From 0bb757c3b9e9a14d70470c1d251c7dbadc1ee590 Mon Sep 17 00:00:00 2001 From: Zelos Zhu Date: Thu, 1 Aug 2024 23:28:56 +0000 Subject: [PATCH 1/9] get live on github --- .github/CODEOWNERS | 3 + NEWS.md | 4 + R/data.R | 12 ++ data-raw/batch_run.sh | 4 + data-raw/dm_peds.R | 46 +++++++ data-raw/vs_peds.R | 261 +++++++++++++++++++++++++++++++++++++++ data/dm_peds.rda | Bin 0 -> 1071 bytes data/vs_peds.rda | Bin 0 -> 3931 bytes man/dm_peds.Rd | 19 +++ man/vs_peds.Rd | 19 +++ staged_dependencies.yaml | 3 + 11 files changed, 371 insertions(+) create mode 100644 data-raw/dm_peds.R create mode 100644 data-raw/vs_peds.R create mode 100644 data/dm_peds.rda create mode 100644 data/vs_peds.rda create mode 100644 man/dm_peds.Rd create mode 100644 man/vs_peds.Rd diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS index e19b8b2..f3dcde7 100644 --- a/.github/CODEOWNERS +++ b/.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 diff --git a/NEWS.md b/NEWS.md index 25d0152..e61f934 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,7 @@ +# pharmaversesdtm 1.1.0 + +- Pediatrics data for anthropologic measures (`dm_peds` and `vs_peds`) was added. + # pharmaversesdtm 1.0.0 ## New Features diff --git a/R/data.R b/R/data.R index 7569331..288cf21 100644 --- a/R/data.R +++ b/R/data.R @@ -316,3 +316,15 @@ #' #' @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" diff --git a/data-raw/batch_run.sh b/data-raw/batch_run.sh index 049b95e..08c5212 100644 --- a/data-raw/batch_run.sh +++ b/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 diff --git a/data-raw/dm_peds.R b/data-raw/dm_peds.R new file mode 100644 index 0000000..8e1711f --- /dev/null +++ b/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 ---- +data("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) diff --git a/data-raw/vs_peds.R b/data-raw/vs_peds.R new file mode 100644 index 0000000..dee1557 --- /dev/null +++ b/data-raw/vs_peds.R @@ -0,0 +1,261 @@ +# Dataset: vs_peds +# Description: Create VS test SDTM dataset for pediatric studies + +# Load libraries ----- +library(dplyr) +library(admiral) + +# Read input test data from pharmaversesdtm ---- +data("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 %>% + mutate( + VSSEQ = row_number(), + 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) diff --git a/data/dm_peds.rda b/data/dm_peds.rda new file mode 100644 index 0000000000000000000000000000000000000000..4683e013934c15c006996ee4167edaa866e7a4ca GIT binary patch literal 1071 zcmV+~1kn3JT4*^jL0KkKS#lp%2ml5bf5iX)-?s1v|M36!-r&FY|KLCXKmb4q&;(gc z1JTuq1D(QB2oyBQrqt1s(qschfuleJL7}5SdO?tA0#OAvnxW|p2AVPfpfmsg00000 z03t+*C#k9Wnl#F2dXE}V4H|lY8U{u{GzX|3su~CChZ-3)(RrV$!0z 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z0=9rg*u=9x59kW_;fby&%@fH2>8**3#yZzsi(|JtCx}JILIWS*SUvkUpxv{Wp#{Q9 zjhBl#peNL`%QMiWt2-xD-gH(|^j`7CSjhJV%chbG@1h>~c?aq{i*R{!CyKPz@NjDy zf;)X5Uj5}b{)Bg1#e0n@`@P(Nu`ja~TBsUzduv}evvoIpJ_d|K8^*b>8OBBJVY`K< L5f@`-7cc!Ee&%6W literal 0 HcmV?d00001 diff --git a/man/dm_peds.Rd b/man/dm_peds.Rd new file mode 100644 index 0000000..a8e4dea --- /dev/null +++ b/man/dm_peds.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{dm_peds} +\alias{dm_peds} +\title{Demographic Dataset-pediatrics} +\format{ +An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 5 rows and 26 columns. +} +\source{ +Constructed by \code{{admiralpeds}} developers +} +\usage{ +dm_peds +} +\description{ +An updated SDTM DM dataset with pediatric patients +} +\keyword{datasets} diff --git a/man/vs_peds.Rd b/man/vs_peds.Rd new file mode 100644 index 0000000..b8b733b --- /dev/null +++ b/man/vs_peds.