## Data

get_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

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