I am trying to create a phylo correlogram based on my data using phyloCorrelogram from the phylosignal package in order to test for presence of a phylogenetic signal. My data is in the so-called phylo4d format and is called tree.
Now, when I run phyloCorrelogram(tree), I am returned the following error:
library("phylobase")
library("ape")
library("phylosignal") # contains phyloCorrelogram()
> phyloCorrelogram(tree, ci.bs = 10, n.points = 10)
Error in boot::boot(X, function(x, z) moranTest(xr = x[z], Wr = prop.table(Wi[z, :
no data in call to 'boot'
I have already done an elaborate search on the internet to look for ways how to solve this issue, but without success.
Since the dimension of the data that I am using is too large to post it here, I have posted my data in .rda format on dropbox.
Does anyone know the flaw?
You have no data associated to your tree. Your tree is a phylo4d object which has the "tree" information but no data attached to it. You need something like that
library(phylobase)
g1 <- as(geospiza_raw$tree, "phylo4")
geodata <- geospiza_raw$data
g2 <- phylo4d(g1, geodata)
pc <- phyloCorrelogram(g2)