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 using periods outside the supplied events, estimates expected deaths across the observed series, 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
Documentation: https://shanlong-who.github.io/exmort/
Guides
| Guide | What you will learn |
|---|---|
| Getting started | Install the package, run a built-in example and export a report |
| Preparing data | Fill the weekly or monthly workbook and define the event calendar |
| Models and interpretation | Compare baselines, read uncertainty and explain excess deaths and P-scores |
The website contains documentation. Launch the Shiny calculator from R to perform an analysis.
Installation
Install from CRAN:
install.packages("exmort")Development version from GitHub:
# install.packages("remotes")
remotes::install_github("shanlong-who/exmort")Usage
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.
Start with Data → Upload Data → Built-in example data, select a country and its mortality and event sheets, then click Merge Built-in Data. Review View Data, open Model, choose a group and click Run Model. Inspect Tables and Plots before generating an HTML report.
The current models use periods outside the supplied events (event_index == "0") as their baseline. These may include observations after an event; review the input time range and event calendar carefully.
Use RStudio’s Stop button or Escape in the console to stop the app.
Optional features
-
Word (.docx) reports need the
officedownpackage:install.packages("officedown"). -
PDF reports need a LaTeX installation, e.g.
tinytex::install_tinytex().