Package {exmort}

Title: All-Cause and Excess Mortality Calculator
Version: 0.1.0
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>) 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().
License: GPL-3
Encoding: UTF-8
Language: en-GB
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
Config/testthat/edition: 3
SystemRequirements: pandoc (>= 1.14) for report rendering; a LaTeX installation (for example TinyTeX) is required only for PDF reports.
URL: https://github.com/shanlong-who/exmort
BugReports: https://github.com/shanlong-who/exmort/issues
Config/roxygen2/version: 8.0.0
NeedsCompilation: no
Packaged: 2026-07-21 11:13:54 UTC; User
Author: Shanlong Ding [aut, cre], World Health Organization Regional Office for the Western Pacific [cph, fnd]
Maintainer: Shanlong Ding <dings@who.int>
Repository: CRAN
Date/Publication: 2026-07-30 16:30:08 UTC

exmort: All-Cause and Excess Mortality Calculator

Description

An interactive 'shiny' application for estimating all-cause mortality and excess mortality from country-level weekly or monthly death counts. See run_app to start the application.

Details

The @importFrom tags below register one function from each runtime dependency. The application code lives under inst/app and attaches these packages itself at run time; the tags exist so that every package in the DESCRIPTION Imports field is recorded in the NAMESPACE and installed alongside exmort.

Author(s)

Maintainer: Shanlong Ding dings@who.int

Authors:

Other contributors:

See Also

Useful links:

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(), ...)

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()
}