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insightsengineering · Apr 3, 2024 · b56f9a0 · b56f9a0
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -21,11 +21,11 @@ License: Apache License 2.0 | file LICENSE
 URL: https://github.com/insightsengineering/scda.test/
 BugReports: https://github.com/insightsengineering/scda.test/issues
 Depends:
-    formatters (>= 0.5.5),
+    formatters (>= 0.5.5.9018),
     R (>= 4.2),
-    rlistings (>= 0.2.7),
-    rtables (>= 0.6.6),
-    tern (>= 0.9.3)
+    rlistings (>= 0.2.7.9011),
+    rtables (>= 0.6.6.9011),
+    tern (>= 0.9.3.9028)
 Imports:
     pharmaverseadam (>= 0.2.0),
     random.cdisc.data (>= 0.3.14.9006)

diff --git a/tests/testthat/test-listing_adal02.R b/tests/testthat/test-listing_adal02.R
@@ -72,10 +72,10 @@ testthat::test_that("ADAL02 listing is produced correctly", {
     ) %>%
     select(USUBJID, unique(adab_x$VISN[order(adab_x$NFRLT)]), PTES)
 
-  formatters::var_labels(out) <- names(out)
+  var_labels(out) <- names(out)
 
   out <- out %>%
-    formatters::var_relabel(
+    var_relabel(
       USUBJID = "Subject ID",
       PTES = "Patient Treatment\nEmergent ADA Status"
     )

diff --git a/tests/testthat/test-listing_ael01.R b/tests/testthat/test-listing_ael01.R
@@ -3,7 +3,7 @@ testthat::test_that("AEL01 listing is produced correctly", {
     select(AESOC, AEDECOD, AELLT, AETERM) %>%
     unique()
 
-  formatters::var_labels(out) <- c(
+  var_labels(out) <- c(
     AESOC = "MedDRA System Organ Class",
     AEDECOD = "MedDRA Preferred Term",
     AELLT = "MedDRA Lowest Level Term",

diff --git a/tests/testthat/test-listing_ael01_nollt.R b/tests/testthat/test-listing_ael01_nollt.R
@@ -3,7 +3,7 @@ testthat::test_that("AEL01_NOLLT listing is produced correctly", {
     select(AESOC, AEDECOD, AETERM) %>%
     unique()
 
-  formatters::var_labels(out) <- c(
+  var_labels(out) <- c(
     AESOC = "MedDRA System Organ Class",
     AEDECOD = "MedDRA Preferred Term",
     AETERM = "Investigator-Specified\nAdverse Event Term"
@@ -14,8 +14,8 @@ testthat::test_that("AEL01_NOLLT listing is produced correctly", {
     key_cols = c("AESOC", "AEDECOD"),
     disp_cols = names(out),
     default_formatting = list(
-      all = formatters::fmt_config(align = "left"),
-      numeric = formatters::fmt_config(align = "center")
+      all = fmt_config(align = "left"),
+      numeric = fmt_config(align = "center")
     ),
     main_title = "Listing of Preferred Terms and Investigator-Specified Adverse Event Terms"
   ) %>% head(50), "sorting incoming data by key columns")

diff --git a/tests/testthat/test-listing_ael02.R b/tests/testthat/test-listing_ael02.R
@@ -28,7 +28,7 @@ testthat::test_that("AEL02 listing is produced correctly", {
     ) %>%
     select(CPID, ASR, TRT01A, AEDECOD, Date_First, ASTDY, Duration, Serious, AESEV, Related, Outcome, Treated, Action)
 
-  formatters::var_labels(out) <- c(
+  var_labels(out) <- c(
     CPID = "Center/Patient ID",
     ASR = "Age/Sex/Race",
     TRT01A = "Treatment",

diff --git a/tests/testthat/test-listing_ael02_ed.R b/tests/testthat/test-listing_ael02_ed.R
@@ -43,7 +43,7 @@ testthat::test_that("AEL02_ED listing is produced correctly", {
       ADURN, AESER_F, AESEV, AEREL_F, AEOUT_F, AECONTRT_F, AEACN_F
     )
 
-  formatters::var_labels(out) <- c(
+  var_labels(out) <- c(
     cent_subj  = "Center/Patient ID",
     ASR        = "Age/Sex/Race",
     TRT01A     = "Treatment",

diff --git a/tests/testthat/test-listing_ael03.R b/tests/testthat/test-listing_ael03.R
@@ -37,7 +37,7 @@ testthat::test_that("AEL03 listing is produced correctly", {
     ) %>%
     select(CPID, ASR, TRT01A, AEDECOD, Date_First, ASTDY, Duration, AESEV, Related, Outcome, Treated, Action, SERREAS)
 
