Feature Request: `assign_datetime` algorithm

Feature Idea

The assign_datetime algorithm will be implemented as a function. As referred in the documentation, this will be used to assign a value.

Algorithm Description - One-to-one mapping of the raw date and/or time source to a target SDTM variable in iso8601 format

Example mappings - CM.CMSTDTC AE.AEENDTC

function call

assign_datetime(
    raw_dat,
    raw_var,
    raw_fmt,
    raw_unk,
    tgt_var,
    tgt_dat,
    id_vars
 )

Input: raw_dat The raw dataset.

raw_var The raw variable.

raw_fmt - Format of the raw variable

raw_unk - Format of the unknown date and time components.

tgt_var The target SDTM variable.

tgt_dat - Optional parameter. This is the target_dataset that was created in the previous step.

id_vars - Optional parameter. A vector with the string that will be used to merge to the target_dataset

Output: A dataframe with oak_id_vars and target_sdtm_variable if tgt_dat & id_vars are not provided tgt_dat with one additional variable target_sdtm_variable

Relevant Input

sdtm spec

study_number	raw_source_model	raw_dataset	raw_dataset_ordinal	raw_dataset_label	raw_variable	raw_variable_label	raw_variable_ordinal	raw_variable_type	raw_data_format	raw_codelist	study_specific	annotation_ordinal	mapping_is_dataset	annotation_text	target_sdtm_domain	target_sdtm_variable	target_sdtm_variable_role	target_sdtm_variable_codelist_code	target_sdtm_variable_controlled_terms_or_format	target_sdtm_variable_ordinal	origin	mapping_algorithm	entity_sub_algorithm	target_hardcoded_value	target_term_value	target_term_code	condition_ordinal	condition_group_ordinal	condition_left_raw_dataset	condition_left_raw_variable	condition_left_sdtm_domain	condition_left_sdtm_variable	condition_operator	condition_right_text_value	condition_right_sdtm_domain	condition_right_sdtm_variable	condition_right_raw_dataset	condition_right_raw_variable	condition_next_logical_operator	merge_type	merge_left	merge_right	merge_condition	unduplicate_keys	groupby_keys	target_resource_raw_dataset	target_resource_raw_variable
lp_study	e-CRF	MD1	27	Concomitant Medications	MDBDR	Start date	5	DateTime	dd- MMM- yyyy	NA	FALSE	1	FALSE	CM.CMSTDTC	CM	CMSTDTC	Timing Variable	NA	ISO 8601	39	CRF	ASSIGN_NO_CT	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
lp_study	e-CRF	MD1	27	Concomitant Medications	MDEDR	End date	10	DateTime	dd- MMM- yyyy	NA	FALSE	1	FALSE	CM.CMENDTC	CM	CMENDTC	Timing Variable	NA	ISO 8601	40	CRF	ASSIGN_NO_CT	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
lp_study	e-CRF	MD1	27	Concomitant Medications	MDETM	End time	11	DateTime	HH nn	NA	FALSE	1	FALSE	CM.CMENDTC	CM	CMENDTC	Timing Variable	NA	ISO 8601	40	CRF	ASSIGN_NO_CT	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA

raw_datasaet = MD1	oak_id	raw_source	patient_number	MDBDR	MDEDR
1	MD1	375	NA	NA	NA
2	MD1	375	15-Sep-20	NA	NA
3	MD1	376	17-Feb-21	17-Feb-21	NA
4	MD1	377	4-Oct-20	NA	NA
5	MD1	377	20-Jan-20	20-Jan-20	10:00:00
6	MD1	377	UN-UNK-2019	UN-UNK-2019	NA
7	MD1	377	20-UNK-2019	20-UNK-2019	NA
8	MD1	378	UN-UNK-2020	UN-UNK-2020	NA
9	MD1	378	26-Jan-20	26-Jan-20	07:00:00
10	MD1	378	28-Jan-20	1-Feb-20	NA
11	MD1	378	12-Feb-20	18-Feb-20	NA
12	MD1	379	10-UNK-2020	20-UNK-2020	NA
13	MD1	379	NA	NA	NA
14	MD1	379	NA	17-Feb-20	NA

raw_var = "MDBDR"

raw_fmt = "d-m-y"

raw_unk = c("UN", "UNK")

tar_var = "CMSTDTC"

tar_dat = cm_inter - Let's assume CMTRT, CMINDC variables are already derived and CMSTDTC is the third variable being processed

