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Extract portable symptom definitions from a comparison

Source: R/definitions.R
extract_definitions.Rd

Pulls the top symptom combinations of each optimized scenario out of a compare_optimizations result and returns them as a compact, shareable object. Each definition is described only by its symptom indices and the rule needed to apply it (how many must be present, and whether cluster representation is required), so the object contains no participant-level data and can be shared across sites.

Usage

extract_definitions(comparison, n = 5)

Arguments

comparison

A ptsdiag_comparison object from compare_optimizations.

n

Integer. Number of top combinations to keep per optimized scenario (default 5). Capped at the number available.

Value

A named list (one element per optimized scenario). Each element is a list with:

  • symptoms: list of integer vectors (the top-n combinations).

  • n_required: integer threshold for that scenario.

  • hierarchical: logical, whether cluster representation is required.

Details

For each type = "optimize" scenario in the comparison, the rule (n_required, hierarchical) is read from comparison$config, so the only thing the user supplies is how many combinations to carry per scenario. Fixed scenarios (e.g. ICD-11) are skipped, because their symptom set is published rather than derived.

The result pairs with evaluate_definitions: extract the definitions from one sample, then evaluate them in any sample.

See also

evaluate_definitions, as_definitions for building the same object from combinations imported with read_combinations, compare_optimizations.

Examples

# \donttest{
# Use a 250-row subset and a small 4-symptom search to keep the example
# fast; omit `scenarios` to run the three default rules
ptsd <- rename_ptsd_columns(simulated_ptsd[1:250, ],
                            id_col = c("patient_id", "age", "sex"))
comp <- compare_optimizations(
  ptsd,
  scenarios = list(
    "3/4 Non-hierarchical" = list(n_symptoms = 4, n_required = 3,
                                  hierarchical = FALSE)
  ),
  n_top = 10, show_progress = FALSE
)
#> ℹ Evaluated 4845 combinations. Best: 6, 7, 12, 17
definitions <- extract_definitions(comp, n = 5)
lapply(definitions, function(d) d$symptoms)
#> $`3/4 Non-hierarchical`
#> $`3/4 Non-hierarchical`[[1]]
#> [1]  6  7 12 17
#> 
#> $`3/4 Non-hierarchical`[[2]]
#> [1]  4  6  7 12
#> 
#> $`3/4 Non-hierarchical`[[3]]
#> [1]  4  6  7 19
#> 
#> $`3/4 Non-hierarchical`[[4]]
#> [1]  6  7 12 13
#> 
#> $`3/4 Non-hierarchical`[[5]]
#> [1]  6  7 12 15
#> 
#> 
# }