Package: epinowcast 0.3.0.1000
![](https://github.com/epiforecasts/epinowcast/raw/HEAD/man/figures/logo.png)
epinowcast: Flexible Hierarchical Nowcasting
Tools to enable flexible and efficient hierarchical nowcasting of right-truncated epidemiological time-series using a semi-mechanistic Bayesian model with support for a range of reporting and generative processes. Nowcasting, in this context, is gaining situational awareness using currently available observations and the reporting patterns of historical observations. This can be useful when tracking the spread of infectious disease in real-time: without nowcasting, changes in trends can be obfuscated by partial reporting or their detection may be delayed due to the use of simpler methods like truncation. While the package has been designed with epidemiological applications in mind, it could be applied to any set of right-truncated time-series count data.
Authors:
epinowcast_0.3.0.1000.tar.gz
epinowcast_0.3.0.1000.zip(r-4.5)epinowcast_0.3.0.1000.zip(r-4.4)epinowcast_0.3.0.1000.zip(r-4.3)
epinowcast_0.3.0.1000.tgz(r-4.4-any)epinowcast_0.3.0.1000.tgz(r-4.3-any)
epinowcast_0.3.0.1000.tar.gz(r-4.5-noble)epinowcast_0.3.0.1000.tar.gz(r-4.4-noble)
epinowcast_0.3.0.1000.tgz(r-4.4-emscripten)epinowcast_0.3.0.1000.tgz(r-4.3-emscripten)
epinowcast.pdf |epinowcast.html✨
epinowcast/json (API)
NEWS
# Install 'epinowcast' in R: |
install.packages('epinowcast', repos = c('https://epiforecasts.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/epinowcast/epinowcast/issues
- 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 5 days agofrom:640d176b35. Checks:OK: 1 WARNING: 6. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Sep 03 2024 |
R-4.5-win | WARNING | Sep 03 2024 |
R-4.5-linux | WARNING | Sep 03 2024 |
R-4.4-win | WARNING | Sep 03 2024 |
R-4.4-mac | WARNING | Sep 03 2024 |
R-4.3-win | WARNING | Sep 03 2024 |
R-4.3-mac | WARNING | Sep 03 2024 |
Exports:add_pmfscheck_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_cumulative_to_incidenceenw_delay_metadataenw_designenw_effects_metadataenw_exampleenw_expectationenw_extend_dateenw_filter_delayenw_filter_reference_datesenw_filter_report_datesenw_fit_optsenw_flag_observed_observationsenw_formulaenw_formula_as_data_listenw_get_cacheenw_impute_na_observationsenw_incidence_to_cumulativeenw_incidence_to_linelistenw_latest_dataenw_linelist_to_incidenceenw_manual_formulaenw_metadataenw_metadata_delayenw_missingenw_missing_referenceenw_modelenw_nowcast_samplesenw_nowcast_summaryenw_obsenw_one_hot_encode_featureenw_pathfinderenw_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_sampleenw_score_nowcastenw_set_cacheenw_simulate_missing_referenceenw_stan_to_renw_summarise_samplesenw_unset_cacheepinowcastextract_sparse_matrixrerwsimulate_double_censored_pmf
Dependencies:abindbackportsbootcheckmateclicmdstanrcolorspacecpp11data.tabledistributionalfansifarvergenericsggplot2gluegtableisobandjsonlitelabelinglatticelifecyclelme4lubridatemagrittrMASSMatrixmatrixStatsmgcvminqamunsellnlmenloptrnumDerivpillarpkgconfigposteriorprocessxpspurrrR6RColorBrewerRcppRcppEigenrlangscalestensorAtibbletimechangeutf8vctrsviridisLitewithr
Discretised distributions
Rendered fromdistributions.Rmd
usingknitr::rmarkdown
on Sep 03 2024.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.Rmd
usingknitr::rmarkdown
on Sep 03 2024.Last update: 2024-08-23
Started: 2023-09-05
Getting Started with Epinowcast: Nowcasting
Rendered fromepinowcast.Rmd
usingknitr::rmarkdown
on Sep 03 2024.Last update: 2024-08-23
Started: 2023-11-22
Hierarchical nowcasting of age stratified COVID-19 hospitalisations in Germany
Rendered fromgermany-age-stratified-nowcasting.Rmd
usingknitr::rmarkdown
on Sep 03 2024.Last update: 2024-08-23
Started: 2021-11-01
Model definition and implementation
Rendered frommodel.Rmd
usingknitr::rmarkdown
on Sep 03 2024.Last update: 2024-01-03
Started: 2021-11-04
Case studies
Rendered frompackage-use-cases.Rmd
usingknitr::rmarkdown
on Sep 03 2024.Last update: 2024-09-02
Started: 2024-09-02
Resources to help with model fitting using Stan
Rendered fromstan-help.Rmd
usingknitr::rmarkdown
on Sep 03 2024.Last update: 2024-01-03
Started: 2023-12-13