-  formatters::var_labels(out) <- c(
+  var_labels(out) <- c(
     CPID = "Center/Patient ID",
     ASR = "Age/Sex/Race",
     TRT01A = "Treatment",

diff --git a/tests/testthat/test-listing_ael04.R b/tests/testthat/test-listing_ael04.R
@@ -9,7 +9,7 @@ testthat::test_that("AEL04 listing is produced correctly", {
     arrange(SUBJID) %>%
     select(ID, AGSXRC, TRT01A, TRTSD, EOSDY, DTHADY, DTHCAUS, ADTHAUT)
 
-  formatters::var_labels(out) <- c(
+  var_labels(out) <- c(
     ID = "Center/Patient ID",
     AGSXRC = "Age/Sex/Race",
     TRT01A = "Treatment",

diff --git a/tests/testthat/test-listing_cml01.R b/tests/testthat/test-listing_cml01.R
@@ -14,7 +14,7 @@ testthat::test_that("CML01 listing is produced correctly", {
       CMSTRFL, CMENRFL, CMDOSE, CMDOSU, CMDOSFRQ, CMROUTE
     )
 
-  formatters::var_labels(out) <- c(
+  var_labels(out) <- c(
     ID = "Center/Patient ID",
     AGSXRC = "Age/Sex/Race",
     TRT01A = "Treatment",

diff --git a/tests/testthat/test-listing_cml02a_gl.R b/tests/testthat/test-listing_cml02a_gl.R
@@ -3,7 +3,7 @@ testthat::test_that("CML02A_GL listing is produced correctly", {
     select(ATC2, CMDECOD, CMTRT) %>%
     unique()
 
-  formatters::var_labels(out) <- c(
+  var_labels(out) <- c(
     ATC2 = "ATC Class Level 2",
     CMDECOD = "WHODrug Preferred Name",
     CMTRT = "Investigator-Specified\nTreatment Term"

diff --git a/tests/testthat/test-listing_cml02b_gl.R b/tests/testthat/test-listing_cml02b_gl.R
@@ -3,7 +3,7 @@ testthat::test_that("CML02B_GL listing is produced correctly", {
     select(ATC1, ATC2, ATC3, ATC4, CMDECOD, CMTRT) %>%
     unique()
 
-  formatters::var_labels(out) <- c(
+  var_labels(out) <- c(
     ATC1 = "ATC Class Level 1",
     ATC2 = "ATC Class Level 2",
     ATC3 = "ATC Class Level 3",

diff --git a/tests/testthat/test-listing_dsl01.R b/tests/testthat/test-listing_dsl01.R
@@ -9,7 +9,7 @@ testthat::test_that("DSL01 listing is produced correctly", {
     ) %>%
     select(ID, ASR, ARMCD, SSADM, STDWD, DISCONT)
 
-  formatters::var_labels(out) <- c(
+  var_labels(out) <- c(
     ID = "Center/Patient ID",
     ASR = "Age/Sex/Race",
     ARMCD = "Treatment",

diff --git a/tests/testthat/test-listing_dsl02.R b/tests/testthat/test-listing_dsl02.R
@@ -16,7 +16,7 @@ testthat::test_that("DSL02 listing is produced correctly", {
     filter(DISCONT == "Yes") %>%
     select(ID, ASR, TRT01A, SSADTM, EOSDY, SSAEDY, RANDEDY, DCSREAS)
 
-  formatters::var_labels(out) <- c(
+  var_labels(out) <- c(
     ID = "Center/Patient ID",
     ASR = "Age/Sex/Race",
     TRT01A = "Treatment",

diff --git a/tests/testthat/test-listing_dsur4.R b/tests/testthat/test-listing_dsur4.R
@@ -5,7 +5,7 @@ testthat::test_that("DSUR4 listing is produced correctly", {
     select(ARM, ID, DTHCAUS)
   death_num <- length(unique(out$ID))
 
