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Phylogenetic Independent Contrasts in R

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Phylogenetic Independent Contrasts in R

JOSÉ Luiz
Dear list members,

I repeat to fail in running a phylogenetic independent Contrasts analysis
in the ape package. I'm new in this kind of analysis. Apparently, the
length of phenotypic and of phylogenetic data do not match.

I'm using the following script:

phy=read.newick(file.choose())#open my tree with adjusted branches
phytree=collapse.singles(phy)
phytree=multi2di(phytree)# remove polytomies in the tree randomly - only
dichotomous trees work in this package
is.binary.tree(phytree)

names(phytree)
[1] "edge"        "Nnode"       "tip.label"   "edge.length" "node.label"

data = read.csv(file.choose(), sep = ';')#trait data

names(data)
 [1] "LDMC"    "Lhum"    "Larea"   "SLA"     "Shum"    "Sdens"   "Bark"
 "Vdiam"   "Vdens"   "Vindex"
[11] "Slength" "Sdiam"   "Litter"  "Vlitter"

pic(data, phytree, scaled = TRUE, var.contrasts = FALSE)

Error in pic(data, phytree, scaled = TRUE, var.contrasts = FALSE) :
  length of phenotypic and of phylogenetic data do not match

the length of PHYTREE is 5
the length of DATA is 14

I don't understand how pic doesn't use species as length. I thank anyone
who can help.

José Luiz Silva

Brazil

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