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Flag Observations Before or After a Condition is Fulfilled

Source: R/derive_var_relative_flag.R
derive_var_relative_flag.Rd

Flag all observations before or after the observation where a specified condition is fulfilled for each by group. For example, the function could be called to flag for each subject all observations before the first disease progression or to flag all AEs after a specific AE.

Usage

derive_var_relative_flag(
  dataset,
  by_vars,
  order,
  new_var,
  condition,
  mode,
  selection,
  inclusive,
  flag_no_ref_groups = TRUE,
  check_type = "warning"
)

Arguments

dataset

Input dataset

The variables specified by the by_vars and order arguments are expected to be in the dataset.

by_vars

Grouping variables

Permitted Values: list of variables created by exprs() e.g. exprs(USUBJID, VISIT)

order

Sort order

Within each by group the observations are ordered by the specified order.

For handling of NAs in sorting variables see Sort Order.

Permitted Values: list of expressions created by exprs(), e.g., exprs(ADT, desc(AVAL))

new_var

New variable

The variable is added to the input dataset and set to "Y" for all observations before or after the condition is fulfilled. For all other observations it is set to NA.

condition

Condition for Reference Observation

The specified condition determines the reference observation. In the output dataset all observations before or after (selection argument) the reference observation are flagged.

mode

Selection mode (first or last)

If "first" is specified, for each by group the observations before or after (selection argument) the observation where the condition (condition argument) is fulfilled the first time is flagged in the output dataset. If "last" is specified, for each by group the observations before or after (selection argument) the observation where the condition (condition argument) is fulfilled the last time is flagged in the output dataset.

Permitted Values: "first", "last"

selection

Flag observations before or after the reference observation?

Permitted Values: "before", "after"

inclusive

Flag the reference observation?

Permitted Values: TRUE, FALSE

flag_no_ref_groups

Should by groups without reference observation be flagged?

Permitted Values: TRUE, FALSE

check_type

Check uniqueness?

If "warning" or "error" is specified, the specified message is issued if the observations of the input dataset are not unique with respect to the by variables and the order.

Permitted Values: "none", "warning", "error"

Value

The input dataset with the new variable (new_var) added

Details

For each by group (by_vars argument) the observations before or after (selection argument) the observations where the condition (condition argument) is fulfilled the first or last time (order argument and mode argument) is flagged in the output dataset.

See also

General Derivation Functions for all ADaMs that returns variable appended to dataset: derive_var_extreme_flag(), derive_var_joined_exist_flag(), derive_var_merged_ef_msrc(), derive_var_merged_exist_flag(), derive_var_merged_summary(), derive_var_obs_number(), derive_vars_computed(), derive_vars_joined(), derive_vars_merged_lookup(), derive_vars_merged(), derive_vars_transposed()

Examples

library(tibble)
library(dplyr, warn.conflicts = FALSE)

# Flag all AEs after the first COVID AE
adae <- tribble(
  ~USUBJID, ~ASTDY, ~ACOVFL, ~AESEQ,
  "1",           2, NA,           1,
  "1",           5, "Y",          2,
  "1",           5, NA,           3,
  "1",          17, NA,           4,
  "1",          27, "Y",          5,
  "1",          32, NA,           6,
  "2",           8, NA,           1,
  "2",          11, NA,           2,
)

derive_var_relative_flag(
  adae,
  by_vars = exprs(USUBJID),
  order = exprs(ASTDY, AESEQ),
  new_var = PSTCOVFL,
  condition = ACOVFL == "Y",
  mode = "first",
  selection = "after",
  inclusive = FALSE,
  flag_no_ref_groups = FALSE
)
#> # A tibble: 8 × 5
#>   USUBJID ASTDY ACOVFL AESEQ PSTCOVFL
#>   <chr>   <dbl> <chr>  <dbl> <chr>   
#> 1 1           2 NA         1 NA      
#> 2 1           5 Y          2 NA      
#> 3 1           5 NA         3 Y       
#> 4 1          17 NA         4 Y       
#> 5 1          27 Y          5 Y       
#> 6 1          32 NA         6 Y       
#> 7 2           8 NA         1 NA      
#> 8 2          11 NA         2 NA      

response <- tribble(
  ~USUBJID, ~AVISITN, ~AVALC,
  "1",      0,        "PR",
  "1",      1,        "CR",
  "1",      2,        "CR",
  "1",      3,        "SD",
  "1",      4,        "NE",
  "2",      0,        "SD",
  "2",      1,        "PD",
  "2",      2,        "PD",
  "3",      0,        "SD",
  "4",      0,        "SD",
  "4",      1,        "PR",
  "4",      2,        "PD",
  "4",      3,        "SD",
  "4",      4,        "PR"
)

# Flag observations up to first PD for each patient
response %>%
  derive_var_relative_flag(
    by_vars = exprs(USUBJID),
    order = exprs(AVISITN),
    new_var = ANL02FL,
    condition = AVALC == "PD",
    mode = "first",
    selection = "before",
    inclusive = TRUE
  )
#> # A tibble: 14 × 4
#>    USUBJID AVISITN AVALC ANL02FL
#>    <chr>     <dbl> <chr> <chr>  
#>  1 1             0 PR    Y      
#>  2 1             1 CR    Y      
#>  3 1             2 CR    Y      
#>  4 1             3 SD    Y      
#>  5 1             4 NE    Y      
#>  6 2             0 SD    Y      
#>  7 2             1 PD    Y      
#>  8 2             2 PD    NA     
#>  9 3             0 SD    Y      
#> 10 4             0 SD    Y      
#> 11 4             1 PR    Y      
#> 12 4             2 PD    Y      
#> 13 4             3 SD    NA     
#> 14 4             4 PR    NA     

# Flag observations up to first PD excluding baseline (AVISITN = 0) for each patient
response %>%
  restrict_derivation(
    derivation = derive_var_relative_flag,
    args = params(
      by_vars = exprs(USUBJID),
      order = exprs(AVISITN),
      new_var = ANL02FL,
      condition = AVALC == "PD",
      mode = "first",
      selection = "before",
      inclusive = TRUE
    ),
    filter = AVISITN > 0
  ) %>%
  arrange(USUBJID, AVISITN)
#> # A tibble: 14 × 4
#>    USUBJID AVISITN AVALC ANL02FL
#>    <chr>     <dbl> <chr> <chr>  
#>  1 1             0 PR    NA     
#>  2 1             1 CR    Y      
#>  3 1             2 CR    Y      
#>  4 1             3 SD    Y      
#>  5 1             4 NE    Y      
#>  6 2             0 SD    NA     
#>  7 2             1 PD    Y      
#>  8 2             2 PD    NA     
#>  9 3             0 SD    NA     
#> 10 4             0 SD    NA     
#> 11 4             1 PR    Y      
#> 12 4             2 PD    Y      
#> 13 4             3 SD    NA     
#> 14 4             4 PR    NA