Hi all,
I'm trying to use Rphylopars to impute some missing data, but am having some
strange results with my empirical data.
The phylopars should return a `data.frame` of the original data with the
missing (NA) values calculated given the phylogenetic data and evolutionary
model. However, my known values are being changed in the output. For example:
> head(empirical.data)
species Trait
1 Species_1 14.0
2 Species_2 12.0
> head(p_BM$anc_recon)
species Trait
1 Species_1 12.0
2 Species_2 8.9
The function works fine when I use different combinations of simulated data:
* simulated traits + simulated phylogeny works fine
* simulated traits + empirical phylogeny works fine
* empirical data + simulated phylogeny works fine
The phylogeny has no 0 branch lengths, is binary, and ultrametric. I have tried
log-transforming the data. I have also tried sequentially dropping one tip at a
time from the tree and re-running to see if any single tip is causing the
problem. Different models also have the same effect.
If anyone has any thoughts i'd appreciate it.
Nick
--
Nick Crouch
http://nickcrouch.github.io/
Postdoctoral scholar, Jablonski lab
The University of Chicago
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