test_that("bind no class", { x <- 1 expect_error(bind(x)) }) test_that("bind a cohort_table", { cohort1 <- dplyr::tibble( cohort_definition_id = 1, subject_id = 1:3, cohort_start_date = as.Date("2010-01-01"), cohort_end_date = as.Date("2010-01-05") ) cohort2 <- dplyr::tibble( cohort_definition_id = c(2, 2, 3, 3, 3), subject_id = c(1, 2, 3, 1, 2), cohort_start_date = as.Date("2010-01-01"), cohort_end_date = as.Date("2010-01-05") ) cohort3 <- dplyr::tibble( cohort_definition_id = 1:5, subject_id = c(1, 2, 3, 1, 2), cohort_start_date = as.Date("2010-01-01"), cohort_end_date = as.Date("2010-01-05") ) cohort4 <- cohort3 attr(cohort4, "cohort_set") <- dplyr::tibble( cohort_definition_id = 1:5, cohort_name = c("first_cohort", "second_cohort", "third_cohort", "fourth_cohort", "fifth_cohort") ) cdm <- cdmFromTables( tables = list( "person" = dplyr::tibble( person_id = c(1, 2, 3), gender_concept_id = 0, year_of_birth = 1990, race_concept_id = 0, ethnicity_concept_id = 0 ), "observation_period" = dplyr::tibble( observation_period_id = 1:3, person_id = 1:3, observation_period_start_date = as.Date("2000-01-01"), observation_period_end_date = as.Date("2025-12-31"), period_type_concept_id = 0 ) ), cdmName = "mock", cohortTables = list( "cohort1" = cohort1, "cohort2" = cohort2, "cohort3" = cohort3, "cohort4" = cohort4 ) ) expect_no_error(newcdm <- bind(cdm$cohort1, cdm$cohort2, name = "new_cohort")) expect_true("new_cohort" %in% names(newcdm)) expect_true(inherits(newcdm$new_cohort, "cohort_table")) expect_true(all(c("cohort_set", "cohort_attrition") %in% names(attributes(newcdm$new_cohort)))) expect_identical( settings(newcdm$new_cohort) |> data.frame(), settings(newcdm$cohort1) |> dplyr::bind_rows(settings(newcdm$cohort2)) |> data.frame() ) expect_identical( attrition(newcdm$new_cohort) |> data.frame(), attrition(newcdm$cohort1) |> dplyr::bind_rows(attrition(newcdm$cohort2)) |> data.frame() ) expect_error(bind(cdm$cohort1, cdm$cohort2)) expect_error(bind(cdm$cohort1, cdm$cohort2, name = NA_character_)) expect_error(bind(cdm$cohort1, cdm$cohort2, name = 1)) expect_error(bind(cdm$cohort1, cdm$cohort2, name = c("a", "b"))) expect_no_error(bind(cdm$cohort1, name = "new_cohort")) expect_error(bind(cdm$cohort1, cdm$cohort3, name = "new_cohort")) expect_error(bind(cdm$cohort2, cdm$cohort3, name = "new_cohort")) expect_error(bind(cdm$cohort1, cdm$cohort2, cdm$cohort3, name = "new_cohort")) expect_no_error(newcdm <- bind(cdm$cohort1, cdm$cohort4, name = "new_cohort")) expect_no_error(newcdm <- bind(cdm$cohort2, cdm$cohort4, name = "new_cohort")) expect_no_error(newcdm <- bind(cdm$cohort3, cdm$cohort4, name = "new_cohort")) expect_no_error(newcdm <- bind(cdm$cohort1, cdm$cohort2, cdm$cohort4, name = "new_cohort")) expect_equal(newcdm$new_cohort |> dplyr::tally() |> dplyr::pull(), 13) expect_equal(settings(newcdm$new_cohort)$cohort_definition_id, 1:8) expect_equal( settings(newcdm$new_cohort)$cohort_name, c( settings(newcdm$cohort1)$cohort_name, settings(newcdm$cohort2)$cohort_name, settings(newcdm$cohort4)$cohort_name ) ) expect_equal(attrition(newcdm$new_cohort) |> nrow(), 8) cohort1 <- dplyr::tibble( cohort_definition_id = 1, subject_id = 1:3, cohort_start_date = as.Date("2010-01-01"), cohort_end_date = as.Date("2010-01-05"), extra_column1 = 1 ) cohort2 <- dplyr::tibble( cohort_definition_id = c(2, 2, 3, 3, 3), subject_id = c(1, 2, 3, 1, 2), cohort_start_date = as.Date("2010-01-01"), cohort_end_date = as.Date("2010-01-05"), extra_column2 = TRUE, extra_column3 = "fjhhl" ) cohort3 <- dplyr::tibble( cohort_definition_id = 1:5, subject_id = c(1, 2, 3, 1, 2), cohort_start_date = as.Date("2010-01-01"), cohort_end_date = as.Date("2010-01-05") ) attr(cohort3, "cohort_set") <- dplyr::tibble( cohort_definition_id = 1:5, cohort_name = c( "first_cohort", "second_cohort", "third_cohort", "fourth_cohort", "fifth_cohort" ) ) cdm <- cdmFromTables( tables = list( "person" = dplyr::tibble( person_id = c(1, 2, 3), gender_concept_id = 0, year_of_birth = 1990, race_concept_id = 0, ethnicity_concept_id = 0 ), "observation_period" = dplyr::tibble( observation_period_id = 1:3, person_id = 1:3, observation_period_start_date = as.Date("2000-01-01"), observation_period_end_date = as.Date("2025-12-31"), period_type_concept_id = 0 ) ), cdmName = "mock", cohortTables = list( "cohort1" = cohort1, "cohort2" = cohort2, "cohort3" = cohort3 ) ) expect_no_error( cdm <- bind(cdm$cohort1, cdm$cohort2, cdm$cohort3, name = "cohort6") ) expect_true(all( c("cohort_definition_id", "subject_id", "cohort_start_date", "cohort_end_date", "extra_column1", "extra_column2", "extra_column3") %in% colnames(cdm$cohort6) )) }) test_that("bind summarised_result", { x <- dplyr::tibble( "group_name" = "overall", "group_level" = "overall", "strata_name" = c("age_group", "age_group", "sex", "sex"), "strata_level" = c("<40", ">40", "Female", "Male"), "variable_name" = "number subjects", "variable_level" = NA_character_, "estimate_name" = "count", "estimate_type" = "integer", "estimate_value" = sample.int(100, 4) |> as.character(), "additional_name" = "overall", "additional_level" = "overall" ) # empty summarisedResult res1 <- emptySummarisedResult() # no settings res2 <- x |> dplyr::mutate("result_id" = 1L, "cdm_name" = "cprd_gold") |> newSummarisedResult() res3 <- x |> dplyr::mutate("result_id" = 1L, "cdm_name" = "cprd_gold") |> newSummarisedResult(settings = dplyr::tibble( "result_id" = 1L, result_type = "custom" )) res4 <- x |> dplyr::mutate("result_id" = 3L, "cdm_name" = "cprd_gold") |> newSummarisedResult(settings = dplyr::tibble( "result_id" = 3L, result_type = "custom", param = TRUE )) res5 <- x |> dplyr::mutate("result_id" = 1L, "cdm_name" = "eunomia") |> newSummarisedResult(settings = dplyr::tibble( "result_id" = 1L, result_type = "custom" )) res6 <- x |> dplyr::mutate("result_id" = 5L, "cdm_name" = "cprd_gold") |> newSummarisedResult(settings = dplyr::tibble( "result_id" = 5L, washout = 35 )) # two summarised_result expect_no_error(new1 <- bind(res1, res2, res3, res4, res5, res6)) expect_identical(settings(new1), dplyr::tibble( "result_id" = c(1L, 2L, 3L, 4L), "result_type" = c(NA, "custom", "custom", NA), "param" = c(NA, NA, TRUE, NA), "washout" = c(NA, NA, NA, 35) )) attr(new1, "settings") <- NULL expect_identical( new1 |> dplyr::count(.data$result_id) |> dplyr::as_tibble(), dplyr::tibble("result_id" = c(1L, 2L, 3L, 4L), "n" = c(4L, 8L, 4L, 4L)) ) # one of the summarised_result does not have settings expect_no_error(new2 <- bind(res2, res3)) # if we bind the same summarised_result we get an error because number of # subjects is repeated expect_error(new3 <- bind(res2, res2)) # repeated settings expect_no_error(new4 <- bind(res3, res5)) expect_identical(new4$result_id |> unique(), 1L) expect_identical( new4 |> settings() |> dplyr::pull("result_id") |> unique(), 1L ) # repeated settings and empty stetings expect_no_error(new5 <- bind(res3, res5, res2)) expect_identical(new5$result_id |> unique(), c(1L, 2L)) expect_identical( new5 |> settings() |> dplyr::pull("result_id") |> unique(), c(1L, 2L) ) })