Remove default decorator and update docs #1348

vedhav · 2025-02-20T13:55:11Z

Have the same standards as tmg for the decorators

Here's the app to test decorators for all 36 modules

# Load packages
pkgload::load_all()

# Decorators ------------------------------------------------------------------
insert_rrow_decorator <- function(default_caption = "I am a good new row", .var_to_replace = "table") {
  teal_transform_module(
    label = "New rtables row",
    ui = function(id) shiny::textInput(shiny::NS(id, "new_row"), "New row", value = default_caption),
    server = make_teal_transform_server(
      substitute(
        {
          .var_to_replace <- rtables::insert_rrow(.var_to_replace, rtables::rrow(new_row))
        },
        env = list(.var_to_replace = as.name(.var_to_replace))
      )
    )
  )
}
add_title_decorator <- function(default_check = TRUE, .var_to_replace = "plot") {
  teal_transform_module(
    label = "Title",
    ui = function(id) shiny::checkboxInput(NS(id, "flag"), "Add title?", TRUE),
    server = make_teal_transform_server(
      substitute(
        {
          if (flag) {
            .var_to_replace <-
              .var_to_replace + ggplot2::ggtitle("Title added by decorator")
          }
        },
        env = list(.var_to_replace = as.name(.var_to_replace))
      )
    )
  )
}
caption_decorator <- function(default_caption = "I am a good decorator", .var_to_replace = "plot") {
  teal_transform_module(
    label = "Caption",
    ui = function(id) shiny::textInput(shiny::NS(id, "footnote"), "Footnote", value = default_caption),
    server = make_teal_transform_server(
      substitute(
        {
          .var_to_replace <- .var_to_replace + ggplot2::labs(caption = footnote)
        },
        env = list(.var_to_replace = as.name(.var_to_replace))
      )
    )
  )
}
change_theme_decorator <- function(default_check = TRUE, .var_to_replace = "plot") {
  teal_transform_module(
    label = "Theme",
    ui = function(id) shiny::checkboxInput(NS(id, "flag"), "Apply dark theme?", TRUE),
    server = make_teal_transform_server(
      substitute(
        {
          if (flag) .var_to_replace <- .var_to_replace + ggplot2::theme_dark()
        },
        env = list(.var_to_replace = as.name(.var_to_replace))
      )
    )
  )
}
add_cowplot_title_decorator <- function(default_check = TRUE, .var_to_replace = "plot") {
  teal_transform_module(
    label = "Cowplot title",
    ui = function(id) shiny::checkboxInput(NS(id, "flag"), "Add title?", TRUE),
    server = make_teal_transform_server(
      substitute(
        {
          if (flag) {
            .var_to_replace <-
              .var_to_replace +
              ggplot2::ggtitle("Title added by decorator") +
              cowplot::theme_cowplot()
          }
        },
        env = list(.var_to_replace = as.name(.var_to_replace))
      )
    )
  )
}
rlisting_footer <- function(default_footer = "I am a good footer", .var_to_replace = "table_listing") {
  teal_transform_module(
    label = "New row",
    ui = function(id) shiny::textInput(shiny::NS(id, "footer"), "footer", value = default_footer),
    server = make_teal_transform_server(
      substitute(
        {
          rlistings::main_footer(.var_to_replace) <- footer
        },
        env = list(.var_to_replace = as.name(.var_to_replace))
      )
    )
  )
}
head_decorator <- function(default_value = 6, .var_to_replace = "object") {
  teal_transform_module(
    label = "Head",
    ui = function(id) shiny::numericInput(shiny::NS(id, "n"), "N rows", value = default_value),
    server = make_teal_transform_server(
      substitute(
        {
          .var_to_replace <- utils::head(.var_to_replace, n = n)
        },
        env = list(.var_to_replace = as.name(.var_to_replace))
      )
    )
  )
}

# End of decorators -----------------------------------------------------------

library(dplyr)

# arm_ref_comp <- list(ARMCD = list(ref = "ARM B", comp = c("ARM A", "ARM C")))

arm_ref_comp <- list(
  ACTARMCD = list(ref = "ARM B", comp = c("ARM A", "ARM C")),
  ARM = list(ref = "B: Placebo", comp = c("A: Drug X", "C: Combination"))
)

data <- within(teal_data(), {
  ADSL <- tmc_ex_adsl |>
    mutate(ITTFL = factor("Y") |> with_label("Intent-To-Treat Population Flag")) |>
    mutate(DTHFL = case_when(!is.na(DTHDT) ~ "Y", TRUE ~ "") |> with_label("Subject Death Flag"))

  ADAE <- tmc_ex_adae |>
    filter(!((AETOXGR == 1) & (AESEV == "MILD") & (ARM == "A: Drug X")))

  ADAE$ASTDY <- structure(
    as.double(ADAE$ASTDY, unit = attr(ADAE$ASTDY, "units", exact = TRUE)),
    label = attr(ADAE$ASTDY, "label", exact = TRUE)
  )

  .lbls_adae <- col_labels(tmc_ex_adae)
  ADAE <- tmc_ex_adae %>%
    mutate_if(is.character, as.factor) #' be certain of having factors
  col_labels(ADAE) <- .lbls_adae

  ADTTE <- tmc_ex_adtte

  ADLB <- tmc_ex_adlb |>
    mutate(AVISIT == forcats::fct_reorder(AVISIT, AVISITN, min)) |>
    mutate(
      ONTRTFL = case_when(
        AVISIT %in% c("SCREENING", "BASELINE") ~ "",
        TRUE ~ "Y"
      ) |> with_label("On Treatment Record Flag")
    )

  ADVS <- tmc_ex_advs

  ADRS <- tmc_ex_adrs |>
    mutate(
      AVALC = d_onco_rsp_label(AVALC) |>
        with_label("Character Result/Finding")
    ) |>
    filter(PARAMCD != "OVRINV" | AVISIT == "FOLLOW UP") |>
    filter(PARAMCD %in% c("BESRSPI", "INVET"))

  ADAETTE <- tmc_ex_adaette %>%
    filter(PARAMCD %in% c("AETTE1", "AETTE2", "AETTE3")) %>%
    mutate(is_event = CNSR == 0) %>%
    mutate(n_events = as.integer(is_event))

  .add_event_flags <- function(dat) {
    dat <- dat %>%
      mutate(
        TMPFL_SER = AESER == "Y",
        TMPFL_REL = AEREL == "Y",
        TMPFL_GR5 = AETOXGR == "5",
        TMP_SMQ01 = !is.na(SMQ01NAM),
        TMP_SMQ02 = !is.na(SMQ02NAM),
        TMP_CQ01 = !is.na(CQ01NAM)
      )
    column_labels <- list(
      TMPFL_SER = "Serious AE",
      TMPFL_REL = "Related AE",
      TMPFL_GR5 = "Grade 5 AE",
      TMP_SMQ01 = aesi_label(dat[["SMQ01NAM"]], dat[["SMQ01SC"]]),
      TMP_SMQ02 = aesi_label("Y.9.9.9.9/Z.9.9.9.9 AESI"),
      TMP_CQ01 = aesi_label(dat[["CQ01NAM"]])
    )
    col_labels(dat)[names(column_labels)] <- as.character(column_labels)
    dat
  }

