Updates following NEST package releases (#181)

Closes #157
insightsengineering · Jan 3, 2024 · 1e75fb3 · 1e75fb3
1 parent 73f5ff9
commit 1e75fb3
Show file tree

Hide file tree

Showing 6 changed files with 11 additions and 21 deletions.
diff --git a/book/graphs/pharmacokinetic/pkcg03.qmd b/book/graphs/pharmacokinetic/pkcg03.qmd
@@ -42,10 +42,10 @@ result <- g_lineplot(
   variables = control_lineplot_vars(
     x = "NFRLT",
     y = "AVAL",
-    strata = "ARM",
+    group_var = "ARM",
     paramcd = "PARAM",
     y_unit = "AVALU",
-    cohort_id = "USUBJID"
+    subject_var = "USUBJID"
   ),
   alt_counts_df = adsl_f,
   y_lab = "Concentration",
@@ -78,10 +78,10 @@ result <- g_lineplot(
   variables = control_lineplot_vars(
     x = "NFRLT",
     y = "avalog",
-    strata = "ARM",
+    group_var = "ARM",
     paramcd = "PARAM",
     y_unit = "AVALU",
-    cohort_id = "USUBJID"
+    subject_var = "USUBJID"
   ),
   alt_counts_df = adsl_f,
   y_lab = "Concentration",

diff --git a/book/graphs/pharmacokinetic/pkpg01.qmd b/book/graphs/pharmacokinetic/pkpg01.qmd
@@ -56,7 +56,7 @@ result <- g_lineplot(
   variables = control_lineplot_vars(
     x = "Time",
     y = "AVAL",
-    strata = "ARM",
+    group_var = "ARM",
     paramcd = "PARAM1",
     y_unit = "AVALU"
   ),
@@ -112,7 +112,7 @@ result <- g_lineplot(
   variables = control_lineplot_vars(
     x = "Time",
     y = "AVAL",
-    strata = "ARM",
+    group_var = "ARM",
     paramcd = "PARAM1",
     y_unit = "AVALU"
   ),

diff --git a/book/tables/efficacy/mmrmt01.qmd b/book/tables/efficacy/mmrmt01.qmd
@@ -46,7 +46,7 @@ var_labels(adqs_f) <- var_labels(adqs)
 
 ### Considering the treatment variable in the model
 
-```{r variant1, test = list(result_v1 = "result")}
+```{r variant1, test = list(result_v1 = "result"), message=FALSE}
 mmrm_results <- fit_mmrm(
   vars = list(
     response = "CHG",

diff --git a/book/tables/efficacy/ratet01.qmd b/book/tables/efficacy/ratet01.qmd
@@ -32,7 +32,7 @@ anl <- df_explicit_na(anl)
 
 ```{r variant1, test = list(result_v1 = "result")}
 lyt <- basic_table(show_colcounts = TRUE) %>%
-  split_cols_by("ARM", ref_group = "B: Placebo") %>%
+  split_cols_by("ARM", ref_group = "B: Placebo", split_fun = ref_group_position("first")) %>%
   analyze_vars(
     "AVAL_f",
     var_labels = "Number of exacerbations per patient",

diff --git a/book/tables/lab-results/lbt15.qmd b/book/tables/lab-results/lbt15.qmd
@@ -12,16 +12,6 @@ subtitle: Laboratory Test Shifts to NCI CTCAE Grade 3-4 Post-Baseline
 
 Because the `scda` dataset `adlb` doesn't have the `PARCAT1` variable, this variable is created from `LBCAT` in pre-processing.
 
-adlb \<- adlb %\>%
-
-mutate(
-
-PARAM = with_label(.data\$PARAM, "Laboratory Test"),
-
-ANRIND = with_label(.data\$ANRIND, "Direction of Abnormality")
-
-)
-
 ```{r setup, message=FALSE}
 #| code-fold: show
 

diff --git a/package/DESCRIPTION b/package/DESCRIPTION
@@ -22,8 +22,10 @@ Suggests:
     ggpubr,
     ggrepel,
     grid,
+    knitr,
     lubridate,
     nestcolor,
+    quarto,
     renv,
     rlistings (>= 0.2.7),
     rtables (>= 0.6.6),
@@ -39,11 +41,9 @@ Suggests:
     tern (>= 0.9.3.9002),
     tern.mmrm (>= 0.2.2),
     tern.rbmi,
+    testthat (>= 3.0.0),
     tibble,
     tidyr,
-    knitr,
-    quarto,
-    testthat (>= 3.0.0),
     vdiffr (>= 1.0.0),
     withr
 Encoding: UTF-8