Herbivores clustering

🐛 Fixing errors
🚧 Increasing max_vem_steps

Herbivores
⏲️ Switch to future

code/applications/herbivores/01_herbivores_prepare_data.R

@@ -23,12 +23,15 @@ binary_interaction_data <- interaction_data %>%
             insectspecies,
             sep = "_"
         )
-    ) %>% select(-c(insectorder:plantspecies, interquant))
+    ) %>%
+    select(-c(insectorder:plantspecies, interquant))
 
 netlist <- lapply(vec_web, function(web) {
     web_interaction_data <- binary_interaction_data[which(binary_interaction_data[["web"]] == web), ]
-    incidence_matrix <- table(web_interaction_data[["plantname"]], 
-        web_interaction_data[["insectname"]])
+    incidence_matrix <- (table(
+        web_interaction_data[["plantname"]],
+        web_interaction_data[["insectname"]]
+    ) != 0L) * 1L
 })
 
 names(netlist) <- vec_web

code/applications/herbivores/02_herbivores_clustering.R

@@ -2,6 +2,9 @@ library(colSBM)
 library(dplyr)
 library(tidyr)
 library(here)
+library(future.apply)
+
+plan(multicore)
 
 application_name <- "herbivores"
 
@@ -55,14 +58,15 @@ list_collection <- clusterize_bipartite_networks(
         nb_cores = parallelly::availableCores(omit = 1L) %/% 2L,
         verbosity = 2L,
         plot_details = 0L,
-        backend = "parallel"
-    )
+        backend = "future"
+    ),
+    fit_opts = list(max_vem_steps = 500L)
 )
 
 save_file <- file.path(
     save_folder, paste0(
         sprintf("%s_collection_", application_name),
-        model, "_", start_time, ".Rds"
+        model, "_", start_time, "maxsteps_500.Rds"
     )
 )