bind.relative: Bind tips to their designated relatives

In jinyizju/V.PhyloMaker: Make phylogenetic hypotheses for vascular plants, etc.

Description

This function binds a list of species to their designated species- and genus-level relatives in the phylogeny.

Usage

bind.relative(sp.list, tree = GBOTB.extended, nodes = nodes.info.1, output.sp.list = TRUE)

Arguments

sp.list	The user-provided species list.
tree	The backbone phylogeny. The default is GBOTB.extended.
nodes	The nodes information of the backbone phylogeny. The default is nodes.info.1
output.sp.list	Whether or not to output the species list, with each species' status of binded to its designated relative or not. The default is TRUE.

Value

phylo	The updated phylogeny, with species binded to the designated relative
species.list	The species list with the information of each species status of binded to its designated relative or not.
nodes.info	The nodes information of the updated phylogeny.

Author(s)

Yi Jin

Examples

### make the example file
c1 <- c("Carya floridana", "Carya pallida", "Epiprinus siletianus", "Platycarya strobilacea", "Tilia amurensis", "Apodanthes caseariae", "Pilostyles blanchetii")
c2 <- c("Carya", "Carya", "Epiprinus", "Platycarya", "Tilia", "Apodanthes", "Pilostyles")
c3 <- c("Juglandaceae", "Juglandaceae", "Euphorbiaceae", "Juglandaceae", "Malvaceae", "Apodanthaceae", "Apodanthaceae")
c4 <- c("", "Carya floridana", "", "", "", "", "")
c5 <- c("", "", "", "Cyclocarya", "", "", "")
example <- data.frame(species = c1, genus = c2, family = c3, species.relative = c4, genus.relative = c5)

### run the function with phylo.maker.
result <- bind.relative(example)
result1 <- phylo.maker(sp.list = result$species.list, tree = result$phylo, nodes = result$nodes.info, scenarios = "S3")

### run phylo.maker only.
result2 <- phylo.maker(sp.list = example, scenarios="S3")

### compare the phylogeny with and without incorporting bind.relative. node age is displayed.
par(mfrow=c(1,2))
plot.phylo(result1$scenario.3, cex =1.5, main = "bind.relative + phylo.maker")
nodelabels(round(branching.times(result1$scenario.3), 1), cex = 1)
plot.phylo(result2$scenario.3, cex = 1.5, main = "phylo.maker")
nodelabels(round(branching.times(result2$scenario.3), 1), cex = 1)

jinyizju/V.PhyloMaker documentation built on July 12, 2021, 12:15 a.m.