library(microbiome)
library(sbm)

source("load-europe.R")

base_otu <- cpd_phyloseq_europe

taxoEstimateBipartiteSBM <- function(phyloseq_obj, taxonomic_level = "kingdom") {
    taxolevel_otu <- microbiome::aggregate_taxa(phyloseq_obj, taxonomic_level)
    taxolevel_mat <- phyloseq::otu_table(taxolevel_otu) |> as.matrix()

    taxolevel_lbm <- estimateBipartiteSBM(netMat = taxolevel_mat, model = "poisson", dimLabels = c(row = taxonomic_level, col = "sample"))

    rownames(taxolevel_lbm$probMemberships[[1]]) <- rownames(taxolevel_mat)
    rownames(taxolevel_lbm$probMemberships[[2]]) <- colnames(taxolevel_mat)

    return(taxolevel_lbm)
}

kingdom_lbm <- taxoEstimateBipartiteSBM(
    phyloseq_obj = base_otu,
    taxonomic_level = "kingdom"
)

kingdom_lbm$memberships

phylum_lbm <- taxoEstimateBipartiteSBM(
    phyloseq_obj = base_otu,
    taxonomic_level = "phylum"
)

phylum_lbm$memberships

mydf <- otu_table(aggregate_taxa(cpd_phyloseq_europe, "phylum"))
library(ggplot2)