update, prepare new release 0.2.16 [skip vbump]

.lintr

@@ -1,5 +1,5 @@
 linters: linters_with_defaults(
   line_length_linter = line_length_linter(120),
-  cyclocomp_linter = NULL,
-  object_usage_linter = NULL
+  object_usage_linter = NULL,
+  pipe_consistency_linter = NULL
   )

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: chevron
 Title: Standard TLGs for Clinical Trials Reporting
-Version: 0.2.15.9000
+Version: 0.2.16
 Date: 2026-10-28
 Authors@R: c(
     person("Liming", "Li", , "liming.li@roche.com", role = "aut",
@@ -72,7 +72,7 @@ Config/Needs/verdepcheck: mllg/checkmate, tidyverse/dplyr,
     yihui/knitr, rstudio/rmarkdown, r-lib/testthat, tidyverse/tidyr,
     r-lib/vdiffr, r-lib/withr
 Config/Needs/website: insightsengineering/nesttemplate
-Config/roxygen2/version: 8.1.0
+Config/roxygen2/version: 8.1.1
 Config/testthat/edition: 3
 Encoding: UTF-8
 Language: en-US

NEWS.md

@@ -1,8 +1,11 @@
-# chevron 0.2.15.9000
+# chevron 0.2.16
+
+* Updated `rspt01` tests and documentation for `tern` >= 0.9.12, which no longer accepts `"ha"` and `"schouten"` as stratified methods; the examples now use `"cmh_sato"`.
+* Converted the derived `*_main` functions of `cmt02_pt`, `coxt02`, `egt01`, `egt02_2`, `rmpt03`, `rmpt04`, `rmpt05`, `vst01` and `vst02` from `modify_default_args()` wrappers into explicit forwarding functions so their requirements are picked up by the test traceability report (no change to output).
 
 # chevron 0.2.15
 
-* Skip test to avoid cran check fails for tern.
+* Skip test to avoid CRAN check fails for tern.
 
 # chevron 0.2.14
 

R/cmt02_pt.R

@@ -7,11 +7,23 @@
 #' @returns the main function returns an `rtables` object.
 #' @export
 #'
-cmt02_pt_main <- modify_default_args(
-  cmt01a_main,
-  row_split_var = NULL,
-  summary_labels = quote(list(TOTAL = cmt01_label))
-)
+cmt02_pt_main <- function(adam_db,
+                          arm_var = "ARM",
+                          lbl_overall = NULL,
+                          row_split_var = NULL,
+                          medname_var = "CMDECOD",
+                          summary_labels = list(TOTAL = cmt01_label),
+                          ...) {
+  cmt01a_main(
+    adam_db = adam_db,
+    arm_var = arm_var,
+    lbl_overall = lbl_overall,
+    row_split_var = row_split_var,
+    medname_var = medname_var,
+    summary_labels = summary_labels,
+    ...
+  )
+}
 
 #' @describeIn cmt02_pt Preprocessing
 #'

R/coxt02.R

@@ -8,7 +8,27 @@
 #'
 #' @export
 #'
-coxt02_main <- modify_default_args(coxt01_main, multivar = TRUE)
+coxt02_main <- function(adam_db,
+                        arm_var = "ARM",
+                        time_var = "AVAL",
+                        event_var = "EVENT",
+                        covariates = c("SEX", "RACE", "AAGE"),
+                        strata = NULL,
+                        lbl_vars = "Effect/Covariate Included in the Model",
+                        multivar = TRUE,
+                        ...) {
+  coxt01_main(
+    adam_db = adam_db,
+    arm_var = arm_var,
+    time_var = time_var,
+    event_var = event_var,
+    covariates = covariates,
+    strata = strata,
+    lbl_vars = lbl_vars,
+    multivar = multivar,
+    ...
+  )
+}
 
 #' `COXT02` Multi-Variable Cox Regression Model Table.
 #'

R/egt01.R

@@ -10,7 +10,33 @@
 #'
 #' @export
 #'
-egt01_main <- modify_default_args(cfbt01_main, dataset = "adeg", precision = quote(list(default = 0L)))
+egt01_main <- function(adam_db,
+                       dataset = "adeg",
+                       arm_var = "ACTARM",
+                       lbl_overall = NULL,
+                       row_split_var = NULL,
+                       summaryvars = c("AVAL", "CHG"),
+                       visitvar = "AVISIT",
+                       precision = list(default = 0L),
+                       page_var = "PARAMCD",
+                       .stats = c("n", "mean_sd", "median", "range"),
+                       skip = list(CHG = "BASELINE"),
+                       ...) {
+  cfbt01_main(
+    adam_db = adam_db,
+    dataset = dataset,
+    arm_var = arm_var,
+    lbl_overall = lbl_overall,
+    row_split_var = row_split_var,
+    summaryvars = summaryvars,
+    visitvar = visitvar,
+    precision = precision,
+    page_var = page_var,
+    .stats = .stats,
+    skip = skip,
+    ...
+  )
+}
 
 #' @describeIn egt01 Preprocessing
 #'

R/egt02.R

@@ -124,7 +124,19 @@ egt02_1 <- chevron_t(
 #'
 #' @export
 #'
-egt02_2_main <- modify_default_args(egt02_1_main, exclude_base_abn = TRUE)
+egt02_2_main <- function(adam_db,
+                         arm_var = "ACTARM",
+                         lbl_overall = NULL,
+                         exclude_base_abn = TRUE,
+                         ...) {
+  egt02_1_main(
+    adam_db = adam_db,
+    arm_var = arm_var,
+    lbl_overall = lbl_overall,
+    exclude_base_abn = exclude_base_abn,
+    ...
+  )
+}
 
