Merge pull request #115 from pharmaverse/admiralpeds_data_migration

Closes #88 Use pharmaversesdtm to host admiralpeds test data

.github/CODEOWNERS

@@ -19,3 +19,6 @@ data-raw/oe_ophtha.R @manciniedoardo
 data-raw/qs_ophtha.R @manciniedoardo
 data-raw/sc_ophtha.R @manciniedoardo
 
+# admiralpeds
+data-raw/dm_peds.R @fanny-gautier
+data-raw/vs_peds.R @fanny-gautier

NEWS.md

@@ -1,3 +1,9 @@
+# pharmaversesdtm (development version)
+
+## New Features
+
+- Pediatrics data for anthropometric measures (`dm_peds` and `vs_peds`) was added (#88).
+
 # pharmaversesdtm 1.0.0
 
 ## New Features

R/data.R

@@ -316,3 +316,17 @@
 #'
 #' @source Constructed by `{admiralvaccine}` developers
 "suppis_vaccine"
+
+#' Demographic Dataset-pediatrics
+#'
+#' An updated SDTM DM dataset with pediatric patients
+#'
+#' @source Constructed by `{admiralpeds}` developers
+"dm_peds"
+
+#' Vital signs Dataset-pediatrics
+#'
+#' An updated SDTM VS dataset with anthropometric measurements for pediatric patients
+#'
+#' @source Constructed by `{admiralpeds}` developers
+"vs_peds"

data-raw/batch_run.sh

@@ -32,3 +32,7 @@ Rscript data-raw/sc_ophtha.R
 Rscript data-raw/tr_onco.R
 Rscript data-raw/tu_onco.R
 Rscript data-raw/rs_onco.R
+
+# admiralpeds build from program
+Rscript data-raw/dm_peds.R
+Rscript data-raw/vs_peds.R

data-raw/dm_peds.R

@@ -0,0 +1,46 @@
+# Dataset: dm_peds
+# Description: Create DM test SDTM dataset for pediatric studies
+
+# Load libraries -----
+library(dplyr)
+library(admiral)
+
+# Read input test data from pharmaversesdtm ----
+dm <- pharmaversesdtm::dm
+
+# Convert blank to NA ----
+dm <- convert_blanks_to_na(dm)
+
+# Subset to first 5 patients only (which is enough for our examples) ----
+dm_subset <- dm %>%
+  filter(USUBJID %in% c(
+    "01-701-1015", "01-701-1023", "01-701-1028",
+    "01-701-1033", "01-701-1034"
+  ))
+
+# Add birth dates/age realistic for pediatrics in line with treatment dates ----
+dm_peds <- dm_subset %>%
+  mutate(BRTHDTC = case_when(
+    USUBJID == "01-701-1015" ~ "2013-01-02",
+    USUBJID == "01-701-1023" ~ "2010-08-05",
+    USUBJID == "01-701-1028" ~ "2010-07-19",
+    USUBJID == "01-701-1033" ~ "2014-01-01",
+    USUBJID == "01-701-1034" ~ "2014-06-01"
+  )) %>%
+  mutate(AGE = case_when(
+    USUBJID == "01-701-1015" ~ 1,
+    USUBJID == "01-701-1023" ~ 2,
+    USUBJID == "01-701-1028" ~ 3,
+    USUBJID == "01-701-1033" ~ 0,
+    USUBJID == "01-701-1034" ~ 0
+  ))
+
+# Variable labels ----
+attr(dm_peds$BRTHDTC, "label") <- "Date/Time of Birth"
+attr(dm_peds$AGE, "label") <- "Age"
+
+# Label dataset ----
+attr(dm_peds, "label") <- "Demographics"
+
+# Save dataset ----
+usethis::use_data(dm_peds, overwrite = TRUE)