  ADEX <- tmc_ex_adex

  set.seed(1, kind = "Mersenne-Twister")
  .labels <- col_labels(ADEX, fill = FALSE)
  ADEX <- ADEX %>%
    distinct(USUBJID, .keep_all = TRUE) %>%
    mutate(
      PARAMCD = "TDURD",
      PARAM = "Overall duration (days)",
      AVAL = sample(x = seq(1, 200), size = n(), replace = TRUE),
      AVALU = "Days"
    ) %>%
    bind_rows(ADEX)
  col_labels(ADEX) <- .labels

  ADCM <- tmc_ex_adcm

  ADMH <- tmc_ex_admh

  ADCM$CMASTDTM <- ADCM$ASTDTM
  ADCM$CMAENDTM <- ADCM$AENDTM

  ADEG <- tmc_ex_adeg

  # smq
  .names_baskets <- grep("^(SMQ|CQ).*NAM$", names(ADAE), value = TRUE)
  .names_scopes <- grep("^SMQ.*SC$", names(ADAE), value = TRUE)

  .cs_baskets <- choices_selected(
    choices = variable_choices(ADAE, subset = .names_baskets),
    selected = .names_baskets
  )

  .cs_scopes <- choices_selected(
    choices = variable_choices(ADAE, subset = .names_scopes),
    selected = .names_scopes,
    fixed = TRUE
  )

  # summary
  ADSL$EOSDY[1] <- NA_integer_
  ADQS <- tmc_ex_adqs %>%
    filter(ABLFL != "Y" & ABLFL2 != "Y") %>%
    mutate(
      AVISIT = as.factor(AVISIT),
      AVISITN = rank(AVISITN) %>%
        as.factor() %>%
        as.numeric() %>%
        as.factor(),
      AVALBIN = AVAL < 50 # Just as an example to get a binary endpoint.
    ) %>%
    droplevels()
})
join_keys(data) <- default_cdisc_join_keys[names(data)]
adcm_keys <- c("STUDYID", "USUBJID", "ASTDTM", "CMSEQ", "ATC1", "ATC2", "ATC3", "ATC4")
join_keys(data)["ADCM", "ADCM"] <- adcm_keys

# Use in choices selected -----------------------------------------------------

ADSL <- data[["ADSL"]]
ADQS <- data[["ADQS"]]
ADAE <- data[["ADAE"]]
ADTTE <- data[["ADTTE"]]
ADLB <- data[["ADLB"]]
ADAE <- data[["ADAE"]]
ADVS <- data[["ADVS"]]
ADRS <- data[["ADRS"]]
ADAETTE <- data[["ADAETTE"]]
ADEX <- data[["ADEX"]]
ADCM <- data[["ADCM"]]
ADMH <- data[["ADMH"]]
ADEG <- data[["ADEG"]]

# Init ------------------------------------------------------------------------

init(
  data = data,
  modules = modules(
    tm_a_mmrm(
      label = "tm_a_mmrm",
      dataname = "ADQS",
      aval_var = choices_selected(c("AVAL", "CHG"), "AVAL"),
      id_var = choices_selected(c("USUBJID", "SUBJID"), "USUBJID"),
      arm_var = choices_selected(c("ARM", "ARMCD"), "ARM"),
      visit_var = choices_selected(c("AVISIT", "AVISITN"), "AVISIT"),
      arm_ref_comp = arm_ref_comp,
      paramcd = choices_selected(
        choices = value_choices(data[["ADQS"]], "PARAMCD", "PARAM"),
        selected = "FKSI-FWB"
      ),
      cov_var = choices_selected(c("BASE", "AGE", "SEX", "BASE:AVISIT"), NULL),
      decorators = list(
        lsmeans_table = insert_rrow_decorator("New row for lsmeans_table", .var_to_replace = "lsmeans_table"),
        lsmeans_plot = add_title_decorator("New title for lsmeans_plot", .var_to_replace = "lsmeans_plot"),
        covariance_table = insert_rrow_decorator("New row for covariance_table", .var_to_replace = "covariance_table"),
        fixed_effects_table = insert_rrow_decorator("New row for fixed_effects_table", .var_to_replace = "fixed_effects_table"),
        diagnostic_table = insert_rrow_decorator("New row for diagnostic_table", .var_to_replace = "diagnostic_table"),
        diagnostic_plot = add_title_decorator("New title for diagnostic_plot", .var_to_replace = "diagnostic_plot")
      )
    )
  )
) |> runApp()

