Package: surveil 0.3.0

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).

Authors:Connor Donegan [aut, cre]

surveil_0.3.0.tar.gz
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surveil_0.3.0.tgz(r-4.4-arm64)surveil_0.3.0.tgz(r-4.3-arm64)
surveil_0.3.0.tar.gz(r-4.5-noble)surveil_0.3.0.tar.gz(r-4.4-noble)
surveil.pdf |surveil.html
surveil/json (API)
NEWS

# Install 'surveil' in R:
install.packages('surveil', repos = c('https://connordonegan.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/connordonegan/surveil/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • cancer - US cancer incidence by age, 1999-2017
  • msa - Colorectal cancer incidence by Texas MSA, 1999-2017, ages 50-79
  • standard - 2000 U.S. standard million population

On CRAN:

bayesian-statisticscancerhealth-equitypublic-healthrstan

4.94 score 2 stars 11 scripts 262 downloads 9 exports 66 dependencies

Last updated 4 months agofrom:847d19fc67. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 05 2024
R-4.5-win-x86_64NOTENov 05 2024
R-4.5-linux-x86_64NOTENov 05 2024
R-4.4-win-x86_64NOTENov 05 2024
R-4.4-mac-aarch64NOTENov 05 2024
R-4.3-win-x86_64NOTENov 05 2024
R-4.3-mac-aarch64NOTENov 05 2024

Exports:apcgroup_difflkjnormalstan_rwstandardizetheiltheil2waic

Dependencies:abindarrayhelpersbackportsBHcallrcheckmateclicodacolorspacecpp11descdistributionaldplyrfansifarvergenericsggdistggplot2gluegridExtragtableinlineisobandlabelinglatticelifecycleloomagrittrMASSMatrixmatrixStatsmgcvmunsellnlmenumDerivpillarpkgbuildpkgconfigposteriorprocessxpspurrrquadprogQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelrlangrstanrstantoolsscalesStanHeadersstringistringrsvUnittensorAtibbletidybayestidyrtidyselectutf8vctrsviridisLitewithr

Age-standardized rates

Rendered fromage-standardization.Rmdusingknitr::rmarkdownon Nov 05 2024.

Last update: 2024-07-08
Started: 2022-03-29

MCMC with surveil

Rendered fromsurveil-mcmc.Rmdusingknitr::rmarkdownon Nov 05 2024.

Last update: 2024-07-08
Started: 2022-07-29

Measuring health inequality

Rendered frommeasuring-inequality.Rmdusingknitr::rmarkdownon Nov 05 2024.

Last update: 2024-07-08
Started: 2024-07-08

Using surveil for public health research

Rendered fromsurveil-demo.Rmdusingknitr::rmarkdownon Nov 05 2024.

Last update: 2024-07-08
Started: 2022-07-29

Readme and manuals

Help Manual

Help pageTopics
The 'surveil' packagesurveil-package surveil
Annual and cumulative percent changeapc apc.stand_surveil apc.surveil
US cancer incidence by age, 1999-2017cancer
Measures of pairwise inequalitygroup_diff group_diff.list group_diff.surveil
Colorectal cancer incidence by Texas MSA, 1999-2017, ages 50-79msa
Methods for fitted 'surveil' modelsplot.list plot.surveil print.surveil
Methods for Theil's indexplot.theil plot.theil_list print.theil print.theil_list
Methods for APC objectsplot.apc print.apc
Methods for age-standardized ratesplot.stand_surveil print.stand_surveil
Prior distributionslkj normal priors
Time series models for mortality and disease incidencestan_rw
2000 U.S. standard million populationstandard
Age-standardized ratesstandardize
Methods for 'surveil_diff' objectsplot.surveil_diff print.surveil_diff surveil_diff
Theil's inequality indextheil theil.list theil.surveil theil2
Widely Applicable Information Criteriawaic