Hi,
I am trying to use the collies.test and maxlik.betasplit tests in apTreeshape R
package.
I have a set of DNA sequence in fasta format. I am following the steps below.
1. I construct a NJ using the ape R package using the nj(dist.dna(dataset).
2. After I use the "as.treeshape" form the apTreeshape package I get the
following message when I try to plot my tree (after "converting" to treeshape
format)
Error in plot.window(...) : need finite 'xlim' values
In addition: Warning messages:
1: In min(x) : no non-missing arguments to min; returning Inf
2: In max(x) : no non-missing arguments to max; returning -Inf
3: In min(x) : no non-missing arguments to min; returning Inf
4: In max(x) : no non-missing arguments to max; returning -Inf
3. So I decided to use the as.treeshape(tree, model = "yule"). After doing this
I can plot my tree as reshape, but when I perform one of the tests I get the
following message
when using the maxlik.betasplit
"There were 50 or more warnings (use warnings() to see the first 50)"
and when using the collies.test
"Warning message:
In if (class(tree) != "treeshape") { :
the condition has length > 1 and only the first element will be used"
My questions: What are the reasons for these warnings? Can I ignore these
"warnings"? How can I solve this "problem" and convert my NJ generated using
ape in a treeshape class?
Thanks!
Fabricia.
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