R/tableCohortOverlap.R

In CohortCharacteristics: Summarise and Visualise Characteristics of Patients in the OMOP CDM

# Copyright 2024 DARWIN EU (C)
#
# This file is part of CohortCharacteristics
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

#' Format a summariseOverlapCohort result into a visual table.
#'
#' `r lifecycle::badge("experimental")`
#'
#' @inheritParams resultDoc
#' @inheritParams uniqueCombinationsDoc
#' @inheritParams tableDoc
#'
#' @return A formatted table.
#'
#' @export
#'
#' @examples
#' \donttest{
#' library(CohortCharacteristics)
#'
#' cdm <- mockCohortCharacteristics()
#'
#' overlap <- summariseCohortOverlap(cdm$cohort2)
#'
#' tableCohortOverlap(overlap)
#'
#' mockDisconnect(cdm = cdm)
#' }
#'
tableCohortOverlap <- function(result,
                               uniqueCombinations = TRUE,
                               type = "gt",
                               header = c("variable_name"),
                               groupColumn = c("cdm_name"),
                               hide = c("variable_level", settingsColumns(result))) {
  omopgenerics::assertLogical(uniqueCombinations, length = 1)
  result |>
    tableCohortCharacteristics(
      resultType = "summarise_cohort_overlap",
      header = header,
      groupColumn = groupColumn,
      hide = hide,
      rename = c("CDM name" = "cdm_name"),
      modifyResults = \(x, ...) {
        if (uniqueCombinations) {
          x <- getUniqueCombinationsSr(x)
        }
        return(x)
      },
      estimateName = c("N (%)" = "<count> (<percentage>%)"),
      type = type
    )
}