%19 run in a plain check · 27 never run
Exported functions with examples: 100%
Documented parameters: 98%
Return-value docs: 100%
Help pages citing references: 23%

Vignettes (1)

Drawing PK curves with pmxTools HTML

How these are measured

Downloads

14.4K

CRAN downloads in the past year

Rank #3,850 · ~40/day · ~1.2K/mo

Releases R versions

Daily download trend is not available in this view yet.

87630 days

2.4K90 days

14.4K1 year

Compare downloads with other packages →

Also on98 r2u2 autocran108 c2d4u

How downloads are counted

Repository

kestrel99/pmxtools ↗Account: kestrel99

37Stars

11Forks

3Open issues

0Open PRs

3Releases

172Commits

4Commit identities

simulationnonmempharmacokinetics

172 commits · Last activity 2026-10-09 · +2.8% stars, 30d · Default branch at 1.6.0.9000, ahead of CRAN 1.6 (checked 2026-10-18)

Responsiveness

How these are sampled

PRs merged (all time): 88%
Median days to close, 50 most recently updated closed issues: 28
Median days to close, 50 most recently updated closed PRs: 16

Stars over time

2025-03-07 · 312026-09-26 · 37

How these are measured

PracticesBeta

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

Checks run against github.com/kestrel99/pmxtools on 2026-10-18.

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 (3)

pkgdown

GitHub Pages site last deployed 2026-10-09 · The repository has a site deploy workflow

pkgdown site last built 2026-10-09

Coverage (1)

Coverage reporting (Codecov)

Reproducibility and dev environment (1)

data-raw/

Show all practicesHide 2 practices

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 2026-08-27
Pull request it wrote: opened by a project member
Commits: at least 7 crediting it in the message

Models named in its commits

Claude Opus 57 commits · Aug 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 pmxTools adds 42 packages (23 with compiled code, 38 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, patchwork 3.2 MB.

Depends (2)

R >= 4.0.0patchwork

Imports (14)

ggplot2 chron xml2 dplyr purrr tibble tidyr ggdist scalesMASSstringr PKNCA magrittr data.tree

LinkingTo (0)

none

Suggests (4)

testthat vdiffr knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Suggested by 3

Suggests, most downloaded first

rxode2 mrgsolve PKNCA

How these are counted

Code & Tests

People & History

People (9)

Justin Wilkins

Bill Denney

Author · added in 0.1.3

Author

Contributor

Contributor

Contributor

Contributor

Contributor

Contributor · added in 1.2.3

Releases (9)

Pick two releases to compare their code metrics.

1.6Latest
record
2026-10-07 · current release · diff ↗ ·
added 2 exports
cut_quantile, datamap
R
R 4.6.0 released · 2026-04-24
1.5
record
2025-08-25 · diff ↗
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
1.3
record
2023-02-21 · diff ↗ ·
added 9 exports
blq_log_trans, blq_trans, breaks_blq_general, estimate_lloq, ftrans_blq_linear, ftrans_blq_log, itrans_blq_linear, itrans_blq_log, label_blq
R
R 4.2.0 released · 2022-04-22
1.2.3
record
2022-04-06 · diff ↗ ·
added 5 exports
count_na, dgr_table, fmt_signif, gcv, plot_dist
R
R 4.1.0 released · 2021-05-18
1.2.1
record
2020-08-26 · diff ↗ ·
added 5 exports
gcv_convert, get_probinfo, read_nm_all, read_nm_multi_table, read_nm_std_ext
R
R 4.0.0 released · 2020-04-24
1.0
record
2020-01-10 · diff ↗ ·
added 1 export
rnm
0.1.3
record
2019-10-28 · diff ↗ ·
added 8 exports
calc_derived, calc_sd_1cmt, calc_sd_2cmt, calc_sd_3cmt, calc_ss_1cmt, calc_ss_2cmt, calc_ss_3cmt, plot_scm
R
R 3.6.0 released · 2019-04-26
unarchivedReturned to CRAN
2019-03-11

Show 5 earlier eventsHide 5 earlier events

0.1.1
record
2019-03-11 · diff ↗
archivedRemoved from CRAN
2019-01-30
requires archived package 'xpose'
R
R 3.5.0 released · 2018-04-23
0.1.0
record
2018-03-14
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2018-03-14
Total releases: 9 / 8 yrs
License: GPL-2 OSI
Minimum R: ≥ 4.0.0
Download size: 969 KB

Appears in task views

Analysis of Pharmacokinetic Data

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("pmxTools")

Format

Wilkins, J., Denney, B., Gibiansky, L., Hooker, A., Johnson, J., Jonsson, E. N., Karlsson, M. O., Nayak, S., & Schoemaker, R. (2026). pmxTools: Pharmacometric and Pharmacokinetic Toolkit (Version 1.6) [Computer software]. https://doi.org/10.32614/CRAN.package.pmxTools

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 pmxTools version 1.6 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, 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 →