wrong node label in drop.tip.singleton

[MarioJose]

Dear @liamrevell,

I'm using the function 'drop.tip.singleton' and having some problems with node labels. The final tree has some node labels of excluded nodes. For instance:

# Pool tree of which I want remove some tips
pool <- "((((((((annona_cacans,annona_sylvatica,annona_montana,annona_dioica,annona_coriacea,annona_cornifolia,annona_dolabripetala,annona_neosalicifolia,annona_neosericea,annona_nutans,annona_crotonifolia,annona_crassiflora)annona,(rollinia_sylvatica,rollinia_emarginata,rollinia_mucosa,rollinia_sericea)rollinia),(guatteria_australis,guatteria_nigrescens)guatteria),(duguetia_furfuracea,duguetia_lanceolata)duguetia),(xylopia_sericea,xylopia_brasiliensis,xylopia_aromatica,xylopia_emarginata)xylopia),(porcelia_macrocarpa)porcelia),((unonopsis_lindmanii)unonopsis,(ephedranthus_parviflorus)ephedranthus)),(anaxagorea_phaeocarpa)anaxagorea)annonaceae;"

# Species of my sample of which I want to keep in pool tree.
samp <- c("annona_cacans","annona_coriacea","annona_crassiflora","annona_dolabripetala","annona_neosalicifolia","annona_neosericea","annona_nutans","annona_sylvatica","duguetia_furfuracea","duguetia_lanceolata","xylopia_aromatica")

# Reading pool tree
tpool <- read.newick(text=pool)

# Removing tips of pool tree that is not in my sample
tsamp <- drop.tip.singleton(tpool, tpool$tip.label[!(tpool$tip.label %in% samp)])

# Final tree
write.tree(tsamp)

"((((((((annona_cacans,annona_sylvatica,annona_coriacea,annona_dolabripetala,annona_neosalicifolia,annona_neosericea,annona_nutans,annona_crassiflora)annona)),(duguetia_furfuracea,duguetia_lanceolata)rollinia),(xylopia_aromatica)guatteria))))annonaceae;"

Note that 'rollinia' and 'guetteria' nodes labels must be dropped, but the function changed 'duguetia' and 'xylopia' nodes labels to labels of nodes that was deleted.

Best regards,

Mario

[MarioJose]

Dear @liamrevell,

I wrote the function drop.tip.label that solve the problem. It can remove tips and preserve singletons.

All the best,

Mario

[MarioJose]

Dear @liamrevell,

I just update phytools to 0.6-20 version and the problem persist.

All the best,

Mario

[liamrevell]

ape::drop.tip now has an option (collapse.singles=TRUE) that drops tips from a tree with non-splitting nodes, and that also allows the resulting tree to contain these nodes. I recommend using that function.