R/ep.ca.R

#' @export
ep.ca <- function(DATA, asymmetric = F, k = 0, compact = T, graphs = F, tol = .Machine$double.eps){

  if(any(is.na(DATA))){
    stop("No NAs allowed.")
  }

  DATA <- table.scale(DATA, type="ca") # no user choice here.
  wi <- rowSums(DATA)
  wj <- colSums(DATA)

  k <- ceiling(abs(k))
  res <- gsvd( sweep(sweep(DATA, 1, wi, "/"), 2, wj), wi, 1/wj)
  res$fi <- sweep(res$fi, 1, wi, "/")

  res$asymmetric <- asymmetric
  if(asymmetric){
    res$fj <- sweep(res$fj,2,res$d,"/")
  }

  res$compact <- F
  if(compact){
    res <- list(fi=res$fi, fj=res$fj, tau = res$tau, d.orig=res$d.orig, u=res$u, v=res$v)
  }
  res$wi <- wi
  res$wj <- wj
  res$data.attributes <- attributes(DATA) ## maybe it's none?
  res$analysis <- "ca"
  class(res) <- "expo"


  if(graphs){
    max.lims <- apply(rbind(res$fi[,1:2], res$fj[,1:2]),2,max) * 1.25
    min.lims <- apply(rbind(res$fi[,1:2], res$fj[,1:2]),2,min) * 1.25
    xlims <- c(min.lims[1],max.lims[1])
    ylims <- c(min.lims[2],max.lims[2])
    c1.label <- paste0("Component 1: ", round(res$tau[1],digits=3), " % variance" )
    c2.label <- paste0("Component 2: ", round(res$tau[2],digits=3), " % variance" )

    plot(res,type="row.scores", main="Row component scores", xlim = xlims, ylim = ylims, xlab= c1.label, ylab = c2.label)
    plot(res,type="col.scores", main="Column component scores", xlim = xlims, ylim = ylims, xlab= c1.label, ylab = c2.label)
    plot(res,type="scree")
  }

  return(res)
}
derekbeaton/ExPosition2 documentation built on May 10, 2019, 8:25 a.m.