diff --git a/NEWS.md b/NEWS.md index dbfbf1f6..25839aa8 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,9 @@ # teal.transform 0.1.1.9009 +### Breaking changes + +* Following changes to the output of `teal.slice::FilteredData$get_call()` the data merge functionality no longer expects input datanames to have the suffix `_FILTERED`. + ### New features * `data_extract_ui`, `data_extract_srv`, `data_extract_multiple_srv` can be initialized by the list of (optionally `reactive`) `data.frame` objects. diff --git a/R/data_merge_module.R b/R/data_merge_module.R index c6296976..db9d9846 100644 --- a/R/data_merge_module.R +++ b/R/data_merge_module.R @@ -259,7 +259,6 @@ data_merge_srv <- function(id = "merge_id", ) ch <- teal.code::chunks_new() datasets_list_nr <- sapply(datasets$datanames(), simplify = FALSE, datasets$get_data, filtered = TRUE) - names(datasets_list_nr) <- paste0(names(datasets_list_nr), "_FILTERED") teal.code::chunks_reset(envir = list2env(datasets_list_nr), chunks = ch) for (chunk in merged_data$expr) teal.code::chunks_push(expression = chunk, chunks = ch) diff --git a/R/get_dplyr_call.R b/R/get_dplyr_call.R index f09d63af..c277a66a 100644 --- a/R/get_dplyr_call.R +++ b/R/get_dplyr_call.R @@ -216,7 +216,7 @@ get_dplyr_call <- function(selector_list, n_selectors <- length(selector_list) - dataname_filtered <- as.name(paste0(selector_list[[idx]]$dataname, "_FILTERED")) + dataname_filtered <- as.name(selector_list[[idx]]$dataname) filter_call <- get_filter_call(selector_list[[idx]]$filters, selector_list[[idx]]$dataname, datasets) diff --git a/tests/testthat/test-dplyr_call_examples.R b/tests/testthat/test-dplyr_call_examples.R index 0da8745a..0c3707ce 100644 --- a/tests/testthat/test-dplyr_call_examples.R +++ b/tests/testthat/test-dplyr_call_examples.R @@ -146,7 +146,7 @@ testthat::test_that("Single wide dataset", { testthat::expect_identical( get_dplyr_call(merged_selectors1, join_keys = jk1), quote( - ADSL_FILTERED %>% + ADSL %>% dplyr::select(STUDYID, USUBJID, AGE) ) ) @@ -176,7 +176,7 @@ testthat::test_that("Single wide dataset", { testthat::expect_identical( get_dplyr_call(merged_selectors2, join_keys = jk2), quote( - ADSL_FILTERED %>% + ADSL %>% dplyr::select(STUDYID, USUBJID, AGE, SEX) ) ) @@ -214,7 +214,7 @@ testthat::test_that("Single wide dataset", { testthat::expect_identical( get_dplyr_call(merged_selectors3, join_keys = jk3), quote( - ADSL_FILTERED %>% + ADSL %>% dplyr::select(STUDYID, USUBJID, AGE, SEX, BMRKR1) ) ) @@ -268,7 +268,7 @@ testthat::test_that("Single wide dataset", { testthat::expect_identical( get_dplyr_call(merged_selectors4, join_keys = jk4), quote( - ADSL_FILTERED %>% + ADSL %>% dplyr::select(STUDYID, USUBJID, AGE, SEX, BMRKR1, STRATA, ARMCD, COUNTRY) ) ) @@ -322,7 +322,7 @@ testthat::test_that("Single wide dataset", { testthat::expect_identical( get_dplyr_call(merged_selectors5, join_keys = jk5), quote( - ADSL_FILTERED %>% + ADSL %>% dplyr::select(STUDYID, USUBJID, STRATA, ARMCD, BMRKR1, COUNTRY) ) ) @@ -352,7 +352,7 @@ testthat::test_that("Single wide dataset", { testthat::expect_identical( get_dplyr_call(merged_selectors6, join_keys = jk6), quote( - ADSL_FILTERED %>% + ADSL %>% dplyr::filter(SEX == "F") %>% dplyr::select(STUDYID, USUBJID, AGE) ) @@ -383,7 +383,7 @@ testthat::test_that("Single wide dataset", { testthat::expect_identical( get_dplyr_call(merged_selectors7, join_keys = jk7), quote( - ADSL_FILTERED %>% + ADSL %>% dplyr::filter(STUDYID == "STUDY1") %>% dplyr::select(STUDYID, USUBJID, AGE) ) @@ -414,7 +414,7 @@ testthat::test_that("Single wide dataset", { testthat::expect_identical( get_dplyr_call(merged_selectors8, join_keys = jk8), quote( - ADSL_FILTERED %>% + ADSL %>% dplyr::filter(STUDYID == "STUDY1") %>% dplyr::select(USUBJID, AGE) ) @@ -445,7 +445,7 @@ testthat::test_that("Single wide dataset", { testthat::expect_identical( get_dplyr_call(merged_selectors9, join_keys = jk9), quote( - ADSL_FILTERED %>% + ADSL %>% dplyr::filter(STUDYID == "STUDY1") %>% dplyr::select(USUBJID, AGE, STUDYID) ) @@ -493,11 +493,11 @@ testthat::test_that("Multiple wide dataset", { ), list( quote( - ADSL_FILTERED %>% + ADSL %>% dplyr::select(STUDYID, USUBJID, AGE) ), quote( - ADSL2_FILTERED %>% + ADSL2 %>% dplyr::select(STUDYID, USUBJID, SEX, STRATA) ) ) @@ -544,11 +544,11 @@ testthat::test_that("Multiple wide dataset", { ), list( quote( - ADSL_FILTERED %>% + ADSL %>% dplyr::select(STUDYID, USUBJID, AGE) ), quote( - ADSL2_FILTERED %>% + ADSL2 %>% dplyr::select(STUDYID, USUBJID) ) ) @@ -613,17 +613,17 @@ testthat::test_that("Multiple wide dataset", { ), list( quote( - ADSL_FILTERED %>% + ADSL %>% dplyr::select(STUDYID, USUBJID, AGE) %>% dplyr::rename(x1.AGE = AGE) ), quote( - ADSL2_FILTERED %>% + ADSL2 %>% dplyr::select(STUDYID, USUBJID, AGE, SEX, STRATA, BMRKR1) %>% dplyr::rename(x2.AGE = AGE, x2.SEX = SEX, x2.STRATA = STRATA) ), quote( - ADSL3_FILTERED %>% + ADSL3 %>% dplyr::select(STUDYID, USUBJID, AGE, SEX, STRATA) %>% dplyr::rename(x3.AGE = AGE, x3.SEX = SEX, x3.STRATA = STRATA) ) @@ -690,17 +690,17 @@ testthat::test_that("Multiple wide dataset", { ), list( quote( - ADSL_FILTERED %>% + ADSL %>% dplyr::select(STUDYID, USUBJID, AGE) %>% dplyr::rename(x1.AGE = AGE) ), quote( - ADSL2_FILTERED %>% + ADSL2 %>% dplyr::select(STUDYID, USUBJID, AGE, SEX) %>% dplyr::rename(x2.AGE = AGE) ), quote( - ADSL3_FILTERED %>% + ADSL3 %>% dplyr::select(STUDYID, USUBJID) ) ) @@ -774,17 +774,17 @@ testthat::test_that("Multiple wide dataset", { ), list( quote( - ADSL_FILTERED %>% + ADSL %>% dplyr::select(STUDYID, USUBJID, AGE) %>% dplyr::rename(x1.AGE = AGE) ), quote( - ADSL2_FILTERED %>% + ADSL2 %>% dplyr::select(STUDYID, USUBJID, AGE, SEX, STRATA, BMRKR1) %>% dplyr::rename(x2.AGE = AGE, x2.SEX = SEX, x2.STRATA = STRATA) ), quote( - ADSL3_FILTERED %>% + ADSL3 %>% dplyr::select(STUDYID, USUBJID, AGE, SEX, STRATA) %>% dplyr::rename(x4.AGE = AGE, x4.SEX = SEX, x4.STRATA = STRATA) ) @@ -823,7 +823,7 @@ testthat::test_that("Single long dataset", { testthat::expect_identical( get_dplyr_call(merged_selectors1, join_keys = jk1), quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD == "BESRSPI") %>% dplyr::select(STUDYID, USUBJID, PARAMCD, AVISIT, AGE) ) @@ -854,7 +854,7 @@ testthat::test_that("Single long dataset", { testthat::expect_identical( get_dplyr_call(merged_selectors1, join_keys = jk1), quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD == "BESRSPI") %>% dplyr::select(STUDYID, USUBJID, AVISIT, AGE) ) @@ -888,7 +888,7 @@ testthat::test_that("Single long dataset", { testthat::expect_equal( get_dplyr_call(merged_selectors2, join_keys = jk2), quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD == "BESRSPI" & AVISIT %in% c("BASELINE", "SCREENING")) %>% dplyr::select(STUDYID, USUBJID, AVISIT, AGE, SEX) @@ -934,7 +934,7 @@ testthat::test_that("Single long dataset", { testthat::expect_equal( deparse(get_dplyr_call(merged_selectors3, join_keys = jk3), 120), deparse(quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD == "BESRSPI" & AVISIT %in% c("BASELINE", "SCREENING")) %>% dplyr::select(STUDYID, USUBJID, PARAMCD, AVISIT, AGE, SEX, BMRKR1) @@ -986,13 +986,13 @@ testthat::test_that("Single long dataset", { ), list( quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD == "BESRSPI" & AVISIT %in% c("BASELINE", "SCREENING")) %>% dplyr::select(STUDYID, USUBJID, AVISIT, AGE) %>% dplyr::rename(x1.AGE = AGE) ), quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD == "BESRSPI" & AVISIT %in% c("BASELINE", "SCREENING")) %>% dplyr::select(STUDYID, USUBJID, PARAMCD, AVISIT, SEX, AGE, BMRKR1) %>% dplyr::rename(x2.AGE = AGE) @@ -1047,13 +1047,13 @@ testthat::test_that("Single long dataset", { ), list( quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD == "BESRSPI" & AVISIT == "BASELINE") %>% dplyr::select(STUDYID, USUBJID, AGE) %>% dplyr::rename(x1.AGE = AGE) ), quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD == "BESRSPI" & AVISIT == "SCREENING") %>% dplyr::select(STUDYID, USUBJID, SEX, AGE, BMRKR1) %>% dplyr::rename(x2.AGE = AGE) @@ -1104,13 +1104,13 @@ testthat::test_that("Single long