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

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

data("simulated_ptsd")
ptsd <- rename_ptsd_columns(simulated_ptsd[1:120, ],
                            id_col = c("patient_id", "age", "sex"))

comp <- compare_optimizations(
  ptsd,
  n_top         = 10,
  include_icd11 = TRUE,
  score_by      = "balanced_accuracy",
  show_progress = FALSE
)
print(comp)

## ----table-2------------------------------------------------------------------
tbl <- summarize_top_combinations(comp, top_n = 10, as_percent = TRUE)
head(tbl, 12)

## ----heatmap, fig.alt = "Heatmap of PCL-5 symptom selection frequency across optimization scenarios"----
plot_symptom_frequency(comp, type = "relative")

## ----table heat---------------------------------------------------------------
freq   <- symptom_frequency(comp)
counts <- xtabs(Count ~ Symptom + Approach, data = freq)
wide   <- as.data.frame.matrix(counts, optional = TRUE)
wide   <- cbind(Symptom = as.integer(rownames(wide)), wide)

knitr::kable(
  wide,
  row.names = FALSE,
  caption = "Number of times each PCL-5 item is selected among the top combinations - ICD-11 not included"
)

## ----custom, eval = FALSE-----------------------------------------------------
# my_scenarios <- list(
#   "5/7 Hierarchical"     = list(n_symptoms = 7, n_required = 5, hierarchical = TRUE),
#   "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),
#   "ICD-11"               = list(type = "fixed", criterion = "icd11")
# )
# 
# compare_optimizations(ptsd, scenarios = my_scenarios, n_top = 10,
#                       score_by = "balanced_accuracy", show_progress = FALSE)