R Observatory: Metrics for joineRML version 0.4.8

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

joineRML

0.4.8Package record

Joint Modelling of Multivariate Longitudinal Data and Time-to-Event Outcomes

2packages dependsuggested by 2

105.4Kdownloads / year

95.4%test coverage

13/13flavors OK

Overview

About

Maintained by Graeme L. HickeyCRAN page ↗GitHub ↗Website ↗Issues ↗Declared funder: Medical Research Council

Fits the joint model proposed by Henderson and colleagues (2000) doi:10.1093/biostatistics/1.4.465, but extended to the case of multiple continuous longitudinal measures. The time-to-event data is modelled using a Cox proportional hazards regression model with time-varying covariates. The multiple longitudinal outcomes are modelled using a multivariate version of the Laird and Ware linear mixed model. The association is captured by a multivariate latent Gaussian process. The model is estimated using a Monte Carlo Expectation Maximization algorithm. This project was funded by the Medical Research Council (Grant number MR/M013227/1).

Changes in 0.4.8

Bug fixes

bootSE() parallel branch condition was ncores >= 1L (always TRUE), making the serial code path with the progress bar unreachable. Corrected to ncores > 1L.
mjoint() now correctly throttles the number of threads used by RcppArmadillo during the MCEM algorithm via armadillo_throttle_cores() (restored on exit).
simData() now uses drop = FALSE when subsetting the random effects matrices in the Gompertz (model = "intslope") survival-time calculation, preventing a latent dimension-dropping error when only a single subject remains in the branch.
Internal initial-value calculation for the survival sub-model (initsSurv()) no longer relies on a leaked loop variable when indexing timeVar; it now uses the (outcome-invariant) first time variable explicitly in the balanced-data case.

Minor improvements

plot.ranef.mjoint() now uses geom_errorbar(orientation = "y") instead of the deprecated geom_errorbarh(), eliminating ggplot2 4.0 deprecation warnings.
simData() now reports the simulated event rate via message() rather than cat(), so output can be suppressed with suppressMessages().
vcov.mjoint() now warns when it falls back to the Moore-Penrose pseudo-inverse, as the approximate standard errors may be unreliable in that case.
Fixed documentation typos: "left hand-hand side" in mjoint(), "comprised on" in the package description, and "The choice os" in dynSurv() and dynLong().

Dependency changes

Minimum R version raised to 4.1.0.

From NEWS.md in the release

Install

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

install.packages("joineRML", 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("graemeleehickey/joineRML")

Development version from graemeleehickey/joineRML. 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-joinerml

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-joineRML

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-joineRML

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: 9.5 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK12 OK2026-04-25
NOTE12 OK, 2 NOTE2026-04-22
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-18

Show 1 earlier changeHide 1 earlier change

NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.4.8

READMEYes · 700 wordsVignettesYes · 3 · dynamicNEWSYes · 100% structured · mentions 0.4.8Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 32 (2 internal)includes a package overview page
Examples that run: 5%1 run in a plain check · 18 never run
Exported functions with examples: 78%
Documented parameters: 98%
Return-value docs: 78%
Help pages citing references: 81%

Vignettes (3)

How these are measured

Downloads

105.4K

CRAN downloads in the past year

Rank #1,351 · ~289/day · ~8.8K/mo

Releases R versions

Daily download trend is not available in this view yet.

