Package: fiphde 2.1.0

VP Nagraj

fiphde: Forecasting Influenza in Support of Public Health Decision Making

Miscellaneous functions for retrieving data, creating and evaluating time series forecasting models for influenza-like illness (ILI) and influenza hospitalizations in the United States.

Authors:VP Nagraj [aut, cre], Desiree Williams [aut], Shakeel Jessa [aut], Chris Hulme-Lowe [aut], Stephen Turner [aut]

fiphde_2.1.0.tar.gz
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fiphde.pdf |fiphde.html✨
fiphde/json (API)
NEWS

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

Bug tracker:https://github.com/signaturescience/fiphde/issues

Pkgdown site:https://signaturescience.github.io

On CRAN:

4.26 score 3 stars 9 scripts 31 exports 117 dependencies

Last updated 2 months agofrom:1ab58967a2. Checks:8 OK. Indexed: no.

TargetResultLatest binary
Doc / VignettesOKJan 26 2025
R-4.5-winOKJan 26 2025
R-4.5-macOKJan 26 2025
R-4.5-linuxOKJan 26 2025
R-4.4-winOKJan 26 2025
R-4.4-macOKJan 26 2025
R-4.3-winOKJan 26 2025
R-4.3-macOKJan 26 2025

Exports:%>%clin_nowcastfiphde_launcherforecast_categoricalforecast_iliformat_for_submissionget_cdc_clinget_cdc_hospget_cdc_iliget_hdgov_hospget_nhsn_weeklyget_nowcast_iliglm_wrapis_mondaymake_tsibblemmwr_week_to_datemnzmnz_replacens_imputeplot_forecastplot_forecast_categoricalpois_forcprep_hdgov_hospprep_nhsn_weeklyreplace_ili_nowcastsmoothiethis_mondaythis_saturdayts_fit_forecastts_format_for_submissionvalidate_forecast

Dependencies:abindanytimearmaskpassbackportsbase64encBHbitbit64bootbslibcachemcheckmateciToolsclicliprcodacodetoolscolorspacecommonmarkcpp11crayoncurldigestdistfromqdistributionaldplyrellipsisfablefabletoolsfansifarverfastmapfontawesomefsfurrrfuturegenericsggdistggplot2globalsgluegtablehardhathmshtmltoolshttpuvhttrisobandjquerylibjsonlitelabelinglaterlatticelifecyclelistenvlme4lubridatemagrittrMASSMatrixmemoisemgcvmimeminqaMMWRweekmunsellnlmenloptrnumDerivopensslparallellypillarpkgconfigprettyunitsprogressprogressrpromisespurrrquadprogR6rappdirsrbibutilsRColorBrewerRcppRcppEigenRdpackreadrreformulasrlangrsamplesassscalesshinyslidersourcetoolsstringistringrsurvivalsystibbletidyrtidyselecttimechangetrendevaltrendingtsibbletzdbutf8vctrsviridisLitevroomwarpwithrxtableyardstickzeallot

Basic Usage

Rendered frombasic_usage.Rmdusingknitr::rmarkdownon Jan 26 2025.

Last update: 2024-01-11
Started: 2022-06-02

Readme and manuals

Help Manual

Help pageTopics
Make clean column names.mcga
Nowcast clinical laboratory percent positive flu dataclin_nowcast
Calculate categorical probability densitydensity_probs
FIPHDE explorer app launcherfiphde_launcher
Forecast categorical targetsforecast_categorical
Forecast ILIforecast_ili
Format forecasts for submissionformat_for_submission
Retrieve clinical laboratory percent positive flu dataget_cdc_clin
Retrieve hospitalization data from FluSurv-NETget_cdc_hosp
Retrieve ILI data from ILINetget_cdc_ili
Retrieve hospitalization data from HHSget_hdgov_hosp
Retrieve weekly NHSN flu hospitalization dataget_nhsn_weekly
Retrieve ILI nowcastget_nowcast_ili
Retrieve data from RESP-NETget_respnet
Fit glm modelsglm_fit
Forecast glm modelsglm_forecast
Get quantiles from prediction intervalsglm_quibble
Run glm modeling and forecastingglm_wrap
Laboratory-confirmed influenza hospitalizationshospitalizations
Hubverse formattinghubverse_format
Retrieve ILINet surveillance datailinet
Check Mondayis_monday
Make 'tsibble'make_tsibble
Convert MMWR format to datemmwr_week_to_date
Minimum non-zeromnz
Minimum non-zero replacementmnz_replace
Non-seasonal flu hospitalization imputationns_impute
Plot forecastsplot_forecast
Plot categorical forecastsplot_forecast_categorical
Simple Poisson count forecasterpois_forc
Prep hospitalization dataprep_hdgov_hosp
Prepare NHSN weekly dataprep_nhsn_weekly
Replace ILINet data with nowcastreplace_ili_nowcast
Round and preserve vectorround_preserve
Calculate smoothed and weighted averages of previous observationssmoothie
Get Mondaythis_monday
Get Saturdaythis_saturday
Clean numeric valuesto_num
Fit and forecast with time-series approachests_fit_forecast
Format time series forecastts_format_for_submission
Validate forecast submissionvalidate_forecast
WHO/NREVSS clinical lab surveillance datawho_nrevss