Skip to contents

Generate Hierarchy of events or substances

Source: R/count_reactions.R
hierarchycal_rates.Rd

This function generates a hierarchy of reporting rates for a specified entity and based on different MedDRA or ATC levels and writes the result to a xlsx file.

Usage

hierarchycal_rates(
  pids_cases,
  entity = "reaction",
  file_name = paste0(project_path, "reporting_rates.xlsx"),
  drug_role = c("PS", "SS", "I", "C")
)

Arguments

pids_cases

Vector of primary IDs identifying the sample of interest.

entity

Entity investigated. It can be one of the following:

  • reaction;

  • indication;

  • substance.

file_name

Path to save the XLSX file containing the hierarchy.

drug_role

If entity is substance, it is possible to specify the drug roles that should be considered

Value

An excel file with the hierarchy of interest. For indications and reactions, SOCs are ordered by occurrences and, within, HLGTs, HLTs, PTs. For substances, the ATC hierarchy is followed.

Examples

# The following examples require the MedDRA and the ATC to be imported
if (file.exists("external_sources/meddra_primary")) {
  hierarchycal_rates(pids, "reaction", "reactions_rates.xlsx")
}
if (file.exists("external_sources/meddra_primary")) {
  hierarchycal_rates(pids, "indication", "indications_rates.xlsx")
}
if (file.exists("external_sources/ATC_DiAna")) {
  hierarchycal_rates(pids, "substance", "substances_rates.xlsx")
}