data-raw/vs_peds.R

@@ -0,0 +1,263 @@
+# Dataset: vs_peds
+# Description: Create VS test SDTM dataset for pediatric studies
+
+# Load libraries -----
+library(dplyr)
+library(admiral)
+
+# Read input test data from pharmaversesdtm ----
+vs <- pharmaversesdtm::vs
+
+# Convert blank to NA ----
+vs <- convert_blanks_to_na(vs)
+
+# Subset to 5 patients present in dm_peds and only keep WEIGHT records ----
+vs_subset <- vs %>%
+  filter(USUBJID %in% c(
+    "01-701-1015", "01-701-1023", "01-701-1028",
+    "01-701-1033", "01-701-1034"
+  ) &
+    VSTESTCD %in% c("WEIGHT"))
+
+# Create placeholder records for HEIGHT, BMI and HDCIRC from the WEIGHT records
+vs_subset_height <- vs_subset %>%
+  mutate(VSTESTCD = "HEIGHT")
+vs_subset_bmi <- vs_subset %>%
+  mutate(VSTESTCD = "BMI")
+vs_subset_hdcirc <- vs_subset %>%
+  mutate(VSTESTCD = "HDCIRC")
+
+# Bind new parameter records to original dataset
+vs_subset_full <- bind_rows(
+  vs_subset,
+  vs_subset_height,
+  vs_subset_bmi,
+  vs_subset_hdcirc
+) %>%
+  arrange(USUBJID, VSTESTCD, VISITNUM, VSDY)
+
+# Updating each parameters values and units to be consistent with the ages of these dummy patients
+vs_peds <- vs_subset_full %>%
+  mutate(VSSTRESN = case_when(
+    USUBJID == "01-701-1015" & VSTESTCD == "WEIGHT" ~ case_when(
+      VISIT == "SCREENING 1" ~ 9.11,
+      VISIT == "BASELINE" ~ 9.2,
+      VISIT == "WEEK 2" ~ 9.32,
+      VISIT == "WEEK 4" ~ 9.54,
+      VISIT == "WEEK 6" ~ 9.7,
+      VISIT == "WEEK 8" ~ 9.91,
+      VISIT == "WEEK 12" ~ 10.3,
+      VISIT == "WEEK 16" ~ 10.7,
+      VISIT == "WEEK 20" ~ 11.1,
+      VISIT == "WEEK 24" ~ 11.56,
+      VISIT == "WEEK 26" ~ 11.71,
+    ),
+    USUBJID == "01-701-1015" & VSTESTCD == "HEIGHT" ~ case_when(
+      VISIT == "SCREENING 1" ~ 74.13,
+      VISIT == "BASELINE" ~ 74.41,
+      VISIT == "WEEK 2" ~ 74.71,
+      VISIT == "WEEK 4" ~ 75.32,
+      VISIT == "WEEK 6" ~ 75.93,
+      VISIT == "WEEK 8" ~ 76.54,
+      VISIT == "WEEK 12" ~ 77.72,
+      VISIT == "WEEK 16" ~ 78.96,
+      VISIT == "WEEK 20" ~ 80.22,
+      VISIT == "WEEK 24" ~ 81.43,
+      VISIT == "WEEK 26" ~ 82.03
+    ),
+    USUBJID == "01-701-1015" & VSTESTCD == "HDCIRC" ~ case_when(
+      VISIT == "SCREENING 1" ~ 35.61,
+      VISIT == "BASELINE" ~ 37.24,
+      VISIT == "WEEK 2" ~ 38.57,
+      VISIT == "WEEK 4" ~ 39.84,
+      VISIT == "WEEK 6" ~ 40.95,
+      VISIT == "WEEK 8" ~ 42.14,
+      VISIT == "WEEK 12" ~ 43.67,
+      VISIT == "WEEK 16" ~ 44.79,
+      VISIT == "WEEK 20" ~ 45.92,
+      VISIT == "WEEK 24" ~ 46.88,
+      VISIT == "WEEK 26" ~ 47.56
+    ),
+    USUBJID == "01-701-1023" & VSTESTCD == "WEIGHT" ~ case_when(
+      VISIT == "SCREENING 1" ~ 12.47,
+      VISIT == "BASELINE" ~ 12.89,
+      VISIT == "WEEK 2" ~ 13.14,
+      VISIT == "WEEK 4" ~ 13.45
+    ),
+    USUBJID == "01-701-1023" & VSTESTCD == "HEIGHT" ~ case_when(
+      VISIT == "SCREENING 1" ~ 87.65,
+      VISIT == "BASELINE" ~ 88.25,
+      VISIT == "WEEK 2" ~ 88.75,