init(
  data = data,
  modules = modules(
    tm_a_gee(
      label = "tm_a_gee",
      dataname = "ADQS",
      aval_var = choices_selected("AVALBIN", fixed = TRUE),
      id_var = choices_selected(c("USUBJID", "SUBJID"), "USUBJID"),
      arm_var = choices_selected(c("ARM", "ARMCD"), "ARM"),
      visit_var = choices_selected(c("AVISIT", "AVISITN"), "AVISIT"),
      paramcd = choices_selected(
        choices = value_choices(data[["ADQS"]], "PARAMCD", "PARAM"),
        selected = "FKSI-FWB"
      ),
      cov_var = choices_selected(c("BASE", "AGE", "SEX", "BASE:AVISIT"), NULL),
      decorators = list(table = insert_rrow_decorator())
    ),
    tm_a_mmrm(
      label = "tm_a_mmrm",
      dataname = "ADQS",
      aval_var = choices_selected(c("AVAL", "CHG"), "AVAL"),
      id_var = choices_selected(c("USUBJID", "SUBJID"), "USUBJID"),
      arm_var = choices_selected(c("ARM", "ARMCD"), "ARM"),
      visit_var = choices_selected(c("AVISIT", "AVISITN"), "AVISIT"),
      arm_ref_comp = arm_ref_comp,
      paramcd = choices_selected(
        choices = value_choices(data[["ADQS"]], "PARAMCD", "PARAM"),
        selected = "FKSI-FWB"
      ),
      cov_var = choices_selected(c("BASE", "AGE", "SEX", "BASE:AVISIT"), NULL),
      decorators = list(
        lsmeans_table = insert_rrow_decorator("New row for lsmeans_table", .var_to_replace = "lsmeans_table"),
        lsmeans_plot = add_title_decorator(.var_to_replace = "lsmeans_plot"),
        covariance_table = insert_rrow_decorator("New row for covariance_table", .var_to_replace = "covariance_table"),
        fixed_effects_table = insert_rrow_decorator("New row for fixed_effects_table", .var_to_replace = "fixed_effects_table"),
        diagnostic_table = insert_rrow_decorator("New row for diagnostic_table", .var_to_replace = "diagnostic_table"),
        diagnostic_plot = add_title_decorator(.var_to_replace = "diagnostic_plot")
      )
    ),
    tm_g_barchart_simple(
      label = "tm_g_barchart_simple",
      x = data_extract_spec(
        dataname = "ADSL",
        select = select_spec(
          choices = variable_choices(
            ADSL,
            c(
              "ARM", "ACTARM", "SEX",
              "RACE", "ITTFL", "SAFFL", "STRATA2"
            )
          ),
          selected = "ACTARM",
          multiple = FALSE
        )
      ),
      fill = list(
        data_extract_spec(
          dataname = "ADSL",
          select = select_spec(
            choices = variable_choices(
              ADSL,
              c(
                "ARM", "ACTARM", "SEX",
                "RACE", "ITTFL", "SAFFL", "STRATA2"
              )
            ),
            selected = "SEX",
            multiple = FALSE
          )
        ),
        data_extract_spec(
          dataname = "ADAE",
          select = select_spec(
            choices = variable_choices(ADAE, c("AETOXGR", "AESEV", "AESER")),
            selected = NULL,
            multiple = FALSE
          )
        )
      ),
      x_facet = list(
        data_extract_spec(
          dataname = "ADAE",
          select = select_spec(
            choices = variable_choices(ADAE, c("AETOXGR", "AESEV", "AESER")),
            selected = "AETOXGR",
            multiple = FALSE
          )
        ),
        data_extract_spec(
          dataname = "ADSL",
          select = select_spec(
            choices = variable_choices(
              ADSL,
              c(
                "ARM", "ACTARM", "SEX",
                "RACE", "ITTFL", "SAFFL", "STRATA2"
              )
            ),
            selected = NULL,
            multiple = FALSE
          )
        )
      ),
      y_facet = list(
        data_extract_spec(
          dataname = "ADAE",
          select = select_spec(
            choices = variable_choices(ADAE, c("AETOXGR", "AESEV", "AESER")),
            selected = "AESEV",
            multiple = FALSE
          )
        ),
        data_extract_spec(
          dataname = "ADSL",
          select = select_spec(
            choices = variable_choices(
              ADSL,
              c(
                "ARM", "ACTARM", "SEX",
                "RACE", "ITTFL", "SAFFL", "STRATA2"
              )
            ),
            selected = NULL,
            multiple = FALSE
          )
        )
      ),
      decorators = list(plot = caption_decorator("The best", "plot"))
    ),
    tm_g_ci(
      label = "tm_g_ci",
      x_var = data_extract_spec(
        dataname = "ADSL",
        select = select_spec(
          choices = c("ARMCD", "BMRKR2"),
          selected = c("ARMCD"),
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      y_var = data_extract_spec(
        dataname = "ADLB",
        filter = list(
          filter_spec(
            vars = "PARAMCD",
            choices = levels(ADLB$PARAMCD),
            selected = levels(ADLB$PARAMCD)[1],
            multiple = FALSE,
            label = "Select lab:"
          ),
          filter_spec(
            vars = "AVISIT",
            choices = levels(ADLB$AVISIT),
            selected = levels(ADLB$AVISIT)[1],
            multiple = FALSE,
            label = "Select visit:"
          )
        ),
        select = select_spec(
          label = "Analyzed Value",
          choices = c("AVAL", "CHG"),
          selected = "AVAL",
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      color = data_extract_spec(
        dataname = "ADSL",
        select = select_spec(
          label = "Color by variable",
          choices = c("SEX", "STRATA1", "STRATA2"),
          selected = c("STRATA1"),
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      decorators = list(plot = caption_decorator(.var_to_replace = "plot"))
    ),
    tm_g_forest_rsp(
      label = "tm_g_forest_rsp",
      dataname = "ADRS",
      arm_var = choices_selected(
        variable_choices(ADSL, c("ARM", "ARMCD")),
        "ARMCD"
      ),
      arm_ref_comp = arm_ref_comp,
      paramcd = choices_selected(
        value_choices(ADRS, "PARAMCD", "PARAM"),
        "INVET"
      ),
      subgroup_var = choices_selected(
        variable_choices(ADSL, names(ADSL)),
        c("BMRKR2", "SEX")
      ),
      strata_var = choices_selected(
        variable_choices(ADSL, c("STRATA1", "STRATA2")),
        "STRATA2"
      ),
      plot_height = c(600L, 200L, 2000L),
      default_responses = list(
        BESRSPI = list(
          rsp = c("Stable Disease (SD)", "Not Evaluable (NE)"),
          levels = c(
            "Complete Response (CR)", "Partial Response (PR)", "Stable Disease (SD)",
            "Progressive Disease (PD)", "Not Evaluable (NE)"
          )
        ),
        INVET = list(
          rsp = c("Complete Response (CR)", "Partial Response (PR)"),
          levels = c(
            "Complete Response (CR)", "Not Evaluable (NE)", "Partial Response (PR)",
            "Progressive Disease (PD)", "Stable Disease (SD)"
          )
        ),
        OVRINV = list(
          rsp = c("Progressive Disease (PD)", "Stable Disease (SD)"),
          levels = c("Progressive Disease (PD)", "Stable Disease (SD)", "Not Evaluable (NE)")
        )
      ),
      decorators = list(plot = caption_decorator())
    ),
    tm_g_forest_tte(
      label = "tm_g_forest_tte",
      dataname = "ADTTE",
      arm_var = choices_selected(
        variable_choices(ADSL, c("ARM", "ARMCD")),
        "ARMCD"
      ),
      arm_ref_comp = arm_ref_comp,
      paramcd = choices_selected(
        value_choices(ADTTE, "PARAMCD", "PARAM"),
        "OS"
      ),
      subgroup_var = choices_selected(
        variable_choices(ADSL, names(ADSL)),
        c("BMRKR2", "SEX")
      ),
      strata_var = choices_selected(
        variable_choices(ADSL, c("STRATA1", "STRATA2")),
        "STRATA2"
      ),
      decorators = list(plot = caption_decorator())
    ),
    tm_g_ipp(
      label = "tm_g_ipp",
