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surveil: Time Series Models for Disease Surveillance

Fits time trend models for routine disease surveillance tasks and returns probability distributions for a variety of quantities of interest, including age-standardized rates, period and cumulative percent change, and measures of health inequality. The models are appropriate for count data such as disease incidence and mortality data, employing a Poisson or binomial likelihood and the first-difference (random-walk) prior for unknown risk. Optionally add a covariance matrix for multiple, correlated time series models. Inference is completed using Markov chain Monte Carlo via the Stan modeling language. References: Donegan, Hughes, and Lee (2022) <doi:10.2196/34589>; Stan Development Team (2021) <https://mc-stan.org>; Theil (1972, ISBN:0-444-10378-3).

Version: 0.3.0
Depends: R (≥ 3.5.0)
Imports: rstantools (≥ 2.1.1), methods, Rcpp (≥ 0.12.0), RcppParallel (≥ 5.0.1), rstan (≥ 2.26.0), tidybayes (≥ 3.0.0), dplyr (≥ 1.0.7), rlang (≥ 0.4.0), tidyr (≥ 1.1.0), ggplot2 (≥ 3.0.0), gridExtra (≥ 2.0), scales (≥ 0.4.0), ggdist (≥ 3.0.0)
LinkingTo: BH (≥ 1.66.0), Rcpp (≥ 0.12.0), RcppEigen (≥ 0.3.3.3.0), RcppParallel (≥ 5.0.1), rstan (≥ 2.26.0), StanHeaders (≥ 2.26.0)
Suggests: rmarkdown, knitr, testthat
Published: 2024-07-08
DOI: 10.32614/CRAN.package.surveil
Author: Connor Donegan ORCID iD [aut, cre]
Maintainer: Connor Donegan <connor.donegan at gmail.com>
License: GPL (≥ 3)
URL: https://connordonegan.github.io/surveil/, https://github.com/ConnorDonegan/surveil/
NeedsCompilation: yes
SystemRequirements: GNU make
Citation: surveil citation info
Materials: README NEWS
CRAN checks: surveil results

Documentation:

Reference manual: surveil.pdf
Vignettes: Age-standardized rates
Measuring health inequality
Using surveil for public health research
MCMC with surveil

Downloads:

Package source: surveil_0.3.0.tar.gz
Windows binaries: r-devel: surveil_0.3.0.zip, r-release: surveil_0.3.0.zip, r-oldrel: surveil_0.3.0.zip
macOS binaries: r-release (arm64): surveil_0.3.0.tgz, r-oldrel (arm64): surveil_0.3.0.tgz, r-release (x86_64): surveil_0.3.0.tgz, r-oldrel (x86_64): surveil_0.3.0.tgz
Old sources: surveil archive

Linking:

Please use the canonical form https://CRAN.R-project.org/package=surveil to link to this page.

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.