+      VISIT == "WEEK 4" ~ 89.23
+    ),
+    USUBJID == "01-701-1023" & VSTESTCD == "HDCIRC" ~ case_when(
+      VISIT == "SCREENING 1" ~ 48.34,
+      VISIT == "BASELINE" ~ 48.71,
+      VISIT == "WEEK 2" ~ 49.12,
+      VISIT == "WEEK 4" ~ 49.56
+    ),
+    USUBJID == "01-701-1028" & VSTESTCD == "HEIGHT" ~ case_when(
+      VISIT == "SCREENING 1" ~ 98.32,
+      VISIT == "BASELINE" ~ 98.95,
+      VISIT == "WEEK 2" ~ 99.34,
+      VISIT == "WEEK 4" ~ 99.68,
+      VISIT == "WEEK 6" ~ 100.13,
+      VISIT == "WEEK 8" ~ 100.45,
+      VISIT == "WEEK 12" ~ 101.02,
+      VISIT == "WEEK 16" ~ 101.48,
+      VISIT == "WEEK 20" ~ 101.97,
+      VISIT == "WEEK 24" ~ 102.44,
+      VISIT == "WEEK 26" ~ 102.82
+    ),
+    USUBJID == "01-701-1028" & VSTESTCD == "WEIGHT" ~ case_when(
+      VISIT == "SCREENING 1" ~ 14.65,
+      VISIT == "BASELINE" ~ 14.95,
+      VISIT == "WEEK 2" ~ 15.17,
+      VISIT == "WEEK 4" ~ 15.43,
+      VISIT == "WEEK 6" ~ 15.66,
+      VISIT == "WEEK 8" ~ 15.84,
+      VISIT == "WEEK 12" ~ 16.34,
+      VISIT == "WEEK 16" ~ 16.73,
+      VISIT == "WEEK 20" ~ 17.11,
+      VISIT == "WEEK 24" ~ 17.56,
+      VISIT == "WEEK 26" ~ 17.85
+    ),
+    USUBJID == "01-701-1028" & VSTESTCD == "HDCIRC" ~ case_when(
+      VISIT == "SCREENING 1" ~ 51.34,
+      VISIT == "BASELINE" ~ 51.71,
+      VISIT == "WEEK 2" ~ 52.12,
+      VISIT == "WEEK 4" ~ 52.56,
+      VISIT == "WEEK 6" ~ 52.93,
+      VISIT == "WEEK 8" ~ 53.45,
+      VISIT == "WEEK 12" ~ 54.02,
+      VISIT == "WEEK 16" ~ 54.48,
+      VISIT == "WEEK 20" ~ 54.97,
+      VISIT == "WEEK 24" ~ 55.44,
+      VISIT == "WEEK 26" ~ 55.82
+    ),
+    USUBJID == "01-701-1033" & VSTESTCD == "HEIGHT" ~ case_when(
+      VISIT == "SCREENING 1" ~ 59.45,
+      VISIT == "BASELINE" ~ 60.53,
+      VISIT == "WEEK 2" ~ 61.72,
+      VISIT == "WEEK 4" ~ 62.91
+    ),
+    USUBJID == "01-701-1033" & VSTESTCD == "WEIGHT" ~ case_when(
+      VISIT == "SCREENING 1" ~ 5.62,
+      VISIT == "BASELINE" ~ 5.89,
+      VISIT == "WEEK 2" ~ 6.17,
+      VISIT == "WEEK 4" ~ 6.45
+    ),
+    USUBJID == "01-701-1033" & VSTESTCD == "HDCIRC" ~ case_when(
+      VISIT == "SCREENING 1" ~ 40.34,
+      VISIT == "BASELINE" ~ 40.71,
+      VISIT == "WEEK 2" ~ 41.12,
+      VISIT == "WEEK 4" ~ 41.56
+    ),
+    USUBJID == "01-701-1034" & VSTESTCD == "HEIGHT" ~ case_when(
+      VISIT == "SCREENING 1" ~ 53.65,
+      VISIT == "BASELINE" ~ 54.78,
+      VISIT == "WEEK 2" ~ 55.95,
+      VISIT == "WEEK 4" ~ 57.14,
+      VISIT == "WEEK 6" ~ 58.23,
+      VISIT == "WEEK 8" ~ 59.45,
+      VISIT == "WEEK 12" ~ 60.67,
+      VISIT == "WEEK 16" ~ 61.79,
+      VISIT == "WEEK 20" ~ 62.91,
+      VISIT == "WEEK 24" ~ 64.03,
+      VISIT == "WEEK 26" ~ 65.15
+    ),
+    USUBJID == "01-701-1034" & VSTESTCD == "WEIGHT" ~ case_when(
+      VISIT == "SCREENING 1" ~ 4.25,
+      VISIT == "BASELINE" ~ 4.56,
+      VISIT == "WEEK 2" ~ 4.84,
+      VISIT == "WEEK 4" ~ 5.15,
