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šŸ—ƒļø Decorators feature branch #1252

Merged
merged 94 commits into from
Dec 17, 2024
Merged

šŸ—ƒļø Decorators feature branch #1252

merged 94 commits into from
Dec 17, 2024

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averissimo
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@averissimo averissimo commented Nov 25, 2024 •
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Changes description

  • Adds internal wrapper around srv_decorate_data as utility to append code after decorator (such as print(plot))
  • Implements decorators in modules

Checklist for final review:

Double check check for every module:

  • Works with and without decorators
  • Has param and section in documentation
  • Code shows in "Show R code"
  • Reporter shows both the outputs and code

Todo on feature branch

Example apps

Not all modules could be used in same App as the examples' data are not 100% compatible. Hence the 2 apps below.

Example app 
# Load packages
pkgload::load_all("../teal.modules.clinical", export_all = FALSE)

# 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)))
    )
  )
}

# 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_
})
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_t_summary_by(
      label = "Summary by Row Groups Table",
      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(insert_rrow_decorator())
    ),
    # -------------------------------------------------------------------------
    tm_t_smq(
      label = "Adverse Events by SMQ Table",
      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(insert_rrow_decorator())
    ),
    # -------------------------------------------------------------------------
    tm_t_shift_by_grade(
      label = "Grade Laboratory Abnormality Table",
      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(insert_rrow_decorator())
    ),
    # -------------------------------------------------------------------------
    tm_t_shift_by_arm(
      label = "Shift by Arm Table",
      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(insert_rrow_decorator())
    ),
    # -------------------------------------------------------------------------
    tm_t_shift_by_arm_by_worst(
      label = "Shift by Arm Table (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(insert_rrow_decorator())
    ),
    # -------------------------------------------------------------------------
    tm_t_pp_prior_medication(
      label = "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_pp_medical_history(
      label = "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(insert_rrow_decorator())
    ),
    # -------------------------------------------------------------------------
    tm_t_pp_laboratory(
      label = "Vitals",
      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_basic_info(
      label = "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_mult_events(
      label = "Concomitant Medications by Medication Class and Preferred Name",
      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(insert_rrow_decorator())
    ),
    # -------------------------------------------------------------------------
    tm_t_logistic(
      label = "Logistic Regression",
      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(insert_rrow_decorator())
    ),
    # -------------------------------------------------------------------------
    tm_t_exposure(
      label = "Duration of Exposure Table",
      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(insert_rrow_decorator())
    ),
    # -------------------------------------------------------------------------
    tm_t_events(
      label = "Adverse Event Table",
      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(insert_rrow_decorator())
    ),
    # -------------------------------------------------------------------------
    tm_t_events_patyear(
      label = "AE Rate Adjusted for Patient-Years At Risk Table",
      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(insert_rrow_decorator())
    ),
    # -------------------------------------------------------------------------
    tm_t_events_by_grade(
      label = "Adverse Events by Grade Table",
      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(insert_rrow_decorator())
    ),
    # -------------------------------------------------------------------------
    tm_t_coxreg(
      label = "Cox Reg.",
      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(insert_rrow_decorator())
    ),
    # -------------------------------------------------------------------------
    tm_t_abnormality(
      label = "Abnormality Table",
      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(insert_rrow_decorator("I am a good new row"))
    ),
    # -------------------------------------------------------------------------
    tm_g_pp_vitals(
      label = "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_g_pp_adverse_events(
      label = "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_lineplot(
      label = "Line Plot",
      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(add_cowplot_title_decorator("plot"))
    ),
    # -------------------------------------------------------------------------
    tm_g_km(
      label = "Kaplan-Meier Plot",
      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_barchart_simple(
      label = "ADAE Analysis",
      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'))
    )
  )
) |> shiny::runApp()
Second App 
# Load packages
pkgload::load_all("../teal.modules.clinical", export_all = FALSE)
# Example below

insert_rrow_decorator <- function(default_caption = "I am a good new row", .var_to_replace = "table") {
  teal_transform_module(
    label = "New 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)))
    )
  )
}

# Preparation of the test case - use `EOSDY` and `DCSREAS` variables to demonstrate missing data.
data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl |>
    mutate(
      DTHFL = case_when(
        !is.na(DTHDT) ~ "Y",
        TRUE ~ ""
      ) %>% with_label("Subject Death Flag")
    )
  ADSL$EOSDY[1] <- NA_integer_

  ADAE <- tmc_ex_adae

  .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
  }

  #' Generating user-defined event flags.
  ADAE <- ADAE %>% .add_event_flags()

  .ae_anl_vars <- names(ADAE)[startsWith(names(ADAE), "TMPFL_")]
  .aesi_vars <- names(ADAE)[startsWith(names(ADAE), "TMP_")]

