Helper function to prepare ADLB for count_abnormal_by_worst_grade()

Source: R/abnormal_by_worst_grade.R

[Stable]

Helper function to prepare an ADLB data frame to be used as input in count_abnormal_by_worst_grade(). The following pre-processing steps are applied:

  1. adlb is filtered on variable avisit to only include post-baseline visits.

  2. adlb is filtered on variables worst_flag_low and worst_flag_high so that only worst grades (in either direction) are included.

  3. From the standard lab grade variable atoxgr, the following two variables are derived and added to adlb:

  • A grade direction variable (e.g. GRADE_DIR). The variable takes value "HIGH" when atoxgr > 0, "LOW" when atoxgr < 0, and "ZERO" otherwise.

  • A toxicity grade variable (e.g. GRADE_ANL) where all negative values from atoxgr are replaced by their absolute values.

  1. Unused factor levels are dropped from adlb via droplevels().

h_adlb_abnormal_by_worst_grade(
  adlb,
  atoxgr = "ATOXGR",
  avisit = "AVISIT",
  worst_flag_low = "WGRLOFL",
  worst_flag_high = "WGRHIFL"
)

Arguments

adlb

(data.frame)
ADLB data frame.

atoxgr

(string)
name of the analysis toxicity grade variable. This must be a factor variable.

avisit

(string)
name of the analysis visit variable.

worst_flag_low

(string)
name of the worst low lab grade flag variable. This variable is set to "Y" when indicating records of worst low lab grades.

worst_flag_high

(string)
name of the worst high lab grade flag variable. This variable is set to "Y" when indicating records of worst high lab grades.

Value

h_adlb_abnormal_by_worst_grade() returns the adlb data frame with two new variables: GRADE_DIR and GRADE_ANL.

Examples

h_adlb_abnormal_by_worst_grade(tern_ex_adlb) %>%
  dplyr::select(ATOXGR, GRADE_DIR, GRADE_ANL) %>%
  head(10)
#> # A tibble: 10 × 3
#>    ATOXGR GRADE_DIR GRADE_ANL
#>    <fct>  <fct>     <fct>    
#>  1 -3     LOW       3        
#>  2 0      ZERO      0        
#>  3 0      ZERO      0        
#>  4 2      HIGH      2        
#>  5 0      ZERO      0        
#>  6 0      ZERO      0        
#>  7 -4     LOW       4        
#>  8 1      HIGH      1        
#>  9 -1     LOW       1        
#> 10 0      ZERO      0