Calculate average postmortem interval (PMI - average time from death to MITS in hours) by age and DeCoDe result

calc_pmi_by_age_decode(
  d,
  condition,
  pathogen,
  icds,
  specimen_types = 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`.
pathogen	A string specifying the pathogen to count positive cases of in the TAC results.
icds	A vector of ICD10 codes to check for the DeCoDe result of "Contributing (P2)".
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`.
sites	An optional vector of site names to include in the tabulation. If not provided, all sites will be used. See `valid_sites`.

Examples

specimen_types <- c(
  "Cerebrospinal fluid sample",
  "Tissue specimen from lung",
  "Whole blood",
  "Rectal swab",
  "Plasma or spun blood specimen"
)
calc_pmi_by_age_decode(mock,
  condition = "Streptococcus agalactiae",
  pathogen = "Group B Streptococcus",
  icds = c("P36.0", "A40.1", "P23.3", "G00.2"),
  specimen_types = specimen_types)