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Incorporating cards

Source: vignettes/articles/ARS_example.Rmd
ARS_example.Rmd

Prepare list of data of raw-data 

adam <- list(
  ADVS = arrow::read_parquet(system.file("demo_gsmpharmaverse/data/ADAM/ADAM_ADVS.parquet", package = "workr"))
)
Show ADAM 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 TRT01A PARAMCD AVAL
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 DRUG X SYSBP 158.00
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 DRUG X DIABP 92.00
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 DRUG X PULSE 63.00
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 DRUG X RESP 17.00
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 DRUG X TEMP 40.48
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 DRUG X OXYSAT 98.00

Show YAML’s of cards transformations 

## ```yaml
## meta:
##   ID: table_mean_arterial_pressure
##   Type: ars
##   Description: Create table 1 ARS
##   Priority: 1
## spec:
##   ADVS:
##     _all:
##       required: true
## steps:
##   - output: predose_visit1_map
##     name: workr::RunQuery
##     params:
##       df: ADVS
##       strQuery: "SELECT * FROM df WHERE PARAMCD = 'MAP' AND VISIT = 'VISIT1' AND VSTPT = 'PREDOSE'"
##   - output: table_predose_visit1_map
##     name: cards::ard_summary
##     params:
##       data: predose_visit1_map
##       variables:
##         - AVAL
## ```

This workflow combines aspects of gtsummary and safetyCharts modules to demonstrate how to assemble multiple static outputs or a hybrid approach that may include shiny/web app html-based modules.

ARS_workflows <- workr::MakeWorkflowList(
  strNames = "table_mean_arterial_pressure",
  strPath = "demo_gsmpharmaverse/workflows/3_ADAM_TO_ARS/",
  strPackage = "workr"
)
ARS <- workr::RunWorkflows(lWorkflows = ARS_workflows, lData = adam )
map2(ARS, names(ARS), function(x,y) arrow::write_parquet(x, paste0("demo_gsmpharmaverse/data/ARS/", y,".parquet")))
Show Table 1 ARS (first 6 rows)
variable context stat_name stat_label stat fmt_fun warning error
AVAL summary N N 2 0
AVAL summary mean Mean 93.83333 1
AVAL summary sd SD 28.51997 1
AVAL summary median Median 93.83333 1
AVAL summary p25 Q1 73.66667 1
AVAL summary p75 Q3 114 1
AVAL summary min Min 73.66667 1
AVAL summary max Max 114 1