R/init_tree_priors.R

In beautier: 'BEAUti' from R

#' Initializes all tree priors
#' @inheritParams default_params_doc
#' @param distr_id the first distributions' ID
#' @param param_id the first parameter's ID
#' @return a list of initialized tree priors
#' @author Richèl J.C. Bilderbeek
#' @export
init_tree_priors <- function(
  tree_priors,
  ids,
  distr_id = 0,
  param_id = 0
) {
  check_true(are_tree_priors(tree_priors))

  for (i in seq_along(tree_priors)) {
    tree_prior <- tree_priors[[i]]
    check_true(is_tree_prior(tree_prior))

    if (is_bd_tree_prior(tree_prior)) {
      if (!is_init_bd_tree_prior(tree_prior)) {
        tree_prior <- init_bd_tree_prior(
          tree_prior, distr_id = distr_id, param_id = param_id
        )
      }
    } else if (is_cbs_tree_prior(tree_prior)) {
      # Nothing to do
    } else if (is_ccp_tree_prior(tree_prior)) {
      if (!is_init_ccp_tree_prior(tree_prior)) {
        tree_prior <- init_ccp_tree_prior(
          tree_prior, distr_id = distr_id, param_id = param_id
        )
      }
    } else if (is_cep_tree_prior(tree_prior)) {
      if (!is_init_cep_tree_prior(tree_prior)) {
        tree_prior <- init_cep_tree_prior(
          tree_prior, distr_id = distr_id, param_id = param_id
        )
      }
    } else {
      check_true(is_yule_tree_prior(tree_prior))
      if (!is_init_yule_tree_prior(tree_prior)) {
        tree_prior <- init_yule_tree_prior(
          tree_prior,
          distr_id = distr_id,
          param_id = param_id
        )
      }
    }
    distr_id <- distr_id + get_tree_prior_n_distrs(tree_prior)
    param_id <- param_id + get_tree_prior_n_params(tree_prior)

    if (is_one_na(tree_prior$id)) tree_prior$id <- ids[i]
    tree_priors[[i]] <- tree_prior
  }
  tree_priors
}

#' Initializes a Birth-Death tree prior
#' @inheritParams default_params_doc
#' @return an initialized Birth-Death tree prior
#' @author Richèl J.C. Bilderbeek
#' @export
init_bd_tree_prior <- function(
  bd_tree_prior,
  distr_id,
  param_id
) {
  check_true(is_bd_tree_prior(bd_tree_prior))

  result <- create_bd_tree_prior(
    birth_rate_distr = init_distr(
      bd_tree_prior$birth_rate_distr,
      distr_id,
      param_id
    ),
    death_rate_distr = init_distr(
      bd_tree_prior$death_rate_distr,
      distr_id + 1,
      param_id + get_distr_n_params(bd_tree_prior$birth_rate_distr)
    )
  )

  result
}


#' Initializes a Coalescent Constant Population tree prior
#' @inheritParams default_params_doc
#' @return an initialized Coalescent Constant Population tree prior
#' @author Richèl J.C. Bilderbeek
#' @export
init_ccp_tree_prior <- function(
  ccp_tree_prior,
  distr_id,
  param_id
) {
  check_true(is_ccp_tree_prior(ccp_tree_prior))

  result <- create_ccp_tree_prior(
    pop_size_distr = init_distr(
      ccp_tree_prior$pop_size_distr,
      distr_id,
      param_id
    )
  )
  result
}

#' Initializes a Coalescent Exponential Population tree prior
#' @inheritParams default_params_doc
#' @return an initialized Coalescent Exponential Population tree prior
#' @author Richèl J.C. Bilderbeek
#' @export
init_cep_tree_prior <- function(
  cep_tree_prior,
  distr_id,
  param_id
) {
  check_true(is_cep_tree_prior(cep_tree_prior))
  check_true(!is_one_na(distr_id))
  check_true(!is_one_na(param_id))
  check_true(
    !is_one_na(
      get_distr_n_params(cep_tree_prior$pop_size_distr)
    )
  )

  result <- create_cep_tree_prior(
    pop_size_distr = init_distr(
      cep_tree_prior$pop_size_distr,
      distr_id,
      param_id
    ),
    growth_rate_distr = init_distr(
      cep_tree_prior$growth_rate_distr,
      distr_id + 1,
      param_id + get_distr_n_params(cep_tree_prior$pop_size_distr)
    )
  )

  result
}

#' Initializes a Yule tree prior
#' @inheritParams default_params_doc
#' @return an initialized Yule tree prior
#' @author Richèl J.C. Bilderbeek
#' @export
init_yule_tree_prior <- function(
  yule_tree_prior,
  distr_id,
  param_id
) {
  check_true(is_yule_tree_prior(yule_tree_prior))

  result <- create_yule_tree_prior(
    birth_rate_distr = init_distr(
      yule_tree_prior$birth_rate_distr,
      distr_id,
      param_id
    )
  )

  result
}