diff --git a/DESCRIPTION b/DESCRIPTION index d3422ce0..105bfa4c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -10,7 +10,8 @@ Authors@R: c( person("Stefan", "Bundfuss", role = "aut", comment = c(ORCID = "0009-0005-0027-1198")), person("Zelos", "Zhu", role = "aut"), person("Sadchla", "Mascary", role = "aut"), - person("Vladyslav", "Shuliar", role = "aut", comment = c(ORCID = "0009-0008-2354-8999")) + person("Vladyslav", "Shuliar", role = "aut", comment = c(ORCID = "0009-0008-2354-8999")), + person("Vinh", "Nguyen", role = "aut") ) Description: A set of Study Data Tabulation Model (SDTM) datasets from the Clinical Data Interchange Standards Consortium (CDISC) pilot project used for testing diff --git a/NEWS.md b/NEWS.md index c6d3a139..9fd39d50 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,6 +1,9 @@ # pharmaversesdtm 1.1.0 -## New features +## New Features + +- Oncology response data for GCIG criteria (`rs_onco_ca125` and +`supprs_onco_ca125`) was added. (#124) - Pediatrics data for anthropometric measures (`dm_peds` and `vs_peds`) was added. (#88) diff --git a/R/data.R b/R/data.R index 18e6d25f..d5a16e86 100644 --- a/R/data.R +++ b/R/data.R @@ -178,6 +178,22 @@ #' @author Vinh Nguyen "supprs_onco_imwg" +#' Disease Response (GCIG) +#' +#' A SDTM RS dataset using GCIG criteria. The dataset contains just a few patients. +#' It is intended for vignettes and examples of ADaM dataset creation. +#' +#' @author Vinh Nguyen +"rs_onco_ca125" + +#' Supplemental Qualifiers for RS_ONCO_CA125 +#' +#' A SDTM supplemental RS dataset using GCIG criteria. It is intended to be used +#' together with `rs_onco_ca125`. +#' +#' @author Vinh Nguyen +"supprs_onco_ca125" + #' Supplemental Adverse Events #' #' A SDTM SUPPAE dataset from the CDISC pilot project diff --git a/data-raw/rs_supprs_onco_ca125.R b/data-raw/rs_supprs_onco_ca125.R new file mode 100644 index 00000000..78c7638e --- /dev/null +++ b/data-raw/rs_supprs_onco_ca125.R @@ -0,0 +1,158 @@ +# Datasets: rs_onco_ca125, supprs_onco_ca125 +# Description: RS Oncology and SUPPRS dataset using GCIG criteria + +# Load libraries ----- +library(dplyr) +library(usethis) + +# Create rs_onco_ca125 ---- +rs_onco_ca125 <- tibble::tribble( + ~USUBJID, ~RSSEQ, ~RSTESTCD, ~RSTEST, ~RSCAT, ~RSORRES, ~RSSTRESC, ~VISITNUM, ~VISIT, ~RSDTC, + "01-701-1015", 3L, "OVRLRESP", "Overall Response", "CA125", "Non-Response/ Non-PD", "SD", 2L, "WEEK 3", "2014-01-23", + "01-701-1015", 6L, "OVRLRESP", "Overall Response", "CA125", "Not Evaluable", "NE", 3L, "WEEK 6", "2014-02", + "01-701-1015", 9L, "OVRLRESP", "Overall Response", "CA125", "Response But Not Within Normal Range", "PR", 4L, "WEEK 9", "2014-03-06", + "01-701-1028", 3L, "OVRLRESP", "Overall Response", "CA125", "Progressive Disease", "PD", 2L, "WEEK 3", "2013-08-09", + "01-701-1028", 6L, "OVRLRESP", "Overall Response", "CA125", "Progressive Disease", "PD", 3L, "WEEK 6", "2013-08-30", + "01-701-1028", 9L, "OVRLRESP", "Overall Response", "CA125", "Progressive Disease", "PD", 4L, "WEEK 9", "2013-09-30", + "01-701-1034", 3L, "OVRLRESP", "Overall Response", "CA125", "Response Within Normal Range", "CR", 2L, "WEEK 3", "2014-07-22", + "01-701-1034", 6L, "OVRLRESP", "Overall Response", "CA125", "Response Within Normal Range", "CR", 3L, "WEEK 6", "2014-08-20", + "01-701-1097", 3L, "OVRLRESP", "Overall