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Find optimal hierarchical six-symptom combinations for PTSD diagnosis

Source: R/analysis.R
analyze_best_six_symptoms_four_required_clusters.Rd

`r lifecycle::badge("deprecated")`

Convenience wrapper around optimize_combinations_clusters with the original PCL-5 defaults: 6 symptoms, 4 required, top 3 returned, and standard DSM-5 cluster structure.

Identifies the three best six-symptom combinations for PTSD diagnosis where four symptoms must be present and must include at least one symptom from each DSM-5 criterion cluster.

Usage

analyze_best_six_symptoms_four_required_clusters(
  data,
  score_by = "false_cases",
  DT = FALSE
)

Arguments

data

A dataframe containing exactly 20 columns with PCL-5 item scores (output of rename_ptsd_columns). Each symptom should be scored on a 0-4 scale where:

  • 0 = Not at all

  • 1 = A little bit

  • 2 = Moderately

  • 3 = Quite a bit

  • 4 = Extremely

score_by

Character string specifying optimization criterion:

  • "false_cases": Minimize total misclassifications

  • "newly_nondiagnosed": Minimize false negatives only

DT

Logical. If TRUE, return the summary as an interactive datatable widget. If FALSE (default), return a plain data.frame.

Value

A list containing:

  • best_symptoms: List of three vectors, each containing six symptom numbers representing the best combinations found

  • diagnosis_comparison: Dataframe comparing original DSM-5 diagnosis with diagnoses based on the three best combinations

  • summary: Diagnostic accuracy metrics for each combination. A data.frame by default, or an interactive datatable if DT = TRUE.

Details

The function:

  1. Generates valid combinations ensuring representation from all clusters

  2. Requires 4 symptoms to be present (>=2 on original 0-4 scale) for diagnosis

  3. Validates that present symptoms include at least one from each cluster

  4. Identifies the three combinations that best match the original DSM-5 diagnosis

DSM-5 PTSD symptom clusters:

  • Cluster 1 (B) - Intrusion: Items 1-5

  • Cluster 2 (C) - Avoidance: Items 6-7

  • Cluster 3 (D) - Negative alterations in cognitions and mood: Items 8-14

  • Cluster 4 (E) - Alterations in arousal and reactivity: Items 15-20

Optimization can be based on either:

  • Minimizing false cases (both false positives and false negatives)

  • Minimizing only false negatives (newly non-diagnosed cases)

See also

optimize_combinations_clusters for the generalized version with configurable parameters and custom cluster definitions.

Examples

# Create example data
ptsd_data <- data.frame(matrix(sample(0:4, 200, replace=TRUE), ncol=20))
names(ptsd_data) <- paste0("symptom_", 1:20)

# \donttest{
# Find best hierarchical combinations minimizing false cases
results <- analyze_best_six_symptoms_four_required_clusters(ptsd_data, score_by = "false_cases")
#> Warning: `analyze_best_six_symptoms_four_required_clusters()` was deprecated in PTSDdiag
#> 0.2.1.
#> ℹ Please use `optimize_combinations_clusters()` instead.
#> ℹ Generated 13685 valid cluster-constrained combinations
#> ℹ Evaluated 13685 combinations. Best: 4, 6, 7, 11, 12, 15

# Get symptom numbers
results$best_symptoms
#> [[1]]
#> [1]  4  6  7 11 12 15
#> 
#> [[2]]
#> [1]  1  4  6  8 11 15
#> 
#> [[3]]
#> [1]  1  5  6  8 11 15
#> 

# View raw comparison data
results$diagnosis_comparison
#>    PTSD_orig symptom_4_6_7_11_12_15 symptom_1_4_6_8_11_15 symptom_1_5_6_8_11_15
#> 1       TRUE                   TRUE                  TRUE                  TRUE
#> 2       TRUE                   TRUE                  TRUE                  TRUE
#> 3       TRUE                  FALSE                 FALSE                 FALSE
#> 4       TRUE                   TRUE                 FALSE                 FALSE
#> 5       TRUE                   TRUE                  TRUE                  TRUE
#> 6      FALSE                  FALSE                 FALSE                 FALSE
#> 7      FALSE                  FALSE                 FALSE                 FALSE
#> 8       TRUE                   TRUE                  TRUE                  TRUE
#> 9       TRUE                   TRUE                  TRUE                  TRUE
#> 10      TRUE                   TRUE                  TRUE                  TRUE

# View summary statistics
results$summary
#>                 Scenario combination_id rank Total Diagnosed
#> 1              PTSD_orig           <NA>   NA         8 (80%)
#> 2 symptom_4_6_7_11_12_15 4_6_7_11_12_15    1         7 (70%)
#> 3  symptom_1_4_6_8_11_15  1_4_6_8_11_15    2         6 (60%)
#> 4  symptom_1_5_6_8_11_15  1_5_6_8_11_15    3         6 (60%)
#>   Total Non-Diagnosed True Positive True Negative Newly Diagnosed
#> 1             2 (20%)             8             2               0
#> 2             3 (30%)             7             2               0
#> 3             4 (40%)             6             2               0
#> 4             4 (40%)             6             2               0
#>   Newly Non-Diagnosed True Cases False Cases Sensitivity Specificity PPV    NPV
#> 1                   0         10           0       1.000           1   1 1.0000
#> 2                   1          9           1       0.875           1   1 0.6667
#> 3                   2          8           2       0.750           1   1 0.5000
#> 4                   2          8           2       0.750           1   1 0.5000
# }