R Observatory: Metrics for groupedSurv version 1.0.5.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

groupedSurv

1.0.5.1Package record

Efficient Estimation of Grouped Survival Models Using the Exact Likelihood Function

0packages depend

3.3Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Alexander SibleyCRAN page ↗

These 'Rcpp'-based functions compute the efficient score statistics for grouped time-to-event data (Prentice and Gloeckler, 1978), with the optional inclusion of baseline covariates. Functions for estimating the parameter of interest and nuisance parameters, including baseline hazards, using maximum likelihood are also provided. A parallel set of functions allow for the incorporation of family structure of related individuals (e.g., trios). Note that the current implementation of the frailty model (Ripatti and Palmgren, 2000) is sensitive to departures from model assumptions, and should be considered experimental. For these data, the exact proportional-hazards-model-based likelihood is computed by evaluating multiple variable integration. The integration is accomplished using the 'Cuba' library (Hahn, 2005), and the source files are included in this package. The maximization process is carried out using Brent's algorithm, with the C++ code file from John Burkardt and John Denker (Brent, 2002).

Changes in 1.0.5.1

Fixed version number

From NEWS in the release

Install

R (CRAN)Ubuntu (r2u)

install.packages("groupedSurv", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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-groupedsurv

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

Health

CRAN checks

2NOTE11OK

Check messages

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Alexander Sibley <dcibioinformatics@duke.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jiaxing",
                      family = "Lin",
                      role = "aut"),
               person(given = "Alexander",
                      family = "Sibley",
                      role = c("aut", "cre"),
                      email = "dcibioinformatics@duke.edu"),
               person(given = "Tracy",
                      family = "Truong",
                      role = "aut"),
               person(given = "Kouros",
                      family = "Owzar",
                      role = "aut"),
               person(given = "Zhiguo",
                      family = "Li",
                      role = "aut"),
               person(given = "Layne",
                      family = "Rogers",
                      role = "ctb"),
               person(given = "Yu",
                      family = "Jiang",
                      role = "ctb"),
               person(given = "Janice",
                      family = "McCarthy",
                      role = "ctb"),
               person(given = "Andrew",
                      family = "Allen",
                      role = "ctb"))
as necessary.

CRAN check page ↗

Slowest check: 4.6 min · r-devel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTE2026-10-01
ERROR10 OK, 2 NOTE, 1 ERROR2026-09-24
NOTE11 OK, 2 NOTE2026-09-18
ERROR10 OK, 2 NOTE, 1 ERROR2026-09-15
NOTE11 OK, 2 NOTE2026-09-01

Show 4 earlier changesHide 4 earlier changes

ERROR10 OK, 2 NOTE, 1 ERROR2026-08-25
NOTE10 OK, 4 NOTE2026-04-22
ERROR9 OK, 4 NOTE, 1 ERROR2026-04-18
NOTE10 OK, 4 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.5.1

READMENoVignettesYes · 1 · dynamicNEWSYes · 33% structured · mentions 1.0.5.1Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 11includes a package overview page
Examples that run: 100%10 run in a plain check
Exported functions with examples: 100%
Documented parameters: 98%
Return-value docs: 100%
Help pages citing references: 36%

Vignettes (1)

groupedSurv PDF

How these are measured

Downloads

3.3K

CRAN downloads in the past year

Rank #11,865 · ~9/day · ~277/mo

Releases R versions

Daily download trend is not available in this view yet.

37130 days

91190 days

3.3K1 year

Compare downloads with other packages →

Also on349 r2u

How downloads are counted

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Installing groupedSurv adds 6 packages (2 with compiled code, 18 MB of source tarballs). Heaviest: BH 14 MB, Rcpp 1.8 MB, RcppEigen 1.7 MB. 1 more not on CRAN is not measured.

Depends (0)

none

Imports (5)

Rcpp doParallelparallelforeach qvalue

LinkingTo (3)

Rcpp RcppEigen BH

Suggests (3)

knitr snplist BEDMatrix

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (from the free-text Author field) (9)

Author

Author

Author

Author

Author

Contributor · added in 1.0.5

Yu Jiang

Contributor

Janice McCarthy

Contributor

Andrew Allen

Contributor

Maintainer since 1.0.4.2 (2020), previously Jiaxing Lin (1.0.0 to 1.0.4.1)

Releases (10)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.0.5.1Latest
record
2023-09-28 · current release · diff ↗
R
R 4.3.0 released · 2023-04-21
unarchivedReturned to CRAN
2023-01-25
1.0.5
record
2023-01-25 · diff ↗ ·
removed 1 export
pattern:^[[:alpha:]]+

added 10 exports
alphaEstFam, betaEst, betaEstFam, geneStat, groupedSurv, groupedSurvFam, PvalueFam, thetaEst, varEstFam, varLLFam
archivedRemoved from CRAN
2023-01-24
issues were not corrected in time
1.0.4.3
record
2022-08-05 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.0.4.2
record
2020-11-12 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.0.4.1
record
2020-02-02 · diff ↗
1.0.4
record
2019-12-02 · diff ↗
R
R 3.6.0 released · 2019-04-26

Show 5 earlier eventsHide 5 earlier events

1.0.3
record
2018-06-29 · diff ↗
1.0.2
record
2018-06-23 · diff ↗
1.0.1
record
2018-05-15 · diff ↗
1.0.0
record
2018-05-11
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-05-11
Total releases: 10 / 8 yrs
License: GPL (>= 2) OSI
Download size: 313 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("groupedSurv")

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

It points to 10.1186/s12859-019-2899-x.

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 groupedSurv version 1.0.5.1 [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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