gsm.safetyexamples

Per-participant adverse-event timelines colored by severity, with seriousness highlighting and filters.

gsm.safety 1.0.0 · safety.viz 1.4.0 · rendered 2026-07-23

The chart below is live — rendered by the safety.viz aeTimelines module on the package’s example data, with the full control sidebar.

Render this report from a workflow

The same chart ships as a gsm-idiom report workflow. Run it with gsm.core::RunWorkflow() to produce a standalone HTML report, or use the matching runner script:

lWorkflow <- yaml::read_yaml(
  system.file("workflow", "3_reports", "ae_timelines.yaml", package = "gsm.safety")
)

gsm.core::RunWorkflow(
  lWorkflow = lWorkflow,
  lData = list(dfResults = ExampleData("adae"))
)
Rscript inst/examples/ae-timelines.R <output-dir>
The full ae_timelines.yaml workflow 
meta:
  Type: Report
  ID: ae_timelines
  Output: html
  Name: AE Timelines Report
  Description: Interactive safety.viz adverse-event timelines, one row per participant.
  lSettings:
    color:
      value_col: AESEV
      label: Severity
    highlight:
      value_col: AESER
      label: Serious Event
      value: Y
    filters:
      - value_col: AESER
        label: Serious Event
      - value_col: AESEV
        label: Severity
      - value_col: ARM
        label: Treatment Group
      - value_col: USUBJID
        label: Participant ID
    details:
      - value_col: AEBODSYS
        label: Body System
      - value_col: AEDECOD
        label: Dictionary-Derived Term
    sort_participants: earliest
spec:
  dfResults:
    USUBJID:
      type: character
    AETERM:
      type: character
    ASTDY:
      type: numeric
steps:
  - output: strOutputDir
    name: getwd
  - output: lWidget
    name: gsm.safety::Widget_AeTimelines
    params:
      dfResults: dfResults
      lSettings: lSettings
  - output: strReportPath
    name: gsm.safety::SaveWidgetReport
    params:
      widget: lWidget
      strOutputDir: strOutputDir
      strOutputFile: ID

The live chart

library(gsm.safety)

dfResults <- ExampleData("adae")

Widget_AeTimelines(
  dfResults,
  lSettings = list(
    color = list(
      value_col = "AESEV",
      label = "Severity"
    ),
    highlight = list(
      value_col = "AESER",
      label = "Serious Event",
      value = "Y"
    ),
    filters = list(
      list(value_col = "AESER", label = "Serious Event"),
      list(value_col = "AESEV", label = "Severity"),
      list(value_col = "ARM", label = "Treatment Group"),
      list(value_col = "USUBJID", label = "Participant ID")
    ),
    details = list(
      list(value_col = "AEBODSYS", label = "Body System"),
      list(value_col = "AEDECOD", label = "Dictionary-Derived Term")
    ),
    sort_participants = "earliest"
  )
)