🗃️ Decorators feature branch (#1252) · insightsengineering/teal.modules.clinical@9ec59e9

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🗃️ Decorators feature branch (#1252)

- Partner to insightsengineering/teal#1357
- Introduces decorators to modules. More about decorators in here
insightsengineering/teal#1384
- Part 1 of
insightsengineering/teal#1371 (comment)

### 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

- [x] Link the `teal_transform_module` parameter to an extended
explanation as [suggested
here](https://github.com/insightsengineering/teal.modules.clinical/pull/1252/files/a78c0baa0996fb30fdff551bccb7bab0ec86caa6#r1870909229)
- [x] Meet with SME to validate some changes in template, topics:
  - modules with listing/dt
- Merge all modules
- [x] Part 1 of
insightsengineering/teal#1371 (comment)
- [x] Part 2 of
insightsengineering/teal#1371 (comment)
- [x] Accept changes to snapshots in regression testing
#1304

#### Example apps

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

<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>

---------

Signed-off-by: Marcin <[email protected]>
Signed-off-by: Lluís Revilla <[email protected]>
Signed-off-by: André Veríssimo <[email protected]>
Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com>
Co-authored-by: Marcin <[email protected]>
Co-authored-by: m7pr <[email protected]>
Co-authored-by: Lluís Revilla <[email protected]>
Co-authored-by: Lluís Revilla <[email protected]>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

Loading branch information

7 people authored Dec 17, 2024

1 parent c2c21c7 commit 9ec59e9

.pre-commit-config.yaml

-Original file line number
+Diff line change
@@ Expand Up / @@ -33,7 +33,6 @@ repos: @@
               - methods
               - rlistings
               - rmarkdown
-              - rtables
               - scales
               - shiny
               - shinyjs
@@ Expand All / @@ -48,6 +47,9 @@ repos: @@
               - insightsengineering/teal.widgets
               - insightsengineering/tern.gee
               - insightsengineering/tern.mmrm
+              - insightsengineering/rtables
+              - insightsengineering/rtables.officer
+              - insightsengineering/formatters
               - utils
               - vistime
           - id: spell-check
@@ Expand Down @@

R/argument_convention.R

-Original file line number
+Diff line change
@@ Expand Up / @@ -203,6 +203,14 @@ NULL @@
     #'   value indicating worst grade.
     #' @param worst_flag_var ([teal.transform::choices_selected()])\cr object
     #'   with all available choices and preselected option for variable names that can be used as worst flag variable.
+    #' @param decorators `r lifecycle::badge("experimental")`
+    #' " (`list` of `teal_transform_module`, named `list` of `teal_transform_module` or" `NULL`) optional,
+    #' if not `NULL`, decorator for tables or plots included in the module.
+    #' When a named list of `teal_transform_module`, the decorators are applied to the respective output objects.
+    #'
+    #' Otherwise, the decorators are applied to all objects, which is equivalent as using the name `default`.
+    #'
+    #' See section "Decorating Module" below for more details.
     #'
     #' @return a `teal_module` object.
     #'
@@ Expand Down @@

R/tm_a_gee.R

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -69,9 +69,9 @@ template_a_gee <- function(output_table,
  
          if (output_table == "t_gee_cov") {

            substitute(

              expr = {

                result_table <- tern.gee::as.rtable(model_fit, type = "cov")

                subtitles(result_table) <- st

                main_footer(result_table) <- mf

                table <- tern.gee::as.rtable(model_fit, type = "cov")

                subtitles(table) <- st

                main_footer(table) <- mf

              },

              env = list(

                st = basic_table_args$subtitles,

    @@ -81,9 +81,9 @@ template_a_gee <- function(output_table,
  
          } else if (output_table == "t_gee_coef") {

            substitute(

              expr = {

                result_table <- tern.gee::as.rtable(data.frame(Coefficient = model_fit$coefficients))

                subtitles(result_table) <- st

                main_footer(result_table) <- mf

                table <- tern.gee::as.rtable(data.frame(Coefficient = model_fit$coefficients))

                subtitles(table) <- st

                main_footer(table) <- mf

              },

              env = list(

                conf_level = conf_level,

    @@ -95,17 +95,16 @@ template_a_gee <- function(output_table,
  
            substitute(

              expr = {

                lsmeans_fit_model <- tern.gee::lsmeans(model_fit, conf_level)

                result_table <- rtables::basic_table(show_colcounts = TRUE) %>%

                table <- rtables::basic_table(show_colcounts = TRUE) %>%

                  rtables::split_cols_by(var = input_arm_var, ref_group = model_fit$ref_level) %>%

                  tern.gee::summarize_gee_logistic() %>%

                  rtables::build_table(

                    df = lsmeans_fit_model,

                    alt_counts_df = dataname_lsmeans

                  )

                subtitles(result_table) <- st

                main_footer(result_table) <- mf

                result_table

                subtitles(table) <- st

                main_footer(table) <- mf

              },

              env = list(

                dataname_lsmeans = as.name(dataname_lsmeans),

    @@ -135,6 +134,14 @@ template_a_gee <- function(output_table,
  
    #'

