derive_var_bcvacritxfl {admiralophtha}

Adds CRITx/CRITxFL pairs to BCVA dataset

Description

Adds a criterion variables CRITx and their corresponding flags CRITxFL to a dataset containing BCVA records

Usage

derive_var_bcvacritxfl(
  dataset,
  crit_var,
  bcva_ranges = NULL,
  bcva_uplims = NULL,
  bcva_lowlims = NULL,
  additional_text = "",
  critxfl_index = NULL
)

Arguments

dataset

Input dataset containing BCVA data (usually ADBCVA).

crit_var

Variable with respect to which CRITx/CRITxFL are derived (usually CHG or AVAL).

bcva_ranges

List containing one or more numeric vectors of length 2. For each vector c(a,b) in bcva_ranges, a pair of variables CRITx, CRITxFL is created with the condition: ⁠a <= crit_var <= b⁠. If criterion flags of that type are not required, then leave as NULL.

bcva_uplims

List containing one or more numeric elements. For each element a in bcva_uplims, a pair of variables CRITx, CRITxFL is created with the condition: crit_var <= a. If criterion flags of that type are not required, then leave as NULL.

bcva_lowlims

List containing one or more numeric elements. For each element b in bcva_lowlims, a pair of variables CRITx, CRITxFL is created with the condition: crit_var >= b. If criterion flags of that type are not required, then leave as NULL.

additional_text

string containing additional text to append to CRITx

critxfl_index

positive integer detailing the first value of x to use in CRITxFL. If not supplied, the function takes the first available value of x, counting up from x = 1.

Details

This function works by calling derive_var_bcvacritxfl() once for each of the elements in bcva_ranges, bcva_uplims and bcva_lowlims. NOTE: if crit_var is equal to NA, then the resulting criterion flag is also marked as NA.

Value

The input BCVA dataset with additional column pairsCRITx, CRITxFL.

Author(s)

Edoardo Mancini

Examples

library(tibble)
library(admiral)
library(admiraldev)

adbcva1 <- tribble(
  ~STUDYID, ~USUBJID, ~AVISIT, ~BASETYPE, ~PARAMCD, ~CHG,
  "XXX001", "P01", "BASELINE", "LAST", "SBCVA", 0,
  "XXX001", "P01", "WEEK 2", "LAST", "FBCVA", 2,
  "XXX001", "P02", "BASELINE", "LAST", "SBCVA", -13,
  "XXX001", "P02", "WEEK 2", "LAST", "FBCVA", 5,
  "XXX001", "P03", "BASELINE", "LAST", "SBCVA", NA,
  "XXX001", "P03", "WEEK 2", "LAST", "FBCVA", 17
)

derive_var_bcvacritxfl(
  dataset = adbcva1,
  crit_var = exprs(CHG),
  bcva_ranges = list(c(0, 5), c(-5, -1), c(10, 15)),
  bcva_uplims = list(5, 10),
  bcva_lowlims = list(8),
  additional_text = ""
)

adbcva2 <- tribble(
  ~STUDYID, ~USUBJID, ~AVISIT, ~BASETYPE, ~PARAMCD, ~AVAL, ~CHG,
  "XXX001", "P01", "BASELINE", "LAST", "SBCVA", 4, NA,
  "XXX001", "P01", "BASELINE", "LAST", "SBCVA", 6, NA,
  "XXX001", "P01", "AVERAGE BASELINE", "AVERAGE", "SBCVA", 5, NA,
  "XXX001", "P01", "WEEK 2", "LAST", "SBCVA", -3, NA,
  "XXX001", "P01", "WEEK 4", "LAST", "SBCVA", -10, NA,
  "XXX001", "P01", "WEEK 6", "LAST", "SBCVA", 12, NA,
  "XXX001", "P01", "WEEK 2", "AVERAGE", "SBCVA", -2, -7,
  "XXX001", "P01", "WEEK 4", "AVERAGE", "SBCVA", 6, 1,
  "XXX001", "P01", "WEEK 6", "AVERAGE", "SBCVA", 3, -2
)

restrict_derivation(
  adbcva2,
  derivation = derive_var_bcvacritxfl,
  args = params(
    crit_var = exprs(CHG),
    bcva_ranges = list(c(0, 5), c(-10, 0)),
    bcva_lowlims = list(5),
    additional_text = " (AVERAGE)"
  ),
  filter = PARAMCD %in% c("SBCVA", "FBCVA") & BASETYPE == "AVERAGE"
)