From 96db7c5169210a05617acba9d676afdf2f9dca3d Mon Sep 17 00:00:00 2001
From: Louis <louis.lacoste@agroparistech.fr>
Date: Tue, 24 Feb 2026 14:30:42 +0100
Subject: [PATCH] Code for the multipartite

---
 multipartite_taxtable.R | 42 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)
 create mode 100644 multipartite_taxtable.R

diff --git a/multipartite_taxtable.R b/multipartite_taxtable.R
new file mode 100644
index 0000000..b95655e
--- /dev/null
+++ b/multipartite_taxtable.R
@@ -0,0 +1,42 @@
+library(sbm)
+library(phyloseq)
+library(biomformat)
+library(here)
+source("utils.R")
+
+options(parallelly.availableCores.custom = function() {
+    ncores <- min(parallelly::availableCores(), 64)
+    max(1L, ncores)
+})
+
+message(paste("Number of cores available:", parallelly::availableCores()))
+args <- commandArgs(trailingOnly = TRUE)
+if (length(args) == 0) {
+    author <- "mach"
+} else {
+    author <- args[1]
+}
+
+message("For author: ", author)
+the_data <- import_biom(here("data", author, paste0(author, ".biom")))
+
+epoch <- as.integer(Sys.time())
+
+per_taxa_networks <- collapse_otu_at_taxo(the_data)
+per_taxa_networks <- per_taxa_networks[-1]
+
+lbm_list <- lapply(seq_along(per_taxa_networks), function(idx) {
+    defineSBM(per_taxa_networks[[idx]], model = "poisson", dimLabels = c(row = paste0("Rank", idx + 1), col = "Sample"))
+})
+
+lbm_list_covariates <- lapply(seq_along(per_taxa_networks), function(idx) {
+    covar_sd <- log(rep(1, nrow(per_taxa_networks[[idx]])) %*% t(colSums(per_taxa_networks[[idx]])))
+    defineSBM(per_taxa_networks[[idx]], model = "poisson", dimLabels = c(row = paste0("Rank", idx + 1), col = "Sample"), covariates = list(covar_sd))
+})
+
+
+multipartite_fit <- estimateMultipartiteSBM(listSBM = lbm_list, estimOptions = list(initBM = FALSE))
+
+multipartite_covariates_fit <- estimateMultipartiteSBM(listSBM = lbm_list_covariates, estimOptions = list(initBM = FALSE))
+
+plot(multipartite_covariates_fit)