5.9K30 days

20.9K90 days

105.4K1 year

Compare downloads with other packages →

Also on483 r2u7 autocran195 c2d4u

How downloads are counted

Repository

graemeleehickey/joinerml ↗Account: graemeleehickey

34Stars

13Forks

7Open issues

0Open PRs

12Releases

470Commits

6Commit identities

longitudinal-dataregression-modelsmultivariate-longitudinal-datacoxr-packagesurvivaljoint-modelsrcpp

License file reads as GPL-3.0 · 470 commits · Last activity 2026-06-13 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 88%
Median days to close, 50 most recently updated closed issues: 22
Median days to close, 50 most recently updated closed PRs: 28

Stars over time

2025-10-09 · 322026-07-07 · 34

How these are measured

PracticesBeta

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

Checks run against github.com/graemeleehickey/joinerml 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 2026-06-14 · The repository has a site deploy workflow

pkgdown site last built 2026-06-14

Coverage (1)

Coverage reporting (Codecov)

Reproducibility and dev environment (1)

data-raw/

Show all practicesHide 2 practices

CRAN release process (3)

cran-comments.mdrevdep/CRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

20 external dependencies (excludes base and recommended)

Installing joineRML adds 42 packages (23 with compiled code, 32 MB of source tarballs). Heaviest: ggplot2 6.0 MB, lme4 4.1 MB, nloptr 2.1 MB.

Depends (3)

R >= 4.1.0nlmesurvival

Imports (17)

cobs doParallel foreach generics ggplot2graphicslme4MASSMatrixmvtnormparallelrandtoolbox Rcpp RcppArmadillostatstibbleutils

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (7)

dplyr JM joineR knitr pkgdown rmarkdown testthat (>= 3.0.0)

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

0indirect

Imports 2

Suggested by 2

Depends, Imports or LinkingTo, most downloaded first

JMbdirect jmBIG

Suggests, most downloaded first

broom BCClong

How these are counted

Code & Tests

Datasets

People & History

People (8)

Graeme L. Hickey

Maintainer since 0.4.3 (2020), Author

Alessandro Gasparini

Author · added in 0.4.0

Ruwanthi Kolamunnage-Dona

Author

Pete Philipson

Author

Andrea Jorgensen

Contributor

Dimitris Rizopoulos

Contributor, Data contributor · added in 0.2.0

data/renal.rda, R/hessian.R, R/vcov.R

Paula Williamson

Contributor

Medical Research Council

Funder · added in 0.4.1

Grant number: MR/M013227/1

Previously maintained by Pete Philipson (0.4.2) and Graeme L. Hickey (0.1.0 to 0.4.1).

Releases (15)

Pick two releases to compare their code metrics.

0.4.8Latest
record
2026-06-14 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
0.4.7
record
2025-02-04 · diff ↗
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
0.4.6
record
2023-01-20 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
0.4.5
record
2021-01-05 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.4.4
record
2020-04-09 · diff ↗ ·
added 3 exports
augment, glance, tidy
unarchivedReturned to CRAN
2020-02-17
0.4.3
record
2020-02-17 · diff ↗
archivedRemoved from CRAN
2020-01-10
check problems were not corrected in time
R
R 3.6.0 released · 2019-04-26

Show 12 earlier eventsHide 12 earlier events

0.4.2
record
2018-05-29 · diff ↗
R
R 3.5.0 released · 2018-04-23
0.4.1
record
2018-01-21 · diff ↗
0.4.0
record
2017-11-12 · diff ↗
0.3.0
record
2017-07-23 · diff ↗ ·
added 3 exports
baseHaz, dynLong, dynSurv
0.2.2
record
2017-05-01 · diff ↗
0.2.1
record
2017-04-25 · diff ↗
R
R 3.4.0 released · 2017-04-21
0.2.0
record
2017-03-27 · diff ↗ ·
removed 1 export
pattern:^[[:alpha:]]+
0.1.1
record
2016-12-30 · diff ↗
0.1.0
record
2016-12-27
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2016-12-27
Total releases: 15 / 10 yrs
License: GPL-3 | file LICENSE OSI
Minimum R: ≥ 4.1.0
Bundled data: 958 KB / 4 files
Download size: 1.6 MB

Appears in task views

Survival Analysis

Cite

Cite this package

Run in R for the authors' entry:

citation("joineRML")

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

It points to 10.1186/s12874-018-0502-1.

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 joineRML version 0.4.8 [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.

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