  ADTTE <- tmc_ex_adtte

  # responder

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


  ADQS <- tmc_ex_adqs %>%
    filter(ABLFL != "Y" & ABLFL2 != "Y") %>%
    filter(AVISIT %in% c("WEEK 1 DAY 8", "WEEK 2 DAY 15", "WEEK 3 DAY 22")) %>%
    mutate(
      AVISIT = as.factor(AVISIT),
      AVISITN = rank(AVISITN) %>%
        as.factor() %>%
        as.numeric() %>%
        as.factor() #' making consecutive numeric factor
    )
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

ADSL <- data[["ADSL"]]
ADRS <- data[["ADRS"]]

app <- init(
  data = data,
  modules = modules(
    # -------------------------------------------------------------------------
    tm_a_mmrm(
      label = "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("A", .var_to_replace = "lsmeans_table")
        , lsmeans_plot = add_title_decorator("B", .var_to_replace = "lsmeans_plot")
        , covariance_table = insert_rrow_decorator("C", .var_to_replace = "covariance_table")
        , fixed_effects_table = insert_rrow_decorator("D", .var_to_replace = "fixed_effects_table")
        , diagnostic_table = insert_rrow_decorator(.var_to_replace = "diagnostic_table")
        , diagnostic_plot = add_title_decorator(.var_to_replace = "diagnostic_plot")
      )
    ),
    # -------------------------------------------------------------------------
    tm_t_binary_outcome(
      label = "Responders",
      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(insert_rrow_decorator("I am a new row"))
    ),
    # -------------------------------------------------------------------------
    tm_t_events_summary(
      label = "Adverse 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(insert_rrow_decorator())
    ),
    # -------------------------------------------------------------------------
    tm_t_summary(
      label = "Demographic Table",
      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(insert_rrow_decorator())
    )
  )
) |> shiny::runApp()

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Unit Tests Summary

ā€‡ā€ˆā€‡ā€‡1 filesā€„ā€ƒā€‡ā€ˆā€‡70 suitesā€„ā€ƒā€‚1h 9m 32s ā±ļø
ā€‡ā€ˆ727 testsā€ƒā€‡ā€ˆ614 āœ…ā€ƒ113 šŸ’¤ā€ƒ0 āŒ
1ā€ˆ987 runsā€Šā€ƒ1ā€ˆ759 āœ…ā€ƒ228 šŸ’¤ā€ƒ0 āŒ

Results for commit fad76cd.

ā™»ļø This comment has been updated with latest results.

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Unit Test Performance Difference

Test Suite $Status$ Time on main $Ā±Time$ $Ā±Tests$ $Ā±Skipped$ $Ā±Failures$ $Ā±Errors$
shinytest2-tm_g_forest_rsp šŸ’” $172.55$ $+1.49$ $0$ $0$ $0$ $0$
shinytest2-tm_g_forest_tte šŸ’” $62.13$ $+1.10$ $0$ $0$ $0$ $0$
shinytest2-tm_g_ipp šŸ’” $106.20$ $+1.45$ $0$ $0$ $0$ $0$
shinytest2-tm_g_km šŸ’” $259.29$ $+8.39$ $0$ $0$ $0$ $0$
shinytest2-tm_g_lineplot šŸ’” $84.79$ $+6.52$ $0$ $0$ $0$ $0$
shinytest2-tm_g_pp_adverse_events šŸ’” $120.14$ $+9.05$ $0$ $0$ $0$ $0$
shinytest2-tm_g_pp_patient_timeline šŸ’” $241.61$ $+3.17$ $0$ $0$ $0$ $0$
shinytest2-tm_g_pp_therapy šŸ’” $193.67$ $+3.75$ $0$ $0$ $0$ $0$
shinytest2-tm_t_shift_by_grade šŸ’” $77.92$ $+1.24$ $0$ $0$ $0$ $0$
Additional test case details
Test Suite $Status$ Time on main $Ā±Time$ Test Case
examples šŸ‘¶ $+0.01$ example_normalize_decorators.Rd
examples šŸ‘¶ $+0.01$ example_select_decorators.Rd
examples šŸ‘¶ $+0.01$ example_srv_decorate_teal_data.Rd

Results for commit b8edb52

ā™»ļø This comment has been updated with latest results.

