Adjust otu-table sample names to match sample data when subsetting duplicate samples

[mikemc]

Suppose one wants to create bootstrap replicates of the phyloseq dataset. Doing

smpls <- sample(nsamples(ps), replace = TRUE)
otu1 <- otu_table(ps)[smpls,]
data1 <- sample_data(ps0)[smpls,]
sample_names(otu1) %>% anyDuplicated
sample_names(data1) %>% anyDuplicated
sample_names(data1)

Shows that otu1 has duplicated sample names, for the samples that were drawn multiple times, but that the sample names in data1 are made unique (I think by make.unique()). I suspect this behavior comes down to differences in the matrix and data.frame subsetting methods. However, for phyloseq components, it seems desirable for the sample names to match.