Closes #11 vs_metabolic test data (#25)

* (#11): RoxygenNote updated to 7.3.2

* (#11): Added documentation for vs_metabolic

* (#11): Created vs_metabolic

* (#11): Code formatted using styler

* (#11): Updated as per requested changes

---------

Co-authored-by: SPUJ (Siddhesh Pujari) <[email protected]>

DESCRIPTION

@@ -49,4 +49,4 @@ Encoding: UTF-8
 Language: en-US
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

R/data.R

@@ -4,3 +4,10 @@
 #'
 #' @source Constructed using `dm` from the `{pharmaversesdtm}` package
 "dm_metabolic"
+
+#' Example vital signs dataset
+#'
+#' An example Vital Signs SDTM dataset for metabolic studies.
+#'
+#' @source Constructed using `vs` from the `{pharmaversesdtm}` package and `dm_metabolic` from `{admiralmetabolic}` package
+"vs_metabolic"

data-raw/vs_metabolic.R

@@ -0,0 +1,293 @@
+# Dataset: vs_metabolic
+# Description: Create VS test SDTM dataset for metabolic studies
+
+# Load libraries ----
+
+library(tibble)
+library(dplyr)
+library(pharmaversesdtm)
+library(purrr)
+
+## Read input data ----
+
+data("vs")
+data("dm_metabolic")
+
+# Merge vs with dm_metabolic to use the req subjects ----
+
+vs1 <- dm_metabolic %>%
+  select(USUBJID) %>%
+  left_join(vs, by = c("USUBJID"))
+
+# Create placeholder record for WAIST CIRCUMFERENCE from the WEIGHT records
+vs1_wstcir <- vs1 %>%
+  filter(VSTESTCD == "WEIGHT") %>%
+  mutate(VSTESTCD = "WSTCIR", VSTEST = "Waist Circumference")
+
+vs1_hipcir <- vs1 %>%
+  filter(VSTESTCD == "WEIGHT") %>%
+  mutate(VSTESTCD = "HIPCIR", VSTEST = "Hip Circumference")
+
+# Bind new parameter records to original dataset
+vs_full <- bind_rows(vs1, vs1_wstcir, vs1_hipcir) %>%
+  arrange(USUBJID, VSTESTCD, VISITNUM, VSDY)
+
+# Updating each parameter values for each subject to make them obese
+vs_mb <- vs_full %>%
+  mutate(
+    VSSTRESN =
+      case_when(
+        USUBJID == "01-701-1015" & # PLACEBO
+          VSTESTCD == "WEIGHT" ~ case_when(
+          VISIT == "SCREENING 1" ~ 89.20,
+          VISIT == "BASELINE" ~ 89.10,
+          VISIT == "WEEK 2" ~ 90.20,
+          VISIT == "WEEK 4" ~ 90.42,
+          VISIT == "WEEK 6" ~ 90.54,
+          VISIT == "WEEK 8" ~ 90.81,
+          VISIT == "WEEK 12" ~ 91.20,
+          VISIT == "WEEK 16" ~ 90.31,
+          VISIT == "WEEK 20" ~ 91.37,
+          VISIT == "WEEK 24" ~ 91.55,
+          VISIT == "WEEK 26" ~ 93.10,
+        ),
+        USUBJID == "01-701-1015" & # PLACEBO
+          VSTESTCD == "HEIGHT" ~ case_when(VISIT == "SCREENING 1" ~ 153),
+        USUBJID == "01-701-1015" & # PLACEBO
+          VSTESTCD == "WSTCIR" ~ case_when(
+          VISIT == "SCREENING 1" ~ 99,
+          VISIT == "BASELINE" ~ 99,
+          VISIT == "WEEK 2" ~ 100,
+          VISIT == "WEEK 4" ~ 100.4,
+          VISIT == "WEEK 6" ~ 101,
+          VISIT == "WEEK 8" ~ 101,
+          VISIT == "WEEK 12" ~ 102,
+          VISIT == "WEEK 16" ~ 102.5,
+          VISIT == "WEEK 20" ~ 102.7,
+          VISIT == "WEEK 24" ~ 104,
+          VISIT == "WEEK 26" ~ 105,
+        ),
+        USUBJID == "01-701-1015" & # PLACEBO
+          VSTESTCD == "HIPCIR" ~ case_when(
+          VISIT == "SCREENING 1" ~ 102,
+          VISIT == "BASELINE" ~ 102,
+          VISIT == "WEEK 2" ~ 103,
+          VISIT == "WEEK 4" ~ 103,
+          VISIT == "WEEK 6" ~ 103,
+          VISIT == "WEEK 8" ~ 104,
+          VISIT == "WEEK 12" ~ 104.2,
+          VISIT == "WEEK 16" ~ 104.7,
+          VISIT == "WEEK 20" ~ 105,
+          VISIT == "WEEK 24" ~ 105.1,
+          VISIT == "WEEK 26" ~ 105.2,
