A bug of `prepare_boxly`

[LittleBeannie]

The following code works.

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))

adlb <- boxly_adlb |> 
  filter(TRTA %in% c("Placebo", "Xanomeline High Dose")) |>
  mutate(TRTA = factor(TRTA,
                       levels = c("Placebo", "Xanomeline High Dose"),
                       labels = c("Control", "Experimental"))) |>
  rename(TRT01A = TRTA)

meta_lab <- meta_adam(population = adsl,
                      observation = adlb) |>
  define_plan(plan = plan(analysis = "lab_boxplot",
                          population = "apat",
                          observation = "wk12",
                          parameter = "alp;alt;bili;sodium;urate")) |>
  define_population(name = "apat",
                    group = "TRT01A",
                    subset = SAFFL == "Y",
                    label = "APaT Population") |>
  define_observation(name = "wk12",
                     group = "TRT01A",
                     var = "PARAM",
                     subset = SAFFL == "Y",
                     label = "") |>
  define_analysis(name = "lab_boxplot",
                  label = "Interactive Box Plot",
                  x = "AVISITN", 
                  y = "CHG") |>
  define_parameter(name = "alp",
                   label = "Alanine Aminotransferase (U/L)",
                   subset = PARAM == "Alanine Aminotransferase (U/L)") |>
  define_parameter(name = "alt",
                   label = "Alkaline Phosphatase (U/L)",
                   subset = PARAM == "Alkaline Phosphatase (U/L)") |>
  define_parameter(name = "bili",
                   label = "Bilirubin (umol/L)",
                   subset = PARAM == "Bilirubin (umol/L)") |>
  define_parameter(name = "sodium",
                   label = "Sodium (mmol/L)",
                   subset = PARAM == "Sodium (mmol/L)") |>
  define_parameter(name = "urate",
                   label = "Urate (umol/L)",
                   subset = PARAM == "Urate (umol/L)") |>
  meta_build()

meta_lab |>
  prepare_boxly(population = "apat",
                observation = "apat",
                analysis = "lab_boxplot") |>
  boxly()

> metalite::collect_adam_mapping(meta_lab, "wk12")$var
[1] "PARAM"

However, if I change the observation to "apat", then it breaks!

meta_lab <- meta_adam(population = adsl,
                      observation = adlb) |>
  define_plan(plan = plan(analysis = "lab_boxplot",
                          population = "apat",
                          observation = "apat",
                          parameter = "alp;alt;bili;sodium;urate")) |>
  define_population(name = "apat",
                    group = "TRT01A",
                    subset = SAFFL == "Y",
                    label = "APaT Population") |>
  define_observation(name = "apat",
                     group = "TRT01A",
                     var = "PARAM",
                     subset = SAFFL == "Y",
                     label = "APaT Population") |>
  define_analysis(name = "lab_boxplot",
                  label = "Interactive Box Plot",
                  x = "AVISITN", 
                  y = "CHG") |>
  define_parameter(name = "alp",
                   label = "Alanine Aminotransferase (U/L)",
                   subset = PARAM == "Alanine Aminotransferase (U/L)") |>
  define_parameter(name = "alt",
                   label = "Alkaline Phosphatase (U/L)",
                   subset = PARAM == "Alkaline Phosphatase (U/L)") |>
  define_parameter(name = "bili",
                   label = "Bilirubin (umol/L)",
                   subset = PARAM == "Bilirubin (umol/L)") |>
  define_parameter(name = "sodium",
                   label = "Sodium (mmol/L)",
                   subset = PARAM == "Sodium (mmol/L)") |>
  define_parameter(name = "urate",
                   label = "Urate (umol/L)",
                   subset = PARAM == "Urate (umol/L)") |>
  meta_build()

> metalite::collect_adam_mapping(meta_lab, "apat")$var
NULL

[fukuhiro2023]

Pending.
This relates to the concept of metalite package. If the population name and observation name are the same, the metalite::collect_adam_mapping() retrieves the information for population. To resolve this, metalite functions need to be updated so that it allows the same keyword for population and observation