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Derive AVAL variable for ADIS ADaM domain

Source: R/derive_var_aval_adis.R
derive_var_aval_adis.Rd

Derive AVAL variable for Laboratory Immunology Data ADaM domain. A common rule has been decided for its derivation, based on ISLLOQ, ISULOQ and ISORRES when both ISLLOQ and ISULOQ are present. If ISULOQ is not present, the variables used are ISLLOQ and ISORRES. Please, refers to arguments description for additional details.

Usage

derive_var_aval_adis(
  dataset,
  lower_rule,
  middle_rule,
  upper_rule = NULL,
  round = NULL
)

Arguments

dataset

Input dataset.

lower_rule

Derivation rule when ISSTRESN value is below ISLLOQ. When ISSTRESN is missing, the inequality in ISORRES is checked for the derivation.

middle_rule

Derivation rule when ISSTRESN value is greater than ISLLOQ and lower than ISULOQ. If ISULOQ is not present, derivation rule when ISSTRESN is greater than ISLLOQ. When ISSTRESN is missing, the inequality in ISORRES is checked for the derivation.

upper_rule

Derivation rule when ISSTRESN value is greater than ISULOQ. This is an optional argument since ISULOQ may not be present. When ISSTRESN is missing, the inequality in ISORRES. is checked for the derivation. Default value is NULL.

round

Rounding for AVAL variable. An integer argument which specifies the number of decimals displayed. Default value is NULL.

Value

Dataset with AVAL variable derived.

See also

Other der_var: derive_vars_crit(), derive_vars_event_flag(), derive_vars_max_flag(), derive_vars_merged_vaccine(), derive_vars_params(), derive_vars_vaxdt()

Author

Federico Baratin

Examples

library(tibble)
library(admiral)
library(admiraldev)
library(dplyr)
library(rlang)

input <- tribble(
  ~USUBJID, ~AVISITN, ~PARAMCD, ~PARAM, ~ISORRES, ~ISSTRESN, ~ISLLOQ, ~ISULOQ,
  "ABC-1001", 10, "J0033VN", "J0033VN Antibody", NA, NA, 2, 100,
  "ABC-1001", 10, "I0019NT", "I0019NT Antibody", "3", 3.0, 4, 200,
  "ABC-1001", 10, "M0019LN", "M0019LN Antibody", ">150", NA, 8, 150,
  "ABC-1001", 10, "R0003MA", "R0003MA Antibody", "140.5", 140.5, 4, 120,
  "ABC-1001", 30, "J0033VN", "J0033VN Antibody", "2", 2.0, 2, 100,
  "ABC-1001", 30, "I0019NT", "I0019NT Antibody", NA, NA, 4, 200,
  "ABC-1001", 30, "M0019LN", "M0019LN Antibody", NA, NA, 8, 150,
  "ABC-1001", 30, "R0003MA", "R0003MA Antibody", "98.2", 98.2, 4, 120,
  "ABC-1001", 10, "J0033VNL", "LOG10 (J0033VN Antibody)", NA, NA, 2, 100,
  "ABC-1001", 10, "I0019NTL", "LOG10 (I0019NT Antibody)", "3", 3.0, 4, 200,
  "ABC-1001", 10, "M0019LNL", "LOG10 (M0019LN Antibody)", ">150", NA, 8, 150,
  "ABC-1001", 10, "R0003MAL", "LOG10 (R0003MA Antibody)", "140.5", 140.5, 4, 120,
  "ABC-1001", 30, "J0033VNL", "LOG10 (J0033VN Antibody)", "2", 2.0, 2, 100,
  "ABC-1001", 30, "I0019NTL", "LOG10 (I0019NT Antibody)", NA, NA, 4, 200,
  "ABC-1001", 30, "M0019LNL", "LOG10 (M0019LN Antibody)", NA, NA, 8, 150,
  "ABC-1001", 30, "R0003MAL", "LOG10 (R0003MA Antibody)", "98.2", 98.2, 4, 120,
  "ABC-1002", 10, "J0033VN", "J0033VN Antibody", "3", 3.0, 2, 100,
  "ABC-1002", 10, "I0019NT", "I0019NT Antibody", NA, NA, 4, 200,
  "ABC-1002", 10, "M0019LN", "M0019LN Antibody", NA, NA, 8, 150,
  "ABC-1002", 10, "R0003MA", "R0003MA Antibody", "48.9", 48.9, 4, 120,
  "ABC-1002", 30, "J0033VN", "J0033VN Antibody", NA, NA, 2, 100,
  "ABC-1002", 30, "I0019NT", "I0019NT Antibody", NA, NA, 4, 200,
  "ABC-1002", 30, "M0019LN", "M0019LN Antibody", "5", 5.0, 8, 150,
  "ABC-1002", 30, "R0003MA", "R0003MA Antibody", "228.1", 228.1, 4, 120
)

derive_var_aval_adis(
  dataset = input,
  lower_rule = ISLLOQ / 2,
  middle_rule = ISSTRESN,
  upper_rule = ISULOQ,
  round = 2
)
#> # A tibble: 24 × 9
#>    USUBJID  AVISITN PARAMCD  PARAM          ISORRES ISSTRESN ISLLOQ ISULOQ  AVAL
#>    <chr>      <dbl> <chr>    <chr>          <chr>      <dbl>  <dbl>  <dbl> <dbl>
#>  1 ABC-1001      10 J0033VN  J0033VN Antib… NA          NA        2    100  NA  
#>  2 ABC-1001      10 I0019NT  I0019NT Antib… 3            3        4    200   2  
#>  3 ABC-1001      10 M0019LN  M0019LN Antib… >150        NA        8    150 150  
#>  4 ABC-1001      10 R0003MA  R0003MA Antib… 140.5      140.       4    120 120  
#>  5 ABC-1001      30 J0033VN  J0033VN Antib… 2            2        2    100   2  
#>  6 ABC-1001      30 I0019NT  I0019NT Antib… NA          NA        4    200  NA  
#>  7 ABC-1001      30 M0019LN  M0019LN Antib… NA          NA        8    150  NA  
#>  8 ABC-1001      30 R0003MA  R0003MA Antib… 98.2        98.2      4    120  98.2
#>  9 ABC-1001      10 J0033VNL LOG10 (J0033V… NA          NA        2    100  NA  
#> 10 ABC-1001      10 I0019NTL LOG10 (I0019N… 3            3        4    200   2  
#> # ℹ 14 more rows