assign_datetime() maps one or more variables with date/time components in a
raw dataset to a target SDTM variable following the ISO8601 format.
Usage
assign_datetime(
tgt_dat = NULL,
tgt_var,
raw_dat,
raw_var,
raw_fmt,
raw_unk = c("UN", "UNK"),
id_vars = oak_id_vars(),
.warn = TRUE
)Arguments
- tgt_dat
Target dataset: a data frame to be merged against
raw_datby the variables indicated inid_vars. This parameter is optional, see section Value for how the output changes depending on this argument value.- tgt_var
The target SDTM variable: a single string indicating the name of variable to be derived.
- raw_dat
The raw dataset (dataframe); must include the variables passed in
id_varsandraw_var.- raw_var
The raw variable(s): a character vector indicating the name(s) of the raw variable(s) in
raw_datwith date or time components to be parsed into a ISO8601 format variable intgt_var.- raw_fmt
A date/time parsing format. Either a character vector or a list of character vectors. If a character vector is passed then each element is taken as parsing format for each variable indicated in
raw_var. If a list is provided, then each element must be a character vector of formats. The first vector of formats is used for parsing the first variable inraw_var, and so on.- raw_unk
A character vector of string literals to be regarded as missing values during parsing.
- id_vars
Key variables to be used in the join between the raw dataset (
raw_dat) and the target data set (tgt_dat).- .warn
Whether to warn about parsing failures.
Value
The returned data set depends on the value of tgt_dat:
If no target dataset is supplied, meaning that
tgt_datdefaults toNULL, then the returned data set israw_dat, selected for the variables indicated inid_vars, and a new extra column: the derived variable, as indicated intgt_var.If the target dataset is provided, then it is merged with the raw data set
raw_datby the variables indicated inid_vars, with a new column: the derived variable, as indicated intgt_var.
Examples
# `md1`: an example raw data set.
md1 <-
tibble::tribble(
~oak_id, ~raw_source, ~patient_number, ~MDBDR, ~MDEDR, ~MDETM,
1L, "MD1", 375, NA, NA, NA,
2L, "MD1", 375, "15-Sep-20", NA, NA,
3L, "MD1", 376, "17-Feb-21", "17-Feb-21", NA,
4L, "MD1", 377, "4-Oct-20", NA, NA,
5L, "MD1", 377, "20-Jan-20", "20-Jan-20", "10:00:00",
6L, "MD1", 377, "UN-UNK-2019", "UN-UNK-2019", NA,
7L, "MD1", 377, "20-UNK-2019", "20-UNK-2019", NA,
8L, "MD1", 378, "UN-UNK-2020", "UN-UNK-2020", NA,
9L, "MD1", 378, "26-Jan-20", "26-Jan-20", "07:00:00",
10L, "MD1", 378, "28-Jan-20", "1-Feb-20", NA,
11L, "MD1", 378, "12-Feb-20", "18-Feb-20", NA,
12L, "MD1", 379, "10-UNK-2020", "20-UNK-2020", NA,
13L, "MD1", 379, NA, NA, NA,
14L, "MD1", 379, NA, "17-Feb-20", NA
)
# Using the raw data set `md1`, derive the variable CMSTDTC from MDBDR using
# the parsing format (`raw_fmt`) `"d-m-y"` (day-month-year), while allowing
# for the presence of special date component values (e.g. `"UN"` or `"UNK"`),
# indicating that these values are missing/unknown (unk).
cm1 <-
assign_datetime(
tgt_var = "CMSTDTC",
raw_dat = md1,
raw_var = "MDBDR",
raw_fmt = "d-m-y",
raw_unk = c("UN", "UNK")
)
cm1
#> # A tibble: 14 × 4
#> oak_id raw_source patient_number CMSTDTC
#> <int> <chr> <dbl> <iso8601>
#> 1 1 MD1 375 NA
#> 2 2 MD1 375 2020-09-15
#> 3 3 MD1 376 2021-02-17
#> 4 4 MD1 377 2020-10-04
#> 5 5 MD1 377 2020-01-20
#> 6 6 MD1 377 2019
#> 7 7 MD1 377 2019---20
#> 8 8 MD1 378 2020
#> 9 9 MD1 378 2020-01-26
#> 10 10 MD1 378 2020-01-28
#> 11 11 MD1 378 2020-02-12
#> 12 12 MD1 379 2020---10
#> 13 13 MD1 379 NA
#> 14 14 MD1 379 NA
# Inspect parsing failures associated with derivation of CMSTDTC.
problems(cm1$CMSTDTC)
