Function reference • champs

Data
`get_l2_data()`	Register and download L2 data
`load_data()`	Load and pre-process data from relevant CHAMPS database tables
`valid_conditions()`	Get a list of valid conditions
`valid_pathogens()`	Get a list of valid TAC results pathogens based on the provided CHAMPS data
`valid_sites()`	Get a list of valid site names based on the provided CHAMPS data
`valid_specimen_types()`	Get a list of valid TAC results specimen types based on the provided CHAMPS data
`valid_icds()`	Get a list of DeCoDe "Other Significant Cause" ICD 10 codes that exist in the CHAMPS data
`valid_age_groups()`	Get a list of valid age groups based on the provided CHAMPS data
`valid_age_subcats()`	Get a list of valid age subgroups based on the provided CHAMPS data
`mock`	Mock data with same format as CHAMPS download
`tac_table`	A table of TAC name information
`infectious_causes`	A vector of named infectious causes.
Computing Statistics
`calc_cc_allcases_by_site_age()`	Tabulate the number of cases of a given condition found in the causal chain by site and by age, within the context of all cases
`calc_cc_detected_by_site_age()`	Tabulate the number of cases of a given condition found in the causal chain by site and by age, within the context of cases where the pathogen(s) are detected in TAC results (dying from vs. dying with)
`calc_detected_allcases_by_site_age()`	Tabulate the number of cases where the pathogen(s) are detected in TAC results in the context of all cases by site and by age
`calc_detected_by_decode()`	Tabulate the number of cases where the pathogen(s) are detected in TAC results by DeCoDe result (in causal chain or not, etc.) and by either site or age
`calc_nspecimen_by_pmi()`	Tabulate the number of positive specimens for each case where the pathogen(s) are detected in TAC results by postmortem interval range (PMI - time from death to MITS)
`calc_pmi_by_age_decode()`	Calculate average postmortem interval (PMI - average time from death to MITS in hours) by age and DeCoDe result
`calc_pmi_by_decode_site()`	Calculate average postmortem interval (PMI - average time from death to MITS in hours) by DeCoDe result and site
`calc_pmi_by_specimen_site()`	Calculate average postmortem interval (PMI - average time from death to MITS in hours) by specimen type of NP Only vs. Blood/CSF/Lung and by site
`calc_top_tac_pathogens()`	Tabulate top other pathogens found in the causal chain for cases that have positive TAC results for a given pathogen
`calc_top_dcd_pathogens_by_acq()`	Tabulate top pathogens associated with a condition by site of acquisition
`calc_top_tac_pathogens_cc()`	Tabulate TAC top pathogens detected and causal chain
`calc_top_etiol_by_age()`	Tabulate top etiologies by specified age groups
`calc_cc_allcases_by_age_acq()`	Tabulate cases with condition in causal chain by age and site of acquisition
`calc_syndrome_combinations()`	Tabulate syndrome combinations for a specified condition
`calc_cc_by_age_syndrome()`	Tabulate cases for a condition by age and syndrome
Producing Outputs
`plot_margins_site_age()`	Plot the margins (row and column totals) of a computed CHAMPS table
`heatmap_site_age()`	Plot the percents of a computed CHAMPS table
`plot_top_etiol_by_age()`	Plot the etiologies of a computed CHAMPS table
`plot_syndrome_combinations()`	Plot the syndrome combination tabulations from a computed CHAMPS object
`html_table_site_age()`	Create an html table of a computed CHAMPS object

Reference

Data

Computing Statistics

Producing Outputs