+        ),
+        USUBJID == "01-701-1023" & # PLACEBO
+          VSTESTCD == "WEIGHT" ~ case_when(
+          VISIT == "SCREENING 1" ~ 110.11,
+          VISIT == "BASELINE" ~ 110.02,
+          VISIT == "WEEK 2" ~ 111.31,
+          VISIT == "WEEK 4" ~ 112.21
+        ),
+        USUBJID == "01-701-1023" & # PLACEBO
+          VSTESTCD == "HEIGHT" ~ case_when(VISIT == "SCREENING 1" ~ 169),
+        USUBJID == "01-701-1023" & # PLACEBO
+          VSTESTCD == "WSTCIR" ~ case_when(
+          VISIT == "SCREENING 1" ~ 106,
+          VISIT == "BASELINE" ~ 107,
+          VISIT == "WEEK 2" ~ 107.8,
+          VISIT == "WEEK 4" ~ 109
+        ),
+        USUBJID == "01-701-1023" & # PLACEBO
+          VSTESTCD == "HIPCIR" ~ case_when(
+          VISIT == "SCREENING 1" ~ 110,
+          VISIT == "BASELINE" ~ 110,
+          VISIT == "WEEK 2" ~ 111.4,
+          VISIT == "WEEK 4" ~ 112
+        ),
+        USUBJID == "01-701-1028" & # Insulin
+          VSTESTCD == "WEIGHT" ~ case_when(
+          VISIT == "SCREENING 1" ~ 95.14,
+          VISIT == "BASELINE" ~ 95.11,
+          VISIT == "WEEK 2" ~ 94.23,
+          VISIT == "WEEK 4" ~ 92.11,
+          VISIT == "WEEK 6" ~ 91.55,
+          VISIT == "WEEK 8" ~ 90.24,
+          VISIT == "WEEK 12" ~ 89.33,
+          VISIT == "WEEK 16" ~ 88.82,
+          VISIT == "WEEK 20" ~ 88.15,
+          VISIT == "WEEK 24" ~ 87.06,
+          VISIT == "WEEK 26" ~ 86.12
+        ),
+        USUBJID == "01-701-1028" & # Insulin
+          VSTESTCD == "HEIGHT" ~ case_when(VISIT == "SCREENING 1" ~ 159),
+        USUBJID == "01-701-1028" & # Insulin
+          VSTESTCD == "WSTCIR" ~ case_when(
+          VISIT == "SCREENING 1" ~ 105,
+          VISIT == "BASELINE" ~ 105,
+          VISIT == "WEEK 2" ~ 104,
+          VISIT == "WEEK 4" ~ 102,
+          VISIT == "WEEK 6" ~ 101,
+          VISIT == "WEEK 8" ~ 100,
+          VISIT == "WEEK 12" ~ 99.4,
+          VISIT == "WEEK 16" ~ 99,
+          VISIT == "WEEK 20" ~ 97,
+          VISIT == "WEEK 24" ~ 96,
+          VISIT == "WEEK 26" ~ 95
+        ),
+        USUBJID == "01-701-1028" & # Insulin
+          VSTESTCD == "HIPCIR" ~ case_when(
+          VISIT == "SCREENING 1" ~ 111,
+          VISIT == "BASELINE" ~ 111,
+          VISIT == "WEEK 2" ~ 110,
+          VISIT == "WEEK 4" ~ 112,
+          VISIT == "WEEK 6" ~ 109,
+          VISIT == "WEEK 8" ~ 108,
+          VISIT == "WEEK 12" ~ 107.5,
+          VISIT == "WEEK 16" ~ 106.2,
+          VISIT == "WEEK 20" ~ 104,
+          VISIT == "WEEK 24" ~ 103,
+          VISIT == "WEEK 26" ~ 102
+        ),
+        USUBJID == "01-701-1033" & # Insulin
+          VSTESTCD == "WEIGHT" ~ case_when(
+          VISIT == "SCREENING 1" ~ 101.82,
+          VISIT == "BASELINE" ~ 101.61,
+          VISIT == "WEEK 2" ~ 100.64,
+          VISIT == "WEEK 4" ~ 99.91
+        ),
+        USUBJID == "01-701-1033" & # Insulin
+          VSTESTCD == "HEIGHT" ~ case_when(VISIT == "SCREENING 1" ~ 158),
+        USUBJID == "01-701-1033" & # Insulin
+          VSTESTCD == "WSTCIR" ~ case_when(
+          VISIT == "SCREENING 1" ~ 108,
+          VISIT == "BASELINE" ~ 107,
+          VISIT == "WEEK 2" ~ 107,
+          VISIT == "WEEK 4" ~ 106
+        ),
+        USUBJID == "01-701-1033" & # Insulin
+          VSTESTCD == "HIPCIR" ~ case_when(
+          VISIT == "SCREENING 1" ~ 110,
+          VISIT == "BASELINE" ~ 110,
+          VISIT == "WEEK 2" ~ 108,
+          VISIT == "WEEK 4" ~ 107
+        ),
+        USUBJID == "01-701-1034" & # Insulin
