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Closes #124 rs_ca125: add rs_onco_ca125 #131

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merged 11 commits into from
Jan 15, 2025
Merged

Closes #124 rs_ca125: add rs_onco_ca125 #131

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aea40d1
#123 - Initial commit for RS oncology CA 125 test data
vinhn23 Oct 7, 2024
80ae61a
#123 - Updated object name
vinhn23 Oct 7, 2024
a1127a3
#123 - updated supp data for 1028
vinhn23 Oct 16, 2024
16bfd5c
#123 - Updated per comments
vinhn23 Nov 13, 2024
92e4a85
123 - updated per comment
vinhn23 Nov 22, 2024
d09fc46
#123 - Removed CA2XULRR from the supprs
vinhn23 Dec 20, 2024
6c8ee57
#126 - Updated per comments
vinhn23 Jan 9, 2025
e6702ee
#123 - removed ca125_rs.rda
vinhn23 Jan 10, 2025
3cb5b4c
#124 rs_ca125: update NEWS and documentation
bundfussr Jan 15, 2025
9cf3cc9
Merge branch 'main' into 123_rs_ca125
bundfussr Jan 15, 2025
400e9f2
#124 rs_ca125: style files and fix spelling
bundfussr Jan 15, 2025
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172 changes: 172 additions & 0 deletions data-raw/rs_supprs_onco_ca125.R
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# Datasets: rs_onco_ca125, supprs_onco_ca125
# Description: RS Oncology and SUPPRS dataset using IMWG criteria

