WOD 8/7

Rcodes/simulation/netclustering_analyze.Rmd

@@ -1,5 +1,6 @@
 ```{r libraries, echo = FALSE, include = FALSE}
 require("ggplot2")
+require("ggokabeito")
 require("tidyr")
 require("dplyr")
 require("patchwork")
@@ -10,119 +11,27 @@ require("latex2exp")
 
 ```{r impoting-data, echo = FALSE}
 filenames <- list.files(
-    path = "./Rcodes/simulation/data",
+    path = "./data",
-    pattern = "simulated_collection_clustering_*",
+    pattern = "simulated_collection_data_clustering_*",
     full.names = TRUE
 )
 
-rep(gsub(".*_(iid|pi|rho|pirho)_.*", "\\1", filenames), each = 6)
-
 # data_list <- lapply(filenames, function(file) lapply(readRDS(file), function(model) model$list_clustering))
-data_list <- lapply(filenames, readRDS)
+df_netclust <- do.call("rbind", lapply(filenames, readRDS))
 
+```
 
-for (model in data_list) {
+```{r netclustering-ARI-boxplot, echo = FALSE}
-            list_clustering <- lapply(
+#| dpi = 300,
-                seq_along(model), function(s) model[[s]]$list_of_clusterings
+#| fig.asp = 0.5,
-            )
+#| fig.cap = "\\label{}ARI of the partition obtained by clustering in function of $\\eps$"
-
+df_netclust %>%
-            list_best_partition <- lapply(
+    ggplot() +
-                seq_along(list_clustering), function(s) {
+    aes(x = as.factor(epsilon), y = ARI) +
-                    list(
+    scale_color_okabe_ito() +
-                        epsilon = result_clustering[[s]]$epsilon,
+    scale_fill_okabe_ito() +
-                        best_partition = unlist(extract_best_bipartite_partition(list_clustering[[s]]))
+    xlab(TeX("$\\epsilon$")) +
-                    )
+    guides(fill = guide_legend(title = "Model")) +
-                }
+    ylab("ARI of obtained netclustering") +
-            )
+    geom_boxplot(aes(fill = model))
-            data.frame(
-                epsilon = sapply(
-                    list_best_partition,
-                    function(best_partition) {
-                        best_partition$epsilon
-                    }
-                ),
-                ARI = sapply(
-                    list_best_partition,
-                    function(best_partition) {
-                        aricode::ARI(rep(1:3, each = 3), unlist(
-                            lapply(
-                                seq_along(best_partition$best_partition),
-                                function(idx) {
-                                    setNames(
-                                        rep(idx, 
-                                        best_partition$best_partition[[idx]]$M), 
-                                        best_partition$best_partition[[idx]]$net_id
-                                    )
-                                }
-                            )
-                        ))
-                    }
-                )
-            )
-}
-
-lapply(
-    data_list,
-    function(model) {
-        list_clustering <- lapply(
-        seq_along(model), function(s) model[[s]]$list_of_clusterings
-        )
-
-        list_best_partition <- lapply(
-            seq_along(list_clustering), function(s) {
-                list(
-                    epsilon = result_clustering[[s]]$epsilon,
-                    best_partition = unlist(extract_best_bipartite_partition(list_clustering[[s]]))
-                )
-            }
-        )
-    data.frame(
-        epsilon = sapply(
-            list_best_partition,
-            function(best_partition) {
-                best_partition$epsilon
-            }
-        ),
-        ARI = sapply(
-            list_best_partition,
-            function(best_partition) {
-                aricode::ARI(rep(1:3, each = 3), unlist(
-                    lapply(
-                        seq_along(best_partition$best_partition),
-                        function(idx) {
-                            setNames(
-                                rep(idx, best_partition$best_partition[[idx]]$M), best_partition$best_partition[[idx]]$net_id
