tm_t_events_summary.md
In teal.modules.clinical: 'teal' Modules for Standard Clinical Outputs

template_events_summary generates minimal table

Code
  res
Output
  $data
  {
      anl <- adae
      adsl <- adsl %>% dplyr::mutate(ARM = droplevels(ARM))
      arm_levels <- levels(adsl[["ARM"]])
      anl <- anl %>% dplyr::mutate(ARM = factor(ARM, levels = arm_levels))
      study_id <- unique(anl[["STUDYID"]])
      anl$tmp_aefl <- "Y"
      anl[["AEDECOD"]] <- as.character(anl[["AEDECOD"]])
      anl <- anl %>% dplyr::mutate(USUBJID_AESEQ = paste(USUBJID, 
          AESEQ, sep = "@@"))
      anl <- df_explicit_na(anl, na_level = "<Missing>")
      adsl <- df_explicit_na(adsl, na_level = "<Missing>")
  }

  $layout_parent
  lyt_parent <- rtables::basic_table(show_colcounts = TRUE) %>% 
      rtables::split_cols_by(var = "ARM") %>% rtables::add_overall_col(label = "All Patients") %>% 
      count_values("DTHFL", values = "Y", .labels = c(count_fraction = "Total number of deaths"), 
          .formats = c(count_fraction = format_count_fraction), 
          denom = "N_col") %>% count_values("DCSREAS", values = "ADVERSE EVENT", 
      .labels = c(count_fraction = "Total number of patients withdrawn from study due to an AE"), 
      .formats = c(count_fraction = format_count_fraction), denom = "N_col")

  $table_parent
  table_parent <- rtables::build_table(lyt = lyt_parent, df = adsl, 
      alt_counts_df = adsl)

  $layout_anl
  lyt_anl <- rtables::basic_table(show_colcounts = TRUE) %>% rtables::split_cols_by(var = "ARM") %>% 
      rtables::add_overall_col(label = "All Patients") %>% count_patients_with_event(vars = "USUBJID", 
      filters = c(tmp_aefl = "Y"), denom = "N_col", .stats = "count_fraction", 
      .labels = c(count_fraction = "Total number of patients with at least one adverse event"), 
      .indent_mods = c(count_fraction = 0L), table_names = "total_pts_at_least_one") %>% 
      count_values("STUDYID", values = study_id, .stats = "count", 
          .labels = c(count = "Total AEs"), table_names = "total_aes")

  $table_anl
  table_anl <- rtables::build_table(lyt = lyt_anl, df = anl, alt_counts_df = adsl)

  $table
  {
      rtables::col_info(table_parent) <- rtables::col_info(table_anl)
      table <- rtables::rbind(table_anl, table_parent)
  }

template_events_summary generates table with multiple flags

Code
  res
Output
  $data
  {
      anl <- adae
      adsl <- adsl %>% dplyr::mutate(ARM = droplevels(ARM))
      arm_levels <- levels(adsl[["ARM"]])
      anl <- anl %>% dplyr::mutate(ARM = factor(ARM, levels = arm_levels))
      study_id <- unique(anl[["STUDYID"]])
      anl$tmp_aefl <- "Y"
      anl[["AEDECOD"]] <- as.character(anl[["AEDECOD"]])
      anl <- anl %>% dplyr::mutate(USUBJID_AESEQ = paste(USUBJID, 
          AESEQ, sep = "@@"))
      flag_var_anl_label <- teal.data::col_labels(anl[, c("A", 
          "B", "C")], fill = FALSE)
      flag_var_aesi_label <- teal.data::col_labels(anl[, c("X", 
          "Y")], fill = FALSE)
      anl <- df_explicit_na(anl, na_level = "<Missing>")
      adsl <- df_explicit_na(adsl, na_level = "<Missing>")
  }

  $layout_parent
  lyt_parent <- rtables::basic_table(show_colcounts = TRUE) %>% 
      rtables::split_cols_by(var = "ARM") %>% rtables::add_overall_col(label = "All Patients")

  $table_parent
  table_parent <- rtables::build_table(lyt = lyt_parent, df = adsl, 
      alt_counts_df = adsl)

  $layout_anl
  lyt_anl <- rtables::basic_table(show_colcounts = TRUE) %>% rtables::split_cols_by(var = "ARM") %>% 
      rtables::add_overall_col(label = "All Patients") %>% count_patients_with_event(vars = "USUBJID", 
      filters = c(tmp_aefl = "Y"), denom = "N_col", .stats = "count_fraction", 
      .labels = c(count_fraction = "Total number of patients with at least one adverse event"), 
      .indent_mods = c(count_fraction = 0L), table_names = "total_pts_at_least_one") %>% 
      count_values("STUDYID", values = study_id, .stats = "count", 
          .labels = c(count = "Total AEs"), table_names = "total_aes") %>% 
      count_patients_with_flags(var = "USUBJID", flag_variables = flag_var_anl_label, 
          table_names = "count_subj_anl", denom = "N_col", var_labels = "Total number of patients with at least one", 
          show_labels = "visible") %>% count_patients_with_flags(var = "AEDECOD", 
      flag_variables = flag_var_anl_label, table_names = "count_pt_anl", 
      .stats = "count", .formats = c(count = "xx"), denom = "N_col", 
      var_labels = "Total number of unique preferred terms which are", 
      show_labels = "visible") %>% count_patients_with_flags(var = "USUBJID_AESEQ", 
      flag_variables = flag_var_anl_label, table_names = "count_events_anl", 
      .stats = "count", .formats = c(count = "xx"), denom = "N_col", 
      var_labels = "Total number of adverse events which are", 
      show_labels = "visible") %>% count_patients_with_flags(var = "USUBJID", 
      flag_variables = flag_var_aesi_label, table_names = "count_subj_aesi", 
      denom = "N_col", var_labels = "Medical concepts: number of patients with", 
      show_labels = "visible") %>% count_patients_with_flags(var = "AEDECOD", 
      flag_variables = flag_var_aesi_label, table_names = "count_pt_aesi", 
      .stats = "count", .formats = c(count = "xx"), denom = "N_col", 
      var_labels = "Medical concepts: number of unique preferred terms which are part of", 
      show_labels = "visible") %>% count_patients_with_flags(var = "USUBJID_AESEQ", 
      flag_variables = flag_var_aesi_label, table_names = "count_events_aesi", 
      .stats = "count", .formats = c(count = "xx"), denom = "N_col", 
      var_labels = "Medical concepts: number of adverse events which are part of", 
      show_labels = "visible")

  $table_anl
  table_anl <- rtables::build_table(lyt = lyt_anl, df = anl, alt_counts_df = adsl)

  $table
  {
      rtables::col_info(table_parent) <- rtables::col_info(table_anl)
      table <- rtables::rbind(table_anl[1:2, ], table_anl[3:nrow(table_anl), 
          ])
  }