+          VSTESTCD == "WEIGHT" ~ case_when(
+          VISIT == "SCREENING 1" ~ 108.12,
+          VISIT == "BASELINE" ~ 107.43,
+          VISIT == "WEEK 2" ~ 105.41,
+          VISIT == "WEEK 4" ~ 104.92,
+          VISIT == "WEEK 6" ~ 103.65,
+          VISIT == "WEEK 8" ~ 103.12,
+          VISIT == "WEEK 12" ~ 100.11,
+          VISIT == "WEEK 16" ~ 97.42,
+          VISIT == "WEEK 20" ~ 96.95,
+          VISIT == "WEEK 24" ~ 94.86,
+          VISIT == "WEEK 26" ~ 94.11
+        ),
+        USUBJID == "01-701-1034" & # Insulin
+          VSTESTCD == "HEIGHT" ~ case_when(VISIT == "SCREENING 1" ~ 163),
+        USUBJID == "01-701-1034" & # Insulin
+          VSTESTCD == "WSTCIR" ~ case_when(
+          VISIT == "SCREENING 1" ~ 115,
+          VISIT == "BASELINE" ~ 115,
+          VISIT == "WEEK 2" ~ 114,
+          VISIT == "WEEK 4" ~ 113,
+          VISIT == "WEEK 6" ~ 112,
+          VISIT == "WEEK 8" ~ 113,
+          VISIT == "WEEK 12" ~ 110,
+          VISIT == "WEEK 16" ~ 109.2,
+          VISIT == "WEEK 20" ~ 109,
+          VISIT == "WEEK 24" ~ 108,
+          VISIT == "WEEK 26" ~ 107
+        ),
+        USUBJID == "01-701-1034" & # Insulin
+          VSTESTCD == "HIPCIR" ~ case_when(
+          VISIT == "SCREENING 1" ~ 120,
+          VISIT == "BASELINE" ~ 119.7,
+          VISIT == "WEEK 2" ~ 119.1,
+          VISIT == "WEEK 4" ~ 118.3,
+          VISIT == "WEEK 6" ~ 117.7,
+          VISIT == "WEEK 8" ~ 117,
+          VISIT == "WEEK 12" ~ 116.4,
+          VISIT == "WEEK 16" ~ 115,
+          VISIT == "WEEK 20" ~ 114,
+          VISIT == "WEEK 24" ~ 113,
+          VISIT == "WEEK 26" ~ 113
+        ),
+        TRUE ~ VSSTRESN
+      )
+  )
+
+# Derive BMI values ----
+
+vs_mb_bmi <- vs_mb |>
+  # use body weight as a base for the table
+  filter(VSTESTCD == "WEIGHT") |>
+  mutate(VSSTRESN = as.numeric(VSSTRESN)) |>
+  # rename value to body weight
+  rename(BODYWEIGHT = VSSTRESN) |>
+  # drop irrelevant columns
+  select(-VSORRES, -VSORRESU) |>
+  # add height
+  left_join(
+    vs_mb |>
+      # pick height
+      filter(VSTESTCD == "HEIGHT") |>
+      # Convert height from cm to m
+      mutate(VSSTRESN = as.numeric(VSSTRESN / 100)) |>
+      # rename
+      rename(HEIGHT = VSSTRESN) |>
+      # drop irrelevant
+      select(USUBJID, HEIGHT),
+    by = "USUBJID"
+  ) |>
+  # calculate bmi
+  mutate(
+    VSSTRESN = as.numeric(BODYWEIGHT / (HEIGHT^2)),
+    VSTESTCD = "BMI",
+    VSTEST = "Body Mass Index",
+  ) |>
+  # drop irrelevant
+  select(-BODYWEIGHT, -HEIGHT)
+
+# Bind BMI dataset to vs_mb dataset
+vs_mb <- bind_rows(vs_mb, vs_mb_bmi) %>% arrange(USUBJID, VSTESTCD, VISITNUM, VSDY)
+
+# Formatting the output dataset ----
+
+vs_mb <- vs_mb %>%
+  mutate(
+    VSSEQ = row_number(),
+    VSORRESU = case_when(
+      VSTESTCD == "WEIGHT" ~ "kg",
+      VSTESTCD == "BMI" ~ "kg/m2",
+      VSTESTCD == "WSTCIR" ~ "cm",
+      VSTESTCD == "HIPCIR" ~ "cm",
+      VSTESTCD == "HEIGHT" ~ "cm",
+      TRUE ~ VSORRESU
+    ),
+    VSSTRESC = as.character(VSSTRESN),
+    VSORRES = VSSTRESC,
+    VSSTRESU = VSORRESU,
+  ) %>%
+  arrange(USUBJID, VSTESTCD, VISITNUM, VSDY)
+# get common column names
+
+common_cols <- intersect(names(vs_mb), names(vs))
+
+# assign labels to mb_vs
+
+walk(common_cols, \(x) attr(vs_mb[[x]], "label") <<- attr(vs[[x]], "label"))
+
+# Ordering columns as per vs dataset
+
+vs_metabolic <- vs_mb[, colnames(vs)]
+
+# Label VS dataset ----
+
+attr(vs_metabolic, "label") <- "Vital Signs"
+
+# Save dataset ----
+
+usethis::use_data(vs_metabolic, overwrite = TRUE)