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{vs_peds} +\alias{vs_peds} +\title{Vital signs Dataset-pediatrics} +\format{ +An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 164 rows and 26 columns. +} +\source{ +Constructed by \code{{admiralpeds}} developers +} +\usage{ +vs_peds +} +\description{ +An updated SDTM VS dataset with anthropometric measurements for pediatric patients +} +\keyword{datasets} diff --git a/staged_dependencies.yaml b/staged_dependencies.yaml index c941541..8f379e5 100644 --- a/staged_dependencies.yaml +++ b/staged_dependencies.yaml @@ -12,4 +12,7 @@ downstream_repos: host: https://github.com - repo: pharmaverse/admiralophtha host: https://github.com + - repo: pharmaverse/admiralpeds + host: https://github.com + From 9dd7346cd1b0a220e4c82ceb25511bc7e9924cc2 Mon Sep 17 00:00:00 2001 From: Zelos Zhu Date: Fri, 2 Aug 2024 16:42:32 +0000 Subject: [PATCH 2/9] fix cicd errors --- DESCRIPTION | 2 +- NEWS.md | 2 +- inst/WORDLIST | 5 ++--- 3 files changed, 4 insertions(+), 5 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 8240dd0..fcc579f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -23,7 +23,7 @@ Depends: R (>= 3.5.0) Encoding: UTF-8 LazyData: true Roxygen: list(markdown = TRUE) -RoxygenNote: 7.3.1 +RoxygenNote: 7.3.2 Suggests: devtools, lintr, diff --git a/NEWS.md b/NEWS.md index e61f934..da0c161 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,6 +1,6 @@ # pharmaversesdtm 1.1.0 -- Pediatrics data for anthropologic measures (`dm_peds` and `vs_peds`) was added. +- Pediatrics data for anthropometric measures (`dm_peds` and `vs_peds`) was added. # pharmaversesdtm 1.0.0 diff --git a/inst/WORDLIST b/inst/WORDLIST index 3d26bff..3cad879 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -12,11 +12,10 @@ Immunogenicity MH MedDRA NEI +ONCO Pharmacokinetic -Pharmacokinetics Pharmaverse RECIST -Rodriguez Rohan SDG SDTM @@ -36,7 +35,7 @@ VFQ Vegesna Vinh anonymized +anthropometric iRECIST nolint -ONCO pharmaverse From d32b12eeee5458c7868e5755c71becd3a092c3f0 Mon Sep 17 00:00:00 2001 From: Zelos Zhu Date: Wed, 28 Aug 2024 10:16:46 -0700 Subject: [PATCH 3/9] Update .github/CODEOWNERS Co-authored-by: Ross Farrugia <82581364+rossfarrugia@users.noreply.github.com> --- .github/CODEOWNERS | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS index f3dcde7..4bc6dc5 100644 --- a/.github/CODEOWNERS +++ b/.github/CODEOWNERS @@ -21,4 +21,4 @@ data-raw/sc_ophtha.R @manciniedoardo # admiralpeds data-raw/dm_peds.R @fanny-gautier -data_raw/vs_peds.R @fanny-gautier +data-raw/vs_peds.R @fanny-gautier From 5269047359c1eae729f9bdf3963af2a8324b507f Mon Sep 17 00:00:00 2001 From: Zelos Zhu Date: Wed, 28 Aug 2024 10:16:58 -0700 Subject: [PATCH 4/9] Update NEWS.md Co-authored-by: Ross Farrugia <82581364+rossfarrugia@users.noreply.github.com> --- NEWS.