Prepare list of data of raw-data
lData <- list(
dm_raw = read.csv(system.file("raw_data/dm.csv", package = "sdtm.oak")),
vs_raw = read.csv(system.file("raw_data/vitals_raw_data.csv", package = "sdtm.oak")),
study_ct = read.csv(system.file("raw_data/sdtm_ct.csv", package = "sdtm.oak"))
)Show Raw DM preview (first 6 rows)
| STUDYID | DOMAIN | USUBJID | SUBJID | RFSTDTC | RFENDTC | RFXSTDTC | RFXENDTC | RFICDTC | RFPENDTC | DTHDTC | DTHFL | SITEID | INVID | INVNAM | BRTHDTC | AGE | AGEU | SEX | RACE | ETHNIC | ARMCD | ARM | ACTARMCD | ACTARM | COUNTRY | DMDTC | DMDY | RACE1 | RACE2 | RACE3 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| test_study | DM | test_study-375 | test_study-375 | 1999-04-14T08:36 | 2013-01-21 | 2023-04-14T08:36 | 2021-01-11T07:50 | 2007-01-15 | 2020-04-02 | 2020-04-02 | Y | 111111 | 90009 | Dr doctor9 | NA | NA | NA | F | MULTIPLE | NA | NA | NA | NA | NA | US | NA | NA | NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER | WHITE | NA |
| test_study | DM | test_study-376 | test_study-376 | 2001-03-21 | 2007-05-21 | 2020-03-21 | 2017-09-14T18:49 | NA | 2011-12-18 | 2011-12-18 | NA | 111111 | 90009 | Dr doctor9 | 1981-02-26T18:07 | 42 | YEARS | M | MULTIPLE | NOT HISPANIC OR LATINO | NA | NA | NA | NA | US | NA | NA | BLACK OR AFRICAN AMERICAN | AMERICAN INDIAN OR ALASKA NATIVE | UNKNOWN |
| test_study | DM | test_study-377 | test_study-377 | 1999-03-14 | 2021-05-05 | 2020-03-14 | 2013-08-23T12:37 | 2015-10-07 | 2021-05-05 | 2019-06-29 | NA | 111111 | 90009 | Dr doctor9 | 1968-03-19T04:36 | 56 | YEARS | NA | MULTIPLE | NOT REPORTED | NA | NA | NA | NA | US | NA | NA | ASIAN | AMERICAN INDIAN OR ALASKA NATIVE | UNKNOWN |
| test_study | DM | test_study-378 | test_study-378 | 2003-02-06T06:33 | 2021-04-24T09:06 | 2021-02-06T06:33 | 2021-04-24T09:06 | 2018-10-20 | 2017-04-11 | 2017-04-11 | NA | 111111 | 90009 | Dr doctor9 | 1979-09-24 | 45 | YEARS | M | BLACK OR AFRICAN AMERICAN | HISPANIC OR LATINO | NA | NA | NA | NA | US | NA | NA | NA | NA | NA |
| test_study | DM | test_study-379 | test_study-379 | 2003-02-06T06:33 | 2021-04-24T09:06 | 2022-02-06T06:33 | 2021-04-24T09:06 | 2018-10-20 | 2017-04-11 | 2017-04-11 | Y | 111111 | 90009 | Dr doctor9 | 1963-09-24 | 61 | YEARS | M | BLACK OR AFRICAN AMERICAN | HISPANIC OR LATINO | NA | NA | NA | NA | US | NA | NA | NA | NA | NA |
Show Raw VS preview (first 6 rows)
| STUDY | PATNUM | SUBJSTAT | SITENM | INSTANCE | FORM | FORML | DATAPGID | RECORDID | RECPOS | ASMNTDN | TMPTC | VTLD | VTLTM | SUBPOS | SYS_BP | DIA_BP | PULSE | RESPRT | TEMP | TEMPLOC | OXY_SAT | LAT | LOC | VSO2SRC | NEWS107 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Test Study | 375 | Randomized | Test Study | VISIT1 | VTLS1 | Vital Signs | 1752329 | 5734754 | 0 | 0 | Pre-dose | 16-May-15 | 7:25 | PRONE | 158 | 92 | 63 | 17 | 40.48 | SKIN | 98 | RIGHT | FINGER | MASK OXYGEN THERAPY | UNRESPONSIVE |
| Test Study | 375 | Randomized | Test Study | VISIT1 | VTLS1 | Vital Signs | 8153061 | 3712412 | 1 | 0 | Post-dose | 16-May-15 | 10:25 | SEMI-RECUMBENT | 94 | 78 | 76 | 20 | 36.75 | TYMPANIC MEMBRANE | 99 | LEFT | FINGER | ROOM AIR | NEW CONFUSION |
| Test Study | 375 | Randomized | Test Study | Screening | VTLS1 | Vital Signs | 3463516 | 1229594 | 0 | 0 | 6-May-18 | 2:01 | PRONE | 117 | 62 | 66 | 15 | 29.45 | ORAL CAVITY | 96 | LEFT | FINGER | ROOM AIR | VERBAL RESPONSIVE | |
| Test Study | 376 | Randomized | Test Study | Screening | VTLS1 | Vital Signs | 8423253 | 9767053 | 0 | 1 | NA | NA | NA | NA | NA | NA | |||||||||
| Test Study | 376 | Randomized | Test Study | VISIT1 | VTLS1 | Vital Signs | 1211365 | 1567778 | 0 | 0 | Pre-dose | 23-Oct-08 | 1:19 | PRONE | 85 | 68 | 73 | 21 | 38.25 | AXILLA | 93 | RIGHT | FINGER | ROOM AIR | ALERT |
| Test Study | 376 | Randomized | Test Study | VISIT1 | VTLS1 | Vital Signs | 5880552 | 7060998 | 0 | 0 | Post-dose | 23-Oct-08 | 3:19 | PRONE | 126 | 81 | 56 | 18 | 38.08 | TYMPANIC MEMBRANE | 93 | LEFT | FINGER | MASK OXYGEN THERAPY | PAIN RESPONSIVE |
Show Study CT preview (first 6 rows)
| codelist_code | term_code | term_value | collected_value | term_preferred_term | term_synonyms |