Response", "CA125", "Non-Response/ Non-PD", "SD", 2L, "WEEK 3", "2014-01-22", + "01-701-1115", 3L, "OVRLRESP", "Overall Response", "CA125", "Response But Not Within Normal Range", "PR", 2L, "WEEK 3", "2012-12-21", + "01-701-1115", 6L, "OVRLRESP", "Overall Response", "CA125", "Response But Not Within Normal Range", "PR", 3L, "WEEK 6", "2013-01-11", + "01-701-1115", 9L, "OVRLRESP", "Overall Response", "CA125", "Response Within Normal Range", "CR", 4L, "WEEK 9", "2013-02-01", + "01-701-1118", 3L, "OVRLRESP", "Overall Response", "CA125", "Non-Response/ Non-PD", "SD", 2L, "WEEK 3", "2014-04-02", + "01-701-1118", 6L, "OVRLRESP", "Overall Response", "CA125", "Response Within Normal Range", "CR", 3L, "WEEK 6", "2014-04-23", + "01-701-1118", 9L, "OVRLRESP", "Overall Response", "CA125", "Not Evaluable", "NE", 4L, "WEEK 9", "2014-05-14", + "01-701-1118", 12L, "OVRLRESP", "Overall Response", "CA125", "Response Within Normal Range", "CR", 5L, "WEEK 12", "2014-06-04", + "01-701-1130", 3L, "OVRLRESP", "Overall Response", "CA125", "Non-Response/ Non-PD", "SD", 2L, "WEEK 3", "2014-03-08", + "01-701-1130", 6L, "OVRLRESP", "Overall Response", "CA125", "Progressive Disease", "PD", 3L, "WEEK 6", "2014-03-29", + "01-701-1130", 9L, "OVRLRESP", "Overall Response", "CA125", "Progressive Disease", "PD", 4L, "WEEK 9", "2014-04-19", + "01-701-1133", 3L, "OVRLRESP", "Overall Response", "CA125", "Response But Not Within Normal Range", "PR", 2L, "WEEK 3", "2012-11-18", + "01-701-1133", 6L, "OVRLRESP", "Overall Response", "CA125", "Progressive Disease", "PD", 3L, "WEEK 6", "2012-12-09", + "01-701-1133", 9L, "OVRLRESP", "Overall Response", "CA125", "Progressive Disease", "PD", 4L, "WEEK 9", "2012-12-30", + "01-701-1015", 12L, "OVRLRESP", "Overall Response", "RECIST 1.1", "SD", "SD", 2L, "WEEK 3", "2014-01-23", + "01-701-1015", 15L, "OVRLRESP", "Overall Response", "RECIST 1.1", "NE", "NE", 3L, "WEEK 6", "2014-02", + "01-701-1015", 18L, "OVRLRESP", "Overall Response", "RECIST 1.1", "PR", "PR", 4L, "WEEK 9", "2014-03-06", + "01-701-1028", 12L, "OVRLRESP", "Overall Response", "RECIST 1.1", "PR", "PR", 2L, "WEEK 3", "2013-08-09", + "01-701-1028", 15L, "OVRLRESP", "Overall Response", "RECIST 1.1", "PD", "PD", 3L, "WEEK 6", "2013-08-30", + "01-701-1028", 18L, "OVRLRESP", "Overall Response", "RECIST 1.1", "PD", "PD", 4L, "WEEK 9", "2013-09-30", + "01-701-1034", 12L, "OVRLRESP", "Overall Response", "RECIST 1.1", "CR", "CR", 2L, "WEEK 3", "2014-07-22", + "01-701-1034", 15L, "OVRLRESP", "Overall Response", "RECIST 1.1", "CR", "CR", 3L, "WEEK 6", "2014-08-20", + "01-701-1097", 12L, "OVRLRESP", "Overall Response", "RECIST 1.1", "SD", "SD", 2L, "WEEK 3", "2014-01-22", + "01-701-1115", 12L, "OVRLRESP", "Overall Response", "RECIST 1.1", "SD", "SD", 2L, "WEEK 3", "2012-12-21", + "01-701-1115", 15L, "OVRLRESP", "Overall Response", "RECIST 1.1", "PR", "PR", 3L, "WEEK 6", "2013-01-11", + "01-701-1115", 18L, "OVRLRESP", "Overall Response", "RECIST 1.1", "CR", "CR", 4L, "WEEK 9", "2013-02-01", + "01-701-1118", 12L, "OVRLRESP", "Overall Response", "RECIST 1.1", "SD", "SD", 2L, "WEEK 3", "2014-04-02", + "01-701-1118", 15L, "OVRLRESP", "Overall Response", "RECIST 1.1", "CR", "CR", 3L, "WEEK 6", "2014-04-23", + "01-701-1118", 18L, "OVRLRESP", "Overall Response", "RECIST 1.1", "NE", "NE", 4L, "WEEK 9", "2014-05-14", + "01-701-1118", 21L, "OVRLRESP", "Overall