From 97b4a435973cac868b3c8ccd5e4d865f4e984888 Mon Sep 17 00:00:00 2001
From: Louis <louis.lacoste@agroparistech.fr>
Date: Thu, 19 Feb 2026 10:40:01 +0100
Subject: [PATCH] Usage of Blockmodels with poisson covariates to correct
 sequencing effort

---
 blockmodels_correct_sampling_effort.R | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)
 create mode 100644 blockmodels_correct_sampling_effort.R

diff --git a/blockmodels_correct_sampling_effort.R b/blockmodels_correct_sampling_effort.R
new file mode 100644
index 0000000..8b29eb4
--- /dev/null
+++ b/blockmodels_correct_sampling_effort.R
@@ -0,0 +1,16 @@
+library(blockmodels)
+library(phyloseq)
+library(biomformat)
+source("utils.R")
+
+the_data <- import_biom("data/ravel/ravel.biom")
+
+
+per_taxa_networks <- collapse_otu_at_taxo(the_data)
+
+covar_mat <- t(colSums(per_taxa_networks[[2]]) %*% t(rep(1, nrow(per_taxa_networks[[2]]))))
+
+fitted_model <- BM_poisson_covariates("LBM", adj = per_taxa_networks[[2]], covariates = list(covar_mat))
+fitted_model$estimate()
+
+fitted_model$model_parameters[[which.max(fitted_model$ICL)]]