      dataname = "ADLB",
      arm_var = choices_selected(
        value_choices(ADLB, "ARMCD"),
        "ARM A"
      ),
      paramcd = choices_selected(
        value_choices(ADLB, "PARAMCD"),
        "ALT"
      ),
      aval_var = choices_selected(
        variable_choices(ADLB, c("AVAL", "CHG")),
        "AVAL"
      ),
      avalu_var = choices_selected(
        variable_choices(ADLB, c("AVALU")),
        "AVALU",
        fixed = TRUE
      ),
      id_var = choices_selected(
        variable_choices(ADLB, c("USUBJID")),
        "USUBJID",
        fixed = TRUE
      ),
      visit_var = choices_selected(
        variable_choices(ADLB, c("AVISIT")),
        "AVISIT"
      ),
      baseline_var = choices_selected(
        variable_choices(ADLB, c("BASE")),
        "BASE",
        fixed = TRUE
      ),
      add_baseline_hline = FALSE,
      separate_by_obs = FALSE,
      decorators = list(plot = caption_decorator(.var_to_replace = "plot"))
    ),
    tm_g_km(
      label = "tm_g_km",
      dataname = "ADTTE",
      arm_var = choices_selected(
        variable_choices(ADSL, c("ARM", "ARMCD", "ACTARMCD")),
        "ARM"
      ),
      paramcd = choices_selected(
        value_choices(ADTTE, "PARAMCD", "PARAM"),
        "OS"
      ),
      arm_ref_comp = arm_ref_comp,
      strata_var = choices_selected(
        variable_choices(ADSL, c("SEX", "BMRKR2")),
        "SEX"
      ),
      facet_var = choices_selected(
        variable_choices(ADSL, c("SEX", "BMRKR2")),
        NULL
      ),
      decorators = list(plot = add_cowplot_title_decorator(TRUE, "plot"))
    ),
    tm_g_lineplot(
      label = "tm_g_lineplot",
      dataname = "ADLB",
      strata = choices_selected(
        variable_choices(ADSL, c("ARM", "ARMCD", "ACTARMCD")),
        "ARM"
      ),
      y = choices_selected(
        variable_choices(ADLB, c("AVAL", "BASE", "CHG", "PCHG")),
        "AVAL"
      ),
      param = choices_selected(
        value_choices(ADLB, "PARAMCD", "PARAM"),
        "ALT"
      ),
      decorators = list(plot = add_cowplot_title_decorator("plot"))
    ),
    tm_g_pp_adverse_events(
      label = "tm_g_pp_adverse_events",
      dataname = "ADAE",
      parentname = "ADSL",
      patient_col = "USUBJID",
      plot_height = c(600L, 200L, 2000L),
      aeterm = choices_selected(
        choices = variable_choices(ADAE, "AETERM"),
        selected = "AETERM"
      ),
      tox_grade = choices_selected(
        choices = variable_choices(ADAE, "AETOXGR"),
        selected = "AETOXGR"
      ),
      causality = choices_selected(
        choices = variable_choices(ADAE, "AEREL"),
        selected = "AEREL"
      ),
      outcome = choices_selected(
        choices = variable_choices(ADAE, "AEOUT"),
        selected = "AEOUT"
      ),
      action = choices_selected(
        choices = variable_choices(ADAE, "AEACN"),
        selected = "AEACN"
      ),
      time = choices_selected(
        choices = variable_choices(ADAE, "ASTDY"),
        selected = "ASTDY"
      ),
      decod = NULL,
      decorators = list(
        plot = caption_decorator("I am a good caption", "plot"),
        table = rlisting_footer(.var_to_replace = "table")
      )
    ),
    tm_g_pp_patient_timeline(
      label = "tm_g_pp_patient_timeline",
      dataname_adae = "ADAE",
      dataname_adcm = "ADCM",
      parentname = "ADSL",
      patient_col = "USUBJID",
      plot_height = c(600L, 200L, 2000L),
      cmdecod = choices_selected(
        choices = variable_choices(data[["ADCM"]], "CMDECOD"),
        selected = "CMDECOD",
      ),
      aeterm = choices_selected(
        choices = variable_choices(data[["ADAE"]], "AETERM"),
        selected = c("AETERM")
      ),
      aetime_start = choices_selected(
        choices = variable_choices(data[["ADAE"]], "ASTDTM"),
        selected = c("ASTDTM")
      ),
      aetime_end = choices_selected(
        choices = variable_choices(data[["ADAE"]], "AENDTM"),
        selected = c("AENDTM")
      ),
      dstime_start = choices_selected(
        choices = variable_choices(data[["ADCM"]], "CMASTDTM"),
        selected = c("CMASTDTM")
      ),
      dstime_end = choices_selected(
        choices = variable_choices(data[["ADCM"]], "CMAENDTM"),
        selected = c("CMAENDTM")
      ),
      aerelday_start = choices_selected(
        choices = variable_choices(data[["ADAE"]], "ASTDY"),
        selected = c("ASTDY")
      ),
      aerelday_end = choices_selected(
        choices = variable_choices(data[["ADAE"]], "AENDY"),
        selected = c("AENDY")
      ),
      dsrelday_start = choices_selected(
        choices = variable_choices(data[["ADCM"]], "ASTDY"),
        selected = c("ASTDY")
      ),
      dsrelday_end = choices_selected(
        choices = variable_choices(data[["ADCM"]], "AENDY"),
        selected = c("AENDY")
      ),
      decorators = list(plot = caption_decorator())
    ),
    tm_g_pp_therapy(
      label = "tm_g_pp_therapy",
      dataname = "ADCM",
      parentname = "ADSL",
      patient_col = "USUBJID",
      plot_height = c(600L, 200L, 2000L),
      atirel = choices_selected(
        choices = variable_choices(ADCM, "ATIREL"),
        selected = c("ATIREL")
      ),
      cmdecod = choices_selected(
        choices = variable_choices(ADCM, "CMDECOD"),
        selected = "CMDECOD"
      ),
      cmindc = choices_selected(
        choices = variable_choices(ADCM, "CMINDC"),
        selected = "CMINDC"
      ),
      cmdose = choices_selected(
        choices = variable_choices(ADCM, "CMDOSE"),
        selected = "CMDOSE"
      ),
      cmtrt = choices_selected(
        choices = variable_choices(ADCM, "CMTRT"),
        selected = "CMTRT"
      ),
      cmdosu = choices_selected(
        choices = variable_choices(ADCM, "CMDOSU"),
        selected = c("CMDOSU")
      ),
      cmroute = choices_selected(
        choices = variable_choices(ADCM, "CMROUTE"),
        selected = "CMROUTE"
      ),
      cmdosfrq = choices_selected(
        choices = variable_choices(ADCM, "CMDOSFRQ"),
        selected = "CMDOSFRQ"
      ),
      cmstdy = choices_selected(
        choices = variable_choices(ADCM, "ASTDY"),
        selected = "ASTDY"
      ),
      cmendy = choices_selected(
        choices = variable_choices(ADCM, "AENDY"),
        selected = "AENDY"
      ),
      decorators = list(plot = caption_decorator("Marcin", "plot"), table = head_decorator(2, "table"))
    ),
    tm_g_pp_vitals(
      label = "tm_g_pp_vitals",
      dataname = "ADVS",
      parentname = "ADSL",
      patient_col = "USUBJID",
      plot_height = c(600L, 200L, 2000L),
      paramcd = choices_selected(
        choices = variable_choices(ADVS, "PARAMCD"),
        selected = "PARAMCD"
      ),
      xaxis = choices_selected(
        choices = variable_choices(ADVS, "ADY"),
        selected = "ADY"
      ),
      aval_var = choices_selected(
        choices = variable_choices(ADVS, "AVAL"),
        selected = "AVAL"
      ),
      decorators = list(plot = add_title_decorator("plot"))
    ),
    tm_t_abnormality(
      label = "tm_t_abnormality",
      dataname = "ADLB",
      arm_var = choices_selected(
        choices = variable_choices(ADSL, subset = c("ARM", "ARMCD")),
        selected = "ARM"
      ),
      add_total = FALSE,
      by_vars = choices_selected(
        choices = variable_choices(ADLB, subset = c("LBCAT", "PARAM", "AVISIT")),
        selected = c("LBCAT", "PARAM"),
        keep_order = TRUE
      ),
      baseline_var = choices_selected(
        variable_choices(ADLB, subset = "BNRIND"),
        selected = "BNRIND", fixed = TRUE
      ),
      grade = choices_selected(
        choices = variable_choices(ADLB, subset = "ANRIND"),
        selected = "ANRIND",
        fixed = TRUE
      ),
      abnormal = list(low = "LOW", high = "HIGH"),
      exclude_base_abn = FALSE,
