diff --git a/lbm_at_diff_taxo_seq.R b/lbm_at_diff_taxo_seq.R index dfe0d02..7c663d5 100644 --- a/lbm_at_diff_taxo_seq.R +++ b/lbm_at_diff_taxo_seq.R @@ -6,6 +6,7 @@ library(R.utils) library(stringr) library(sbm) library(blockmodels) +library(tictoc) the_data <- import_biom("data/mach/kinetic.biom") @@ -28,14 +29,17 @@ the_data <- import_biom("data/mach/kinetic.biom") # And to compute with the dispatcher the previous values to init the models with ICL and memberships per_taxa_networks <- collapse_otu_at_taxo(the_data) +tic() r2_model <- BM_poisson( membership_type = "LBM", adj = per_taxa_networks[[2]], # Account for the root verbosity = 6, plotting = "", - ncores = parallelly::availableCores() + ncores = 1, # parallelly::availableCores(), + autosave = "r2test.Rds" ) r2_model$estimate() -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) +toc() +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") 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) 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)