R Observatory: Metrics for wnpmle version 0.1.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

wnpmle

0.1.3Package record

Weighted NPMLE for Recurrent Events with a Competing Terminal Event

0packages depend

1.2Kdownloads / year

43.1%test coverage

13/13flavors OK

Overview

About

Maintained by Anna BellachCRAN page ↗GitHub ↗Issues ↗

Provides regression modeling and prediction for the marginal mean of recurrent events in the presence of a competing terminal event using the weighted nonparametric maximum likelihood estimator (wNPMLE) of Bellach and Kosorok (2026) doi:10.48550/arXiv.2605.25934. Two classes of transformation models are implemented: Box-Cox transformation models and logarithmic transformation models. These extend the proportional means model of Ghosh and Lin (2002) doi:10.17615/pt0g-y207 and the transformation model framework of Zeng and Lin (2006) doi:10.1093/biomet/93.3.627. Parameter estimation is performed using automatic differentiation through the Template Model Builder (TMB) framework. Standard errors are computed using sandwich variance estimators that account for estimation of the inverse-probability censoring weights following Bellach, Kosorok, Rüschendorf and Fine (2019) doi:10.1080/01621459.2017.1401540.

Changes in 0.1.3

The censoring-corrected sandwich variance (se = "sandwich_adj", the default) now follows the formula in Bellach and Kosorok (2026, Appendix B.3) exactly. Two coding issues in the correction term were fixed: the correction is now subtracted from the subject-wise scores (which are on the negative log-likelihood scale), and two internal matrices are now filled in the right order. In the settings checked, the effect on the standard errors was in the fourth decimal place or smaller.
Subject-wise scores and the censoring correction are now computed with TMB (new templates in inst/tmb/), which makes se = "sandwich" and se = "sandwich_adj" much faster for larger data sets.
Compiled TMB templates are now kept between R sessions (in tools::R_user_dir("wnpmle", "cache")), so they are compiled only once per installed version instead of once per session. A different folder can be set with options(wnpmle.cache_dir = ...) or the environment variable WNPMLE_CACHE_DIR, e.g. to share one compiled copy between cluster jobs.

Show all changes in 0.1.3Hide the rest of the changes in 0.1.3

The meat of the sandwich is computed with crossprod(), which uses much less memory.
New example data readmission_prep(): hospital readmissions of 403 colorectal cancer patients with death as terminal event (Gonzalez et al., 2005; copy of the readmission data from frailtypack). The vignette now uses these data as its main example, including model selection with plot_loglik(). The bladder quick start now compares the Ghosh-Lin fit with the estimates reported by Ghosh and Lin (2002).
predict() now handles factor covariates (same coding as in the fit), and uses the correct limit log(1 + x) for the Box-Cox model at rho = 0.
summary() now returns an object that is printed once (before, printing the result of summary() showed the coefficients twice).
plot_loglik(): wider default PDF (width, height arguments), titles no longer overlap, and the points rho = 1 and r = 1 are labelled.
Documentation: "sandwich_adj" is listed as the default for se; references now cite the arXiv preprint of Bellach and Kosorok (2026) with its DOI, and DOIs were added to all references where available.

From NEWS.md in the release

Install

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

install.packages("wnpmle", 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("abellach/wnpmle")

Development version from abellach/wnpmle. 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-wnpmle

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-wnpmle

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-wnpmle

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: 12.8 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK7 OK2026-06-19

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.3

READMEYes · 413 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 0.1.3Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 15 (1 internal)includes a package overview page
Examples that run: 40%2 run in a plain check · 3 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 95%
Return-value docs: 100%
Help pages citing references: 27%

Vignettes (1)

Getting Started with wnpmle HTML

How these are measured

Downloads

1.2K

CRAN downloads in the past year

Rank #15,327 · ~3/day · ~97/mo

Releases R versions

Daily download trend is not available in this view yet.

29630 days

80290 days

1.2K1 year

Compare downloads with other packages →

Also on21 r2u2 autocran

How downloads are counted

Repository

abellach/wnpmle ↗Account: abellach

0Stars

0Forks

0Open issues

0Open PRs

1Releases

74Commits

1Commit identities

74 commits · Last activity 2026-10-18

Responsiveness

not measured

Releases over time

2026-06-20 · 12026-07-07 · 1

How these are measured

PracticesBeta

3 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/abellach/wnpmle on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Installing wnpmle adds 3 packages (3 with compiled code, 4.2 MB of source tarballs). Heaviest: Rcpp 1.8 MB, RcppEigen 1.7 MB, TMB 763 KB.

Depends (1)

R >= 4.1.0

Imports (8)

TMBsurvivalmethodsMASSgraphicsgrDevicestoolsutils

LinkingTo (0)

none

Suggests (3)

testthat knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (1)

Anna Bellach

Author, Maintainer since 0.1.2 (2026)

Releases (2)

Pick two releases to compare their code metrics.

0.1.3Latest
record
2026-10-08 · current release · diff ↗ ·
added 1 export
readmission_prep
·
listed once in CRAN's queue
Seen in one reading of CRAN's incoming queue, at 2026-10-08 20:25 UTC, so it stayed less than the time between readings.
0.1.2
record
2026-06-18
R
R 4.6.0 released · 2026-04-24

Across CRAN, the median accepted release of the past year spent 26 hours in the queue, 90% under 11 days.How queue time is measured

Package metadata

First published: 2026-06-18
Total releases: 2 / 1 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.1.0
Download size: 138 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("wnpmle")

Format

Bellach, A. (2026). wnpmle: Weighted NPMLE for Recurrent Events with a Competing Terminal Event (Version 0.1.3) [Computer software]. https://doi.org/10.32614/CRAN.package.wnpmle

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 wnpmle version 0.1.3 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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