Package: EpiNow 0.2.0

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_0.2.0.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:

    4.74 score 33 stars 111 scripts 46 exports 103 dependencies

    Last updated 5 years agofrom:2af218312a (on v0.4.0). Checks:OK: 1 ERROR: 8. Indexed: yes.

    TargetResultDate
    Doc / VignettesOKOct 31 2024
    R-4.5-win-x86_64ERROROct 31 2024
    R-4.5-linux-x86_64ERROROct 31 2024
    R-4.4-win-x86_64ERROROct 31 2024
    R-4.4-mac-x86_64ERROROct 31 2024
    R-4.4-mac-aarch64ERROROct 31 2024
    R-4.3-win-x86_64ERROROct 31 2024
    R-4.3-mac-x86_64ERROROct 31 2024
    R-4.3-mac-aarch64ERROROct 31 2024

    Exports:add_datesadjust_for_truncationclean_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_maplinelist_from_case_countsload_nowcast_resultlognorm_dist_defmake_confmap_prob_changenowcast_pipelineplot_confidenceplot_forecastplot_gridplot_pipelineplot_summarypull_max_varrbinom_sizeregional_rt_pipelineregional_summaryreport_littlerreport_nowcastreport_reffreport_summaryrt_pipelinesample_approx_distsample_delaysplit_linelist_by_daysummarise_castsummarise_resultssummarise_to_csvtheme_map

    Dependencies:abindaweekbackportsbase64encBHcallrcheckmateclicoarseDataToolscodacodetoolscolorspacecowplotcpp11data.tabledescdigestdistributionaldplyrEpiEstimEpiSoonevaluatefansifarverfitdistrplusfurrrfuturefuture.applygenericsggplot2globalsgluegridExtragtableHDIntervalhighrincidenceinlineisobandknitrlabelinglatticelifecyclelistenvloolubridatemagrittrMASSMatrixMatrixModelsmatrixStatsmcmcMCMCpackMetricsmgcvmunsellnlmenumDerivparallellypatchworkpillarpkgbuildpkgconfigplyrposteriorprocessxpspurrrquantregQuickJSRR.devicesR.methodsS3R.ooR.utilsR6RColorBrewerRcppRcppArmadilloRcppEigenRcppParallelreshape2rlangrstanrstantoolsscalesscoringRulesscoringutilsSparseMStanHeadersstringistringrsurvivaltensorAtibbletidyrtidyselecttimechangeutf8vctrsviridisLitewithrxfunyaml

    Readme and manuals

    Help Manual

    Help pageTopics
    Add Dates from Daataadd_dates
    Adjust Case Counts for Truncationadjust_for_truncation
    Clean Nowcasts for a Supplied Dateclean_nowcasts
    Generate a country map for a single variable.country_map
    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
    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
    Draw with an offset from a negative binomial distributionrbinom_size
    Regional Realtime Pipelineregional_rt_pipeline
    Generate Regional Summary Outputregional_summary
    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
    Convert a linelist into a nested tibble 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