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Display Only SOC in the AE-Specific Tables

Source: vignettes/customize-display-only-soc.Rmd
customize-display-only-soc.Rmd

The interactive AE forest plots include AE-specific tables that present both numerical and visual summaries for each AE SOC/PT terms. In this vignette, we demonstrate how to display only SOC terms in the table.

Step 1: build your metadata

Building interactive AE forest plots starts with constructing the metadata. The detailed procedure for building metadata is covered in the vignette Generate Interactive AE Forest Plots with Drill Down to AE Listing. Therefore, in this vignette, we will skip those details and directly use the metadata created there.

adsl <- forestly_adsl
adae <- forestly_adae

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

meta <- meta_adam(population = adsl, observation = adae) |>
  define_plan(plan = plan(
    analysis = "ae_forestly",
    population = "apat",
    observation = "apat",
    parameter = "any;drug-related"
  )) |>
  define_analysis(name = "ae_forestly", label = "Interactive Forest Plot") |>
  define_population(
    name = "apat", group = "TRTA", id = "USUBJID",
    subset = SAFFL == "Y", label = "All Patient as Treated"
  ) |>
  define_observation(
    name = "apat", group = "TRTA",
    subset = SAFFL == "Y", label = "All Patient as Treated"
  ) |>
  define_parameter(
    name = "any",
    subset = NULL,
    label = "Any AEs",
    var = "AEDECOD", soc = "AEBODSYS"
  ) |>
  define_parameter(
    name = "drug-related",
    subset = toupper(AREL) == "RELATED",
    label = "Drug-related AEs",
    var = "AEDECOD", soc = "AEBODSYS"
  ) |>
  meta_build()

Step 2: display only SOC

Users can control the display of SOC and/or PT terms using the components = … argument in the prepare_ae_forestly().

In the example below, we display only SOC terms in the forest plot, so the “Adverse Events” column contains only SOC terms in the table.

meta |>
  prepare_ae_forestly(components = "soc") |>
  format_ae_forestly() |>
  ae_forestly()