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Generate a subject disposition summary

Source: R/query.R
lg_disposition.Rd

Produces a CONSORT-style subject disposition table from every documented exclusion in the active session – both lg_filter() calls and any lg_join() call (type = "inner"/"right") that dropped unmatched rows of x. Both are exclusions in the same sense (rows removed from the pipeline with a mandatory documented reason), so both must be reflected here for the totals to match lg_exclusions().

Usage

lg_disposition(by = c("reason", "population", "dataset"))

Arguments

by

Character. How to group: "reason" (default) returns the exact step-by-step funnel. "population" groups by population flag. "dataset" groups by dataset ID.

Value

A data.frame. For by = "reason": columns step, reason, n_excluded, n_remaining. For by = "population" or "dataset": columns group, n_excluded, n_remaining.

Details

With the default by = "reason", this returns one row per contributing step (filter or row-dropping join), in the exact chronological order they were executed, with the number of subjects excluded at that step and the number remaining immediately afterward – i.e. the actual funnel.

by = "population" and by = "dataset" aggregate exclusions that share a population flag or dataset across possibly multiple steps, in the order each group first appears. Note that lg_join() has no population argument, so join-caused exclusions always fall into the "(none)" group under by = "population".

See also

lg_exclusions(), lg_trace()

Examples

lg_start()
#> lineager: session started
adsl <- lg_tag(
  data.frame(
    USUBJID = sprintf("%02d", 1:5),
    RANDFL = c("Y","Y","N","Y","Y"),
    SAFFL  = c("Y","Y","N","Y","N")
  ),
  dataset_id = "ADSL5"
)
#> lineager: tagged 'ADSL5' — 5 rows, 3 cols
lg_filter(adsl, RANDFL == "Y",
  reason = "Not randomised (RANDFL != 'Y')",
  reason_code = "NOT_RANDOMISED", population = "RANDFL"
)
#> lineager: [ADSL5] filter 'Not randomised (RANDFL != 'Y')' — 5 in, 4 out, 1 excluded
#> <lg_df> 'ADSL5'  [4 × 4]
#>   USUBJID RANDFL SAFFL
#> 1      01      Y     Y
#> 2      02      Y     Y
#> 3      04      Y     Y
#> 4      05      Y     N

lg_disposition()
#>   step                         reason n_excluded n_remaining
#> 1    1 Not randomised (RANDFL != 'Y')          1           4