# Load libraries -----
library(dplyr)
library(usethis)

# Create rs_onco_ca125 ----
rs_onco_ca125 <-tibble::tribble(
~USUBJID, ~RSSEQ, ~RSTESTCD, ~RSTEST, ~RSCAT, ~RSORRES, ~RSSTRESC, ~RSEVAL, ~VISITNUM, ~VISIT, ~RSDTC,
"01-701-1015", 3L, "OVRLRESP", "Overall Response", "CA125", "Non-Response/ Non-PD", "SD", "INVESTIGATOR", 2L, "WEEK 3", "2014-01-23",
"01-701-1015", 6L, "OVRLRESP", "Overall Response", "CA125", "Not Evaluable", "NE", "INVESTIGATOR", 3L, "WEEK 6", "2014-02",
"01-701-1015", 9L, "OVRLRESP", "Overall Response", "CA125", "Response But Not Within Normal Range", "PR", "INVESTIGATOR", 4L, "WEEK 9", "2014-03-06",
"01-701-1028", 3L, "OVRLRESP", "Overall Response", "CA125", "Progressive Disease", "PD", "INVESTIGATOR", 2L, "WEEK 3", "2013-08-09",
"01-701-1028", 6L, "OVRLRESP", "Overall Response", "CA125", "Progressive Disease", "PD", "INVESTIGATOR", 3L, "WEEK 6", "2013-08-30",
"01-701-1028", 9L, "OVRLRESP", "Overall Response", "CA125", "Progressive Disease", "PD", "INVESTIGATOR", 4L, "WEEK 9", "2013-09-30",
"01-701-1034", 3L, "OVRLRESP", "Overall Response", "CA125", "Response Within Normal Range", "CR", "INVESTIGATOR", 2L, "WEEK 3", "2014-07-22",
"01-701-1034", 6L, "OVRLRESP", "Overall Response", "CA125", "Response Within Normal Range", "CR", "INVESTIGATOR", 3L, "WEEK 6", "2014-08-20",
"01-701-1097", 3L, "OVRLRESP", "Overall Response", "CA125", "Non-Response/ Non-PD", "SD", "INVESTIGATOR", 2L, "WEEK 3", "2014-01-22",
"01-701-1115", 3L, "OVRLRESP", "Overall Response", "CA125", "Response But Not Within Normal Range", "PR", "INVESTIGATOR", 2L, "WEEK 3", "2012-12-21",
"01-701-1115", 6L, "OVRLRESP", "Overall Response", "CA125", "Response But Not Within Normal Range", "PR", "INVESTIGATOR", 3L, "WEEK 6", "2013-01-11",
"01-701-1115", 9L, "OVRLRESP", "Overall Response", "CA125", "Response Within Normal Range", "CR", "INVESTIGATOR", 4L, "WEEK 9", "2013-02-01",
"01-701-1118", 3L, "OVRLRESP", "Overall Response", "CA125", "Non-Response/ Non-PD", "SD", "INVESTIGATOR", 2L, "WEEK 3", "2014-04-02",
"01-701-1118", 6L, "OVRLRESP", "Overall Response", "CA125", "Response Within Normal Range", "CR", "INVESTIGATOR", 3L, "WEEK 6", "2014-04-23",
"01-701-1118", 9L, "OVRLRESP", "Overall Response", "CA125", "Not Evaluable", "NE", "INVESTIGATOR", 4L, "WEEK 9", "2014-05-14",
"01-701-1118", 12L, "OVRLRESP", "Overall Response", "CA125", "Response Within Normal Range", "CR", "INVESTIGATOR", 5L, "WEEK 12", "2014-06-04",
"01-701-1130", 3L, "OVRLRESP", "Overall Response", "CA125", "Non-Response/ Non-PD", "SD", "INVESTIGATOR", 2L, "WEEK 3", "2014-03-08",
"01-701-1130", 6L, "OVRLRESP", "Overall Response", "CA125", "Progressive Disease", "PD", "INVESTIGATOR", 3L, "WEEK 6", "2014-03-29",
"01-701-1130", 9L, "OVRLRESP", "Overall Response", "CA125", "Progressive Disease", "PD", "INVESTIGATOR", 4L, "WEEK 9", "2014-04-19",
"01-701-1133", 3L, "OVRLRESP", "Overall Response", "CA125", "Response But Not Within Normal Range", "PR", "INVESTIGATOR", 2L, "WEEK 3", "2012-11-18",
"01-701-1133", 6L, "OVRLRESP", "Overall Response", "CA125", "Progressive Disease", "PD", "INVESTIGATOR", 3L, "WEEK 6", "2012-12-09",
"01-701-1133", 9L, "OVRLRESP", "Overall Response", "CA125", "Progressive Disease", "PD", "INVESTIGATOR", 4L, "WEEK 9", "2012-12-30",
"01-701-1015", 12L, "OVRLRESP", "Overall Response", "RECIST 1.1", "SD", "SD", "INVESTIGATOR", 2L, "WEEK 3", "2014-01-23",
"01-701-1015", 15L, "OVRLRESP", "Overall Response", "RECIST 1.1", "NE", "NE", "INVESTIGATOR", 3L, "WEEK 6", "2014-02",
"01-701-1015", 18L, "OVRLRESP", "Overall Response", "RECIST 1.1", "PR", "PR", "INVESTIGATOR", 4L, "WEEK 9", "2014-03-06",
"01-701-1028", 12L, "OVRLRESP", "Overall Response", "RECIST 1.1", "PR", "PR", "INVESTIGATOR", 2L, "WEEK 3", "2013-08-09",
"01-701-1028", 15L, "OVRLRESP", "Overall Response", "RECIST 1.1", "PD", "PD", "INVESTIGATOR", 3L, "WEEK 6", "2013-08-30",
"01-701-1028", 18L, "OVRLRESP", "Overall Response", "RECIST 1.1", "PD", "PD", "INVESTIGATOR", 4L, "WEEK 9", "2013-09-30",
"01-701-1034", 12L, "OVRLRESP", "Overall Response", "RECIST 1.1", "CR", "CR", "INVESTIGATOR", 2L, "WEEK 3", "2014-07-22",
"01-701-1034", 15L, "OVRLRESP", "Overall Response", "RECIST 1.1", "CR", "CR", "INVESTIGATOR", 3L, "WEEK 6", "2014-08-20",
"01-701-1097", 12L, "OVRLRESP", "Overall Response", "RECIST 1.1", "SD", "SD", "INVESTIGATOR", 2L, "WEEK 3", "2014-01-22",
"01-701-1115", 12L, "OVRLRESP", "Overall Response", "RECIST 1.1", "SD", "SD", "INVESTIGATOR", 2L, "WEEK 3", "2012-12-21",
"01-701-1115", 15L, "OVRLRESP", "Overall Response", "RECIST 1.1", "PR", "PR", "INVESTIGATOR", 3L, "WEEK 6", "2013-01-11",
"01-701-1115", 18L, "OVRLRESP", "Overall Response", "RECIST 1.1", "CR", "CR", "INVESTIGATOR", 4L, "WEEK 9", "2013-02-01",
"01-701-1118", 12L, "OVRLRESP", "Overall Response", "RECIST 1.1", "SD", "SD", "INVESTIGATOR", 2L, "WEEK 3", "2014-04-02",
"01-701-1118", 15L, "OVRLRESP", "Overall Response", "RECIST 1.1", "CR", "CR", "INVESTIGATOR", 3L, "WEEK 6", "2014-04-23",
"01-701-1118", 18L, "OVRLRESP", "Overall Response", "RECIST 1.1", "NE", "NE", "INVESTIGATOR", 4L, "WEEK 9", "2014-05-14",
"01-701-1118", 21L, "OVRLRESP", "Overall Response", "RECIST 1.1", "CR", "CR", "INVESTIGATOR", 5L, "WEEK 12", "2014-06-04",
"01-701-1130", 12L, "OVRLRESP", "Overall Response", "RECIST 1.1", "SD", "SD", "INVESTIGATOR", 2L, "WEEK 3", "2014-03-08",
