surveil: Time Series Models for Disease Surveillance

Fits time series models for routine disease surveillance tasks and returns probability distributions for a variety of quantities of interest, including measures of health inequality, period and cumulative percent change, and age-standardized rates. Calculates Theil's index to measure inequality among multiple groups, and can be extended to measure inequality across multiple groups nested within geographies. Inference is completed using Markov chain Monte Carlo via the Stan modeling language. The models are appropriate for rare disease incidence and mortality data, employing a Poisson likelihood and first-difference (random-walk) prior for unknown risk, and optional covariance matrix for multiple correlated time series models. References: Brandt and Williams (2007, ISBN:978-1-4129-0656-2); Clayton (1996, ISBN-13:978-0-412-05551-5); Stan Development Team (2021) <>; Theil (1972, ISBN:0-444-10378-3).

Version: 0.1.1
Depends: R (≥ 3.5.0)
Imports: rstantools (≥ 2.1.1), methods, Rcpp (≥ 0.12.0), RcppParallel (≥ 5.0.1), rstan (≥ 2.18.1), 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 (≥, RcppParallel (≥ 5.0.1), rstan (≥ 2.18.1), StanHeaders (≥ 2.18.0)
Suggests: rmarkdown, knitr, testthat
Published: 2022-01-03
Author: Connor Donegan ORCID iD [aut, cre]
Maintainer: Connor Donegan <connor.donegan at>
License: GPL (≥ 3)
NeedsCompilation: yes
SystemRequirements: GNU make
Citation: surveil citation info
Materials: README NEWS
CRAN checks: surveil results


Reference manual: surveil.pdf
Vignettes: Public health surveillance with surveil


Package source: surveil_0.1.1.tar.gz
Windows binaries: r-devel:, r-devel-UCRT:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): surveil_0.1.1.tgz, r-release (x86_64): surveil_0.1.1.tgz, r-oldrel: surveil_0.1.0.tgz
Old sources: surveil archive


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