From 26cac246fccca2d27e0f1f072f179c9e1176f272 Mon Sep 17 00:00:00 2001
From: Edoardo Mancini <53403957+manciniedoardo@users.noreply.github.com>
Date: Tue, 5 Nov 2024 09:29:13 +0000
Subject: [PATCH] Closes #39: CoEQ test data (#45)

* Closes #39: CoEQ test data

* #39 chore: styler updates

* #39 chore: spelling

* Apply suggestions from code review

#39: implemented suggestions from code review

Co-authored-by: Anders Askeland <anders.askeland@gmail.com>

* #39 updated disclaimer based on review

* #39 fixed typo in QSSCATSs

* #39 fixed typo in data.R

* Apply suggestions from code review

Co-authored-by: Anders Askeland <anders.askeland@gmail.com>

* Apply suggestions from code review

Co-authored-by: Andrii Yurovskyi <a.yurovskyi@icloud.com>

* #39 updates following review

---------

Co-authored-by: Anders Askeland <anders.askeland@gmail.com>
Co-authored-by: Andrii Yurovskyi <a.yurovskyi@icloud.com>
---
 R/data.R                |  11 ++++
 data-raw/qs_metabolic.R | 123 ++++++++++++++++++++++++++++++++++++++++
 data/qs_metabolic.rda   | Bin 0 -> 6255 bytes
 inst/WORDLIST           |   1 +
 man/qs_metabolic.Rd     |  23 ++++++++
 5 files changed, 158 insertions(+)
 create mode 100644 data-raw/qs_metabolic.R
 create mode 100644 data/qs_metabolic.rda
 create mode 100644 man/qs_metabolic.Rd

diff --git a/R/data.R b/R/data.R
index d44d3db..26b7c43 100644
--- a/R/data.R
+++ b/R/data.R
@@ -11,3 +11,14 @@
 #'
 #' @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 within `{admiralmetabolic}` and `pharmaverse`-related examples/documentation. 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"
diff --git a/data-raw/qs_metabolic.R b/data-raw/qs_metabolic.R
new file mode 100644
index 0000000..acefe61
--- /dev/null
+++ b/data-raw/qs_metabolic.R
@@ -0,0 +1,123 @@
+#' Dataset: qs_metabolic
+#' Description: Create QS test SDTM dataset for metabolic studies,
+#' containing COEQ data (Control of Eating Questionnaire)
+#' Note: the University of Leeds are the copyright holders of the CoEQ and the test data included within {admiralmetabolic}
+#' is for not-for-profit use only within `{admiralmetabolic}` and `pharmaverse`-related examples/documentation. 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(stringr)
+
+# 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, ~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 ----
+visit_schedule <- vs_metabolic %>%
+  select(STUDYID, USUBJID, VISIT, VISITNUM, VISITDY, VSDTC, VSDY) %>%
+  filter(str_detect(VISIT, "AMBUL|RETRIEVAL", negate = TRUE)) %>%
+  rename(QSDTC = VSDTC, QSDY = VSDY) %>%
+  distinct()
+
+# Cross join to get questions at each visit ----
+qs_metabolic_shell <- visit_schedule %>%
+  cross_join(coeq_structure)
+
+# Simulate question answers ----
+qs_metabolic_results <- qs_metabolic_shell %>%
+  mutate(
+    DOMAIN = "QS",
+    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, 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 ----
+labels <- list(
+  DOMAIN = "Domain Abbreviation",
+  QSBLFL = "Baseline Flag",
+  QSCAT = "Category for Questionnaire",
+  QSTEST = "Questionnaire Test Name",
+  QSTESTCD = "Questionnaire Test Short Name",
+  QSORRES = "Result or Finding in Original Units",
+  QSORRESU = "Original Units",
+  QSSTRESC = "Character Result/Finding in Std Format",
+  QSSTRESN = "Numeric Result/Finding in Standard Units",
+  QSSTRESU = "Standard Units",
+  QSSEQ = "Sequence Number"
+)
+
+for (var in names(labels)) {
+  attr(qs_metabolic_seq[[var]], "label") <- labels[[var]]
+}
+
+# Label QS dataset ----
+attr(qs_metabolic_seq, "label") <- "Questionnaires"
+
+# Final dataset ----
+qs_metabolic <- qs_metabolic_seq
+
+# Save dataset ----
+usethis::use_data(qs_metabolic, overwrite = TRUE)
diff --git a/data/qs_metabolic.rda b/data/qs_metabolic.rda
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diff --git a/inst/WORDLIST b/inst/WORDLIST
index 26e8d42..c469925 100644
--- a/inst/WORDLIST
+++ b/inst/WORDLIST
@@ -10,6 +10,7 @@ Biologics
 BMI
 CDISC
 Changelog
+CoEQ
 DM
 Farrugia
 GSK
diff --git a/man/qs_metabolic.Rd b/man/qs_metabolic.Rd
new file mode 100644
index 0000000..e726f83
--- /dev/null
+++ b/man/qs_metabolic.Rd
@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data.R
+\docType{data}
+\name{qs_metabolic}
+\alias{qs_metabolic}
+\title{Example questionnaire dataset}
+\format{
+An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 966 rows and 18 columns.
+}
+\source{
+Constructed using \code{dm_metabolic} from \code{{admiralmetabolic}} package
+}
+\usage{
+qs_metabolic
+}
+\description{
+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 within \code{{admiralmetabolic}} and \code{pharmaverse}-related examples/documentation. Any persons
+or companies wanting to use the CoEQ should request a license to do so from the following
+\href{https://licensing.leeds.ac.uk/product/control-of-eating-questionnaire-coeq}{link}.
+}
+\keyword{datasets}