45 lines
1.5 KiB
R
45 lines
1.5 KiB
R
source("utils.R")
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source("utils-bm-seq.R")
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library(biomformat)
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library(phyloseq)
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library(R.utils)
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library(stringr)
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library(sbm)
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library(blockmodels)
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library(tictoc)
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the_data <- import_biom("data/mach/kinetic.biom")
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# fit_res <- lapply(per_taxa_network, function(network) {
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# withTimeout(
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# expr = {
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# fit <- estimateBipartiteSBM(network, model = "poisson", estimOptions = list(plot = 0))
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# }, timeout = 300,
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# onTimeout = "warning"
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# )
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# if (exists("fit")) {
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# out <- fit
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# } else {
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# out <- NULL
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# }
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# return(fit)
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# })
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# To init a BM model I need to provide memberships and ICL
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# And to compute with the dispatcher the previous values to init the models with ICL and memberships
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per_taxa_networks <- collapse_otu_at_taxo(the_data)
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tic()
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r2_model <- BM_poisson(
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membership_type = "LBM",
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adj = per_taxa_networks[[2]], # Account for the root
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verbosity = 6,
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plotting = "",
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ncores = 1, # parallelly::availableCores(),
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autosave = "r2test.Rds"
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)
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r2_model$estimate()
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toc()
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r3_model <- bm_propagate_taus_all_models(phyloseq_data = the_data, rank_id_start = 2, target_rank_id = 3, per_taxa_networks = per_taxa_networks, first_model = r2_model, autosave = "r3test.Rds")
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r4_model <- bm_propagate_taus_all_models(phyloseq_data = the_data, rank_id_start = 3, per_taxa_networks = per_taxa_networks, first_model = r3_model)
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r5_model <- bm_propagate_taus_all_models(phyloseq_data = the_data, rank_id_start = 4, per_taxa_networks = per_taxa_networks, first_model = r4_model)
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