|---|---|---|---|---|---|
| C66726 | C25158 | CAPSULE | Capsule | Capsule Dosage Form | cap |
| C66726 | C25394 | PILL | Pill | Pill Dosage Form | |
| C66726 | C29167 | LOTION | Lotion | Lotion Dosage Form | |
| C66726 | C42887 | AEROSOL | Aerosol | Aerosol Dosage Form | aer |
| C66726 | C42944 | INHALANT | Inhalant | Inhalant Dosage Form | |
| C66726 | C42946 | INJECTION | Injection | Injectable Dosage Form |
Show YAML’s of sdtm.oak transformations
## ```yaml
## meta:
## ID: DM
## Type: SDTM
## Description: Transform Raw DM to SDTM DM
## Priority: 1
## spec:
## dm_raw:
## STUDYID:
## type: character
## USUBJID:
## type: character
## steps:
## - output: dm
## name: workr::RunQuery
## params:
## df: dm_raw
## strQuery: "SELECT STUDYID, USUBJID, 'DRUG X' as TRT01A FROM df"
## ```## ```yaml
## meta:
## ID: VS
## Type: SDTM
## Description: Transform Raw VS to SDTM VS following sdtm.oak article
## Priority: 1
## spec:
## # Read in data
## vs_raw:
## _all:
## required: true
## study_ct:
## _all:
## required: true
## steps:
## # Create oak_id_vars
## - output: vs_raw
## name: sdtm.oak::generate_oak_id_vars
## params:
## raw_dat: vs_raw
## pat_var: "PATNUM"
## raw_src: "vitals"
## # Map topic variable SYSBP and its qualifiers.
## - output: vs_sysbp
## name: sdtm.oak::hardcode_ct
## params:
## raw_dat: vs_raw
## raw_var: "SYS_BP"
## tgt_var: "VSTESTCD"
## tgt_val: "SYSBP"
## ct_spec: study_ct
## ct_clst: "C66741"
## - output: vs_sysbp
## name: workr::RunQuery
## params:
## df: vs_sysbp
## strQuery: "SELECT * FROM df WHERE VSTESTCD IS NOT NULL"
## # Map topic variable SYSBP and its qualifiers.
## - output: vs_sysbp
## name: sdtm.oak::hardcode_ct
## params:
## tgt_dat: vs_sysbp
## raw_dat: vs_raw
## raw_var: "SYS_BP"
## tgt_var: "VSTEST"
## tgt_val: "Systolic Blood Pressure"
## ct_spec: study_ct
## ct_clst: "C67153"
## - output: vs_sysbp
## name: sdtm.oak::assign_no_ct
## params:
## tgt_dat: vs_sysbp
## raw_dat: vs_raw
## raw_var: "SYS_BP"
## tgt_var: "VSORRES"
## - output: vs_sysbp
## name: sdtm.oak::hardcode_ct
## params:
## tgt_dat: vs_sysbp
## raw_dat: vs_raw
## raw_var: "SYS_BP"
## tgt_var: "VSORRESU"
## tgt_val: "mmHg"
## ct_spec: study_ct
## ct_clst: "C66770"
## - output: vs_sysbp
## name: sdtm.oak::assign_ct
## params:
## tgt_dat: vs_sysbp
## raw_dat: vs_raw
## raw_var: "SUBPOS"
## tgt_var: "VSPOS"
## ct_spec: study_ct
## ct_clst: "C71148"
##
## # Map topic variable DIABP and its qualifiers.
