R: Optimize PTSD Diagnostic Criteria

# Optimize PTSD Diagnostic Criteria

## Documentation for package ‘PTSDdiag’ version 0.5.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

analyze_best_six_symptoms_four_required | Find optimal non-hierarchical six-symptom combinations for PTSD diagnosis
analyze_best_six_symptoms_four_required_clusters | Find optimal hierarchical six-symptom combinations for PTSD diagnosis
apply_symptom_combinations | Apply pre-specified symptom combinations to new data
as_definitions | Convert imported combination specifications into definitions
as_set_matrix | Coerce a combination specification to an integer matrix
ba_ci | Interval for balanced accuracy
binarize_data | Binarize PCL-5 symptom scores
bootstrap_stability | Bootstrap stability of near-optimal symptom combinations
calculate_ptsd_total | Calculate PTSD total score
chance_baseline | Chance baseline for each item
check_pcl5_data | Check PCL-5 item data before starting the workflow
compare_diagnostic_systems | Compare multiple diagnostic systems against a reference standard
compare_optimizations | Run multiple PTSD optimization scenarios in one call
compare_rule_forms | Compare plateaus and stability across rule forms
compute_plateau | Find the plateau of near-optimal symptom combinations
create_caps5_diagnosis | Compute CAPS-5 DSM-5-TR PTSD diagnosis
create_icd11_diagnosis | Apply ICD-11 PTSD diagnostic criteria to PCL-5 data
create_ptsd_diagnosis_binarized | Determine PTSD diagnosis based on DSM-5 criteria using binarized scores
create_ptsd_diagnosis_nonbinarized | Determine PTSD diagnosis based on DSM-5 criteria using non-binarized scores
create_readable_summary | Create readable summary of PTSD diagnostic changes
cross_validation | Perform k-fold cross-validation for PTSD diagnostic models
diagnostic_metrics | All diagnostic accuracy metrics for one or more two-by-two tables
evaluate_definitions | Evaluate symptom definitions against a sample
evaluate_sets | Evaluate given symptom combinations in one sample
exact_ci | Clopper-Pearson (exact) interval for a binomial proportion
extract_definitions | Extract portable symptom definitions from a comparison
five_number | Five-number summary of a numeric vector, as a one-row data frame
fmt_est_ci | Format an estimate and its interval for a table
fmt_ratio_ci | Format a ratio and its interval for a table
format_set_items | Convert between combination ids and item numbers
format_set_labels | Convert between combination ids and item numbers
holdout_validation | Perform holdout validation for PTSD diagnostic models
icd11_items | The ICD-11 PTSD criterion as PCL-5 items
icd11_performance | ICD-11 performance in one sample
kappa_ci | Cohen's kappa for a two-by-two table, with a large-sample interval
lr_ci | Likelihood ratios with log-normal (Simel) intervals
n_candidates | Size of a candidate space
optimize_combinations | Find optimal symptom combinations for diagnosis (non-hierarchical)
optimize_combinations_clusters | Find optimal symptom combinations for diagnosis (hierarchical/cluster-based)
pcl5_item_labels | PCL-5 item labels, in DSM-5-TR order
plot_symptom_frequency | Heatmap of PCL-5 symptom selection frequency across optimization scenarios
plot_symptom_selection | Plot symptom selection against the chance baseline
print.ptsdiag_comparison | Print method for ptsdiag_comparison objects
print.ptsdiag_plateau | Print method for ptsdiag_plateau objects
print.ptsdiag_rule_forms | Print method for ptsdiag_rule_forms objects
print.ptsdiag_stability | Print method for ptsdiag_stability objects
print.ptsdiag_transport | Print method for ptsdiag_transport objects
read_combinations | Read symptom combinations from a JSON file
read_transport | Read a return bundle
rename_caps5_columns | Rename CAPS-5 symptom columns
rename_ptsd_columns | Rename PTSD symptom (= PCL-5 item) columns
score_all_combinations | Score every candidate symptom combination
set_id_to_items | Convert between combination ids and item numbers
simulated_ptsd | Simulated PCL-5 (PTSD Checklist) Data
simulated_ptsd_genpop | Simulated General Population PCL-5 Data
summarize_ptsd | Summarize PTSD scores and diagnoses
summarize_ptsd_changes | Summarize changes in PTSD diagnostic metrics
summarize_top_combinations | Build a tidy comparison table of top combinations across scenarios
symptom_frequency | Per-symptom inclusion counts across optimization scenarios
symptom_selection | Symptom selection across the plateau, against chance
transport_plateau | Summarise a transported plateau for release
wilson_ci | Wilson score interval for a binomial proportion
write_combinations | Write symptom combinations to a JSON file
write_transport | Write a return bundle