physeq and even sampling depth

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 phyloseq dev was pretty critical of rareifying, so he's not showing it in many tutorials. See his paper here and this followup.

Now, in the mid 2020s, the focus has shifted to compositional methods. I would consider these!

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