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Request to close issue 86 #99

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merged 15 commits into from
May 28, 2024
Merged

Request to close issue 86 #99

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bff1b9c
86 - Inital commit of RS/SUPPRS for IMWG vignette
vinhn23 Mar 5, 2024
a9155be
#86 - Corrected VPGR to VGPR
vinhn23 Mar 20, 2024
b61b0e1
#86 - Added more examples
vinhn23 May 22, 2024
cbc7dc4
#86 -Corrected IDVARVAL value
vinhn23 May 22, 2024
683cbbb
#86 - Updated example
vinhn23 May 22, 2024
8780ccc
Merge branch 'main' into 86_rs_imwg
bundfussr May 24, 2024
1c967af
#86 rs_imwg: update comments and documentation
bundfussr May 24, 2024
79334b8
#86 rs_imwg: style files
bundfussr May 24, 2024
e154e59
#86 rs_imwg: update man
bundfussr May 24, 2024
1033e84
#86 rs_imwg: add Changelog item
bundfussr May 24, 2024
c8d316d
#86 rs_imwg: fix spelling
bundfussr May 24, 2024
b651ede
#86 rs_imwg: fix typo
bundfussr May 28, 2024
fc42519
Merge branch 'main' into 86_rs_imwg
sadchla-codes May 28, 2024
39f3331
More updates on label
sadchla-codes May 28, 2024
ed07bd3
update wordlist
sadchla-codes May 28, 2024
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8 changes: 6 additions & 2 deletions NEWS.md
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Expand Up @@ -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

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16 changes: 16 additions & 0 deletions R/data.R
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Expand Up @@ -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
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128 changes: 128 additions & 0 deletions data-raw/rs_supprs_onco_imwg.R
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# 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
)

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attr(supprs_onco_imwg, "label") <- "Supplemental Qualifiers for RS_ONCO_IMWG"

usethis::use_data(supprs_onco_imwg, overwrite = TRUE)
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9 changes: 3 additions & 6 deletions inst/WORDLIST
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@@ -1,16 +1,13 @@
ADEG
ADaM
AE
AELAT
CDISC
Contestí
DM
DS
EG
EXLAT
EXLOC
GRPID
Gopi
IMWG
Immunogenicity
MH
MedDRA
Expand All @@ -37,9 +34,9 @@ TAs
Thampi
VFQ
Vegesna
ae
Vinh
anonymized
iRECIST
nolint
ONCO
pharmaverse
qs
20 changes: 20 additions & 0 deletions man/rs_onco_imwg.Rd
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