Incorrect pseudorooting detected - use fixPseudoroot() function to correct trait tree topology

[YanCheer]

When I tried to run getAllResiduals (avianRERw = getAllResiduals(Trees, useSpecies=Trees$masterTree$tip.label, transform = "sqrt", weighted = T, scale = T), it reported that

matchNodesInject(tree1, tree2):
Incorrect pseudorooting detected - use fixPseudoroot() function to correct trait tree topology

How can I address this issue??
Please! Thank you very much!

[nclark-lab]

Hello,
This error occurs when the trait tree rooting does not match that of the trees object. After your trait tree is created, run this function as it will fix the rooting if it is possible.

yourTraitTree <- fixPseudoroot( yourTraitTree , yourTreesObj )

Let me know if it works!

[YanCheer]

Hello Professor,
Two points show up there:

1. In this step running getAllResiduals, I did not provide a binary trait tree or any continous variable to the getAllResiduals function as shown in the above command line. So, I think it might be not related to the inconsistency between rootings of trait tree and trees object.
2. This reminds me that my input trees object contains trees that are not rooted by an outgroup species. It is because that I have more than 300 species to analyze, and some species may disappear in some trees. So, it is hard to fix a root at a specific outgroup species for several thousand gene trees that I am not sure which one has which species missed, which sometimes is the specified outgroup. I wonder if it requires a pre-specified, fixed root of the input trees for RERconverge to take following analyses? How can I do if a specified root is missed in a subset of the trees?

Thanks, Professor!
Chen Yan