diff --git a/NEWS.md b/NEWS.md index 62df931..9325520 100644 --- a/NEWS.md +++ b/NEWS.md @@ -2,8 +2,12 @@ ## New Features - - Add URINE records to `pc` and `pp`. (#90) - - Update `PPCAT` so that it corresponds to `PCTEST`. (#91) +- Add URINE records to `pc` and `pp`. (#90) + +- Update `PPCAT` so that it corresponds to `PCTEST`. (#91) + +- Oncology response data for IMWG criteria (`rs_onco_imwg` and `supprs_onco_imwg`) +was added. (#86) # pharmaversesdtm 0.2.0 diff --git a/R/data.R b/R/data.R index b4a0c3f..c4ef5d7 100644 --- a/R/data.R +++ b/R/data.R @@ -162,6 +162,22 @@ #' @author Rohan Thampi "rs_onco_irecist" +#' Disease Response (IMWG) +#' +#' A SDTM RS dataset using IMWG criteria. The dataset contains just a few patients. +#' It is intended for vignettes and examples of ADaM dataset creation. +#' +#' @author Vinh Nguyen +"rs_onco_imwg" + +#' Supplemental Qualifiers for RS_ONCO_IMWG +#' +#' A SDTM supplemental RS dataset using IMWG criteria. It is intended to be used +#' together with `rs_onco_imwg`. +#' +#' @author Vinh Nguyen +"supprs_onco_imwg" + #' Supplemental Adverse Events #' #' A SDTM SUPPAE dataset from the CDISC pilot project diff --git a/data-raw/rs_supprs_onco_imwg.R b/data-raw/rs_supprs_onco_imwg.R new file mode 100644 index 0000000..b7e52ad --- /dev/null +++ b/data-raw/rs_supprs_onco_imwg.R @@ -0,0 +1,128 @@ +# Datasets: rs_onco_imwg, supprs_onco_imwg +# Description: RS Oncology and SUPPRS dataset using IMWG criteria + +# Load libraries ----- +library(dplyr) + +# Create rs_onco_imwg ---- +rs_onco_imwg <- tibble::tribble( + ~USUBJID, ~RSSEQ, ~RSLNKGRP, ~RSTESTCD, ~RSTEST, ~RSORRES, ~RSSTRESC, ~RSSTAT, ~RSREASND, ~RSEVAL, ~VISITNUM, ~VISIT, ~RSDTC, ~RSDY, + "01-701-1015", 7L, "A2", "OVRLRESP", "Overall Response", "PD", "PD", NA, NA, "INVESTIGATOR", 7, "WEEK 6", "2014-02-12", 42L, + "01-701-1028", 7L, "A2", "OVRLRESP", "Overall Response", "sCR", "sCR", NA, NA, "INVESTIGATOR", 7, "WEEK 6", "2013-08", NA, + "01-701-1028", 16L, "A3", "OVRLRESP", "Overall Response", "sCR", "sCR", NA, NA, "INVESTIGATOR", 9, "WEEK 12", "2013-10-09", 84L, + "01-701-1028", 21L, "A4", "OVRLRESP", "Overall Response", "CR", "CR", NA, NA, "INVESTIGATOR", 10, "WEEK 18", "2013-11-20", 126L, + "01-701-1034", 7L, "A2", "OVRLRESP", "Overall Response", "CR", "CR", NA, NA, "INVESTIGATOR", 7, "WEEK 6", "2014-08-11", 42L, + "01-701-1034", 16L, "A3", "OVRLRESP", "Overall Response", "CR", "CR", NA, NA, "INVESTIGATOR", 9, "WEEK 12", "2014-09-25", 84L, + "01-701-1034", 26L, NA, "OVRLRESP", "Overall Response", "sCR", "sCR", NA, NA, "INVESTIGATOR", 10, "WEEK 18", "2014-11-04", 126L, + "01-701-1097", 7L, "A2", "OVRLRESP", "Overall Response", "PD", "PD", NA, NA, "INVESTIGATOR", 7, "WEEK 6", "2014-02-11", 42L, + "01-701-1115", 7L, "A2", "OVRLRESP", "Overall