Package: epinowcast 0.3.0

Sam Abbott

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:Sam Abbott [aut, cre], Adrian Lison [aut], Sebastian Funk [aut], Carl Pearson [aut], Hugo Gruson [aut], Felix Guenther [aut], Michael DeWitt [aut], Hannah Choi [ctb], Pratik Gupte [ctb], Joel Hellewell [ctb], Luis Rivas [ctb], Sang Woo Park [ctb], Nathan McIntosh [ctb], James Mba Azam [ctb], Kath Sherratt [ctb], Nikos Bosse [ctb]

epinowcast_0.3.0.tar.gz
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epinowcast_0.3.0.tgz(r-4.4-any)epinowcast_0.3.0.tgz(r-4.3-any)
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epinowcast.pdf |epinowcast.html✨
epinowcast/json (API)
NEWS

Peer review:

Bug tracker:https://github.com/epinowcast/epinowcast/issues

On CRAN:

cmdstanreffective-reproduction-number-estimationepidemiologyinfectious-disease-surveillancenowcastingoutbreak-analysispandemic-preparednessreal-time-infectious-disease-modellingstan

73 exports 52 stars 3.89 score 52 dependencies

Last updated 4 months agofrom:8a9cda94d0 (on v0.3.0)

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_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