Tabulate TAC top pathogens detected and causal chain
calc_top_tac_pathogens_cc( d, condition, specimen_types = NULL, specimen_abbrv = NULL, age_groups = NULL, sites = NULL )
A data object obtained from
A string specifying the condition to tabulate causal chain
presence for. To list all possibilities, see
An optional vector of specimen types to include as columns in the table.
An optional vector of abbreviations to use for the specified
Optional vector of age groups.
An optional vector of site names to include in the tabulation.
If not provided, all sites will be used. See
calc_top_tac_pathogens_cc(mock, condition = "Lower respiratory infections", age_groups = c( "Infant (28 days to less than 12 months)", "Child (12 months to less than 60 Months)"), specimen_types = c( "Nasopharyngeal and Oropharyngeal swab", "Tissue specimen from lung"), specimen_abbrv = c("# NP+", "# Lung+") )