In TGuillerme/Inapp: Reconstruction of Inapplicable Discrete Characters on Phylogenetic Trees

Before starting

You'll need ape and RCurl (for downloading the code) installed. You can install everything by copy/pasting the following (the code checks what's needed).

if(!require(ape)) install.packages("ape")
if(!require(devtools)) install.packages("devtools")

After, you need to load all the code that's on the morphy-developement repo:

source_url("https://raw.githubusercontent.com/mbrazeau/Morphy/development/R/InApp/plot.algorithm.R")

Plotting the algorithm results

The algorithm is pretty easy, it intakes as arguments: * tree the tree in phylo format * character the character either as a list, a vector of states or a character * passes the passes to plot (for example passes = c(1,4)) only plots the first downpass and the second uppass (it does all the passes though, it's just visual).

Otherwise it has couple of other graphical options but we don't care for now.

Here it goes; plotting a silly character on a random tree with 5 taxa (rtree(5)) and only the first down and uppass (displayed as x: y where x is the pass number and y the nodal state for that pass:

set.seed(1) # for repeatability
tree_5t <- rtree(5)
plot.inapplicable.algorithm(tree_5t, "11111", passes = c(1,2))

Note that you can use the stree function (check ?stree) that allows to generate less random trees (balanced, or ladderised left/right).

For the tree, you can also import your own trees using the read.tree or read.nexus from ape or just by typing the tree manually. Here's the balance 12 tip tree with the classical Maddison problem:

tree_12t <- read.tree(text = "((((((1,2),3),4),5),6),(7,(8,(9,(10,(11,12))))));")
plot.inapplicable.algorithm(tree_12t, "1100----1100")

character argument

The character argument can intake the character as in morphy-like (the easiest) with - being inapplicable (of course!) and ? being all states present. The code transforms the character string (123-?) into the normal characters and attributes them to the taxa in the order of appearance:

plot.inapplicable.algorithm(tree_5t, "123-?")

But you can also input the character as properly read by the code (a list) with - being -1 and ? being all states:

character <- list(c(1),c(2),c(3),c(-1), c(-1,1,2,3))
plot.inapplicable.algorithm(tree_5t, character, passes = c(1,2))

TGuillerme/Inapp documentation built on Feb. 4, 2024, 7:26 a.m.