Hi,
I wonder if there is a method in mother to replicate the ‘sub.sample’ command and apply these results to other commands.
For example, if I perform 1,000 subsampings,
Can I obtain the average alpha diversity indices and the standard deviations? or most probable bary-curtis dendrogram and the bootstrap values on the nodes?
Thank you.
hyungz.
Can I obtain the average alpha diversity indices and the standard deviations?
rarefaction.single(calc=sobs-shannon) will do what you want
most probable bary-curtis dendrogram and the bootstrap values on the nodes
this is still in the experimental phase, but the code is in there (shhhh…)
tree.shared(shared=…, calc=braycurtis, subsample=1000)
When we use the subsample option within a tree.shared command, how is the subsample chosen? lowest sample #? or 10% of data
yeah, you either tell it how many you want, or it will pick the smallest group size.
Ok so running this, I subsampled to the lowest group # 1000 times correct?
tree.shared(shared=bc_bac.final2.an.shared, calc=thetayc, subsample=1000, processors=4)
that will actually subsample to 1000 sequences per sample 1000 times
oh, how would I specify 1000 reps with 1500 sequences/sample?
subsample=1500