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

template_logistic generates correct expressions

Code
  res
Output
  $arm_lab
  arm_var_lab <- teal.data::col_labels(ANL["ARMCD"], fill = FALSE)

  $data
  {
      ANL <- ANL %>% dplyr::filter(ARMCD %in% c("ARM A", "ARM B", 
          "ARM C")) %>% dplyr::mutate(ARMCD = combine_levels(ARMCD, 
          levels = c("ARM A", "ARM B"), new_level = "ARM A/ARM B")) %>% 
          dplyr::mutate(ARMCD = stats::relevel(ARMCD, ref = "ARM A/ARM B")) %>% 
          dplyr::mutate(ARMCD = droplevels(ARMCD))
      ANL <- ANL %>% dplyr::mutate(Response = AVALC %in% "CR") %>% 
          df_explicit_na(na_level = "_NA_")
  }

  $relabel
  teal.data::col_labels(ANL["ARMCD"]) <- arm_var_lab

  $model
  mod <- fit_logistic(ANL, variables = list(response = "Response", 
      arm = "ARMCD", covariates = c("AGE", "SEX"), interaction = "AGE")) %>% 
      broom::tidy(conf_level = 0.95, at = c(30, 40)) %>% df_explicit_na(na_level = "_NA_")

  $table
  {
      table <- rtables::basic_table(title = "Summary of Logistic Regression Analysis for Best Confirmed Overall Response by Investigator for CR Responders") %>% 
          summarize_logistic(conf_level = 0.95, drop_and_remove_str = "_NA_") %>% 
          rtables::append_topleft("BESRSPI") %>% rtables::build_table(df = mod)
  }

Code
  res
Output
  $arm_lab
  arm_var_lab <- teal.data::col_labels(ANL["ARMCD"], fill = FALSE)

  $data
  {
      ANL <- ANL %>% dplyr::filter(ARMCD %in% c("ARM A", "ARM B", 
          "ARM C")) %>% dplyr::mutate(ARMCD = combine_levels(ARMCD, 
          levels = c("ARM A", "ARM B"), new_level = "ARM A/ARM B")) %>% 
          dplyr::mutate(ARMCD = stats::relevel(ARMCD, ref = "ARM A/ARM B")) %>% 
          dplyr::mutate(ARMCD = droplevels(ARMCD))
      ANL <- ANL %>% dplyr::mutate(Response = AVALC %in% "CR") %>% 
          df_explicit_na(na_level = "_NA_")
  }

  $relabel
  teal.data::col_labels(ANL["ARMCD"]) <- arm_var_lab

  $model
  mod <- fit_logistic(ANL, variables = list(response = "Response", 
      arm = "ARMCD", covariates = c("AGE", "SEX"), interaction = "AGE")) %>% 
      broom::tidy(conf_level = 0.95, at = c(30, 40)) %>% df_explicit_na(na_level = "_NA_")

  $table
  {
      table <- rtables::basic_table(title = "Summary of Logistic Regression Analysis for Best Confirmed Overall Response by Investigator for CR Responders") %>% 
          summarize_logistic(conf_level = 0.95, drop_and_remove_str = "_NA_") %>% 
          rtables::append_topleft("BESRSPI") %>% rtables::build_table(df = mod)
  }

template_logistic generates correct expressions for no arm variable

Code
  res
Output
  $data
  {
      ANL <- ANL %>% dplyr::mutate(Response = AVALC %in% "CR") %>% 
          df_explicit_na(na_level = "_NA_")
  }

  $model
  mod <- fit_logistic(ANL, variables = list(response = "Response", 
      arm = NULL, covariates = c("AGE", "SEX"), interaction = "AGE")) %>% 
      broom::tidy(conf_level = 0.95, at = c(30, 40)) %>% df_explicit_na(na_level = "_NA_")

  $table
  {
      table <- rtables::basic_table(title = "Summary of Logistic Regression Analysis for Best Confirmed Overall Response by Investigator for CR Responders") %>% 
          summarize_logistic(conf_level = 0.95, drop_and_remove_str = "_NA_") %>% 
          rtables::append_topleft("BESRSPI") %>% rtables::build_table(df = mod)
  }