Package: epitraxr 0.5.1

Andrew Pulsipher

epitraxr: Manipulate 'EpiTrax' Data and Generate Reports

A fast, flexible tool for generating disease surveillance reports from data exported from 'EpiTrax', a central repository for epidemiological data used by public health officials. It provides functions to manipulate 'EpiTrax' datasets, tailor reports to internal or public use, and export reports in CSV, Excel 'xlsx', or PDF formats.

Authors:Andrew Pulsipher [aut, cre], Nate Lanza [aut, ctb], Madeline George [ctb], Zachary Heuscher [ctb], Centers for Disease Control and Prevention's Center for Forecasting and Outbreak Analytics [fnd]

epitraxr_0.5.1.tar.gz
epitraxr_0.5.1.zip(r-4.7-any)epitraxr_0.5.1.zip(r-4.6-any)epitraxr_0.5.1.zip(r-4.5-any)
epitraxr_0.5.1.tgz(r-4.6-any)epitraxr_0.5.1.tgz(r-4.5-any)
epitraxr_0.5.1.tar.gz(r-4.7-any)epitraxr_0.5.1.tar.gz(r-4.6-any)
epitraxr_0.5.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
epitraxr/json (API)

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

Bug tracker:https://github.com/epiforesite/epitraxr/issues

Pkgdown/docs site:https://epiforesite.github.io

On CRAN:

Conda:

5.56 score 3 stars 8 scripts 396 downloads 57 exports 6 dependencies

Last updated from:e125d5d861. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK173
source / vignettesOK204
linux-releaseOK123
macos-releaseOK98
macos-oldrelOK85
windows-develOK80
windows-releaseOK73
windows-oldrelOK120
wasm-releaseOK117

Exports:clear_old_reportscompute_trendconvert_counts_to_ratecreate_epitrax_from_filecreate_filesystemcreate_public_report_combined_month_ytdcreate_public_report_monthcreate_public_report_ytdcreate_report_annual_countscreate_report_grouped_statscreate_report_monthly_avgscreate_report_monthly_countscreate_report_monthly_medianscreate_report_ytd_countscreate_report_ytd_mediansepitrax_ireport_annual_countsepitrax_ireport_monthly_avgsepitrax_ireport_monthly_counts_all_yrsepitrax_ireport_ytd_counts_for_monthepitrax_preport_combined_month_ytdepitrax_preport_month_crosssectionsepitrax_preport_ytd_ratesepitrax_report_grouped_statsepitrax_report_monthly_mediansepitrax_report_ytd_mediansepitrax_set_config_from_fileepitrax_set_config_from_listepitrax_set_report_diseasesepitrax_write_csvsepitrax_write_pdf_grouped_statsepitrax_write_pdf_public_reportsepitrax_write_xlsxsepitraxr_configformat_epitrax_dataget_month_countsget_report_configget_report_diseasesget_report_diseases_internalget_report_diseases_publicget_yrsmmwr_week_to_monthread_epitrax_datareshape_annual_widereshape_monthly_widerun_appset_na_0setup_epitraxsetup_filesystemstandardize_report_diseasesvalidate_configvalidate_datavalidate_epitraxvalidate_filesystemwrite_report_csvwrite_report_pdfwrite_report_pdf_groupedwrite_report_xlsx

Dependencies:cpp11genericslubridatetimechangewritexlyaml

epitraxr
Introduction to epitraxr | EpiTrax Data | Disease Lists | Generating Reports: Standard Mode | Generating Reports: Piped Mode (recommended)
Rendered fromepitraxr.Rmdusingknitr::rmarkdown

Last update: 2025-09-03
Started: 2025-08-14

Piped Mode
Overview | Pipe Setup | Create an epitrax object | Add Disease Lists | Add Config | Convenient Setup | Running Report Generators | Exporting Reports | Setup Filesystem | Export to CSV | Full Pipe: Putting It All Together
Rendered frompiped-mode.Rmdusingknitr::rmarkdown