-  formatters::var_labels(out) <- c(
+  var_labels(out) <- c(
     ARM = "Treatment Group",
     ID = "Center/Patient ID",
     DTHCAUS = "Cause of Death"

diff --git a/tests/testthat/test-listing_egl01.R b/tests/testthat/test-listing_egl01.R
@@ -35,7 +35,7 @@ testthat::test_that("EGL01 listing is produced correctly", {
     select(
       CRTNPT, AGSXRC, TRT01A, AVISIT, ADY, AVAL_ANRIND_HR, CHG_HR, AVAL_ANRIND_QT, CHG_QT, AVAL_ANRIND_RR, CHG_RR
     ) %>%
-    formatters::var_relabel(
+    var_relabel(
       CRTNPT = "Center/Subject ID",
       AGSXRC = "Age/Sex/Race",
       TRT01A = "Treatment",

diff --git a/tests/testthat/test-listing_exl01.R b/tests/testthat/test-listing_exl01.R
@@ -7,7 +7,7 @@ testthat::test_that("EXL01 listing is produced correctly", {
     arrange(CRTNPT, AVISIT) %>%
     select(CRTNPT, AVISIT, EXSTDY, EXENDY, TRT01A, AVAL, AVALU, EXDOSFRQ, EXROUTE)
 
-  formatters::var_labels(out) <- c(
+  var_labels(out) <- c(
     CRTNPT = "Center/Subject ID",
     AVISIT = "Visit",
     EXSTDY = "Study Day\nFrom",

diff --git a/tests/testthat/test-listing_lbl01.R b/tests/testthat/test-listing_lbl01.R
@@ -33,8 +33,8 @@ testthat::test_that("LBL01 listing is produced correctly", {
     ungroup() %>%
     select(CPID, TRT01A, ADY, DLD, unique(adlb_x$PARAM_U))
 
-  formatters::var_labels(out) <- names(out)
-  out <- out %>% formatters::var_relabel(
+  var_labels(out) <- names(out)
+  out <- out %>% var_relabel(
     TRT01A = "Treatment",
     CPID = "Center/Patient ID",
     ADY = "Study\nDay",

diff --git a/tests/testthat/test-listing_lbl01_rls.R b/tests/testthat/test-listing_lbl01_rls.R
@@ -37,8 +37,8 @@ testthat::test_that("LBL01_RLS listing is produced correctly", {
     ungroup() %>%
     select(CPID, TRT01A, ADY, DLD, unique(adlb_x$PARAM_U))
 
-  formatters::var_labels(out) <- names(out)
-  out <- out %>% formatters::var_relabel(
+  var_labels(out) <- names(out)
+  out <- out %>% var_relabel(
     TRT01A = "Treatment",
     CPID = "Center/Patient ID",
     ADY = "Study\nDay",

diff --git a/tests/testthat/test-listing_lbl02a.R b/tests/testthat/test-listing_lbl02a.R
@@ -26,8 +26,8 @@ testthat::test_that("LBL02A listing is produced correctly", {
   out <- adlb_x %>%
     select(LBTEST_U, TRT01A, CPID, ADY, ADTM, DLD, AVAL, LBNRNG, ANRIND_GR)
 
-  formatters::var_labels(out) <- names(out)
-  out <- out %>% formatters::var_relabel(
+  var_labels(out) <- names(out)
+  out <- out %>% var_relabel(
     LBTEST_U = "Lab Test (Unit)",
     TRT01A = "Treatment",
     CPID = "Center/Patient ID",

diff --git a/tests/testthat/test-listing_lbl02a_rls.R b/tests/testthat/test-listing_lbl02a_rls.R
@@ -47,9 +47,9 @@ testthat::test_that("LBL02A_RLS listing is produced correctly", {
   out <- adlb_x %>%
     select(LBTEST_U, TRT01A, CPID, ADY, DLD, AVAL, PCHG, STD_RNG, LBNRNG, CRC, ANRIND)
 
-  formatters::var_labels(out) <- names(out)
+  var_labels(out) <- names(out)
   out <- out %>%
-    formatters::var_relabel(
+    var_relabel(
       LBTEST_U = "Lab Test (Unit)",
       TRT01A = "Treatment",
       CPID = "Center/Patient ID",

diff --git a/tests/testthat/test-listing_lbl02b.R b/tests/testthat/test-listing_lbl02b.R
@@ -30,9 +30,9 @@ testthat::test_that("LBL02B listing is produced correctly", {
   out <- adlb_x %>%
     select(LBTEST, TRT01A, CPID, ADY, ADTM, DLD, AVAL, AVALU, LBNRNG, ANRIND_GR)
 
