Closes #39: CoEQ test data

R/data.R

@@ -11,3 +11,13 @@
 #'
 #' @source Constructed using `vs` from the `{pharmaversesdtm}` package and `dm_metabolic` from `{admiralmetabolic}` package
 "vs_metabolic"
+
+#' Example questionnaire dataset
+#'
+#' An example questionnaire SDTM dataset (containing Control of Eating Questionnaire, COEQ, test data) for metabolic studies. Note that University
+#' of Leeds are the copyright holders of the CoEQ and the test data included within `{admiralmetabolic}`is for not-for-profit use only. Any persons
+#' or companies wanting to use the CoEQ should request a license to do so from the following
+#' [link](https://licensing.leeds.ac.uk/product/control-of-eating-questionnaire-coeq).
+#'
+#' @source Constructed using `dm_metabolic` from `{admiralmetabolic}` package
+"qs_metabolic"

data-raw/qs_metabolic.R

@@ -0,0 +1,104 @@
+#' Dataset: qs_metabolic
+#' Description: Create QS test SDTM dataset for metabolic studies,
+#' containing COEQ data (Control of Eating Questionnaire)
+#' Note that University  of Leeds are the copyright holders of the CoEQ and the test data included within
+#' `{admiralmetabolic}`is for not-for-profit use only. Any persons  or companies wanting to use the CoEQ
+#' should request a license to do so from the following
+#' [link](https://licensing.leeds.ac.uk/product/control-of-eating-questionnaire-coeq).
+
+# Load libraries ----
+
+library(tibble)
+library(dplyr)
+library(pharmaversesdtm)
+library(purrr)
+
+# Set seed for random data generation ----
+set.seed(3.14159265)
+
+# Read input data ----
+
+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 CRAVING", "COEQ15", "Fruit or fruit juice",
+  "COEQ", "SPECIFIC CRAVING", "COEQ16", "Dairy foods (cheese, yoghurts, milk, etc)",
+  "COEQ", "SPECIFIC CRAVING", "COEQ17", "Starchy foods (bread, rice, pasta, etc)",
+  "COEQ", "SPECIFIC CRAVING", "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?",
+)
+
+# Use visit schedule and days from VS ----
+visit_schedule <- vs_metabolic %>%
+  select(STUDYID, USUBJID, VISIT, VISITNUM, VISITDY, VSDTC, VSDY) %>%
+  filter(!grepl("AMBUL|RETRIEVAL", VISIT)) %>%
+  rename(QSDTC = VSDTC, QSDY = VSDY) %>%
+  distinct()
+
+# Cross join to get questions at each visit ----
+qs_metabolic_shell <- visit_schedule %>%
+  dplyr::cross_join(coeq_structure)
+
+# Simulate question answers ----
+qs_metabolic_results <- qs_metabolic_shell %>%
+  mutate(
+    DOMAIN = "QS",
+    QSORRES = floor(runif(1) * 10) + round(runif(1)),
+    QSORRESU = "cm",
+    QSSTRESU = "cm",
+    QSSTRESN = QSORRES,
+    QSSTRESC = as.character(QSORRES),
+    QSBLFL = ifelse(VISIT == "BASELINE", "Y", NA_character_)
+  )
+
+# 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
+  ) %>%
+  arrange(STUDYID, USUBJID, VISITNUM, QSTESTCD) %>%
+  group_by(USUBJID) %>%
+  mutate(QSSEQ = row_number()) %>%
+  ungroup()
+
+# Add labels to variables that don't have them yet ----
+attr(qs_metabolic_seq$DOMAIN, "label") <- "Domain Abbreviation"
+attr(qs_metabolic_seq$QSBLFL, "label") <- "Baseline Flag"
+attr(qs_metabolic_seq$QSCAT, "label") <- "Category for Questionnaire"
+attr(qs_metabolic_seq$QSSCAT, "label") <- "Subcategory for Questionnaire"
+attr(qs_metabolic_seq$QSTEST, "label") <- "Questionnaire Test Name"
+attr(qs_metabolic_seq$QSTESTCD, "label") <- "Questionnaire Test Short Name"
+attr(qs_metabolic_seq$QSORRES, "label") <- "Result or Finding in Original Units"
+attr(qs_metabolic_seq$QSORRESU, "label") <- "Original Units"
+attr(qs_metabolic_seq$QSSTRESC, "label") <- "Character Result/Finding in Std Format"
+attr(qs_metabolic_seq$QSSTRESN, "label") <- "Numeric Result/Finding in Standard Units"
+attr(qs_metabolic_seq$QSSTRESU, "label") <- "Standard Units"
+attr(qs_metabolic_seq$QSSEQ, "label") <- "Sequence Number"
+
+# Label QS dataset ----
+attr(qs_metabolic_seq, "label") <- "Questionnaire"
+
+# Final dataset ----
+qs_metabolic <- qs_metabolic_seq
+
+# Save dataset ----
+usethis::use_data(qs_metabolic, overwrite = TRUE)

inst/WORDLIST

@@ -10,6 +10,7 @@ Biologics
 BMI
 CDISC
 Changelog
+CoEQ
 DM
 Farrugia
 GSK