# update_to_priors -------------------------------------------------------

#' @keywords internal
.update_to_priors <- function(model, verbose = TRUE) {
  UseMethod(".update_to_priors")
}



#' @keywords internal
#' @importFrom stats update getCall
.update_to_priors.stanreg <- function(model, verbose = TRUE) {
  if (!requireNamespace("rstanarm")) {
    stop("Package \"rstanarm\" needed for this function to work. Please install it.")
  }

  prior_PD <- stats::getCall(model)$prior_PD
  if (!is.null(prior_PD) && isTRUE(eval(parse(text = prior_PD)))) {
    return(model)
  }

  if (verbose) {
    message("Computation of Bayes factors: sampling priors, please wait...")
  }

  prior_dists <- sapply(rstanarm::prior_summary(model), `[[`, "dist")
  if (anyNA(prior_dists)) {
    stop(
      "Cannot compute Bayes factors with flat priors (such as when priors are ",
      "set to 'NULL' in a 'stanreg' model), as Bayes factors inform about the raltive ",
      "likelihood of two 'hypotheses', and flat priors provide no likelihood.\n",
      "See '?bayesfactor_parameters' for more information.\n",
      call. = FALSE
    )
  }

  model_prior <- suppressWarnings(
    stats::update(model, prior_PD = TRUE, refresh = 0)
  )

  model_prior
}



#' @keywords internal
#' @importFrom stats update
#' @importFrom utils capture.output
#' @importFrom methods is
.update_to_priors.brmsfit <- function(model, verbose = TRUE) {
  if (!requireNamespace("brms")) {
    stop("Package \"brms\" needed for this function to work. Please install it.")
  }

  if (isTRUE(attr(model$prior, "sample_prior") == "only")) {
    return(model)
  }

  if (verbose) {
    message("Computation of Bayes factors: sampling priors, please wait...")
  }

  utils::capture.output(
    model_prior <- try(suppressMessages(suppressWarnings(
      stats::update(model, sample_prior = "only", refresh = 0)
    )), silent = TRUE)
  )

  if (is(model_prior, "try-error")) {
    if (grepl("proper priors", model_prior)) {
      stop(
        "Cannot compute Bayes factors with flat priors (such as the default ",
        "priors for fixed-effects in a 'brmsfit' model), as Bayes factors inform about ",
        "the raltive likelihood of two 'hypotheses', and flat priors provide no ",
        "likelihood.\n",
        "See '?bayesfactor_parameters' for more information.\n",
        call. = FALSE
      )
    } else {
      stop(model_prior)
    }
  }

  model_prior
}


# clean priors and posteriors ---------------------------------------------

#' @keywords internal
.clean_priors_and_posteriors <- function(posterior, prior,
                                         verbose = TRUE, ...) {
  UseMethod(".clean_priors_and_posteriors")
}

#' @keywords internal
#' @importFrom insight get_parameters
.clean_priors_and_posteriors.stanreg <- function(posterior, prior,
                                                 verbose = TRUE,
                                                 effects, component, ...) {
  # Get Priors
  if (is.null(prior)) {
    prior <- posterior
  }

  prior <- .update_to_priors(prior, verbose = verbose)
  prior <- insight::get_parameters(prior, effects = effects, component = component, ...)
  posterior <- insight::get_parameters(posterior, effects = effects, component = component, ...)

  list(posterior = posterior,
       prior = prior)
}

#' @keywords internal
.clean_priors_and_posteriors.brmsfit <- .clean_priors_and_posteriors.stanreg

#' @keywords internal
#' @importFrom stats update
.clean_priors_and_posteriors.emmGrid <- function(posterior, prior,
                                                 verbose = TRUE) {
  if (!requireNamespace("emmeans")) {
    stop("Package 'emmeans' required for this function to work. Please install it by running `install.packages('emmeans')`.")
  }

  if (is.null(prior)) {
    prior <- posterior
    warning(
      "Prior not specified! ",
      "Please provide the original model to get meaningful results."
    )
  } else if (!inherits(prior, "emmGrid")) { # then is it a model
    prior <- .update_to_priors(prior, verbose = verbose)
    prior <- emmeans::ref_grid(prior)
    prior <- prior@post.beta

    if (!isTRUE(all.equal(colnames(prior), colnames(posterior@post.beta)))) {
      stop(
        "Unable to reconstruct prior estimates.\n",
        "Perhaps the emmGrid object has been transformed? See function details.\n",
        call. = FALSE
      )
    }
    prior <- stats::update(posterior, post.beta = prior)
  }

  prior <- .clean_emmeans_draws(prior)
  posterior <- .clean_emmeans_draws(posterior)

  list(posterior = posterior,
       prior = prior)
}


# BMA ---------------------------------------------------------------------

#' @keywords internal
#' @importFrom stats as.formula terms terms.formula
.get_model_table <- function(BFGrid, priorOdds = NULL, add_effects_table = TRUE, ...) {
  denominator <- attr(BFGrid, "denominator")
  BFGrid <- rbind(BFGrid[denominator, ], BFGrid[-denominator, ])
  attr(BFGrid, "denominator") <- 1