#> # A tibble: 3 × 2
#> ..i MDBDR
#> <int> <chr>
#> 1 1 NA
#> 2 13 NA
#> 3 14 NA
# `cm_inter`: an example target data set.
cm_inter <-
tibble::tibble(
oak_id = 1L:14L,
raw_source = "MD1",
patient_number = c(
375, 375, 376, 377, 377, 377, 377, 378,
378, 378, 378, 379, 379, 379
),
CMTRT = c(
"BABY ASPIRIN",
"CORTISPORIN",
"ASPIRIN",
"DIPHENHYDRAMINE HCL",
"PARCETEMOL",
"VOMIKIND",
"ZENFLOX OZ",
"AMITRYPTYLINE",
"BENADRYL",
"DIPHENHYDRAMINE HYDROCHLORIDE",
"TETRACYCLINE",
"BENADRYL",
"SOMINEX",
"ZQUILL"
),
CMINDC = c(
"NA",
"NAUSEA",
"ANEMIA",
"NAUSEA",
"PYREXIA",
"VOMITINGS",
"DIARHHEA",
"COLD",
"FEVER",
"LEG PAIN",
"FEVER",
"COLD",
"COLD",
"PAIN"
)
)
# Same derivation as above but now involving the merging with the target
# data set `cm_inter`.
cm2 <-
assign_datetime(
tgt_dat = cm_inter,
tgt_var = "CMSTDTC",
raw_dat = md1,
raw_var = "MDBDR",
raw_fmt = "d-m-y"
)
cm2
#> # A tibble: 14 × 6
#> oak_id raw_source patient_number CMTRT CMINDC CMSTDTC
#> <int> <chr> <dbl> <chr> <chr> <iso86>
#> 1 1 MD1 375 BABY ASPIRIN NA NA …
#> 2 2 MD1 375 CORTISPORIN NAUSEA 2020-0…
#> 3 3 MD1 376 ASPIRIN ANEMIA 2021-0…
#> 4 4 MD1 377 DIPHENHYDRAMINE HCL NAUSEA 2020-1…
#> 5 5 MD1 377 PARCETEMOL PYREX… 2020-0…
#> 6 6 MD1 377 VOMIKIND VOMIT… 2019 …
#> 7 7 MD1 377 ZENFLOX OZ DIARH… 2019--…
#> 8 8 MD1 378 AMITRYPTYLINE COLD 2020 …
#> 9 9 MD1 378 BENADRYL FEVER 2020-0…
#> 10 10 MD1 378 DIPHENHYDRAMINE HYDROCHLORIDE LEG P… 2020-0…
#> 11 11 MD1 378 TETRACYCLINE FEVER 2020-0…
#> 12 12 MD1 379 BENADRYL COLD 2020--…
#> 13 13 MD1 379 SOMINEX COLD NA …
#> 14 14 MD1 379 ZQUILL PAIN NA …
# Inspect parsing failures associated with derivation of CMSTDTC.
problems(cm2$CMSTDTC)
#> # A tibble: 3 × 2
#> ..i MDBDR
#> <int> <chr>
#> 1 1 NA
#> 2 13 NA
#> 3 14 NA
# Derive CMSTDTC using both MDEDR and MDETM variables.
# Note that the format `"d-m-y"` is used for parsing MDEDR and `"H:M:S"` for
# MDETM (correspondence is by positional matching).
cm3 <-
assign_datetime(
tgt_var = "CMSTDTC",
raw_dat = md1,
raw_var = c("MDEDR", "MDETM"),
raw_fmt = c("d-m-y", "H:M:S"),
raw_unk = c("UN", "UNK")
)
cm3
#> # A tibble: 14 × 4
#> oak_id raw_source patient_number CMSTDTC
#> <int> <chr> <dbl> <iso8601>
#> 1 1 MD1 375 NA
#> 2 2 MD1 375 NA
#> 3 3 MD1 376 2021-02-17
#> 4 4 MD1 377 NA
#> 5 5 MD1 377 2020-01-20T10:00:00
#> 6 6 MD1 377 2019
#> 7 7 MD1 377 2019---20
#> 8 8 MD1 378 2020
#> 9 9 MD1 378 2020-01-26T07:00:00
#> 10 10 MD1 378 2020-02-01
#> 11 11 MD1 378 2020-02-18
#> 12 12 MD1 379 2020---20
#> 13 13 MD1 379 NA
#> 14 14 MD1 379 2020-02-17
# Inspect parsing failures associated with derivation of CMSTDTC.
problems(cm3$CMSTDTC)
#> # A tibble: 12 × 3
#> ..i MDEDR MDETM
#> <int> <chr> <chr>
#> 1 1 NA NA
#> 2 2 NA NA
#> 3 3 17-Feb-21 NA
#> 4 4 NA NA
#> 5 6 UN-UNK-2019 NA
#> 6 7 20-UNK-2019 NA
#> 7 8 UN-UNK-2020 NA
#> 8 10 1-Feb-20 NA
#> 9 11 18-Feb-20 NA
#> 10 12 20-UNK-2020 NA
#> 11 13 NA NA
#> 12 14 17-Feb-20 NA