R/use_calibrations_bladj_matched.R

In datelife: Scientific Data on Time of Lineage Divergence for Your Taxa

#' Use calibrations to date a topology with the BLADJ algorithm.
#'
#' @description The function prepares the input for BLADJ and calls [make_bladj_tree()]
#' @param calibrations A `data.frame` of secondary calibrations for any pair of taxon
#' names in `phy`, usually obtained with [get_all_calibrations()].
#' @param type The type of age to use as calibration. Options are "median", "mean", "min", or "max".
#' @param root_age Numeric specifying an age for the root, provided by the user.
#'        Only used if there are no time calibrations for the root node in the chronograms database.
#'        If `NULL` or not numeric, the maximum calibration age plus one unit of the sd
#### '    At some point I tried using the mean of differences between ages available for the tree
#'        (calculated with [stats::sd()])
#'        of all node ages available for the tree will be used as root calibration.
#'        If there is only one calibration available for the whole tree, the root
#'        node age will be proportional to 1.1 of the age of that calibration.
#' @return A `phylo` object with branch lengths proportional to time.
#' @details
#' The BLADJ algorithm is part of the Phylocom software, presented in Webb et al.
#' (2008) \doi{10.1093/bioinformatics/btn358}.
#' @references
#' Webb, C. O., Ackerly, D. D., & Kembel, S. W. (2008). "Phylocom: software for
#' the analysis of phylogenetic community structure and trait evolution".
#' Bioinformatics, 24(18), \doi{10.1093/bioinformatics/btn358}.

#' @export
use_calibrations_bladj.matchedCalibrations <- function(calibrations,
                                                       type = "mean",
                                                       root_age = NULL) {
  #
  message("... Using secondary calibrations with BLADJ.")
  is_good_calibrations <- inherits(calibrations, "congruifiedCalibrations") | !inherits(calibrations, "matchedCalibrations")
  if (!is_good_calibrations) {
    stop("'calibrations' must be a `matchedCalibrations` or `congruifiedCalibrations` object.\n")
  }
  type <- match.arg(tolower(type), c("mean", "min", "max", "median"))
  if (!all(calibrations$MinAge == calibrations$MaxAge)) {
    stop("Min and max calibrations provided are different, please choose one.")
  }
  if (nrow(calibrations) < 1) {
    stop("Nodes in 'calibrations' (determined by taxon pairs) do not match any nodes
						in 'phy'.\n\t Dating analysis is not possible with this set of calibrations.")
  }
  if ("mean" %in% type) {
    #node_ages <- sapply(calibrations$phy$calibration_distribution, mean)
    node_ages <- sapply(unique(calibrations$mrca_node_name), function(x) {
      node <- calibrations$mrca_node_name == x
      mean(calibrations$MinAge[node])})
  }
  if ("min" %in% type) {
    node_ages <- sapply(attributes(calibrations)$phy$calibration_distribution, min)
  }
  if ("max" %in% type) {
    node_ages <- sapply(attributes(calibrations)$phy$calibration_distribution, max)
  }
  if ("median" %in% type) {
    node_ages <- sapply(attributes(calibrations)$phy$calibration_distribution, stats::median)
  }
  # check that the root node has a calibration
  # otherwise, add one
  # bladj does not run if there is no calibration for the root
  # bladj will run if calibrations are in conflict
  node_names <- names(node_ages)
  # length(node_names)
  root_node_name <- paste0("n", ape::Ntip(attributes(calibrations)$phy) + 1)
  # check if the root is available in the data set
  # if not, add a root age and name:
  if (!root_node_name %in% node_names) {
    warning("An age for the root is not available in the data set.")
    # assign a RANDOM age for the root if none is provided by the user:
    if (is.null(root_age)) {
      if (length(node_ages) > 1) {
        root_age <- max(node_ages) + stats::sd(node_ages)
        # root_age <- max(node_ages) + mean(abs(diff(sort(node_ages))))
      } else {
        # if there is only one calibration the line above will give NaN
        root_age <- 1.1 * max(node_ages)
      }
      warn <- paste("We are using a RANDOM ROOT value of",
                    root_age, "Myrs.")
      warning(warn)
      warning("You can provide an informative age for the root (from the literature)",
              "using the argument 'root_age = `, to get a more accurate chronogram estimate.")
    }
    # add root node name and age:
    node_ages <- c(root_age, node_ages)
    node_names <- c(root_node_name, node_names)
  }
  # create the chronogram
  chronogram <- make_bladj_tree(
    tree = attributes(calibrations)$phy, nodeages = node_ages,
    nodenames = node_names
  )
  # TODO: something about these extra list elements, set up as attributes??
  chronogram$dating_method <- "bladj"
  # chronogram$calibration_distribution <- calibrations$phy$calibration_distribution
  chronogram$calibrations <- calibrations
  chronogram$used_calibrations <- stats::setNames(node_ages, node_names)
  return(chronogram)
}