R/tree_influ_phylm.R

In sensiPhy: Sensitivity Analysis for Comparative Methods

#' Interaction between phylogenetic uncertainty and influential species detection - Phylogenetic Linear Regression
#'
#' Performs leave-one-out deletion analysis for phylogenetic linear regression,
#' and detects influential species while evaluating uncertainty in trees topology.
#'
#' @param formula The model formula
#' @param data Data frame containing species traits with row names matching tips
#' in \code{phy}.
#' @param phy A phylogeny (class 'phylo') matching \code{data}.
#' @param model The phylogenetic model to use (see Details). Default is \code{lambda}.
#' @param cutoff The cutoff value used to identify for influential species
#' (see Details)
#' @param n.tree Number of times to repeat the analysis with n different trees picked 
#' randomly in the multiPhylo file.
#' @param track Print a report tracking function progress (default = TRUE)
#' @param ... Further arguments to be passed to \code{phylolm}
#' @details
#' This function sequentially removes one species at a time, fits a phylogenetic
#' linear regression model using \code{\link[phylolm]{phylolm}}, stores the
#' results and detects influential species. It repeats this operation using n trees, 
#' randomly picked in a multiPhylo file.
#'
#' All phylogenetic models from \code{phylolm} can be used, i.e. \code{BM},
#' \code{OUfixedRoot}, \code{OUrandomRoot}, \code{lambda}, \code{kappa},
#' \code{delta}, \code{EB} and \code{trend}. See ?\code{phylolm} for details.
#'
#' \code{influ_phylm} detects influential species based on the standardised
#' difference in intercept and/or slope when removing a given species compared
#' to the full model including all species. Species with a standardised difference
#' above the value of \code{cutoff} are identified as influential. The default
#' value for the cutoff is 2 standardised differences change.
#'
#' Currently, this function can only implement simple linear models (i.e. \eqn{trait~
#' predictor}). In the future we will implement more complex models.
#'
#' Output can be visualised using \code{sensi_plot}.
#'
#' @return The function \code{influ_phylm} returns a list with the following
#' components:
#' @return \code{cutoff}: The value selected for \code{cutoff}
#' @return \code{formula}: The formula
#' @return \code{full.model.estimates}: Coefficients, aic and the optimised
#' value of the phylogenetic parameter (e.g. \code{lambda}) for the full model
#' without deleted species.
#' @return \code{influential_species}: List of influential species, both
#' based on standardised difference in intercept and in the slope of the
#' regression. Species are ordered from most influential to less influential and
#' only include species with a standardised difference > \code{cutoff}.
#' @return \code{sensi.estimates}: A data frame with all simulation
#' estimates. Each row represents a deleted clade for a given random tree. Columns report the calculated
#' regression intercept (\code{intercept}), difference between simulation
#' intercept and full model intercept (\code{DIFintercept}), the standardised
#' difference (\code{sDIFintercept}), the percentage of change in intercept compared
#' to the full model (\code{intercept.perc}) and intercept p-value
#' (\code{pval.intercept}). All these parameters are also reported for the regression
#' slope (\code{DIFestimate} etc.). Additionally, model aic value (\code{AIC}) and
#' the optimised value (\code{optpar}) of the phylogenetic parameter
#' (e.g. \code{kappa} or \code{lambda}, depending on the phylogenetic model used) are
#' reported.
#' @return \code{data}: Original full dataset.
#' @return \code{errors}: Species where deletion resulted in errors.
#' @author Gustavo Paterno, Caterina Penone & Gijsbert D.A. Werner
#' @seealso \code{\link[phylolm]{phylolm}}, \code{\link{tree_phylm}}, 
#' \code{\link{influ_phylm}}, \code{\link{tree_influ_phyglm}}, \code{\link{sensi_plot}}
#' @references 
#' 
#' Paterno, G. B., Penone, C. Werner, G. D. A. 
#' \href{http://doi.wiley.com/10.1111/2041-210X.12990}{sensiPhy: 
#' An r-package for sensitivity analysis in phylogenetic 
#' comparative methods.} Methods in Ecology and Evolution 
#' 2018, 9(6):1461-1467
#'
#' Ho, L. S. T. and Ane, C. 2014. "A linear-time algorithm for 
#' Gaussian and non-Gaussian trait evolution models". Systematic Biology 63(3):397-408.
#' @examples 
#' \dontrun{
#' # Load data:
#' data(alien)
#' # run analysis:
#' tree_influ <- tree_influ_phylm(log(gestaLen) ~ log(adultMass), phy = alien$phy, 
#' data = alien$data, n.tree = 5)
#' # To check summary results:
#'summary(tree_influ)
#'# Visual diagnostics
#'sensi_plot(tree_influ)
#'sensi_plot(tree_influ, graphs = 1)
#'sensi_plot(tree_influ, graphs = 2)
#'
#' data(alien)
#' tree_influ <- tree_influ_phylm(log(gestaLen) ~ log(adultMass), phy = alien$phy, 
#' data = alien$data[1:25, ], n.tree = 2)
#'summary(tree_influ)
#'}
#' @export