    #' @inherit module_arguments return seealso

    #'

    #' @section Decorating Module:

    #'

    #' This module generates the following objects, which can be modified in place using decorators:

    #' - `table` (`ElementaryTable` - output of `rtables::build_table`)

    #'

    #' For additional details and examples of decorators, refer to the vignette

    #' `vignette("decorate-modules-output", package = "teal")` or the [`teal_transform_module()`] documentation.

    #'

    #' @examplesShinylive

    #' library(teal.modules.clinical)

    #' interactive <- function() TRUE

    @@ -200,7 +207,8 @@ tm_a_gee <- function(label,
  
                         conf_level = teal.transform::choices_selected(c(0.95, 0.9, 0.8), 0.95, keep_order = TRUE),

                         pre_output = NULL,

                         post_output = NULL,

                         basic_table_args = teal.widgets::basic_table_args()) {

                         basic_table_args = teal.widgets::basic_table_args(),

                         decorators = NULL) {

      message("Initializing tm_a_gee (prototype)")

      cov_var <- teal.transform::add_no_selected_choices(cov_var, multiple = TRUE)

    @@ -218,6 +226,8 @@ tm_a_gee <- function(label,
  
      checkmate::assert_class(pre_output, classes = "shiny.tag", null.ok = TRUE)

      checkmate::assert_class(post_output, classes = "shiny.tag", null.ok = TRUE)

      checkmate::assert_class(basic_table_args, "basic_table_args")

      decorators <- normalize_decorators(decorators)

      assert_decorators(decorators, "table", null.ok = TRUE)

      args <- as.list(environment())

    @@ -243,7 +253,8 @@ tm_a_gee <- function(label,
  
            parentname = parentname,

            arm_ref_comp = arm_ref_comp,

            label = label,

            basic_table_args = basic_table_args

            basic_table_args = basic_table_args,

            decorators = decorators

          )

        ),

        datanames = teal.transform::get_extract_datanames(data_extract_list)

    @@ -358,7 +369,8 @@ ui_gee <- function(id, ...) {
  
              "Coefficients" = "t_gee_coef"

            ),

            selected = "t_gee_lsmeans"

          )

          ),

          ui_decorate_teal_data(ns("decorator"), decorators = select_decorators(a$decorators, "table"))

        ),

        forms = tagList(

          teal.widgets::verbatim_popup_ui(ns("rcode"), button_label = "Show R code")

    @@ -385,7 +397,8 @@ srv_gee <- function(id,
  
                        label,

                        plot_height,

                        plot_width,

                        basic_table_args) {

                        basic_table_args,

                        decorators) {

      with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")

      with_filter <- !missing(filter_panel_api) && inherits(filter_panel_api, "FilterPanelAPI")

      checkmate::assert_class(data, "reactive")

    @@ -546,19 +559,26 @@ srv_gee <- function(id,
  
          output_title

        })

        table_r <- reactive({

          table_q()[["result_table"]]

        })

        decorated_table_q <- srv_decorate_teal_data(

          id = "decorator",

          data = table_q,

          decorators = select_decorators(decorators, "table"),

          expr = table

        )

        # Outputs to render.

        table_r <- reactive(decorated_table_q()[["table"]])

        teal.widgets::table_with_settings_srv(

          id = "table",

          table_r = table_r

        )

        # Render R code

        source_code_r <- reactive(teal.code::get_code(req(decorated_table_q())))

        teal.widgets::verbatim_popup_srv(

          id = "rcode",

          verbatim_content = reactive(teal.code::get_code(table_q())),

          verbatim_content = source_code_r,

          title = label

        )

    @@ -582,7 +602,7 @@ srv_gee <- function(id,
  
              card$append_text("Comment", "header3")

              card$append_text(comment)

            }

            card$append_src(teal.code::get_code(table_q()))

            card$append_src(source_code_r())

            card

          }

          teal.reporter::simple_reporter_srv("simple_reporter", reporter = reporter, card_fun = card_fun)

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