R/SOWH.R

In KlausVigo/phangorn: Phylogenetic Reconstruction and Analysis

#' Swofford-Olsen-Waddell-Hillis Test
#'
#' This function computes the Swofford--Olsen--Waddell--Hillis (SOWH) test, a
#' parametric bootstrap test. The function is computational very demanding and
#' likely to be very slow.
#'
#' \code{SOWH.test} performs a parametric bootstrap test to compare two trees.
#' It makes extensive use \code{simSeq} and \code{optim.pml} and can take quite
#' long.
#'
#' @param x an object of class \code{"pml"}.
#' @param n the number of bootstrap replicates.
#' @param restricted list of restricted parameter settings.
#' @param optNni Logical value indicating whether topology gets optimized
#' (NNI).
#' @param trace Show output during computations.
#' @param \dots Further arguments passed to \code{"optim.pml"}.
#' @return an object of class SOWH. That is a list with three elements, one is
#' a matrix containing for each bootstrap replicate the (log-) likelihood of
#' the restricted and unrestricted estimate and two pml objects of the
#' restricted and unrestricted model.
#' @author Klaus Schliep \email{klaus.schliep@@gmail.com}
#' @seealso \code{\link{pml}}, \code{\link{pmlPart}}, \code{\link{pmlCluster}},
#' \code{\link{simSeq}}, \code{\link{SH.test}}
#' @references Goldman, N., Anderson, J. P., and Rodrigo, A. G. (2000)
#' Likelihood -based tests of topologies in phylogenetics. \emph{Systematic
#' Biology} \bold{49} 652-670.
#'
#' Swofford, D.L., Olsen, G.J., Waddell, P.J. and Hillis, D.M. (1996)
#' Phylogenetic Inference in Hillis, D.M., Moritz, C. and Mable, B.K. (Eds.)
#' \emph{Molecular Systematics} (2nd ed.) 407-514, Sunderland, MA: Sinauer
#' @keywords models
#' @examples
#'
#' # in real analysis use larger n, e.g. 500 preferably more
#' \dontrun{
#' data(Laurasiatherian)
#' dm <- dist.logDet(Laurasiatherian)
#' tree <- NJ(dm)
#' fit <- pml(tree, Laurasiatherian)
#' fit <- optim.pml(fit, TRUE)
#' set.seed(6)
#' tree <- rNNI(fit$tree, 1)
#' fit <- update(fit, tree = tree)
#' (res <- SOWH.test(fit, n=100))
#' summary(res)
#' }
#'
#' @export SOWH.test
SOWH.test <- function(x, n = 100, restricted = list(optNni = FALSE),
                      optNni = TRUE, trace = 1, ...) {
  res <- matrix(NA, n, 2)
  extras <- match.call(expand.dots = FALSE)$...

  optU <- list (optNni = optNni, optBf = FALSE, optQ = FALSE,
    optInv = FALSE, optGamma = FALSE, optEdge = TRUE, optRate = FALSE,
    optRooted = FALSE, model = NULL)

  if (!is.null(extras)) {
    namAll <-  names(extras)
    for (i in seq_along(extras)) optU[[namAll[i]]] <- extras[[i]]
  }
  optR <- optU
  namR <- names(restricted)
  for (i in seq_along(namR)) optR[[namR[i]]] <- restricted[[i]]
  restr <- optim.pml(x, optNni = optR$optNni, optBf = optR$optBf,
                     optQ = optR$optQ, optInv = optR$optInv,
                     optGamma = optR$optGamma, optEdge = optR$optEdge,
                     optRate = optR$optRate, optRooted = optR$optRooted,
                     model = optR$model, pml.control(trace = trace - 1L))
  unrestr <- optim.pml(restr, optNni = optU$optNni, optBf = optU$optBf,
                       optQ = optU$optQ, optInv = optU$optInv,
                       optGamma = optU$optGamma, optEdge = optU$optEdge,
                       optRate = optU$optRate, optRooted = optU$optRooted,
                       model = optU$model, pml.control(trace = trace - 1L))
  for (i in 1:n) {
    if (trace > 0) cat("iteration: ", i, "\n")
    newData <- simSeq(restr)
    restrTmp <- update(restr, data = newData)
    unrestrTmp <- restrTmp
    restrTmp <- optim.pml(restrTmp, optNni = optR$optNni, optBf = optR$optBf,
                          optQ = optR$optQ, optInv = optR$optInv,
                          optGamma = optR$optGamma, optEdge = optR$optEdge,
                          optRate = optR$optRate, optRooted = optR$optRooted,
                          model = optR$model, pml.control(trace = trace - 1L))
    unrestrTmp <- optim.pml(unrestrTmp, optNni = optU$optNni,
                            optBf = optU$optBf, optQ = optU$optQ,
                            optInv = optU$optInv, optGamma = optU$optGamma,
                            optEdge = optU$optEdge, optRate = optU$optRate,
                            optRooted = optU$optRooted, model = optU$model,
                            pml.control(trace = trace - 1L))
    res[i, 1] <- logLik(restrTmp)
    res[i, 2] <- logLik(unrestrTmp)
  }
  result <- list("LL" = res, "restr" = restr, "unrestr" = unrestr)
  class(result) <- "SOWH"
  result
}


#' @export
print.SOWH <- function(x, digits = 4L, ...) {
  resLL <- logLik(x$restr)
  unresLL <- logLik(x$unrestr)
  diffLL <- unresLL - resLL
  pval <- sum( (x$LL[, 2] - x$LL[, 1]) > diffLL) / nrow(x$LL)
  res <- c(resLL, unresLL, diffLL, pval)
  names(res) <- c("ln L restr", "ln L unrestr", "Diff ln L", "p-value")
  print(res, digits = digits)
  invisible(x)
}


#' @export
summary.SOWH <- function(object, digits = 4L, plot = TRUE, ...) {
  resLL <- logLik(object$restr)
  unresLL <- logLik(object$unrestr)
  diffLL <- unresLL - resLL
  pval <- sum( (object$LL[, 2] - object$LL[, 1]) > diffLL) / nrow(object$LL)
  res <- c(resLL, unresLL, diffLL, pval)
  names(res) <- c("ln L restr", "ln L unrestr", "Diff ln L", "p-value")
  print(res, digits = digits)
  if (plot) {
    d <- object$LL[, 2] - object$LL[, 1]
    hist(d, freq = FALSE, xlim = c(0, 1.2 * max(d, diffLL)))
    abline(v = diffLL, col = "red")
  }
  invisible(object)
}