Optimize PTSD Diagnostic Criteria

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Documentation for package ‘PTSDdiag’ version 0.5.0

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

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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