Package: epinowcast 0.6.0.1000

epinowcast: A Bayesian Framework for Real-time Infectious Disease Surveillance
A modular Bayesian framework for real-time infectious disease surveillance. Provides tools for nowcasting, reproduction number estimation, delay estimation, and forecasting from data subject to reporting delays, right-truncation, missing data, and incomplete ascertainment. Users can build models suited to their setting using a flexible formula interface supporting fixed effects, random effects, random walks, and time-varying parameters, with options including parametric and non-parametric delay distributions with optional modifiers (via discrete-time hazard models), renewal processes, observation models, missing data imputation, and stratified analyses with partial pooling. By jointly estimating disease dynamics and reporting patterns, our framework enables earlier and more reliable detection of trends. While designed with epidemiological applications in mind, the framework can be applied to any right-truncated time series count data.
Authors:
epinowcast_0.6.0.1000.tar.gz
epinowcast_0.6.0.1000.zip(r-4.7)epinowcast_0.6.0.1000.zip(r-4.6)epinowcast_0.6.0.1000.zip(r-4.5)
epinowcast_0.6.0.1000.tgz(r-4.6-any)epinowcast_0.6.0.1000.tgz(r-4.5-any)
epinowcast_0.6.0.1000.tar.gz(r-4.7-any)epinowcast_0.6.0.1000.tar.gz(r-4.6-any)
epinowcast_0.6.0.1000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
epinowcast/json (API)
NEWS
| # Install 'epinowcast' in R: |
| install.packages('epinowcast', repos = c('https://bisaloo.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/epinowcast/epinowcast/issues
Pkgdown/docs site:https://package.epinowcast.org
- germany_covid19_hosp - Hospitalisations in Germany by date of report and reference
cmdstanreffective-reproduction-number-estimationepidemiologyinfectious-disease-surveillancenowcastingoutbreak-analysispandemic-preparednessreal-time-infectious-disease-modellingstan
Last updated from:54492aaf5b. Checks:9 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 349 | ||
| source / vignettes | OK | 279 | ||
| linux-release-x86_64 | OK | 361 | ||
| macos-release-arm64 | OK | 317 | ||
| macos-oldrel-arm64 | OK | 342 | ||
| windows-devel | OK | 320 | ||
| windows-release | OK | 289 | ||
| windows-oldrel | OK | 315 | ||
| wasm-release | OK | 150 |
Exports:add_pmfsararimaarmacheck_max_delaycoerce_dateconvolution_matrixenw_add_cumulativeenw_add_cumulative_membershipenw_add_delayenw_add_incidenceenw_add_latest_obs_to_nowcastenw_add_max_reportedenw_add_metaobs_featuresenw_add_pooling_effectenw_aggregate_cumulativeenw_assign_groupenw_complete_datesenw_construct_dataenw_dayofweek_structural_reportingenw_delay_categoriesenw_delay_quantilesenw_designenw_effects_metadataenw_exampleenw_expectationenw_extend_dateenw_filter_delayenw_filter_reference_datesenw_filter_reference_dates_by_report_startenw_filter_report_datesenw_fit_optsenw_flag_observed_observationsenw_formulaenw_formula_as_data_listenw_get_cacheenw_get_dataenw_impute_na_observationsenw_incidence_to_linelistenw_latest_dataenw_linelist_to_incidenceenw_manual_formulaenw_metadataenw_metadata_delayenw_missingenw_missing_referenceenw_modelenw_nowcast_samplesenw_nowcast_summaryenw_obsenw_obs_at_delayenw_one_hot_encode_featureenw_pathfinderenw_plot_delay_countsenw_plot_delay_cumulativeenw_plot_delay_fractionenw_plot_delay_quantilesenw_plot_nowcast_quantilesenw_plot_obsenw_plot_pp_quantilesenw_plot_quantilesenw_plot_themeenw_posteriorenw_pp_summaryenw_preprocess_dataenw_priors_as_data_listenw_quantiles_to_longenw_referenceenw_replace_priorsenw_reportenw_reporting_triangleenw_reporting_triangle_to_longenw_retrospectiveenw_rolling_sumenw_sampleenw_set_cacheenw_simulate_missing_referenceenw_stan_to_renw_structural_reporting_metadataenw_summarise_samplesenw_unset_cacheepinowcastextract_sparse_matrixmarerw
Dependencies:abindbackportscheckmateclicpp11data.tabledistributionalfarvergenericsggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMatrixmatrixStatsnumDerivpillarpkgconfigposteriorpurrrR6rbibutilsRColorBrewerRdpackreformulasrlangS7scalestensorAtibbleutf8vctrsviridisLitewithr
ARIMA latent residuals: maths, priors, and usage
Rendered fromarima.Rmdusingknitr::rmarkdownon Jun 04 2026.Last update: 2026-06-04
Started: 2026-06-04
Comparing Inference Methods
Rendered frominference-methods.Rmdusingknitr::rmarkdownon Jun 04 2026.Last update: 2026-04-22
Started: 2026-04-20
Discretised distributions
Rendered fromdistributions.Rmdusingknitr::rmarkdownon Jun 04 2026.Last update: 2024-01-03
Started: 2023-04-28
Estimating the effective reproduction number in real-time for a single timeseries with reporting delays
Rendered fromsingle-timeseries-rt-estimation.Rmdusingknitr::rmarkdownon Jun 04 2026.Last update: 2026-04-21
Started: 2023-09-05
Getting Started with Epinowcast: Nowcasting
Rendered fromepinowcast.Rmdusingknitr::rmarkdownon Jun 04 2026.Last update: 2026-05-05
Started: 2023-11-22
Hierarchical nowcasting of age stratified COVID-19 hospitalisations in Germany
Rendered fromgermany-age-stratified-nowcasting.Rmdusingknitr::rmarkdownon Jun 04 2026.Last update: 2026-02-16
Started: 2021-11-01
Latent process and periodic options for the growth-rate model
Rendered fromlatent-processes.Rmdusingknitr::rmarkdownon Jun 04 2026.Last update: 2026-06-04
Started: 2026-06-04
Model definition and implementation
Rendered frommodel.Rmdusingknitr::rmarkdownon Jun 04 2026.Last update: 2026-06-04
Started: 2021-11-04
Model Features Summary
Rendered fromfeatures.Rmdusingknitr::rmarkdownon Jun 04 2026.Last update: 2026-06-04
Started: 2025-10-10
Case studies
Rendered frompackage-use-cases.Rmdusingknitr::rmarkdownon Jun 04 2026.Last update: 2026-02-13
Started: 2024-09-02
Resources to help with model fitting using Stan
Rendered fromstan-help.Rmdusingknitr::rmarkdownon Jun 04 2026.Last update: 2026-04-02
Started: 2023-12-13
Temporal aggregation guide
Rendered fromtemporal-aggregation.Rmdusingknitr::rmarkdownon Jun 04 2026.Last update: 2026-05-05
Started: 2026-05-01
Visualising Preprocessed Data
Rendered frompreprocess-visualisation.Rmdusingknitr::rmarkdownon Jun 04 2026.Last update: 2026-05-05
Started: 2026-04-16
