To calculate alpha-diversity within
phyloseq you need a table of absolute abundance. The only way to reverse from relative to absolute abundances is if you have the total no. of reads per sample. I guess that you do not have this information. If you have you can multiply the relative abundance of each taxa/OTU/ASV by the total no. of reads per sample. This should yield a absolute abundance table (it may not, because relative abundances could have been rounded).
Still you can just calculate the basic alpha-diversity metric, the distinct no. of observed taxa/OTUs/ASVs/features per sample, that are those higher than zero. Though you can't do it in
phyloseq, the R code to do it is quite simple. Let me know if you want to do this.
I believe that you can do beta-diversity analysis. You might need to transform to absolute counts by multiplying each taxa abundance by one million - counts per million:
GP1 = transform_sample_counts(GP1, function(x) 1E6 * x/sum(x)). In your case since you have relative abundance, you just need:
GP1 = transform_sample_counts(GP1, function(x) 1E6 * x) (have a look at phyloseq).
I hope this helps,