R Observatory: Metrics for popEpi version 0.5.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

popEpi

0.5.0Package record

Functions for Epidemiological Analysis using Population Data

1packages dependsuggested by 1

44.2Kdownloads / year

62.3%test coverage

8/13flavors OK

Overview

About

Maintained by Joonas MiettinenCRAN page ↗GitHub ↗Issues ↗

Enables computation of epidemiological statistics, including those where counts or mortality rates of the reference population are used. Currently supported: excess hazard models (Dickman, Sloggett, Hills, and Hakulinen (2012) doi:10.1002/sim.1597), rates, mean survival times, relative/net survival (in particular the Ederer II (Ederer and Heise (1959)) and Pohar Perme (Pohar Perme, Stare, and Esteve (2012) doi:10.1111/j.1541-0420.2011.01640.x) estimators), and standardized incidence and mortality ratios, all of which can be easily adjusted for by covariates such as age. Fast splitting and aggregation of 'Lexis' objects (from package 'Epi') and other computations achieved using 'data.table'.

Changes in 0.5.0

popEpi::Lexis_dt

New function Lexis_dt, a wrapper of Epi::Lexis which also sets class to

c("Lexis", "data.table", "data.frame").

popEpi::Lexis_fpa

Lexis_fpa output is now also a data.table, so the complete class vector

is c("Lexis", "data.table", "data.frame").

popEpi::splitMulti

Fixed popEpi::splitMulti when merge = FALSE. Did not include lex.dur

previously which caused an error.

From NEWS.md in the release

Install

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

install.packages("popEpi", 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("FinnishCancerRegistry/popEpi")

Development version from FinnishCancerRegistry/popEpi. 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-popepi

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-popEpi

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-popEpi

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

5NOTE8OK

Check messages

NOTER code for possible problemsr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64

Found calls to structure() using deprecated special names:
  popEpi/tests/testthat/test_epi.R (.Names: 1)
'.Names' should be changed to 'names'.

CRAN check page ↗

Slowest check: 7.5 min · r-release-macos-x86_64

Status changes

NOTE8 OK, 5 NOTENow
NOTE12 OK, 1 NOTE2026-07-15
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.5.0

READMEYes · 195 wordsVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 0.5.0Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 64 (1 internal)includes a package overview page
Examples that run: 100%36 run in a plain check
Exported functions with examples: 76%
Documented parameters: 99%
Return-value docs: 97%
Help pages citing references: 9%

Vignettes (2)

How these are measured

Downloads

44.2K

CRAN downloads in the past year

Rank #1,984 · ~121/day · ~3.7K/mo

Releases R versions

Daily download trend is not available in this view yet.

3.3K30 days

9.5K90 days

44.2K1 year

Compare downloads with other packages →

Also on1.4K r2u4 autocran159 c2d4u

How downloads are counted

Repository

finnishcancerregistry/popepi ↗Organization: FinnishCancerRegistry

9Stars

8Forks

19Open issues

0Open PRs

2Releases

1,511Commits

7Commit identities

survivalepidemiologyradjust-estimatesage-adjustingdirect-adjustingr-packageindirect-adjusting

1,511 commits · Last activity 2026-10-21 · 0% stars, 30d · Default branch at 0.5.0.9028, ahead of CRAN 0.5.0 (checked 2026-10-22)

Responsiveness

How these are sampled

PRs merged (all time): 67%
Median days to close, 50 most recently updated closed issues: 2,131
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2024-05-20 · 82026-07-07 · 9

How these are measured

PracticesBeta

5 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/finnishcancerregistry/popepi on 2026-10-22.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux

Docs source (1)

README.Rmd

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

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

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Installing popEpi adds 25 packages (17 with compiled code, 18 MB of source tarballs). Heaviest: data.table 5.7 MB, Epi 3.3 MB, Rcpp 1.8 MB.

