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Derive Lab Toxicity Grade 0 - 4

Source: R/derive_var_atoxgr.R
derive_var_atoxgr_dir.Rd

Derives a character lab grade based on severity/toxicity criteria.

Usage

derive_var_atoxgr_dir(
  dataset,
  new_var,
  tox_description_var,
  meta_criteria,
  criteria_direction,
  get_unit_expr
)

Arguments

dataset

Input data set

The columns specified by tox_description_var parameter is expected.

new_var

Name of the character grade variable to create, for example, ATOXGRH or ATOXGRL.

tox_description_var

Variable containing the description of the grading criteria. For example: "Anemia" or "INR Increased".

meta_criteria

Metadata data set holding the criteria (normally a case statement)

Permitted Values: atoxgr_criteria_ctcv4, atoxgr_criteria_ctcv5

admiral metadata data set atoxgr_criteria_ctcv4 implements Common Terminology Criteria for Adverse Events (CTCAE) v4.0 admiral metadata data set atoxgr_criteria_ctcv5 implements Common Terminology Criteria for Adverse Events (CTCAE) v5.0

The metadata should have the following variables:

  • TERM: variable to hold the term describing the criteria applied to a particular lab test, eg. "Anemia" or "INR Increased". Note: the variable is case insensitive.

  • DIRECTION: variable to hold the direction of the abnormality of a particular lab test value. "L" is for LOW values, "H" is for HIGH values. Note: the variable is case insensitive.

  • SI_UNIT_CHECK: variable to hold unit of particular lab test. Used to check against input data if criteria is based on absolute values.

  • VAR_CHECK: variable to hold comma separated list of variables used in criteria. Used to check against input data that variables exist.

  • GRADE_CRITERIA_CODE: variable to hold code that creates grade based on defined criteria.

criteria_direction

Direction (L= Low, H = High) of toxicity grade.

Permitted Values: "L", "H"

get_unit_expr

An expression providing the unit of the parameter

The result is used to check the units of the input parameters. Compared with SI_UNIT_CHECK in metadata (see meta_criteria parameter).

Permitted Values: A variable containing unit from the input dataset, or a function call, for example, get_unit_expr = extract_unit(PARAM).

Value

The input dataset with the character variable added

Details

new_var is derived with values NA, "0", "1", "2", "3", "4", where "4" is the most severe grade

  • "4" is where the lab value satisfies the criteria for grade 4.

  • "3" is where the lab value satisfies the criteria for grade 3.

  • "2" is where the lab value satisfies the criteria for grade 2.

  • "1" is where the lab value satisfies the criteria for grade 1.

  • "0" is where a grade can be derived and is not grade "1", "2", "3" or "4".

  • NA is where a grade cannot be derived.

See also

BDS-Findings Functions that returns variable appended to dataset: derive_var_analysis_ratio(), derive_var_anrind(), derive_var_atoxgr(), derive_var_basetype(), derive_var_base(), derive_var_chg(), derive_var_ontrtfl(), derive_var_pchg(), derive_var_shift()

Examples

library(tibble)

data <- tribble(
  ~ATOXDSCL,                     ~AVAL,  ~ANRLO,   ~ANRHI, ~PARAM,
  "Hypoglycemia",                119,    4,        7,      "Glucose (mmol/L)",
  "Hypoglycemia",                120,    4,        7,      "Glucose (mmol/L)",
  "Anemia",                      129,    120,      180,    "Hemoglobin (g/L)",
  "White blood cell decreased",  10,     5,        20,     "White blood cell (10^9/L)",
  "White blood cell decreased",  15,     5,        20,     "White blood cell (10^9/L)",
  "Anemia",                      140,    120,      180,    "Hemoglobin (g/L)"
)

derive_var_atoxgr_dir(data,
  new_var = ATOXGRL,
  tox_description_var = ATOXDSCL,
  meta_criteria = atoxgr_criteria_ctcv4,
  criteria_direction = "L",
  get_unit_expr = extract_unit(PARAM)
)
#> # A tibble: 6 x 6
#>   ATOXDSCL                    AVAL ANRLO ANRHI PARAM                     ATOXGRL
#>   <chr>                      <dbl> <dbl> <dbl> <chr>                     <chr>  
#> 1 Anemia                       129   120   180 Hemoglobin (g/L)          0      
#> 2 Anemia                       140   120   180 Hemoglobin (g/L)          0      
#> 3 Hypoglycemia                 119     4     7 Glucose (mmol/L)          0      
#> 4 Hypoglycemia                 120     4     7 Glucose (mmol/L)          0      
#> 5 White blood cell decreased    10     5    20 White blood cell (10^9/L) 0      
#> 6 White blood cell decreased    15     5    20 White blood cell (10^9/L) 0      

data <- tribble(
  ~ATOXDSCH,                     ~AVAL,  ~ANRLO,   ~ANRHI, ~PARAM,
  "Hyperglycemia",               119,    4,        7,      "Glucose (mmol/L)",
  "Hyperglycemia",               120,    4,        7,      "Glucose  (mmol/L)",
  "GGT increased",               129,    0,        30,     "Gamma Glutamyl Transferase (U/L)",
  "Lymphocyte count increased",  4,      1,        4,      "Lymphocytes Abs (10^9/L)",
  "Lymphocyte count increased",  2,      1,        4,      "Lymphocytes Abs (10^9/L)",
  "GGT increased",               140,    120,      180,    "Gamma Glutamyl Transferase (U/L)"
)

derive_var_atoxgr_dir(data,
  new_var = ATOXGRH,
  tox_description_var = ATOXDSCH,
  meta_criteria = atoxgr_criteria_ctcv4,
  criteria_direction = "H",
  get_unit_expr = extract_unit(PARAM)
)
#> # A tibble: 6 x 6
#>   ATOXDSCH                  AVAL ANRLO ANRHI PARAM                       ATOXGRH
#>   <chr>                    <dbl> <dbl> <dbl> <chr>                       <chr>  
#> 1 GGT increased              129     0    30 Gamma Glutamyl Transferase… 2      
#> 2 GGT increased              140   120   180 Gamma Glutamyl Transferase… 0      
#> 3 Hyperglycemia              119     4     7 Glucose (mmol/L)            4      
#> 4 Hyperglycemia              120     4     7 Glucose  (mmol/L)           4      
#> 5 Lymphocyte count increa…     4     1     4 Lymphocytes Abs (10^9/L)    0      
#> 6 Lymphocyte count increa…     2     1     4 Lymphocytes Abs (10^9/L)    0