Closes #41 : Add ADCOEQ for review (#58)

* #41 : Add ADCOEQ for review * adcoeq (#41) : Addressed comments * adcoeq (#41) : Added PARAMN * adcoeq (#41) : Minor updates * adcoeq (#41) : Updated AVISIT logic for Baseline * Minor update Co-authored-by: Anders Askeland <[email protected]> --------- Co-authored-by: SPUJ (Siddhesh Pujari) <[email protected]> Co-authored-by: Anders Askeland <[email protected]>
pharmaverse · Dec 16, 2024 · f94f7c9 · f94f7c9
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+# Name: ADCOEQ
+#
+# Label: Control of Eating Questionnaires Analysis dataset
+#
+# Input: adsl, qs
+
+# License ----
+
+# Note that University of Leeds are the copyright holders of the Control of Eating
+# Questionnaire (CoEQ) and the test data included within `{admiralmetabolic}` as
+# well as the ADCOEQ code are 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).
+
+# Attach/load required packages ----
+library(admiral)
+library(admiralmetabolic)
+library(tibble)
+library(dplyr)
+library(stringr)
+
+# Define project options/variables ----
+# Use the admiral option functionality to store subject key variables in one
+# place (note: `subject_keys` defaults to STUDYID and USUBJID)
+set_admiral_options(subject_keys = exprs(STUDYID, USUBJID))
+
+# Store ADSL variables required for derivations as an R object, enabling
+# simplified usage throughout the program
+adsl_vars <- exprs(TRTSDT, TRTEDT, TRT01P, TRT01A)
+
+# Read in data ----
+# See the "Read in Data" vignette section for more information:
+# (https://pharmaverse.github.io/admiral/articles/bds_finding.html#readdata)
+
+# Read data
+qs_metabolic <- admiralmetabolic::qs_metabolic
+adsl <- admiral::admiral_adsl
+
+# Convert SAS missing character values to NA
+adcoeq <- qs_metabolic %>%
+  convert_blanks_to_na()
+adsl <- adsl %>%
+  convert_blanks_to_na()
+
+# Merge ADSL variables (stored in `adsl_vars`) needed for ADQS
+adcoeq <- adcoeq %>%
+  derive_vars_merged(
+    dataset_add = adsl,
+    new_vars = adsl_vars,
+    by_vars = get_admiral_option("subject_keys")
+  )
+
+# Add analysis parameter variables
+adcoeq <- adcoeq %>%
+  mutate(
+    PARAMCD = QSTESTCD,
+    PARAM = QSTEST,
+    PARAMN = as.numeric(str_extract(QSTESTCD, "\\d+")),
+    PARCAT1 = QSCAT
+  )
+
+# Derive Date/Time and Analysis Day ----
+# See the "Derive/Impute Numeric Date/Time and Analysis Day" vignette section
+# for more information:
+# (https://pharmaverse.github.io/admiral/articles/bds_finding.html#datetime)
+
+# Add questionnaire analysis date (ADT) and treatment start date (TRTSDT)
+adcoeq <- adcoeq %>%
+  derive_vars_dt(
+    new_vars_prefix = "A",
+    dtc = QSDTC
+  ) %>%
+  derive_vars_dy(
+    reference_date = TRTSDT,
+    source_vars = exprs(ADT)
+  )
+
+# Derive visit info ----
+# See the "Visit and Period Variables" vignette for more information:
+# (https://pharmaverse.github.io/admiral/articles/visits_periods.html)
+
+# Derive analysis visit (AVISIT, AVISITN)
+adcoeq <- adcoeq %>%
+  mutate(
+    AVISIT = case_when(
+      is.na(VISIT) ~ NA_character_,
+      str_detect(VISIT, "UNSCHED|RETRIEVAL|AMBUL") ~ NA_character_,
+      TRUE ~ str_to_title(VISIT)
+    ),
+    AVISITN = case_when(
+      AVISIT == "Baseline" ~ 0,
+      str_detect(AVISIT, "Screen") ~ -1,
+      str_detect(VISIT, "WEEK") ~ as.integer(str_extract(VISIT, "\\d+")),
+      TRUE ~ NA_integer_
+    )
+  )
+
+# Derive results ----
+# See the "Derive Results (AVAL, AVALC)" vignette section for more information:
+# (https://pharmaverse.github.io/admiral/articles/bds_finding.html#aval)
+
+# Derive analysis result (AVAL, AVALC)
+adcoeq <- adcoeq %>%
+  mutate(
+    # Invert the original scores for COEQ item 6 as they indicate anxiety and
+    # is used in calculating the subscale for "Positive Mood"
+    AVAL = if_else(PARAMCD == "COEQ06", 100 - QSSTRESN, QSSTRESN),
+    AVALC = if_else(PARAMCD == "COEQ20", QSORRES, NA_character_)
+  )
+
+
+# Derive summary records ----
+
+# See the "Example 2 (Deriving a Summary Record)" vignette section for more
+# information:
+# (https://pharmaverse.github.io/admiral/articles/bds_finding.html#example-2-deriving-a-summary-record)
+
+# For the Control of Eating Questionnaire, four subscales are derived.
+# These subscales are derived as the mean across a subset of the
+# various items/questions.
+
+# The subscales are defined as follows:
+
+# 1) Craving Control: Calculate mean of items 9, 10, 11, 12 and 19.
+
+# 2) Craving for Sweet: Calculate mean of items 3, 13, 14 and 15.
