View source: R/period_dataset.R
create_period_dataset | R Documentation |
The function creates a reference dataset for subperiods, periods, or phases
from the ADSL
dataset. The reference dataset can be used to derive
subperiod, period, or phase variables like ASPER
, ASPRSDT
, ASPREDT
,
APERIOD
, APERSDT
, APEREDT
, TRTA
, APHASEN
, PHSDTM
, PHEDTM
, ...
in OCCDS and BDS datasets.
create_period_dataset(
dataset,
new_vars,
subject_keys = get_admiral_option("subject_keys")
)
dataset |
Input dataset The variables specified by the |
new_vars |
New variables A named list of variables like If the lower case letter "w" is used it refers to a phase variable, if the lower case letters "xx" are used it refers to a period variable, and if both "xx" and "w" are used it refers to a subperiod variable. Only one type must be used, e.g., all right hand side values must refer to period variables. It is not allowed to mix for example period and subperiod variables. If period and subperiod variables are required, separate reference datasets must be created. |
subject_keys |
Variables to uniquely identify a subject A list of expressions where the expressions are symbols as returned by
|
For each subject and each subperiod/period/phase where at least one
of the source variable is not NA
an observation is added to the output
dataset.
Depending on the type of the source variable (subperiod, period, or phase)
the variable ASPER
, APERIOD
, or APHASEN
is added and set to the
number of the subperiod, period, or phase.
The variables specified for new_vars
(left hand side) are added to the
output dataset and set to the value of the source variable (right hand
side).
A period reference dataset (see "Details" section)
derive_vars_period()
Creating auxiliary datasets:
consolidate_metadata()
,
create_query_data()
,
create_single_dose_dataset()
library(tibble)
library(dplyr, warn.conflicts = FALSE)
library(lubridate)
# Create reference dataset for periods
adsl <- tribble(
~USUBJID, ~AP01SDT, ~AP01EDT, ~AP02SDT, ~AP02EDT, ~TRT01A, ~TRT02A,
"1", "2021-01-04", "2021-02-06", "2021-02-07", "2021-03-07", "A", "B",
"2", "2021-02-02", "2021-03-02", "2021-03-03", "2021-04-01", "B", "A",
) %>%
mutate(
across(matches("AP\\d\\d[ES]DT"), ymd)
) %>%
mutate(
STUDYID = "xyz"
)
create_period_dataset(
adsl,
new_vars = exprs(APERSDT = APxxSDT, APEREDT = APxxEDT, TRTA = TRTxxA)
)
# Create reference dataset for phases
adsl <- tribble(
~USUBJID, ~PH1SDT, ~PH1EDT, ~PH2SDT, ~PH2EDT, ~APHASE1, ~APHASE2,
"1", "2021-01-04", "2021-02-06", "2021-02-07", "2021-03-07", "TREATMENT", "FUP",
"2", "2021-02-02", "2021-03-02", NA, NA, "TREATMENT", NA
) %>%
mutate(
across(matches("PH\\d[ES]DT"), ymd)
) %>%
mutate(
STUDYID = "xyz"
)
create_period_dataset(
adsl,
new_vars = exprs(PHSDT = PHwSDT, PHEDT = PHwEDT, APHASE = APHASEw)
)
# Create reference datasets for subperiods
adsl <- tribble(
~USUBJID, ~P01S1SDT, ~P01S1EDT, ~P01S2SDT, ~P01S2EDT, ~P02S1SDT, ~P02S1EDT,
"1", "2021-01-04", "2021-01-19", "2021-01-20", "2021-02-06", "2021-02-07", "2021-03-07",
"2", "2021-02-02", "2021-03-02", NA, NA, "2021-03-03", "2021-04-01"
) %>%
mutate(
across(matches("P\\d\\dS\\d[ES]DT"), ymd)
) %>%
mutate(
STUDYID = "xyz"
)
create_period_dataset(
adsl,
new_vars = exprs(ASPRSDT = PxxSwSDT, ASPREDT = PxxSwEDT)
)
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