admiral: ADaM in R Asset Library

# Name: ADAE
#
# Label: Adverse Event Analysis Dataset
#
# Input: ae, adsl, suppae, ex_single
library(admiral)
library(admiral.test) # Contains example datasets from the CDISC pilot project
library(dplyr)
library(lubridate)

# ---- Load source datasets ----

# Use e.g. haven::read_sas to read in .sas7bdat, or other suitable functions
# as needed and assign to the variables below.
# For illustration purposes read in admiral test data

data("ae")
data("suppae")
data("adsl")
data("ex_single")

ae <- convert_blanks_to_na(ae)
suppae <- convert_blanks_to_na(suppae)
ex <- convert_blanks_to_na(ex_single)


# ---- Derivations ----

# Get list of ADSL vars required for derivations
adsl_vars <- vars(TRTSDT, TRTEDT, DTHDT, EOSDT)

adae <- ae %>%
  # join supplementary qualifier variables
  derive_vars_suppqual(suppae) %>%

  # join adsl to ae
  left_join(
    select(adsl, STUDYID, USUBJID, !!!adsl_vars),
    by = c("STUDYID", "USUBJID")
  ) %>%

  # derive analysis start time
  derive_vars_dtm(
    dtc = AESTDTC,
    new_vars_prefix = "AST",
    date_imputation = "first",
    time_imputation = "first",
    min_dates = vars(TRTSDT)
  ) %>%

  # derive analysis end time
  derive_vars_dtm(
    dtc = AEENDTC,
    new_vars_prefix = "AEN",
    date_imputation = "last",
    time_imputation = "last",
    max_dates = vars(DTHDT, EOSDT)
  ) %>%

  # derive analysis end/start date
  derive_vars_dtm_to_dt(vars(ASTDTM, AENDTM)) %>%

  # derive analysis start relative day
  derive_var_astdy(
    reference_date = TRTSDT,
    date = ASTDT
  ) %>%

  # derive analysis end relative day
  derive_var_aendy(
    reference_date = TRTSDT,
    date = AENDT
  ) %>%

  # derive analysis duration (value and unit)
  derive_vars_duration(
    new_var = ADURN,
    new_var_unit = ADURU,
    start_date = ASTDT,
    end_date = AENDT,
    in_unit = "days",
    out_unit = "days",
    add_one = TRUE,
    trunc_out = FALSE
  )


adae <- adae %>%

  # derive last dose date/time
  derive_var_last_dose_date(
    ex,
    filter_ex = (EXDOSE > 0 | (EXDOSE == 0 & grepl("PLACEBO", EXTRT))) &
      nchar(EXENDTC) >= 10,
    dose_date = EXSTDTC,
    analysis_date = ASTDT,
    new_var = LDOSEDTM,
    single_dose_condition = (EXSTDTC == EXENDTC),
    output_datetime = TRUE
  ) %>%

  # derive severity / causality / ...
  mutate(
    ASEV = AESEV,
    AREL = AEREL
  ) %>%

  # derive treatment emergent flag
  mutate(
    TRTEMFL = ifelse(ASTDT >= TRTSDT & ASTDT <= TRTEDT + days(30), "Y", NA_character_)
  ) %>%

  # derive occurrence flags: first occurence of most severe AE
  # create numeric value ASEVN for severity
  mutate(
    ASEVN = as.integer(factor(ASEV, levels = c("MILD", "MODERATE", "SEVERE", "DEATH THREATENING")))
  ) %>%
  derive_var_extreme_flag(
    by_vars = vars(USUBJID),
    order = vars(ASTDTM, AESEQ),
    new_var = AOCCIFL,
    filter = TRTEMFL == "Y",
    mode = "last"
  )

# Join all ADSL with AE
adae <- adae %>%
  left_join(select(adsl, !!!admiral:::negate_vars(adsl_vars)),
            by = c("STUDYID", "USUBJID")
  )


# ---- Save output ----

save(adae, file = "data/adae.rda", compress = "bzip2")