Merck / Merck/forestly

Improvement of `format_ae_listing()`

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Dominant language
R
Stars
22
Forks
6
Avg merge
1d 12h
Merged PRs (30d)
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Description

The following code works without AREL in the ae_listing_display =.... After a quick debuging, the error seems to come from format_ae_listing() (maybe from https://github.com/Merck/forestly/blob/main/R/ae_listing.R#L313-L398).

In format_ae_listing(), we defaultly requried some variables for AE listing, including the following:

Furthermore, we did some data manuplication (see below links), which is NOT required. We are suggested to display what's exactly the data. These manuplication can be time consuming.

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()

meta |>
  prepare_ae_forestly(ae_listing_display = c("USUBJID", "SITEID", "SEX", "RACE", "AGE", "AREL")) |>
  format_ae_forestly() |>
  ae_forestly()

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start in R/ae_listing.R, especially format_ae_listing() and the linked ranges around lines 206-398, then reproduce the example using prepare_ae_forestly() and format_ae_forestly(). Check which required variables and data manipulations break listings without AREL; done means the listing works with the shown inputs and displays the source data without unnecessary transformations.

Written by the indexing model from the issue text.

Assessment

Tech stack
r
Domain
data
Issue type
Refactor
Difficulty
3/5
Estimated time
1-2 days
Activity status
Quiet
Clarity
Mostly clear
Newbie friendliness
65/100

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