rt <- function (phy) {

}

#' Phylogenetic beta diversity standardized for species beta diversity

#'

#' This function computes the standard effect size of phylogenetic beta

#' diversity by correcting for changes in species beta diversity. The

#' novelty of this function is its ability to utilize sparse community

#' matrix making it possible to efficiently randomize very large

#' community matrices spanning thousands of taxa and sites.

#'

#' @param x  a (sparse) community matrix, i.e., an object of class

#' matrix or Matrix.

#' @param phy a phylogenetic tree (object of class phylo).

#' @param reps Number of replications.

#' @param index.family the family of dissimilarity indices including

#' \dQuote{simpson}, \dQuote{sorensen} and \dQuote{jaccard}.

#' @param model The null model for separating patterns from processes and

#' for contrasting against alternative hypotheses. Available null models

#' include:

#' \itemize{

#' \item \dQuote{tipshuffle}: shuffles phylogenetic tip labels multiple times.

#' \item \dQuote{rowwise}: shuffles sites (i.e., varying richness) and

#' keeping species occurrence frequency constant.

#' \item \dQuote{colwise}: shuffles species occurrence frequency and

#' keeping site richness constant.}

#'

#' @param \dots Further arguments passed to or from other methods.

#' @rdname phylobeta_ses

#' @importFrom stats sd

#' @importFrom ape keep.tip

#' @references

#' Proches, S., Wilson, J.R.U. & Cowling, R.M. (2006) How much evolutionary

#' history in a 10 x 10m plot? \emph{Proceedings of Royal Society B}

#' \strong{273}: 1143-1148.

#' @examples

#' library(ape)

#' library(Matrix)

#' tree <- read.tree(text ="((t1:1,t2:1)N2:1,(t3:1,t4:1)N3:1)N1;")

#' com <- sparseMatrix(c(1,3,4,1,4,5,1,2,3,4,5,6,3,4,6),

#'   c(1,1,1,2,2,2,3,3,3,3,3,3,4,4,4),x=1,

#'   dimnames = list(paste0("g", 1:6), tree$tip.label))

#'

#' phylobeta_ses(com, tree, model="rowwise")

#'

#' @return A data frame of results for each community or grid cell

#' \itemize{

#'   \item phylobeta_obs: Observed phylobeta in community

#'   \item phylobeta_rand_mean: Mean phylobeta in null communities

#'   \item phylobeta_rand_sd: Standard deviation of phylobeta in null communities

#'   \item phylobeta_obs_z: Standardized effect size of phylobeta vs.

#'   null communities \eqn{= (phylobeta_obs - phylobeta_rand_mean)

#'   / phylobeta_rand_sd}

#'   \item reps: Number of replicates

#' }

#' @export

phylobeta_ses <- function(x, phy, index.family="simpson",

                   model = c("tipshuffle", "rowwise", "colwise"),

                   reps = 1000, ...) {

    }

    }

}

mean_dist <- function(files, trace = 1, ...){