Defines functions org_matrix

Documented in org_matrix

#' Organize rows and columns of a matrix
#' @param m A matrix with individuals ordered identically in rows and columns.
#' @param method The method to be used to reorganize the matrix.
#' \code{method="alpha"} is the default and will organize rows/columns based
#' on alphanumeric order of rownames/colnames. \code{method="wins"} will
#' return a matrix ordered in descending order of summed rows (i.e. total
#' competitive interactions won). If rows have tied number of total wins,
#' they will be returned in the order of the inputted matrix.
#'  \code{method="ds"} Will return a matrix ordered by David's Score.
#' @return The same matrix \code{m} with reordered rows/columns
#' @examples
#' org_matrix(bonobos)
#' org_matrix(mouse, method="wins")
#' org_matrix(people, method="ds")
#' @export

#Organizing a matrix by highest to lowest wins
org_matrix <- function(m, method="alpha"){

if (method=="alpha"){
  m <- as.matrix(m)
  xr<- rownames(m)
  m <- m[order(xr),order(xr)]

if (method=="wins"){
  m <- as.matrix(m)
  xr<-rowSums(m, na.rm=T)
  m <- m[order(xr, decreasing=T),order(xr, decreasing=T)]

  if (method=="ds"){
    dsm <- ds(m)
    m <- m[names(dsm1),names(dsm1)]

jalapic/compete documentation built on Nov. 22, 2017, 2:10 a.m.