m7pr and others added 26 commits November 26, 2024 16:42
@m7pr
Merge branch 'main' into 1187_decorate_output@main
537b2c1
@m7pr
add decorators @param to standard template arguments
84a00fd
@m7pr
move decorators parameter to module templeate parameters
58e65bf
@m7pr
bring check_decorators from tmg
b684fa5
@dependabot-preview
[skip roxygen] [skip vbump] Roxygen Man Pages Auto Update
0805fa4
@m7pr
rename decorators to transformators in ui_decorate_teal_data
29f22c7
@m7pr
Merge branch '1187_decorate_output@main' of https://github.com/insighā€¦
3df00dc 
ā€¦tsengineering/teal.modules.clinical into 1187_decorate_output@main
@dependabot-preview
[skip roxygen] [skip vbump] Roxygen Man Pages Auto Update
dc682cd
@m7pr
introduce decorators for tm_g_pp_vitals
93c6af5
@m7pr
revert changes for vitals
1899063
@averissimo
fix: update wrapper to use 'inner' in srv_decorate_teal_data
64b9d1d
@m7pr
Merge branch 'main' into 1187_decorate_output@main
af2a623 
Signed-off-by: Marcin <[email protected]>
@dependabot-preview
[skip roxygen] [skip vbump] Roxygen Man Pages Auto Update
b033451
@m7pr
add normalize_decorators
064bcb2
@m7pr
fix normalize_decorators
a677777
@dependabot-preview
[skip roxygen] [skip vbump] Roxygen Man Pages Auto Update
1e9a78c
@m7pr
update utils from tmg
55cd3d3
@llrs-roche @m7pr
introduce decorators for tm_g_ci (#1265)
b565310 
Part of insightsengineering/teal#1371

WIP

<details>
<summary> Example with decorator </summary>

```r
devtools::load_all("../teal")
devtools::load_all(".")
library(nestcolor)

data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl
  ADLB <- tmc_ex_adlb
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

ADSL <- data[["ADSL"]]
ADLB <- data[["ADLB"]]

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)))
    )
  )
}



app <- init(
  data = data,
  modules = modules(
    tm_g_ci(
      label = "Confidence Interval Plot",
      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(caption_decorator(.var_to_replace = "plot"))
    )
  )
)
shinyApp(app$ui, app$server)
```

</details>

---------

Co-authored-by: Marcin <[email protected]>
Co-authored-by: m7pr <[email protected]>
@llrs-roche @m7pr
Introduce decorators to tm_g_forest_rsp (#1266)
2276fca 
Part of insightsengineering/teal#1371

This module also returns a plot from `cowplot`, and I am not sure if the
example I got works well (I am not that familiar with it).

<details>
<summary>Draft of an example</summary>

````r
devtools::load_all("../teal.reporter")
devtools::load_all("../teal")
devtools::load_all(".")
library(nestcolor)
library(dplyr)

caption_decorator <- function(annotation = "I am a good decorator", var_to_decorate = "plot") {
  teal_transform_module(
    label = "Annotation",
    ui = function(id) shiny::textInput(shiny::NS(id, "annotation"), "Annotation", value = annotation),
    server = make_teal_transform_server(
      substitute({
        var_to_decorate <- cowplot::add_sub(var_to_decorate, annotation)
      }, env = list(var_to_decorate = as.name(var_to_decorate)))
    )
  )
}

data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl
  ADRS <- tmc_ex_adrs %>%
    mutate(AVALC = d_onco_rsp_label(AVALC) %>%
             with_label("Character Result/Finding")) %>%
    filter(PARAMCD != "OVRINV" | AVISIT == "FOLLOW UP")
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

ADSL <- data[["ADSL"]]
ADRS <- data[["ADRS"]]

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

app <- init(
  data = data,
  modules = modules(
    tm_g_forest_rsp(
      label = "Forest Response",
      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(caption_decorator())
    )
  )
)
shinyApp(app$ui, app$server)


```

</details>

---------

Co-authored-by: Marcin <[email protected]>
Co-authored-by: m7pr <[email protected]>
@m7pr
introduce decorators for tm_g_forest_tte (#1264)
fd17aed 
Part of insightsengineering/teal#1371

<details><summary> Working Example </summary>

```r
devtools::load_all("../teal.reporter")
devtools::load_all("../teal")
devtools::load_all(".")
library(nestcolor)
library(dplyr)

caption_decorator <- function(annotation = "I am a good decorator", var_to_decorate = "plot") {
  teal_transform_module(
    label = "Annotation",
    ui = function(id) shiny::textInput(shiny::NS(id, "annotation"), "Annotation", value = annotation),
    server = make_teal_transform_server(
      substitute({
        var_to_decorate <- cowplot::add_sub(var_to_decorate, annotation)
      }, env = list(var_to_decorate = as.name(var_to_decorate)))
    )
  )
}

data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl
  ADTTE <- tmc_ex_adtte
  ADSL$RACE <- droplevels(ADSL$RACE) %>% with_label("Race")
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

ADSL <- data[["ADSL"]]
ADTTE <- data[["ADTTE"]]

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

app <- init(
  data = data,
  modules = modules(
    tm_g_forest_tte(
      label = "Forest Survival",
      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(caption_decorator())
    )
  )
)
shinyApp(app$ui, app$server)


```

</details>
@m7pr
introduce decorators for tm_a_gee (#1262)
4e747f9 
Part of insightsengineering/teal#1371