tree_influ_phylm <- function(formula,
                             data,
                             phy,
                             n.tree = 2,
                             cutoff = 2,
                             model = "lambda",
                             track = TRUE,
                             ...) {
  # Error checking:
  if (!inherits(data, "data.frame"))
    stop("data must be class 'data.frame'")
  if (!inherits(formula, "formula"))
    stop("formula must be class 'formula'")
  if (!inherits(phy, "multiPhylo"))
    stop("phy must be class 'multiPhylo'")
  if (length(phy) < n.tree)
    stop("'times' must be smaller (or equal) than the number of trees in the 'multiPhylo' object")
  if ((model == "trend") && (sum(is.ultrametric(phy)) > 1))
    stop("Trend is unidentifiable for ultrametric trees., see ?phylolm for details")
  else
    
    #Match data and phy
    data_phy <- match_dataphy(formula, data, phy, ...)
  phy <- data_phy$phy
  full.data <- data_phy$data
  
  # If the class of tree is multiphylo pick n=n.tree random trees
  trees <- sample(length(phy), n.tree, replace = F)
  
  
  #List to store information
  tree.influ <- list ()
  
  #Start tree loop here
  if (track == TRUE)
    pb <- utils::txtProgressBar(min = 0, max = n.tree, style = 3)
  counter = 1
  
  for (j in trees) {
    #Match data order to tip order
    full.data <- full.data[phy[[j]]$tip.label, ]
    
    #Select tree
    tree <- phy[[j]]
    
    tree.influ[[counter]] <-
      influ_phylm(
        formula,
        data = full.data,
        phy = tree,
        model,
        cutoff,
        track = FALSE,
        verbose = FALSE,
        ...
      )
    
    if (track == TRUE)
      utils::setTxtProgressBar(pb, counter)
    counter = counter + 1
  }
  
  if (track == TRUE)
    close(pb)
  names(tree.influ) <- trees
  
  # Merge lists into data.frames between iterations:
  full.estimates  <-
    suppressWarnings(recombine(tree.influ, slot1 = 4, slot2 = 1))
  
  #influ species slope
  influ.sp.estimate <-
    (lapply(tree.influ, function(x)
      x$influential.species$influ.sp.estimate))
  influ.sp.estimate <- as.data.frame(as.matrix(influ.sp.estimate))
  names(influ.sp.estimate) <- "influ.sp.estimate"
  influ.sp.estimate$tree <- row.names(influ.sp.estimate)
  
  #influ species intercept
  influ.sp.intercept <-
    (lapply(tree.influ, function(x)
      x$influential.species$influ.sp.intercept))
  influ.sp.intercept <- as.data.frame(as.matrix(influ.sp.intercept))
  names(influ.sp.intercept) <- "influ.sp.intercept"
  influ.sp.intercept$tree <- row.names(influ.sp.intercept)
  
  #influ.estimates
  influ.estimates <- recombine(tree.influ, slot1 = 6)
  influ.estimates$info <- NULL
  
  #Generates output:
  res <- list(
    call = match.call(),
    cutoff = cutoff,
    formula = formula,
    full.model.estimates = full.estimates,
    influential.species = list(
      influ.sp.estimate = influ.sp.estimate,
      influ.sp.intercept = influ.sp.intercept
    ),
    sensi.estimates = influ.estimates,
    data = full.data
  )
  
  
  class(res) <- "sensiTree_Influ"
  ### Warnings:
  if (length(res$errors) > 0) {
    warning("Some species deletion presented errors, please check: output$errors")
  }
  else {
    res$errors <- "No errors found."
  }
  return(res)
}