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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.

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.