Response", "PD", "PD", NA, NA, "INVESTIGATOR", 7, "WEEK 6", "2013-01-10", 42L, + "01-701-1118", 7L, "A2", "OVRLRESP", "Overall Response", "sCR", "sCR", NA, NA, "INVESTIGATOR", 7, "WEEK 6", "2014-04-23", 42L, + "01-701-1118", 16L, "A3", "OVRLRESP", "Overall Response", "VGPR", "VGPR", NA, NA, "INVESTIGATOR", 9, "WEEK 12", "2014-06-05", 84L, + "01-701-1118", 26L, NA, "OVRLRESP", "Overall Response", "CR", "CR", NA, NA, "INVESTIGATOR", 10.1, "WEEK 18", "2014-07-16", 126L, + "01-701-1118", 34L, "A4", "OVRLRESP", "Overall Response", "VGPR", "VGPR", NA, NA, "INVESTIGATOR", 12, "WEEK 24", "2014-08-27", 168L, + "01-701-1130", 7L, "A2", "OVRLRESP", "Overall Response", "VGPR", "VGPR", NA, NA, "INVESTIGATOR", 7, "WEEK 6", "2014-03-29", 42L, + "01-701-1130", 16L, "A3", "OVRLRESP", "Overall Response", "sCR", "sCR", NA, NA, "INVESTIGATOR", 9, "WEEK 12", "2014-05-16", 84L, + "01-701-1130", 26L, NA, "OVRLRESP", "Overall Response", "VGPR", "VGPR", NA, NA, "INVESTIGATOR", 10, "WEEK 18", "2014-06-21", 126L, + "01-701-1130", 34L, "A4", "OVRLRESP", "Overall Response", "VGPR", "VGPR", NA, NA, "INVESTIGATOR", 12, "WEEK 24", "2014-08-02", 168L, + "01-701-1133", 7L, "A2", "OVRLRESP", "Overall Response", "sCR", "sCR", NA, NA, "INVESTIGATOR", 7, "WEEK 6", "2012-12-11", 42L, + "01-701-1133", 16L, "A3", "OVRLRESP", "Overall Response", "PR", "PR", NA, NA, "INVESTIGATOR", 9, "WEEK 12", "2013-01-22", 84L, + "01-701-1133", 26L, NA, "OVRLRESP", "Overall Response", "CR", "CR", NA, NA, "INVESTIGATOR", 10.1, "WEEK 18", "2013-03-04", 126L, + "01-701-1133", 34L, "A4", "OVRLRESP", "Overall Response", "PR", "PR", NA, NA, "INVESTIGATOR", 12, "WEEK 24", "2013-04-18", 168L, + "01-701-1146", 7L, "A2", "OVRLRESP", "Overall Response", "PD", "PD", NA, NA, "INVESTIGATOR", 7, "WEEK 6", "2013-06-30", 42L, + "01-701-1148", 7L, "A2", "OVRLRESP", "Overall Response", "VGPR", "VGPR", NA, NA, "INVESTIGATOR", 7, "WEEK 6", "2013-10-03", 42L, + "01-701-1148", 16L, "A3", "OVRLRESP", "Overall Response", "PR", "PR", NA, NA, "INVESTIGATOR", 9, "WEEK 12", "2013-11-17", 84L, + "01-701-1148", 26L, NA, "OVRLRESP", "Overall Response", "PR", "PR", NA, NA, "INVESTIGATOR", 10.1, "WEEK 18", "2013-12-27", 126L, + "01-701-1148", 36L, "A4", "OVRLRESP", "Overall Response", "PR", "PR", NA, NA, "INVESTIGATOR", 12, "WEEK 24", "2014-02-08", 168L, + "01-701-1153", 7L, "A2", "OVRLRESP", "Overall Response", "sCR", "sCR", NA, NA, "INVESTIGATOR", 7, "WEEK 6", "2013-11-04", 42L, + "01-701-1153", 16L, "A3", "OVRLRESP", "Overall Response", "MR", "MR", NA, NA, "INVESTIGATOR", 9, "WEEK 12", "2013-12-16", 84L, + "01-701-1153", 26L, NA, "OVRLRESP", "Overall Response", "sCR", "sCR", NA, NA, "INVESTIGATOR", 9.2, "UNSCHEDULED 9.2", "2014-01-08", NA, + "01-701-1153", 35L, NA, "OVRLRESP", "Overall