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().
| Version: | 0.1.0 |
| 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 |
| Published: | 2026-07-30 |
| DOI: | 10.32614/CRAN.package.exmort |
| Author: | Shanlong Ding [aut, cre], World Health Organization Regional Office for the Western Pacific [cph, fnd] |
| Maintainer: | Shanlong Ding <dings at who.int> |
| BugReports: | https://github.com/shanlong-who/exmort/issues |
| License: | GPL-3 |
| URL: | https://github.com/shanlong-who/exmort |
| NeedsCompilation: | no |
| SystemRequirements: | pandoc (>= 1.14) for report rendering; a LaTeX installation (for example TinyTeX) is required only for PDF reports. |
| Language: | en-GB |
| Materials: | README, NEWS |
| CRAN checks: | exmort results |
| Reference manual: | exmort.html , exmort.pdf |
| Package source: | exmort_0.1.0.tar.gz |
| Windows binaries: | r-devel: exmort_0.1.0.zip, r-release: exmort_0.1.0.zip, r-oldrel: exmort_0.1.0.zip |
| macOS binaries: | r-release (arm64): exmort_0.1.0.tgz, r-oldrel (arm64): exmort_0.1.0.tgz, r-release (x86_64): exmort_0.1.0.tgz, r-oldrel (x86_64): exmort_0.1.0.tgz |
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