oak_id	raw_source	patient_number	CMTRT	CMINDC
1	MD1	375	BABY ASPIRIN	NA
2	MD1	375	CORTISPORIN	NAUSEA
3	MD1	376	ASPIRIN	ANEMIA
4	MD1	377	DIPHENHYDRAMINE HCL	NAUSEA
5	MD1	377	PARCETEMOL	PYREXIA
6	MD1	377	VOMIKIND	VOMITINGS
7	MD1	377	ZENFLOX OZ	DIARHHEA
8	MD1	378	AMITRYPTYLINE	COLD
9	MD1	378	BENADRYL	FEVER
10	MD1	378	DIPHENHYDRAMINE HYDROCHLORIDE	LEG PAIN
11	MD1	378	TETRACYCLINE	FEVER
12	MD1	379	BENADRYL	COLD
13	MD1	379	SOMINEX	COLD
14	MD1	379	ZQUILL	PAIN

id_vars - oak_id_vars()

Relevant Output

Option 1 - When used without merde and id_vars. The function call is

assign_datetime(
raw_dat = MD1
raw_var = "MDBDR",
raw_fmt = "d-m-y",
raw_unk = c("UN", "UNK"),
tar_var = "CMSTDTC")

output dataset from the function

oak_id	raw_source	patient_number	CMSTDTC
1	MD1	375	NA
2	MD1	375	2020-09-15
3	MD1	376	2021-02-17
4	MD1	377	2020-10-04
5	MD1	377	2020-01-20
6	MD1	377	2019
7	MD1	377	2019---20
8	MD1	378	2020
9	MD1	378	2020-01-26
10	MD1	378	2020-01-28
11	MD1	378	2020-02-12
12	MD1	379	2020---10
13	MD1	379	NA
14	MD1	379	NA

Option 2 - When used with merging and id_vars

assign_datetime(
raw_dat = MD1
raw_var = "MDBDR",
raw_fmt = "d-m-y",
raw_unk = c("UN", "UNK"),
tar_var = "CMSTDTC"),
tar_dat = cm_inter,
id_vars = oak_id_vars())

Output dataset

oak_id	raw_source	patient_number	CMTRT	CMINDC	CMSTDTC
1	MD1	375	BABY ASPIRIN	NA	NA
2	MD1	375	CORTISPORIN	NAUSEA	2020-09-15
3	MD1	376	ASPIRIN	ANEMIA	2021-02-17
4	MD1	377	DIPHENHYDRAMINE HCL	NAUSEA	2020-10-04
5	MD1	377	PARCETEMOL	PYREXIA	2020-01-20
6	MD1	377	VOMIKIND	VOMITINGS	2019
7	MD1	377	ZENFLOX OZ	DIARHHEA	2019---20
8	MD1	378	AMITRYPTYLINE	COLD	2020
9	MD1	378	BENADRYL	FEVER	2020-01-26
10	MD1	378	DIPHENHYDRAMINE HYDROCHLORIDE	LEG PAIN	2020-01-28
11	MD1	378	TETRACYCLINE	FEVER	2020-02-12
12	MD1	379	BENADRYL	COLD	2020---10
13	MD1	379	SOMINEX	COLD	NA
14	MD1	379	ZQUILL	PAIN	NA

Reproducible Example/Pseudo Code

library(sdtm.oak)
library(dplyr)

#Option 1 - Just to derive CMSTDTC

assign_datetime(
raw_dat = MD1
raw_var = "MDBDR",
raw_fmt = "d-m-y",
raw_unk = c("UN", "UNK"),
tar_var = "CMSTDTC")

#Option 2 - Derive cmstdtc along and merge it

cm <- cm_daw_data |>
  # Derive topic variable
  assign_no_ct(
    raw_dataset = MD1, 
    raw_variable = MDRAW,
    target_sdtm_var = CMTRT
  )  |>
  assign_no_ct(
    raw_dataset = MD1,
    raw_variable = MDIND,
    target_sdtm_var = CMINDC,
    merge_to_topic_by = c("oak_id","raw_source","patient_number")
  ) |>
assign_datetime(
raw_dat = MD1
raw_var = "MDBDR",
raw_fmt = "d-m-y",
raw_unk = c("UN", "UNK"),
tar_var = "CMSTDTC"),
tar_dat = cm_inter,
id_vars = oak_id_vars())

pharmaverse / sdtm.oak