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Derive Lab High toxicity Grade 0 - 4 and Low Toxicity Grades 0 - (-4)

Source: R/derive_var_atoxgr.R
derive_var_atoxgr.Rd

Derives character lab grade based on high and low severity/toxicity grade(s).

Usage

derive_var_atoxgr(
  dataset,
  lotox_description_var = ATOXDSCL,
  hitox_description_var = ATOXDSCH
)

Arguments

dataset

Input dataset

The variables specified by the lotox_description_var and hitox_description_var arguments are expected to be in the dataset. ATOXGRL, and ATOXGRH are expected as well.

lotox_description_var

Variable containing the toxicity grade description for low values, eg. "Anemia"

hitox_description_var

Variable containing the toxicity grade description for high values, eg. "Hemoglobin Increased".

Value

The input data set with the character variable added

Details

Created variable ATOXGR will contain values "-4", "-3", "-2", "-1" for low values and "1", "2", "3", "4" for high values, and will contain "0" if value is gradable and does not satisfy any of the criteria for high or low values. ATOXGR is set to missing if information not available to give a grade.

Function applies the following rules:

  • High and low missing - overall missing

  • Low grade not missing and > 0 - overall holds low grade

  • High grade not missing and > 0 - overall holds high grade

  • (Only high direction OR low direction is NORMAL) and high grade normal - overall NORMAL

  • (Only low direction OR high direction is NORMAL) and low grade normal - overall NORMAL

  • otherwise set to missing

See also

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

Examples

library(tibble)

adlb <- tribble(
  ~ATOXDSCL,          ~ATOXDSCH,        ~ATOXGRL,      ~ATOXGRH,
  "Hypoglycemia",     "Hyperglycemia",  NA_character_, "0",
  "Hypoglycemia",     "Hyperglycemia",  "0",           "1",
  "Hypoglycemia",     "Hyperglycemia",  "0",           "0",
  NA_character_,      "INR Increased",  NA_character_, "0",
  "Hypophosphatemia", NA_character_,    "1",           NA_character_
)

derive_var_atoxgr(adlb)
#> # A tibble: 5 × 5
#>   ATOXDSCL         ATOXDSCH      ATOXGRL ATOXGRH ATOXGR
#>   <chr>            <chr>         <chr>   <chr>   <chr> 
#> 1 Hypoglycemia     Hyperglycemia NA      0       NA    
#> 2 Hypoglycemia     Hyperglycemia 0       1       1     
#> 3 Hypoglycemia     Hyperglycemia 0       0       0     
#> 4 NA               INR Increased NA      0       0     
#> 5 Hypophosphatemia NA            1       NA      -1