Exposure Duration Table

In metalite.sl: Subject-Level Analysis Using 'metalite'

library(metalite)
library(metalite.sl)

Create Exposure Duration Table

The exposure duration analysis aims to provide table to summarize by each identified duration category. The development of exposure duration analysis involves functions:

• meta_sl_exposure_example: build the metadata (meta object) for analysis.
• prepare_exp_duration: prepare analysis raw datasets.
• format_exp_duration: prepare analysis outdata with proper format.
• rtf_exp_duration: transfer (mock) output dataset to RTF table.

knitr::include_graphics("pdf/exp0duration.pdf")

Build a metadata

There are two steps in meta_sl_exposure_example function in order to build the metadata (meta object): processing the ADaM dataset and save meta information for A&R reporting.

Step1: ADEXSUM, the ADaM dataset for Drug Exposrue Summary Data, is utilized to:

• Sum up duration by STUDYID SITENUM USUBJID SUBJID APERIOD EXTRT ADOSEFRM PARAMCD.
• Subset the exposure data by upcase(trim(left(paramcd))) = "TRTDUR".
• Get the exposure duration adexsum$AVAL for all participants.
• Assign duration category adexsum$EXDURGR i.e.">=1 day", ">=7 days",">=28 days", ">=12 weeks" and ">=24 weeks".

adsl <- r2rtf::r2rtf_adsl
adexsum <- data.frame(USUBJID = adsl$USUBJID)
adexsum$TRTA <- factor(adsl$TRT01A,
  levels = c("Placebo", "Xanomeline Low Dose", "Xanomeline High Dose"),
  labels = c("Placebo", "Low Dose", "High Dose")
)

adexsum$APERIODC <- "Base"
adexsum$APERIOD <- 1

set.seed(123) # Set a seed for reproducibility
adexsum$AVAL <- sample(x = 0:(24 * 7), size = length(adexsum$USUBJID), replace = TRUE)
adexsum$EXDURGR <- "not treated"
adexsum$EXDURGR[adexsum$AVAL >= 1] <- ">=1 day"
adexsum$EXDURGR[adexsum$AVAL >= 7] <- ">=7 days"
adexsum$EXDURGR[adexsum$AVAL >= 28] <- ">=28 days"
adexsum$EXDURGR[adexsum$AVAL >= 12 * 7] <- ">=12 weeks"
adexsum$EXDURGR[adexsum$AVAL >= 24 * 7] <- ">=24 weeks"

adexsum$EXDURGR <- factor(adexsum$EXDURGR,
  levels = c("not treated", ">=1 day", ">=7 days", ">=28 days", ">=12 weeks", ">=24 weeks")
)
unique(adexsum$EXDURGR)

Step2: Save analysis plan and metadata(parameter and analysis) information, then build meta object.

plan <- metalite::plan(
  analysis = "exp_dur", population = "apat",
  observation = "apat", parameter = "expdur"
)

meta <- metalite::meta_adam(
  population = adexsum,
  observation = adexsum
) |>
  metalite::define_plan(plan) |>
  metalite::define_population(
    name = "apat",
    group = "TRTA",
    subset = quote(APERIOD == 1 & AVAL > 0)
  ) |>
  metalite::define_parameter(
    name = "expdur",
    var = "AVAL",
    label = "Exposure Duration (Days)",
    vargroup = "EXDURGR"
  ) |>
  metalite::define_analysis(
    name = "exp_dur",
    title = "Summary of Exposure Duration",
    label = "exposure duration table"
  ) |>
  metalite::meta_build()

Analysis preparation

The input of the function prepare_exp_duration() is a meta object created by the metalite package. The resulting output comprises a collection of raw datasets for analysis and reporting.

outdata <- prepare_exp_duration(meta)
outdata

Number of participants in population

outdata$n[, 1:5]

Number of participants in each duration category

charn <- data.frame(outdata$char_n[1])
head(charn[, 1:5], 6)

Proportion of participants in each duration category

charp <- data.frame(outdata$char_prop[1])
head(charp[, 1:5], 6)

Statistical summary of exposure duration for each treatment

chars <- data.frame(outdata$char_n[1])
tail(chars[, 1:5], 8)

Format output

format_exp_duration to prepare analysis dataset before generate RTF output

tbl <- format_exp_duration(outdata, display_col = c("n", "prop", "total"))
head(tbl$tbl)

Output as RTF

rtf_exp_duration to generate RTF output

outdata <- format_exp_duration(outdata, display_col = c("n", "prop", "total")) |>
  rtf_exp_duration(
    source = "Source:  [CDISCpilot: adam-adexsum]",
    path_outdata = tempfile(fileext = ".Rdata"),
    path_outtable = "outtable/exp0duration.rtf"
  )

knitr::include_graphics("pdf/exp0duration.pdf")

metalite.sl documentation built on April 3, 2025, 8:52 p.m.