Alternative to
#1259

<details><summary> Working Example </summary>

```r
devtools::load_all("../teal.reporter")
devtools::load_all("../teal")
devtools::load_all(".")

insert_rrow_decorator <- function(default_caption = "I am a good new row", .var_to_replace = "table") {
  teal_transform_module(
    label = "New 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)))
    )
  )
}

library(dplyr)

data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl
  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)]

app <- init(
  data = data,
  modules = modules(
    tm_a_gee(
      label = "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(insert_rrow_decorator("Hello world", "table"))
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}


```

</details>
@m7pr
introduce decorators for tm_g_ipp (#1263)
fcc3682 
Part of insightsengineering/teal#1371

<details><summary> Working Example </summary>

```r

devtools::load_all("../teal")
devtools::load_all(".")

library(nestcolor)
library(dplyr)

data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl %>%
    slice(1:20) %>%
    df_explicit_na()
  ADLB <- tmc_ex_adlb %>%
    filter(USUBJID %in% ADSL$USUBJID) %>%
    df_explicit_na() %>%
    filter(AVISIT != "SCREENING")
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

ADSL <- data[["ADSL"]]
ADLB <- data[["ADLB"]]

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)))
    )
  )
}

app <- init(
  data = data,
  modules = modules(
    tm_g_ipp(
      label = "Individual Patient Plot",
      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(caption_decorator(.var_to_replace = "plot"))
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}

```

</details>
@dependabot-preview
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31fdab6
@llrs-roche @m7pr
introduce decorators to tm_g_pp_patient_timeline (#1270)
98520eb 
Part of insightsengineering/teal#1371

<details>
<summary>Example using cowplot::add_sub with ggplot2</summary>

```r
devtools::load_all("../teal.modules.general")
devtools::load_all("../teal.reporter")
devtools::load_all("../teal")
devtools::load_all(".")
library(nestcolor)
library(dplyr)

data <- teal_data()
data <- within(data, {
  ADAE <- tmc_ex_adae
  ADSL <- tmc_ex_adsl %>%
    filter(USUBJID %in% ADAE$USUBJID)
  ADCM <- tmc_ex_adcm %>%
    mutate(
      CMSTDY = case_when(
        CMCAT == "medcl B" ~ 20,
        CMCAT == "medcl C" ~ 150,
        TRUE ~ 1
      ) %>% with_label("Study Day of Start of Medication"),
      CMENDY = case_when(
        CMCAT == "medcl B" ~ 700,
        CMCAT == "medcl C" ~ 1000,
        TRUE ~ 500
      ) %>% with_label("Study Day of End of Medication"),
      CMASTDTM = ASTDTM,
      CMAENDTM = AENDTM
    )
})

join_keys(data) <- default_cdisc_join_keys[c("ADSL", "ADAE", "ADCM")]
adcm_keys <- c("STUDYID", "USUBJID", "ASTDTM", "CMSEQ", "ATC1", "ATC2", "ATC3", "ATC4")
join_keys(data)["ADCM", "ADCM"] <- adcm_keys
join_keys(data)["ADAE", "ADCM"] <- c("STUDYID", "USUBJID")


caption_decorator <- function(annotation = "I am a good decorator", var_to_decorate = "plot") {
  teal_transform_module(
    label = "Annotation",
    ui = function(id) shiny::textInput(shiny::NS(id, "annotation"), "Annotation", value = annotation),
    server = make_teal_transform_server(
      substitute({
        var_to_decorate <- cowplot::add_sub(var_to_decorate, annotation)
      }, env = list(var_to_decorate = as.name(var_to_decorate)))
    )
  )
}


app <- init(
  data = data,
  modules = modules(
    tm_g_pp_patient_timeline(
      label = "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(caption_decorator())
    )
  )
)
shinyApp(app$ui, app$server)
```

</details>

---------

Co-authored-by: m7pr <[email protected]>
@dependabot-preview
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5cf2166
@m7pr
introduce decorators for tm_g_pp_therapy (#1268)
f462d60 
Part of insightsengineering/teal#1371

<details><summary> Working Example </summary>

```r
devtools::load_all("../teal.reporter")
devtools::load_all("../teal")
devtools::load_all(".")

library(nestcolor)
library(dplyr)

data <- teal_data()
data <- within(data, {
  ADCM <- tmc_ex_adcm
  ADSL <- tmc_ex_adsl %>% filter(USUBJID %in% ADCM$USUBJID)
  ADCM$CMASTDTM <- ADCM$ASTDTM
  ADCM$CMAENDTM <- ADCM$AENDTM
})

join_keys(data) <- default_cdisc_join_keys[c("ADSL", "ADCM")]
adcm_keys <- c("STUDYID", "USUBJID", "ASTDTM", "CMSEQ", "ATC1", "ATC2", "ATC3", "ATC4")
join_keys(data)["ADCM", "ADCM"] <- adcm_keys

ADSL <- data[["ADSL"]]
ADCM <- data[["ADCM"]]

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)))
    )
  )
}

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)))
    )
  )
}

app <- init(
  data = data,
  modules = modules(
    tm_g_pp_therapy(
      label = "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'))
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}
```

