Closes #23: ADVS template program

inst/ad_advs.R

@@ -0,0 +1,260 @@
+# Name: ADVS
+#
+# Label: Vital Signs Analysis dataset
+#
+# Input: adsl, vs
+
+
+# Attach/load required packages ----
+library(admiral)
+library(admiralmetabolic)
+library(tibble)
+library(dplyr)
+library(stringr)
+
+
+# Define look-up tables ----
+# See function documentation for `derive_vars_merged_lookup()` and
+# `derive_vars_cat()` for information of how look-up tables can be used:
+# (https://pharmaverse.github.io/admiral/reference/derive_vars_merged_lookup.html)
+# (https://pharmaverse.github.io/admiral/reference/derive_vars_cat.html)
+
+# Parameter look-up
+param_lookup <- tribble(
+  ~VSTESTCD, ~PARAMCD, ~PARAM, ~PARAMN, ~PARCAT1, ~PARCAT1N,
+  "HEIGHT", "HEIGHT", "Height (cm)", 1, "Subject Characteristic", 1,
+  "WEIGHT", "WEIGHT", "Weight (kg)", 2, "Subject Characteristic", 1,
+  "BMI", "BMI", "Body Mass Index(kg/m^2)", 3, "Subject Characteristic", 1,
+  "HIPCIR", "HIPCIR", "Hip Circumference (cm)", 4, "Subject Characteristic", 1,
+  "WSTCIR", "WSTCIR", "Waist Circumference (cm)", 5, "Subject Characteristic", 1,
+  "DIABP", "DIABP", "Diastolic Blood Pressure (mmHg)", 6, "Vital Sign", 2,
+  "PULSE", "PULSE", "Pulse Rate (beats/min)", 7, "Vital Sign", 2,
+  "SYSBP", "SYSBP", "Systolic Blood Pressure (mmHg)", 8, "Vital Sign", 2,
+  "TEMP", "TEMP", "Temperature (C)", 9, "Vital Sign", 2
+)
+
+# Analysis categories look-up (conditional look-up)
+avalcat_lookup <- exprs(
+  ~PARAMCD, ~condition,                ~AVALCAT1,           ~AVALCA1N,
+  "BMI",    AVAL < 18.5,               "Underweight",       1,
+  "BMI",    AVAL >= 18.5 & AVAL < 25,  "Normal weight",     2,
+  "BMI",    AVAL >= 25 & AVAL < 30,    "Overweight",        3,
+  "BMI",    AVAL >= 30 & AVAL < 35,    "Obesity class I",   4,
+  "BMI",    AVAL >= 35 & AVAL < 40,    "Obesity class II",  5,
+  "BMI",    AVAL >= 40,                "Obesity class III", 6,
+  "BMI",    is.na(AVAL),               NA_character_,       NA_integer_
+)
+
+# 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
+vs_metabolic <- admiralmetabolic::vs_metabolic
+adsl <- admiral::admiral_adsl
+
+# Convert SAS empty values to NA
+advs <- vs_metabolic |>
+  convert_blanks_to_na()
+adsl <- adsl |>
+  convert_blanks_to_na()
+
+# Merge ADSL variables (TRTSDT, TRTEDT, TRT01P, TRT01A) needed for ADVS
+# derivations
+advs <- advs |>
+  derive_vars_merged(
+    dataset_add = adsl,
+    new_vars = exprs(TRTSDT, TRTEDT, TRT01P, TRT01A),
+    by_vars = exprs(STUDYID, USUBJID)
+  )
+
+# Add parameter (PARAMCD) info to enable later ADVS derivations. Additional
+# parameter information will be merged again, after all AVDS derivations are
+# completed.
