Add `var = ...` to `define_population` and `define_observation`
Open
@lm3388 is already working on this.
Since Apr 14, 2026.
- Dominant language
- R
- Stars
- 22
- Forks
- 6
- Avg merge
- 1d 12h
- Merged PRs (30d)
- 7
Description
Add var = ... to define_population() and define_observation() in the vignette of https://merck.github.io/forestly/articles/forestly.html like code below.
adsl <- r2rtf::r2rtf_adsl |>
filter(TRT01P %in% c("Placebo", "Xanomeline High Dose")) |>
mutate(TRT01P = factor(TRT01P,
levels = c("Placebo", "Xanomeline High Dose"),
labels = c("Control", "Experimental")),
TRT01A = factor(TRT01A,
levels = c("Placebo", "Xanomeline High Dose"),
labels = c("Control", "Experimental")),
RACE = stringr::str_to_sentence(RACE))
adae <- forestly_adae |>
filter(TRTA %in% c("Placebo", "Xanomeline High Dose")) |>
rename(TRT01A = TRTA) |>
mutate(TRT01A = factor(TRT01A,
levels = c("Placebo", "Xanomeline High Dose"),
labels = c("Control", "Experimental")))
meta_ae_forest <- meta_adam(population = adsl,
observation = adae) |>
define_plan(plan = plan(analysis = "ae_forestly",
population = "apat",
observation = "apat",
parameter = "any;drug-related;serious;drug-related-serious")) |>
define_analysis(name = "ae_forestly",
label = "Interactive Forest Plot") |>
define_population(name = "apat",
group = "TRT01A",
id = "USUBJID",
subset = SAFFL == "Y",
label = "All Patient as Treated",
var = c("USUBJID", "SAFFL", "TRT01A", "SITEID", "SEX", "RACE", "AGE")) |>
define_observation(name = "apat",
group = "TRT01A",
subset = SAFFL == "Y",
label = "All Patient as Treated",
var = c("USUBJID", "SAFFL", "TRT01A", "AEDECOD", "AEBODSYS",
"AEREL", "AESER", "AEOUT", "AEACN", "AESDTH", "ASTDT", "AENDT")
) |>
define_parameter(name = "any",
subset = NULL,
label = "Any AEs",
var = "AEDECOD",
soc = "AEBODSYS") |>
define_parameter(name = "drug-related",
subset = toupper(AEREL) %in% c("PROBABLE", "POSSIBLE"),
label = "Drug-related AEs",
var = "AEDECOD", soc = "AEBODSYS") |>
define_parameter(name = "serious",
subset = AESER == "Y",
label = "Serious AEs",
var = "AEDECOD", soc = "AEBODSYS") |>
define_parameter(name = "drug-related-serious",
subset = AESER == "Y" & toupper(AEREL) %in% c("PROBABLE", "POSSIBLE"),
label = "Drug-related serious AEs",
var = "AEDECOD", soc = "AEBODSYS") |>
meta_build()
meta_ae_forest |>
prepare_ae_forestly(ae_listing_display = c("USUBJID", "SITEID", "SEX", "RACE", "AGE",
"AEREL", "AESER", "AEOUT", "AEACN", "AESDTH", "ASTDT", "AENDT")) |>
format_ae_forestly(display = c("n", "prop", "fig_prop", "fig_diff")) |>
ae_forestly()
Contributor guide
No contributing guide indexed for this repository
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Assessment
This issue has not been assessed yet.