</details>
averissimo and others added 5 commits December 10, 2024 17:41
@averissimo @m7pr
Adds decorators to tm_t_summary_by (#1294)
8986e27 
Part of insightsengineering/teal#1371

<details>
<summary>Working example</summary>

```r
pkgload::load_all("../teal.modules.clinical", export_all = FALSE)
# Example below

insert_rrow_decorator <- function(default_caption = "I am a good new row", .var_to_replace = "table") {
  teal_transform_module(
    label = "New 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)))
    )
  )
}

data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl
  ADLB <- tmc_ex_adlb
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

ADSL <- data[["ADSL"]]
ADLB <- data[["ADLB"]]

app <- init(
  data = data,
  modules = modules(
    tm_t_summary_by(
      label = "Summary by Row Groups Table",
      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(insert_rrow_decorator())
    )
  )
) |> shiny::runApp()
```

</details>

---------

Co-authored-by: Marcin <[email protected]>
@averissimo
Adds decorators to tm_t_shift_by_arm (#1287)
772c14b 
Part of insightsengineering/teal#1371

<details>
<summary>Working example</summary>

```r
pkgload::load_all("../teal.modules.clinical", export_all = FALSE)
# Example below

insert_rrow_decorator <- function(default_caption = "I am a good new row", .var_to_replace = "table") {
  teal_transform_module(
    label = "New 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)))
    )
  )
}

data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl
  ADEG <- tmc_ex_adeg
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

ADSL <- data[["ADSL"]]
ADEG <- data[["ADEG"]]

init(
  data = data,
  modules = modules(
    tm_t_shift_by_arm(
      label = "Shift by Arm Table",
      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(insert_rrow_decorator())
    )
  )
) |> shiny::runApp()
```

</details>
@averissimo @m7pr
Adds decorators to tm_t_shift_by_arm_by_worst (#1286)
582ceb3 
Part of insightsengineering/teal#1371

<details>
<summary>Working example</summary>

```r
pkgload::load_all("../teal.modules.clinical", export_all = FALSE)
# Example below

insert_rrow_decorator <- function(default_caption = "I am a good new row", .var_to_replace = "table") {
  teal_transform_module(
    label = "New 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)))
    )
  )
}

data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl
  ADEG <- tmc_ex_adeg
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

ADSL <- data[["ADSL"]]
ADEG <- data[["ADEG"]]

init(
  data = data,
  modules = modules(
    tm_t_shift_by_arm_by_worst(
      label = "Shift by Arm Table",
      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(insert_rrow_decorator())
    )
  )
) |> shiny::runApp()
```

</details>

---------

Co-authored-by: Marcin <[email protected]>
@averissimo
feat: pass qenv.error to module when template code fails
66e7b36
@averissimo
Merge branch 'main' into 1187_decorate_output@main
d403e95
averissimo
averissimo commented Dec 10, 2024
View reviewed changes
R/utils.R Show resolved Hide resolved
llrs-roche and others added 13 commits December 11, 2024 10:01
@llrs-roche @averissimo
Introduce decorators for tm_t_exposure (#1279)
d1d8df8 
Part of insightsengineering/teal#1371

<details>
<summary>Example with decorator</summary>

```r
devtools::load_all("../teal")
devtools::load_all("../tern")
devtools::load_all(".")

insert_rrow_decorator <- function(default_caption = "I am a good new row", .var_to_replace = "table") {
  teal_transform_module(
    label = "New 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)))
    )
  )
}
library(dplyr)

data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl
  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
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

app <- init(
  data = data,
  modules = modules(
    tm_t_exposure(
      label = "Duration of Exposure Table",
      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(insert_rrow_decorator())
    )
  ),
  filter = teal_slices(teal_slice("ADSL", "SAFFL", selected = "Y"))
)
shinyApp(app$ui, app$server)
```

</details>

Note: I placed the decorated right above some options to add additional
columns and rows.
Perhaps we need to review where to place it. I would group these three
options in a single panel

---------

Signed-off-by: LluĆ­s Revilla <[email protected]>
Co-authored-by: AndrĆ© VerĆ­ssimo <[email protected]>
@dependabot-preview
[skip roxygen] [skip vbump] Roxygen Man Pages Auto Update
c146b11
@averissimo
Adds decorators to tm_t_pp_laboratory (#1291)
83d9fb0 
Part of insightsengineering/teal#1371

