Merge branch 'main' into 120_cm_CMENRTPT

# Conflicts:
#	NEWS.md

.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

DESCRIPTION

@@ -9,7 +9,8 @@ Authors@R: c(
   person("Pooja", "Kumari", role = "aut"),
   person("Stefan", "Bundfuss", role = "aut", comment = c(ORCID = "0009-0005-0027-1198")),
   person("Zelos", "Zhu", role = "aut"),
-  person("Sadchla", "Mascary", role = "aut")
+  person("Sadchla", "Mascary", role = "aut"),
+  person("Vladyslav", "Shuliar", role = "aut", comment = c(ORCID = "0009-0008-2354-8999"))
   )
 Description: A set of Study Data Tabulation Model (SDTM) datasets from the Clinical
     Data Interchange Standards Consortium (CDISC) pilot project used for testing

NEWS.md

@@ -1,9 +1,18 @@
-# pharmaversesdtm 1.0.1
+# pharmaversesdtm (development version)
 
-## New Features
+# New features
+
+- Pediatrics data for anthropometric measures (`dm_peds` and `vs_peds`) was added (#88).
 
 - Add `CMENRTPT` to `cm`. (#120)
 
+<details>
+<summary>Developer Notes</summary>
+
+- Activated automatic version bumping CICD workflow. (#122)
+
+</details>
+>>>>>>> main
 