Response", "RECIST 1.1", "CR", "CR", 5L, "WEEK 12", "2014-06-04", + "01-701-1130", 12L, "OVRLRESP", "Overall Response", "RECIST 1.1", "SD", "SD", 2L, "WEEK 3", "2014-03-08", + "01-701-1130", 15L, "OVRLRESP", "Overall Response", "RECIST 1.1", "PD", "PD", 3L, "WEEK 6", "2014-03-29", + "01-701-1130", 18L, "OVRLRESP", "Overall Response", "RECIST 1.1", "PD", "PD", 4L, "WEEK 9", "2014-04-19", + "01-701-1133", 12L, "OVRLRESP", "Overall Response", "RECIST 1.1", "PR", "PR", 2L, "WEEK 3", "2012-11-18", + "01-701-1133", 15L, "OVRLRESP", "Overall Response", "RECIST 1.1", "PR", "PR", 3L, "WEEK 6", "2012-12-09", + "01-701-1133", 18L, "OVRLRESP", "Overall Response", "RECIST 1.1", "PR", "PR", 4L, "WEEK 9", "2012-12-30", + "01-701-1015", 21L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Stable Disease", "SD", 2L, "WEEK 3", "2014-01-23", + "01-701-1015", 24L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Not Evaluable", "NE", 3L, "WEEK 6", "2014-02", + "01-701-1015", 27L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Partial Response", "PR", 4L, "WEEK 9", "2014-03-06", + "01-701-1028", 21L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Progressive Disease", "PD", 2L, "WEEK 3", "2013-08-09", + "01-701-1028", 24L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Progressive Disease", "PD", 3L, "WEEK 6", "2013-08-30", + "01-701-1028", 27L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Progressive Disease", "PD", 4L, "WEEK 9", "2013-09-30", + "01-701-1034", 21L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Complete Response", "CR", 2L, "WEEK 3", "2014-07-22", + "01-701-1034", 24L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Complete Response", "CR", 3L, "WEEK 6", "2014-08-20", + "01-701-1097", 21L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Stable Disease", "SD", 2L, "WEEK 3", "2014-01-22", + "01-701-1115", 21L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Partial Response", "PR", 2L, "WEEK 3", "2012-12-21", + "01-701-1115", 24L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Partial Response", "PR", 3L, "WEEK 6", "2013-01-11", + "01-701-1115", 27L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Complete Response", "CR", 4L, "WEEK 9", "2013-02-01", + "01-701-1118", 21L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Stable Disease", "SD", 2L, "WEEK 3", "2014-04-02", + "01-701-1118", 24L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Complete Response", "CR", 3L, "WEEK 6", "2014-04-23", + "01-701-1118", 27L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Not Evaluable", "NE", 4L, "WEEK 9", "2014-05-14", + "01-701-1118", 30L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Complete Response", "CR", 5L, "WEEK 12", "2014-06-04", + "01-701-1130", 21L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Stable Disease", "SD", 2L, "WEEK 3", "2014-03-08", + "01-701-1130", 24L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Progressive Disease", "PD", 3L, "WEEK 6", "2014-03-29", + "01-701-1130", 27L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Progressive Disease", "PD", 4L, "WEEK 9", "2014-04-19", + "01-701-1133", 21L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Partial Response", "PR", 2L, "WEEK 3", "2012-11-18", + "01-701-1133", 24L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Progressive Disease", "PD", 