## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)

## ----setup--------------------------------------------------------------------
library(PCBN)

## -----------------------------------------------------------------------------
DAG = create_empty_DAG(7)
DAG = bnlearn::set.arc(DAG, 'U1', 'U2')
DAG = bnlearn::set.arc(DAG, 'U1', 'U3')
DAG = bnlearn::set.arc(DAG, 'U1', 'U4')
DAG = bnlearn::set.arc(DAG, 'U2', 'U4')
DAG = bnlearn::set.arc(DAG, 'U3', 'U4')
DAG = bnlearn::set.arc(DAG, 'U4', 'U6')
DAG = bnlearn::set.arc(DAG, 'U5', 'U6')
DAG = bnlearn::set.arc(DAG, 'U4', 'U7')
DAG = bnlearn::set.arc(DAG, 'U6', 'U7')

## ----fig.height=8, fig.width=8------------------------------------------------
DAG |> bnlearn::as.igraph() |>
  igraph::plot.igraph(size = 20, label.cex = 2
                      # , layout = igraph::layout_as_tree
  )

## -----------------------------------------------------------------------------
order_hash = r2r::hashmap()
order_hash[['U4']] = c("U2", "U1", "U3")
order_hash[['U6']] = c("U4", "U5")
order_hash[['U7']] = c("U4", "U6")
complete_and_check_orders(DAG, order_hash)

fam = matrix(c(0, 1, 1, 1, 0, 0, 0,
               0, 0, 0, 1, 0, 0, 0,
               0, 0, 0, 1, 0, 0, 0,
               0, 0, 0, 0, 0, 1, 1,
               0, 0, 0, 0, 0, 1, 0,
               0, 0, 0, 0, 0, 0, 1,
               0, 0, 0, 0, 0, 0, 0), 
             byrow = TRUE, ncol = 7)
tau = 0.2 * fam

my_PCBN = new_PCBN(
  DAG, order_hash,
  copula_mat = list(tau = tau, fam = fam))

N = 100
mydata = PCBN_sim(my_PCBN, N = N)

## -----------------------------------------------------------------------------
e = default_envir()

## -----------------------------------------------------------------------------
BiCopCondFit(data = mydata, DAG = DAG, v = "U1", w = "U2",
             cond_set = c(), familyset = 1, order_hash = order_hash, e = e,
             method = "mle")

## -----------------------------------------------------------------------------
copula_key = e$keychain[[list(margins = c("U1", "U2"), cond = character(0))]]

e$copula_hash[[copula_key]]

## -----------------------------------------------------------------------------
print(data.tree::FromListSimple(copula_key))

## -----------------------------------------------------------------------------
BiCopCondFit(data = mydata, DAG = DAG, v = "U1", w = "U3",
             cond_set = c(), familyset = 1, order_hash = order_hash,
             e = e, method = "mle")

## -----------------------------------------------------------------------------
BiCopCondFit(data = mydata, DAG = DAG, v = "U2", w = "U4",
             cond_set = c(), familyset = 1, order_hash = order_hash,
             e = e, method = "mle")

## -----------------------------------------------------------------------------
BiCopCondFit(data = mydata, DAG = DAG, v = "U1", w = "U4",
             cond_set = c("U2"), familyset = 1, order_hash = order_hash,
             e = e, method = "mle")

## -----------------------------------------------------------------------------
BiCopCondFit(data = mydata, DAG = DAG, v = "U3", w = "U4",
             cond_set = c("U1", "U2"), familyset = 1, order_hash = order_hash,
             e = e, method = "mle")

## -----------------------------------------------------------------------------
e$keychain[[list(margins = c("U2", "U4"), cond = character(0))]] |>
  data.tree::FromListSimple() |>
  print()

## -----------------------------------------------------------------------------
e$keychain[[list(margins = c("U1", "U4"), cond = c("U2"))]] |>
  data.tree::FromListSimple() |>
  print()

## -----------------------------------------------------------------------------
e$keychain[[list(margins = c("U3", "U4"), cond = c("U1", "U2"))]] |>
  data.tree::FromListSimple() |>
  print()

## -----------------------------------------------------------------------------
e$keychain[[list(margin = c("U4"), cond = c("U1", "U2"))]] |>
  data.tree::FromListSimple() |>
  print()

## -----------------------------------------------------------------------------
e$keychain[[list(margin = c("U3"), cond = c("U1", "U2"))]]

## -----------------------------------------------------------------------------
remove_CondInd(DAG = DAG, node = "U3", cond_set = c("U1", "U2"))

## -----------------------------------------------------------------------------
e$margin_hash[[ e$keychain[[list(margin = c("U3"), cond = c("U1"))]] ]]  |>
  head()

## -----------------------------------------------------------------------------
BiCopCondFit(data = mydata, DAG = DAG, v = "U4", w = "U6",
             cond_set = c(), familyset = 1, order_hash = order_hash,
             e = e, method = "mle")

## -----------------------------------------------------------------------------
BiCopCondFit(data = mydata, DAG = DAG, v = "U5", w = "U6",
             cond_set = c("U4"), familyset = 1, order_hash = order_hash,
             e = e, method = "mle")

## -----------------------------------------------------------------------------
BiCopCondFit(data = mydata, DAG = DAG, v = "U4", w = "U7",
             cond_set = c(), familyset = 1, order_hash = order_hash,
             e = e, method = "mle")

## -----------------------------------------------------------------------------
BiCopCondFit(data = mydata, DAG = DAG, v = "U6", w = "U7",
             cond_set = c("U4"), familyset = 1, order_hash = order_hash,
             e = e, method = "mle")