oi: Identification of Stem-Lineage-Edges and MRCAs

In ips: Interfaces to Phylogenetic Software in R

Identification of Stem-Lineage-Edges and MRCAs

Description

noi (node of interest) identifies the most recent common ancestor (MRCA) and eoi (edge of interest) its subtending stem-lineage edge of one or more sets of taxa/tips.

Usage

eoi(phy, node, group, regex = FALSE, stem = FALSE, monophyletic = FALSE)

noi(phy, group, regex = FALSE, stem = FALSE, monophyletic = FALSE)

Arguments

phy	An object of class phylo.
node	A vector of mode "numeric" giving the nodes numbers of the nodes whose subtending stem-lineages will be identified.
group	A vector or list of vectors of mode character specifying the taxon set(s). Will be ignored if node is given.
regex	A logical, if regex = TRUE, taxon sets are matched to the tip labels as regular expressions of the form "taxon1|taxon2"; otherwise strings will be matched exactly (see which).
stem	Logical, ...
monophyletic	Logical, ...

Value

A vector of mode "numeric" containing node numbers.

See Also

mrca; descendants for the contrary operation to noi.

Examples

# molecular phylogeny of Ips bark beetles
# ---------------------------------------
data(ips.tree)
ips.tree <- ladderize(ips.tree)
ips.tree <- fixNodes(ips.tree)
clade1 <- descendants(ips.tree, 44, labels = TRUE)
mrca <- noi(ips.tree, clade1)
stem_lineage <- eoi(ips.tree, mrca)
ecol <- rep("black", Nedge(ips.tree))
ecol[stem_lineage] <- "red"
plot(ips.tree, no.margin = TRUE, edge.color = ecol)
nodelabels(node = mrca, pch = 22, col = "blue")
#gen <- sapply(viperidae$tip.label, function(x) unlist(strsplit(x, "_"))[1])
#tax <- data.frame(genus = gen, species = viperidae$tip.label, row.names = NULL)

# group can be a list
# -------------------
#myclades <- split(tax$species, tax$genus)
#nds <- noi(viperidae, myclades)
#plot(viperidae)
#nodeInfo(nds)

# group might contain tip numbers
# -------------------------------
#group <- list(c(17, 22), c(13, 1))
#plot(viperidae)
#append2tips(phy, tips = unlist(group), pch = 19)
#nds <- noi(viperidae, myclades)
#nodeInfo(nds)

# the 'group' argument can also take regular expressions
# ------------------------------------------------------
#rex <- "aspis"
#node <- noi(viperidae, rex, regex = TRUE)
#plot.phylo(viperidae, tip.color = 0, edge.color = 0)
#box.clades(viperidae, nodes = node, col = "#D2A6A7", align = "all")
#plot.phylo.upon(viperidae)
#nodelabels(node = node, pch = 21, cex = 1.2, col = "red", bg = "#D2A6A7")

# if the 'group' argument is a list of elements of length 2,
# n = length(group) nodes of interest will be returned
# ----------------------------------------------------
#group <- list(
#    c("Vipera_berus", "Vipera_ursinii"),
#    c("Vipera_aspis_ssp._aspis", "Vipera_latastei"),
#    c("Vipera_ammodytes_ssp._ammodytes",
#        "Vipera_ammodytes_ssp._montandoni"),
#    c("Macrovipera_lebetina", "Vipera_wagneri")
#)
#clades <- noi(viperidae, group)
#plot.phylo(viperidae, tip.color = 0, edge.color = 0)
#box.clades(viperidae, nodes = clades, col = c("#FFFFA5", "#D2A6A7",
#    "#A7D2A5", "#A5A6D2"), align = "all")
#plot.phylo.upon(viperidae)

ips documentation built on May 29, 2024, 4:39 a.m.