clean up

R/bootstrap.R

@@ -206,42 +206,3 @@ bootstrap.phyDat <- function(x, FUN, bs = 100, multicore = FALSE,
   }
   res
 }
-
-
-cladeMatrix <- function(x, rooted = FALSE) {
-  if (!rooted) x <- unroot(x)
-  pp <- prop.part(x)
-  pplabel <- attr(pp, "labels")
-  if (!rooted) pp <- SHORTwise(pp)
-  x <- .uncompressTipLabel(x)
-  nnodes <- Nnode(x)
-  class(x) <- NULL
-  # nnodes <- sapply(x, Nnode)
-  l <- length(x)
-  from <- cumsum(c(1, nnodes[-l]))
-  to <- cumsum(nnodes)
-  ivec <- integer(to[l])
-  pvec <- c(0, to)
-  res <- vector("list", l)
-  k <- 1
-  for (i in 1:l) {
-    ppi <- prop.part(x[[i]])
-    if (!rooted) ppi <- SHORTwise(ppi)
-    indi <- sort(fmatch(ppi, pp))
-    ivec[from[i]:to[i]] <- indi
-  }
-  X <- sparseMatrix(i = ivec, p = pvec, dims = c(length(pp), l))
-  list(X = X, prop.part = pp)
-}
-
-
-moving_average <- function(obj, window = 50) {
-  fun <- function(x) {
-    cx <- c(0, cumsum(x))
-    (cx[(window + 1):length(cx)] - cx[1:(length(cx) - window)]) / (window)
-  }
-  res <- apply(obj$X, 1, fun)
-  rownames(res) <- c()
-}
-
-