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Simulate synthetic ADaM datasets from a previously-saved study summary.

Source: R/simulate_study.R
simulate_study_from_summary.Rd

Reads a study summary written by glimpse_study() and produces synthetic datasets, decoupling simulation from the original .sas7bdat files.

Usage

simulate_study_from_summary(study_summary_path, output_dir, seed = NULL)

Arguments

study_summary_path

character - path to the .rds study summary written by glimpse_study().

output_dir

character - directory to write syn_{key}.rds files to. Created if missing.

seed

integer or NULL - simulation seed. When NULL (default), the seed stored in the study summary is used; if the study summary has no seed, it falls back to 123. Override to draw a different synthetic replicate from the same summaries.

Value

NULL (invisibly). Synthetic datasets are saved as syn_{key}.rds files in output_dir. Each dataset has a synadam_version attribute.

See also

glimpse_study(), simulate_study().

Examples

# Generate a config and glimpse the datasets into a study summary.
yaml_path <- generate_study_config(
  adam_dir,
  output_dir = file.path(tempdir(), "syn_data")
)
study_summary_path <- tempfile(fileext = ".rds")
glimpse_study(yaml_path, study_summary_path)
#> ----- Glimpsing adsl (adsl) dataset -----
#> Loading dataset from /tmp/Rtmpm0P6Ux/adam_dir/adsl.sas7bdat
#> Glimpsing treatment/flag columns
#> 2 treatment/flag combination(s) with count = 1 were masked and added to the most common combination.
#> Glimpsing column(s): REGION1, REGION1N
#> Glimpsing column(s): STUDYID
#> Glimpsing column(s): USUBJID
#> Glimpsing column(s): SUBJID
#> Glimpsing column(s): SITEID
#> Glimpsing column(s): AGE
#> Glimpsing column(s): AGEU
#> Glimpsing column(s): SEX
#> Glimpsing column(s): RACE
#> Glimpsing column(s): ETHNIC
#> Glimpsing column(s): COUNTRY
#> Glimpsing column(s): HEIGHTBL
#> Glimpsing column(s): WEIGHTBL
#> Glimpsing column(s): BMIBL
#> Glimpsing column(s): TRTSDT
#> Simulating column(s): treatment, flag
#> Simulating column(s): REGION1, REGION1N
#> Simulating column(s): STUDYID
#> Simulating column(s): USUBJID
#> Simulating column(s): SUBJID
#> Simulating column(s): SITEID
#> Simulating column(s): AGE
#> Simulating column(s): AGEU
#> Simulating column(s): SEX
#> Simulating column(s): RACE
#> Simulating column(s): ETHNIC
#> Simulating column(s): COUNTRY
#> Simulating column(s): HEIGHTBL
#> Simulating column(s): WEIGHTBL
#> Simulating column(s): BMIBL
#> Simulating column(s): TRTSDT
#> ----- Glimpsing adae (occds) dataset -----
#> Loading dataset from /tmp/Rtmpm0P6Ux/adam_dir/adae.sas7bdat
#> Glimpsing occurrence counts, ID and sequence columns
#> Glimpsing ADSL columns from synthetic ADSL
#> Glimpsing column(s): AESEV, AESEVN
#> Glimpsing column(s): AEBODSYS
#> Glimpsing column(s): AEDECOD
#> Glimpsing column(s): AESER
#> Glimpsing column(s): AEREL
#> Glimpsing column(s): ASTDT
#> Glimpsing column(s): AENDT
#> Saving study summary to /tmp/Rtmpm0P6Ux/file442831255562.rds...

# Simulate synthetic datasets from the saved study summary.
out_dir <- file.path(tempdir(), "syn_data")
simulate_study_from_summary(study_summary_path, out_dir)
#> ----- Simulating adsl -----
#> Simulating column(s): treatment, flag
#> Simulating column(s): REGION1, REGION1N
#> Simulating column(s): STUDYID
#> Simulating column(s): USUBJID
#> Simulating column(s): SUBJID
#> Simulating column(s): SITEID
#> Simulating column(s): AGE
#> Simulating column(s): AGEU
#> Simulating column(s): SEX
#> Simulating column(s): RACE
#> Simulating column(s): ETHNIC
#> Simulating column(s): COUNTRY
#> Simulating column(s): HEIGHTBL
#> Simulating column(s): WEIGHTBL
#> Simulating column(s): BMIBL
#> Simulating column(s): TRTSDT
#> Saving adsl to /tmp/Rtmpm0P6Ux/syn_data/syn_adsl.rds...
#> ----- Simulating adae -----
#> Simulating occurrence counts
#> Simulating sequence column
#> Simulating column(s): AESEV, AESEVN
#> Simulating column(s): AEBODSYS
#> Simulating column(s): AEDECOD
#> Simulating column(s): AESER
#> Simulating column(s): AEREL
#> Simulating column(s): ASTDT
#> Simulating column(s): AENDT
#> Saving adae to /tmp/Rtmpm0P6Ux/syn_data/syn_adae.rds...
list.files(out_dir, pattern = "\\.rds$")
#> [1] "syn_adae.rds" "syn_adsl.rds"