 # pharmaversesdtm 1.0.0
 

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/eg.R

@@ -0,0 +1,190 @@
+# Dataset: eg
+# Description: Standard EG dataset generated using random data. Patients and visit schedule are copied from CDISC pilot study Vital Signs dataset.
+
+# Load necessary libraries ----
+library(dplyr)
+library(metatools)
+
+# Read input data ----
+data("vs")
+
+# Set seed for reproducibility ----
+set.seed(123)
+
+# Extract unique date/time of measurements for each subject and visit ----
+egdtc <- vs %>%
+  select(USUBJID, VISIT, VSDTC) %>%
+  distinct() %>%
+  rename(EGDTC = VSDTC)
+
+# Generate patients data ----
+eg <- expand.grid(
+  USUBJID = unique(vs$USUBJID),
+  EGTESTCD = c("QT", "HR", "RR", "ECGINT"),
+  EGTPT = c("AFTER LYING DOWN FOR 5 MINUTES", "AFTER STANDING FOR 1 MINUTE", "AFTER STANDING FOR 3 MINUTES"),
+  VISIT = c(
+    "SCREENING 1",
+    "SCREENING 2",
+    "BASELINE",
+    "AMBUL ECG PLACEMENT",
+    "WEEK 2",
+    "WEEK 4",
+    "AMBUL ECG REMOVAL",
+    "WEEK 6",
+    "WEEK 8",
+    "WEEK 12",
+    "WEEK 16",
+    "WEEK 20",
+    "WEEK 24",
+    "WEEK 26",
+    "RETRIEVAL"
+  ), stringsAsFactors = FALSE
+) %>%
+  # The original CDISC dataset kept no information about ECG Interpretation on specified visits
+  # Remove entries with specific visit names where EGTESTCD == "ECGINT"
+  filter(!(EGTESTCD == "ECGINT" & VISIT %in% c("AMBUL ECG PLACEMENT", "AMBUL ECG REMOVAL", "RETRIEVAL", "SCREENING 2"))) %>%
+  # Remove duplicates for other visit names where EGTESTCD == "ECGINT"
+  group_by(USUBJID, VISIT) %>%
+  filter(!(EGTESTCD == "ECGINT" & duplicated(EGTESTCD))) %>%
+  ungroup() %>%
+  inner_join(egdtc, by = c("USUBJID", "VISIT")) %>%
+  mutate(
+    STUDYID = "CDISCPILOT01",
+    DOMAIN = "EG",
+    EGTEST = c("QT" = "QT Duration", "HR" = "Heart Rate", "RR" = "RR Duration", "ECGINT" = "ECG Interpretation")[EGTESTCD],
+    EGORRESU = c("QT" = "mmHg", "HR" = "BEATS/MIN", "RR" = "mmHg", "ECGINT" = "LB")[EGTESTCD],
+    EGELTM = ifelse(
+      EGTESTCD == "ECGINT", "",
+      c("AFTER LYING DOWN FOR 5 MINUTES" = "PT5M", "AFTER STANDING FOR 1 MINUTE" = "PT1M", "AFTER STANDING FOR 3 MINUTES" = "PT3M")[EGTPT]
+    ),
+    # Generate random results based on test type and time point
+    EGSTRESN = case_when(
+      EGTESTCD == "RR" & EGELTM == "PT5M" ~ floor(rnorm(n(), 543.9985, 80)),
+      EGTESTCD == "RR" & EGELTM == "PT3M" ~ floor(rnorm(n(), 536.0161, 80)),
+      EGTESTCD == "RR" & EGELTM == "PT1M" ~ floor(rnorm(n(), 532.3233, 80)),
+      EGTESTCD == "HR" & EGELTM == "PT5M" ~ floor(rnorm(n(), 70.04389, 8)),
+      EGTESTCD == "HR" & EGELTM == "PT3M" ~ floor(rnorm(n(), 74.27798, 8)),
+      EGTESTCD == "HR" & EGELTM == "PT1M" ~ floor(rnorm(n(), 74.77461, 8)),
+      EGTESTCD == "QT" & EGELTM == "PT5M" ~ floor(rnorm(n(), 450.9781, 60)),
+      EGTESTCD == "QT" & EGELTM == "PT3M" ~ floor(rnorm(n(), 457.7265, 60)),
+      EGTESTCD == "QT" & EGELTM == "PT1M" ~ floor(rnorm(n(), 455.3394, 60))
+    ),
+    EGSTRESC = ifelse(EGTESTCD == "ECGINT", sample(c("NORMAL", "ABNORMAL"), 1), as.character(EGSTRESN)),
+    EGORRES = EGSTRESC,
+    EGSTRESU = c("QT" = "msec", "HR" = "BEATS/MIN", "RR" = "msec", "ECGINT" = NA)[EGTESTCD],
+    EGSTAT = "",
+    EGLOC = "",
+    EGBLFL = ifelse(VISIT == "BASELINE", "Y", ""),
+    VISITNUM = c(
+      "SCREENING 1" = 1,
+      "SCREENING 2" = 2,
+      "BASELINE" = 3,
+      "AMBUL ECG PLACEMENT" = 3.5,
+      "WEEK 2" = 4,
+      "WEEK 4" = 5,
+      "AMBUL ECG REMOVAL" = 6,
+      "WEEK 6" = 7,
+      "WEEK 8" = 8,
+      "WEEK 12" = 9,
+      "WEEK 16" = 10,
+      "WEEK 20" = 11,
+      "WEEK 24" = 12,
+      "WEEK 26" = 13,
+      "RETRIEVAL" = 201
+    )[VISIT],
+    VISITDY = c(
+      "SCREENING 1" = -7,
+      "SCREENING 2" = -1,
+      "BASELINE" = 1,
+      "AMBUL ECG PLACEMENT" = 13,
+      "WEEK 2" = 14,
+      "WEEK 4" = 28,
+      "AMBUL ECG REMOVAL" = 30,
+      "WEEK 6" = 42,
+      "WEEK 8" = 56,
+      "WEEK 12" = 84,
+      "WEEK 16" = 112,
+      "WEEK 20" = 140,
+      "WEEK 24" = 168,
+      "WEEK 26" = 182,
+      "RETRIEVAL" = 168
+    )[VISIT],
+    EGTPTNUM = ifelse(
+      EGTESTCD == "ECGINT",
+      NA,
+      c(
+        "AFTER LYING DOWN FOR 5 MINUTES" = 815,
+        "AFTER STANDING FOR 1 MINUTE" = 816,
+        "AFTER STANDING FOR 3 MINUTES" = 817
+      )[EGTPT]
+    ),
+    EGTPTREF = EGTPTREF <- case_when(
+      EGTESTCD == "ECGINT" ~ "",
+      EGELTM == "PT5M" ~ "PATIENT SUPINE",
+      TRUE ~ "PATIENT STANDING"
+    ),
+    EGDY = VISITDY,
+    EGTPT = ifelse(EGTESTCD == "ECGINT", "", EGTPT)
+  ) %>%
+  arrange(USUBJID, EGTESTCD, VISITNUM) %>%
+  # Generate sequence number
+  group_by(USUBJID) %>%
+  mutate(EGSEQ = row_number() %>% as.numeric()) %>%
+  ungroup() %>%
+  select(
+    STUDYID,
+    DOMAIN,
+    USUBJID,
+    EGSEQ,
+    EGTESTCD,
+    EGTEST,
+    EGORRES,
+    EGORRESU,
+    EGSTRESC,
+    EGSTRESN,
+    EGSTRESU,
+    EGSTAT,
+    EGLOC,
+    EGBLFL,
+    VISITNUM,
+    VISIT,
+    VISITDY,
+    EGDTC,
+    EGDY,
+    EGTPT,
+    EGTPTNUM,
+    EGELTM,
+    EGTPTREF
+  ) %>%
+  add_labels(
+    STUDYID = "Study Identifier",
+    DOMAIN = "Domain Abbreviation",
+    USUBJID = "Unique Subject Identifier",
+    EGSEQ = "Sequence Number",
+    EGTESTCD = "ECG Test Short Name",
+    EGTEST = "ECG Test Name",
+    EGORRES = "Result or Finding in Original Units",
+    EGORRESU = "Original Units",
+    EGELTM = "Elapsed Time",
+    EGSTRESC = "Character Result/Finding in Std Format",
+    EGSTRESN = "Numeric Result/Finding in Standard Units",
+    EGSTRESU = "Standard Units",
+    EGSTAT = "Completion Status",
+    EGLOC = "Location of Vital Signs Measurement",
+    EGBLFL = "Baseline Flag",
+    VISITNUM = "Visit Number",
+    VISIT = "Visit Name",
+    VISITDY = "Planned Study Day of Visit",
+    EGDTC = "Date/Time of Measurements",
+    EGDY = "Study Day of Vital Signs",
+    EGTPT = "Planned Time Point Number",
+    EGTPTNUM = "Time Point Number",
+    EGELTM = "Planned Elapsed Time from Time Point Ref",
+    EGTPTREF = "Time Point Reference"
+  )
+
+# Label the dataset ----
+attr(eg, "label") <- "Electrocardiogram"
+
+# Save the dataset ----
+usethis::use_data(eg, overwrite = TRUE)