Depends (1)

R >= 3.5

Imports (6)

data.table directadjusting Epi (>= 2.0)methodssplinessurvival

LinkingTo (0)

none

Suggests (6)

knitr mstate relsurv rmarkdown roxygen2 testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

TwoTimeScales

Suggests, most downloaded first

Epi

How these are counted

Code & Tests

Datasets

People & History

People (3)

Joonas Miettinen

Maintainer, Author · added in 0.3.0

Matti Rantanen

Author · added in 0.3.0

Karri Seppa

Contributor · added in 0.3.0

Maintainer since 0.2.1 (2015)

Listed in earlier versions (4)

Show 4 peopleHide 4 people

J Miettinen

no longer listed · 0.2.1

J Pitkaniemi

no longer listed · 0.2.1

M Rantanen

no longer listed · 0.2.1

K Seppa

no longer listed · 0.2.1

Releases (19)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.5.0Latest
record
2026-02-12 · current release · diff ↗ ·
added 1 export
Lexis_dt
0.4.14
record
2026-02-12 · diff ↗
R
R 4.5.0 released · 2025-04-11
0.4.13
record
2025-01-31 · diff ↗
0.4.12
record
2024-05-10 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.4.11
record
2023-08-23 · diff ↗
R
R 4.3.0 released · 2023-04-21
unarchivedReturned to CRAN
2022-09-25
0.4.10
record
2022-09-25 · diff ↗
archivedRemoved from CRAN
2022-08-24
issues were not corrected in time
R
R 4.2.0 released · 2022-04-22
unarchivedReturned to CRAN
2021-10-29
0.4.9
record
2021-10-29 · diff ↗ ·
added 10 exports
array_to_long_df, array_to_long_dt, array_to_ratetable, long_df_to_array, long_df_to_ratetable, long_dt_to_array, long_dt_to_ratetable, ratetable_to_array, ratetable_to_long_df, ratetable_to_long_dt
archivedRemoved from CRAN
2021-10-13
check problems were not corrected in time

Show 19 earlier eventsHide 19 earlier events

R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
0.4.8
record
2019-09-28 · diff ↗ ·
added 1 export
Surv
R
R 3.6.0 released · 2019-04-26
0.4.7
record
2019-03-18 · diff ↗
0.4.6
record
2019-02-14 · diff ↗
0.4.5
record
2018-05-16 · diff ↗
R
R 3.5.0 released · 2018-04-23
0.4.4
record
2017-11-14 · diff ↗
0.4.3
record
2017-09-05 · diff ↗
0.4.2
record
2017-08-10 · diff ↗
R
R 3.4.0 released · 2017-04-21
0.4.1
record
2016-11-08 · diff ↗ ·
added 3 exports
sir_ag, sir_exp, sir_lex
0.4.0
record
2016-09-23 · diff ↗ ·
removed 1 export
shift.var

added 3 exports
Lexis_fpa, rate_ratio, sir_ratio
R
R 3.3.0 released · 2016-05-03
0.3.1
record
2016-04-25 · diff ↗
0.3.0
record
2016-03-31 · diff ↗ ·
removed 12 exports
as.data.frame.ratetable, as.data.table.ratetable, as.pe.Lexis, as.pe.data.table, as.pe.list, lines.survtab, plot.pe, plot.sir, plot.sirspline, plot.survtab, print.sir, print.sirspline

added 8 exports
adjust, aggre, as.aggre, prepExpo, rate, relpois_ag, setaggre, survtab_ag
0.2.1
record
2015-09-29
R
R 3.2.0 released · 2015-04-16

Package metadata

First published: 2015-09-29
Total releases: 19 / 11 yrs
License: MIT + file LICENSE OSI · relicensed from GPL-3 in 0.4.11
Minimum R: ≥ 3.5
Bundled data: 294 KB / 7 files
Download size: 1.2 MB

Appears in task views

Epidemiology

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("popEpi")

Format

Miettinen, J., Rantanen, M., & Seppa, K. (2026). popEpi: Functions for Epidemiological Analysis using Population Data (Version 0.5.0) [Computer software]. https://doi.org/10.32614/CRAN.package.popEpi

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 popEpi version 0.5.0 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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