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
)

Arguments

d A data object obtained from load_data. A string specifying the condition to tabulate causal chain presence for. To list all possibilities, see valid_conditions. An optional vector of specimen types to include as columns in the table. An optional vector of abbreviations to use for the specified specimen_types. calculation. If not provided, all specimen types will be used. See valid_specimen_types. Optional vector of age groups. See valid_age_groups. An optional vector of site names to include in the tabulation. If not provided, all sites will be used. See valid_sites.

Examples

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+")
)