feat: #2142 working enhanced function

pharmaverse · Oct 26, 2023 · 346f595 · 346f595
1 parent 70836b5
commit 346f595
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Showing 15 changed files with 75 additions and 65 deletions.
diff --git a/R/derive_summary_records.R b/R/derive_summary_records.R
@@ -155,9 +155,9 @@ derive_summary_records <- function(dataset,
     required_vars = expr_c(by_vars),
     optional = TRUE
   )
-  assert_varval_list(set_values_to, optional = TRUE)
-  assert_expr_list(missing_values, named = TRUE, optional = TRUE)
+
   assert_varval_list(set_values_to)
+  assert_expr_list(missing_values, named = TRUE, optional = TRUE)
 
   if (!missing(analysis_var) || !missing(summary_fun)) {
     deprecate_warn(
@@ -170,29 +170,15 @@ derive_summary_records <- function(dataset,
     set_values_to <- exprs(!!analysis_var := {{ summary_fun }}(!!analysis_var), !!!set_values_to)
   }
 
-  # Summarise the analysis value and bind to the original dataset
-  # bind_rows(
-  #   dataset,
-  #   get_summary_records(
-  #     dataset,
-  #     by_vars = by_vars,
-  #     filter = !!filter,
-  #     set_values_to = set_values_to
-  #   )
-  #   analysis_var <- assert_symbol(enexpr(analysis_var))
-  #   assert_s3_class(summary_fun, "function")
-  #   set_values_to <- exprs(!!analysis_var := {{ summary_fun }}(!!analysis_var), !!!set_values_to)
-  # }
-
   if (is.null(dataset_add)) {
     dataset_add <- dataset
   }
 
   summary_records <- dataset_add %>%
     group_by(!!!by_vars) %>%
-    filter_if(filter) %>%
-    ungroup() %>%
-    process_set_values_to(set_values_to)
+    filter_if(filter)  %>%
+    summarise(!!!set_values_to) %>%
+    ungroup()
 
   df_return <- bind_rows(
     dataset,
@@ -215,6 +201,16 @@ derive_summary_records <- function(dataset,
     )
   }
 
+  if (!is.null(missing_values)) {
+    update_missings <- map2(
+      syms(names(missing_values)),
+      missing_values,
+      ~ expr(if_else(is.na(!!missing_var), !!.y, !!.x))
+    )
+    names(update_missings) <- names(missing_values)
+    df_return <- df_return %>%
+      mutate(!!!update_missings)
+  }
 
   return(df_return)
 }
diff --git a/R/get_summary_records.R b/R/get_summary_records.R
@@ -163,13 +163,13 @@ get_summary_records <- function(dataset,
                                 summary_fun,
                                 set_values_to = NULL) {
   # lifecycle::signal_stage("superseded", "get_summary_records()", "derive_summary_records(dataset_add= )")
-  inform(
-    message = paste0(
-      "`get_summary_records()` has been superseded, ",
-      "please use the `dataset_add` argument in `derive_summary_records()`",
-      sep = ""
-    )
-  )
+  # inform(
+  #   message = paste0(
+  #     "`get_summary_records()` has been superseded, ",
+  #     "please use the `dataset_add` argument in `derive_summary_records()`",
+  #     sep = ""
+  #   )
+  # )
   assert_vars(by_vars)
   filter <- assert_filter_cond(enexpr(filter), optional = TRUE)
   assert_data_frame(

diff --git a/man/derive_summary_records.Rd b/man/derive_summary_records.Rd
diff --git a/man/derive_var_extreme_flag.Rd b/man/derive_var_extreme_flag.Rd
diff --git a/man/derive_var_joined_exist_flag.Rd b/man/derive_var_joined_exist_flag.Rd
diff --git a/man/derive_var_merged_exist_flag.Rd b/man/derive_var_merged_exist_flag.Rd
diff --git a/man/derive_var_merged_summary.Rd b/man/derive_var_merged_summary.Rd
diff --git a/man/derive_var_obs_number.Rd b/man/derive_var_obs_number.Rd
diff --git a/man/derive_var_relative_flag.Rd b/man/derive_var_relative_flag.Rd
diff --git a/man/derive_vars_joined.Rd b/man/derive_vars_joined.Rd
diff --git a/man/derive_vars_merged.Rd b/man/derive_vars_merged.Rd
diff --git a/man/derive_vars_merged_lookup.Rd b/man/derive_vars_merged_lookup.Rd
diff --git a/man/derive_vars_transposed.Rd b/man/derive_vars_transposed.Rd
diff --git a/man/get_summary_records.Rd b/man/get_summary_records.Rd
diff --git a/tests/testthat/test-derive_summary_records.R b/tests/testthat/test-derive_summary_records.R
@@ -143,3 +143,41 @@ test_that("derive_summary_records Test 4: deprecation warning for analysis_var a
     keys = c("subj", "visit", "seq", "type")
   )
 })
+
+test_that("make sure dataset_add works", {
+  input <- tibble::tribble(
+    ~subj, ~visit,       ~val, ~seq,
+    "1",        1,         10,    1,
+    "1",        1,         14,    2,
+    "1",        1,          9,    3,
+    "1",        2,         11,    4,
+    "2",        2,   NA_real_,    1
+  )
+  input_add <- tibble::tribble(
+    ~subj, ~visit,       ~add_val, ~seq,
+    "1",        1,            100,    1,
+    "1",        1,            140,    2,
+    "1",        1,             90,    3
+  )
+  expected_output<- bind_rows(
+    input,
+    tibble::tribble(
+      ~subj, ~visit,       ~val,    ~type,
+      "1",        1,        110, "AVERAGE"
+    )
+  )
+  actual_output <- input %>%
+    derive_summary_records(
+      dataset_add = input_add,
+      by_vars = exprs(subj, visit),
+      set_values_to = exprs(
+        val = mean(add_val, na.rm = TRUE),
+        type = "AVERAGE"
+      )
+    )
+  expect_dfs_equal(
+    base = expected_output,
+    compare = actual_output,
+    keys = c("subj", "visit", "seq", "type")
+  )
+})