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 
[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:
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