Update use of deprecated strat argument from tern (#1081)

Fixes #1080

NEWS.md

@@ -7,6 +7,7 @@
 ### Miscellaneous
 * Removed `formatters` from dependencies and replaced the use of its functions relating to variable labels with functions from `teal.data`.
 * Replaced instances of deprecated `na_level` argument to `tern` functions with `na_str`.
+* Updated all template functions to use argument/list element name `strata` instead of `strat` in all `tern` function inputs following the deprecation of this argument/name within `tern`.
 
 # teal.modules.clinical 0.9.0
 

R/tm_g_forest_rsp.R

@@ -137,7 +137,7 @@ template_forest_rsp <- function(dataname = "ANL",
     substitute(
       expr = df <- extract_rsp_subgroups(
         variables = list(
-          rsp = "is_rsp", arm = arm_var, subgroups = subgroup_var, strat = strata_var
+          rsp = "is_rsp", arm = arm_var, subgroups = subgroup_var, strata = strata_var
         ),
         data = anl,
         conf_level = conf_level

R/tm_g_forest_tte.R

@@ -124,7 +124,7 @@ template_forest_tte <- function(dataname = "ANL",
           is_event = "is_event",
           arm = arm_var,
           subgroups = subgroup_var,
-          strat = strata_var
+          strata = strata_var
         ),
         control = control_coxph(conf_level = conf_level),
         data = anl

R/tm_g_km.R

@@ -99,7 +99,7 @@ template_g_km <- function(dataname = "ANL",
 
   y$variables <- if (length(strata_var) != 0) {
     substitute(
-      expr = variables <- list(tte = tte, is_event = "is_event", arm = arm, strat = strata_var),
+      expr = variables <- list(tte = tte, is_event = "is_event", arm = arm, strata = strata_var),
       env = list(tte = aval_var, arm = arm_var, strata_var = strata_var)
     )
   } else {

R/tm_t_tte.R

@@ -296,7 +296,7 @@ template_tte <- function(dataname = "ANL",
           vars = aval_var,
           is_event = "is_event",
           var_labels = paste0("Stratified By: ", paste(strata_var, collapse = ", ")),
-          strat = strata_var,
+          strata = strata_var,
           control = control_coxph(
             pval_method = pval_method,
             ties = ties,

R/utils.R

@@ -89,7 +89,7 @@ get_var_labels <- function(datasets, dataname, vars) {
 #'   basic_table() %>%
 #'     split_cols_by(var = "ARMCD") %>%
 #'     test_proportion_diff(
-#'       vars = "rsp", method = "cmh", variables = list(strata = "strat")
+#'       vars = "rsp", method = "cmh", variables = list(strata = "strata")
 #'     ) %>%
 #'     build_table(df = dta)
 #' })
@@ -155,7 +155,7 @@ pipe_expr <- function(exprs, pipe_str = "%>%") {
 #'   lyt,
 #'   substitute(
 #'     test_proportion_diff(
-#'       vars = "rsp", method = "cmh", variables = list(strata = "strat")
+#'       vars = "rsp", method = "cmh", variables = list(strata = "strata")
 #'     )
 #'   )
 #' )

tests/testthat/_snaps/tm_g_forest_rsp.md

@@ -21,7 +21,7 @@
       $summary
       {
           df <- extract_rsp_subgroups(variables = list(rsp = "is_rsp", 
-              arm = "ARMCD", subgroups = c("SEX", "STRATA2"), strat = NULL), 
+              arm = "ARMCD", subgroups = c("SEX", "STRATA2"), strata = NULL), 
               data = adrs, conf_level = 0.95)
       }
       

tests/testthat/_snaps/tm_g_forest_tte.md

@@ -21,7 +21,7 @@
       {
           df <- extract_survival_subgroups(variables = list(tte = "AVAL", 
               is_event = "is_event", arm = "ARMCD", subgroups = c("SEX", 
-                  "BMRKR2"), strat = "STRATA2"), control = control_coxph(conf_level = 0.9), 
+                  "BMRKR2"), strata = "STRATA2"), control = control_coxph(conf_level = 0.9), 
               data = anl)
       }
       

tests/testthat/_snaps/utils.md

@@ -3,7 +3,7 @@
     Code
       res
     Output
-      [1] "rtables::basic_table() %>% rtables::split_cols_by(var = \"ARMCD\") %>%      tern::test_proportion_diff(vars = \"rsp\", method = \"cmh\",          variables = list(strata = \"strat\")) %>% rtables::build_table(df = dta)"
+      [1] "rtables::basic_table() %>% rtables::split_cols_by(var = \"ARMCD\") %>%      tern::test_proportion_diff(vars = \"rsp\", method = \"cmh\",          variables = list(strata = \"strata\")) %>% rtables::build_table(df = dta)"
 
 # add_expr adds expressions to expression list
 
@@ -17,7 +17,7 @@
       rtables::split_cols_by(var = arm)
       
       [[3]]
-      tern::test_proportion_diff(vars = "rsp", method = "cmh", variables = list(strata = "strat"))
+      tern::test_proportion_diff(vars = "rsp", method = "cmh", variables = list(strata = "strata"))
       
       [[4]]
       rtables::build_table(df = dta)
@@ -29,7 +29,7 @@
       res
     Output
       rtables::basic_table() %>% rtables::split_cols_by(var = arm) %>% 
-          test_proportion_diff(vars = "rsp", method = "cmh", variables = list(strata = "strat")) %>% 
+          test_proportion_diff(vars = "rsp", method = "cmh", variables = list(strata = "strata")) %>% 
           rtables::build_table(df = dta)
 
 # bracket_expr concatenates expressions into a single expression

tests/testthat/test-utils.R

@@ -3,7 +3,7 @@ testthat::test_that("h_concat_expr returns a string for long expression", {
     rtables::basic_table() %>%
       rtables::split_cols_by(var = "ARMCD") %>%
       tern::test_proportion_diff(
-        vars = "rsp", method = "cmh", variables = list(strata = "strat")
+        vars = "rsp", method = "cmh", variables = list(strata = "strata")
       ) %>%
       rtables::build_table(df = dta)
   )
@@ -34,7 +34,7 @@ testthat::test_that("add_expr adds expressions to expression list", {
     lyt,
     substitute(
       tern::test_proportion_diff(
-        vars = "rsp", method = "cmh", variables = list(strata = "strat")
+        vars = "rsp", method = "cmh", variables = list(strata = "strata")
       )
     )
   )
@@ -54,7 +54,7 @@ testthat::test_that("add_expr manages expression list which can be used by pipe_
     lyt,
     substitute(
       test_proportion_diff(
-        vars = "rsp", method = "cmh", variables = list(strata = "strat")
+        vars = "rsp", method = "cmh", variables = list(strata = "strata")
       )
     )
   )