Manipulate 'EpiTrax' Data and Generate Reports

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Documentation for package ‘epitraxr’ version 0.5.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

clear_old_reports	Clear out old reports before generating new ones.
compute_trend	Compute the report trend
convert_counts_to_rate	Convert case counts to rate
create_epitrax_from_file	Create an EpiTrax object from data file
create_filesystem	Create filesystem
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
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
epitraxr_config	Create epitraxr config object
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
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
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
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
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
format_epitrax_data	Format EpiTrax data for report generation
get_month_counts	Get monthly counts for each disease
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
get_yrs	Get unique years from the data
mmwr_week_to_month	Convert MMWR week to calendar month
read_epitrax_data	Read in EpiTrax data
reshape_annual_wide	Reshape data with each year as a separate column
reshape_monthly_wide	Reshape data with each month as a separate column
run_app	Launch the epitraxr Shiny Application
setup_epitrax	Setup EpiTrax object with configuration and disease lists
setup_filesystem	Setup the report filesystem
set_na_0	Set NA values to 0
standardize_report_diseases	Standardize diseases for report
validate_config	Validate config
validate_data	Validate input EpiTrax data
validate_epitrax	Validate EpiTrax object
validate_filesystem	Validate filesystem structure
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