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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 80ae61a
#123 - Updated object name
vinhn23 a1127a3
#123 - updated supp data for 1028
vinhn23 16bfd5c
#123 - Updated per comments
vinhn23 92e4a85
123 - updated per comment
vinhn23 d09fc46
#123 - Removed CA2XULRR from the supprs
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,172 @@ | ||
| # 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", | ||
| "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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@vinhn23 , why have some patients
CAELEPREand someCA2XULRR?Should we have
CAELEPREfor all patients?There was a problem hiding this comment.
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CAELEPRE are for subjects with PD. CA2XULRR has been removed per request from @starosto .