      decorators = list(table = insert_rrow_decorator("I am a good new row"))
    ),
    tm_t_abnormality_by_worst_grade(
      label = "tm_t_abnormality_by_worst_grade",
      dataname = "ADLB",
      arm_var = choices_selected(
        choices = variable_choices(ADSL, subset = c("ARM", "ARMCD")),
        selected = "ARM"
      ),
      paramcd = choices_selected(
        choices = value_choices(ADLB, "PARAMCD", "PARAM"),
        selected = c("ALT", "CRP", "IGA")
      ),
      add_total = FALSE,
      decorators = list(table = insert_rrow_decorator("I am a good new row"))
    ),
    tm_t_ancova(
      label = "tm_t_ancova",
      dataname = "ADQS",
      avisit = choices_selected(
        choices = value_choices(ADQS, "AVISIT"),
        selected = "WEEK 1 DAY 8"
      ),
      arm_var = choices_selected(
        choices = variable_choices(ADSL, c("ARM", "ACTARMCD", "ARMCD")),
        selected = "ARMCD"
      ),
      arm_ref_comp = arm_ref_comp,
      aval_var = choices_selected(
        choices = variable_choices(ADQS, c("CHG", "AVAL")),
        selected = "CHG"
      ),
      cov_var = choices_selected(
        choices = variable_choices(ADQS, c("BASE", "STRATA1", "SEX")),
        selected = "STRATA1"
      ),
      paramcd = choices_selected(
        choices = value_choices(ADQS, "PARAMCD", "PARAM"),
        selected = "FKSI-FWB"
      ),
      interact_var = choices_selected(
        choices = variable_choices(ADQS, c("BASE", "STRATA1", "SEX")),
        selected = "STRATA1"
      ),
      decorators = list(table = insert_rrow_decorator("I am a good new row"))
    ),
    tm_t_binary_outcome(
      label = "tm_t_binary_outcome",
      dataname = "ADRS",
      paramcd = choices_selected(
        choices = value_choices(ADRS, "PARAMCD", "PARAM"),
        selected = "BESRSPI"
      ),
      arm_var = choices_selected(
        choices = variable_choices(ADRS, c("ARM", "ARMCD", "ACTARMCD")),
        selected = "ARM"
      ),
      arm_ref_comp = arm_ref_comp,
      strata_var = choices_selected(
        choices = variable_choices(ADRS, c("SEX", "BMRKR2", "RACE")),
        selected = "RACE"
      ),
      default_responses = list(
        BESRSPI = list(
          rsp = c("Complete Response (CR)", "Partial Response (PR)"),
          levels = c(
            "Complete Response (CR)", "Partial Response (PR)",
            "Stable Disease (SD)", "Progressive Disease (PD)"
          )
        ),
        INVET = list(
          rsp = c("Stable Disease (SD)", "Not Evaluable (NE)"),
          levels = c(
            "Complete Response (CR)", "Not Evaluable (NE)", "Partial Response (PR)",
            "Progressive Disease (PD)", "Stable Disease (SD)"
          )
        ),
        OVRINV = list(
          rsp = c("Progressive Disease (PD)", "Stable Disease (SD)"),
          levels = c("Progressive Disease (PD)", "Stable Disease (SD)", "Not Evaluable (NE)")
        )
      ),
      decorators = list(table = insert_rrow_decorator("I am a new row"))
    ),
    tm_t_coxreg(
      label = "tm_t_coxreg",
      dataname = "ADTTE",
      arm_var = choices_selected(c("ARM", "ARMCD", "ACTARMCD"), "ARM"),
      arm_ref_comp = arm_ref_comp,
      paramcd = choices_selected(
        value_choices(ADTTE, "PARAMCD", "PARAM"), "OS"
      ),
      strata_var = choices_selected(
        c("COUNTRY", "STRATA1", "STRATA2"), "STRATA1"
      ),
      cov_var = choices_selected(
        c("AGE", "BMRKR1", "BMRKR2", "REGION1"), "AGE"
      ),
      multivariate = TRUE,
      decorators = list(table = insert_rrow_decorator())
    ),
    tm_t_events(
      label = "tm_t_events",
      dataname = "ADAE",
      arm_var = choices_selected(c("ARM", "ARMCD"), "ARM"),
      llt = choices_selected(
        choices = variable_choices(ADAE, c("AETERM", "AEDECOD")),
        selected = c("AEDECOD")
      ),
      hlt = choices_selected(
        choices = variable_choices(ADAE, c("AEBODSYS", "AESOC")),
        selected = "AEBODSYS"
      ),
      add_total = TRUE,
      event_type = "adverse event",
      decorators = list(table = insert_rrow_decorator())
    ),
    tm_t_events_by_grade(
      label = "tm_t_events_by_grade",
      dataname = "ADAE",
      arm_var = choices_selected(c("ARM", "ARMCD"), "ARM"),
      llt = choices_selected(
        choices = variable_choices(ADAE, c("AETERM", "AEDECOD")),
        selected = c("AEDECOD")
      ),
      hlt = choices_selected(
        choices = variable_choices(ADAE, c("AEBODSYS", "AESOC")),
        selected = "AEBODSYS"
      ),
      grade = choices_selected(
        choices = variable_choices(ADAE, c("AETOXGR", "AESEV")),
        selected = "AETOXGR"
      ),
      decorators = list(table = insert_rrow_decorator())
    ),
    tm_t_events_patyear(
      label = "tm_t_events_patyear",
      dataname = "ADAETTE",
      arm_var = choices_selected(
        choices = variable_choices(ADSL, c("ARM", "ARMCD")),
        selected = "ARMCD"
      ),
      add_total = TRUE,
      events_var = choices_selected(
        choices = variable_choices(ADAETTE, "n_events"),
        selected = "n_events",
        fixed = TRUE
      ),
      paramcd = choices_selected(
        choices = value_choices(ADAETTE, "PARAMCD", "PARAM"),
        selected = "AETTE1"
      ),
      decorators = list(table = insert_rrow_decorator())
    ),
    tm_t_events_summary(
      label = "tm_t_events_summary",
      dataname = "ADAE",
      arm_var = choices_selected(
        choices = variable_choices("ADSL", c("ARM", "ARMCD")),
        selected = "ARM"
      ),
      flag_var_anl = choices_selected(
        choices = variable_choices("ADAE", data[[".ae_anl_vars"]]),
        selected = data[[".ae_anl_vars"]][1],
        keep_order = TRUE,
        fixed = FALSE
      ),
      flag_var_aesi = choices_selected(
        choices = variable_choices("ADAE", data[[".aesi_vars"]]),
        selected = data[[".aesi_vars"]][1],
        keep_order = TRUE,
        fixed = FALSE
      ),
      add_total = TRUE,
      decorators = list(table = insert_rrow_decorator())
    ),
    tm_t_exposure(
      label = "tm_t_exposure",
      dataname = "ADEX",
      paramcd = choices_selected(
        choices = value_choices(data[["ADEX"]], "PARAMCD", "PARAM"),
        selected = "TDURD"
      ),
      col_by_var = choices_selected(
        choices = variable_choices(data[["ADEX"]], subset = c("SEX", "ARM")),
        selected = "SEX"
      ),
      row_by_var = choices_selected(
        choices = variable_choices(data[["ADEX"]], subset = c("RACE", "REGION1", "STRATA1", "SEX")),
        selected = "RACE"
      ),
      parcat = choices_selected(
        choices = value_choices(data[["ADEX"]], "PARCAT2"),
        selected = "Drug A"
      ),
      add_total = FALSE,
      decorators = list(table = insert_rrow_decorator())
    ),
    tm_t_logistic(
      label = "tm_t_logistic",
      dataname = "ADRS",
      arm_var = choices_selected(
        choices = variable_choices(ADRS, c("ARM", "ARMCD")),
        selected = "ARM"
      ),
      arm_ref_comp = arm_ref_comp,
      paramcd = choices_selected(
        choices = value_choices(ADRS, "PARAMCD", "PARAM"),
        selected = "BESRSPI"
      ),
      cov_var = choices_selected(
        choices = c("SEX", "AGE", "BMRKR1", "BMRKR2"),
        selected = "SEX"
      ),
      decorators = list(table = insert_rrow_decorator())
    ),
    tm_t_mult_events(
      label = "tm_t_mult_events",
      dataname = "ADCM",
      arm_var = choices_selected(c("ARM", "ARMCD"), "ARM"),
      seq_var = choices_selected("CMSEQ", selected = "CMSEQ", fixed = TRUE),
      hlt = choices_selected(
        choices = variable_choices(ADCM, c("ATC1", "ATC2", "ATC3", "ATC4")),
        selected = c("ATC1", "ATC2", "ATC3", "ATC4")
      ),
      llt = choices_selected(choices = variable_choices(ADCM, c("CMDECOD")), selected = c("CMDECOD")),
      add_total = TRUE,
