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adsl <- r2rtf::r2rtf_adsl
adsl$TRTA <- adsl$TRT01A
adsl$TRTA <- factor(adsl$TRTA,
levels = c("Placebo", "Xanomeline Low Dose", "Xanomeline High Dose"),
labels = c("Placebo", "Low Dose", "High Dose")
)
# Create a variable EOSSTT indicating the end of end of study status
metadata_ae <- metalite.ae::meta_ae_example()
adae <- metadata_ae$data_observation
# If no value populate for AEACN in AE, then generate dummy values
if (length(unique(adae$AEACN)) == 1) {
adae$AEACN <- sample(
x = c("DOSE NOT CHANGED", "DRUG INTERRUPTED", "DRUG WITHDRAWN", "NOT APPLICABLE", "UNKNOWN"),
size = length(adae$USUBJID),
prob = c(0.7, 0.1, 0.05, 0.1, 0.05), replace = TRUE
)
}
metadata_ae$data_observation <- adae
# Treatment Disposition
# For discontinued due to AE
adaedisc <- subset(adae[which(adae$AEACN == "DRUG WITHDRAWN"), ], select = c(USUBJID, AEACN))
adaedisc <- adaedisc[!duplicated(adaedisc), ]
adsl <- merge(adsl, adaedisc, by = "USUBJID", all.x = TRUE)
adsl$EOTSTT <- ifelse(adsl$AEACN == "DRUG WITHDRAWN", "Discontinued", NA)
adsl$DCTREAS <- ifelse(adsl$EOTSTT == "Discontinued", "Adverse Event", NA)
# sample assignment cannot be NA value
adsl$EOTSTT[is.na(adsl$EOTSTT)] <- "temp"
adsl$DCTREAS[is.na(adsl$DCTREAS)] <- "temp"
adsl[adsl$EOTSTT != "Discontinued", "EOTSTT"] <- sample(
x = c("Complete", "Discontinued", "Participants Ongoing"),
size = length(adsl[adsl[["EOTSTT"]] != "Discontinued", "USUBJID"]),
prob = c(0.6, 0.2, 0.2), replace = TRUE
)
adsl[adsl$EOTSTT == "Discontinued" & adsl$DCTREAS != "Adverse Event", "DCTREAS"] <- sample(
x = c("Withdrawal By Subject", "Lack of Efficacy", "Lost to Follow-Up"),
size = length(adsl[adsl$EOTSTT == "Discontinued" & adsl$DCTREAS != "Adverse Event", "USUBJID"]),
prob = c(0.3, 0.4, 0.3), replace = TRUE
)
adsl[adsl[["EOTSTT"]] != "Discontinued", "DCTREAS"] <- NA
# Trial Disposition
adsl$EOSSTT <- adsl$EOTSTT
adsl$DCSREAS <- adsl$DCTREAS
adsl$DCSREAS <- ifelse(adsl$DCSREAS == "Adverse Event", "Other", adsl$DCTREAS)
head(adsl)
#> USUBJID STUDYID SUBJID SITEID SITEGR1 ARM
#> 1 01-701-1015 CDISCPILOT01 1015 701 701 Placebo
#> 2 01-701-1023 CDISCPILOT01 1023 701 701 Placebo
#> 3 01-701-1028 CDISCPILOT01 1028 701 701 Xanomeline High Dose
#> 4 01-701-1033 CDISCPILOT01 1033 701 701 Xanomeline Low Dose
#> 5 01-701-1034 CDISCPILOT01 1034 701 701 Xanomeline High Dose
#> 6 01-701-1047 CDISCPILOT01 1047 701 701 Placebo
#> TRT01P TRT01PN TRT01A TRT01AN TRTSDT
#> 1 Placebo 0 Placebo 0 2014-01-02
#> 2 Placebo 0 Placebo 0 2012-08-05
#> 3 Xanomeline High Dose 81 Xanomeline High Dose 81 2013-07-19
#> 4 Xanomeline Low Dose 54 Xanomeline Low Dose 54 2014-03-18
#> 5 Xanomeline High Dose 81 Xanomeline High Dose 81 2014-07-01
#> 6 Placebo 0 Placebo 0 2013-02-12
