### how do i vary the versions of bgms with easybgm 
##### CROSS-SECTIONAL
###-------------
### Estimation checks 
###-------------

test_that("easybgm returns expected structure across valid type–package combos", {
  set.seed(123)
  
  # Subsample small data to stay fast on CRAN
  data("Wenchuan", package = "bgms")
  dat <- na.omit(Wenchuan)[1:20, 1:5]
  p <- ncol(dat)
  itr <- 10
  
  # Test only core combinations
  combos <- list(
    ### BGGM
    list(type = "continuous", pkg = "BGGM", sv = F, cnt = F),
    list(type = "continuous", pkg = "BGGM", sv = T, cnt = T),
    list(type = "mixed", pkg = "BGGM", sv = T, cnt = T),
    ### BDGRAPH
    list(type = "mixed",      pkg = "BDgraph", sv = F, cnt = F),
    list(type = "continuous",  pkg = "BDgraph", sv = F, cnt = F),
    ### bgms
    list(type = "binary",     pkg = "bgms", sv = F, cnt = F), 
    list(type = "binary",     pkg = "bgms", sv = T, cnt = T), 
    list(type = "blume-capel", pkg = "bgms", sv = T, cnt = T), 
    list(type = "binary", pkg = "bgms", sv = T, cnt = T, sbm = "Stochastic-Block") 
  )
  
  for (cmb in combos) {
    t <- cmb$type
    pkg <- cmb$pkg
    sv <- cmb$sv
    cnt <- cmb$cnt
    if(!is.null(cmb$sbm)) {sbm <- cmb$sbm}
    
    not_cont <- if (t == "mixed") c(TRUE, TRUE, rep(FALSE, p - 2)) else NULL
    
    if(t == "blume-capel"){
      suppressWarnings({
        res <- easybgm(
          data       = dat,
          type       = t,
          package    = pkg,
          iter       = itr,          # tiny for speed
          save       = sv,
          centrality = cnt,
          progress   = FALSE,
          not_cont   = not_cont, 
          baseline_category = 2
        )
      })} else if(!is.null(cmb$sbm)){
        suppressWarnings({
          res <- easybgm(
            data       = dat,
            type       = t,
            package    = pkg,
            iter       = itr,          # tiny for speed
            save       = sv,
            centrality = cnt,
            progress   = FALSE, 
            edge_prior = sbm
          )
        })
      } else {
        suppressWarnings({
          res <- easybgm(
            data       = dat,
            type       = t,
            package    = pkg,
            iter       = itr,          # tiny for speed
            save       = sv,
            centrality = cnt,
            progress   = FALSE,
            not_cont   = not_cont
          )
        })
      }
    
    # --- class check ---
    expect_true(inherits(res, c("easybgm")))
    expect_true(any(grepl("package_", class(res))))  # backend tag present
    
    # --- field presence check ---
    expect_true(all(c("parameters", "inc_probs", "inc_BF", "structure", "model") %in% names(res)))
    
    # --- dimensions check ---
    expect_equal(dim(res$parameters), c(p, p))
    expect_equal(dim(res$inc_probs),  c(p, p))
    expect_equal(dim(res$inc_BF),     c(p, p))
    expect_equal(dim(res$structure),  c(p, p))
    
    # --- sanity check ---
    expect_false(all(is.na(res$parameters)))
    expect_false(all(is.na(res$inc_probs))) 
    
    if(sv == TRUE && pkg == "BGGM") {
      k <- p*(p-1)/2
      expect_equal(dim(res$samples_posterior), c(itr, k))
      expect_equal(dim(res$centrality),  c(itr, p))
    } 
    if(sv == TRUE && pkg == "bgms"){
      k <- p*(p-1)/2
      expect_equal(dim(res$samples_posterior), c(4*itr, k))
      expect_equal(dim(res$centrality),  c(4*itr, p))
    }
    if(!is.null(cmb$sbm)){
      expect_equal(length(res$sbm), 4)
    }
    print(paste0("Finished easybgm: Package: ", cmb$pkg, "; Type: ", cmb$type, "; Centrality: ", cmb$cnt))
    
  }
})