<details>
<summary>Working example</summary>

```r
pkgload::load_all("../teal.modules.clinical", export_all = FALSE)
# Example below

rlisting_footer <- function(default_footer = "I am a good footer", .var_to_replace = "table") {
  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)))
    )
  )
}

dt_decorator <- function(.color1 = "#f9f9f9", .color2 = "#f0f0f0", .var_to_replace = "table") {
  teal_transform_module(
    label = "Table color",
    ui = function(id) {
      selectInput(
        NS(id, "style"),
        "Table Style",
        choices = c("Default", "Color1", "Color2"),
        selected = "Default"
      )
    },
    server = function(id, data) {
      moduleServer(id, function(input, output, session) {
        logger::log_info("šŸ”µ Table row color called to action!", namespace = "teal.modules.general")
        reactive({
          req(data(), input$style)
          logger::log_info("changing the Table row color '{input$style}'", namespace = "teal.modules.general")
          teal.code::eval_code(data(), substitute({
            .var_to_replace <- switch(
              style,
              "Color1" = DT::formatStyle(
                .var_to_replace,
                columns = attr(.var_to_replace$x, "colnames")[-1],
                target = "row",
                backgroundColor = .color1
              ),
              "Color2" = DT::formatStyle(
                .var_to_replace,
                columns = attr(.var_to_replace$x, "colnames")[-1],
                target = "row",
                backgroundColor = .color2
              ),
              .var_to_replace
            )
          }, env = list(
            style = input$style,
            .var_to_replace = as.name(.var_to_replace),
            .color1 = .color1,
            .color2 = .color2
          )))
        })
      })
    }
  )
}

data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl
  ADLB <- tmc_ex_adlb
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

ADSL <- data[["ADSL"]]
ADLB <- data[["ADLB"]]

init(
  data = data,
  modules = modules(
    tm_t_pp_laboratory(
      label = "Vitals",
      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_listing = rlisting_footer()
      )
    )
  )
) |> shiny::runApp()
```

</details>
@averissimo
Adds decorators to tm_t_pp_basic_info (#1282)
95f11f3 
Part of insightsengineering/teal#1371

<details>
<summary>Working example</summary>

```r
# Load packages
pkgload::load_all("../teal.modules.clinical", export_all = FALSE)
# Example below

insert_rlisting_footer_decorator <- function(default_caption = "I am a good new footer", .var_to_replace = "table") {
  teal_transform_module(
    label = "New row",
    ui = function(id) shiny::textInput(shiny::NS(id, "new_footer"), "New footer", value = default_caption),
    server = make_teal_transform_server(
      substitute({
        rlistings::main_footer(.var_to_replace) <- new_footer
      }, env = list(.var_to_replace = as.name(.var_to_replace)))
    )
  )
}

data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

ADSL <- data[["ADSL"]]

init(
  data = data,
  modules = modules(
    tm_t_pp_basic_info(
      label = "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 = insert_rlisting_footer_decorator(.var_to_replace = "table")
      )
    )
  )
) |> shiny::runApp()
```

</details>
@averissimo
Adds decorators to tm_t_pp_prior_medication (#1288)
b85523c 
Part of insightsengineering/teal#1371

<details>
<summary>Working example</summary>

```r
# Load packages
pkgload::load_all("../teal.modules.clinical", export_all = FALSE)
# Example below

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)))
    )
  )
}

library(dplyr)
data <- teal_data()
data <- within(data, {
  ADCM <- tmc_ex_adcm
  ADSL <- tmc_ex_adsl %>% filter(USUBJID %in% ADCM$USUBJID)
  ADCM$CMASTDTM <- ADCM$ASTDTM
  ADCM$CMAENDTM <- ADCM$AENDTM
})
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

ADSL <- data[["ADSL"]]
ADCM <- data[["ADCM"]]

init(
  data = data,
  modules = modules(
    tm_t_pp_prior_medication(
      label = "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")
      )
    )
  )
) |> shiny::runApp()
```

</details>
@llrs-roche @averissimo @m7pr
Introduce decorators for tm_t events by grade (#1276)
eb42bae 
Part of insightsengineering/teal#1371

<details>
<summary>Example with decorators</summary>

```r
load_all("../teal")
load_all(".")
library(dplyr)

data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl
  .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
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

ADSL <- data[["ADSL"]]
ADAE <- data[["ADAE"]]

insert_rrow_decorator <- function(default_caption = "I am a good new row", .var_to_replace = "table") {
  teal_transform_module(
    label = "New 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)))
    )
  )
}

app <- init(
  data = data,
  modules = modules(
    tm_t_events_by_grade(
      label = "Adverse Events by Grade Table",
      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(insert_rrow_decorator())
    )
  )
)
shinyApp(app$ui, app$server)

```

</details>

---------

Signed-off-by: LluĆ­s Revilla <[email protected]>
Co-authored-by: AndrĆ© VerĆ­ssimo <[email protected]>
Co-authored-by: Marcin <[email protected]>
@github-actions
[skip roxygen] [skip vbump] Roxygen Man Pages Auto Update
b2919f6
@averissimo
docs: remove roxygen inline call
5c90ece
@averissimo
Merge branch 'main' into 1187_decorate_output@main
274d2b6
@github-actions
[skip roxygen] [skip vbump] Roxygen Man Pages Auto Update
f439cd4
@averissimo
fix: linter error
00c8c0b
@averissimo @m7pr
Adds decorators to tm_a_mmrm (#1300)
a855989 
Part of insightsengineering/teal#1371