      event_type = "treatment",
      decorators = list(table = insert_rrow_decorator())
    ),
    tm_t_pp_basic_info(
      label = "tm_t_pp_basic_info",
      dataname = "ADSL",
      patient_col = "USUBJID",
      vars = choices_selected(choices = variable_choices(ADSL), selected = c("ARM", "AGE", "SEX", "COUNTRY", "RACE", "EOSSTT")),
      decorators = list(
        table = rlisting_footer(.var_to_replace = "table")
      )
    ),
    tm_t_pp_laboratory(
      label = "tm_t_pp_laboratory",
      dataname = "ADLB",
      patient_col = "USUBJID",
      paramcd = choices_selected(
        choices = variable_choices(ADLB, "PARAMCD"),
        selected = "PARAMCD"
      ),
      param = choices_selected(
        choices = variable_choices(ADLB, "PARAM"),
        selected = "PARAM"
      ),
      timepoints = choices_selected(
        choices = variable_choices(ADLB, "ADY"),
        selected = "ADY"
      ),
      anrind = choices_selected(
        choices = variable_choices(ADLB, "ANRIND"),
        selected = "ANRIND"
      ),
      aval_var = choices_selected(
        choices = variable_choices(ADLB, "AVAL"),
        selected = "AVAL"
      ),
      avalu_var = choices_selected(
        choices = variable_choices(ADLB, "AVALU"),
        selected = "AVALU"
      ),
      decorators = list(table = rlisting_footer(.var_to_replace = "table"))
    ),
    tm_t_pp_medical_history(
      label = "tm_t_pp_medical_history",
      dataname = "ADMH",
      parentname = "ADSL",
      patient_col = "USUBJID",
      mhterm = choices_selected(
        choices = variable_choices(ADMH, c("MHTERM")),
        selected = "MHTERM"
      ),
      mhbodsys = choices_selected(
        choices = variable_choices(ADMH, "MHBODSYS"),
        selected = "MHBODSYS"
      ),
      mhdistat = choices_selected(
        choices = variable_choices(ADMH, "MHDISTAT"),
        selected = "MHDISTAT"
      ),
      decorators = list(table = insert_rrow_decorator())
    ),
    tm_t_pp_prior_medication(
      label = "tm_t_pp_prior_medication",
      dataname = "ADCM",
      parentname = "ADSL",
      patient_col = "USUBJID",
      atirel = choices_selected(
        choices = variable_choices(ADCM, "ATIREL"),
        selected = "ATIREL"
      ),
      cmdecod = choices_selected(
        choices = variable_choices(ADCM, "CMDECOD"),
        selected = "CMDECOD"
      ),
      cmindc = choices_selected(
        choices = variable_choices(ADCM, "CMINDC"),
        selected = "CMINDC"
      ),
      cmstdy = choices_selected(
        choices = variable_choices(ADCM, "ASTDY"),
        selected = "ASTDY"
      ),
      decorators = list(
        table = rlisting_footer(.var_to_replace = "table")
      )
    ),
    tm_t_shift_by_arm(
      label = "tm_t_shift_by_arm",
      dataname = "ADEG",
      arm_var = choices_selected(
        variable_choices(ADSL, subset = c("ARM", "ARMCD")),
        selected = "ARM"
      ),
      paramcd = choices_selected(
        value_choices(ADEG, "PARAMCD"),
        selected = "HR"
      ),
      visit_var = choices_selected(
        value_choices(ADEG, "AVISIT"),
        selected = "POST-BASELINE MINIMUM"
      ),
      aval_var = choices_selected(
        variable_choices(ADEG, subset = "ANRIND"),
        selected = "ANRIND",
        fixed = TRUE
      ),
      baseline_var = choices_selected(
        variable_choices(ADEG, subset = "BNRIND"),
        selected = "BNRIND",
        fixed = TRUE
      ),
      useNA = "ifany",
      decorators = list(table = insert_rrow_decorator())
    ),
    tm_t_shift_by_arm_by_worst(
      label = "tm_t_shift_by_arm_by_worst",
      dataname = "ADEG",
      arm_var = choices_selected(
        variable_choices(ADSL, subset = c("ARM", "ARMCD")),
        selected = "ARM"
      ),
      paramcd = choices_selected(
        value_choices(ADEG, "PARAMCD"),
        selected = "ECGINTP"
      ),
      worst_flag_var = choices_selected(
        variable_choices(ADEG, c("WORS02FL", "WORS01FL")),
        selected = "WORS02FL"
      ),
      worst_flag = choices_selected(
        value_choices(ADEG, "WORS02FL"),
        selected = "Y",
        fixed = TRUE
      ),
      aval_var = choices_selected(
        variable_choices(ADEG, c("AVALC", "ANRIND")),
        selected = "AVALC"
      ),
      baseline_var = choices_selected(
        variable_choices(ADEG, c("BASEC", "BNRIND")),
        selected = "BASEC"
      ),
      useNA = "ifany",
      decorators = list(table = insert_rrow_decorator())
    ),
    tm_t_shift_by_grade(
      label = "tm_t_shift_by_grade",
      dataname = "ADLB",
      arm_var = choices_selected(
        choices = variable_choices(ADSL, subset = c("ARM", "ARMCD")),
        selected = "ARM"
      ),
      paramcd = choices_selected(
        choices = value_choices(ADLB, "PARAMCD", "PARAM"),
        selected = "ALT"
      ),
      worst_flag_var = choices_selected(
        choices = variable_choices(ADLB, subset = c("WGRLOVFL", "WGRLOFL", "WGRHIVFL", "WGRHIFL")),
        selected = c("WGRLOVFL")
      ),
      worst_flag_indicator = choices_selected(
        value_choices(ADLB, "WGRLOVFL"),
        selected = "Y", fixed = TRUE
      ),
      anl_toxgrade_var = choices_selected(
        choices = variable_choices(ADLB, subset = c("ATOXGR")),
        selected = c("ATOXGR"),
        fixed = TRUE
      ),
      base_toxgrade_var = choices_selected(
        choices = variable_choices(ADLB, subset = c("BTOXGR")),
        selected = c("BTOXGR"),
        fixed = TRUE
      ),
      add_total = FALSE,
      decorators = list(table = insert_rrow_decorator())
    ),
    tm_t_smq(
      label = "tm_t_smq",
      dataname = "ADAE",
      arm_var = choices_selected(
        choices = variable_choices(data[["ADSL"]], subset = c("ARM", "SEX")),
        selected = "ARM"
      ),
      add_total = FALSE,
      baskets = data[[".cs_baskets"]],
      scopes = data[[".cs_scopes"]],
      llt = choices_selected(
        choices = variable_choices(data[["ADAE"]], subset = c("AEDECOD")),
        selected = "AEDECOD"
      ),
      decorators = list(table = insert_rrow_decorator())
    ),
    tm_t_summary(
      label = "tm_t_summary",
      dataname = "ADSL",
      arm_var = choices_selected(c("ARM", "ARMCD"), "ARM"),
      add_total = TRUE,
      summarize_vars = choices_selected(
        c("SEX", "RACE", "BMRKR2", "EOSDY", "DCSREAS", "AGE"),
        c("SEX", "RACE")
      ),
      useNA = "ifany",
      decorators = list(table = insert_rrow_decorator())
    ),
    tm_t_summary_by(
      label = "tm_t_summary_by",
      dataname = "ADLB",
      arm_var = choices_selected(
        choices = variable_choices(ADSL, c("ARM", "ARMCD")),
        selected = "ARM"
      ),
      add_total = TRUE,
      by_vars = choices_selected(
        choices = variable_choices(ADLB, c("PARAM", "AVISIT")),
        selected = c("AVISIT")
      ),
      summarize_vars = choices_selected(
        choices = variable_choices(ADLB, c("AVAL", "CHG")),
        selected = c("AVAL")
      ),
      useNA = "ifany",
      paramcd = choices_selected(
        choices = value_choices(ADLB, "PARAMCD", "PARAM"),
        selected = "ALT"
      ),
      decorators = list(table = insert_rrow_decorator())
    ),
    tm_t_tte(
      label = "tm_t_tte",
      dataname = "ADTTE",
      arm_var = choices_selected(variable_choices(ADSL, c("ARM", "ARMCD", "ACTARMCD")), "ARM"),
      arm_ref_comp = arm_ref_comp,
      paramcd = choices_selected(value_choices(ADTTE, "PARAMCD", "PARAM"), "OS"),
      strata_var = choices_selected(variable_choices(ADSL, c("SEX", "BMRKR2")), "SEX"),
      time_points = choices_selected(c(182, 243), 182),
      event_desc_var = choices_selected(variable_choices(ADTTE, "EVNTDESC"), "EVNTDESC", fixed = TRUE),
      decorators = list(table = insert_rrow_decorator())
    )
  )
) |> shiny::runApp()

