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Adding autosave capabilities

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Louis 2026-01-27 09:52:03 +01:00
parent e236b687ca
commit d46e7e8913
1 changed files with 7 additions and 4 deletions
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11
utils-bm-seq.R
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@ -63,9 +63,11 @@ bm_estimate_with_inits <- function(bm_model, reinitialization_effort = 1) {
cat("With ascending number of groups\n") cat("With ascending number of groups\n")
ra <- bm_model$estim_ascend(reinitialization_effort, changing_effort) ra <- bm_model$estim_ascend(reinitialization_effort, changing_effort)
bm_model$save_now() # Using blockmodels save capabilities
cat("With descending number of groups\n") cat("With descending number of groups\n")
rb <- bm_model$estim_descend(reinitialization_effort) rb <- bm_model$estim_descend(reinitialization_effort)
bm_model$save_now()
l <- ra || rb l <- ra || rb
n <- n + 1 n <- n + 1
@ -73,7 +75,7 @@ bm_estimate_with_inits <- function(bm_model, reinitialization_effort = 1) {
} }
} }
bm_propagate_taus_all_models <- function(phyloseq_data, rank_id_start = 2, target_rank_id = rank_id_start + 1, first_model = NULL, per_taxa_networks = collapse_otu_at_taxo(phyloseq_data), sd_noise = 0.001, ncores = parallelly::availableCores(), verbosity = 2L) { bm_propagate_taus_all_models <- function(phyloseq_data, rank_id_start = 2, target_rank_id = rank_id_start + 1, first_model = NULL, per_taxa_networks = collapse_otu_at_taxo(phyloseq_data), sd_noise = 0.001, ncores = parallelly::availableCores(), verbosity = 2L, autosave = character(0)) {
removed_root <- FALSE removed_root <- FALSE
# Detect if first rank (higher) is fully collapsed # Detect if first rank (higher) is fully collapsed
if (nrow(per_taxa_networks[[1]]) <= 1L) { if (nrow(per_taxa_networks[[1]]) <= 1L) {
@ -81,7 +83,6 @@ bm_propagate_taus_all_models <- function(phyloseq_data, rank_id_start = 2, targe
removed_root <- TRUE removed_root <- TRUE
per_taxa_networks <- per_taxa_networks[-1] per_taxa_networks <- per_taxa_networks[-1]
} }
result_list <- list()
# Init # Init
net_id_start <- ifelse(removed_root, rank_id_start - 1, rank_id_start) net_id_start <- ifelse(removed_root, rank_id_start - 1, rank_id_start)
if (missing(first_model)) { if (missing(first_model)) {
@ -90,7 +91,8 @@ bm_propagate_taus_all_models <- function(phyloseq_data, rank_id_start = 2, targe
adj = per_taxa_networks[[net_id_start]], # Account for the root adj = per_taxa_networks[[net_id_start]], # Account for the root
verbosity = verbosity, verbosity = verbosity,
plotting = "", plotting = "",
ncores = ncores ncores = ncores,
autosave = autosave
) )
first_model$estimate() first_model$estimate()
} }
@ -110,7 +112,8 @@ bm_propagate_taus_all_models <- function(phyloseq_data, rank_id_start = 2, targe
adj = per_taxa_networks[[target_net_id]], # Account for the root adj = per_taxa_networks[[target_net_id]], # Account for the root
verbosity = verbosity, verbosity = verbosity,
plotting = "", plotting = "",
ncores = ncores ncores = ncores,
autosave = autosave
) )
lapply(seq_along(propagated_models), function(current_q) { lapply(seq_along(propagated_models), function(current_q) {