+advs <- advs |>
+  derive_vars_merged_lookup(
+    dataset_add = param_lookup,
+    new_vars = exprs(PARAMCD),
+    by_vars = exprs(VSTESTCD)
+  )
+
+
+# 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 vital sign analysis date (ADT) and treatment start date (TRTSDT)
+advs <- advs |>
+  derive_vars_dt(new_vars_prefix = "A", dtc = VSDTC)
+advs <- advs |>
+  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 time point (ATPT, ATPTN) and analysis visit (AVISIT, AVISITN)
+advs <- advs |>
+  mutate(
+    ATPT = VSTPT,
+    ATPTN = VSTPTNUM,
+    AVISIT = case_when(
+      is.na(VISIT) ~ NA_character_,
+      str_detect(VISIT, "SCREEN|UNSCHED|RETRIEVAL|AMBUL") ~ NA_character_,
+      TRUE ~ str_to_title(VISIT)
+    ),
+    AVISITN = case_when(
+      VISIT == "BASELINE" ~ 0,
+      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)
+advs <- advs |>
+  mutate(
+    AVAL = VSSTRESN
+  )
+
+
+# Derive domain specific variables ----
+# See the "Derive Additional Parameters" vignette section for more information:
+# (https://pharmaverse.github.io/admiral/articles/bds_finding.html#derive_param)
+
+# Derive BMI
+advs <- advs |>
+  filter(VSTESTCD != "BMI") |>
+  derive_param_bmi(
+    by_vars = exprs(
+      STUDYID, USUBJID, TRTSDT, TRTEDT, TRT01P, TRT01A, VISIT,
+      VISITNUM, ADT, ADY, VSTPT, VSTPTNUM
+    ),
+    set_values_to = exprs(
+      PARAMCD = "BMI",
+      DOMAIN = "VS"
+    ),
+    get_unit_expr = VSSTRESU,
+    filter = VSSTAT != "NOT DONE" | is.na(VSSTAT),
+    constant_by_vars = exprs(USUBJID)
+  )
+
+
+# Derive categorization variables ----
+# See the "Derive Categorization Variables" vignette section for more
+# information:
+# (https://pharmaverse.github.io/admiral/articles/bds_finding.html#cat)
+
+# Derive BMI class (AVALCAT1, AVALCA1N)
+advs <- advs |>
+  derive_vars_cat(
+    definition = avalcat_lookup,
+    by_vars = exprs(PARAMCD)
+  )
+
+
+# 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)
+advs <- advs |>
+  restrict_derivation(
+    derivation = derive_var_extreme_flag,
+    args = params(
+      by_vars = exprs(STUDYID, USUBJID, PARAMCD),
+      order = exprs(ADT, VSTPTNUM, VISITNUM),
+      new_var = ABLFL,
+      mode = "last"
+    ),
+    filter = (!is.na(AVAL) & ADT <= TRTSDT)
+  )
+
+# Derive baseline analysis value (BASE)
+advs <- advs |>
+  derive_var_base(
+    by_vars = exprs(STUDYID, USUBJID, PARAMCD),
+    source_var = AVAL,
+    new_var = BASE
+  )
+
+# Derive absolute (CHG) and relative (PCHG) change from baseline
+advs <- advs |>
+  derive_var_chg()
+advs <- advs |>
+  derive_var_pchg()
+
+
+# Derive criterion variables ----
+# See the "Derive Criterion Variables" vignette section for more information:
+# (https://pharmaverse.github.io/admiral/articles/bds_finding.html#crit_vars)
+
+# Set weight loss criterion flags (CRIT1, CRIT1FL)
+advs <- advs |>
+  derive_vars_crit_flag(
+    condition = PCHG <= -5 & PARAMCD == "WEIGHT",
+    description = "Achievement of ≥ 5% weight reduction from baseline",
+    crit_nr = 1,
+    values_yn = TRUE,
+    create_numeric_flag = FALSE
+  ) |>
+  derive_vars_crit_flag(
+    condition = PCHG <= -10 & PARAMCD == "WEIGHT",
+    description = "Achievement of ≥ 10% weight reduction from baseline",
+    crit_nr = 2,
+    values_yn = TRUE,
+    create_numeric_flag = FALSE
+  )
+
+
+# Assign parameter variables ----
+# See the "Assign PARAMCD, PARAM, PARAMN, PARCAT1" vignette section for more
+# information:
+# (https://pharmaverse.github.io/admiral/articles/bds_finding.html#paramcd)
+
+# Add all parameter variables (PARAM, PARAMN, PARCAT1)
+advs <- advs |>
+  derive_vars_merged_lookup(
+    dataset_add = param_lookup,
+    new_vars = exprs(PARAMCD, PARAM, PARAMN, PARCAT1, PARCAT1N),
+    by_vars = exprs(PARAMCD)
+  )
+
+
+# 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
+advs <- advs %>%
+  derive_vars_merged(
+    dataset_add = select(adsl, !!!negate_vars(TRTSDT, TRTEDT, TRT01P, TRT01A)),
+    by_vars = exprs(STUDYID, USUBJID)
+  )
+
+
+# Add Labels and Attributes ----
+# This process is commonly based on your 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(advs, file = file.path(dir, "advs.rda"), compress = "bzip2")