tests/testthat/_snaps/utils.md

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

h_concat_expr returns a string for long expression

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Output
  [1] "rtables::basic_table() %>% rtables::split_cols_by(var = \"ARMCD\") %>% \n    tern::test_proportion_diff(vars = \"rsp\", method = \"cmh\", \n        variables = list(strata = \"strata\")) %>% rtables::build_table(df = dta)"

add_expr adds expressions to expression list

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Output
  [[1]]
  rtables::basic_table()

  [[2]]
  rtables::split_cols_by(var = arm)

  [[3]]
  tern::test_proportion_diff(vars = "rsp", method = "cmh", variables = list(strata = "strata"))

  [[4]]
  rtables::build_table(df = dta)

add_expr manages expression list which can be used by pipe_expr

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Output
  rtables::basic_table() %>% rtables::split_cols_by(var = arm) %>% 
      test_proportion_diff(vars = "rsp", method = "cmh", variables = list(strata = "strata")) %>% 
      rtables::build_table(df = dta)

bracket_expr concatenates expressions into a single expression

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Output
  {
      anl <- subset(adrs, PARAMCD == "INVET")
      anl$rsp_lab <- tern::d_onco_rsp_label(anl$AVALC)
      anl$is_rsp <- anl$rsp_lab %in% c("Complete Response (CR)", 
          "Partial Response (PR)")
  }

bracket_expr returns a single evaluable expression

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Output

                             FALSE TRUE
    Complete Response (CR)       0   60
    Partial Response (PR)        0   45
    Stable Disease (SD)         50    0
    Progressive Disease (PD)    39    0
    Not Evaluable (NE)           6    0

prepare_arm with standard inputs

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Output
  adrs %>% dplyr::filter(ARMCD %in% c("ARM A", "ARM B", "ARM C")) %>% 
      dplyr::mutate(ARMCD = stats::relevel(ARMCD, ref = "ARM A")) %>% 
      dplyr::mutate(ARMCD = droplevels(ARMCD))

prepare_arm combine ref arms

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Output
  adrs %>% 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))

prepare_arm combine ref arms and use new level

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Output
  adrs %>% 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 = "Control")) %>% dplyr::mutate(ARMCD = stats::relevel(ARMCD, 
      ref = "Control")) %>% dplyr::mutate(ARMCD = droplevels(ARMCD))

prepare_arm_levels with standard inputs

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Output
  {
      adae <- adae %>% dplyr::mutate(ARMCD = droplevels(ARMCD))
      arm_levels <- levels(adae[["ARMCD"]])
      adsl <- adsl %>% dplyr::filter(ARMCD %in% arm_levels)
      adsl <- adsl %>% dplyr::mutate(ARMCD = droplevels(ARMCD))
  }

prepare_arm_levels can use parentname arm levels

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Output
  {
      adsl <- adsl %>% dplyr::mutate(ARMCD = droplevels(ARMCD))
      arm_levels <- levels(adsl[["ARMCD"]])
      adae <- adae %>% dplyr::mutate(ARMCD = factor(ARMCD, levels = arm_levels))
  }

color_lab_values main

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Output
                                                                                       3 HIGH 
     "<span style='color:red!important'>3<i class='glyphicon glyphicon-arrow-up'></i></span>" 
                                                                                     2 NORMAL 
                            "<span style='color:grey!important'>2<i class='NULL'></i></span>" 
                                                                                       5 HIGH 
     "<span style='color:red!important'>5<i class='glyphicon glyphicon-arrow-up'></i></span>" 
                                                                                            4 
                                                                                          "4" 
                                                                                        0 LOW 
  "<span style='color:blue!important'>0<i class='glyphicon glyphicon-arrow-down'></i></span>"

teal.modules.clinical documentation built on April 4, 2025, 12:35 a.m.