+      VISIT == "WEEK 6" ~ 5.47,
+      VISIT == "WEEK 8" ~ 5.79,
+      VISIT == "WEEK 12" ~ 6.11,
+      VISIT == "WEEK 16" ~ 6.43,
+      VISIT == "WEEK 20" ~ 6.75,
+      VISIT == "WEEK 24" ~ 7.07,
+      VISIT == "WEEK 26" ~ 7.39
+    ),
+    USUBJID == "01-701-1034" & VSTESTCD == "HDCIRC" ~ case_when(
+      VISIT == "SCREENING 1" ~ 38.45,
+      VISIT == "BASELINE" ~ 38.92,
+      VISIT == "WEEK 2" ~ 39.34,
+      VISIT == "WEEK 4" ~ 39.78,
+      VISIT == "WEEK 6" ~ 40.23,
+      VISIT == "WEEK 8" ~ 40.65,
+      VISIT == "WEEK 12" ~ 41.07,
+      VISIT == "WEEK 16" ~ 41.48,
+      VISIT == "WEEK 20" ~ 41.89,
+      VISIT == "WEEK 24" ~ 42.30,
+      VISIT == "WEEK 26" ~ 42.72
+    ),
+    TRUE ~ VSSTRESN
+  ))
+
+# Derive BMI values ----
+vs_peds <- vs_peds %>%
+  arrange(USUBJID, VISITNUM, VSTESTCD, VSDY) %>%
+  group_by(USUBJID, VISITNUM) %>%
+  mutate(
+    VSSTRESN = case_when(
+      VSTESTCD == "BMI" ~ {
+        weight <- VSSTRESN[VSTESTCD == "WEIGHT"]
+        height <- VSSTRESN[VSTESTCD == "HEIGHT"] / 100 # Convert height from cm to m
+        as.numeric(weight / (height^2)) # BMI calculation
+      },
+      TRUE ~ VSSTRESN
+    )
+  ) %>%
+  ungroup()
+
+# Formatting the output dataset ----
+vs_peds <- vs_peds %>%
+  group_by(STUDYID, USUBJID) %>%
+  mutate(VSSEQ = row_number()) %>%
+  ungroup() %>%
+  mutate(
+    VSPOS = NA_character_,
+    VSORRESU = case_when(
+      VSTESTCD == "HEIGHT" ~ "cm",
+      VSTESTCD == "WEIGHT" ~ "kg",
+      VSTESTCD == "BMI" ~ "kg/m2",
+      VSTESTCD == "HDCIRC" ~ "cm",
+      TRUE ~ NA_character_
+    ),
+    VSTEST = case_when(
+      VSTESTCD == "HEIGHT" ~ "Height",
+      VSTESTCD == "WEIGHT" ~ "Weight",
+      VSTESTCD == "BMI" ~ "BMI",
+      VSTESTCD == "HDCIRC" ~ "Head Circumference",
+      TRUE ~ NA_character_
+    ),
+    VSSTRESC = as.character(VSSTRESN),
+    VSORRES = VSSTRESC,
+    VSSTRESU = VSORRESU,
+    VSSTAT = NA_character_,
+    VSLOC = NA_character_,
+    VSBLFL = if_else(VISITNUM == 2, "Y", NA_character_),
+    VISITDY = NA_integer_,
+    VSDY = NA_integer_,
+    VSEVAL = NA_character_,
+    EPOCH = "Epoch"
+  ) %>%
+  arrange(USUBJID, VSTESTCD, VISITNUM, VSDY)
+
+# Get common column names with VS
+common_cols <- intersect(names(vs), names(vs_peds))
+
+# Copy attributes (including labels) from vs to vs_peds for common columns
+for (col in common_cols) {
+  attributes(vs_peds[[col]]) <- attributes(vs[[col]])
+}
+# Set the labels for non-commn variables
+attr(vs_peds$VSEVAL, "label") <- "Evaluator"
+attr(vs_peds$EPOCH, "label") <- "Epoch"
+
+# Label dataset ----
+attr(vs_peds, "label") <- "Vital Signs"
+
+# Save dataset ----
+usethis::use_data(vs_peds, overwrite = TRUE)

inst/WORDLIST

@@ -12,12 +12,11 @@ Immunogenicity
 MH
 MedDRA
 NEI
+ONCO
 ORCID
 Pharmacokinetic
-Pharmacokinetics
 Pharmaverse
 RECIST
-Rodriguez
 Rohan
 SDG
 SDTM
@@ -37,7 +36,7 @@ VFQ
 Vegesna
 Vinh
 anonymized
+anthropometric
 iRECIST
 nolint
-ONCO
 pharmaverse