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x = c("DOSE NOT CHANGED", "DRUG INTERRUPTED", "DRUG WITHDRAWN", "NOT APPLICABLE", "UNKNOWN"),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- subset(adae[which(adae$AEACN == "DRUG WITHDRAWN"), ], select = c(USUBJID, AEACN))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- ifelse(adsl$AEACN == "DRUG WITHDRAWN", "Discontinued", NA)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 <NA>
#> EOTSTT DCTREAS EOSSTT DCSREAS
#> 1 Participants Ongoing <NA> Participants Ongoing <NA>
#> 2 Complete <NA> Complete <NA>
#> 3 Participants Ongoing <NA> Participants Ongoing <NA>
#> 4 Complete <NA> Complete <NA>
#> 5 Complete <NA> Complete <NA>
#> 6 Participants Ongoing <NA> Participants Ongoing <NA>
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()
