R/derive_var_relative_flag.R
derive_var_relative_flag.RdFlag 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.
derive_var_relative_flag(
dataset,
by_vars,
order,
new_var,
condition,
mode,
selection,
inclusive,
flag_no_ref_groups = TRUE,
check_type = "warning"
)Input dataset
The variables specified by the by_vars and order arguments are expected to be in the dataset.
none
Grouping variables
none
Sort order
Within each by group the observations are ordered by the specified order.
For handling of NAs in sorting variables see Sort Order.
list of expressions created by exprs(), e.g.,
exprs(ADT, desc(AVAL))
none
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.
none
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.
none
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.
"first", "last"
none
Flag observations before or after the reference observation?
"before", "after"
none
Flag the reference observation?
TRUE, FALSE
none
Should by groups without reference observation be flagged?
TRUE, FALSE
TRUE
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.
"none", "warning", "error"
"warning"
The input dataset with the new variable (new_var) added
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.
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_cat(),
derive_vars_computed(),
derive_vars_joined(),
derive_vars_joined_summary(),
derive_vars_merged(),
derive_vars_merged_lookup(),
derive_vars_transposed()
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