Closes #39: CoEQ test data

data-raw/qs_metabolic.R

@@ -10,8 +10,6 @@
 
 library(tibble)
 library(dplyr)
-library(pharmaversesdtm)
-library(purrr)
 library(stringr)
 
 # Set seed for random data generation ----
@@ -23,28 +21,28 @@ vs_metabolic <- admiralmetabolic::vs_metabolic
 
 # Set up questions, codes and categories ----
 coeq_structure <- tibble::tribble(
-  ~QSCAT, ~QSSCAT, ~QSTESTCD, ~QSTEST,
-  "COEQ", "EATING", "COEQ01", "How hungry have you felt?",
-  "COEQ", "EATING", "COEQ02", "How full have you felt?",
-  "COEQ", "EATING", "COEQ03", "How strong was your desire to eat sweet foods?",
-  "COEQ", "EATING", "COEQ04", "How strong was your desire to eat savoury foods?",
-  "COEQ", "EMOTIONS", "COEQ05", "How happy have you felt?",
-  "COEQ", "EMOTIONS", "COEQ06", "How anxious have you felt?",
-  "COEQ", "EMOTIONS", "COEQ07", "How alert have you felt?",
-  "COEQ", "EMOTIONS", "COEQ08", "How contented have you felt?",
-  "COEQ", "GENERAL CRAVINGS", "COEQ09", "During the last 7 days how often have you had food cravings?",
-  "COEQ", "GENERAL CRAVINGS", "COEQ10", "How strong have any food cravings been?",
-  "COEQ", "GENERAL CRAVINGS", "COEQ11", "How difficult has it been to resist any food cravings?",
-  "COEQ", "GENERAL CRAVINGS", "COEQ12", "How often have you eaten in response to food cravings?",
-  "COEQ", "GENERAL CRAVINGS", "COEQ13", "Chocolate or chocolate flavoured foods",
-  "COEQ", "SPECIFIC CRAVINGS", "COEQ14", "Other sweet foods (cakes, pastries, biscuits, etc)",
-  "COEQ", "SPECIFIC CRAVINGS", "COEQ15", "Fruit or fruit juice",
-  "COEQ", "SPECIFIC CRAVINGS", "COEQ16", "Dairy foods (cheese, yoghurts, milk, etc)",
-  "COEQ", "SPECIFIC CRAVINGS", "COEQ17", "Starchy foods (bread, rice, pasta, etc)",
-  "COEQ", "SPECIFIC CRAVINGS", "COEQ18", "Savoury foods (french fries, crisps, burgers, pizza, etc)",
-  "COEQ", "CONTROL EATING", "COEQ19", "Generally, how difficult has it been to control your eating?",
-  "COEQ", "CONTROL EATING", "COEQ20", "Which one food makes it most difficult for you to control eating?",
-  "COEQ", "CONTROL EATING", "COEQ21", "How difficult has it been to resist eating this food during the last 7 days?",
+  ~QSCAT, ~QSTESTCD, ~QSTEST,
+  "COEQ", "COEQ01", "How hungry have you felt?",
+  "COEQ", "COEQ02", "How full have you felt?",
+  "COEQ", "COEQ03", "How strong was your desire to eat sweet foods?",
+  "COEQ", "COEQ04", "How strong was your desire to eat savoury foods?",
+  "COEQ", "COEQ05", "How happy have you felt?",
+  "COEQ", "COEQ06", "How anxious have you felt?",
+  "COEQ", "COEQ07", "How alert have you felt?",
+  "COEQ", "COEQ08", "How contented have you felt?",
+  "COEQ", "COEQ09", "During the last 7 days how often have you had food cravings?",
+  "COEQ", "COEQ10", "How strong have any food cravings been?",
+  "COEQ", "COEQ11", "How difficult has it been to resist any food cravings?",
+  "COEQ", "COEQ12", "How often have you eaten in response to food cravings?",
+  "COEQ", "COEQ13", "Chocolate or chocolate flavoured foods",
+  "COEQ", "COEQ14", "Other sweet foods (cakes, pastries, biscuits, etc)",
+  "COEQ", "COEQ15", "Fruit or fruit juice",
+  "COEQ", "COEQ16", "Dairy foods (cheese, yoghurts, milk, etc)",
+  "COEQ", "COEQ17", "Starchy foods (bread, rice, pasta, etc)",
+  "COEQ", "COEQ18", "Savoury foods (french fries, crisps, burgers, pizza, etc)",
+  "COEQ", "COEQ19", "Generally, how difficult has it been to control your eating?",
+  "COEQ", "COEQ20", "Which one food makes it most difficult for you to control eating?",
+  "COEQ", "COEQ21", "How difficult has it been to resist eating this food during the last 7 days?",
 )
 
 # Use visit schedule and days from VS ----
@@ -62,19 +60,34 @@ qs_metabolic_shell <- visit_schedule %>%
 qs_metabolic_results <- qs_metabolic_shell %>%
   mutate(
     DOMAIN = "QS",
-    QSORRES = round(runif(n(), min = 0, max = 100)),
-    QSORRESU = "cm",
-    QSSTRESU = "cm",
-    QSSTRESN = QSORRES,
-    QSSTRESC = as.character(QSORRES),
+    QSORRES = as.character(round(runif(n(), min = 0, max = 100))),
+    QSORRESU = "mm",
+    QSSTRESU = "mm",
+    QSSTRESN = as.numeric(QSORRES),
+    QSSTRESC = QSORRES,
     QSBLFL = if_else(VISIT == "BASELINE", "Y", NA_character_)
+  ) %>%
+  # Update the free text question (COEQ20)
+  mutate(
+    QSSTRESC = case_when(
+      QSTESTCD == "COEQ20" & QSSTRESN < 33 ~ "Ice Cream",
+      QSTESTCD == "COEQ20" & QSSTRESN < 66 ~ "Pizza",
+      QSTESTCD == "COEQ20" ~ "Pasta",
+      TRUE ~ QSSTRESC
+    )
+  ) %>%
+  mutate(
+    QSSTRESN = if_else(QSTESTCD == "COEQ20", NA, QSSTRESN),
+    QSORRES = if_else(QSTESTCD == "COEQ20", QSSTRESC, QSORRES),
+    QSORRESU = if_else(QSTESTCD == "COEQ20", NA_character_, QSORRESU),
+    QSSTRESU = if_else(QSTESTCD == "COEQ20", NA_character_, QSSTRESU),
   )
 
 # Order variables, sort and add sequence number ----
 qs_metabolic_seq <- qs_metabolic_results %>%
   select(
     STUDYID, USUBJID, DOMAIN, VISIT, VISITNUM, VISITDY, QSBLFL, QSDTC, QSDY,
-    QSCAT, QSSCAT, QSTEST, QSTESTCD, QSORRES, QSORRESU, QSSTRESC, QSSTRESN, QSSTRESU
+    QSCAT, QSTEST, QSTESTCD, QSORRES, QSORRESU, QSSTRESC, QSSTRESN, QSSTRESU
   ) %>%
   arrange(STUDYID, USUBJID, VISITNUM, QSTESTCD) %>%
   group_by(USUBJID) %>%
@@ -86,7 +99,6 @@ labels <- list(
   DOMAIN = "Domain Abbreviation",
   QSBLFL = "Baseline Flag",
   QSCAT = "Category for Questionnaire",
-  QSSCAT = "Subcategory for Questionnaire",
   QSTEST = "Questionnaire Test Name",
   QSTESTCD = "Questionnaire Test Short Name",
   QSORRES = "Result or Finding in Original Units",