Write a key as Newick, with safe labels or node annotations

The dimoose method $toNewick() writes quoted Newick, which is correct but which several parsers (ape, scikit-bio, toytree) mangle. This wrapper adds two options for interoperating with the wider phylogenetics ecosystem.

Usage

toNewick(
  key,
  labels = c("quoted", "safe"),
  annotate = c("none", "nhx", "beast")
)

Arguments

key

A dimoose key.

labels

"quoted" (the default, identical to key$toNewick()) or "safe", which replaces every label with an ASCII id (n<couplet> for couplets, t<n> for taxa) and returns the mapping in a side table, so fragile parsers never see spaces or punctuation. The real text travels in the companion table (this is also the Newick-plus-table shape Taxonium reads).

annotate

"none" (default), "nhx" or "beast": attach each lead's Character text to the node it leads to, as an NHX ([&&NHX:lead=...]) or BEAST-style ([&lead=...]) comment. Values are sanitized (, : ; = " [ ] and newlines removed) because Newick comments cannot carry them. Only one of labels = "safe" or annotate applies at a time; annotate wins if both are given.

[ ]: R:%20

Value

For labels = "quoted" or any annotate, a single Newick string. For labels = "safe" with annotate = "none", a list of newick (the string) and labels (a data frame of id and label).

See also

toTreedata(), toAuspiceJSON()

Examples

k <- arachnidaKey()
cat(toNewick(k, annotate = "nhx"))
#> ((Araneae[&&NHX:lead=Opisthosoma petiolate (Figures 5-5 and 5-9 through 5-13)],Acari[&&NHX:lead=Opisthosoma not petiolate  but broadly joined to prosoma (Figures 5-15 through 5-22)])2[&&NHX:lead=Opisthosoma (abdomen) unsegmented or  if segmented  with spinnerets posteriorly on ventral side (Figures 5-5 and 5-8  ALS PLS PMS)],((Scorpiones[&&NHX:lead=Opisthosoma ending in a sting (Figure 5-3)  first pair of legs not greatly elongated  second ventral segment of opisthosoma with a pair of comblike organs],(Palpigradi[&&NHX:lead=Pedipalps slender  similar to legs (Figure 5-4A)  minute forms  5 mm or less in length],(Uropygi[&&NHX:lead=With two median eyes on a tubercle anteriorly and a group of three eyes on each lateral margin  tail long  filiform  and many-segmented  pedipalps nearly straight or curved mesad  extending forward  and moving laterally (Figure 5-4B)  body blackish  more than 50 mm in length],Schizomida[&&NHX:lead=Eyes lacking  tail short  one- to four-segmented  pedipalps arching upward  forward  and downward and moving vertically  body yellowish or brownish  less than 8 mm in length])6[&&NHX:lead=Pedipalps usually much stouter than any of the legs (Figure 5-4B)  mostly larger forms])5[&&NHX:lead=Opisthosoma not ending in a sting  first pair of legs longer than other pairs (Figure 5-4A B)  second ventral segment of opisthosoma without comblike organs])4[&&NHX:lead=Opisthosoma with a tail-like prolongation that is either thick and terminating in a sting (Figure 5-3) or slender and more or less whiplike (Figure 5-4A B)  mostly tropical],(Pseudoscorpiones[&&NHX:lead=Pedipalps chelate (pincerlike) (Figure 5-23)  body more or less oval  flattened  usually less than 5 mm in length],(Solifugae[&&NHX:lead=Chelicerae very large  usually about as long as prosoma  and extending forward  and body slightly narrowed in middle (Figure 5-4C)  color pale yellow to brownish  length 20 to 30 mm  mostly nocturnal desert forms occurring in western United States],((Schizomida[&&NHX:lead=Prosoma longer than wide  lateral margins nearly parallel  and with a transverse membranous suture in caudal third  opisthosoma with a very short terminal appendage  length 5-8 mm (see also couplet 6')],Amblypygi[&&NHX:lead=Prosoma wider than long  lateral margins rounded or arched  and without a transverse suture  opisthosoma without a terminal appendage  length variable  up to about 50 mm])10[&&NHX:lead=First pair of legs very long  with long tarsi  opisthosoma constricted at base  mainly tropical],(Ricinulei[&&NHX:lead=Orange-red to brown arachnids  about 3 mm in length  with broad flap at anterior end of prosoma concealing chelicerae  legs not unusually long  animal somewhat mitelike or ticklike in appearance  recorded from Rio Grande Valley of Texas],Opiliones[&&NHX:lead=Size and color variable  but without broad flap at anterior end of prosoma covering chelicerae  legs variable in length  often very long and slender (Figure 5-14)  widely distributed])11[&&NHX:lead=First legs similar to the others and (except in the Opiliones) not usually long  opisthosoma not particularly constricted at base])9[&&NHX:lead=Without the preceding combination of characters])8[&&NHX:lead=Pedipalps raptorial or leglike  but not chelate  body not particularly flattened  size variable])7[&&NHX:lead=Opisthosoma without a tail-like prolongation or with a very short leaflike appendage])3[&&NHX:lead=Opisthosoma distinctly segmented  without spinnerets])1;