Helper function to analyze patients for s_count_abnormal_lab_worsen_by_baseline()

Source: R/abnormal_lab_worsen_by_baseline.R

[Stable]

Helper function to count the number of patients and the fraction of patients according to highest post-baseline lab grade variable .var, baseline lab grade variable baseline_var, and the direction of interest specified in direction_var.

h_worsen_counter(df, id, .var, baseline_var, direction_var)

Arguments

df

(data.frame)
data set containing all analysis variables.

id

(string)
subject variable name.

.var

(string)
single variable name that is passed by rtables when requested by a statistics function.

baseline_var

(string)
name of the baseline lab grade variable.

direction_var

(string)
name of the direction variable specifying the direction of the shift table of interest. Only lab records flagged by L, H or B are included in the shift table.

  • L: low direction only

  • H: high direction only

  • B: both low and high directions

Value

The counts and fraction of patients whose worst post-baseline lab grades are worse than their baseline grades, for post-baseline worst grades "1", "2", "3", "4" and "Any".

Examples

library(dplyr)

# The direction variable, GRADDR, is based on metadata
adlb <- tern_ex_adlb %>%
  mutate(
    GRADDR = case_when(
      PARAMCD == "ALT" ~ "B",
      PARAMCD == "CRP" ~ "L",
      PARAMCD == "IGA" ~ "H"
    )
  ) %>%
  filter(SAFFL == "Y" & ONTRTFL == "Y" & GRADDR != "")

df <- h_adlb_worsen(
  adlb,
  worst_flag_low = c("WGRLOFL" = "Y"),
  worst_flag_high = c("WGRHIFL" = "Y"),
  direction_var = "GRADDR"
)

# `h_worsen_counter`
h_worsen_counter(
  df %>% filter(PARAMCD == "CRP" & GRADDR == "Low"),
  id = "USUBJID",
  .var = "ATOXGR",
  baseline_var = "BTOXGR",
  direction_var = "GRADDR"
)
#> $fraction
#> $fraction$`1`
#>   num denom 
#>    25   180 
#> 
#> $fraction$`2`
#>   num denom 
#>    15   186 
#> 
#> $fraction$`3`
#>   num denom 
#>    18   191 
#> 
#> $fraction$`4`
#>   num denom 
#>    17   196 
#> 
#> $fraction$Any
#>   num denom 
#>    75   196 
#> 
#>