 #' `EGT02_2` ECG Abnormalities Table.
 #'

R/rmpt03.R

@@ -12,12 +12,23 @@
 #'
 #' @export
 #'
-rmpt03_main <- modify_default_args(
-  rmpt01_main,
-  summaryvars = "AGEGR1",
-  col_split_var = "SEX",
-  overall_col_lbl = "All Genders"
-)
+rmpt03_main <- function(adam_db,
+                        summaryvars = "AGEGR1",
+                        show_tot = TRUE,
+                        row_split_var = NULL,
+                        col_split_var = "SEX",
+                        overall_col_lbl = "All Genders",
+                        ...) {
+  rmpt01_main(
+    adam_db = adam_db,
+    summaryvars = summaryvars,
+    show_tot = show_tot,
+    row_split_var = row_split_var,
+    col_split_var = col_split_var,
+    overall_col_lbl = overall_col_lbl,
+    ...
+  )
+}
 
 #' @describeIn rmpt03 Preprocessing
 #'

R/rmpt04.R

@@ -14,7 +14,23 @@
 #'
 #' @export
 #'
-rmpt04_main <- modify_default_args(rmpt01_main, summaryvars = "ETHNIC")
+rmpt04_main <- function(adam_db,
+                        summaryvars = "ETHNIC",
+                        show_tot = TRUE,
+                        row_split_var = NULL,
+                        col_split_var = NULL,
+                        overall_col_lbl = NULL,
+                        ...) {
+  rmpt01_main(
+    adam_db = adam_db,
+    summaryvars = summaryvars,
+    show_tot = show_tot,
+    row_split_var = row_split_var,
+    col_split_var = col_split_var,
+    overall_col_lbl = overall_col_lbl,
+    ...
+  )
+}
 
 #' @describeIn rmpt04 Preprocessing
 #'

R/rmpt05.R

@@ -14,7 +14,23 @@
 #'
 #' @export
 #'
-rmpt05_main <- modify_default_args(rmpt01_main, summaryvars = "RACE")
+rmpt05_main <- function(adam_db,
+                        summaryvars = "RACE",
+                        show_tot = TRUE,
+                        row_split_var = NULL,
+                        col_split_var = NULL,
+                        overall_col_lbl = NULL,
+                        ...) {
+  rmpt01_main(
+    adam_db = adam_db,
+    summaryvars = summaryvars,
+    show_tot = show_tot,
+    row_split_var = row_split_var,
+    col_split_var = col_split_var,
+    overall_col_lbl = overall_col_lbl,
+    ...
+  )
+}
 
 #' @describeIn rmpt05 Preprocessing
 #'

R/rspt01.R

@@ -15,9 +15,9 @@
 #' @param methods (`list`) a named list, use a named list to control, for example:
 #' `methods = list(prop_conf_method = "wald",
 #'                diff_conf_method = "wald",
-#'                strat_diff_conf_method = "ha",
+#'                strat_diff_conf_method = "cmh_sato",
 #'                diff_pval_method = "fisher",
-#'                strat_diff_pval_method = "schouten")`
+#'                strat_diff_pval_method = "cmh_sato")`
 #' `prop_conf_method` controls the methods of calculating proportion confidence interval,
 #' `diff_conf_method` controls the methods of calculating unstratified difference confidence interval,
 #' `strat_diff_conf_method` controls the methods of calculating stratified difference confidence interval,

R/vst01.R

@@ -8,11 +8,33 @@
 #'
 #' @export
 #'
-vst01_main <- modify_default_args(
-  cfbt01_main,
-  dataset = "advs",
-  precision = quote(list(DIABP = 0, PUL = 0, SYSBP = 0, default = 2L))
-)
+vst01_main <- function(adam_db,
+                       dataset = "advs",
+                       arm_var = "ACTARM",
+                       lbl_overall = NULL,
+                       row_split_var = NULL,
+                       summaryvars = c("AVAL", "CHG"),
+                       visitvar = "AVISIT",
+                       precision = list(DIABP = 0, PUL = 0, SYSBP = 0, default = 2L),
+                       page_var = "PARAMCD",
+                       .stats = c("n", "mean_sd", "median", "range"),
+                       skip = list(CHG = "BASELINE"),
+                       ...) {
+  cfbt01_main(
+    adam_db = adam_db,
+    dataset = dataset,
+    arm_var = arm_var,
+    lbl_overall = lbl_overall,
+    row_split_var = row_split_var,
+    summaryvars = summaryvars,
+    visitvar = visitvar,
+    precision = precision,
+    page_var = page_var,
+    .stats = .stats,
+    skip = skip,
+    ...
+  )
+}
 
 #' @describeIn vst01 Preprocessing
 #'

R/vst02.R

@@ -135,7 +135,19 @@ vst02_1 <- chevron_t(
 #'
 #' @export
 #'
-vst02_2_main <- modify_default_args(vst02_1_main, exclude_base_abn = TRUE)
+vst02_2_main <- function(adam_db,
+                         arm_var = "ACTARM",
+                         lbl_overall = NULL,
+                         exclude_base_abn = TRUE,
+                         ...) {
+  vst02_1_main(
+    adam_db = adam_db,
+    arm_var = arm_var,
+    lbl_overall = lbl_overall,
+    exclude_base_abn = exclude_base_abn,
+    ...
+  )
+}
 #' `VST02` Vital Sign Abnormalities Table.
 #'
 #' Vital Sign Parameters outside Normal Limits Among Patients without Abnormality at Baseline.