<details>
<summary>Working example</summary>

```r
# Load packages
pkgload::load_all("../teal.modules.clinical", export_all = FALSE)
# Example below

insert_rrow_decorator <- function(default_caption = "I am a good new row", .var_to_replace = "table") {
  teal_transform_module(
    label = "New 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 = "Theme",
    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))
      )
    )
  )
}

library(dplyr)

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

data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl
  ADQS <- tmc_ex_adqs %>%
    filter(ABLFL != "Y" & ABLFL2 != "Y") %>%
    filter(AVISIT %in% c("WEEK 1 DAY 8", "WEEK 2 DAY 15", "WEEK 3 DAY 22")) %>%
    mutate(
      AVISIT = as.factor(AVISIT),
      AVISITN = rank(AVISITN) %>%
        as.factor() %>%
        as.numeric() %>%
        as.factor() #' making consecutive numeric factor
    )
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

init(
  data = data,
  modules = modules(
    tm_a_mmrm(
      label = "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("A", .var_to_replace = "lsmeans_table")
        , lsmeans_plot = add_title_decorator("B", .var_to_replace = "lsmeans_plot")
        , covariance_table = insert_rrow_decorator("C", .var_to_replace = "covariance_table")
        , fixed_effects_table = insert_rrow_decorator("D", .var_to_replace = "fixed_effects_table")
        , diagnostic_table = insert_rrow_decorator(.var_to_replace = "diagnostic_table")
        , diagnostic_plot = add_title_decorator(.var_to_replace = "diagnostic_plot")
      )
    )
  )
) |> shiny::runApp()
```

</details>

---------

Co-authored-by: Marcin <[email protected]>
@averissimo
fix: tm_t_coxreg bug
0a06fbb
@m7pr
Copy link
Contributor

m7pr commented Dec 13, 2024

Hey @averissimo 16 tests are failiing, let me know if you need help fixing those!

@averissimo
fix: adverse events error
6d4ce5b
@averissimo
Uses same code for source code generation in modules (#1301)
8a9edd2 
Part of insightsengineering/teal#1371

### Example app with all modules / decorators

<details>
<summary>Example app</summary>

```r
# Load packages
pkgload::load_all("../teal.modules.clinical", export_all = FALSE)

# 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)))
    )
  )
}

# 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_
})
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_t_summary_by(
      label = "Summary by Row Groups Table",
      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(insert_rrow_decorator())
    ),
    # -------------------------------------------------------------------------
    tm_t_smq(
      label = "Adverse Events by SMQ Table",
      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(insert_rrow_decorator())
    ),
    # -------------------------------------------------------------------------
    tm_t_shift_by_grade(
      label = "Grade Laboratory Abnormality Table",
      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(insert_rrow_decorator())
    ),
    # -------------------------------------------------------------------------
    tm_t_shift_by_arm(
      label = "Shift by Arm Table",
      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(insert_rrow_decorator())
    ),
    # -------------------------------------------------------------------------
    tm_t_shift_by_arm_by_worst(
      label = "Shift by Arm Table (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(insert_rrow_decorator())
    ),
    # -------------------------------------------------------------------------
    tm_t_pp_prior_medication(
      label = "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_pp_medical_history(
      label = "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(insert_rrow_decorator())
    ),
    # -------------------------------------------------------------------------
    tm_t_pp_laboratory(
      label = "Vitals",
      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_basic_info(
      label = "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_mult_events(
      label = "Concomitant Medications by Medication Class and Preferred Name",
      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(insert_rrow_decorator())
    ),
    # -------------------------------------------------------------------------
    tm_t_logistic(
      label = "Logistic Regression",
      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(insert_rrow_decorator())
    ),
    # -------------------------------------------------------------------------
    tm_t_exposure(
      label = "Duration of Exposure Table",
      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(insert_rrow_decorator())
    ),
    # -------------------------------------------------------------------------
    tm_t_events(
      label = "Adverse Event Table",
      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(insert_rrow_decorator())
    ),
    # -------------------------------------------------------------------------
    tm_t_events_patyear(
      label = "AE Rate Adjusted for Patient-Years At Risk Table",
      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(insert_rrow_decorator())
    ),
    # -------------------------------------------------------------------------
    tm_t_events_by_grade(
      label = "Adverse Events by Grade Table",
      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(insert_rrow_decorator())
    ),
    # -------------------------------------------------------------------------
    tm_t_coxreg(
      label = "Cox Reg.",
      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(insert_rrow_decorator())
    ),
    # -------------------------------------------------------------------------
    tm_t_abnormality(
      label = "Abnormality Table",
      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(insert_rrow_decorator("I am a good new row"))
    ),
    # -------------------------------------------------------------------------
    tm_g_pp_vitals(
      label = "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_g_pp_adverse_events(
      label = "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_lineplot(
      label = "Line Plot",
      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(add_cowplot_title_decorator("plot"))
    ),
    # -------------------------------------------------------------------------
    tm_g_km(
      label = "Kaplan-Meier Plot",
      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_barchart_simple(
      label = "ADAE Analysis",
      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'))
    )
  )
) |> shiny::runApp()