-  formatters::var_labels(out) <- names(out)
+  var_labels(out) <- names(out)
   out <- out %>%
-    formatters::var_relabel(
+    var_relabel(
       LBTEST = "Lab Test",
       TRT01A = "Treatment",
       CPID = "Center/Patient ID",

diff --git a/tests/testthat/test-listing_mhl01.R b/tests/testthat/test-listing_mhl01.R
@@ -9,7 +9,7 @@ testthat::test_that("MHL01 listing is produced correctly", {
     ) %>%
     select(ID, ASR, TRT01A, MHBODSYS, MHDECOD, TRTSDTM, ASTDTM, ASTDY, AENDTM, AENDY, ATIREL)
 
-  formatters::var_labels(out) <- c(
+  var_labels(out) <- c(
     ID = "Center/Patient ID",
     ASR = "Age/Sex/Race",
     TRT01A = "Treatment",

diff --git a/tests/testthat/test-listing_pkcl01.R b/tests/testthat/test-listing_pkcl01.R
@@ -5,7 +5,7 @@ testthat::test_that("PKCL01 listing is produced correctly", {
     filter(PARAM == analyte) %>%
     select(ARM, USUBJID, VISIT, NFRLT, AFRLT, AVAL)
 
-  formatters::var_labels(out) <- c(
+  var_labels(out) <- c(
     ARM = "Treatment Group",
     USUBJID = "Subject ID",
     VISIT = "Visit",

diff --git a/tests/testthat/test-listing_pkcl02.R b/tests/testthat/test-listing_pkcl02.R
@@ -42,8 +42,8 @@ testthat::test_that("PKCL02 listing is produced correctly", {
       values_from = VALUE
     )
 
-  formatters::var_labels(out) <- names(out)
-  out <- out %>% formatters::var_relabel(
+  var_labels(out) <- names(out)
+  out <- out %>% var_relabel(
     TRT01A = "Treatment Group",
     USUBJID = "Subject ID",
     VISIT = "Visit"

diff --git a/tests/testthat/test-listing_pkpl01.R b/tests/testthat/test-listing_pkpl01.R
@@ -20,8 +20,8 @@ testthat::test_that("PKPL01 listing is produced correctly", {
       values_from = AVAL
     )
 
-  formatters::var_labels(out) <- names(out)
-  out <- out %>% formatters::var_relabel(
+  var_labels(out) <- names(out)
+  out <- out %>% var_relabel(
     TRT01A = "Treatment Group",
     USUBJID = "Subject ID",
     AVISIT = "Visit"

diff --git a/tests/testthat/test-listing_pkpl02.R b/tests/testthat/test-listing_pkpl02.R
@@ -17,8 +17,8 @@ testthat::test_that("PKPL02 listing is produced correctly", {
       values_from = AVAL
     )
 
-  formatters::var_labels(out) <- names(out)
-  out <- out %>% formatters::var_relabel(
+  var_labels(out) <- names(out)
+  out <- out %>% var_relabel(
     TRT01A = "Treatment Group",
     USUBJID = "Subject ID",
     AVISIT = "Visit"

diff --git a/tests/testthat/test-listing_pkpl04.R b/tests/testthat/test-listing_pkpl04.R
@@ -32,8 +32,8 @@ testthat::test_that("PKPL04 listing is produced correctly", {
     ) %>%
     select(names(.)[c(1:2, 4, 6, 3, 5, 7)])
 
-  formatters::var_labels(out) <- names(out)
-  out <- out %>% formatters::var_relabel(USUBJID = "Subject ID")
+  var_labels(out) <- names(out)
+  out <- out %>% var_relabel(USUBJID = "Subject ID")
 
   testthat::expect_message(result <- as_listing(
     out,

diff --git a/tests/testthat/test-listing_vsl01.R b/tests/testthat/test-listing_vsl01.R
@@ -36,7 +36,7 @@ testthat::test_that("VSL01 listing is produced correctly", {
       AVAL_ANRIND_DIABP, CHG_DIABP, AVAL_ANRIND_SYSBP, CHG_SYSBP, AVAL_ANRIND_PULSE, CHG_PULSE,
       AVAL_ANRIND_RESP, CHG_RESP
     ) %>%
-    formatters::var_relabel(
+    var_relabel(
       CRTNPT = "Center/Subject ID",
       AGSXRC = "Age/Sex/Race",
       TRT01A = "Treatment",

diff --git a/tests/testthat/test-pagination_listing.R b/tests/testthat/test-pagination_listing.R
@@ -40,7 +40,7 @@ result <- adae_raw %>%
   select(CPID, ASR, TRT01A, AEDECOD, Date_First, ASTDY, Duration, AESEV, Related, Outcome, Treated, Action, SERREAS)
 