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index da0c161..8e7918d 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,6 +1,6 @@ # pharmaversesdtm 1.1.0 -- Pediatrics data for anthropometric measures (`dm_peds` and `vs_peds`) was added. +- Pediatrics data for anthropometric measures (`dm_peds` and `vs_peds`) was added (#88). # pharmaversesdtm 1.0.0 From d152cc9780e09fe677bf10ff4afd68e21eb39d1b Mon Sep 17 00:00:00 2001 From: Zelos Zhu Date: Wed, 28 Aug 2024 17:19:17 +0000 Subject: [PATCH 5/9] remaining feedback changes --- NEWS.md | 2 ++ R/data.R | 1 + 2 files changed, 3 insertions(+) diff --git a/NEWS.md b/NEWS.md index 8e7918d..f2e3389 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # pharmaversesdtm 1.1.0 +## New Features + - Pediatrics data for anthropometric measures (`dm_peds` and `vs_peds`) was added (#88). # pharmaversesdtm 1.0.0 diff --git a/R/data.R b/R/data.R index 288cf21..b741a4b 100644 --- a/R/data.R +++ b/R/data.R @@ -326,5 +326,6 @@ #' Vital signs Dataset-pediatrics #' #' An updated SDTM VS dataset with anthropometric measurements for pediatric patients +#' #' @source Constructed by `{admiralpeds}` developers "vs_peds" From d70eb0a0dc80cadccf4a1b70a02d21953cd42a16 Mon Sep 17 00:00:00 2001 From: Fanny-Gautier Date: Fri, 13 Sep 2024 13:09:53 +0200 Subject: [PATCH 6/9] #88 fix VSSEQ derivation --- data-raw/vs_peds.R | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/data-raw/vs_peds.R b/data-raw/vs_peds.R index dee1557..5050568 100644 --- a/data-raw/vs_peds.R +++ b/data-raw/vs_peds.R @@ -213,8 +213,10 @@ vs_peds <- vs_peds %>% # Formatting the output dataset ---- vs_peds <- vs_peds %>% + group_by(STUDYID, USUBJID) %>% + mutate(VSSEQ = row_number()) %>% + ungroup() %>% mutate( - VSSEQ = row_number(), VSPOS = NA_character_, VSORRESU = case_when( VSTESTCD == "HEIGHT" ~ "cm", From 2aeca5ac71472d37675b52909e32f99f92e566bf Mon Sep 17 00:00:00 2001 From: Zelos Zhu Date: Mon, 16 Sep 2024 19:41:54 +0000 Subject: [PATCH 7/9] use :: formatting --- data-raw/dm_peds.R | 2 +- data-raw/vs_peds.R | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/data-raw/dm_peds.R b/data-raw/dm_peds.R index 8e1711f..7e3eab8 100644 --- a/data-raw/dm_peds.R +++ b/data-raw/dm_peds.R @@ -6,7 +6,7 @@ library(dplyr) library(admiral) # Read input test data from pharmaversesdtm ---- -data("dm") +dm <- pharmaversesdtm::dm # Convert blank to NA ---- dm <- convert_blanks_to_na(dm) diff --git a/data-raw/vs_peds.R b/data-raw/vs_peds.R index 5050568..2e54fd7 100644 --- a/data-raw/vs_peds.R +++ b/data-raw/vs_peds.R @@ -6,7 +6,7 @@ library(dplyr) library(admiral) # Read input test data from pharmaversesdtm ---- -data("vs") +vs <- pharmaversesdtm::vs # Convert blank to NA ---- vs <- convert_blanks_to_na(vs) From 8d7889866d705af2f593298c91bcbca0085206c9 Mon Sep 17 00:00:00 2001 From: Ross Farrugia <82581364+rossfarrugia@users.noreply.github.com> Date: Wed, 18 Sep 2024 13:05:13 +0100 Subject: [PATCH 8/9] minor blank row added for consistency --- R/data.R | 1 + 1 file changed, 1 insertion(+) diff --git a/R/data.R b/R/data.R index b741a4b..18e6d25 100644 --- a/R/data.R +++ b/R/data.R @@ -320,6 +320,7 @@ #' Demographic Dataset-pediatrics #' #' An updated SDTM DM dataset with pediatric patients +#' #' @source Constructed by `{admiralpeds}` developers "dm_peds" From 5b88bf32ddf2482fc8d9d16620d2008e56885f74 Mon Sep 17 00:00:00 2001 From: Ross Farrugia <82581364+rossfarrugia@users.noreply.github.com> Date: Wed, 18 Sep 2024 13:11:02 +0100 Subject: [PATCH 9/9] Updated version to development, so that vbump CI can do its magic until ready to go 1.1.0 --- NEWS.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index f2e3389..442c489 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# pharmaversesdtm 1.1.0 +# pharmaversesdtm (development version) ## New Features