library(MicroBioMap)
library(phyloseq)
library(mia)

cpd <- getCompendium()
cpd_phyloseq <- convertToPhyloseq(x = cpd)
sample_data(cpd_phyloseq)$geo_loc_name |> grepl(pattern = "europe")
rm(cpd)
gc()
sample_data(cpd_phyloseq)
cpd_phyloseq_europe <- subset_samples(cpd_phyloseq, grepl("europe", geo_loc_name))
rm(cpd_phyloseq)
gc()
saveRDS(cpd_phyloseq_europe, "data/hmc-phyloseq-europe.Rds")