Brian O'Meara bomeara

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bomeara / # treepl - 2018-08-07_14-05-22.txt

Created August 7, 2018 19:44

treepl (brewsci/bio/treepl) on macOS 10.13.6 - Homebrew build logs

	Homebrew build logs for brewsci/bio/treepl on macOS 10.13.6
	Build date: 2018-08-07 14:05:22

bomeara / distances.R

Last active August 9, 2019 08:08

Solution to @joel_nitta's "Heya phylotweeps! Anybody know of the right model to use for ancestral state reconstruction on a multivariate trait when the parts of the trait must sum to 1? Thinking OU but not sure how to implement it🤔 @Lagomarsino_L @kfeilich @omearabrian"

	chunks <- seq(from=0, to=1, length.out=7) # how finely we want to divide each univariate character

	# 0.0000000 0.1666667 0.3333333 0.5000000 0.6666667 0.8333333 1.0000000

	possible_states <- expand.grid(a=chunks, b=chunks, c=chunks) # all possible combinations (not adding up to 1).
	#Doing just three chars here, you can add more: d=chunks, e=chunks....
	sums <- apply(possible_states,1, sum)
	possible_states <- possible_states[which(abs(sums-1)<0.00001),] # now limiting to those that add up to 1
	rownames(possible_states) <- sequence(nrow(possible_states)) - 1 # state 0, 1, 2...