Response", "SD", "SD", NA, NA, "INVESTIGATOR", 9.3, "UNSCHEDULED 9.3", "2013-12-30", NA, + "01-701-1153", 43L, "A4", "OVRLRESP", "Overall Response", "MR", "MR", NA, NA, "INVESTIGATOR", 12, "WEEK 24", "2014-03-11", 168L, + "01-701-1203", 7L, "A2", "OVRLRESP", "Overall Response", "CR", "CR", NA, NA, "INVESTIGATOR", 7, "WEEK 6", "2013-03-16", 42L, + "01-701-1203", 16L, "A3", "OVRLRESP", "Overall Response", "MR", "MR", NA, NA, "INVESTIGATOR", 9, "WEEK 12", "2013-05-09", 84L, + "01-701-1203", 26L, NA, "OVRLRESP", "Overall Response", "CR", "CR", NA, NA, "INVESTIGATOR", 10.1, "WEEK 18", "2013-06-08", 126L, + "01-701-1203", 34L, "A4", "OVRLRESP", "Overall Response", "SD", "SD", NA, NA, "INVESTIGATOR", 12, "WEEK 24", "2013-07-22", 168L, + "01-701-1211", 7L, "A2", "OVRLRESP", "Overall Response", "VGPR", "VGPR", NA, NA, "INVESTIGATOR", 7, "WEEK 6", "2012-12-25", 42L, + "01-701-1211", 16L, "A3", "OVRLRESP", "Overall Response", "MR", "MR", NA, NA, "INVESTIGATOR", 9, "WEEK 12", "2013-01-14", 84L, + "01-701-1239", 7L, "A2", "OVRLRESP", "Overall Response", "PR", "PR", NA, NA, "INVESTIGATOR", 7, "WEEK 6", "2014-02-19", 42L, + "01-701-1239", 16L, "A3", "OVRLRESP", "Overall Response", "MR", "MR", NA, NA, "INVESTIGATOR", 9, "WEEK 12", "2014-04-02", 84L, + "01-701-1239", 26L, NA, "OVRLRESP", "Overall Response", "MR", "MR", NA, NA, "INVESTIGATOR", 10.1, "WEEK 18", "2014-05-14", 126L, + "01-701-1239", 34L, "A4", "OVRLRESP", "Overall Response", "VGPR", "VGPR", NA, NA, "INVESTIGATOR", 12, "WEEK 24", "2014-06-27", 168L, + "01-701-1275", 7L, "A2", "OVRLRESP", "Overall Response", "MR", "MR", NA, NA, "INVESTIGATOR", 7, "WEEK 6", "2014-03-22", 42L, + "01-701-1275", 16L, "A3", "OVRLRESP", "Overall Response", "PR", "PR", NA, NA, "INVESTIGATOR", 9, "WEEK 12", "2014-05-03", 84L, + "01-701-1287", 7L, "A2", "OVRLRESP", "Overall Response", "PR", "PR", NA, NA, "INVESTIGATOR", 7, "WEEK 6", "2014-03-06", 42L, + "01-701-1287", 16L, "A3", "OVRLRESP", "Overall Response", "PR", "PR", NA, NA, "INVESTIGATOR", 9, "WEEK 12", "2014-04-17", 84L, + "01-701-1287", 26L, NA, "OVRLRESP", "Overall Response", "PD", "PD", NA, NA, "INVESTIGATOR", 10.1, "WEEK 18", "2014-05-29", 126L, + "01-701-1287", 36L, "A4", "OVRLRESP", "Overall Response", "PD", "PD", NA, NA, "INVESTIGATOR", 12, "WEEK 24", "2014-07-12", 168L, + "01-701-1294", 7L, "A2", "OVRLRESP", "Overall Response", "PR", "PR", NA, NA, "INVESTIGATOR", 7, "WEEK 6", "2013-05-08", 42L, + "01-701-1294", 16L, "A3", "OVRLRESP", "Overall Response", "SD", "SD", NA, NA, "INVESTIGATOR", 9, "WEEK 12", "2013-06-14", 84L, + "01-701-1302", 7L, "A2", "OVRLRESP", "Overall Response", "PD", "PD", NA, NA, "INVESTIGATOR", 7, "WEEK 6", "2013-10-08", 42L, + "01-701-1302", 16L, "A3", "OVRLRESP", "Overall Response", "CR", "CR", NA, NA, "INVESTIGATOR", 9, "WEEK 12", "2013-11-05", 