3L, "WEEK 6", "2012-12-09", + "01-701-1133", 27L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Progressive Disease", "PD", 4L, "WEEK 9", "2012-12-30" +) %>% + mutate( + STUDYID = "CDISCPILOT01", + DOMAIN = "RS", + RSEVAL = "INVESTIGATOR" + ) %>% + relocate( + STUDYID, DOMAIN, USUBJID, RSSEQ, RSTESTCD, RSTEST, RSCAT, RSORRES, + RSSTRESC, RSEVAL, VISITNUM, VISIT, RSDTC + ) + +attr(rs_onco_ca125, "label") <- "Disease Response (CA125)" + +usethis::use_data(rs_onco_ca125, overwrite = TRUE) + +# Create supprs_onco_imwg ---- +supprs_onco_ca125 <- tibble::tribble( + ~USUBJID, ~IDVARVAL, ~QNAM, ~QLABEL, ~QVAL, + "01-701-1133", 3L, "CA125EFL", "CA-125 response evaluable", "Y", + "01-701-1133", 6L, "CA125EFL", "CA-125 response evaluable", "Y", + "01-701-1133", 9L, "CA125EFL", "CA-125 response evaluable", "Y", + "01-701-1133", 3L, "CAELEPRE", "Elevated pre-treatment CA-125", "Y", + "01-701-1133", 6L, "CAELEPRE", "Elevated pre-treatment CA-125", "Y", + "01-701-1133", 9L, "CAELEPRE", "Elevated pre-treatment CA-125", "Y", + "01-701-1133", 3L, "CA50RED", ">=50% reduction from baseline", "Y", + "01-701-1133", 6L, "CANORM2X", "CA125 normal, lab increased >=2x ULRR", "Y", + "01-701-1133", 9L, "CANORM2X", "CA125 normal, lab increased >=2x ULRR", "Y", + "01-701-1130", 3L, "CA125EFL", "CA-125 response evaluable", "Y", + "01-701-1130", 6L, "CA125EFL", "CA-125 response evaluable", "Y", + "01-701-1130", 9L, "CA125EFL", "CA-125 response evaluable", "Y", + "01-701-1130", 3L, "CAELEPRE", "Elevated pre-treatment CA-125", "Y", + "01-701-1130", 6L, "CAELEPRE", "Elevated pre-treatment CA-125", "Y", + "01-701-1130", 9L, "CAELEPRE", "Elevated pre-treatment CA-125", "Y", + "01-701-1130", 6L, "CNOTNORM", "CA125 not norm, lab increased >=2x nadir", "Y", + "01-701-1130", 9L, "CNOTNORM", "CA125 not norm, lab increased >=2x nadir", "Y", + "01-701-1028", 3L, "CA125EFL", "CA-125 response evaluable", "N", + "01-701-1028", 6L, "CA125EFL", "CA-125 response evaluable", "N", + "01-701-1028", 9L, "CA125EFL", "CA-125 response evaluable", "N", + "01-701-1028", 3L, "CAELEPRE", "Elevated pre-treatment CA-125", "N", + "01-701-1028", 6L, "CAELEPRE", "Elevated pre-treatment CA-125", "N", + "01-701-1028", 9L, "CAELEPRE", "Elevated pre-treatment CA-125", "N", + "01-701-1028", 3L, "CANORM2X", "CA125 normal, lab increased >=2x ULRR", "Y", + "01-701-1028", 6L, "CANORM2X", "CA125 normal, lab increased >=2x ULRR", "Y", + "01-701-1028", 9L, "CANORM2X", "CA125 normal, lab increased >=2x ULRR", "Y", + "01-701-1034", 3L, "CA125EFL", "CA-125 response evaluable", "Y", + "01-701-1034", 6L, "CA125EFL", "CA-125 response evaluable", "Y", + "01-701-1034", 3L, "CA50RED", ">=50% reduction from baseline", "Y", + "01-701-1034", 6L, "CA50RED", ">=50% reduction from baseline", "Y", + "01-701-1097", 3L, "CA125EFL", "CA-125 response evaluable", "Y", + "01-701-1015", 3L, "CA125EFL", "CA-125 response evaluable", "Y", + "01-701-1015", 6L, "CA125EFL", "CA-125 response evaluable", "Y", + "01-701-1015", 9L, "CA125EFL", "CA-125 response evaluable", "Y", + "01-701-1015", 9L, "CA50RED", ">=50% reduction from baseline", "Y", + "01-701-1015", 6L, "MOUSEANT", "Received mouse antibodies", "Y", + "01-701-1015", 24L, "MOUSEANT", "Received mouse antibodies", "Y", + "01-701-1115", 3L, "CA125EFL", "CA-125 response evaluable", "Y", + "01-701-1115", 6L, "CA125EFL", "CA-125 