dataset", { ), list( quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD == "BESRSPI" & AVISIT == "BASELINE") %>% dplyr::select(STUDYID, USUBJID, AGE) %>% dplyr::rename(x1.AGE = AGE) ), quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD == "BESRSPI") %>% dplyr::select(STUDYID, USUBJID, AVISIT, SEX, AGE, BMRKR1) %>% dplyr::rename(x2.AGE = AGE) @@ -1164,14 +1164,14 @@ testthat::test_that("Single long dataset", { ), list( deparse(quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD == "BESRSPI" & AVISIT %in% c("BASELINE", "SCREENING")) %>% dplyr::select(STUDYID, USUBJID, AVISIT, AGE) %>% dplyr::rename(x1.AGE = AGE) ), 120), deparse(quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD == "BESRSPI" & AVISIT %in% c("SCREENING", "FOLLOW UP")) %>% dplyr::select(STUDYID, USUBJID, AVISIT, SEX, AGE, BMRKR1) %>% @@ -1227,14 +1227,14 @@ testthat::test_that("Single long dataset", { ), list( quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD == "BESRSPI" & AVISIT %in% c("BASELINE", "SCREENING") & SEX %in% c("F", "M")) %>% dplyr::select(STUDYID, USUBJID, AVISIT, AGE) %>% dplyr::rename(x1.AGE = AGE) ), quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD == "INVET" & AVISIT %in% c("SCREENING", "FOLLOW UP")) %>% dplyr::select(STUDYID, USUBJID, AVISIT, SEX, AGE, BMRKR1) %>% @@ -1303,19 +1303,19 @@ testthat::test_that("Single long dataset", { ), list( quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD == "INVET" & AVISIT %in% c("BASELINE", "SCREENING") & SEX %in% c("F", "M")) %>% dplyr::select(STUDYID, USUBJID, AVISIT, AGE) %>% dplyr::rename(x1.AGE = AGE) ), quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD == "BESRSPI" & AVISIT == "SCREENING") %>% dplyr::select(STUDYID, USUBJID) ), quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD == "BESRSPI" & AVISIT %in% c("SCREENING", "FOLLOW UP")) %>% dplyr::select(STUDYID, USUBJID, AVISIT, AVAL, AGE) %>% @@ -1353,7 +1353,7 @@ testthat::test_that("Single long dataset", { testthat::expect_identical( get_dplyr_call(merged_selectors9, join_keys = jk9), quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD == "BESRSPI") %>% dplyr::select(STUDYID, USUBJID, AVISIT, PARAMCD, AVAL) %>% tidyr::pivot_longer(cols = "AVAL", names_to = "MEASURE", values_to = "VALUE") %>% @@ -1395,7 +1395,7 @@ testthat::test_that("Single long dataset", { testthat::expect_equal( get_dplyr_call(merged_selectors10, join_keys = jk10), quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD == "BESRSPI" & AVISIT %in% c("BASELINE", "SCREENING")) %>% dplyr::select(STUDYID, USUBJID, PARAMCD, AVISIT, AVAL) %>% @@ -1439,7 +1439,7 @@ testthat::test_that("Single long dataset", { testthat::expect_equal( get_dplyr_call(merged_selectors11, join_keys = jk11), quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD == "BESRSPI" & SEX %in% c("M", "F")) %>% dplyr::select(STUDYID, USUBJID, AVISIT, PARAMCD, AVAL) %>% @@ -1493,7 +1493,7 @@ testthat::test_that("Single long dataset", { testthat::expect_equal( get_dplyr_call(merged_selectors12, 1L, jk12), quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD == "BESRSPI" & AVISIT %in% c("BASELINE", "SCREENING")) %>% dplyr::select(STUDYID, USUBJID, PARAMCD, AVISIT, AVAL) %>% tidyr::pivot_longer(cols = "AVAL", names_to = "MEASURE", values_to = "VALUE") %>% @@ -1550,7 +1550,7 @@ testthat::test_that("Single long dataset", { ), list( quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD == "INVET" & AVISIT %in% c("BASELINE", "SCREENING")) %>% dplyr::select(STUDYID, USUBJID, PARAMCD, AVISIT, AVAL) %>% @@ -1560,7 +1560,7 @@ testthat::test_that("Single long dataset", { tidyr::pivot_wider(names_from = "KEY", values_from = "VALUE") ), quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD == "BESRSPI" & AVISIT %in% c("SCREENING", "FOLLOW UP")) %>% dplyr::select(STUDYID, USUBJID, PARAMCD, AVISIT, AVAL) %>% @@ -1625,7 +1625,7 @@ testthat::test_that("Single long dataset", { ), list( quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD == "BESRSPI" & AVISIT %in% c("BASELINE", "SCREENING")) %>% dplyr::select(STUDYID, USUBJID, PARAMCD, AVISIT) %>% @@ -1634,7 +1634,7 @@ testthat::test_that("Single long dataset", { tidyr::pivot_wider(names_from = "KEY", values_from = "VALUE") ), quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD == "BESRSPI" & AVISIT %in% c("SCREENING", "FOLLOW UP")) %>% dplyr::select(STUDYID, USUBJID, PARAMCD, AVISIT, AVAL) %>% @@ -1695,7 +1695,7 @@ testthat::test_that("Single long dataset", { ), list( quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(SEX %in% c("M", "F")) %>% dplyr::select(STUDYID, USUBJID, PARAMCD, AVISIT, AVAL) %>% dplyr::rename(x1.AVAL = AVAL) %>% @@ -1704,7 +1704,7 @@ testthat::test_that("Single long dataset", { tidyr::pivot_wider(names_from = "KEY", values_from = "VALUE") ), quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD == "BESRSPI" & AVISIT %in% c("SCREENING", "FOLLOW UP")) %>% dplyr::select(STUDYID, USUBJID, PARAMCD, AVISIT, AVAL) %>% @@ -1779,7 +1779,7 @@ testthat::test_that("Single long dataset", { ), list( deparse(quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(AVISIT %in% c("BASELINE", "SCREENING") & SEX %in% c("F", "M")) %>% dplyr::select(STUDYID, USUBJID, PARAMCD, AVISIT, AVAL) %>% dplyr::rename(x1.AVAL = AVAL) %>% @@ -1788,7 +1788,7 @@ testthat::test_that("Single long dataset", { tidyr::pivot_wider(names_from = "KEY", values_from = "VALUE") ), 120), deparse(quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD == "INVET" & AVISIT == "SCREENING") %>% dplyr::select(STUDYID, USUBJID, PARAMCD, AVISIT, AVAL) %>% @@ -1798,7 +1798,7 @@ testthat::test_that("Single long dataset", { tidyr::pivot_wider(names_from = "KEY", values_from = "VALUE") ), 120), deparse(quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD == "BESRSPI" & AVISIT %in% c("SCREENING", "FOLLOW UP")) %>% dplyr::select(STUDYID, USUBJID, PARAMCD, AVISIT, AVAL, AGE) %>% dplyr::rename(x3.AVAL = AVAL) %>% @@ -1879,7 +1879,7 @@ testthat::test_that("Single long dataset", { ), list( deparse(quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD %in% c("BESRSPI", "INVET") & AVISIT %in% c("BASELINE", "SCREENING") & SEX %in% c("F", "M")) %>% @@ -1890,7 +1890,7 @@ testthat::test_that("Single long dataset", { tidyr::pivot_wider(names_from = "KEY", values_from = "VALUE") ), 200), deparse(quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD == "BESRSPI" & AVISIT == "SCREENING") %>% dplyr::select(STUDYID, USUBJID, PARAMCD, AVISIT, AVAL) %>% dplyr::rename(x2.AVAL = AVAL) %>% @@ -1899,7 +1899,7 @@ testthat::test_that("Single long dataset", { tidyr::pivot_wider(names_from = "KEY", values_from = "VALUE") ), 200), deparse(quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD == "BESRSPI" & AVISIT %in% c("SCREENING", "FOLLOW UP")) %>% dplyr::select(STUDYID, USUBJID, PARAMCD, AVISIT, AVAL, AGE) %>% dplyr::rename(x3.AVAL = AVAL) %>% @@ -1953,7 +1953,7 @@ testthat::test_that("Single long dataset", { testthat::expect_identical( get_dplyr_call(merged_selectors18, join_keys = jk18), quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD == "BESRSPI") %>% dplyr::select(STUDYID, USUBJID, AVISIT, PARAMCD, AVAL) %>% tidyr::pivot_longer(cols = "AVAL", names_to = "MEASURE", values_to = "VALUE") %>% @@ -2024,7 +2024,7 @@ testthat::test_that("Single long dataset", { ), list( quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD == "BESRSPI" & AVISIT %in% c("BASELINE", "SCREENING") & SEX %in% c("F", "M")) %>% @@ -2032,13 +2032,13 @@ testthat::test_that("Single long dataset", { dplyr::rename(x1.PARAMCD = PARAMCD, x1.AGE = AGE) ), quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD == "BESRSPI" & AVISIT == "SCREENING") %>% dplyr::select(STUDYID, USUBJID, PARAMCD, AVISIT) %>% dplyr::rename(x2.PARAMCD = PARAMCD, x2.AVISIT = AVISIT) ), quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD == "BESRSPI" & AVISIT %in% c("SCREENING", "FOLLOW UP")) %>% dplyr::select(STUDYID, USUBJID, AVISIT, PARAMCD, AVAL, AGE) %>% @@ -2089,7 +2089,7 @@ testthat::test_that("Single long dataset", { testthat::expect_equal( get_dplyr_call(merged_selectors21, join_keys = jk21), quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter((PARAMCD == "BESRSPI" & AVISIT == "SCREENING") & SEX == "F") %>% dplyr::select(STUDYID, USUBJID, AGE, SEX) # attribute of the data_extract ) @@ -2195,34 +2195,34 @@ testthat::test_that("Single long dataset", { testthat::expect_equal( list( - get_dplyr_call(merged_selectors22, 1L, jk22), - get_dplyr_call(merged_selectors22, 2L, jk22), - get_dplyr_call(merged_selectors22, 3L, jk22) + deparse1(get_dplyr_call(merged_selectors22, 1L, jk22)), + deparse1(get_dplyr_call(merged_selectors22, 2L, jk22)), + deparse1(get_dplyr_call(merged_selectors22, 3L, jk22)) ), list( # x1 and x3 are from the identical dataset - select(s) are combined # so output are just three ANLs instead of four - quote( - ADRS_FILTERED %>% + deparse1(quote( + ADRS %>% dplyr::filter((PARAMCD == "BESRSPI" & AVISIT == "SCREENING") & SEX == "F") %>% dplyr::select(STUDYID, USUBJID, AGE, PARAMCD, COUNTRY, AVISIT) %>% dplyr::rename(x1.AGE = AGE, x1.PARAMCD = PARAMCD, x1.AVISIT = AVISIT) - ), - quote( - ADRS_FILTERED %>% + )), + deparse1(quote( + ADRS %>% dplyr::filter((PARAMCD == "BESRSPI" & AVISIT == "BASELINE") & SEX == "M") %>% dplyr::select(STUDYID, USUBJID, AGE, AVISIT) %>% dplyr::rename(x2.AGE = AGE, x2.AVISIT = AVISIT) - ), - quote( - ADRS_FILTERED %>% + )), + deparse1(quote( + ADRS %>% dplyr::filter((PARAMCD == "INVET" & AVISIT == "BASELINE") & SEX == "F") %>% dplyr::select(STUDYID, USUBJID, PARAMCD, AVISIT, AVAL, AGE) %>% dplyr::rename(x4.AGE = AGE) %>% tidyr::pivot_longer(cols = c("AVAL", "x4.AGE"), names_to = "MEASURE", values_to = "VALUE") %>% tidyr::unite(KEY, MEASURE, PARAMCD, AVISIT) %>% tidyr::pivot_wider(names_from = "KEY", values_from = "VALUE") - ) + )) ) ) # AVISIT should be included in select @@ -2270,12 +2270,12 @@ testthat::test_that("Multiple long datasets", { ), list( quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::select(STUDYID, USUBJID, AVAL) %>% dplyr::rename(x1.AVAL = AVAL) ), quote( - ADTTE_FILTERED %>% + ADTTE %>% dplyr::select(STUDYID, USUBJID, AVAL, AGE) %>% dplyr::rename(x2.AVAL = AVAL) ) @@ -2323,12 +2323,12 @@ testthat::test_that("Multiple long datasets", { ), list( quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::select(USUBJID, STUDYID, AVAL) %>% dplyr::rename(x1.AVAL = AVAL) ), quote( - ADTTE_FILTERED %>% + ADTTE %>% dplyr::select(STUDYID, USUBJID, AVAL, AGE) %>% dplyr::rename(x2.AVAL = AVAL) ) @@ -2382,13 +2382,13 @@ testthat::test_that("Multiple long datasets", { ), list( quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD == "BESRSPI" & AVISIT == "SCREENING") %>% dplyr::select(STUDYID, USUBJID, AVAL) %>% dplyr::rename(x1.AVAL = AVAL) ), quote( - ADTTE_FILTERED %>% + ADTTE %>% dplyr::select(STUDYID, USUBJID, AVAL, AGE) %>% dplyr::rename(x2.AVAL = AVAL) ) @@ -2438,13 +2438,13 @@ testthat::test_that("Multiple long datasets", { ), list( quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD == "BESRSPI" & AVISIT == "SCREENING") %>% dplyr::select(STUDYID, USUBJID, AVAL) %>% dplyr::rename(x1.AVAL = AVAL) ), deparse(quote( - ADTTE_FILTERED %>% + ADTTE %>% dplyr::filter(PARAMCD %in% c("EFS", "PFS")) %>% dplyr::select(STUDYID, USUBJID, AVAL, AGE) %>% dplyr::rename(x2.AVAL = AVAL) @@ -2496,12 +2496,12 @@ testthat::test_that("Multiple long datasets", { ), list( deparse(quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD == "BESRSPI" & AVISIT == "SCREENING") %>% dplyr::select(STUDYID, USUBJID) ), 120), deparse(quote( - ADTTE_FILTERED %>% + ADTTE %>% dplyr::filter(PARAMCD %in% c("EFS", "PFS")) %>% dplyr::select(STUDYID, USUBJID, AVAL, AGE) ), 120) @@ -2552,13 +2552,13 @@ testthat::test_that("Multiple long datasets", { ), list( quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD == "BESRSPI" & AVISIT == "SCREENING") %>% dplyr::select(STUDYID, USUBJID, AVAL) %>% dplyr::rename(x1.AVAL = AVAL) ), deparse(quote( - ADTTE_FILTERED %>% + ADTTE %>% dplyr::filter(PARAMCD %in% c("EFS", "PFS")) %>% dplyr::select(STUDYID, USUBJID, PARAMCD, AVAL, AGE) %>% dplyr::rename(x2.AVAL = AVAL) %>% @@ -2617,7 +2617,7 @@ testthat::test_that("Multiple long