R/filter_relative.R
filter_relative.RdFilters the observations before or after the observation where a specified condition is fulfilled for each by group. For example, the function could be called to select for each subject all observations before the first disease progression.
filter_relative(
dataset,
by_vars,
order,
condition,
mode,
selection,
inclusive,
keep_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
Condition for Reference Observation
The specified condition determines the reference observation. The output
dataset contains all observations before or after (selection parameter)
the reference observation.
none
Selection mode (first or last)
If "first" is specified, for each by group the observations before or
after (selection parameter) the observation where the condition
(condition parameter) is fulfilled the first time is included in the
output dataset. If "last" is specified, for each by group the
observations before or after (selection parameter) the observation where
the condition (condition parameter) is fulfilled the last time is
included in the output dataset.
"first", "last"
none
Select observations before or after the reference observation?
"before", "after"
none
Include the reference observation?
TRUE, FALSE
none
Should by groups without reference observation be kept?
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"
A dataset containing for each by group the observations before or after the observation where the condition was fulfilled the first or last time
For each by group ( by_vars parameter) the observations before or
after (selection parameter) the observations where the condition
(condition parameter) is fulfilled the first or last time (order
parameter and mode parameter) is included in the output dataset.
Utilities for Filtering Observations:
count_vals(),
filter_exist(),
filter_extreme(),
filter_joined(),
filter_not_exist(),
max_cond(),
min_cond()
library(tibble)
response <- tribble(
~USUBJID, ~AVISITN, ~AVALC,
"1", 1, "PR",
"1", 2, "CR",
"1", 3, "CR",
"1", 4, "SD",
"1", 5, "NE",
"2", 1, "SD",
"2", 2, "PD",
"2", 3, "PD",
"3", 1, "SD",
"4", 1, "SD",
"4", 2, "PR",
"4", 3, "PD",
"4", 4, "SD",
"4", 5, "PR"
)
# Select observations up to first PD for each patient
response %>%
filter_relative(
by_vars = exprs(USUBJID),
order = exprs(AVISITN),
condition = AVALC == "PD",
mode = "first",
selection = "before",
inclusive = TRUE
)
#> # A tibble: 11 × 3
#> USUBJID AVISITN AVALC
#> <chr> <dbl> <chr>
#> 1 1 1 PR
#> 2 1 2 CR
#> 3 1 3 CR
#> 4 1 4 SD
#> 5 1 5 NE
#> 6 2 1 SD
#> 7 2 2 PD
#> 8 3 1 SD
#> 9 4 1 SD
#> 10 4 2 PR
#> 11 4 3 PD
# Select observations after last CR, PR, or SD for each patient
response %>%
filter_relative(
by_vars = exprs(USUBJID),
order = exprs(AVISITN),
condition = AVALC %in% c("CR", "PR", "SD"),
mode = "last",
selection = "after",
inclusive = FALSE
)
#> # A tibble: 3 × 3
#> USUBJID AVISITN AVALC
#> <chr> <dbl> <chr>
#> 1 1 5 NE
#> 2 2 2 PD
#> 3 2 3 PD
# Select observations from first response to first PD
response %>%
filter_relative(
by_vars = exprs(USUBJID),
order = exprs(AVISITN),
condition = AVALC %in% c("CR", "PR"),
mode = "first",
selection = "after",
inclusive = TRUE,
keep_no_ref_groups = FALSE
) %>%
filter_relative(
by_vars = exprs(USUBJID),
order = exprs(AVISITN),
condition = AVALC == "PD",
mode = "first",
selection = "before",
inclusive = TRUE
)
#> # A tibble: 7 × 3
#> USUBJID AVISITN AVALC
#> <chr> <dbl> <chr>
#> 1 1 1 PR
#> 2 1 2 CR
#> 3 1 3 CR
#> 4 1 4 SD
#> 5 1 5 NE
#> 6 4 2 PR
#> 7 4 3 PD