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Changelog

Source: NEWS.md

joineR 1.2.9

Bug fixes

  • emUpdate() and emUpdateCR() now issue a warning() on non-convergence instead of silently calling print(), making it possible for callers to catch non-convergence programmatically.

  • survst() no longer unconditionally forces the first subject’s censoring indicator to 1 before passing data to coxph(). A proper stop() is raised if no events are observed. The rs index vector is now computed correctly via findInterval(), clamping subjects who precede the first event time to risk set 1 rather than producing NA.

  • survst() and survstCR() now correctly index loglik[2] (the fitted model log-likelihood) rather than storing the full length-2 vector in $log.like.

  • Bootstrap confidence intervals in jointSE() now use quantile() instead of a manual sorted-index lookup, fixing an off-by-one error for small n.boot values.

Improvements

  • joint() and jointSE() arguments gpt, lgpt, max.it, and tol now have explicit default values in the function signatures, replacing the previous missing() pattern. Defaults are visible in auto-complete and ?joint.

  • jointSE() output now includes a p-value column containing two-sided Wald p-values for all fixed-effect and association parameters. Variance component rows (U_*, Residual) return NA as Wald tests are not appropriate for positive-constrained parameters. Closes #58.

  • jointSE() confidence intervals are now computed for all values of n.boot. Previously, runs with fewer than 100 bootstrap samples silently returned 0 for both CI bounds; now the empirical percentile CIs are always returned and a warning() is issued when n.boot < 100 to alert the user that the intervals may be unreliable.

  • tidy() and glance() methods are now available for joint objects, providing a tidy broom-style interface. tidy() returns a data frame of parameter estimates (one row per term) and optionally accepts a jointSE() result to add standard errors, Wald statistics, p-values, and confidence intervals. glance() returns a single-row summary of model-level statistics including log-likelihood, AIC, BIC, number of observations, number of subjects, convergence status, and EM iteration count. Closes #59.

  • simjoint() no longer prints a progress line via cat() from the internal simdat() function. It now emits a message() at the simjoint() level, which can be suppressed with suppressMessages().

  • survival has been moved from Depends to Imports. Surv is re-exported so existing user code does not require changes.

  • Test coverage improved from 89% to 93%.

  • Code formatted with air.

Housekeeping

  • Added a pkgdown site with Bootstrap 5, full dark mode (light switch), and a structured reference index. A pkgdown.yaml GitHub Actions workflow builds and deploys the site to GitHub Pages on push and release.

  • Added a render-readme.yaml GitHub Actions workflow that automatically re-renders README.md from README.Rmd when README.Rmd is changed.

  • Updated R-CMD-check.yaml and test-coverage.yaml GitHub Actions workflows to use actions/checkout@v6, codecov-action@v7, and upload-artifact@v7.

  • DESCRIPTION URL field now includes the pkgdown site, CRAN page, and GitHub repository.

  • README badges updated: removed defunct AppVeyor and Depsy badges; added pkgdown deployment badge and lifecycle (stable) badge.

  • Updated README with new MRC logo and fixed badges.

  • Fixed deprecated documentation for joineR-package.R.

  • Added reverse dependency checks.

  • Removed dead commented-out code blocks in survst.R and prepSurvData.R.

  • Removed no-op fd <- fd / sd <- sd assignments in emUpdate().

  • The internal helper sortJointData() (previously sort.dat() defined inside joint() on every call) is now a file-level internal function, avoiding a spurious S3 method consistency note in R CMD check.

  • Fixed copy-paste error in @param ylab documentation for jointplot() (was labelled “x-axis”).

  • Renamed variable t to obs_time in jointplot() to avoid shadowing base::t().

  • Fixed typo “am Expectation Maximization” → “an” in DESCRIPTION.

  • Updated test suite: removed deprecated context() calls and replaced expect_is() with expect_s3_class() throughout. Fixed typo “seperate” → “separate” in one test name. Enabled testthat edition 3.

joineR 1.2.8

CRAN release: 2023-01-22

Bugs

  • Fixes CRAN CMD check when run using ATLAS (alternative BLAS/LAPACK implementation). Issue was in the tests.

joineR 1.2.7

CRAN release: 2023-01-18

Bugs

  • Fixed bug for case when all subjects experience events.

  • Change to survival::basehaz arguments.

  • Fixed a NOTE on checking for class type.s

Housekeeping

  • Edited NEWS v1.1 entry.

joineR 1.2.6

CRAN release: 2021-06-01

Bugs

  • Fixed bug for covariates in competing risks models.

Housekeeping

  • Changed package maintainer to Graeme Hickey.

joineR 1.2.5

CRAN release: 2020-02-08

Bugs

  • Fixed error when ID column was not the first column in the dataset.

joineR 1.2.4

CRAN release: 2018-05-17

Housekeeping

  • Added Zenodo badge to README.

  • Added further ORCID IDs for authors.

  • Changed package maintainer to Pete Philipson.

joineR 1.2.3

CRAN release: 2018-02-06

Bugs

  • Fixed errors when subjects IDs were character format.

Housekeeping

  • Added ORCID IDs for authors.

  • Added Depsy badge to README.

joineR 1.2.2

CRAN release: 2017-09-14

Minor update

  • Modified the control parameters for the call to nlme::lme() that is used to generate initial parameter estimates. In some bootstrap settings, this was throwing an error, leading to the entire bootstrap run to cease.

Housekeeping

  • Added hex sticker badge.

joineR 1.2.1

CRAN release: 2017-07-24

Minor updates

  • Added Rd file for joint.object to describe what is contained in an object of class joint.

  • Added the ubiquitous aids dataset for teaching purposes.

Bugs

Fixed an error in the liver dataset.

Maintenance

  • Updated the documentation for the datasets.

  • Added ByteCompile: true to the DESCRIPTION.

joineR 1.2.0

CRAN release: 2017-05-19

Major updates

  • joint now allows for competing risks data (2 failure types) as per the model developed by Williamson et al. (2008). Other functions have been upgraded to handle the competing risks data.

  • A second vignette for the competing risks model is available.

Minor updates

  • R version 3.4.0 deprecated the recycling of 1x1 matrices, and led to warnings being thrown. This is now fixed.

Maintenance

  • General code and documentation tidy-up.

  • New unit tests added to increase code coverage.

joineR 1.1.0

CRAN release: 2017-02-02

Minor updates

  • Add simjoint function to simulate data from joint models with several types of association structures.

  • Removed jlike function and integrated likelihood calculation directly into em.alg function.

  • Minor bug fixes to the joint and em.alg functions.

Maintenance

  • Added a NEWS.md file to track changes to the package.

  • Added some unit tests + code coverage monitoring integration.

  • Converted Rd files to roxygen.

  • Converted Sweave vignette to rmarkdown.

  • Updates to vignette and documentation.

  • Minor updates to DESCRIPTION and NAMESPACE to pass R CMD checks, provide additional information, and removed dependency of boot and gdata packages.

  • Added a README.Rmd.

  • Added project to GitHub with integrated Travis CI and appveyor.

joineR 1.1

  • First version of software with subsequent minor patches. No NEWS file was maintained prior to version 1.1.