Merge branch 'main' into 245_pdt02@main

insightsengineering · Jan 20, 2023 · 4f50873 · 4f50873
2 parents 3f5db6a + 444e79e
commit 4f50873
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Type: Package
 Package: chevron
 Title: Standard TLGs For Clinical Trials Reporting
-Version: 0.1.1.9028
-Date: 2023-01-16
+Version: 0.1.1.9029
+Date: 2023-01-20
 Authors@R: c(
     person("Benoit", "Falquet", , "[email protected]", role = c("aut", "cre")),
     person("Adrian", "Waddell", , "[email protected]", role = "aut"),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,3 @@
-# chevron 0.1.1.9028
+# chevron 0.1.1.9029
 
 * First release with implementation of: `AET01`, `AET02`, `AET03`, `AET04`, `CMT01A`, `CMT02_PT`, `DMT01`, `DST01`, `DTHT01`, `EGT01`, `EGT02`, `EXT01`, `LBT01`, `MHT01`, `MNG01`, `VST01`, `VST02`.
diff --git a/R/lbt01.R b/R/lbt01.R
@@ -117,12 +117,17 @@ lbt01_1_lyt <- function(armvar,
 
         # Create context dependent function.
         n_fun <- sum(!is.na(x), na.rm = TRUE)
-        mean_sd_fun <- c(mean(x, na.rm = TRUE), sd(x, na.rm = TRUE))
-        median_fun <- median(x, na.rm = TRUE)
-        min_max_fun <- c(min(x), max(x))
+        if (n_fun == 0) {
+          mean_sd_fun <- c(NA, NA)
+          median_fun <- NA
+          min_max_fun <- c(NA, NA)
+        } else {
+          mean_sd_fun <- c(mean(x, na.rm = TRUE), sd(x, na.rm = TRUE))
+          median_fun <- median(x, na.rm = TRUE)
+          min_max_fun <- c(min(x), max(x))
+        }
 
         # Identify context-
-        is_baseline <- .spl_context$value[2] == "BASELINE"
         is_chg <- .var == "CHG"
 
         is_baseline <- .spl_context$value[which(.spl_context$split == "AVISIT")] == "BASELINE"
@@ -141,6 +146,12 @@ lbt01_1_lyt <- function(armvar,
             "Mean (SD)" = h_format_dec(format = "%f (%f)", digits = pcs + 1),
             "Median" = h_format_dec(format = "%f", digits = pcs + 1),
             "Min - Max" = h_format_dec(format = "%f - %f", digits = pcs)
+          ),
+          .format_na_strs = list(
+            "n" = "NE",
+            "Mean (SD)" = "NE (NE)",
+            "Median" = "NE",
+            "Min - Max" = "NE - NE"
           )
         )
       },

diff --git a/R/utils.R b/R/utils.R
@@ -349,17 +349,14 @@ h_format_dec <- function(digits = NA, format = NA) {
 
   if (is.na(format)) {
     NULL
-
   } else {
-
     function(x, ...) {
       checkmate::assert_numeric(x)
 
       digit_string <- ifelse(is.na(digits), "", paste0(".", digits))
       new_format <- gsub("%([a-z])", paste0("%", digit_string, "\\1"), format)
-      fun <- formatters::sprintf_format(new_format)
 
-      fun(x)
+      formatters::sprintf_format(new_format)(x)
     }
   }
 }
diff --git a/tests/testthat/_snaps/lbt01.md b/tests/testthat/_snaps/lbt01.md
@@ -0,0 +1,20 @@
+# lbt01_1 can handle n = 0 and outputs NE instead of infs and NAs
+
+    Code
+      res
+    Output
+                                                 A: Drug X   
+                                               Value at Visit
+        —————————————————————————————————————————————————————
+        Alanine Aminotransferase Measurement                 
+          BASELINE                                           
+            n                                        0       
+            Mean (SD)                             NE (NE)    
+            Median                                   NE      
+            Min - Max                             NE - NE    
+          WEEK 1 DAY 8                                       
+            n                                        0       
+            Mean (SD)                             NE (NE)    
+            Median                                   NE      
+            Min - Max                             NE - NE    
+
diff --git a/tests/testthat/test-lbt01.R b/tests/testthat/test-lbt01.R
@@ -0,0 +1,12 @@
+test_that("lbt01_1 can handle n = 0 and outputs NE instead of infs and NAs", {
+  proc_data <- syn_data %>%
+    dm_zoom_to("adlb") %>%
+    filter(PARAM != "ALT" & ACTARM != "A: Drug X") %>%
+    dm_update_zoomed()
+
+  res <- expect_silent(
+    run(lbt01_1, proc_data, precision = c("ALT" = 0, "CRP" = 1))
+  )
+  res <- res[1:11, 1]
+  expect_snapshot(res)
+})