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`.
condition	A string specifying the condition to tabulate causal chain presence for. To list all possibilities, see `valid_conditions`.
specimen_types	An optional vector of specimen types to include as columns in the table.
specimen_abbrv	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`.
age_groups	Optional vector of age groups. See `valid_age_groups`.
sites	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+")
)