newick_string: Generate Newick Tree Format Parenthetic Strings

In SoilTaxonomy: A System of Soil Classification for Making and Interpreting Soil Surveys

Generate Newick Tree Format Parenthetic Strings

Description

This function generates Newick tree format strings for a single tree. Taxa are assigned relative positions within their parent to indicate the order that they "key out."

Usage

newick_string(
  x = NULL,
  level = c("suborder", "greatgroup", "subgroup"),
  what = c("taxon", "code")
)

Arguments

x	Optional: a taxon name to get children of.
level	Level to build the tree at. One of "suborder", "greatgroup", "subgroup". Defaults to "suborder" when x is not specified. When x is specified but level is not specified, level is calculated from taxon_to_level(x).
what	Either "taxon" (default; for taxon names (quoted for subgroups)) or "code"

Details

The output from this function is a character string with parenthetical format encoding a single tree suitable for input into functions such as ape::read.tree(). Multiple trees can be combined together in the file or text string supplied to your tree-parsing function of choice.

Value

character. A single tree in parenthetical Newick or New Hampshire format.

Examples

if (requireNamespace("ape")) {
  par(mar = c(0, 0, 0, 0))

  # "fan"
  mytr <- ape::read.tree(text = newick_string(level = "suborder"))
  plot(mytr, "f", rotate.tree = 180, cex = 0.75)

  # "cladogram"
  mytr <- ape::read.tree(text = newick_string("durixeralfs", level = "subgroup"))
  plot(mytr, "c")

  # "cladogram" (using taxon codes instead of subgroups)
  mytr <- ape::read.tree(text = newick_string("xeralfs", level = "subgroup", what = "code"))
  plot(mytr, "c")

  dev.off()
}

SoilTaxonomy documentation built on Nov. 17, 2023, 1:07 a.m.