Re: [R-sig-phylo] Count the number of character/state changes in a tree
Hi Luiz,
didn’t try that out, but here is some code I wrote for some of the
megaphylogenies I produced where you don’t want to search in a pdf or so where
the transitions are…
It’s two months ago so don’t know if it was totally save
I think you should make sure the order of the tree and tip.states fit.
If I look at it now there might be shorter solutions ;-)
Have fun,
Franz
# Franz Krah
# count origins
# 02 - 04 - 2015
origins - function(phy, tip.states, node.states, threshold.states=75,
threshold.nodes=80)
{
if (!is.rooted(phy))
stop( phy is not rooted )
if (!any(as.numeric(tip.states)1))
stop( tips need to be a binary in form O/1 )
nodes - data.frame(node.states)
names(nodes) - c(0:(length(nodes[1,])-1))
# threshold states
sortStates - function(x, threshold){
yy - (x threshold)
states - matrix(,length(x[,1]))
for (i in 1:length(x[,1]))
{
# if both threshold
if (sum(yy[1,])==0)
states[i] - NA
# if one is threshold
if (!sum(yy[i,])==0)
states[i] - which(x[i,]threshold)-1
}
return(states)
}
states - sortStates(nodes, threshold=threshold.states)
states - data.frame(states, tn=phy$node.label)
# threshold nodes
states - ifelse(states$tn threshold.nodes,NA, states$states)
cstates - data.frame(states=c(as.vector(tip.states),states))
if (length(cstates$states)!=(length(phy$edge[,1])+1))
stop( phy and edge+tips length are not the same )
l_nodes - cstates$states[phy$edge[,1]]
r_nodes - cstates$states[phy$edge[,2]]
diff - (as.numeric(l_nodes) - as.numeric(r_nodes))
wins - sum(diff 0, na.rm=T)
loss - sum(diff 0, na.rm=T)
equal - sum(diff==0, na.rm=T)
dep_nod - which(!is.na(states)) # depest node above threshold
dep_nod - states[dep_nod[1]]
res - c(wins, loss, equal)
names(res) - c(won,lost,equal)
out - paste(State of deepest node above threshold:, dep_nod, sep= )
res - list(out, res)
print(res)
}
On 03 Mar 2015, at 14:04, Luiz Max Carvalho luizepidemiolo...@gmail.com
wrote:
Dear Phylofolks,
Suppose I have a phylo object phy and the states at all nodes (internal and
external). Would the following function give me the number of state changes?
get.changes - function(tree, states){
sum(apply(phy$edge, 1, function(x) states[x[1]]!=states[x[2]]))
}
If not, what would?
Thanks in advance,
Luiz
--
Luiz Max Fagundes de Carvalho
PhD student, Institute of Evolutionary Biology, School of Biological
Sciences,
Ashworth Laboratories, Ash 2, office 123
University of Edinburgh, United Kingdom.
http://br.linkedin.com/pub/luiz-max-carvalho/49/687/283
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[R-sig-phylo] Count the number of character/state changes in a tree
Dear Phylofolks,
Suppose I have a phylo object phy and the states at all nodes (internal and
external). Would the following function give me the number of state changes?
get.changes - function(tree, states){
sum(apply(phy$edge, 1, function(x) states[x[1]]!=states[x[2]]))
}
If not, what would?
Thanks in advance,
Luiz
--
Luiz Max Fagundes de Carvalho
PhD student, Institute of Evolutionary Biology, School of Biological
Sciences,
Ashworth Laboratories, Ash 2, office 123
University of Edinburgh, United Kingdom.
http://br.linkedin.com/pub/luiz-max-carvalho/49/687/283
[[alternative HTML version deleted]]
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Re: [R-sig-phylo] Count the number of character/state changes in a tree
If the vector states is indexed by the node numbers of phy$edge, then
the following seems like it should work:
get.changes-function(tree,states)
sum(apply(tree$edge,1,function(x,s) s[x[1]]!=s[x[2]],s=states))
This will of course only be the minimum number of changes given your
states at tips internal nodes it will not account for multiple
changes along a single edge. Where do your states at internal nodes come
from?
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 3/3/2015 2:04 PM, Luiz Max Carvalho wrote:
Dear Phylofolks,
Suppose I have a phylo object phy and the states at all nodes (internal and
external). Would the following function give me the number of state changes?
get.changes - function(tree, states){
sum(apply(phy$edge, 1, function(x) states[x[1]]!=states[x[2]]))
}
If not, what would?
Thanks in advance,
Luiz
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[R-sig-phylo] Stuck with Phylomatic tree!
Dear friends, I am trying to adjust the leghts of a tree I created using 113 tree species in Phylomatic using the bladj function in Phylocom. Unfortunately, the program crashes when I use the tree without the final note about the impossibility of matching four of the species (when I exclude the final note), or produces an empty output file when I use the newick file with the final note. I tried to open it directly in R using the read.newick() function written by Liam J. Revell ( http://www.phytools.org/read.newick/v0.4/read.newick.R) since the tree probably has single nodes. However, it did not work and produced an eternal loop I guess (working simbol never turned off). I plan to use the tree in further ecological analysis and the steps would be to adjust ages with Phylocom, then cut off single nodes in R and then to proceed with analyses. I am, however, stuck. Could you plase help me? I am new to phylogenetic analyses so I apologize if I be repetitive, but I could not find an answer searching previous correspondence. What should I do? Is there a way to produce a tree directly in R? Here is the newick tree, in case you may find it useful to take a look. Thank you very much in advance, Alexandre
