Fixing regex

merge-lbm-seq.R

@@ -6,7 +6,7 @@ path <- args[1]
 
 
 
-base_folder <- str_remove(string = path, pattern = "/tmp[0-9]*$")
+base_folder <- str_remove(string = path, pattern = "/tmp[0-9]*/?$")
 print(base_folder)
 epoch <- str_extract(string = path, pattern = "(?<=tmp)([0-9]*)")
 

multipartite_taxtable.R

@@ -0,0 +1,42 @@
+library(sbm)
+library(phyloseq)
+library(biomformat)
+library(here)
+source("utils.R")
+
+options(parallelly.availableCores.custom = function() {
+    ncores <- min(parallelly::availableCores(), 64)
+    max(1L, ncores)
+})
+
+message(paste("Number of cores available:", parallelly::availableCores()))
+args <- commandArgs(trailingOnly = TRUE)
+if (length(args) == 0) {
+    author <- "mach"
+} else {
+    author <- args[1]
+}
+
+message("For author: ", author)
+the_data <- import_biom(here("data", author, paste0(author, ".biom")))
+
+epoch <- as.integer(Sys.time())
+
+per_taxa_networks <- collapse_otu_at_taxo(the_data)
+per_taxa_networks <- per_taxa_networks[-1]
+
+lbm_list <- lapply(seq_along(per_taxa_networks), function(idx) {
+    defineSBM(per_taxa_networks[[idx]], model = "poisson", dimLabels = c(row = paste0("Rank", idx + 1), col = "Sample"))
+})
+
+lbm_list_covariates <- lapply(seq_along(per_taxa_networks), function(idx) {
+    covar_sd <- log(rep(1, nrow(per_taxa_networks[[idx]])) %*% t(colSums(per_taxa_networks[[idx]])))
+    defineSBM(per_taxa_networks[[idx]], model = "poisson", dimLabels = c(row = paste0("Rank", idx + 1), col = "Sample"), covariates = list(covar_sd))
+})
+
+
+multipartite_fit <- estimateMultipartiteSBM(listSBM = lbm_list, estimOptions = list(initBM = FALSE))
+
+multipartite_covariates_fit <- estimateMultipartiteSBM(listSBM = lbm_list_covariates, estimOptions = list(initBM = FALSE))
+
+plot(multipartite_covariates_fit)