+
+# 3) Craving for Savoury: Calculate mean of items 4, 16, 17 and 18.
+
+# 4) Positive Mood: Calculate mean of items 5, 7, 8 and 6 (reversed).
+
+# Derive four subscales
+adcoeq <- adcoeq %>%
+  call_derivation(
+    derivation = derive_summary_records,
+    variable_params = list(
+      params(
+        filter_add = PARAMCD %in% c(
+          "COEQ09", "COEQ10", "COEQ11", "COEQ12", "COEQ19"
+        ) & AVISITN >= 0,
+        set_values_to = exprs(
+          AVAL = mean(AVAL, na.rm = TRUE),
+          PARAMCD = "COEQCRCO",
+          PARAM = "COEQ - Craving Control",
+          PARAMN = 22
+        )
+      ),
+      params(
+        filter_add = PARAMCD %in% c("COEQ03", "COEQ13", "COEQ14", "COEQ15") &
+          AVISITN >= 0,
+        set_values_to = exprs(
+          AVAL = mean(AVAL, na.rm = TRUE),
+          PARAMCD = "COEQCRSW",
+          PARAM = "COEQ - Craving for Sweet",
+          PARAMN = 23
+        )
+      ),
+      params(
+        filter_add = PARAMCD %in% c("COEQ04", "COEQ16", "COEQ17", "COEQ18") &
+          AVISITN >= 0,
+        set_values_to = exprs(
+          AVAL = mean(AVAL, na.rm = TRUE),
+          PARAMCD = "COEQCRSA",
+          PARAM = "COEQ - Craving for Savoury",
+          PARAMN = 24
+        )
+      ),
+      params(
+        filter_add = PARAMCD %in% c("COEQ05", "COEQ07", "COEQ08", "COEQ06") &
+          AVISITN >= 0,
+        set_values_to = exprs(
+          AVAL = mean(AVAL, na.rm = TRUE),
+          PARAMCD = "COEQPOMO",
+          PARAM = "COEQ - Positive Mood",
+          PARAMN = 25
+        )
+      )
+    ),
+    dataset_add = adcoeq,
+    by_vars = exprs(
+      STUDYID, USUBJID, AVISIT, AVISITN, ADT, ADY, PARCAT1,
+      TRTSDT, TRTEDT, TRT01P, TRT01A
+    )
+  )
+
+
+# Derive Baseline variables ----
+# See the "Derive Baseline" and "Derive Change from Baseline " vignette sections
+# for more information:
+# (https://pharmaverse.github.io/admiral/articles/bds_finding.html#baseline)
+# (https://pharmaverse.github.io/admiral/articles/bds_finding.html#bchange)
+
+# Add baseline flag (ABLFL)
+adcoeq <- adcoeq %>%
+  restrict_derivation(
+    derivation = derive_var_extreme_flag,
+    args = params(
+      by_vars = exprs(!!!get_admiral_option("subject_keys"), PARAMCD),
+      order = exprs(ADT, AVISITN),
+      new_var = ABLFL,
+      mode = "last"
+    ),
+    filter = (!is.na(AVAL) & ADT <= TRTSDT)
+  )
+
+# Derive baseline analysis value (BASE)
+adcoeq <- adcoeq %>%
+  derive_var_base(
+    by_vars = exprs(!!!get_admiral_option("subject_keys"), PARAMCD),
+    source_var = AVAL,
+    new_var = BASE
+  )
+
+# Derive absolute (CHG) and relative (PCHG) change from baseline
+adcoeq <- adcoeq %>%
+  restrict_derivation(
+    derivation = derive_var_chg,
+    filter = AVISITN > 0
+  ) %>%
+  restrict_derivation(
+    derivation = derive_var_pchg,
+    filter = AVISITN > 0
+  )
+
+# Assign ASEQ ----
+# See the "Assign ASEQ" vignette section for more information:
+# https://pharmaverse.github.io/admiral/articles/bds_finding.html#aseq
+
+# Calculate ASEQ
+adcoeq <- adcoeq %>%
+  derive_var_obs_number(
+    new_var = ASEQ,
+    by_vars = exprs(STUDYID, USUBJID),
+    order = exprs(PARAMCD, ADT, AVISITN),
+    check_type = "error"
+  )
+
+# Add ADSL variables ----
+# See the "Add ADSL variables" vignette section for more information:
+# (https://pharmaverse.github.io/admiral/articles/bds_finding.html#adsl_vars)
+
+# Add all ADSL variables besides TRTSDT, TRTEDT, TRT01P, TRT01A (stored in
+# `adsl_vars`)
+adcoeq <- adcoeq %>%
+  derive_vars_merged(
+    dataset_add = select(adsl, !!!negate_vars(adsl_vars)),
+    by_vars = get_admiral_option("subject_keys")
+  )
+
+# Add Labels and Attributes ----
+# This process is usually based on one's metadata. As such, no specific example
+# will be given. See the "Add Labels and Attributes" vignette section for
+# description of several open source R packages which can be used to handle
+# metadata.
+# (https://pharmaverse.github.io/admiral/articles/bds_finding.html#attributes)
+
+
+# Save output ----
+
+# Change to whichever directory you want to save the dataset in
+dir <- tools::R_user_dir("admiral_templates_data", which = "cache") # Cache
+if (!file.exists(dir)) {
+  # Create the folder
+  dir.create(dir, recursive = TRUE, showWarnings = FALSE)
+}
+save(adcoeq, file = file.path(dir, "adcoeq.rda"), compress = "bzip2")