PoonLab / clustuneR

Implementing clustering algorithms on genetic data and finding optimal parameters through the performance of predictive growth models.
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Warning raised by extend.tree #11

Closed ArtPoon closed 11 months ago

ArtPoon commented 2 years ago
> phy.extend <- extend.tree(phy, seq.info, seqs, mc.cores=4, log.file="data/be.log")

Warning messages:

1: In eval(jsub, SDenv, parent.frame()) :
 NAs introduced by coercion

2: 
In annotate.growth(t, growth.info.trees, mc.cores = mc.cores) :

  Not all newly added sequences are noted in the seq.info of the tree
ArtPoon commented 2 years ago

I determined that this is expected behaviour associated with the root node of the tree not carrying a numeric value:

> head(t$node.label)
[1] "Root"  "0.960" "0.945" "0.827" "0.619" "0.432"

We can ignore this warning, but a more elegant workaround would be to replace Root with 1.0.

liamxg commented 11 months ago
image
liamxg commented 11 months ago

@ArtPoon how to solve this?

ArtPoon commented 11 months ago

@liamxg - Please see my question in #16

ArtPoon commented 11 months ago

The above problem is fixed in current development branches, closing for now.