Cleaner implementation of benchmark lbm seq
This commit is contained in:
Louis
parent
20d26e8634
commit
40068f8d00
1 changed files with 31 additions and 125 deletions
|
|
@ -33,132 +33,38 @@ if (!dir.exists(tmp_folder)) {
|
||||||
|
|
||||||
per_taxa_networks <- collapse_otu_at_taxo(the_data)
|
per_taxa_networks <- collapse_otu_at_taxo(the_data)
|
||||||
|
|
||||||
|
prev_model <- NULL
|
||||||
|
|
||||||
switch(mode,
|
sequential <- FALSE
|
||||||
"seq" = {
|
|
||||||
message("Will use SEQ")
|
if (mode == "seq" || mode == "para") {
|
||||||
r2_mbm_seq <- microbenchmark("Rank2seq" = {
|
sequential <- TRUE
|
||||||
r2_model_seq <- BM_poisson(
|
}
|
||||||
|
|
||||||
|
ncores <- ifelse(mode == "para", parallelly::availableCores(), 1L)
|
||||||
|
|
||||||
|
model_list <- list()
|
||||||
|
net_ids <- seq_along(per_taxa_networks)[-1]
|
||||||
|
|
||||||
|
|
||||||
|
for (idx in net_ids) {
|
||||||
|
if (!sequential || is.null(prev_model)) {
|
||||||
|
current_model <- BM_poisson(
|
||||||
membership_type = "LBM",
|
membership_type = "LBM",
|
||||||
adj = per_taxa_networks[[2]], # Account for the root
|
adj = per_taxa_networks[[idx]], # Account for the root
|
||||||
verbosity = 6,
|
verbosity = 6,
|
||||||
plotting = "",
|
plotting = "",
|
||||||
autosave = here(tmp_folder, "r2_seq.Rds"),
|
autosave = here(tmp_folder, paste0("r", idx, "_", mode, ".Rds")),
|
||||||
ncores = 1L
|
ncores = ncores
|
||||||
)
|
)
|
||||||
r2_model_seq$estimate()
|
current_model$estimate()
|
||||||
}, times = 3L)
|
} else {
|
||||||
r3_mbm_seq <- microbenchmark("Rank3seq" = {
|
# We transfer
|
||||||
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"))
|
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")))
|
||||||
}, times = 3L)
|
}
|
||||||
r4_mbm_seq <- microbenchmark("Rank4seq" = {
|
prev_model <- current_model
|
||||||
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"))
|
model_list <- append(model_list, current_model)
|
||||||
}, times = 3L)
|
}
|
||||||
r5_mbm_seq <- microbenchmark("Rank5seq" = {
|
|
||||||
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"))
|
|
||||||
}, times = 3L)
|
|
||||||
mbm_seq <- rbind(r2_mbm_seq, r3_mbm_seq, r4_mbm_seq, r5_mbm_seq)
|
|
||||||
|
|
||||||
out_seq <- list(
|
names(model_list) <- paste0("Rank", net_ids)
|
||||||
benchmark = mbm_seq,
|
saveRDS(model_list, here(named_data_folder, paste0(mode, "_", epoch, ".Rds")))
|
||||||
models = list(
|
|
||||||
Rank2 = r2_model_seq,
|
|
||||||
Rank3 = r3_model_seq,
|
|
||||||
Rank4 = r4_model_seq,
|
|
||||||
Rank5 = r5_model_seq
|
|
||||||
)
|
|
||||||
)
|
|
||||||
|
|
||||||
saveRDS(out_seq, here(named_data_folder, "seq.Rds"))
|
|
||||||
},
|
|
||||||
"para" = {
|
|
||||||
message("Will use PARA")
|
|
||||||
|
|
||||||
r2_mbm_para <- microbenchmark("Rank2para" = {
|
|
||||||
r2_model_para <- BM_poisson(
|
|
||||||
membership_type = "LBM",
|
|
||||||
adj = per_taxa_networks[[2]], # Account for the root
|
|
||||||
verbosity = 6,
|
|
||||||
plotting = "",
|
|
||||||
ncores = parallelly::availableCores(), autosave = here(tmp_folder, "r2_para.Rds")
|
|
||||||
)
|
|
||||||
r2_model_para$estimate()
|
|
||||||
}, times = 3L)
|
|
||||||
r3_mbm_para <- microbenchmark("Rank3para" = {
|
|
||||||
r3_model_para <- bm_propagate_taus_all_models(phyloseq_data = the_data, rank_id_start = 2, target_rank_id = 3, per_taxa_networks = per_taxa_networks, first_model = r2_model_para, ncores = parallelly::availableCores(), autosave = here(tmp_folder, "r3_para.Rds"))
|
|
