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Usage of Blockmodels with poisson covariates to correct sequencing effort

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Louis 2026-02-19 10:40:01 +01:00
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blockmodels_correct_sampling_effort.R Normal file
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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)]]