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_cc_detected_by_site_age(
  d,
  condition,
  pathogen,
  sites = NULL,
  specimen_types = 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`.
pathogen	A string specifying the pathogen to count positive cases of in the TAC results.
sites	An optional vector of site names to include in the tabulation. If not provided, all sites will be used. See `valid_sites`.
specimen_types	An optional vector of specimen types to include in the calculation. If not provided, all specimen types will be used. See `valid_specimen_types`.

Examples

specimen_types <- c(
  "Cerebrospinal fluid sample",
  "Tissue specimen from lung",
  "Whole blood",
  "Rectal swab",
  "Plasma or spun blood specimen"
)

calc_cc_detected_by_site_age(mock,
  condition = "Streptococcus agalactiae",
  pathogen = "Group B Streptococcus",
  specimen_types = specimen_types)