Tabulate top other pathogens found in the causal chain for cases that have positive TAC results for a given pathogen

calc_top_tac_pathogens(
d,
condition,
pathogen,
icds,
specimen_types = 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. A string specifying the pathogen to count positive cases of in the TAC results. A vector of ICD10 codes to check for the DeCoDe result of "Contributing (P2)". An optional vector of specimen types to include in the calculation. If not provided, all specimen types will be used. See valid_specimen_types. 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_top_tac_pathogens(mock,
condition = "Streptococcus agalactiae",
pathogen = "Group B Streptococcus",
icds = c("P36.0", "A40.1", "P23.3", "G00.2"),
specimen_types = specimen_types)