  # Prior and post odds
  Modelnames <- BFGrid$Model
  if (!is.null(priorOdds)) {
    priorOdds <- c(1, priorOdds)
  } else {
    priorOdds <- rep(1, length(Modelnames))
  }

  posterior_odds <- priorOdds * BFGrid$BF

  priorProbs <- priorOdds / sum(priorOdds)
  postProbs <- posterior_odds / sum(posterior_odds)

  df.model <- data.frame(
    Modelnames,
    priorProbs,
    postProbs,
    stringsAsFactors = FALSE
  )

  # add effects table
  if (add_effects_table) {
    for (m in seq_len(nrow(df.model))) {
      tmp_terms <- .make_terms(df.model$Modelnames[m])
      if (length(tmp_terms) > 0) {
        missing_terms <- !tmp_terms %in% colnames(df.model) # For R < 3.6.0
        if (any(missing_terms)) df.model[, tmp_terms[missing_terms]] <- NA # For R < 3.6.0
        df.model[m, tmp_terms] <- TRUE
      }
    }
  }

  df.model[is.na(df.model)] <- FALSE

  df.model
}

# make_BF_plot_data -------------------------------------------------------

#' @importFrom stats median mad approx
#' @importFrom utils stack
#' @keywords internal
.make_BF_plot_data <- function(posterior, prior, direction, null,
                               extend_scale = 0.05, precision = 2^8, ...) {
  if (!requireNamespace("logspline")) {
    stop("Package \"logspline\" needed for this function to work. Please install it.")
  }

  estimate_samples_density <- function(samples) {
    nm <- .safe_deparse(substitute(samples))
    samples <- utils::stack(samples)
    samples <- split(samples, samples$ind)

    samples <- lapply(samples, function(data) {
      # 1. estimate density
      x <- data$values

      x_range <- range(x)
      x_rangex <- stats::median(x) + 7 * stats::mad(x) * c(-1, 1)
      x_range <- c(
        max(c(x_range[1], x_rangex[1])),
        min(c(x_range[2], x_rangex[2]))
      )

      extension_scale <- diff(x_range) * extend_scale
      x_range[1] <- x_range[1] - extension_scale
      x_range[2] <- x_range[2] + extension_scale

      x_axis <- seq(x_range[1], x_range[2], length.out = precision)
      f_x <- .logspline(x, ...)
      y <- logspline::dlogspline(x_axis, f_x)
      d_points <- data.frame(x = x_axis, y = y)

      # 2. estimate points
      d_null <- stats::approx(d_points$x, d_points$y, xout = null)
      d_null$y[is.na(d_null$y)] <- 0

      # 3. direction?
      if (direction > 0) {
        d_points <- d_points[d_points$x > min(null), , drop = FALSE]
        norm_factor <- 1 - logspline::plogspline(min(null), f_x)
        d_points$y <- d_points$y / norm_factor
        d_null$y <- d_null$y / norm_factor
      } else if (direction < 0) {
        d_points <- d_points[d_points$x < max(null), , drop = FALSE]
        norm_factor <- logspline::plogspline(max(null), f_x)
        d_points$y <- d_points$y / norm_factor
        d_null$y <- d_null$y / norm_factor
      }

      d_points$ind <- d_null$ind <- data$ind[1]
      list(d_points, d_null)
    })

    # 4a. organize
    point0 <- lapply(samples, function(.) as.data.frame(.[[2]]))
    point0 <- do.call("rbind", point0)

    samplesX <- lapply(samples, function(.) .[[1]])
    samplesX <- do.call("rbind", samplesX)

    samplesX$Distribution <- point0$Distribution <- nm
    rownames(samplesX) <- rownames(point0) <- c()

    list(samplesX, point0)
  }

  # 4b. orgenize
  posterior <- estimate_samples_density(posterior)
  prior <- estimate_samples_density(prior)

  list(
    plot_data = rbind(posterior[[1]], prior[[1]]),
    d_points = rbind(posterior[[2]], prior[[2]])
  )
}

# As numeric vector -------------------------------------------------------

#' @export
as.numeric.bayesfactor_inclusion <- function(x, ...) {
  if ("data.frame" %in% class(x)) {
    return(as.numeric(as.vector(x$BF)))
  } else {
    return(as.vector(x))
  }
}

#' @export
as.numeric.bayesfactor_models <- as.numeric.bayesfactor_inclusion

#' @export
as.numeric.bayesfactor_parameters <- as.numeric.bayesfactor_inclusion

#' @export
as.numeric.bayesfactor_restricted <- as.numeric.bayesfactor_inclusion

#' @export
as.double.bayesfactor_inclusion <- as.numeric.bayesfactor_inclusion

#' @export
as.double.bayesfactor_models <- as.numeric.bayesfactor_inclusion

#' @export
as.double.bayesfactor_parameters <- as.numeric.bayesfactor_inclusion

#' @export
as.double.bayesfactor_restricted <- as.numeric.bayesfactor_inclusion



# logspline ---------------------------------------------------------------

#' @keywords internal
.logspline <- function(x, ...) {
  if (!requireNamespace("logspline")) {
    stop("Package \"logspline\" needed for this function to work. Please install it.")
  }

  # arg_names <- names(formals(logspline::logspline, envir = parent.frame()))
  arg_names <- names(formals(logspline::logspline)) # support R<3.6.0
  in_args <- list(...)

  in_args <- in_args[names(in_args) %in% arg_names]
  in_args <- c(list(x = x), in_args)
  suppressWarnings(do.call(logspline::logspline, in_args))
}