Last update: 2025-09-03
Started: 2025-08-18

Readme and manuals

Help Manual

Help pageTopics
Clear out old reports before generating new ones.clear_old_reports
Compute the report trendcompute_trend
Convert case counts to rateconvert_counts_to_rate
Create an EpiTrax object from data filecreate_epitrax_from_file
Create filesystemcreate_filesystem
Create combined monthly and year-to-date public reportcreate_public_report_combined_month_ytd
Create a monthly cross-section public reportcreate_public_report_month
Create a YTD public reportcreate_public_report_ytd
Create annual counts reportcreate_report_annual_counts
Create grouped disease statistics reportcreate_report_grouped_stats
Create monthly averages reportcreate_report_monthly_avgs
Create monthly counts reportcreate_report_monthly_counts
Create monthly medians reportcreate_report_monthly_medians
Create year-to-date (YTD) counts reportcreate_report_ytd_counts
Create year-to-date (YTD) medians reportcreate_report_ytd_medians
Create annual counts internal report from an EpiTrax objectepitrax_ireport_annual_counts
Create monthly averages internal report from an EpiTrax objectepitrax_ireport_monthly_avgs
Create monthly counts internal report for all years from an EpiTrax objectepitrax_ireport_monthly_counts_all_yrs
Create year-to-date (YTD) counts internal report for a given month from an EpiTrax objectepitrax_ireport_ytd_counts_for_month
Create combined monthly/YTD stats public report from an EpiTrax objectepitrax_preport_combined_month_ytd
Create monthly cross-section reports from an EpiTrax objectepitrax_preport_month_crosssections
Create year-to-date (YTD) rates public report from an EpiTrax objectepitrax_preport_ytd_rates
Create grouped disease statistics report from an EpiTrax objectepitrax_report_grouped_stats
Create monthly medians report from an EpiTrax objectepitrax_report_monthly_medians
Create year-to-date (YTD) medians report from an EpiTrax objectepitrax_report_ytd_medians
Set report configuration of EpiTrax object from config fileepitrax_set_config_from_file
Set report configuration of EpiTrax object from listepitrax_set_config_from_list
Set report diseases in EpiTrax objectepitrax_set_report_diseases
Write reports from EpiTrax object to CSV filesepitrax_write_csvs
Write grouped statistics reports from EpiTrax object to PDF filesepitrax_write_pdf_grouped_stats
Create formatted PDF report of monthly cross-section reportsepitrax_write_pdf_public_reports
Write reports from EpiTrax object to Excel filesepitrax_write_xlsxs
Create epitraxr config objectepitraxr_config
Format EpiTrax data for report generationformat_epitrax_data
Get monthly counts for each diseaseget_month_counts
Read in the report config YAML fileget_report_config
Get both internal and public disease listsget_report_diseases
Get the internal disease listget_report_diseases_internal
Get the public disease listget_report_diseases_public
Get unique years from the dataget_yrs
Convert MMWR week to calendar monthmmwr_week_to_month
Read in EpiTrax dataread_epitrax_data
Reshape data with each year as a separate columnreshape_annual_wide
Reshape data with each month as a separate columnreshape_monthly_wide
Launch the epitraxr Shiny Applicationrun_app
Set NA values to 0set_na_0
Setup EpiTrax object with configuration and disease listssetup_epitrax
Setup the report filesystemsetup_filesystem
Standardize diseases for reportstandardize_report_diseases
Validate configvalidate_config
Validate input EpiTrax datavalidate_data
Validate EpiTrax objectvalidate_epitrax
Validate filesystem structurevalidate_filesystem
Write report CSV fileswrite_report_csv
Write general PDF report of disease stats from R Markdown templatewrite_report_pdf
Write PDF grouped report from R Markdown templatewrite_report_pdf_grouped
Write report Excel fileswrite_report_xlsx