"01-701-1130", 15L, "OVRLRESP", "Overall Response", "RECIST 1.1", "PD", "PD", "INVESTIGATOR", 3L, "WEEK 6", "2014-03-29",
"01-701-1130", 18L, "OVRLRESP", "Overall Response", "RECIST 1.1", "PD", "PD", "INVESTIGATOR", 4L, "WEEK 9", "2014-04-19",
"01-701-1133", 12L, "OVRLRESP", "Overall Response", "RECIST 1.1", "PR", "PR", "INVESTIGATOR", 2L, "WEEK 3", "2012-11-18",
"01-701-1133", 15L, "OVRLRESP", "Overall Response", "RECIST 1.1", "PR", "PR", "INVESTIGATOR", 3L, "WEEK 6", "2012-12-09",
"01-701-1133", 18L, "OVRLRESP", "Overall Response", "RECIST 1.1", "PR", "PR", "INVESTIGATOR", 4L, "WEEK 9", "2012-12-30",
"01-701-1015", 21L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Stable Disease", "SD", "INVESTIGATOR", 2L, "WEEK 3", "2014-01-23",
"01-701-1015", 24L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Not Evaluable", "NE", "INVESTIGATOR", 3L, "WEEK 6", "2014-02",
"01-701-1015", 27L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Partial Response", "PR", "INVESTIGATOR", 4L, "WEEK 9", "2014-03-06",
"01-701-1028", 21L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Progressive Disease", "PD", "INVESTIGATOR", 2L, "WEEK 3", "2013-08-09",
"01-701-1028", 24L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Progressive Disease", "PD", "INVESTIGATOR", 3L, "WEEK 6", "2013-08-30",
"01-701-1028", 27L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Progressive Disease", "PD", "INVESTIGATOR", 4L, "WEEK 9", "2013-09-30",
"01-701-1034", 21L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Complete Response", "CR", "INVESTIGATOR", 2L, "WEEK 3", "2014-07-22",
"01-701-1034", 24L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Complete Response", "CR", "INVESTIGATOR", 3L, "WEEK 6", "2014-08-20",
"01-701-1097", 21L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Stable Disease", "SD", "INVESTIGATOR", 2L, "WEEK 3", "2014-01-22",
"01-701-1115", 21L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Partial Response", "PR", "INVESTIGATOR", 2L, "WEEK 3", "2012-12-21",
"01-701-1115", 24L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Partial Response", "PR", "INVESTIGATOR", 3L, "WEEK 6", "2013-01-11",
"01-701-1115", 27L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Complete Response", "CR", "INVESTIGATOR", 4L, "WEEK 9", "2013-02-01",
"01-701-1118", 21L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Stable Disease", "SD", "INVESTIGATOR", 2L, "WEEK 3", "2014-04-02",
"01-701-1118", 24L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Complete Response", "CR", "INVESTIGATOR", 3L, "WEEK 6", "2014-04-23",
"01-701-1118", 27L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Not Evaluable", "NE", "INVESTIGATOR", 4L, "WEEK 9", "2014-05-14",
"01-701-1118", 30L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Complete Response", "CR", "INVESTIGATOR", 5L, "WEEK 12", "2014-06-04",
"01-701-1130", 21L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Stable Disease", "SD", "INVESTIGATOR", 2L, "WEEK 3", "2014-03-08",
"01-701-1130", 24L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Progressive Disease", "PD", "INVESTIGATOR", 3L, "WEEK 6", "2014-03-29",
"01-701-1130", 27L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Progressive Disease", "PD", "INVESTIGATOR", 4L, "WEEK 9", "2014-04-19",
"01-701-1133", 21L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Partial Response", "PR", "INVESTIGATOR", 2L, "WEEK 3", "2012-11-18",
"01-701-1133", 24L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Progressive Disease", "PD", "INVESTIGATOR", 3L, "WEEK 6", "2012-12-09",
"01-701-1133", 27L, "OVRLRESP", "Overall Response", "RECIST 1.1 - CA125", "Progressive Disease", "PD", "INVESTIGATOR", 4L, "WEEK 9", "2012-12-30"
) %>%
mutate(
STUDYID = "CDISCPILOT01",
DOMAIN = "RS",
# RSCAT = "IMWG",
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", 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",
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"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, "CA2XULRR", "CA-125 pre-treatment 2x ULRR", "Y",
"01-701-1034", 6L, "CA2XULRR", "CA-125 pre-treatment 2x ULRR", "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",
"01-701-1097", 3L, "CA2XULRR", "CA-125 pre-treatment 2x ULRR", "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", 3L, "CA2XULRR", "CA-125 pre-treatment 2x ULRR", "Y",
"01-701-1015", 6L, "CA2XULRR", "CA-125 pre-treatment 2x ULRR", "Y",
"01-701-1015", 9L, "CA2XULRR", "CA-125 pre-treatment 2x ULRR", "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, "CA2XULRR", "CA-125 pre-treatment 2x ULRR", "Y",
"01-701-1115", 6L, "CA2XULRR", "CA-125 pre-treatment 2x ULRR", "Y",
"01-701-1115", 9L, "CA2XULRR", "CA-125 pre-treatment 2x ULRR", "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", 3L, "CA2XULRR", "CA-125 pre-treatment 2x ULRR", "Y",
"01-701-1118", 6L, "CA2XULRR", "CA-125 pre-treatment 2x ULRR", "Y",
"01-701-1118", 9L, "CA2XULRR", "CA-125 pre-treatment 2x ULRR", "Y",
"01-701-1118", 12L, "CA2XULRR", "CA-125 pre-treatment 2x ULRR", "Y",
"01-701-1118", 3L, "CA50RED", ">=50% reduction from baseline", "Y",
"01-701-1118", 9L, "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)
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