Hello, Can anyone guide on how can i rarefy my phyloseq object created so that i can use it to calculate my diversity metrics. I created my phyloseq object here (phyloseq object). The various tutorial I went through are confusing. My physeq object as a whole will used as a input file for rarefying or I first subject my feature table to rarefraction and then create a phyloseq object???
Thank you
The function phyloseq::rarefy_even_depth() is used in this tutorial:
https://joey711.github.io/phyloseq-demo/Restroom-Biogeography.html
Back in the mid 2010s, the Paul J. McMurdie was extremely critical of rareifying, so he's not showing it in many tutorials. See his scathing paper here and this measured response.
Now, in the mid 2020s, the focus has shifted to compositional methods.
That's what I would consider today.
Ten years later, Rarefaction is currently the best approach to control for uneven sequencing effort in amplicon sequence analyses. Go figure! 
And now we have better resampling methods: check out the new boostrapping plugin Qiime2 Boots! 