R/tm_a_gee.R

Signed-off-by: Vedha Viyash <[email protected]>

vedhav · 2025-02-21T05:44:02Z

Here is the status of decorators QC:

✅ tm_a_gee - table (ElementaryTable)
✅ tm_a_mmrm - lsmeans_plot (ggplot2), diagnostic_plot (TableTree), lsmeans_table (TableTree), covariance_table (TableTree), fixed_effects_table (TableTree), diagnostic_table (TableTree)
✅ tm_g_barchart_simple - plot (ggplot2)
✅ tm_g_ci - plot (ggplot2)
❌ tm_g_forest_rsp - plot (ggplot2) [plot decorator does not seem to work]
❌ tm_g_forest_tte - plot (ggplot2) [plot decorator does not seem to work]
✅ tm_g_ipp - plot (ggplot2)
✅ tm_g_km - plot (ggplot2)
✅ tm_g_lineplot - plot (ggplot2)
❌ tm_g_pp_adverse_events - plot (ggplot2), table (listing_df) [change to DT]
✅ tm_g_pp_patient_timeline - plot (ggplot2)
❌ tm_g_pp_therapy - plot (ggplot2), table (listing_df) [change to DT]
✅ tm_g_pp_vitals - plot (ggplot2)
✅ tm_t_abnormality - table (ElementaryTable)
✅ tm_t_abnormality_by_worst_grade - table (ElementaryTable)
✅ tm_t_ancova - table (ElementaryTable)
✅ tm_t_binary_outcome - table (TableTree)
✅ tm_t_coxreg - table (TableTree)
✅ tm_t_events - table (TableTree)
✅ tm_t_events_by_grade - table (TableTree)
✅ tm_t_events_patyear - table (TableTree)
✅ tm_t_events_summary - table (ableTree)
✅ tm_t_exposure - table (TableTree)
✅ tm_t_logistic - table (ElementaryTable)
✅ tm_t_mult_events - table (TableTree)
❌ tm_t_pp_basic_info - table (listing_df) [change to DT]
❌ tm_t_pp_laboratory - table (listing_df) [change to DT]
✅ tm_t_pp_medical_history - table (TableTree)
❌ tm_t_pp_prior_medication - table (listing_df) [change to DT]
✅ tm_t_shift_by_arm - table (TableTree)
✅ tm_t_shift_by_arm_by_worst - table (TableTree)
✅ tm_t_shift_by_grade - table (TableTree)
✅ tm_t_smq - table (TableTree)
✅ tm_t_summary - table (TableTree)
✅ tm_t_summary_by - table (TableTree)
✅ tm_t_tte - table (TableTree)

vedhav · 2025-02-21T07:01:16Z

I wanted to verify the class of the output objects and here's the inspection of all the output object class:
Note this was fixed in commit 8917513

Module	Output	Class	Doc Class	Documented properly
tm_a_gee	table	ElementaryTable	ElementaryTable	✅
tm_a_mmrm	lsmeans_table	TableTree	TableTree	✅
tm_a_mmrm	lsmeans_plot	ggplot	ggplot2	❌
tm_a_mmrm	covariance_table	ElementaryTable	TableTree	❌
tm_a_mmrm	fixed_effects_table	ElementaryTable	TableTree	❌
tm_a_mmrm	diagnostic_table	ElementaryTable	TableTree	❌
tm_a_mmrm	diagnostic_plot	ggplot	TableTree	❌
tm_g_barchart_simple	plot	ggplot	ggplot2	❌
tm_g_ci	plot	ggplot	ggplot2	❌
tm_g_forest_rsp	plot	ggplot	ggplot2	❌
tm_g_forest_tte	plot	ggplot	ggplot2	❌
tm_g_ipp	plot	ggplot	ggplot2	❌
tm_g_km	plot	ggplot	ggplot2	❌
tm_g_lineplot	plot	ggplot	ggplot2	❌
tm_g_pp_adverse_events	table	listing_df	listing_df	✅
tm_g_pp_adverse_events	plot	ggplot	ggplot2	❌
tm_g_pp_patient_timeline	plot	ggplot	ggplot2	❌
tm_g_pp_therapy	plot	ggplot	ggplot2	❌
tm_g_pp_vitals	plot	ggplot	ggplot2	❌
tm_t_abnormality	table	TableTree	ElementaryTable	❌
tm_t_abnormality_by_worst_grade	table	TableTree	ElementaryTable	❌
tm_t_ancova	table	TableTree	ElementaryTable	❌
tm_t_binary_outcome	table	TableTree	TableTree	✅
tm_t_coxreg	table	TableTree	TableTree	✅
tm_t_events	table	TableTree	TableTree	✅
tm_t_events_by_grade	table	TableTree	TableTree	✅
tm_t_events_patyear	table	ElementaryTable	TableTree	❌
tm_t_events_summary	table	TableTree	TableTree	✅
tm_t_exposure	table	ElementaryTable	TableTree	❌
tm_t_logistic	table	TableTree	ElementaryTable	❌
tm_t_mult_events	table	TableTree	TableTree	✅
tm_t_pp_basic_info	table	listing_df	listing_df	✅
tm_t_pp_laboratory	table	listing_df	listing_df	✅
tm_t_pp_medical_history	table	TableTree	TableTree	✅
tm_t_pp_prior_medication	table	listing_df	listing_df	✅
tm_t_shift_by_arm	table	TableTree	TableTree	✅
tm_t_shift_by_arm_by_worst	table	TableTree	TableTree	✅
tm_t_shift_by_grade	table	TableTree	TableTree	✅
tm_t_smq	table	TableTree	TableTree	✅
tm_t_summary	table	TableTree	TableTree	✅
tm_t_summary_by	table	TableTree	TableTree	✅
tm_t_tte	table	TableTree	TableTree	✅

github-actions · 2025-02-21T07:10:35Z

Unit Tests Summary

1 files 70 suites 1h 12m 36s ⏱️
726 tests 614 ✅ 112 💤 0 ❌
1 986 runs 1 759 ✅ 227 💤 0 ❌

Results for commit c525a64.

