Prepare list of data of raw-data
sdtm <- list(
SDTM_DM = arrow::read_parquet(system.file("demo_gsmpharmaverse/data/SDTM/SDTM_DM.parquet", package = "workr")),
SDTM_VS = arrow::read_parquet(system.file("demo_gsmpharmaverse/data/SDTM/SDTM_VS.parquet", package = "workr"))
)Show Raw DM preview (first 6 rows)
| STUDYID | USUBJID | TRT01A |
|---|---|---|
| test_study | test_study-375 | DRUG X |
| test_study | test_study-376 | DRUG X |
| test_study | test_study-377 | DRUG X |
| test_study | test_study-378 | DRUG X |
| test_study | test_study-379 | DRUG X |
Show Raw VS preview (first 6 rows)
| oak_id | raw_source | patient_number | VSTESTCD | VSTEST | VSORRES | VSORRESU | VSPOS | VSLOC | VSLAT | VSDTC | VSTPT | VSTPTNUM | VISIT | VISITNUM | STUDYID | DOMAIN | VSCAT | USUBJID |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | vitals | 375 | SYSBP | Systolic Blood Pressure | 158.00 | mmHg | PRONE | NA | NA | 2015-05-16T07:25 | PREDOSE | 1 | VISIT1 | VISIT1 | test_study | VS | VITAL SIGNS | test_study-375 |
| 1 | vitals | 375 | DIABP | Diastolic Blood Pressure | 92.00 | mmHg | PRONE | NA | NA | 2015-05-16T07:25 | PREDOSE | 1 | VISIT1 | VISIT1 | test_study | VS | VITAL SIGNS | test_study-375 |
| 1 | vitals | 375 | PULSE | Pulse Rate | 63.00 | beats/min | NA | NA | NA | 2015-05-16T07:25 | PREDOSE | 1 | VISIT1 | VISIT1 | test_study | VS | VITAL SIGNS | test_study-375 |
| 1 | vitals | 375 | RESP | Respiratory Rate | 17.00 | breaths/min | NA | NA | NA | 2015-05-16T07:25 | PREDOSE | 1 | VISIT1 | VISIT1 | test_study | VS | VITAL SIGNS | test_study-375 |
| 1 | vitals | 375 | TEMP | Temperature | 40.48 | C | NA | SKIN | NA | 2015-05-16T07:25 | PREDOSE | 1 | VISIT1 | VISIT1 | test_study | VS | VITAL SIGNS | test_study-375 |
| 1 | vitals | 375 | OXYSAT | Oxygen Saturation | 98.00 | % | NA | FINGER | RIGHT | 2015-05-16T07:25 | PREDOSE | 1 | VISIT1 | VISIT1 | test_study | VS | VITAL SIGNS | test_study-375 |
Show YAML’s of admiral transformations
## ```yaml
## meta:
## ID: ADVS
## Type: ADAM
## Description: Create Basic ADVS
## Priority: 1
## spec:
## SDTM_DM:
## _all:
## required: true
## SDTM_VS:
## _all:
## required: true
## steps:
## - output: initial_advs
## name: admiral::derive_vars_merged
## params:
## dataset: SDTM_VS
## dataset_add: SDTM_DM
## new_vars: !expr exprs(TRT01A)
## by_vars: !expr exprs(STUDYID, USUBJID)
## - output: advs
## name: dplyr::mutate
## params:
## .data: initial_advs
## PARAMCD: !expr rlang::expr(.data[["VSTESTCD"]])
## AVAL: !expr rlang::expr(.data[["VSORRES"]])
## - output: advs
## name: admiral::derive_param_map
## params:
## dataset: advs
## by_vars: !expr exprs(STUDYID, USUBJID, TRT01A, VSDTC, VISIT, VISITNUM, VSTPT, VSTPTNUM)
## sysbp_code: 'SYSBP'
## diabp_code: 'DIABP'
## get_unit_expr: !expr rlang::expr(.data[["VSORRESU"]])
## ```This workflow was inspired by portions of this admiral
vignette.
ADAM_workflows <- workr::MakeWorkflowList(
strNames = "ADVS",
strPath = "demo_gsmpharmaverse/workflows/2_SDTM_TO_ADAM/",
strPackage = "workr"
)
ADAM <- workr::RunWorkflows(lWorkflows = ADAM_workflows, lData = sdtm)map2(ADAM, names(ADAM), function(x,y) arrow::write_parquet(x, paste0("demo_gsmpharmaverse/data/ADAM/",y,".parquet"))Show ADVS (first 6 rows)
| oak_id | raw_source | patient_number | VSTESTCD | VSTEST | VSORRES | VSORRESU | VSPOS | VSLOC | VSLAT | VSDTC | VSTPT | VSTPTNUM | VISIT | VISITNUM | STUDYID | DOMAIN | VSCAT | USUBJID | TRT01A | PARAMCD | AVAL |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | 2015-05-16T07:25 | PREDOSE | 1 | VISIT1 | VISIT1 | test_study | NA | NA | test_study-375 | DRUG X | MAP | 114.00000 |
| NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | 2015-05-16T10:25 | POSTDOSE | 2 | VISIT1 | VISIT1 | test_study | NA | NA | test_study-375 | DRUG X | MAP | 83.33333 |
| NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | 2018-05-06T02:01 | SCREENING | 1 | test_study | NA | NA | test_study-375 | DRUG X | MAP | 80.33333 | ||
| NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | 2008-10-23T01:19 | PREDOSE | 1 | VISIT1 | VISIT1 | test_study | NA | NA | test_study-376 | DRUG X | MAP | 73.66667 |
| NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | 2008-10-23T03:19 | POSTDOSE | 2 | VISIT1 | VISIT1 | test_study | NA | NA | test_study-376 | DRUG X | MAP | 96.00000 |