response evaluable", "Y", + "01-701-1115", 9L, "CA125EFL", "CA-125 response evaluable", "Y", + "01-701-1115", 3L, "CA50RED", ">=50% reduction from baseline", "Y", + "01-701-1115", 6L, "CA50RED", ">=50% reduction from baseline", "Y", + "01-701-1115", 9L, "CA50RED", ">=50% reduction from baseline", "Y", + "01-701-1118", 3L, "CA125EFL", "CA-125 response evaluable", "Y", + "01-701-1118", 6L, "CA125EFL", "CA-125 response evaluable", "Y", + "01-701-1118", 9L, "CA125EFL", "CA-125 response evaluable", "Y", + "01-701-1118", 12L, "CA125EFL", "CA-125 response evaluable", "Y", + "01-701-1118", 6L, "CA50RED", ">=50% reduction from baseline", "Y", + "01-701-1118", 12L, "CA50RED", ">=50% reduction from baseline", "Y" +) %>% + mutate( + STUDYID = "CDISCPILOT01", + RDOMAIN = "RS", + IDVAR = "RSSEQ", + QORIG = "CRF", + IDVARVAL = as.character(IDVARVAL) + ) %>% + relocate( + STUDYID, RDOMAIN, USUBJID, IDVAR, IDVARVAL, QNAM, QLABEL, QVAL, QORIG + ) + +attr(supprs_onco_ca125, "label") <- "Supplemental Qualifiers for RS_ONCO_CA125" + +usethis::use_data(supprs_onco_ca125, overwrite = TRUE) diff --git a/data/rs_onco_ca125.rda b/data/rs_onco_ca125.rda new file mode 100644 index 00000000..469d0554 Binary files /dev/null and b/data/rs_onco_ca125.rda differ diff --git a/data/supprs_onco_ca125.rda b/data/supprs_onco_ca125.rda new file mode 100644 index 00000000..e3c01deb Binary files /dev/null and b/data/supprs_onco_ca125.rda differ diff --git a/inst/WORDLIST b/inst/WORDLIST index 07264906..1e554729 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -2,10 +2,12 @@ ADEG ADaM AE CDISC +CICD Contesti DM DS EG +GCIG Gopi IMWG Immunogenicity @@ -34,10 +36,8 @@ TAs Thampi VFQ Vegesna -Vinh anonymized anthropometric iRECIST nolint pharmaverse -CICD diff --git a/man/pharmaversesdtm-package.Rd b/man/pharmaversesdtm-package.Rd index bedb19c1..480a2393 100644 --- a/man/pharmaversesdtm-package.Rd +++ b/man/pharmaversesdtm-package.Rd @@ -30,6 +30,7 @@ Authors: \item Zelos Zhu \item Sadchla Mascary \item Vladyslav Shuliar (\href{https://orcid.org/0009-0008-2354-8999}{ORCID}) + \item Vinh Nguyen } } diff --git a/man/rs_onco_ca125.Rd b/man/rs_onco_ca125.Rd new file mode 100644 index 00000000..af99d649 --- /dev/null +++ b/man/rs_onco_ca125.Rd @@ -0,0 +1,20 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{rs_onco_ca125} +\alias{rs_onco_ca125} +\title{Disease Response (GCIG)} +\format{ +An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 66 rows and 13 columns. +} +\usage{ +rs_onco_ca125 +} +\description{ +A SDTM RS dataset using GCIG criteria. The dataset contains just a few patients. +It is intended for vignettes and examples of ADaM dataset creation. +} +\author{ +Vinh Nguyen +} +\keyword{datasets} diff --git a/man/supprs_onco_ca125.Rd b/man/supprs_onco_ca125.Rd new file mode 100644 index 00000000..02175132 --- /dev/null +++ b/man/supprs_onco_ca125.Rd @@ -0,0 +1,20 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{supprs_onco_ca125} +\alias{supprs_onco_ca125} +\title{Supplemental Qualifiers for RS_ONCO_CA125} +\format{ +An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 49 rows and 9 columns. +} +\usage{ +supprs_onco_ca125 +} +\description{ +A SDTM supplemental RS dataset using GCIG criteria. It is intended to be used +together with \code{rs_onco_ca125}. +} +\author{ +Vinh Nguyen +} +\keyword{datasets}