Package: EpiNow 0.3.0

Sam Abbott

EpiNow: Estimate Realtime Case Counts and Time-varying Epidemiological Parameters

To identify changes in the reproduction number, rate of spread, and doubling time during the course of outbreaks whilst accounting for potential biases due to delays in case reporting.

Authors:Sam Abbott [aut, cre], Joel Hellewell [aut], James Munday [aut], Robin Thompson [aut], Sebastian Funk [aut]

EpiNow_0.3.0.tar.gz

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EpiNow.pdf |EpiNow.html✨
EpiNow/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/epiforecasts/epinow/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

51 exports 33 stars 2.46 score 104 dependencies

Last updated 4 years agofrom:917c73397c

Exports:add_datesadjust_for_truncationadjust_infection_to_reportclean_nowcastscountry_mapdist_fitdist_skelepi_measures_pipelineestimate_doubling_timeestimate_little_restimate_r_in_windowestimate_R0estimate_time_varying_rgamma_dist_defgenerate_pseudo_linelistget_dist_defget_local_import_case_countsget_regionsget_timeseriesglobal_mapgrowth_to_Rlinelist_from_case_countsload_nowcast_resultlognorm_dist_defmake_confmap_prob_changenowcast_pipelineplot_confidenceplot_forecastplot_gridplot_pipelineplot_summarypull_max_varR_to_growthrbinom_sizeregional_rt_pipelineregional_summaryreport_casesreport_littlerreport_nowcastreport_reffreport_summaryrt_pipelinesample_approx_distsample_delaysimulate_casessplit_linelist_by_daysummarise_castsummarise_resultssummarise_to_csvtheme_map

Dependencies:abindaweekbackportsbase64encBHcallrcheckmateclicoarseDataToolscodacodetoolscolorspacecowplotcpp11data.tabledescdigestdistributionaldplyrEpiEstimEpiSoonevaluatefansifarverfitdistrplusfurrrfuturefuture.applygenericsggplot2globalsgluegridExtragtableHDIntervalhighrincidenceinlineisobandknitrlabelinglatticelifecyclelistenvloolubridatemagrittrMASSMatrixMatrixModelsmatrixStatsmcmcMCMCpackMetricsmgcvmunsellnlmenumDerivparallellypatchworkpillarpkgbuildpkgconfigplyrposteriorprocessxpspurrrquantregQuickJSRR.devicesR.methodsS3R.ooR.utilsR6RColorBrewerRcppRcppArmadilloRcppEigenRcppParallelreshape2rlangrstanrstantoolsscalesscoringRulesscoringutilsSparseMStanHeadersstringistringrsurvivaltensorAtibbletidyrtidyselecttimechangetruncnormutf8vctrsviridisLitewithrxfunyaml

Getting started

Rendered fromgetting-started.Rmdusingknitr::rmarkdownon Jun 28 2024.

Last update: 2020-05-28
Started: 2020-05-28

Readme and manuals

Help Manual

Help pageTopics
Add Dates from Daataadd_dates
Adjust Case Counts for Truncationadjust_for_truncation
Adjust from Case Counts by Infection Date to Date of Reportadjust_infection_to_report
Clean Nowcasts for a Supplied Dateclean_nowcasts
Generate a country map for a single variable.country_map
Covid Generation Time Estimatescovid_generation_times
Covid Generation Time Estimates - Summarycovid_generation_times_summary
Covid Incubation Periodcovid_incubation_period
Covid Generation Serial Intervalscovid_serial_intervals
Fit an integer adjusted exponential or gamma distributiondist_fit
Distribution Skeletondist_skel
Estimate time-varying measures and forecastepi_measures_pipeline
Estimate the doubling timeestimate_doubling_time
Estimate restimate_little_r
Estimate r in a set time windowestimate_r_in_window
Estimate the time varying R0 - using EpiEstimestimate_R0
Estimate time varying restimate_time_varying_r
Generate a Gamma Distribution Definition Based on Parameter Estimatesgamma_dist_def
Generate a sample linelist from the observed linelist and sampled linelistsgenerate_pseudo_linelist
Get a Parameters that Define a Discrete Distributionget_dist_def
Combine total and imported case countsget_local_import_case_counts
Get Folders with Nowcast Resultsget_regions
Get Timeseries from EpiNowget_timeseries
Generate a global map for a single variable.global_map
Convert Growth Rates to Reproduction numbers.growth_to_R
Sample a linelist from case counts and a reporting delay distributionlinelist_from_case_counts
Load nowcast resultsload_nowcast_result
Generate a Log Normal Distribution Definition Based on Parameter Estimateslognorm_dist_def
Format Credible Intervalsmake_conf
Categorise the Probability of Change for Rtmap_prob_change
Impute Cases Date of Infectionnowcast_pipeline
Plot a Time Series with Confidence.plot_confidence
Add a Forecast to a Plotplot_forecast
Plot a Grid of Plotsplot_grid
Plot Pipeline Resultsplot_pipeline
Plot a Summary of the Latest Resultsplot_summary
Extract a the Maximum Value of a Variable Based on a Filterpull_max_var
Convert Reproduction Numbers to Growth RatesR_to_growth
Draw with an offset from a negative binomial distributionrbinom_size
Regional Realtime Pipelineregional_rt_pipeline
Generate Regional Summary Outputregional_summary
Report case counts by date of reportreport_cases
Report Rate of Growth Estimatesreport_littler
Report Case Nowcast Estimatesreport_nowcast
Report Effective Reproduction Number Estimatesreport_reff
Provide Summary Statistics on an Rt Pipelinereport_summary
Real-time Pipelinert_pipeline
Approximate Sampling a Distribution using Countssample_approx_dist
Sample Onset Dates for Cases missing themsample_delay
Simulate Cases by Date of Infection, Onset and Reportsimulate_cases
Convert a linelist into a nested `data.table`` of linelists by daysplit_linelist_by_day
Summarise a nowcastsummarise_cast
Summarise Realtime Resultssummarise_results
Summarise rt and cases as a csvsummarise_to_csv
Custom Map Themetheme_map