Package 'exmort' reference manual

Package 'exmort'

Title:	All-Cause and Excess Mortality Calculator
Description:	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().
Authors:	Shanlong Ding [aut, cre], World Health Organization Regional Office for the Western Pacific [cph, fnd]
Maintainer:	Shanlong Ding <[email protected]>
License:	GPL-3
Version:	0.1.1
Built:	2026-10-09 13:10:04 UTC
Source:	https://github.com/shanlong-who/exmort

Title:

All-Cause and Excess Mortality Calculator

Description:

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().

Authors:

Shanlong Ding [aut, cre], World Health Organization Regional Office for the Western Pacific [cph, fnd]

Maintainer:

Shanlong Ding <[email protected]>

License:

GPL-3

Version:

0.1.1

Built:

2026-10-09 13:10:04 UTC

Source:

https://github.com/shanlong-who/exmort

Help Index

Launch the All-Cause and Excess Mortality Calculator

Description

Starts the bundled 'shiny' application in your default web browser. The app runs entirely on your own machine and does not upload any data.

Usage

run_app(launch.browser = interactive(), ...)
run_app(launch.browser = interactive(), ...)

Arguments

launch.browser

Logical; whether to open the app in a web browser. Defaults to interactive().

...

Additional arguments passed on to runApp (for example port or host).

Details

The application is copied to a per-session temporary directory before it is launched, so it never writes into the (possibly read-only) package installation directory.

Value

Called for its side effect of running the Shiny application; invisibly returns NULL when the app is closed.

Examples

if (interactive()) {
  # Launch the calculator in your browser:
  run_app()
}

if (interactive()) {
  # Launch the calculator in your browser:
  run_app()
}