||||||
}, times = 3L)
|
|
||||||
r4_mbm_para <- microbenchmark("Rank4para" = {
|
|
||||||
r4_model_para <- bm_propagate_taus_all_models(phyloseq_data = the_data, rank_id_start = 3, per_taxa_networks = per_taxa_networks, first_model = r3_model_para, ncores = parallelly::availableCores(), autosave = here(tmp_folder, "r4_para.Rds"))
|
|
||||||
}, times = 3L)
|
|
||||||
r5_mbm_para <- microbenchmark("Rank5para" = {
|
|
||||||
r5_model_para <- bm_propagate_taus_all_models(phyloseq_data = the_data, rank_id_start = 4, per_taxa_networks = per_taxa_networks, first_model = r4_model_para, ncores = parallelly::availableCores(), autosave = here(tmp_folder, "r5_para.Rds"))
|
|
||||||
}, times = 3L)
|
|
||||||
mbm_para <- rbind(r2_mbm_para, r3_mbm_para, r4_mbm_para, r5_mbm_para)
|
|
||||||
|
|
||||||
out_para <- list(
|
|
||||||
benchmark = mbm_para,
|
|
||||||
models = list(
|
|
||||||
Rank2 = r2_model_para,
|
|
||||||
Rank3 = r3_model_para,
|
|
||||||
Rank4 = r4_model_para,
|
|
||||||
Rank5 = r5_model_para
|
|
||||||
)
|
|
||||||
)
|
|
||||||
saveRDS(out_para, here(named_data_folder, "para.Rds"))
|
|
||||||
},
|
|
||||||
"notrans" = { # No transfer
|
|
||||||
message("Will use NO TRANSFER")
|
|
||||||
r2_mbm_notrans <- microbenchmark("Rank2notrans" = {
|
|
||||||
r2_model_notrans <- BM_poisson(
|
|
||||||
membership_type = "LBM",
|
|
||||||
adj = per_taxa_networks[[2]], # Account for the root
|
|
||||||
verbosity = 6,
|
|
||||||
ncores = parallelly::availableCores(), autosave = here(tmp_folder, "r2_notrans.Rds")
|
|
||||||
)
|
|
||||||
r2_model_notrans$estimate()
|
|
||||||
}, times = 3L)
|
|
||||||
r3_mbm_notrans <- microbenchmark("Rank3notrans" = {
|
|
||||||
r3_model_notrans <- BM_poisson(
|
|
||||||
membership_type = "LBM",
|
|
||||||
adj = per_taxa_networks[[3]], # Account for the root
|
|
||||||
verbosity = 6,
|
|
||||||
plotting = "",
|
|
||||||
ncores = parallelly::availableCores(), autosave = here(tmp_folder, "r3_notrans.Rds")
|
|
||||||
)
|
|
||||||
r3_model_notrans$estimate()
|
|
||||||
}, times = 3L)
|
|
||||||
r4_mbm_notrans <- microbenchmark("Rank4notrans" = {
|
|
||||||
r4_model_notrans <- BM_poisson(
|
|
||||||
membership_type = "LBM",
|
|
||||||
adj = per_taxa_networks[[4]], # Account for the root
|
|
||||||
verbosity = 6,
|
|
||||||
plotting = "",
|
|
||||||
ncores = parallelly::availableCores(), autosave = here(tmp_folder, "r4_notrans.Rds")
|
|
||||||
)
|
|
||||||
r4_model_notrans$estimate()
|
|
||||||
}, times = 3L)
|
|
||||||
r5_mbm_notrans <- microbenchmark("Rank5notrans" = {
|
|
||||||
r5_model_notrans <- BM_poisson(
|
|
||||||
membership_type = "LBM",
|
|
||||||
adj = per_taxa_networks[[5]], # Account for the root
|
|
||||||
verbosity = 6,
|
|
||||||
plotting = "",
|
|
||||||
ncores = parallelly::availableCores(), autosave = here(tmp_folder, "r5_notrans.Rds")
|
|
||||||
)
|
|
||||||
r5_model_notrans$estimate()
|
|
||||||
}, times = 3L)
|
|
||||||
mbm_notrans <- rbind(r2_mbm_notrans, r3_mbm_notrans, r4_mbm_notrans, r5_mbm_notrans)
|
|
||||||
|
|
||||||
out_notrans <- list(
|
|
||||||
benchmark = mbm_notrans,
|
|
||||||
models = list(
|
|
||||||
Rank2 = r2_model_notrans,
|
|
||||||
Rank3 = r3_model_notrans,
|
|
||||||
Rank4 = r4_model_notrans,
|
|
||||||
Rank5 = r5_model_notrans
|
|
||||||
)
|
|
||||||
)
|
|
||||||
saveRDS(out_notrans, here(named_data_folder, "notrans.Rds"))
|
|
||||||
},
|
|
||||||
stop("Nothing selected, exiting")
|
|
||||||
)
|
|
||||||
|
|
|
||||||
Loading…
Add table
Reference in a new issue