| derive_var_extreme_flag {admiral} | R Documentation |
Add a Variable Flagging the First or Last Observation Within Each By Group
Description
Add a variable flagging the first or last observation within each by group
Usage
derive_var_extreme_flag(
dataset,
by_vars,
order,
new_var,
mode,
true_value = "Y",
false_value = NA_character_,
flag_all = FALSE,
check_type = "warning"
)
Arguments
dataset |
Input dataset The variables specified by the |
by_vars |
Grouping variables Permitted Values: list of variables created by |
order |
Sort order The first or last observation is determined with respect to the specified order. For handling of Permitted Values: list of variables or functions of variables |
new_var |
Variable to add The specified variable is added to the output dataset. It is set to the value
set in Permitted Values: list of name-value pairs |
mode |
Flag mode Determines of the first or last observation is flagged. Permitted Values: |
true_value |
True value The value for the specified variable Permitted Values: An atomic scalar |
false_value |
False value The value for the specified variable Permitted Values: An atomic scalar |
flag_all |
Flag setting A logical value where if set to |
check_type |
Check uniqueness? If Default: Permitted Values: |
Details
For each group (with respect to the variables specified for the
by_vars parameter), new_var is set to "Y" for the first or last observation
(with respect to the order specified for the order parameter and the flag mode
specified for the mode parameter). In the case where the user wants to flag multiple records
of a grouping, for example records that all happen on the same visit and time, the argument
flag_all can be set to TRUE.
Otherwise, new_var is set to NA. Thus, the direction of "worst" is considered fixed for
all parameters in the dataset depending on the order and the mode, i.e. for every
parameter the first or last record will be flagged across the whole dataset.
Value
The input dataset with the new flag variable added
See Also
General Derivation Functions for all ADaMs that returns variable appended to dataset:
derive_var_joined_exist_flag(),
derive_var_merged_ef_msrc(),
derive_var_merged_exist_flag(),
derive_var_merged_summary(),
derive_var_obs_number(),
derive_var_relative_flag(),
derive_vars_computed(),
derive_vars_joined(),
derive_vars_merged(),
derive_vars_merged_lookup(),
derive_vars_transposed()
Examples
library(tibble)
library(dplyr, warn.conflicts = FALSE)
example_vs <- tribble(
~USUBJID, ~VSTESTCD, ~VISIT, ~VISITNUM, ~VSTPTNUM, ~VSSTRESN,
"1001", "DIABP", "SCREENING", 1, 10, 64,
"1001", "DIABP", "SCREENING", 1, 11, 66,
"1001", "DIABP", "BASELINE", 2, 100, 68,
"1001", "DIABP", "BASELINE", 2, 101, 68,
"1001", "DIABP", "WEEK 2", 3, 200, 72,
"1001", "DIABP", "WEEK 2", 3, 201, 71,
"1001", "DIABP", "WEEK 4", 4, 300, 70,
"1001", "DIABP", "WEEK 4", 4, 301, 70
)
# Flag last value for each patient, test, and visit, baseline observations are ignored
example_vs %>%
restrict_derivation(
derivation = derive_var_extreme_flag,
args = params(
by_vars = exprs(USUBJID, VSTESTCD, VISIT),
order = exprs(VSTPTNUM),
new_var = LASTFL,
mode = "last"
),
filter = VISIT != "BASELINE"
) %>%
arrange(USUBJID, VSTESTCD, VISITNUM, VSTPTNUM) %>%
select(USUBJID, VSTESTCD, VISIT, VSTPTNUM, VSSTRESN, LASTFL)
# Baseline (ABLFL) examples:
input <- tribble(
~STUDYID, ~USUBJID, ~PARAMCD, ~AVISIT, ~ADT, ~AVAL, ~DTYPE,
"TEST01", "PAT01", "PARAM01", "BASELINE", as.Date("2021-04-27"), 15.0, NA,
"TEST01", "PAT01", "PARAM01", "BASELINE", as.Date("2021-04-25"), 14.0, NA,
"TEST01", "PAT01", "PARAM01", "BASELINE", as.Date("2021-04-23"), 15.0, "AVERAGE",
"TEST01", "PAT01", "PARAM01", "WEEK 1", as.Date("2021-04-27"), 10.0, "AVERAGE",
"TEST01", "PAT01", "PARAM01", "WEEK 2", as.Date("2021-04-30"), 12.0, NA,
