surveil: Time Series Models for Disease Surveillance (original) (raw)

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 [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:

Downloads:

Linking:

Please use the canonical formhttps://CRAN.R-project.org/package=surveilto link to this page.