exmort: All-Cause and Excess Mortality Calculator

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>) on a user-defined baseline period, projects the expected deaths into the post-baseline period, 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().

Version:	0.1.0
Imports:	base64enc, data.table, dplyr, DT, forecast, ggplot2, ggrepel, htmltools, ISOweek, kableExtra, knitr, lubridate, mgcv, openxlsx, parallel, plotly, reactable, readxl, RColorBrewer, reshape2, rmarkdown, scales, shiny, shinyalert, shinycssloaders, shinyjs, stringr, tibble, tidyr, zoo
Suggests:	officedown, testthat (≥ 3.0.0), tinytex
Published:	2026-07-30
DOI:	10.32614/CRAN.package.exmort
Author:	Shanlong Ding [aut, cre], World Health Organization Regional Office for the Western Pacific [cph, fnd]
Maintainer:	Shanlong Ding <dings at who.int>
BugReports:	https://github.com/shanlong-who/exmort/issues
License:	GPL-3
URL:	https://github.com/shanlong-who/exmort
NeedsCompilation:	no
SystemRequirements:	pandoc (>= 1.14) for report rendering; a LaTeX installation (for example TinyTeX) is required only for PDF reports.
Language:	en-GB
Materials:	README, NEWS
CRAN checks:	exmort results

Documentation:

Reference manual:

exmort.html , exmort.pdf

Downloads:

Package source:	exmort_0.1.0.tar.gz
Windows binaries:	r-devel: exmort_0.1.0.zip, r-release: exmort_0.1.0.zip, r-oldrel: exmort_0.1.0.zip
macOS binaries:	r-release (arm64): exmort_0.1.0.tgz, r-oldrel (arm64): exmort_0.1.0.tgz, r-release (x86_64): exmort_0.1.0.tgz, r-oldrel (x86_64): exmort_0.1.0.tgz

Linking:

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