Usage of Blockmodels with poisson covariates to correct sequencing effort

blockmodels_correct_sampling_effort.R

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+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)]]