How do I shift the edge length of multiple trees in R?
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Entering edit mode
19 months ago
Namenlos • 0

I have a file with the posterior sample of trees produced by RevBayes, the beginning of which looks as follows:

Iteration   Posterior   Likelihood  Prior   timetree
0   -1802.126   -1387.298   -414.8278   ((((Arcadian[&index=24]:0.990245,East_Ionic[&index=23]:0.690245)[&index=25]:0.447748,(((Mycenaean[&index=22]:0.310027,((West_Argolic[&index=21]:0.063518,Lesbian[&index=20]:0.263518)[&index=26]:0.106910,East_Argolic[&index=19]:0.370428)[&index=27]:0.939599)[&index=28]:0.024201,(((Corinthian[&index=18]:0.504267,West_Thessalian_Thessaliotis[&index=17]:0.504267)[&index=29]:0.261774,(Cretan[&index=16]:0.551464,Cypriot[&index=15]:0.651464)[&index=30]:0.114576)[&index=31]:0.109957,((Attic[&index=14]:0.626171,Boeotian[&index=13]:0.626171)[&index=32]:0.133810,((Laconian[&index=12]:0.243437,Megarian[&index=11]:0.343437)[&index=33]:0.265065,Central_Ionic[&index=10]:0.408503)[&index=34]:0.251478)[&index=35]:0.116017)[&index=36]:0.258232)[&index=37]:0.094907,(Theran[&index=9]:1.098901,Elean[&index=8]:1.198901)[&index=38]:0.130235)[&index=39]:0.008857)[&index=40]:0.026457,((Rhodian[&index=7]:0.258910,Pamphylian[&index=6]:0.458910)[&index=41]:1.098605,((Phocian[&index=5]:0.775238,East_Thessalian_Pelasgiotis[&index=4]:0.875238)[&index=42]:0.088669,West_Ionic[&index=3]:0.863907)[&index=43]:0.293609)[&index=44]:0.006934)[&index=45]:0.014444,(Coan[&index=2]:1.478782,Locrian[&index=1]:1.178782)[&index=46]:0.000112)[&index=47]:0.000000;

The file contains thousands of rows like this. For each timetree, I want to shift the age of each branch by 2.1. How do I do this in R? Or is there another way that I can accomplish this?

phylogenetics edge-length R • 592 views
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Entering edit mode

I presume, this is possible, but I am not familiar with the format.

First, check the documentation of the package, if it provides a function for this. Otherwise, you can very likely access the values within the data structure itself.

Can you run str(), class() on a tree and post the results? Possibly - if you have a small tree that you can share, use dput() and post it or save it into a file using saveRDS().

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