## - output: vs_diabp
## name: sdtm.oak::hardcode_ct
## params:
## raw_dat: vs_raw
## raw_var: "DIA_BP"
## tgt_var: "VSTESTCD"
## tgt_val: "DIABP"
## ct_spec: study_ct
## ct_clst: "C66741"
## - output: vs_diabp
## name: workr::RunQuery
## params:
## df: vs_diabp
## strQuery: "SELECT * FROM df WHERE VSTESTCD IS NOT NULL"
## - output: vs_diabp
## name: sdtm.oak::hardcode_ct
## params:
## tgt_dat: vs_diabp
## raw_dat: vs_raw
## raw_var: "DIA_BP"
## tgt_var: "VSTEST"
## tgt_val: "Diastolic Blood Pressure"
## ct_spec: study_ct
## ct_clst: "C67153"
## - output: vs_diabp
## name: sdtm.oak::assign_no_ct
## params:
## tgt_dat: vs_diabp
## raw_dat: vs_raw
## raw_var: "DIA_BP"
## tgt_var: "VSORRES"
## - output: vs_diabp
## name: sdtm.oak::hardcode_ct
## params:
## tgt_dat: vs_diabp
## raw_dat: vs_raw
## raw_var: "DIA_BP"
## tgt_var: "VSORRESU"
## tgt_val: "mmHg"
## ct_spec: study_ct
## ct_clst: "C66770"
## - output: vs_diabp
## name: sdtm.oak::assign_ct
## params:
## tgt_dat: vs_diabp
## raw_dat: vs_raw
## raw_var: "SUBPOS"
## tgt_var: "VSPOS"
## ct_spec: study_ct
## ct_clst: "C71148"
##
## - output: vs_pulse
## name: sdtm.oak::hardcode_ct
## params:
## raw_dat: vs_raw
## raw_var: "PULSE"
## tgt_var: "VSTESTCD"
## tgt_val: "PULSE"
## ct_spec: study_ct
## ct_clst: "C66741"
## - output: vs_pulse
## name: workr::RunQuery
## params:
## df: vs_pulse
## strQuery: "SELECT * FROM df WHERE VSTESTCD IS NOT NULL"
## - output: vs_pulse
## name: sdtm.oak::hardcode_ct
## params:
## tgt_dat: vs_pulse
## raw_dat: vs_raw
## raw_var: "PULSE"
## tgt_var: "VSTEST"
## tgt_val: "Pulse Rate"
## ct_spec: study_ct
## ct_clst: "C67153"
## - output: vs_pulse
## name: sdtm.oak::assign_no_ct
## params:
## tgt_dat: vs_pulse
## raw_dat: vs_raw
## raw_var: "PULSE"
## tgt_var: "VSORRES"
## - output: vs_pulse
## name: sdtm.oak::hardcode_ct
## params:
## tgt_dat: vs_pulse
## raw_dat: vs_raw
## raw_var: "PULSE"
## tgt_var: "VSORRESU"
## tgt_val: "beats/min"
## ct_spec: study_ct
## ct_clst: "C66770"
##
## - output: vs_resp
## name: sdtm.oak::hardcode_ct
## params:
## raw_dat: vs_raw
## raw_var: "RESPRT"
## tgt_var: "VSTESTCD"
## tgt_val: "RESP"
## ct_spec: study_ct
## ct_clst: "C66741"
## - output: vs_resp
## name: workr::RunQuery
## params:
## df: vs_resp
## strQuery: "SELECT * FROM df WHERE VSTESTCD IS NOT NULL"
## - output: vs_resp
## name: sdtm.oak::hardcode_ct
## params:
## tgt_dat: vs_resp
## raw_dat: vs_raw
## raw_var: "RESPRT"
## tgt_var: "VSTEST"
## tgt_val: "Respiratory Rate"
## ct_spec: study_ct
## ct_clst: "C67153"
## - output: vs_resp
## name: sdtm.oak::assign_no_ct
## params:
## tgt_dat: vs_resp
## raw_dat: vs_raw
## raw_var: "RESPRT"
## tgt_var: "VSORRES"
## - output: vs_resp
## name: sdtm.oak::hardcode_ct
## params:
## tgt_dat: vs_resp
## raw_dat: vs_raw
## raw_var: "RESPRT"
## tgt_var: "VSORRESU"
## tgt_val: "breaths/min"
## ct_spec: study_ct
## ct_clst: "C66770"
##
## - output: vs_temp
## name: sdtm.oak::hardcode_ct
## params:
## raw_dat: vs_raw
## raw_var: "TEMP"
## tgt_var: "VSTESTCD"
## tgt_val: "TEMP"
## ct_spec: study_ct
## ct_clst: "C66741"
## - output: vs_temp
## name: workr::RunQuery
## params:
## df: vs_temp
## strQuery: "SELECT * FROM df WHERE VSTESTCD IS NOT NULL"
## - output: vs_temp
## name: sdtm.oak::hardcode_ct
## params:
## tgt_dat: vs_temp
## raw_dat: vs_raw
## raw_var: "TEMP"
## tgt_var: "VSTEST"
## tgt_val: "Temperature"
## ct_spec: study_ct
## ct_clst: "C67153"
## - output: vs_temp
## name: sdtm.oak::assign_no_ct
## params:
## tgt_dat: vs_temp
## raw_dat: vs_raw
## raw_var: "TEMP"
## tgt_var: "VSORRES"
## - output: vs_temp
## name: sdtm.oak::hardcode_ct
## params:
## tgt_dat: vs_temp
## raw_dat: vs_raw
## raw_var: "TEMP"
## tgt_var: "VSORRESU"
## tgt_val: "C"
## ct_spec: study_ct
## ct_clst: "C66770"
## - output: vs_temp
## name: sdtm.oak::assign_ct
## params:
## tgt_dat: vs_temp
## raw_dat: vs_raw
## raw_var: "TEMPLOC"
## tgt_var: "VSLOC"
## ct_spec: study_ct
## ct_clst: "C74456"
##
## - output: vs_oxysat
## name: sdtm.oak::hardcode_ct
## params:
## raw_dat: vs_raw
## raw_var: "OXY_SAT"
## tgt_var: "VSTESTCD"
## tgt_val: "OXYSAT"
## ct_spec: study_ct
## ct_clst: "C66741"
## - output: vs_oxysat
## name: workr::RunQuery
## params:
## df: vs_oxysat
## strQuery: "SELECT * FROM df WHERE VSTESTCD IS NOT NULL"
## - output: vs_oxysat
## name: sdtm.oak::hardcode_ct
## params:
## tgt_dat: vs_oxysat
## raw_dat: vs_raw
## raw_var: "OXY_SAT"
## tgt_var: "VSTEST"
## tgt_val: "Oxygen Saturation"
## ct_spec: study_ct
## ct_clst: "C67153"
## - output: vs_oxysat
## name: sdtm.oak::assign_no_ct
## params:
## tgt_dat: vs_oxysat
## raw_dat: vs_raw
## raw_var: "OXY_SAT"
## tgt_var: "VSORRES"
## - output: vs_oxysat
## name: sdtm.oak::hardcode_ct
## params:
## tgt_dat: vs_oxysat
## raw_dat: vs_raw
## raw_var: "OXY_SAT"
## tgt_var: "VSORRESU"
## tgt_val: "%"
## ct_spec: study_ct
## ct_clst: "C66770"
## - output: vs_oxysat
## name: sdtm.oak::assign_ct
## params:
## tgt_dat: vs_oxysat
## raw_dat: vs_raw
## raw_var: "LAT"
## tgt_var: "VSLAT"
## ct_spec: study_ct
## ct_clst: "C99073"
## - output: vs_oxysat
## name: sdtm.oak::assign_ct
## params:
## tgt_dat: vs_oxysat
## raw_dat: vs_raw
## raw_var: "LOC"
## tgt_var: "VSLOC"
## ct_spec: study_ct
## ct_clst: "C74456"
##
## - output: vs_raw_asmntdn_cond
## name: sdtm.oak::condition_add
## params:
## dat: vs_raw
## '...': !expr rlang::expr(ASMNTDN == 1L)
## - output: vs_vsall
## name: sdtm.oak::hardcode_ct
## params:
## raw_dat: vs_raw_asmntdn_cond
