23 lines
818 B
R
23 lines
818 B
R
library("sbm")
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library("phyloseq")
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library("microbiome")
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source("load-europe.R")
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# Define the taxonomy structure as a multipartite network
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type <- "bipartite"
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model <- "poisson"
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## Define all adjacency matrices
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kingdom_sample_mat <- otu_table(aggregate_taxa(cpd_phyloseq_europe, level = "kingdom"))
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phylum_sample_mat <- otu_table(aggregate_taxa(cpd_phyloseq_europe, level = "phylum"))
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class_sample_mat <- otu_table(aggregate_taxa(cpd_phyloseq_europe, level = "class"))
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order_sample_mat <- otu_table(aggregate_taxa(cpd_phyloseq_europe, level = "order"))
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family_sample_mat <- otu_table(aggregate_taxa(cpd_phyloseq_europe, level = "family"))
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genus_sample_mat <- otu_table(aggregate_taxa(cpd_phyloseq_europe, level = "genus"))
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## Define taxonomic relations
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## Define the SBMs
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KingdomSample <- defineSBM(otu_table())
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