parentChild2taxonTree: Create a Taxonomy-Based Phylogeny ('Taxon Tree') from a Table...

In dwbapst/paleotree: Paleontological and Phylogenetic Analyses of Evolution

Create a Taxonomy-Based Phylogeny ('Taxon Tree') from a Table of Parent-Child Taxon Relationships

Description

This function takes a two-column matrix of taxon names, indicating a set of binary parent-taxon:child-taxon paired relationships with a common root, and returns a 'taxonomy-tree' phylogeny object of class phylo.

Usage

parentChild2taxonTree(parentChild, tipSet = "nonParents", cleanTree = TRUE)

Arguments

parentChild	A two-column matrix of type character where each element is a taxon name. Each row represents a parent-child relationship with first the parent (column 1) taxon name and then the child (column 2).
tipSet	This argument controls which taxa are selected as tip taxa for the output tree. The default tipSet = "nonParents" selects all child taxa which are not listed as parents in parentChild. Alternatively, tipSet = "all" will add a tip to every internal node with the parent-taxon name encapsulated in parentheses.
cleanTree	When TRUE (the default), the tree is run through a series of post-processing, including having singles collapsed, nodes reordered and being written out as a Newick string and read back in, to ensure functionality with ape functions and ape-derived functions. If FALSE, none of this post-processing is done and users should beware, as such trees can lead to hard-crashes of R.

Details

All taxa listed must be traceable via their parent-child relationships to a single, common ancestor which will act as the root node for output phylogeny. Additionally, the root used will be the parent taxon to all tip taxa closest in terms of parent-child relationships to the tip taxa: i.e., the most recent common ancestor. Ancestral taxa which are singular internal nodes that trace to this root are removed, and a message is printed.

Value

A phylogeny of class phylo, with tip taxa as controlled by argument tipSet. The output tree is returned with no edge lengths.

The names of higher taxa than the tips should be appended as the element $node.label for the internal nodes.

Author(s)

David W. Bapst

See Also

makePBDBtaxonTree, taxonTable2taxonTree

Examples

#let's create a small, really cheesy example
pokexample <- rbind(
    cbind("Squirtadae", c("Squirtle","Blastoise","Wartortle")),
    c("Shelloidea","Lapras"), c("Shelloidea","Squirtadae"),
    c("Pokezooa","Shelloidea"), c("Pokezooa","Parasect"),
    c("Rodentapokemorpha","Linoone"), c("Rodentapokemorpha","Sandshrew"),
    c("Rodentapokemorpha","Pikachu"), c("Hirsutamona","Ursaring"),
    c("Hirsutamona","Rodentapokemorpha"), c("Pokezooa","Hirsutamona")
    )

#Default: tipSet = 'nonParents'
pokeTree <- parentChild2taxonTree(
    parentChild = pokexample,
    tipSet = "nonParents")
plot(pokeTree)
nodelabels(pokeTree$node.label)

#Get ALL taxa as tips with tipSet = 'all'
pokeTree <- parentChild2taxonTree(
    parentChild = pokexample,
    tipSet = "all")
plot(pokeTree)
nodelabels(pokeTree$node.label)


## Not run: 

# let's try a dataset where not all the
    # taxon relationships lead to a common root

pokexample_bad <- rbind(
    cbind("Squirtadae", c("Squirtle","Blastoise","Wartortle")),
    c("Shelloidea","Lapras"), c("Shelloidea","Squirtadae"),
    c("Pokezooa","Shelloidea"), c("Pokezooa","Parasect"),
    c("Rodentapokemorpha","Linoone"), c("Rodentapokemorpha","Sandshrew"),
    c("Rodentapokemorpha","Pikachu"), c("Hirsutamona","Ursaring"),
    c("Hirsutamona","Rodentapokemorpha"), c("Pokezooa","Hirsutamona"),
    c("Umbrarcheota","Gengar")
    )

# this should return an error
    # as Gengar doesn't share common root
pokeTree <- parentChild2taxonTree(parentChild = pokexample_bad)


# another example, where a taxon is listed as both parent and child
pokexample_bad2 <- rbind(
    cbind("Squirtadae", c("Squirtle","Blastoise","Wartortle")),
    c("Shelloidea", c("Lapras","Squirtadae","Shelloidea")),
    c("Pokezooa","Shelloidea"), c("Pokezooa","Parasect"),
    c("Rodentapokemorpha","Linoone"), c("Rodentapokemorpha","Sandshrew"),
    c("Rodentapokemorpha","Pikachu"), c("Hirsutamona","Ursaring"),
    c("Hirsutamona","Rodentapokemorpha"), c("Pokezooa","Hirsutamona"),
    c("Umbrarcheota","Gengar")
    )

#this should return an error, as Shelloidea is its own parent
pokeTree <- parentChild2taxonTree(parentChild = pokexample_bad2)


## End(Not run)



# note that we should even be able to do this
    # with ancestor-descendent pairs from
    # simulated datasets from simFossilRecord, like so:
set.seed(444)
record <- simFossilRecord(
    p = 0.1, q = 0.1, nruns = 1,
    nTotalTaxa = c(30, 40), 
    nExtant = 0
    )
taxa <- fossilRecord2fossilTaxa(record)
# need to reorder the columns so parents
    # (ancestors) first, then children 
parentChild2taxonTree(parentChild = taxa[,2:1])
# now note that it issues a warning that
    # the input wasn't type character
    # and it will be coerced to be such

dwbapst/paleotree documentation built on Aug. 30, 2022, 6:44 a.m.