"TEST01", "PAT02", "PARAM01", "SCREENING", as.Date("2021-04-27"), 15.0, "AVERAGE",
"TEST01", "PAT02", "PARAM01", "BASELINE", as.Date("2021-04-25"), 14.0, "AVERAGE",
"TEST01", "PAT02", "PARAM01", "BASELINE", as.Date("2021-04-23"), 15.0, "AVERAGE",
"TEST01", "PAT02", "PARAM01", "WEEK 1", as.Date("2021-04-27"), 10.0, "AVERAGE",
"TEST01", "PAT02", "PARAM01", "WEEK 2", as.Date("2021-04-30"), 12.0, "AVERAGE",
"TEST01", "PAT01", "PARAM02", "SCREENING", as.Date("2021-04-27"), 15.0, "AVERAGE",
"TEST01", "PAT01", "PARAM02", "SCREENING", as.Date("2021-04-25"), 14.0, "AVERAGE",
"TEST01", "PAT01", "PARAM02", "SCREENING", as.Date("2021-04-23"), 15.0, NA,
"TEST01", "PAT01", "PARAM02", "BASELINE", as.Date("2021-04-27"), 10.0, "AVERAGE",
"TEST01", "PAT01", "PARAM02", "WEEK 2", as.Date("2021-04-30"), 12.0, NA,
"TEST01", "PAT02", "PARAM02", "SCREENING", as.Date("2021-04-27"), 15.0, NA,
"TEST01", "PAT02", "PARAM02", "BASELINE", as.Date("2021-04-25"), 14.0, NA,
"TEST01", "PAT02", "PARAM02", "WEEK 1", as.Date("2021-04-23"), 15.0, NA,
"TEST01", "PAT02", "PARAM02", "WEEK 1", as.Date("2021-04-27"), 10.0, NA,
"TEST01", "PAT02", "PARAM02", "BASELINE", as.Date("2021-04-30"), 12.0, NA
)
# Last observation
restrict_derivation(
input,
derivation = derive_var_extreme_flag,
args = params(
by_vars = exprs(USUBJID, PARAMCD),
order = exprs(ADT),
new_var = ABLFL,
mode = "last"
),
filter = AVISIT == "BASELINE"
)
# Worst observation - Direction = High
restrict_derivation(
input,
derivation = derive_var_extreme_flag,
args = params(
by_vars = exprs(USUBJID, PARAMCD),
order = exprs(AVAL, ADT),
new_var = ABLFL,
mode = "last"
),
filter = AVISIT == "BASELINE"
)
# Worst observation - Direction = Lo
restrict_derivation(
input,
derivation = derive_var_extreme_flag,
args = params(
by_vars = exprs(USUBJID, PARAMCD),
order = exprs(desc(AVAL), ADT),
new_var = ABLFL,
mode = "last"
),
filter = AVISIT == "BASELINE"
)
# Average observation
restrict_derivation(
input,
derivation = derive_var_extreme_flag,
args = params(
by_vars = exprs(USUBJID, PARAMCD),
order = exprs(ADT, desc(AVAL)),
new_var = ABLFL,
mode = "last"
),
filter = AVISIT == "BASELINE" & DTYPE == "AVERAGE"
)
# OCCURDS Examples
example_ae <- tribble(
~USUBJID, ~AEBODSYS, ~AEDECOD, ~AESEV, ~AESTDY, ~AESEQ,
"1015", "GENERAL DISORDERS", "ERYTHEMA", "MILD", 2, 1,
"1015", "GENERAL DISORDERS", "PRURITUS", "MILD", 2, 2,
"1015", "GI DISORDERS", "DIARRHOEA", "MILD", 8, 3,
"1023", "CARDIAC DISORDERS", "AV BLOCK", "MILD", 22, 4,
"1023", "SKIN DISORDERS", "ERYTHEMA", "MILD", 3, 1,
"1023", "SKIN DISORDERS", "ERYTHEMA", "SEVERE", 5, 2,
"1023", "SKIN DISORDERS", "ERYTHEMA", "MILD", 8, 3
)
# Most severe AE first occurrence per patient
example_ae %>%
mutate(
TEMP_AESEVN =
as.integer(factor(AESEV, levels = c("SEVERE", "MODERATE", "MILD")))
) %>%
derive_var_extreme_flag(
new_var = AOCCIFL,
by_vars = exprs(USUBJID),
order = exprs(TEMP_AESEVN, AESTDY, AESEQ),
mode = "first"
) %>%
arrange(USUBJID, AESTDY, AESEQ) %>%
select(USUBJID, AEDECOD, AESEV, AESTDY, AESEQ, AOCCIFL)
# Most severe AE first occurrence per patient (flag all cases)
example_ae %>%
mutate(
TEMP_AESEVN =
as.integer(factor(AESEV, levels = c("SEVERE", "MODERATE", "MILD")))
) %>%
derive_var_extreme_flag(
new_var = AOCCIFL,
by_vars = exprs(USUBJID),
order = exprs(TEMP_AESEVN, AESTDY),
mode = "first",
flag_all = TRUE
) %>%
arrange(USUBJID, AESTDY) %>%
select(USUBJID, AEDECOD, AESEV, AESTDY, AOCCIFL)
# Most severe AE first occurrence per patient per body system
example_ae %>%
mutate(
TEMP_AESEVN =
as.integer(factor(AESEV, levels = c("SEVERE", "MODERATE", "MILD")))
) %>%
derive_var_extreme_flag(
new_var = AOCCSIFL,
by_vars = exprs(USUBJID, AEBODSYS),
order = exprs(TEMP_AESEVN, AESTDY, AESEQ),
mode = "first"
) %>%
arrange(USUBJID, AESTDY, AESEQ) %>%
select(USUBJID, AEBODSYS, AESEV, AESTDY, AOCCSIFL)