```

</details>    

<details>
<summary>Second App</summary>

```r
# Load packages
pkgload::load_all("../teal.modules.clinical", export_all = FALSE)
# Example below

insert_rrow_decorator <- function(default_caption = "I am a good new row", .var_to_replace = "table") {
  teal_transform_module(
    label = "New 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)))
    )
  )
}

# Preparation of the test case - use `EOSDY` and `DCSREAS` variables to demonstrate missing data.
data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl |>
    mutate(
      DTHFL = case_when(
        !is.na(DTHDT) ~ "Y",
        TRUE ~ ""
      ) %>% with_label("Subject Death Flag")
    )
  ADSL$EOSDY[1] <- NA_integer_

  ADAE <- tmc_ex_adae

  .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
  }

  #' Generating user-defined event flags.
  ADAE <- ADAE %>% .add_event_flags()

  .ae_anl_vars <- names(ADAE)[startsWith(names(ADAE), "TMPFL_")]
  .aesi_vars <- names(ADAE)[startsWith(names(ADAE), "TMP_")]

  ADTTE <- tmc_ex_adtte

  # responder

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


  ADQS <- tmc_ex_adqs %>%
    filter(ABLFL != "Y" & ABLFL2 != "Y") %>%
    filter(AVISIT %in% c("WEEK 1 DAY 8", "WEEK 2 DAY 15", "WEEK 3 DAY 22")) %>%
    mutate(
      AVISIT = as.factor(AVISIT),
      AVISITN = rank(AVISITN) %>%
        as.factor() %>%
        as.numeric() %>%
        as.factor() #' making consecutive numeric factor
    )
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

ADSL <- data[["ADSL"]]
ADRS <- data[["ADRS"]]

app <- init(
  data = data,
  modules = modules(
    # -------------------------------------------------------------------------
    tm_a_mmrm(
      label = "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("A", .var_to_replace = "lsmeans_table")
        , lsmeans_plot = add_title_decorator("B", .var_to_replace = "lsmeans_plot")
        , covariance_table = insert_rrow_decorator("C", .var_to_replace = "covariance_table")
        , fixed_effects_table = insert_rrow_decorator("D", .var_to_replace = "fixed_effects_table")
        , diagnostic_table = insert_rrow_decorator(.var_to_replace = "diagnostic_table")
        , diagnostic_plot = add_title_decorator(.var_to_replace = "diagnostic_plot")
      )
    ),
    # -------------------------------------------------------------------------
    tm_t_binary_outcome(
      label = "Responders",
      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(insert_rrow_decorator("I am a new row"))
    ),
    # -------------------------------------------------------------------------
    tm_t_events_summary(
      label = "Adverse 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(insert_rrow_decorator())
    ),
    # -------------------------------------------------------------------------
    tm_t_summary(
      label = "Demographic Table",
      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(insert_rrow_decorator())
    )
  )
) |> shiny::runApp()
```

</details>
@averissimo
fix: remove rlang usage
1db24ad
@averissimo
Decorators: Accepts new snapshot from testthat::test() (#1304)
19e8752 
# Pull Request

<!--- Replace `#nnn` with your issue link for reference. -->

Part of
insightsengineering/teal#1371 (comment)

### Changes description

- Tracks changes in the template code of the decorators feature branch
- Renames variables to be `plot`, `table` or (in case of multiple
decoratable elements) `<name>_plot` and `<name>_table`

### Workflow

Manually triggered:
https://github.com/insightsengineering/teal.modules.clinical/actions/runs/12359120026

[![Check
šŸ› ](https://github.com/insightsengineering/teal.modules.clinical/actions/workflows/check.yaml/badge.svg?branch=snapshots%401187_decorate_output%40main)](https://github.com/insightsengineering/teal.modules.clinical/actions/workflows/check.yaml)
@averissimo
fix: adds stats prefix
9c4612c
@averissimo
Merge branch 'main' into 1187_decorate_output@main
fad76cd
m7pr
m7pr approved these changes Dec 17, 2024
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107 files changed! What a journey! Accepting!

@averissimo averissimo merged commit 9ec59e9 into main Dec 17, 2024
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@averissimo averissimo deleted the 1187_decorate_output@main branch December 17, 2024 15:22
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@averissimo @m7pr @pawelru @llrs-roche