♻️ This comment has been updated with latest results.

github-actions · 2025-02-21T07:10:39Z

Unit Test Performance Difference

Test suite performance difference

Test Suite	$Status$	Time on `main`	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
examples	💚	$5.74$	$-4.04$	$-1$	$+112$	$0$	$0$
shinytest2-tm_a_gee	💔	$133.04$	$+2.00$	$0$	$0$	$0$	$0$
shinytest2-tm_g_barchart_simple	💚	$234.84$	$-1.60$	$0$	$0$	$0$	$0$
shinytest2-tm_g_ci	💚	$108.65$	$-3.30$	$0$	$0$	$0$	$0$
shinytest2-tm_g_forest_rsp	💚	$186.98$	$-4.92$	$0$	$0$	$0$	$0$
shinytest2-tm_g_forest_tte	💚	$67.32$	$-2.51$	$0$	$0$	$0$	$0$
shinytest2-tm_g_ipp	💚	$116.57$	$-4.57$	$0$	$0$	$0$	$0$
shinytest2-tm_g_km	💚	$287.26$	$-6.72$	$0$	$0$	$0$	$0$
shinytest2-tm_g_lineplot	💚	$92.83$	$-2.50$	$0$	$0$	$0$	$0$
shinytest2-tm_g_pp_patient_timeline	💔	$249.71$	$+5.18$	$0$	$0$	$0$	$0$
shinytest2-tm_g_pp_therapy	💔	$200.37$	$+6.71$	$0$	$0$	$0$	$0$
shinytest2-tm_g_pp_vitals	💔	$89.43$	$+2.59$	$0$	$0$	$0$	$0$
shinytest2-tm_t_ancova	💔	$99.02$	$+2.67$	$0$	$0$	$0$	$0$
shinytest2-tm_t_events_by_grade	💔	$93.08$	$+1.58$	$0$	$0$	$0$	$0$
shinytest2-tm_t_events_patyear	💔	$52.84$	$+1.04$	$0$	$0$	$0$	$0$
shinytest2-tm_t_events_summary	💔	$69.33$	$+2.16$	$0$	$0$	$0$	$0$
shinytest2-tm_t_exposure	💔	$81.39$	$+1.96$	$0$	$0$	$0$	$0$
shinytest2-tm_t_logistic	💔	$61.69$	$+1.58$	$0$	$0$	$0$	$0$
shinytest2-tm_t_mult_events	💔	$59.85$	$+1.78$	$0$	$0$	$0$	$0$
shinytest2-tm_t_shift_by_arm	💚	$61.97$	$-1.28$	$0$	$0$	$0$	$0$
shinytest2-tm_t_shift_by_grade	💚	$82.96$	$-1.16$	$0$	$0$	$0$	$0$
shinytest2-tm_t_summary	💚	$42.63$	$-1.29$	$0$	$0$	$0$	$0$
shinytest2-tm_t_tte	💔	$69.47$	$+1.07$	$0$	$0$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on `main`	$±Time$	Test Case
examples	💀	$0.01$	$-0.01$	example_normalize_decorators.Rd

Results for commit ded09df

♻️ This comment has been updated with latest results.

…corator outputs

CI fix test Second Attempt https://github.com/insightsengineering/teal.modules.clinical/actions/runs/13453005605/job/37590862923

m7pr · 2025-02-21T09:21:16Z

Hey, reviewed the big app and confirm the status the Vedha reported.

However, there is one more that does not work

tm_g_pp_patient_timeline

R/tm_a_mmrm.R

vignettes/generate_tmc_test_data.Rmd

R/tm_t_exposure.R

m7pr

Left 1 suggestion, and 1 question and found 1 more module that doesn't work.
@vedhav this is excellent job.
Would you be able to create separate issues to fix each of the modules?

vedhav · 2025-02-21T11:19:44Z

Raised a PR #1350 to fix the modules that need to decorate DT objects

vedhav · 2025-02-21T11:41:08Z

Raised a PR #1351 to fix the forest plot modules. Those were the last failing modules. After this all module decorators will work as expected.

feat: remove default decorator and update docs

8d1083c

vedhav added the core label Feb 20, 2025

vedhav commented Feb 20, 2025

View reviewed changes

R/tm_a_gee.R Outdated Show resolved Hide resolved

Update R/tm_a_gee.R

2d60769

Signed-off-by: Vedha Viyash <[email protected]>

vedhav marked this pull request as ready for review February 21, 2025 05:44

vedhav and others added 2 commits February 21, 2025 11:14

Merge branch 'main' into decorator-vignettes@main

d48db0c

[skip roxygen] [skip vbump] Roxygen Man Pages Auto Update

d4d1f47

vedhav and others added 2 commits February 21, 2025 12:48

docs: make sure that we document the proper output object type for de…

8917513

…corator outputs

Fix lintr attempt (#1349)

2eec524

CI fix test Second Attempt https://github.com/insightsengineering/teal.modules.clinical/actions/runs/13453005605/job/37590862923

m7pr reviewed Feb 21, 2025

View reviewed changes

R/tm_a_mmrm.R Outdated Show resolved Hide resolved

llrs-roche reviewed Feb 21, 2025

View reviewed changes

vignettes/generate_tmc_test_data.Rmd Outdated Show resolved Hide resolved

m7pr reviewed Feb 21, 2025

View reviewed changes

R/tm_t_exposure.R Show resolved Hide resolved

review comments

c525a64

m7pr approved these changes Feb 21, 2025

View reviewed changes

vedhav enabled auto-merge (squash) February 21, 2025 09:37

vedhav merged commit 1a1bb10 into main Feb 21, 2025
28 checks passed

vedhav deleted the decorator-vignettes@main branch February 21, 2025 10:49

github-actions bot locked and limited conversation to collaborators Feb 21, 2025

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Remove default decorator and update docs #1348

Remove default decorator and update docs #1348

vedhav commented Feb 20, 2025 •

edited

Loading

vedhav commented Feb 21, 2025

vedhav commented Feb 21, 2025 •

edited

Loading

github-actions bot commented Feb 21, 2025 •

edited

Loading

github-actions bot commented Feb 21, 2025 •

edited

Loading

m7pr commented Feb 21, 2025

m7pr left a comment

vedhav commented Feb 21, 2025

vedhav commented Feb 21, 2025

Remove default decorator and update docs #1348

Remove default decorator and update docs #1348

Conversation

vedhav commented Feb 20, 2025 • edited Loading

vedhav commented Feb 21, 2025

vedhav commented Feb 21, 2025 • edited Loading

github-actions bot commented Feb 21, 2025 • edited Loading

Unit Tests Summary

github-actions bot commented Feb 21, 2025 • edited Loading

Unit Test Performance Difference

m7pr commented Feb 21, 2025

m7pr left a comment

Choose a reason for hiding this comment

vedhav commented Feb 21, 2025

vedhav commented Feb 21, 2025

vedhav commented Feb 20, 2025 •

edited

Loading

vedhav commented Feb 21, 2025 •

edited

Loading

github-actions bot commented Feb 21, 2025 •

edited

Loading

github-actions bot commented Feb 21, 2025 •

edited

Loading