## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment  = "#>",
  fig.width  = 7,
  fig.height = 4
)

## ----setup, message = FALSE---------------------------------------------------
library(PTSDdiag)

data("simulated_ptsd_genpop")
gp   <- simulated_ptsd_genpop[1:120, ]
demo <- c("patient_id", "age", "sex")

# PCL-5 view: rename S1..S20; carry the CAPS-5 columns through untouched
ptsd  <- rename_ptsd_columns(gp,  id_col = c(demo, paste0("C", 1:20)))

# CAPS-5 view: rename C1..C20; carry the PCL-5 columns through untouched
caps5 <- rename_caps5_columns(gp, id_col = c(demo, paste0("S", 1:20)))

## ----caps5-dx-----------------------------------------------------------------
caps5_dx <- create_caps5_diagnosis(caps5)
mean(caps5_dx$PTSD_caps5) * 100

## ----compare------------------------------------------------------------------
compare_diagnostic_systems(
  ptsd,
  caps5_data = caps5,
  icd11      = TRUE,
  reference  = "caps5"
)

## ----caps5-as-fixed-----------------------------------------------------------
comp <- compare_optimizations(
  ptsd,
  scenarios = list(
    "4/6 Hierarchical"     = list(n_symptoms = 6, n_required = 4, hierarchical = TRUE),
    "4/6 Non-hierarchical" = list(n_symptoms = 6, n_required = 4, hierarchical = FALSE),
    "CAPS-5 (reference)"   = list(type = "fixed", criterion = caps5_dx$PTSD_caps5,
                                  symptoms = 1:20)
  ),
  n_top         = 5,
  score_by      = "balanced_accuracy",
  show_progress = FALSE
)
summarize_top_combinations(comp, top_n = 3, as_percent = TRUE)

## ----evaluate-vs-caps5--------------------------------------------------------
definitions <- extract_definitions(comp, n = 3)

evaluate_definitions(ptsd, definitions,
                     reference = caps5_dx$PTSD_caps5, tidy = TRUE)