R Observatory: Metrics for exmort version 0.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

exmort

0.1.1Package record

All-Cause and Excess Mortality Calculator

0packages depend

1.1Kdownloads / year

62.5%test coverage

13/13flavors OK

Overview

About

Maintained by Shanlong DingCRAN page ↗GitHub ↗Website ↗Issues ↗Declared funder: World Health Organization Regional Office for the Western Pacific

An interactive 'shiny' application that estimates all-cause mortality and excess mortality from country-level weekly or monthly death counts. Users supply observed deaths and an event calendar (for example COVID-19 waves or typhoons); the app fits one or more statistical baseline models (historical average, negative binomial regression, quasi-Poisson regression, zero-inflated Poisson regression, ARIMA (autoregressive integrated moving average) and SARIMA (seasonal ARIMA) models, GAM (generalized additive model) splines, and the model of Karlinsky and Kobak (2021) doi:10.7554/eLife.69336) using periods outside the supplied events, estimates expected deaths across the observed series, and reports excess deaths, P-scores (excess deaths as a percentage of expected deaths) and confidence limits with tables, plots and downloadable reports. Launch the application with run_app().

Changes in 0.1.1

Added three vignettes covering installation and launch, input templates and data preparation, and baseline models and result interpretation.
Added a pkgdown documentation website, linked from the package metadata and README, with a function reference and searchable articles.
Added a package hex logo showing expected and observed mortality, used in the README, website and vignettes.
Clarified that baseline models are fitted to all periods outside the supplied events, including any non-event periods after an event.

From NEWS.md in the release

Install

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

install.packages("exmort", 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("shanlong-who/exmort")

Development version from shanlong-who/exmort. 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-exmort

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-exmort

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-exmort

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: 3.6 min · r-release-macos-x86_64

Status changes

OK13 OKNow
OK12 OK2026-08-05
NOTE9 OK, 1 NOTE2026-08-01
OK7 OK2026-07-31

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.1

READMEYes · 389 wordsVignettesYes · 3 · dynamicNEWSYes · 100% structured · mentions 0.1.1Citation fileNoWebsiteYes · pkgdown

Help pages: 2 (1 internal)includes a package overview page
Examples that run: 100%1 run in a plain check (under a condition)
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (3)

How these are measured

Downloads

1.1K

CRAN downloads in the past year

Rank #8,931 · ~3/day · ~89/mo

Releases R versions

Daily download trend is not available in this view yet.

44130 days

1.1K90 days

1.1K1 year

Compare downloads with other packages →

Also on13 r2u

How downloads are counted

Repository

shanlong-who/exmort ↗Account: shanlong-who

0Stars

1Forks

0Open issues

1Open PRs

1Releases

29Commits

1Commit identities

29 commits · Last activity 2026-10-21 · Default branch at 0.1.1.9000, ahead of CRAN 0.1.1 (checked 2026-10-21)

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 0

Forks over time

2026-07-31 · 02026-10-19 · 1

How these are measured

PracticesBeta

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

Checks run against github.com/shanlong-who/exmort on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, and on R-devel

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-10-21 · The repository has a site deploy workflow

pkgdown site last built 2026-10-21

Reproducibility and dev environment (1)

data-raw/

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Show all practicesHide 1 practice

Git structural (1)

.gitattributes

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

AI coding toolsBeta

This repository shows signs of AI coding tools.

Claude Codefirst seen 2026-07-12
Commits: at least 1 crediting it in the message

Models named in its commits

Claude Fable 51 commit · Jul 2026

Counts are commits, not lines of code. Commits by a tool's accounts count once across all of its accounts. Commits crediting it are the largest count among its credit lines, a minimum.How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

32 external dependencies (excludes base and recommended)

Installing exmort adds 105 packages (58 with compiled code, 86 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (0)

none

LinkingTo (0)

none

Suggests (4)

DSIR officedown testthat tinytex

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (2)

Shanlong Ding

Author, Maintainer since 0.1.0 (2026)

World Health Organization Regional Office for the Western Pacific

Copyright holder, Funder

Releases (2)

Pick two releases to compare their code metrics.

0.1.1Latest
record
2026-10-06 · current release · diff ↗
0.1.0
record
2026-07-30
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-07-30
Total releases: 2 / 1 yrs
License: GPL-3 OSI
Download size: 5.6 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("exmort")

Format

Ding, S., & World Health Organization Regional Office for the Western Pacific. (2026). exmort: All-Cause and Excess Mortality Calculator (Version 0.1.1) [Computer software]. https://doi.org/10.32614/CRAN.package.exmort

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 exmort version 0.1.1 [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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