AE summary table — tlf_ae_summary • metalite.ae

AE summary table

Usage

tlf_ae_summary(
  outdata,
  source,
  analysis,
  col_rel_width = NULL,
  text_font_size = 9,
  orientation = "portrait",
  title = c("analysis", "observation", "population"),
  footnotes = NULL,
  path_outdata = NULL,
  path_outtable = NULL
)

Arguments

outdata: An outdata object created by prepare_ae_specific().
source: A character value of the data source.
analysis: One of analysis name existing at outdata$meta$analysis
col_rel_width: Column relative width in a vector e.g. c(2,1,1) refers to 2:1:1. Default is NULL for equal column width.
text_font_size: Text font size. To vary text font size by column, use numeric vector with length of vector equal to number of columns displayed e.g. c(9,20,40).
orientation: Orientation in 'portrait' or 'landscape'.
title: Term "analysis", "observation"and "population") for collecting title from metadata or a character vector of table titles.
footnotes: A character vector of table footnotes.
path_outdata: A character string of the outdata path.
path_outtable: A character string of the outtable path.

Value

RTF file and the source dataset for AE summary table.

Examples

# Define metadata
adsl <- forestly::forestly_adsl
adae <- forestly::forestly_adae

adsl$TRT01A <- factor(
  adsl$TRT01A,
  levels = c("Xanomeline Low Dose", "Placebo"),
  labels = c("Low Dose", "Placebo")
)
adae$TRTA <- factor(
  adae$TRTA,
  levels = c("Xanomeline Low Dose", "Placebo"),
  labels = c("Low Dose", "Placebo")
)

analysis_plan <- metalite::plan(
  analysis = "ae_summary",
  population = "apat",
  observation = "wk12",
  parameter = "any;rel;ser"
)

meta <- metalite::meta_adam(observation = adae, population = adsl) |>
  metalite::define_plan(analysis_plan) |>
  metalite::define_population(
    name = "apat",
    var = c(
      "USUBJID", "SAFFL", "TRT01A", "TRTDUR",
      "SITEID", "SEX", "RACE", "AGE"
    ),
    group = "TRT01A",
    subset = SAFFL == "Y",
    label = "All Participants as Treated"
  ) |>
  metalite::define_observation(
    name = "wk12",
    var = c(
      "USUBJID", "SAFFL", "TRTA", "AEDECOD", "AEBODSYS", "AEREL",
      "AESER", "AEOUT", "AEACN", "AESDTH", "ASTDT", "AENDT"
    ),
    group = "TRTA",
    subset = SAFFL == "Y",
    label = "Weeks 0 to 12"
  ) |>
  metalite::define_parameter(
    name = "any",
    term1 = "",
    term2 = "",
    var = "AEDECOD",
    soc = "AEBODSYS",
    label = "All AEs"
  ) |>
  metalite::define_parameter(
    name = "rel",
    term1 = "Drug-Related",
    term2 = "",
    subset = AEREL %in% c("POSSIBLE", "PROBABLE"),
    var = "AEDECOD",
    soc = "AEBODSYS",
    label = "Drug-related AEs"
  ) |>
  metalite::define_parameter(
    name = "ser",
    term1 = "Serious",
    term2 = "",
    subset = AESER == "Y",
    var = "AEDECOD",
    soc = "AEBODSYS",
    label = "Serious AEs"
  ) |>
  metalite::define_analysis(
    name = "ae_summary",
    title = "Adverse Event Summary"
  ) |>
  metalite::meta_build()

outdata <- prepare_ae_summary(meta,
  population = "apat",
  observation = "wk12",
  parameter = "any;rel;ser"
)
#> any
#> rel
#> ser
outdata |>
  format_ae_summary() |>
  tlf_ae_summary(
    source = "Source:  [CDISCpilot: adam-adsl; adae]",
    analysis = "ae_summary",
    path_outdata = tempfile(fileext = ".Rdata"),
    path_outtable = tempfile(fileext = ".rtf")
  )
#> The outdata is saved in/tmp/RtmpVmZuRp/file221166933e1e.Rdata
#> The output is saved in/tmp/RtmpVmZuRp/file2211a1dc1df.rtf