Package index • epitraxr

Piped mode functions

Setup

Functions to create the epitrax object and prepare it for report generation

setup_epitrax(): Setup EpiTrax object with configuration and disease lists

create_epitrax_from_file(): Create an EpiTrax object from data file

epitrax_set_config_from_file(): Set report configuration of EpiTrax object from config file

epitrax_set_config_from_list(): Set report configuration of EpiTrax object from list

epitrax_set_report_diseases(): Set report diseases in EpiTrax object

Internal reports

Functions that generate exclusively internal reports

epitrax_ireport_annual_counts(): Create annual counts internal report from an EpiTrax object

epitrax_ireport_monthly_avgs(): Create monthly averages internal report from an EpiTrax object

epitrax_ireport_monthly_counts_all_yrs(): Create monthly counts internal report for all years from an EpiTrax object

epitrax_ireport_ytd_counts_for_month(): Create year-to-date (YTD) counts internal report for a given month from an EpiTrax object

Public reports

Functions that generate exclusively public reports

epitrax_preport_combined_month_ytd(): Create combined monthly/YTD stats public report from an EpiTrax object

epitrax_preport_month_crosssections(): Create monthly cross-section reports from an EpiTrax object

epitrax_preport_ytd_rates(): Create year-to-date (YTD) rates public report from an EpiTrax object

Other reports

Functions that generate both internal and public reports

epitrax_report_grouped_stats(): Create grouped disease statistics report from an EpiTrax object

epitrax_report_monthly_medians(): Create monthly medians report from an EpiTrax object

epitrax_report_ytd_medians(): Create year-to-date (YTD) medians report from an EpiTrax object

Export

Functions to export reports

epitrax_write_csvs(): Write reports from EpiTrax object to CSV files

epitrax_write_pdf_grouped_stats(): Write grouped statistics reports from EpiTrax object to PDF files

epitrax_write_pdf_public_reports(): Create formatted PDF report of monthly cross-section reports

epitrax_write_xlsxs(): Write reports from EpiTrax object to Excel files

Standard mode functions

Internal reports

Functions that generate reports intended for internal use

create_report_annual_counts(): Create annual counts report

create_report_grouped_stats(): Create grouped disease statistics report

create_report_monthly_avgs(): Create monthly averages report

create_report_monthly_counts(): Create monthly counts report

create_report_monthly_medians(): Create monthly medians report

create_report_ytd_counts(): Create year-to-date (YTD) counts report

create_report_ytd_medians(): Create year-to-date (YTD) medians report

Public reports

Functions that generate reports intended for public use

create_public_report_combined_month_ytd(): Create combined monthly and year-to-date public report

create_public_report_month(): Create a monthly cross-section public report

create_public_report_ytd(): Create a YTD public report

Data processing

Functions for importing and processing data

read_epitrax_data(): Read in EpiTrax data

mmwr_week_to_month(): Convert MMWR week to calendar month

format_epitrax_data(): Format EpiTrax data for report generation

reshape_monthly_wide(): Reshape data with each month as a separate column

reshape_annual_wide(): Reshape data with each year as a separate column

standardize_report_diseases(): Standardize diseases for report

get_yrs(): Get unique years from the data

get_month_counts(): Get monthly counts for each disease

Filesystem

Setup

Functions for setting up the filesystem

create_filesystem(): Create filesystem

clear_old_reports(): Clear out old reports before generating new ones.

setup_filesystem(): Setup the report filesystem

Reading files

Functions for reading configuration and data files

get_report_config(): Read in the report config YAML file

get_report_diseases(): Get both internal and public disease lists

get_report_diseases_internal(): Get the internal disease list

get_report_diseases_public(): Get the public disease list

Export functions

Functions to export reports

write_report_csv(): Write report CSV files

write_report_pdf(): Write general PDF report of disease stats from R Markdown template

write_report_pdf_grouped(): Write PDF grouped report from R Markdown template

write_report_xlsx(): Write report Excel files

Validation

Functions for validating input data and configurations

validate_epitrax(): Validate EpiTrax object

validate_filesystem(): Validate filesystem structure

validate_config(): Validate config

validate_data(): Validate input EpiTrax data

Utilities

Miscellaneous utility functions

epitraxr_config(): Create epitraxr config object

convert_counts_to_rate(): Convert case counts to rate

compute_trend(): Compute the report trend

set_na_0(): Set NA values to 0

Shiny app

Functions related to the Shiny application

run_app(): Launch the epitraxr Shiny Application