Helper function to prepare ADLB with worst labs

Source: R/abnormal_lab_worsen_by_baseline.R

[Stable]

Helper function to prepare a df for generate the patient count shift table.

h_adlb_worsen(
  adlb,
  worst_flag_low = NULL,
  worst_flag_high = NULL,
  direction_var
)

Arguments

adlb

(data.frame)
ADLB data frame.

worst_flag_low

(named vector)
worst low post-baseline lab grade flag variable. See how this is implemented in the following examples.

worst_flag_high

(named vector)
worst high post-baseline lab grade flag variable. See how this is implemented in the following examples.

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

h_adlb_worsen() returns the adlb data.frame containing only the worst labs specified according to worst_flag_low or worst_flag_high for the direction specified according to direction_var. For instance, for a lab that is needed for the low direction only, only records flagged by worst_flag_low are selected. For a lab that is needed for both low and high directions, the worst low records are selected for the low direction, and the worst high record are selected for the high direction.

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"
)