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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:
Documentation: https://shanlong-who.github.io/exmort/
| 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.
Install from CRAN:
install.packages("exmort")Development version from GitHub:
# install.packages("remotes")
remotes::install_github("shanlong-who/exmort")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.
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.
officedown package:
install.packages("officedown").tinytex::install_tinytex().GPL-3. © World Health Organization Regional Office for the Western Pacific.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.