R Observatory: Metrics for pencal version 2.3.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

pencal

2.3.1Package record

Penalized Regression Calibration for the Dynamic Prediction of Survival

0packages depend

4.9Kdownloads / year

–test coverage

12/13flavors OK

Overview

About

Maintained by Mirko SignorelliCRAN page ↗Website ↗

Computes penalized regression calibration (PRC), a statistical method for the dynamic prediction of survival when many longitudinal predictors are available. See Signorelli (2024) doi:10.32614/RJ-2024-014 and Signorelli et al. (2021) doi:10.1002/sim.9178 for details.

Changes in 2.3.1

Released: April 2026
Changed error to warning for check on times argument in performance_prc. Added same warning to performance_pencox for consistency
Added warning in survpred_prclmm and survpred_prcmplmm telling users that they are trying to predict beyond the last observed time. Added extend = T to summary.survfit call within such functions
Minor updates to help pages (mostly formatting)

From inst/NEWS.md in the release

Install

R (CRAN)Ubuntu (r2u)

install.packages("pencal", 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-pencal

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

1ERROR12OK

Check messages

ERRORpackage dependenciesr-oldrel-macos-arm64

Package required but not available: ‘survcomp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

CRAN check page ↗

Slowest check: 3.7 min · r-oldrel-windows-x86_64

Status changes

ERROR12 OK, 1 ERRORNow
ERROR13 OK, 1 ERROR2026-04-15
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.3.1

READMENoVignettesYes · 1 · staticNEWSYes · 67% structured · mentions 2.3.1Citation fileYes · cites a publicationWebsiteYes

Cites an R Journal article

Help pages: 27 (2 internal)
Examples that run: 78%14 run in a plain check · 4 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 98%
Return-value docs: 93%
Help pages citing references: 100%

Vignettes (1)

pencal: an R Package for the Dynamic Prediction of Survival with Many Longitudinal Predictors PDF

How these are measured

Downloads

4.9K

CRAN downloads in the past year

Rank #6,137 · ~13/day · ~410/mo

Releases R versions

Daily download trend is not available in this view yet.

54830 days

1.4K90 days

4.9K1 year

Compare downloads with other packages →

Also on84 r2u

How downloads are counted

Repository

mirkosignorelli/r ↗

Responsiveness

not measured

How these are measured

PracticesBeta

Repository github.com/mirkosignorelli/r is linked, but repository-practices checks have not run for it yet.

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

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Installing pencal adds 101 packages (52 with compiled code, 91 MB of source tarballs). Heaviest: stringi 11 MB, TH.data 8.2 MB, ggplot2 6.0 MB. 1 more not on CRAN is not measured.

Depends (1)

R >= 4.2.0

Imports (16)

doParallel dplyr foreach glmnet lcmm magicMASSMatrixmethodsnlmepurrr riskRegressionstatssurvcompsurvivalsurvivalROC

LinkingTo (0)

none

Suggests (4)

knitr ptmixed rmarkdown survminer

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 (4)

Contributor

Contributor

Contributor · added in 2.0.1

Releases (27)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
2.3.1Latest
record
2026-04-09 · current release · diff ↗
2.3.0
record
2025-06-05 · diff ↗
R
R 4.5.0 released · 2025-04-11
2.2.4
record
2025-03-10 · diff ↗
2.2.3
record
2025-02-07 · diff ↗
2.2.2
record
2024-06-12 · diff ↗
R
R 4.4.0 released · 2024-04-24
2.2.1
record
2024-03-31 · diff ↗ ·
removed 2 exports
getlmm, getmlpmm

added 1 export
survplot_prc
2.1.1
record
2023-10-28 · diff ↗
2.1.0
record
2023-09-16 · diff ↗
2.0.1
record
2023-08-10 · diff ↗ ·
removed 2 exports
pencox_baseline, performance_pencox_baseline

added 2 exports
pencox, performance_pencox
R
R 4.3.0 released · 2023-04-21
1.3.2
record
2022-12-15 · diff ↗
unarchivedReturned to CRAN
2022-12-09
1.3.1
record
2022-12-09 · diff ↗ ·
added 2 exports
getlmm, getmlpmm

Show 22 earlier eventsHide 22 earlier events

archivedRemoved from CRAN
2022-12-05
requires archived package 'survivalROC'
1.2.2
record
2022-07-20 · diff ↗
1.2.1
record
2022-06-22 · diff ↗
unarchivedReturned to CRAN
2022-05-30
1.2.0
record
2022-05-30 · diff ↗
archivedRemoved from CRAN
2022-05-22
check issues were not corrected in time
1.1.1
record
2022-05-03 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.1.0
record
2022-03-29 · diff ↗
1.0.2
record
2022-02-14 · diff ↗
1.0.1
record
2021-12-01 · diff ↗
1.0.0
record
2021-09-03 · diff ↗
0.4.2
record
2021-05-28 · diff ↗ ·
removed 1 export
survpred_prc

added 2 exports
survpred_prclmm, survpred_prcmlpmm
R
R 4.1.0 released · 2021-05-18
0.4.1
record
2021-04-19 · diff ↗ ·
added 2 exports
pencox_baseline, performance_pencox_baseline
0.3.2
record
2021-03-25 · diff ↗
0.3.1
record
2021-03-16 · diff ↗ ·
removed 2 exports
performance_prclmm, survpred_prclmm

added 6 exports
fit_mlpmms, fit_prcmlpmm, performance_prc, simulate_prcmlpmm_data, summarize_mlpmms, survpred_prc
0.2.2
record
2021-01-15 · diff ↗
0.2.1
record
2021-01-06 · diff ↗
0.1.2
record
2020-12-04 · diff ↗ ·
added 1 export
survpred_prclmm
0.1.1
record
2020-11-25
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-11-25
Total releases: 27 / 6 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.2.0
Bundled data: 996 KB / 3 files
Download size: 1.5 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("pencal")

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

It points to 10.32614/rj-2024-014, 10.1002/sim.9178.

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 pencal version 2.3.1 [Data set]. HJJB, LLC. Data release v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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