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Glimpse an OCCDS dataset.

Source: R/adam_occds.R
glimpse_occds.Rd

Summarizes an OCCDS (Occurrence Data Structure) dataset for simulation. Works with ADAE, ADCM, ADMH, ADDV and other occurrence-based datasets.

Usage

glimpse_occds(
  occds,
  syn_adsl,
  id_cols,
  seq_col,
  flag_cols = character(0),
  ordered_col_sets = list(),
  seed = NULL
)

Arguments

occds

data.frame - input OCCDS dataset e.g. ADAE, ADCM.

syn_adsl

data.frame - synthetic ADSL to obtain subject-level data from. Should be created by simulate_adsl().

id_cols

character - ID column names that identify subjects e.g. c("USUBJID"). These columns must exist in syn_adsl and will be taken from there (never simulated).

seq_col

character - sequence column name e.g. "AESEQ", "CMSEQ".

flag_cols

character - flag columns that will be sampled as Y/N in proportion to input e.g. c("ANL01FL"). Default is an empty character vector (no flag columns).

ordered_col_sets

list<character> - each element is a character vector naming columns whose combinations should be preserved e.g. list(c("REGION1", "REGION1N")). Default is an empty list.

seed

integer - random seed for reproducibility.

Value

summary_occds - summary object for OCCDS simulation.

Examples


# OCCDS simulation needs a synthetic ADSL first to provide the subject spine.
syn_adsl <- simulate_adsl(glimpse_adsl(
  adsl,
  id_cols = c("USUBJID", "SUBJID"),
  treatment_cols = c("TRT01A", "TRT01AN")
))
#> Glimpsing treatment/flag columns
#> 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): SAFFL
#> Glimpsing column(s): ITTFL
#> Glimpsing column(s): EFFFL
#> Glimpsing column(s): REGION1
#> Glimpsing column(s): REGION1N
#> 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): 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): SAFFL
#> Simulating column(s): ITTFL
#> Simulating column(s): EFFFL
#> Simulating column(s): REGION1
#> Simulating column(s): REGION1N
#> Simulating column(s): COUNTRY
#> Simulating column(s): HEIGHTBL
#> Simulating column(s): WEIGHTBL
#> Simulating column(s): BMIBL
#> Simulating column(s): TRTSDT

occds_summary <- glimpse_occds(
  adae,
  syn_adsl,
  id_cols = "USUBJID",
  seq_col = "AESEQ",
  ordered_col_sets = list(c("AEBODSYS", "AEDECOD"))
)
#> Glimpsing occurrence counts, ID and sequence columns
#> Glimpsing ADSL columns from synthetic ADSL
#> Glimpsing column(s): AEBODSYS, AEDECOD
#> 3 ordered column combination(s) with count = 1 were masked and added to the most common combination.
#> Glimpsing column(s): AESEV
#> Glimpsing column(s): AESEVN
#> Glimpsing column(s): AESER
#> Glimpsing column(s): AEREL
#> Glimpsing column(s): ASTDT
#> Glimpsing column(s): AENDT
syn_adae <- simulate_occds(occds_summary, seed = 42)
#> Simulating occurrence counts
#> Simulating sequence column
#> Simulating column(s): AEBODSYS, AEDECOD
#> Simulating column(s): AESEV
#> Simulating column(s): AESEVN
#> Simulating column(s): AESER
#> Simulating column(s): AEREL
#> Simulating column(s): ASTDT
#> Simulating column(s): AENDT
head(syn_adae)
#>          STUDYID   USUBJID AESEQ                               AEBODSYS
#> 1   CDISCPILOT01 USUBJID_1     1             GASTROINTESTINAL DISORDERS
#> 5   CDISCPILOT01 USUBJID_1     2 SKIN AND SUBCUTANEOUS TISSUE DISORDERS
#> 1.1 CDISCPILOT01 USUBJID_2     1             GASTROINTESTINAL DISORDERS
#> 1.2 CDISCPILOT01 USUBJID_3     1             GASTROINTESTINAL DISORDERS
#> 2   CDISCPILOT01 USUBJID_3     2             GASTROINTESTINAL DISORDERS
#> 4   CDISCPILOT01 USUBJID_4     1               NERVOUS SYSTEM DISORDERS
#>       AEDECOD    AESEV AESEVN AESER            AEREL      ASTDT  AENDT
#> 1   DIARRHOEA     MILD      2     N      NOT RELATED 2014-01-25 MASKED
#> 5        RASH     MILD      2     N      NOT RELATED 2014-01-25 MASKED
#> 1.1 DIARRHOEA     MILD      1     N      NOT RELATED 2014-01-25 MASKED
#> 1.2 DIARRHOEA     MILD      2     N      NOT RELATED 2014-01-25 MASKED
#> 2      NAUSEA MODERATE      2     N POSSIBLY RELATED 2014-01-25 MASKED
#> 4    HEADACHE MODERATE      2     N POSSIBLY RELATED 2014-01-25 MASKED