exmort

All-Cause and Excess Mortality Calculator — an R Shiny application for estimating all-cause mortality and excess mortality from country-level weekly or monthly death counts, developed at the WHO Regional Office for the Western Pacific (WPRO).

You supply observed deaths and an event calendar (e.g. COVID-19 waves, typhoons). The app fits one or more statistical baseline models on a user-defined baseline period, projects expected deaths into the post-baseline period, and reports excess deaths, P-scores and confidence limits with tables, plots and downloadable reports.

Baseline models included:

• Historical average
• Negative binomial regression
• Quasi-Poisson regression
• Zero-inflated Poisson
• ARIMA / SARIMA
• Generalized additive model (GAM spline)
• Karlinsky–Kobak model

Installation

From CRAN (once released):

install.packages("exmort")

Development version from GitHub:

# install.packages("remotes")
remotes::install_github("shanlong-who/exmort")

Usage

library(exmort)
run_app()

The app opens in your default web browser and runs entirely on your machine — no data leaves your computer. Built-in example datasets for several countries are included; you can also upload your own workbook using the templates on the Data tab.

Optional features

• Word (.docx) reports need the officedown package: install.packages("officedown").
• PDF reports need a LaTeX installation, e.g. tinytex::install_tinytex().

License

GPL-3. © World Health Organization Regional Office for the Western Pacific.