 # Adding labels
-formatters::var_labels(result) <- c(
+var_labels(result) <- c(
   CPID = "Center/Patient ID",
   ASR = "Age/Sex/Race",
   TRT01A = "Treatment",
@@ -79,7 +79,7 @@ lst_res <- as_listing(
 testthat::test_that("Direct pagination works fine", {
   testthat::expect_equal(nrow(lst_res), 50) # head() worked
 
-  clw <- formatters::propose_column_widths(lst_res) / 2 + 1
+  clw <- propose_column_widths(lst_res) / 2 + 1
 
   pg_lst <- testthat::expect_silent(paginate_listing(lst_res, lpp = 50, colwidths = floor(clw)))
   testthat::expect_equal(length(pg_lst), 10L)

diff --git a/tests/testthat/test-pagination_table.R b/tests/testthat/test-pagination_table.R
@@ -66,7 +66,7 @@ testthat::test_that("Direct pagination with standard values", {
 
 testthat::test_that("Pagination with specific column widths and minimum lines per page", {
   # With combo of rows and cols per page
-  std_col_widths <- formatters::propose_column_widths(raw_result)
+  std_col_widths <- propose_column_widths(raw_result)
   # Min h-width: first value is the row label, second is the largest content, 3 is the inter-space
   cpp_width <- std_col_widths[1] + max(std_col_widths[-1]) + 3
   pag_res <- testthat::expect_silent(
@@ -211,7 +211,7 @@ testthat::test_that("AET04 variant 2 page_by pagination tests", {
   res <- testthat::expect_silent(result)
   pag_res <- testthat::expect_silent(paginate_table(res))
   testthat::expect_setequal(
-    sapply(pag_res, formatters::page_titles),
+    sapply(pag_res, page_titles),
     paste0("AEBODSYS: ", levels(adae$AEBODSYS))
   )
   testthat::expect_snapshot(pag_res[c(2, 5)]) # randomly picked to have a comparison

diff --git a/tests/testthat/test-table_aet06_smq.R b/tests/testthat/test-table_aet06_smq.R
@@ -3,8 +3,8 @@ adsl <- adsl_pharmaverse
 adae <- adae_pharmaverse
 
 testthat::test_that("AET06_SMQ variant 1 is produced correctly", {
-  adsl_labels <- formatters::var_labels(adsl)
-  adae_labels <- formatters::var_labels(adae)
+  adsl_labels <- var_labels(adsl)
+  adae_labels <- var_labels(adae)
 
   adae <- adae %>%
     dplyr::mutate(
@@ -39,7 +39,7 @@ testthat::test_that("AET06_SMQ variant 1 is produced correctly", {
 
   adae_f <- rbind(adae_smq1, adae_smq2, adae_smq3)
 
-  formatters::var_labels(adae_f) <- c(adae_labels, "SMQ" = "Standardised MedDRA Queries")
+  var_labels(adae_f) <- c(adae_labels, "SMQ" = "Standardised MedDRA Queries")
 
   lyt <- basic_table() %>%
     split_cols_by("ARM") %>%
@@ -74,8 +74,8 @@ testthat::test_that("AET06_SMQ variant 1 is produced correctly", {
 })
 
 testthat::test_that("AET06_SMQ variant 2 is produced correctly", {
-  adsl_labels <- formatters::var_labels(adsl)
-  adae_labels <- formatters::var_labels(adae)
+  adsl_labels <- var_labels(adsl)
+  adae_labels <- var_labels(adae)
 
   adsl <- adsl %>%
     dplyr::mutate(
@@ -86,7 +86,7 @@ testthat::test_that("AET06_SMQ variant 2 is produced correctly", {
       AGE65 = factor(AGE65, levels = c(">= 65", "< 65"))
     )
 
-  formatters::var_labels(adsl) <- c(adsl_labels, "AGE65" = "AGE65 GROUP")
+  var_labels(adsl) <- c(adsl_labels, "AGE65" = "AGE65 GROUP")
 
   adae <- adae %>%
     dplyr::mutate(
@@ -126,7 +126,7 @@ testthat::test_that("AET06_SMQ variant 2 is produced correctly", {
 
   adae_f <- rbind(adae_smq1, adae_smq2, adae_smq3)
 
-  formatters::var_labels(adae_f) <- c(adae_labels, "SMQ" = "Standardised MedDRA Queries", "AGE65" = "AGE65 GROUP")
+  var_labels(adae_f) <- c(adae_labels, "SMQ" = "Standardised MedDRA Queries", "AGE65" = "AGE65 GROUP")
 
   lyt <- basic_table() %>%
     split_cols_by("ARM") %>%