R/deprecated.R

Defines functions baseAnalysis baseCreate baseListAnalysis baseListCreate classifyConfigFive classifyConfigFour configFind configTop dists fAvgLadder fColless fNConfig fNLadders fWidths idNodeLabel ladderDist ladderNums laddItr makeTransTree nDescendants nLadders nodeApply nodeFrac nTipChildren nTipDescendants rootLaddDist sortmyepi topSumm treeListSummary

baseAnalysis <- function(...) {
  .Deprecated("phyloTop", package="phyloTop")
}

baseCreate <- function(...) {
  .Deprecated("phyloTop", package="phyloTop")
}

baseListAnalysis <- function(...) {
  .Deprecated("phyloTop", package="phyloTop")
}

baseListCreate <- function(...) {
  .Deprecated("phyloTop", package="phyloTop")
}

classifyConfigFive <- function(...) {
  .Deprecated("nConfig", package="phyloTop")
}

classifyConfigFour <- function(...) {
  .Deprecated("nConfig", package="phyloTop")
}

configFind <- function(...) {
  .Deprecated("nConfig", package="phyloTop")
}

configTop <- function(...) {
  .Deprecated("nConfig", package="phyloTop")
}

dists <- function(...) {
  .Deprecated("getDepths", package="phyloTop")
}

fAvgLadder <- function(...) {
  .Deprecated("avgLadder", package="phyloTop")
}

fColless <- function(...) {
  .Deprecated("colless.phylo", package="phyloTop")
}

fNConfig <- function(...) {
  .Deprecated("nConfig", package="phyloTop")
}

fNLadders <- function(...) {
  .Deprecated("ladderSizes", package="phyloTop")
}

fWidths <- function(...) {
  .Deprecated("widths", package="phyloTop")
}

idNodeLabel <- function(...) {
  .Deprecated("phyloTop", package="phyloTop", 
              "Function deprecated: no longer needed now that functions use phylo objects.")
}

ladderDist <- function(...) {
  .Deprecated("ladderSizes", package="phyloTop")
}

ladderNums <- function(...) {
  .Deprecated("ladderSizes", package="phyloTop")
}

laddItr <- function(...) {
  .Deprecated("ladderSizes", package="phyloTop")
}

makeTransTree <- function(...) {
  .Deprecated("makeEpiRecord", package="phyloTop", 
              "Function deprecated: use instead the new function makeEpiRecord")
}

nDescendants <- function(...) {
  .Deprecated("phyloTop", package="phyloTop",
              "Function deprecated: number of descendants is handled within the relevant functions.")
}

nLadders <- function(...) {
  .Deprecated("ladderSizes", package="phyloTop")
}

nodeApply <- function(...) {
  .Deprecated("phyloTop", package="phyloTop",
              "Function deprecated: no longer needed now that functions use phylo objects.")
}

nodeFrac <- function(...) {
  .Deprecated("phyloTop", package="phyloTop",
              "Function deprecated. See nodeImbFrac and nodeDepthFrac for new node threshold functions.")
}

nTipChildren <- function(...) {
  .Deprecated("nConfig", package="phyloTop")
}

nTipDescendants <- function(...) {
  .Deprecated("treeImb", package="phyloTop")
}

rootLaddDist <- function(...) {
  .Deprecated("ladderSizes", package="phyloTop")
}

sortmyepi <- function(...) {
  .Deprecated("getLabGenealogy", package="phyloTop",
              "Function deprecated: now a line within getLabGenealogy")
}

topSumm <- function(...) {
  .Deprecated("phyloTop", package="phyloTop")
}

treeListSummary <- function(...) {
  .Deprecated("phyloTop", package="phyloTop")
}

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phyloTop documentation built on May 2, 2019, 11:03 a.m.