datasets", { ), list( quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD == "BESRSPI" & AVISIT == "SCREENING") %>% dplyr::select(STUDYID, USUBJID, PARAMCD, AVISIT, AVAL) %>% dplyr::rename(x1.AVAL = AVAL) %>% @@ -2626,7 +2626,7 @@ testthat::test_that("Multiple long datasets", { tidyr::pivot_wider(names_from = "KEY", values_from = "VALUE") ), deparse(quote( - ADTTE_FILTERED %>% + ADTTE %>% dplyr::filter(PARAMCD %in% c("EFS", "PFS")) %>% dplyr::select(STUDYID, USUBJID, PARAMCD, AVAL, AGE) %>% dplyr::rename(x2.AVAL = AVAL) %>% @@ -2694,7 +2694,7 @@ testthat::test_that("Multiple long datasets", { deparse(get_dplyr_call(merged_selectors8, 3L, jk8), width.cutoff = 120) ), list( - deparse(quote(ADRS_FILTERED %>% + deparse(quote(ADRS %>% dplyr::filter(PARAMCD == "BESRSPI" & AVISIT == "SCREENING") %>% dplyr::select(STUDYID, USUBJID, PARAMCD, AVISIT, AVAL) %>% dplyr::rename(x1.AVAL = AVAL) %>% @@ -2702,7 +2702,7 @@ testthat::test_that("Multiple long datasets", { tidyr::unite(KEY, MEASURE, PARAMCD, AVISIT) %>% tidyr::pivot_wider(names_from = "KEY", values_from = "VALUE")), width.cutoff = 120), deparse(quote( - ADTTE_FILTERED %>% + ADTTE %>% dplyr::filter(PARAMCD %in% c("EFS", "PFS")) %>% dplyr::select(STUDYID, USUBJID, PARAMCD, AVAL, AGE) %>% dplyr::rename(x2.AVAL = AVAL, x2.AGE = AGE) %>% @@ -2711,7 +2711,7 @@ testthat::test_that("Multiple long datasets", { tidyr::pivot_wider(names_from = "KEY", values_from = "VALUE") ), width.cutoff = 120), deparse(quote( - ADSL_FILTERED %>% + ADSL %>% dplyr::select(STUDYID, USUBJID, AGE) %>% dplyr::rename(x3.AGE = AGE) ), width.cutoff = 120) @@ -2796,13 +2796,13 @@ testthat::test_that("Multiple long datasets", { ), list( deparse(quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD == "BESRSPI") %>% dplyr::select(STUDYID, USUBJID, AVISIT, AVAL) %>% dplyr::rename(x1.AVAL = AVAL) ), 120), deparse(quote( - ADTTE_FILTERED %>% + ADTTE %>% dplyr::filter(PARAMCD %in% c("EFS", "PFS")) %>% dplyr::select(STUDYID, USUBJID, PARAMCD, AVAL, AGE) %>% dplyr::rename(x2.AVAL = AVAL, x2.AGE = AGE) %>% @@ -2811,12 +2811,12 @@ testthat::test_that("Multiple long datasets", { tidyr::pivot_wider(names_from = "KEY", values_from = "VALUE") ), 120), deparse(quote( - ADSL_FILTERED %>% + ADSL %>% dplyr::select(STUDYID, USUBJID, AGE) %>% dplyr::rename(x3.AGE = AGE) ), 120), deparse(quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD == "BESRSPI" & AVISIT %in% c("SCREENING", "BASELINE")) %>% dplyr::select(STUDYID, USUBJID, AVISIT, AVAL) %>% dplyr::rename(x4.AVAL = AVAL) @@ -2900,13 +2900,13 @@ testthat::test_that("Multiple long datasets", { ), list( quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD == "BESRSPI") %>% dplyr::select(STUDYID, USUBJID, AVAL, AGE) %>% dplyr::rename(x1.AVAL = AVAL, x1.AGE = AGE) ), deparse(quote( - ADTTE_FILTERED %>% + ADTTE %>% dplyr::filter(PARAMCD %in% c("EFS", "PFS")) %>% dplyr::select(STUDYID, USUBJID, PARAMCD, AVAL, AGE) %>% dplyr::rename(x2.AVAL = AVAL, x2.AGE = AGE) %>% @@ -2915,7 +2915,7 @@ testthat::test_that("Multiple long datasets", { tidyr::pivot_wider(names_from = "KEY", values_from = "VALUE") ), 120), quote( - ADSL_FILTERED %>% + ADSL %>% dplyr::select(STUDYID, USUBJID, AGE) %>% dplyr::rename(x3.AGE = AGE) ) @@ -2971,13 +2971,13 @@ testthat::test_that("Multiple long datasets", { ), list( quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter(PARAMCD == "BESRSPI" & AVISIT == "SCREENING" & SEX == "F") %>% dplyr::select(STUDYID, USUBJID, AVAL) %>% dplyr::rename(x1.AVAL = AVAL) ), deparse(quote( - ADTTE_FILTERED %>% + ADTTE %>% dplyr::filter(RACE == "ASIAN" & PARAMCD %in% c("EFS", "PFS")) %>% dplyr::select(STUDYID, USUBJID, AVAL, AGE) %>% dplyr::rename(x2.AVAL = AVAL) @@ -3055,13 +3055,13 @@ testthat::test_that("Multiple long - combined/concatenated filters", { ), list( quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter((PARAMCD == "BESRSPI" & AVISIT == "SCREENING") & SEX == "F") %>% dplyr::select(STUDYID, USUBJID, PARAMCD, AVAL) %>% dplyr::rename(x1.AVAL = AVAL) ), deparse(quote( - ADTTE_FILTERED %>% + ADTTE %>% dplyr::filter(RACE == "ASIAN" & PARAMCD %in% c("EFS", "PFS")) %>% dplyr::select(STUDYID, USUBJID, PARAMCD, AVAL, AGE) %>% dplyr::rename(x2.AVAL = AVAL) @@ -3120,7 +3120,7 @@ testthat::test_that("Multiple long - combined/concatenated filters", { ), list( deparse(quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter((PARAMCD == "BESRSPI" & AVISIT == "SCREENING")) %>% dplyr::select(STUDYID, USUBJID, PARAMCD, AVISIT, AVAL) %>% dplyr::rename(x1.AVAL = AVAL) %>% @@ -3129,7 +3129,7 @@ testthat::test_that("Multiple long - combined/concatenated filters", { tidyr::pivot_wider(names_from = "KEY", values_from = "VALUE") ), width.cutoff = 120), deparse(quote( - ADTTE_FILTERED %>% + ADTTE %>% dplyr::filter(PARAMCD %in% c("EFS", "PFS")) %>% dplyr::select(STUDYID, USUBJID, PARAMCD, AVAL, AGE) %>% dplyr::rename(x2.AVAL = AVAL) %>% @@ -3209,19 +3209,19 @@ testthat::test_that("Multiple long - combined/concatenated filters", { ), list( quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter((PARAMCD == "BESRSPI" & AVISIT == "SCREENING") & SEX == "F") %>% dplyr::select(STUDYID, USUBJID, AVAL) %>% dplyr::rename(x1.AVAL = AVAL) ), deparse(quote( - ADTTE_FILTERED %>% + ADTTE %>% dplyr::filter(RACE == "ASIAN" & PARAMCD %in% c("EFS", "PFS")) %>% dplyr::select(STUDYID, USUBJID, AVAL, AGE) %>% dplyr::rename(x2.AVAL = AVAL) ), 120), quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter((PARAMCD == "OVRINV" & AVISIT == "FOLLOW UP")) %>% dplyr::select(STUDYID, USUBJID, AVAL) %>% dplyr::rename(x3.AVAL = AVAL) @@ -3291,7 +3291,7 @@ testthat::test_that("Multiple long - combined/concatenated filters", { ), list( quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter( (PARAMCD == "BESRSPI" & AVISIT == "END OF INDUCTION" & SEX == "F") | (PARAMCD == "BESRSPI" & AVISIT == "END OF INDUCTION" & SEX == "M") @@ -3300,13 +3300,13 @@ testthat::test_that("Multiple long - combined/concatenated filters", { dplyr::rename(x1.AVAL = AVAL) ), deparse(quote( - ADTTE_FILTERED %>% + ADTTE %>% dplyr::filter(RACE == "ASIAN" & PARAMCD %in% c("EFS", "PFS")) %>% dplyr::select(STUDYID, USUBJID, AVAL, AGE) %>% dplyr::rename(x2.AVAL = AVAL) ), 120), quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter((PARAMCD == "OVRINV" & AVISIT == "FOLLOW UP")) %>% dplyr::select(STUDYID, USUBJID, AVAL) %>% dplyr::rename(x3.AVAL = AVAL) @@ -3362,7 +3362,7 @@ testthat::test_that("Multiple long - combined/concatenated filters", { ), list( quote( - ADRS_FILTERED %>% + ADRS %>% dplyr::filter((PARAMCD == "BESRSPI" & SEX == "F") | (PARAMCD == "BESRSPI" & SEX == "M")) %>% dplyr::select(STUDYID, USUBJID, PARAMCD, AVAL) %>% dplyr::rename(x1.AVAL = AVAL) %>% @@ -3371,7 +3371,7 @@ testthat::test_that("Multiple long - combined/concatenated filters", { tidyr::pivot_wider(names_from = "KEY", values_from = "VALUE") ), deparse(quote( - ADTTE_FILTERED %>% + ADTTE %>% dplyr::filter(RACE == "ASIAN" & PARAMCD %in% c("EFS", "PFS")) %>% dplyr::select(STUDYID, USUBJID, AVAL, AGE) %>% dplyr::rename(x2.AVAL = AVAL) @@ -3442,9 +3442,9 @@ testthat::test_that("Universal example", { paste(merged_datasets$expr), paste( c( - "ANL_1 <- X_FILTERED %>% dplyr::select(A, B, D, E)", - "ANL_2 <- Y_FILTERED %>% dplyr::select(A, B, C, G) %>% dplyr::rename(y.G = G)", - "ANL_3 <- Z_FILTERED %>% dplyr::select(D, C, F, G) %>% dplyr::rename(z.G = G)", + "ANL_1 <- X %>% dplyr::select(A, B, D, E)", + "ANL_2 <- Y %>% dplyr::select(A, B, C, G) %>% dplyr::rename(y.G = G)", + "ANL_3 <- Z %>% dplyr::select(D, C, F, G) %>% dplyr::rename(z.G = G)", "ANL <- ANL_1", "ANL <- dplyr::left_join(ANL, ANL_2, by = c(\"A\", \"B\"))", "ANL <- dplyr::left_join(ANL, ANL_3, by = c(\"D\", \"C\"))" diff --git a/tests/testthat/test-get_dplyr_call.R b/tests/testthat/test-get_dplyr_call.R index 5df5c4ed..61386ada 100644 --- a/tests/testthat/test-get_dplyr_call.R +++ b/tests/testthat/test-get_dplyr_call.R @@ -166,7 +166,7 @@ testthat::test_that("get_dplyr_call - single filter and single select", { )), join_keys = teal.data::join_keys(teal.data::join_key("ADSL", "ADSL", teal.data::get_cdisc_keys("ADSL"))) ), - quote(ADSL_FILTERED %>% dplyr::select(STUDYID, USUBJID)) + quote(ADSL %>% dplyr::select(STUDYID, USUBJID)) ) # filter call, default select @@ -183,7 +183,7 @@ testthat::test_that("get_dplyr_call - single filter and single select", { join_keys = teal.data::join_keys(teal.data::join_key("ADSL", "ADSL", teal.data::get_cdisc_keys("ADSL"))) ), quote( - ADSL_FILTERED %>% + ADSL %>% dplyr::filter(SEX %in% c("F", "M")) %>% dplyr::select(STUDYID, USUBJID) ) @@ -203,7 +203,7 @@ testthat::test_that("get_dplyr_call - single filter and single select", { join_keys = teal.data::join_keys(teal.data::join_key("ADSL", "ADSL", teal.data::get_cdisc_keys("ADSL"))) ), quote( - ADSL_FILTERED %>% + ADSL %>% dplyr::filter(SEX %in% c("F", "M")) %>% dplyr::select(STUDYID, USUBJID, AVAL) ) @@ -223,7 +223,7 @@ testthat::test_that("get_dplyr_call - single filter and single select", { join_keys = teal.data::join_keys(teal.data::join_key("ADSL", "ADSL", teal.data::get_cdisc_keys("ADSL"))) ), quote( - ADSL_FILTERED %>% + ADSL %>% dplyr::filter(SEX == "F") %>% dplyr::select(STUDYID, USUBJID, AVAL, SEX) ) @@ -244,7 +244,7 @@ testthat::test_that("get_dplyr_call - single filter and single select", { join_keys = teal.data::join_keys(teal.data::join_key("ADSL", "ADSL", teal.data::get_cdisc_keys("ADSL"))) ), quote( - ADSL_FILTERED %>% + ADSL %>% dplyr::filter(SEX == "F") %>% dplyr::select(STUDYID, USUBJID, AVAL, SEX) ) @@ -264,7 +264,7 @@ testthat::test_that("get_dplyr_call - single filter and single select", { join_keys = teal.data::join_keys(teal.data::join_key("ADSL", "ADSL", teal.data::get_cdisc_keys("ADSL"))) ), quote( - ADSL_FILTERED %>% + ADSL %>% dplyr::filter(STUDYID == "ANY") %>% dplyr::select(USUBJID, AVAL) ) @@ -284,7 +284,7 @@ testthat::test_that("get_dplyr_call - single filter and single select", { join_keys = teal.data::join_keys(teal.data::join_key("ADSL", "ADSL", teal.data::get_cdisc_keys("ADSL"))) ), quote( - ADSL_FILTERED %>% + ADSL %>% dplyr::filter(STUDYID == "ANY") %>% dplyr::select(STUDYID, USUBJID, AVAL) ) @@ -317,7 +317,7 @@ testthat::test_that("get_dplyr_call - multiple filter(s) or multiple select(s)", join_keys = teal.data::join_keys(teal.data::join_key("ADSL", "ADSL", teal.data::get_cdisc_keys("ADSL"))) ), quote( - ADSL_FILTERED %>% + ADSL %>% dplyr::select(STUDYID, USUBJID, COL_1, COL_2) %>% dplyr::rename(test1.COL_2 = COL_2) ) @@ -340,7 +340,7 @@ testthat::test_that("get_dplyr_call - multiple filter(s) or multiple select(s)", )), join_keys = teal.data::join_keys(teal.data::join_key("ADLB", "ADLB", teal.data::get_cdisc_keys("ADSL"))) ), - quote(ADLB_FILTERED %>% + quote(ADLB %>% dplyr::filter((PARAMCD == "ALBCV" & AVISIT == "SCREENING") | (PARAMCD == "ALBCV" & AVISIT == "BASELINE")) %>% dplyr::select(STUDYID, USUBJID, PARAMCD, AVISIT, AVAL) %>% tidyr::pivot_longer(cols = "AVAL", names_to = "MEASURE", values_to = "VALUE") %>% @@ -366,7 +366,7 @@ testthat::test_that("get_dplyr_call - multiple filter(s) or multiple select(s)", join_keys = teal.data::join_keys(teal.data::join_key("ADLB", "ADLB", teal.data::get_cdisc_keys("ADSL"))) ), quote( - ADLB_FILTERED %>% + ADLB %>% dplyr::filter((PARAMCD == "ALBCV" & AVISIT == "SCREENING") | (PARAMCD == "ALBCV" & AVISIT == "BASELINE")) %>% dplyr::select(STUDYID, USUBJID, AVAL) ) diff --git a/tests/testthat/test-merge_expression_srv.R b/tests/testthat/test-merge_expression_srv.R index 831b9c24..f16df2ec 100644 --- a/tests/testthat/test-merge_expression_srv.R +++ b/tests/testthat/test-merge_expression_srv.R @@ -220,8 +220,8 @@ testthat::test_that("merge_expression_srv returns merge expression when passing testthat::expect_true(inherits(session$returned()$expr[[1]], "<-")) testthat::expect_identical( c( - "ANL_1 <- ADSL_FILTERED %>% dplyr::select(STUDYID, USUBJID, AGE)", - "ANL_2 <- ADLB_FILTERED %>% dplyr::select(STUDYID, USUBJID, AVAL, CHG)", + "ANL_1 <- ADSL %>% dplyr::select(STUDYID, USUBJID, AGE)", + "ANL_2 <- ADLB %>% dplyr::select(STUDYID, USUBJID, AVAL, CHG)", "ANL <- ANL_1", "ANL <- dplyr::full_join(ANL, ANL_2, by = c(\"STUDYID\", \"USUBJID\"))" ),