Cleaner implementation of benchmark lbm seq
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Louis
parent
20d26e8634
commit
40068f8d00
1 changed files with 31 additions and 125 deletions
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@ -33,132 +33,38 @@ if (!dir.exists(tmp_folder)) {
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per_taxa_networks <- collapse_otu_at_taxo(the_data)
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per_taxa_networks <- collapse_otu_at_taxo(the_data)
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prev_model <- NULL
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switch(mode,
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sequential <- FALSE
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"seq" = {
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message("Will use SEQ")
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r2_mbm_seq <- microbenchmark("Rank2seq" = {
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r2_model_seq <- 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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autosave = here(tmp_folder, "r2_seq.Rds"),
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ncores = 1L
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)
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r2_model_seq$estimate()
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}, times = 3L)
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r3_mbm_seq <- microbenchmark("Rank3seq" = {
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r3_model_seq <- 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_seq, ncores = 1, autosave = here(tmp_folder, "r3_seq.Rds"))
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}, times = 3L)
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r4_mbm_seq <- microbenchmark("Rank4seq" = {
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r4_model_seq <- bm_propagate_taus_all_models(phyloseq_data = the_data, rank_id_start = 3, per_taxa_networks = per_taxa_networks, first_model = r3_model_seq, ncores = 1, autosave = here(tmp_folder, "r4_seq.Rds"))
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}, times = 3L)
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r5_mbm_seq <- microbenchmark("Rank5seq" = {
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r5_model_seq <- bm_propagate_taus_all_models(phyloseq_data = the_data, rank_id_start = 4, per_taxa_networks = per_taxa_networks, first_model = r4_model_seq, ncores = 1, autosave = here(tmp_folder, "r5_seq.Rds"))
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}, times = 3L)
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mbm_seq <- rbind(r2_mbm_seq, r3_mbm_seq, r4_mbm_seq, r5_mbm_seq)
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out_seq <- list(
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if (mode == "seq" || mode == "para") {
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benchmark = mbm_seq,
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sequential <- TRUE
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models = list(
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}
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Rank2 = r2_model_seq,
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Rank3 = r3_model_seq,
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ncores <- ifelse(mode == "para", parallelly::availableCores(), 1L)
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Rank4 = r4_model_seq,
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Rank5 = r5_model_seq
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model_list <- list()
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)
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net_ids <- seq_along(per_taxa_networks)[-1]
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for (idx in net_ids) {
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if (!sequential || is.null(prev_model)) {
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current_model <- BM_poisson(
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membership_type = "LBM",
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adj = per_taxa_networks[[idx]], # Account for the root
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verbosity = 6,
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plotting = "",
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autosave = here(tmp_folder, paste0("r", idx, "_", mode, ".Rds")),
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ncores = ncores
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)
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)
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current_model$estimate()
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} else {
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# We transfer
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current_model <- bm_propagate_taus_all_models(phyloseq_data = the_data, rank_id_start = idx - 1, target_rank_id = idx, per_taxa_networks = per_taxa_networks, first_model = prev_model, ncores = ncores, autosave = here(tmp_folder, paste0("r", idx, "_", mode, ".Rds")))
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}
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prev_model <- current_model
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model_list <- append(model_list, current_model)
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}
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saveRDS(out_seq, here(named_data_folder, "seq.Rds"))
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names(model_list) <- paste0("Rank", net_ids)
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},
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saveRDS(model_list, here(named_data_folder, paste0(mode, "_", epoch, ".Rds")))
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"para" = {
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message("Will use PARA")
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r2_mbm_para <- microbenchmark("Rank2para" = {
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r2_model_para <- 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 = parallelly::availableCores(), autosave = here(tmp_folder, "r2_para.Rds")
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)
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r2_model_para$estimate()
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}, times = 3L)
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r3_mbm_para <- microbenchmark("Rank3para" = {
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r3_model_para <- 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_para, ncores = parallelly::availableCores(), autosave = here(tmp_folder, "r3_para.Rds"))
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}, times = 3L)
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r4_mbm_para <- microbenchmark("Rank4para" = {
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r4_model_para <- bm_propagate_taus_all_models(phyloseq_data = the_data, rank_id_start = 3, per_taxa_networks = per_taxa_networks, first_model = r3_model_para, ncores = parallelly::availableCores(), autosave = here(tmp_folder, "r4_para.Rds"))
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}, times = 3L)
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r5_mbm_para <- microbenchmark("Rank5para" = {
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r5_model_para <- bm_propagate_taus_all_models(phyloseq_data = the_data, rank_id_start = 4, per_taxa_networks = per_taxa_networks, first_model = r4_model_para, ncores = parallelly::availableCores(), autosave = here(tmp_folder, "r5_para.Rds"))
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}, times = 3L)
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mbm_para <- rbind(r2_mbm_para, r3_mbm_para, r4_mbm_para, r5_mbm_para)
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out_para <- list(
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benchmark = mbm_para,
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models = list(
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Rank2 = r2_model_para,
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Rank3 = r3_model_para,
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Rank4 = r4_model_para,
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Rank5 = r5_model_para
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)
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)
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saveRDS(out_para, here(named_data_folder, "para.Rds"))
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},
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"notrans" = { # No transfer
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message("Will use NO TRANSFER")
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r2_mbm_notrans <- microbenchmark("Rank2notrans" = {
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r2_model_notrans <- 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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ncores = parallelly::availableCores(), autosave = here(tmp_folder, "r2_notrans.Rds")
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)
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r2_model_notrans$estimate()
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}, times = 3L)
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r3_mbm_notrans <- microbenchmark("Rank3notrans" = {
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r3_model_notrans <- BM_poisson(
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membership_type = "LBM",
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adj = per_taxa_networks[[3]], # Account for the root
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verbosity = 6,
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plotting = "",
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ncores = parallelly::availableCores(), autosave = here(tmp_folder, "r3_notrans.Rds")
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)
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r3_model_notrans$estimate()
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}, times = 3L)
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r4_mbm_notrans <- microbenchmark("Rank4notrans" = {
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r4_model_notrans <- BM_poisson(
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membership_type = "LBM",
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adj = per_taxa_networks[[4]], # Account for the root
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verbosity = 6,
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plotting = "",
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ncores = parallelly::availableCores(), autosave = here(tmp_folder, "r4_notrans.Rds")
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)
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r4_model_notrans$estimate()
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}, times = 3L)
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r5_mbm_notrans <- microbenchmark("Rank5notrans" = {
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r5_model_notrans <- BM_poisson(
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membership_type = "LBM",
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adj = per_taxa_networks[[5]], # Account for the root
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verbosity = 6,
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plotting = "",
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ncores = parallelly::availableCores(), autosave = here(tmp_folder, "r5_notrans.Rds")
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)
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r5_model_notrans$estimate()
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}, times = 3L)
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mbm_notrans <- rbind(r2_mbm_notrans, r3_mbm_notrans, r4_mbm_notrans, r5_mbm_notrans)
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out_notrans <- list(
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benchmark = mbm_notrans,
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models = list(
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Rank2 = r2_model_notrans,
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Rank3 = r3_model_notrans,
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Rank4 = r4_model_notrans,
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Rank5 = r5_model_notrans
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)
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)
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saveRDS(out_notrans, here(named_data_folder, "notrans.Rds"))
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},
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stop("Nothing selected, exiting")
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)
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