###-------------
### Plotting functions test
###-------------

test_that("plotting functions work across valid type–package combos", {
  set.seed(123)

  data("Wenchuan", package = "bgms")
  dat <- na.omit(Wenchuan)[1:20, 1:5]
  p   <- ncol(dat)

  combos <- list(
    list(type = "continuous", pkg = "BGGM"),
    list(type = "mixed",      pkg = "BDgraph"),
    list(type = "binary",     pkg = "bgms")
  )

  for (cmb in combos) {
    t   <- cmb$type
    pkg <- cmb$pkg
    not_cont <- if (t == "mixed") c(TRUE, TRUE, rep(FALSE, p - 2)) else NULL

    suppressMessages({
      res <- easybgm(
        data       = dat,
        type       = t,
        package    = pkg,
        iter       = 10,
        save       = TRUE,
        centrality = TRUE,
        progress   = FALSE,
        not_cont   = not_cont
      )
    })

    # --- edge evidence ---
    g1 <- invisible(plot_edgeevidence(res))
    expect_true(inherits(g1, c("ggplot", "qgraph")))

    # --- network ---
    g2 <- invisible(plot_network(res))
    expect_true(inherits(g2, c("ggplot", "qgraph")))

    # --- structure plots (skip for BGGM) ---
    if (pkg != "BGGM") {
      g3 <- invisible(plot_structure_probabilities(res))
      expect_s3_class(g3, "ggplot")

      g4 <- invisible(plot_complexity_probabilities(res))
      expect_s3_class(g4, "ggplot")

      g5 <- invisible(plot_structure(res))
      expect_true(inherits(g5, c("ggplot", "qgraph")))
    }

    # --- posterior parameter HDI ---
    if(pkg != "BDgraph"){
      g6 <-    suppressWarnings({invisible(plot_parameterHDI(res))})
      expect_s3_class(g6, "ggplot")

      # --- centrality ---
      g7 <- invisible(plot_centrality(res))
      expect_s3_class(g7, "ggplot")
    }
  }
})


##### NETWORK COMPARISON
test_that("easybgm_compare returns expected structure across valid type–package combos", {
  set.seed(123)

  # Subsample small data to stay fast on CRAN
  data("Wenchuan", package = "bgms")
  dat <- as.data.frame(na.omit(Wenchuan)[1:90, 1:5])
  p <- ncol(dat)
  itr <- 10

  # Test only core combinations
  combos <- list(
    ### BGGM
    list(type = "continuous", pkg = "BGGM", sv = F),
    list(type = "continuous", pkg = "BGGM", sv = T),
    list(type = "mixed", pkg = "BGGM", sv = T),
    ### bgms
    list(type = "binary",     pkg = "bgms", sv = F),
    list(type = "binary",     pkg = "bgms", sv = T),
    list(type = "binary",     pkg = "bgms", sv = T, multi_group = T)
  )

  for (cmb in combos) {
    t <- cmb$type
    pkg <- cmb$pkg
    sv <- cmb$sv

    if(!is.null(cmb$multi_group)){
      group <- rep(c(1, 2, 3), each = 30)

      suppressMessages({
        res <- easybgm_compare(
          data       = dat,
          type       = t,
          package    = pkg,
          iter       = itr,          # tiny for speed
          save       = sv,
          group_indicator = group,
          progress   = FALSE
        )
      })
    } else {
      group_dat <- list(dat[1:45, ], dat[46:90, ])
      not_cont <- if (t == "mixed") c(TRUE, TRUE, rep(FALSE, p - 2)) else NULL

      suppressWarnings({
        res <- easybgm_compare(
          data       = group_dat,
          type       = t,
          package    = pkg,
          iter       = itr,          # tiny for speed
          save       = sv,
          progress   = FALSE,
          not_cont   = not_cont
        )
      })
    }
    # --- class check ---
    expect_true(inherits(res, c("easybgm_compare")))
    expect_true(any(grepl("package_", class(res))))  # backend tag present

    # --- field presence check ---
    expect_true(all(c("parameters", "inc_probs", "inc_BF", "structure", "model") %in% names(res)))

    # --- dimensions check ---
    expect_equal(dim(res$parameters), c(p, p))
    expect_equal(dim(res$inc_probs),  c(p, p))
    expect_equal(dim(res$inc_BF),     c(p, p))
    expect_equal(dim(res$structure),  c(p, p))

    # --- sanity check ---
    expect_false(all(is.na(res$parameters)))
    expect_false(all(is.na(res$inc_probs)))

    if(sv == TRUE && pkg != "bgms") {
      k <- p*(p-1)/2
      expect_equal(dim(res$samples_posterior), c(itr, k))
    }
    if(sv == TRUE && pkg == "bgms"){
      k <- p*(p-1)/2
      expect_equal(dim(res$samples_posterior), c(4*itr, k))
    }


    print(paste0("Finished easybgm_compare: Package: ", cmb$pkg, "; Type: ", cmb$type))
  }
})