Hacktoberfest 2026: the issues maintainers tagged for October, open and beginner-friendly. Browse Hacktoberfest issues

Improvement of `format_ae_listing()`

Open
#138 0 comments 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

Assessment

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

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.

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()

Dominant language
R
Stars
22
Forks
6
Avg merge
1d 14h
Merged PRs (30d)
10

Contributor guide

No contributing guide indexed for this repository

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.

More from Merck/forestly

All issues in Merck/forestly

Similar issues

More R issues

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.