Ordering summarised_results object

[mvankessel-EMC]

This is a (slightly altered) snippet of code that I sent to @ariannaa7 on how to order a summarized result:

# Example from CohortCharactersitcs -------------------------------------------
library(omock)
library(dplyr, warn.conflicts = FALSE)
library(DrugUtilisation)
library(CohortCharacteristics)

cdm <- mockCdmFromDataset(datasetName = "GiBleed", source = "duckdb")

cdm <- generateIngredientCohortSet(cdm = cdm, name = "my_cohort", ingredient = c("warfarin", "acetaminophen"))

result <- cdm$my_cohort |>
  PatientProfiles::addSex() |>
  summariseCharacteristics(strata = "sex")

# Code to re-order  -----------------------------------------------------------
# Copy result and rename CDM to have 2 CDM's
resultMultiDb <- result |>
  omopgenerics::bind(
    result |>
      dplyr::mutate(cdm_name = "my cdm")
  )

# CDM name order: GiBleed, my cdm
# Sex strata order: overall, Female, Male
CohortCharacteristics::tableCharacteristics(resultMultiDb)

# Reordering strata to be reversed: Male, Female, Overall
resultReordered <- resultMultiDb |>
  # Add `cdm_order` column, set values will be either 1, 2, or 3
  dplyr::mutate(
    cdm_order = dplyr::case_when(
      .data$cdm_name == "my cdm" ~ 1,
      .data$cdm_name == "GiBleed" ~ 2,
      # Anything that is not specified above
      .default = 3
    )
  ) |>
  dplyr::mutate(
  # Add `sex_order` column, set values will be either 1, 2, or 3
    sex_order = dplyr::case_when(
      # `strata_name == <type>` is the strata type, usually age, sex w/e
      # `strata_level == <group>` are the individual groups within the strata
      .data$strata_name == "sex" & .data$strata_level == "Male" ~ 1,
      .data$strata_name == "sex" & .data$strata_level == "Female" ~ 2,
      .data$strata_name == "sex" & .data$strata_level == "overall" ~ 3,
      .default = 4
    )
  ) |>
  # Re-order by `cdm_order` and `sex_order` columns
  dplyr::arrange(.data$cdm_order, .data$sex_order) |>
  # Remove the `cdm_order` and `sex_order` column
  dplyr::select(-"cdm_order", -"sex_order")

# CDM order: my cdm, GiBleed
# Strata order: Male, Female, overall
CohortCharacteristics::tableCharacteristics(resultReordered)