84L, + "01-701-1345", 7L, "A2", "OVRLRESP", "Overall Response", "MR", "MR", NA, NA, "INVESTIGATOR", 7, "WEEK 6", "2013-11-19", 42L, + "01-701-1345", 16L, "A3", "OVRLRESP", "Overall Response", "MR", "MR", NA, NA, "INVESTIGATOR", 9, "WEEK 12", "2013-12-31", 84L, + "01-701-1345", 26L, NA, "OVRLRESP", "Overall Response", "PD", "PD", NA, NA, "INVESTIGATOR", 10.1, "WEEK 18", "2014-02-11", 126L, + "01-701-1345", 34L, "A4", "OVRLRESP", "Overall Response", "PR", "PR", NA, NA, "INVESTIGATOR", 12, "WEEK 24", "2014-03-18", 168L, + "01-701-1363", 7L, "A2", "OVRLRESP", "Overall Response", "NE", "NE", NA, NA, "INVESTIGATOR", 7, "WEEK 6", "2013-07-10", 42L, + "01-701-1363", 16L, "A3", "OVRLRESP", "Overall Response", "CR", "CR", NA, NA, "INVESTIGATOR", 9, "WEEK 12", "2013-08-21", 84L, + "01-701-1415", 7L, "A2", "OVRLRESP", "Overall Response", "PR", "PR", NA, NA, "INVESTIGATOR", 7, "WEEK 6", "2013-11-04", 42L, + "01-701-1415", 16L, "A3", "OVRLRESP", "Overall Response", "NE", "NE", NA, NA, "INVESTIGATOR", 9, "WEEK 12", "2013-12-21", 84L, + "01-701-1415", 26L, NA, "OVRLRESP", "Overall Response", "MR", "MR", NA, NA, "INVESTIGATOR", 10.1, "WEEK 18", "2014-01-27", 126L, + "01-701-1415", 34L, "A4", "OVRLRESP", "Overall Response", "MR", "MR", NA, NA, "INVESTIGATOR", 12, "WEEK 24", "2014-03-10", 168L, + "01-702-1082", 7L, "A2", "OVRLRESP", "Overall Response", "PD", "PD", NA, NA, "INVESTIGATOR", 7, "WEEK 6", "2013-09-06", 42L, + "01-702-1082", 16L, "A3", "OVRLRESP", "Overall Response", "CR", "CR", NA, NA, "INVESTIGATOR", 9, "WEEK 12", "2013-11-17", 84L, + "01-703-1076", 7L, "A2", "OVRLRESP", "Overall Response", "PR", "PR", NA, NA, "INVESTIGATOR", 7, "WEEK 6", "2013-12-04", 42L, + "01-703-1076", 16L, "A3", "OVRLRESP", "Overall Response", "NE", "NE", NA, NA, "INVESTIGATOR", 9, "WEEK 12", "2013-12-24", 84L +) %>% + mutate( + STUDYID = "CDISCPILOT01", + DOMAIN = "RS", + RSCAT = "IMWG", + RSEVAL = "INVESTIGATOR" + ) %>% + relocate( + STUDYID, DOMAIN, USUBJID, RSSEQ, RSLNKGRP, RSTESTCD, RSTEST, RSCAT, RSORRES, + RSSTRESC, RSSTAT, RSREASND, RSEVAL, VISITNUM, VISIT, RSDTC, + RSDY + ) + +attr(rs_onco_imwg, "label") <- "Disease Response (IMWG)" + +usethis::use_data(rs_onco_imwg, overwrite = TRUE) + +# Create supprs_onco_imwg ---- +supprs_onco_imwg <- tibble::tribble( + ~USUBJID, ~IDVARVAL, ~QNAM, ~QLABEL, ~QVAL, + "01-701-1015", 7L, "PDOFL", "Progressive Disease: Other", "Y", + "01-701-1015", 7L, "DTHPDFL", "Death Due to Progressive Disease", "Y", + "01-701-1097", 7L, "PDOFL", "Progressive Disease: Other", "Y", + "01-701-1097", 7L, "NACTDT", "New Anti-Cancer Therapy Date", "2014-02-10", + "01-701-1115", 7L, "PDIFL", "Progressive Disease: Imaging", "Y", + "01-701-1146", 7L, "PDOFL", "Progressive Disease: Other", "Y", + "01-701-1148", 7L, "NACTDT", "New