Replace instances of deprecated na_level with na_str (#1088)

Fixes #1084
insightsengineering · Feb 28, 2024 · 87bd391 · 87bd391
1 parent 89ae995
commit 87bd391
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Showing 6 changed files with 22 additions and 11 deletions.
diff --git a/NEWS.md b/NEWS.md
@@ -2,12 +2,11 @@
 
 ### Enhancements
 * Updated `tm_g_forest_rsp` and `tm_g_forest_tte` to use refactored version of `g_forest`. Plots are now displayed as `ggplot` objects instead of `grob` objects. Added parameters `font_size` and `rel_width_forest` to control font size and width of plot relative to table, respectively.
-
-### Enhancements
 * Updated `tm_t_summary_by` to allow `NULL` input to `paramcd` argument.
 
 ### 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`.
 
 # teal.modules.clinical 0.9.0
 

diff --git a/R/tm_t_abnormality.R b/R/tm_t_abnormality.R
@@ -108,7 +108,7 @@ template_abnormality <- function(parentname,
         variables = list(anl = grade, split_rows = by_vars),
         abnormal = abnormal,
         method = "default",
-        na_level = na_level
+        na_str = na_level
       ),
       env = list(dataname = as.name("anl"), by_vars = by_vars, grade = grade, abnormal = abnormal, na_level = na_level)
     )

diff --git a/R/tm_t_shift_by_arm.R b/R/tm_t_shift_by_arm.R
@@ -110,7 +110,10 @@ template_shift_by_arm <- function(dataname,
           add_rowcounts() %>%
           analyze_vars(
             baseline_var,
-            denom = "N_row", na_level = na_str, na.rm = na.rm, .stats = "count_fraction"
+            denom = "N_row",
+            na_str = na_str,
+            na.rm = na.rm,
+            .stats = "count_fraction"
           ) %>%
           append_varlabels(dataname, baseline_var, indent = 1L),
         env = list(
@@ -142,7 +145,10 @@ template_shift_by_arm <- function(dataname,
           add_rowcounts() %>%
           analyze_vars(
             baseline_var,
-            denom = "N_row", na_level = na_str, na.rm = na.rm, .stats = "count_fraction"
+            denom = "N_row",
+            na_str = na_str,
+            na.rm = na.rm,
+            .stats = "count_fraction"
           ) %>%
           append_varlabels(dataname, baseline_var, indent = 1L),
         env = list(

diff --git a/R/tm_t_shift_by_arm_by_worst.R b/R/tm_t_shift_by_arm_by_worst.R
@@ -118,7 +118,10 @@ template_shift_by_arm_by_worst <- function(dataname,
           add_rowcounts() %>%
           analyze_vars(
             baseline_var,
-            denom = "N_row", na_level = na_str, na.rm = na.rm, .stats = "count_fraction"
+            denom = "N_row",
+            na_str = na_str,
+            na.rm = na.rm,
+            .stats = "count_fraction"
           ) %>%
           append_varlabels(dataname, baseline_var, indent = 1L),
         env = list(
@@ -149,7 +152,10 @@ template_shift_by_arm_by_worst <- function(dataname,
           add_rowcounts() %>%
           analyze_vars(
             baseline_var,
-            denom = "N_row", na_level = na_str, na.rm = na.rm, .stats = "count_fraction"
+            denom = "N_row",
+            na_str = na_str,
+            na.rm = na.rm,
+            .stats = "count_fraction"
           ) %>%
           append_varlabels(dataname, baseline_var, indent = 1L),
         env = list(

diff --git a/R/tm_t_summary.R b/R/tm_t_summary.R
@@ -155,7 +155,7 @@ template_summary <- function(dataname,
           var_labels = sum_var_labels,
           show_labels = show_labels,
           na.rm = na.rm,
-          na_level = na_level,
+          na_str = na_level,
           denom = denom,
           .stats = stats
         ),
@@ -167,7 +167,7 @@ template_summary <- function(dataname,
           vars = sum_vars,
           show_labels = show_labels,
           na.rm = na.rm,
-          na_level = na_level,
+          na_str = na_level,
           denom = denom,
           .stats = stats
         ),

diff --git a/R/tm_t_summary_by.R b/R/tm_t_summary_by.R
@@ -253,7 +253,7 @@ template_summary_by <- function(parentname,
               vars = sum_vars,
               var_labels = sum_var_labels,
               na.rm = na.rm,
-              na_level = na_level,
+              na_str = na_level,
               denom = denom,
               .stats = stats
             ),
@@ -264,7 +264,7 @@ template_summary_by <- function(parentname,
             expr = analyze_vars(
               vars = sum_vars,
               na.rm = na.rm,
-              na_level = na_level,
+              na_str = na_level,
               denom = denom,
               .stats = stats
             ),