## raw_var: "ASMNTDN"
## tgt_var: "VSTESTCD"
## tgt_val: "VSALL"
## ct_spec: study_ct
## ct_clst: "C66741"
## - output: vs_vsall
## name: workr::RunQuery
## params:
## df: vs_vsall
## strQuery: "SELECT * FROM df WHERE VSTESTCD IS NOT NULL"
## - output: vs_vsall
## name: sdtm.oak::hardcode_ct
## params:
## tgt_dat: vs_vsall
## raw_dat: vs_raw
## raw_var: "ASMNTDN"
## tgt_var: "VSTEST"
## tgt_val: "Vital Signs"
## ct_spec: study_ct
## ct_clst: "C67153"
##
## # Combine all the topic variables into a single data frame and map qualifiers
## # applicable to all topic variables
## - output: vs
## name: dplyr::bind_rows
## params:
## vs_vsall: vs_vsall
## vs_sysbp: vs_sysbp
## vs_diabp: vs_diabp
## vs_pulse: vs_pulse
## vs_resp: vs_resp
## vs_temp: vs_temp
## vs_oxysat: vs_oxysat
## - output: vs
## name: sdtm.oak::assign_datetime
## params:
## tgt_dat: vs
## raw_dat: vs_raw
## raw_var: !expr rlang::expr(c("VTLD", "VTLTM"))
## tgt_var: "VSDTC"
## raw_fmt: !expr rlang::expr(c(list(c("d-m-y", "dd-mmm-yyyy")), "H:M"))
## - output: vs
## name: sdtm.oak::assign_ct
## params:
## tgt_dat: vs
## raw_dat: vs_raw
## raw_var: "TMPTC"
## tgt_var: "VSTPT"
## ct_spec: study_ct
## ct_clst: "TPT"
## - output: vs
## name: sdtm.oak::assign_ct
## params:
## tgt_dat: vs
## raw_dat: vs_raw
## raw_var: "TMPTC"
## tgt_var: "VSTPTNUM"
## ct_spec: study_ct
## ct_clst: "TPTNUM"
## - output: vs
## name: sdtm.oak::assign_ct
## params:
## tgt_dat: vs
## raw_dat: vs_raw
## raw_var: "INSTANCE"
## tgt_var: "VISIT"
## ct_spec: study_ct
## ct_clst: "VISIT"
## - output: vs
## name: sdtm.oak::assign_ct
## params:
## tgt_dat: vs
## raw_dat: vs_raw
## raw_var: "INSTANCE"
## tgt_var: "VISITNUM"
## ct_spec: study_ct
## ct_clst: "VISITNUM"
## - output: vs
## name: dplyr::mutate
## params:
## '.data': vs
## STUDYID: 'test_study'
## DOMAIN: 'VS'
## VSCAT: 'VITAL SIGNS'
## USUBJID: !expr rlang::expr(paste0("test_study", "-", .data$patient_number))
## ```This workflow was designed to mimic and follow this respective
sdtm.oak vignette.
Run Respective Workflows to Arrive at SDTM datasets
SDTM_workflows <- workr::MakeWorkflowList(
strNames = c("VS", "DM"),
strPath = "demo_gsmpharmaverse/workflows/1_RAW_TO_SDTM/",
strPackage = "workr"
)
SDTM <- workr::RunWorkflows(lWorkflows = SDTM_workflows, lData = lData)
# Take Results and save them as parquets in a SDTM folder
# or wherever it needs to be saved, gsm has a load/save configuartion as well
purrr::map2(
SDTM,
names(SDTM),
function(x,y) arrow::write_parquet(x, paste0("demo_gsmpharmaverse/data/SDTM/", y,".parquet"))
)Show SDTM VS (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 |