Anti-Cancer Therapy Date", "2014-02-07", + "01-701-1148", 16L, "NACTDT", "New Anti-Cancer Therapy Date", "2014-02-07", + "01-701-1148", 26L, "NACTDT", "New Anti-Cancer Therapy Date", "2014-02-07", + "01-701-1148", 36L, "NACTDT", "New Anti-Cancer Therapy Date", "2014-02-07", + "01-701-1302", 7L, "PDIFL", "Progressive Disease: Imaging", "Y", + "01-701-1345", 26L, "PDOFL", "Progressive Disease: Other", "Y", + "01-701-1287", 26L, "PDOFL", "Progressive Disease: Other", "Y", + "01-701-1287", 7L, "NACTDT", "New Anti-Cancer Therapy Date", "2014-05-30", + "01-701-1287", 16L, "NACTDT", "New Anti-Cancer Therapy Date", "2014-05-30", + "01-701-1287", 26L, "NACTDT", "New Anti-Cancer Therapy Date", "2014-05-30", + "01-701-1287", 36L, "NACTDT", "New Anti-Cancer Therapy Date", "2014-05-30", + "01-701-1287", 36L, "PDOFL", "Progressive Disease: Other", "Y", + "01-702-1082", 7L, "PDOFL", "Progressive Disease: Other", "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_imwg, "label") <- "Supplemental Qualifiers for RS_ONCO_IMWG" + +usethis::use_data(supprs_onco_imwg, overwrite = TRUE) diff --git a/data/rs_onco_imwg.rda b/data/rs_onco_imwg.rda new file mode 100644 index 0000000..a8eb98a Binary files /dev/null and b/data/rs_onco_imwg.rda differ diff --git a/data/supprs_onco_imwg.rda b/data/supprs_onco_imwg.rda new file mode 100644 index 0000000..1f74c94 Binary files /dev/null and b/data/supprs_onco_imwg.rda differ diff --git a/inst/WORDLIST b/inst/WORDLIST index 0f85756..ad06e8e 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -1,16 +1,13 @@ ADEG ADaM AE -AELAT CDISC Contestí DM DS EG -EXLAT -EXLOC -GRPID Gopi +IMWG Immunogenicity MH MedDRA @@ -37,9 +34,9 @@ TAs Thampi VFQ Vegesna -ae +Vinh anonymized iRECIST nolint +ONCO pharmaverse -qs diff --git a/man/rs_onco_imwg.Rd b/man/rs_onco_imwg.Rd new file mode 100644 index 0000000..9c4ee18 --- /dev/null +++ b/man/rs_onco_imwg.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_imwg} +\alias{rs_onco_imwg} +\title{Disease Response (IMWG)} +\format{ +An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 65 rows and 17 columns. +} +\usage{ +rs_onco_imwg +} +\description{ +A SDTM RS dataset using IMWG 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_imwg.Rd b/man/supprs_onco_imwg.Rd new file mode 100644 index 0000000..5c989ad --- /dev/null +++ b/man/supprs_onco_imwg.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_imwg} +\alias{supprs_onco_imwg} +\title{Supplemental Qualifiers for RS_ONCO_IMWG} +\format{ +An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 19 rows and 9 columns. +} +\usage{ +supprs_onco_imwg +} +\description{ +A SDTM supplemental RS dataset using IMWG criteria. It is intended to be used +together with \code{rs_onco_imwg}. +} +\author{ +Vinh Nguyen +} +\keyword{datasets}