#> TRTEDT TRTDUR AVGDD CUMDOSE AGE AGEGR1 AGEGR1N AGEU RACE RACEN SEX
#> 1 2014-07-02 182 0.0 0 63 <65 1 YEARS WHITE 1 F
#> 2 2012-09-01 28 0.0 0 64 <65 1 YEARS WHITE 1 M
#> 3 2014-01-14 180 77.7 13986 71 65-80 2 YEARS WHITE 1 M
#> 4 2014-03-31 14 54.0 756 74 65-80 2 YEARS WHITE 1 M
#> 5 2014-12-30 183 76.9 14067 77 65-80 2 YEARS WHITE 1 F
#> 6 2013-03-09 26 0.0 0 85 >80 3 YEARS WHITE 1 F
#> ETHNIC SAFFL ITTFL EFFFL COMP8FL COMP16FL COMP24FL DISCONFL
#> 1 HISPANIC OR LATINO Y Y Y Y Y Y
#> 2 HISPANIC OR LATINO Y Y Y N N N Y
#> 3 NOT HISPANIC OR LATINO Y Y Y Y Y Y
#> 4 NOT HISPANIC OR LATINO Y Y Y N N N Y
#> 5 NOT HISPANIC OR LATINO Y Y Y Y Y Y
#> 6 NOT HISPANIC OR LATINO Y Y Y N N N Y
#> DSRAEFL DTHFL BMIBL BMIBLGR1 HEIGHTBL WEIGHTBL EDUCLVL DISONSDT DURDIS
#> 1 25.1 25-<30 147.3 54.4 16 2010-04-30 43.9
#> 2 Y 30.4 >=30 162.6 80.3 14 2006-03-11 76.4
#> 3 31.4 >=30 177.8 99.3 16 2009-12-16 42.8
#> 4 28.8 25-<30 175.3 88.5 12 2009-08-02 55.3
#> 5 26.1 25-<30 154.9 62.6 9 2011-09-29 32.9
#> 6 Y 30.4 >=30 148.6 67.1 8 2009-07-26 42.0
#> DURDSGR1 VISIT1DT RFSTDTC RFENDTC VISNUMEN RFENDT
#> 1 >=12 2013-12-26 2014-01-02 2014-07-02 12 2014-07-02
#> 2 >=12 2012-07-22 2012-08-05 2012-09-02 5 2012-09-02
#> 3 >=12 2013-07-11 2013-07-19 2014-01-14 12 2014-01-14
#> 4 >=12 2014-03-10 2014-03-18 2014-04-14 5 2014-04-14
#> 5 >=12 2014-06-24 2014-07-01 2014-12-30 12 2014-12-30
#> 6 >=12 2013-01-22 2013-02-12 2013-03-29 6 2013-03-29
#> DCDECOD DCREASCD MMSETOT TRTA AEACN
#> 1 COMPLETED Completed 23 Placebo <NA>
#> 2 ADVERSE EVENT Adverse Event 23 Placebo <NA>
#> 3 COMPLETED Completed 23 High Dose <NA>
#> 4 STUDY TERMINATED BY SPONSOR Sponsor Decision 23 Low Dose <NA>
#> 5 COMPLETED Completed 21 High Dose <NA>
#> 6 ADVERSE EVENT Adverse Event 23 Placebo DRUG WITHDRAWN
#> EOTSTT DCTREAS EOSSTT DCSREAS
#> 1 Complete <NA> Complete <NA>
#> 2 Participants Ongoing <NA> Participants Ongoing <NA>
#> 3 Complete <NA> Complete <NA>
#> 4 Complete <NA> Complete <NA>
#> 5 Complete <NA> Complete <NA>
#> 6 Discontinued Adverse Event Discontinued Otherplan <- plan(
analysis = "disp", population = "apat",
observation = "apat", parameter = "disposition;medical-disposition"
)meta <- meta_adam(
population = adsl,
observation = adsl
) |>
define_plan(plan = plan) |>
define_population(
name = "apat",
group = "TRTA",
subset = quote(SAFFL == "Y")
) |>
define_parameter(
name = "disposition",
var = "EOSSTT",
label = "Trial Disposition",
var_lower = "DCSREAS"
) |>
define_parameter(
name = "medical-disposition",
var = "EOTSTT",
label = "Participant Study Medication Disposition",
var_lower = "DCTREAS"
) |>
define_analysis(
name = "disp",
title = "Disposition of Participant",
label = "disposition table"
) |>
meta_build()These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.