Hi Timothee,
Assuming that I figured out your tree format correctly, I have written
you a function to translate your tree-as-data-frame into an object of
class phylo in R. I attach the disclaimer that this is programmed
very inelegantly and may contain errors. It also contains no method for
checking your tree file for errors, thus will probably crash if your
tree doesn't make any sense (say, for example, contains floating
branches not connected to any other nodes). It assumes that you have
installed APE and that, for example (taking your table, below), node
is the ancestor to node 1000 and 0001 (as well as
several other nodes) with the branch length of 27 leading to node
1000 and 83 leading to 0001. If this is the correct
interpretation of your format, the original data file, below, yields a
Newick tree of ((5:78,9:140):27,11:185,12:196,10:176,7:159); where the
taxon labels are determined by the row labels of the data frame. (Note
that this tree is highly polytomous at the root, because a number of
nodes in the data frame, e.g., node 1001, leave one and only one
descendant.)
The input is just the table given below, with the lines above Anc
OffSpr. . . etc. excluded, which you can read in as follows:
tree.data-read.table(filename,colClasses=character)
Then you can load the function from source, as follows:
source(tree.read.R) # this name is just to distinguish it from
read.tree(), an ape function.
And run it as follows:
tree-tree.read(tree.data)
Trees can be printed to file using, for example:
write.tree(tree,filename)
The function is as follows:
tree.read-function(tree.data){
n.tips=0; k=1; tip.label-NA;
edge-matrix(0,nrow(tree.data)-1,2); edge.length-NA;
for (i in 1:nrow(tree.data)){
external=1;
for (j in 1:nrow(tree.data)){
if(tree.data[i,2]==tree.data[j,1]){
external=0;
}
}
n.tips-n.tips+external;
if(external==1){
edge[i-1,2]-n.tips;
tip.label[k]-row.names(tree.data[i,]);
k=k+1;
}
}
node.number-n.tips;
for (i in 2:nrow(tree.data)){
for(j in 1:2){
if(edge[i-1,j]==0){
internal-tree.data[i,j];
node.number-node.number+1;
for(k in i:nrow(tree.data)){
for(l in 1:2){
if(tree.data[k,l]==internal){
edge[k-1,l]=node.number;
}
}
}
}
# find branch length
if(j==2){
anc.height=0;
for(k in 1:nrow(tree.data)){
if(tree.data[i,1]==tree.data[k,2]){
anc.height-as.numeric(tree.data[k,3]);
}
}
edge.length[i-1]-as.numeric(tree.data[i,3])-anc.height;
}
}
}
Nnode-node.number-n.tips;
obj-list(edge=edge,tip.label=tip.label,edge.length=edge.length,Nnode=Nnode);
class(obj) - phylo;
obj-collapse.singles(obj);
obj;
}
I hope this works!
- Liam
Liam J. Revell
NESCent, Duke University
web: http://anolis.oeb.harvard.edu/~liam/
NEW email: lrev...@nescent.org
Timothee POISOT wrote:
Dear users,
I am currently doing a model of community assembly, and I would like to
integrate phylogenetic information. For each organism, I know its ancestor
and the time at which speciation occured. These informations are stored in
a data.frame, an example of which is here :
PhyloTree
Anc OffSpr TimeApp
1 Anc 1
2 1000 28
3 0001 84
4 0010 101
5 1000 1010 106
6 0010 139
7 0100 160
8 0001 1001 161
9 1000 1100 168
10 0010 0011 177
11 1001 10010001 186
12 0010 0110 197
Do you have any idea about how I can proceed to transform this object into
a tree object, such as the one used by APE?
Regards,
Timothée
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