-                            )
-                        }
-                    )
-                ))
-            }
-        )
-    )
-
-}
-)
-    data.frame(
-        epsilon = sapply(
-            list_best_partition,
-            function(best_partition) {
-                best_partition$epsilon
-            }
-        ),
-        ARI = sapply(
-            list_best_partition,
-            function(best_partition) {
-                aricode::ARI(rep(1:3, each = 3), unlist(
-                    lapply(
-                        seq_along(best_partition$best_partition),
-                        function(idx) {
-                            setNames(
-                                rep(idx, best_partition$best_partition[[idx]]$M), best_partition$best_partition[[idx]]$net_id
-                            )
-                        }
-                    )
-                ))
-            }
-        )
-    )
 ```

Rcodes/simulation/netclustering_analyze.tex

@@ -1,13 +1,8 @@
 \section{Network clustering of simulated networks}\label{sec:network-clustering-of-simulated-networks}
 
-\begin{verbatim}
+\begin{figure}
-## character(0)
+\centering
-\end{verbatim}
+\includegraphics{./img/99d363f6aa43bf0eba413cb994dc00b130709107.png}
-
+\caption{\label{}ARI of the partition obtained by clustering in function
-\begin{verbatim}
+of \(\eps\)}
-## list()
+\end{figure}
-\end{verbatim}
-
-\begin{verbatim}
-## Error in eval(expr, envir, enclos): objet 'list_best_partition' introuvable
-\end{verbatim}

Rcodes/simulation/netclustering_check.R

@@ -1,7 +1,8 @@
 require("ggplot2")
 require("tictoc")
+require("colSBM")
 
-devtools::load_all("R/")
+set.seed(1234)
 
 # Generation of conditions
 if (!exists("model_to_test")) {
@@ -17,7 +18,7 @@ nc <- 75
 
 pi <- matrix(c(0.2, 0.3, 0.5), nrow = 1, byrow = TRUE)
 rho <- matrix(c(0.2, 0.3, 0.5), nrow = 1, byrow = TRUE)
-epsilons <- c(0.4)
+epsilons <- seq(0.1, 0.4, by = 0.1)
 
 if (!exists("arg")) {
     arg <- commandArgs(trailingOnly = TRUE)
@@ -31,7 +32,7 @@ if (identical(arg, character(0))) {
 
 conditions <- tidyr::crossing(epsilons, pi, rho, repetitions)
 
-results <- bettermc::mclapply(seq_len(nrow(conditions)), function(s) {
+results <- lapply(seq_len(nrow(conditions)), function(s) {
     eps <- conditions[s, ]$epsilons
     current_pi <- conditions[s, ]$pi
     current_rho <- conditions[s, ]$rho
@@ -70,7 +71,8 @@ results <- bettermc::mclapply(seq_len(nrow(conditions)), function(s) {
         nr, nc,
         current_pi, current_rho,
         alpha_assortative, 3,
-        model = model_to_test
+        model = model_to_test,
+        return_memberships = TRUE
     )
 
     assortative_incidence <- lapply(
@@ -98,7 +100,8 @@ results <- bettermc::mclapply(seq_len(nrow(conditions)), function(s) {
         nr, nc,
         current_pi, current_rho,
         alpha_core_periphery, 3,
-        model = model_to_test
+        model = model_to_test,
+        return_memberships = TRUE
     )
 
     core_periphery_incidence <- lapply(
@@ -126,7 +129,8 @@ results <- bettermc::mclapply(seq_len(nrow(conditions)), function(s) {
         nr, nc,
         current_pi, current_rho,
         alpha_disassortative, 3,
-        model = model_to_test
+        model = model_to_test,
+        return_memberships = TRUE
     )
 
     disassortative_incidence <- lapply(
@@ -184,31 +188,40 @@ results <- bettermc::mclapply(seq_len(nrow(conditions)), function(s) {
         colsbm_model = model_to_test,
         global_opts = list(
             nb_cores = parallel::detectCores() - 1, verbosity = 2,
-            plot_details = 0#,
+            plot_details = 0 # ,
-            #parallelization_vector = c(FALSE, FALSE, FALSE)
+            # parallelization_vector = c(FALSE, FALSE, FALSE)
         ),
         silent_parallelization = TRUE
     )
-    toc()
+
-    return(
+    best_partitions <- unlist(extract_best_bipartite_partition(list_collection))
-        list(
+    clustering <- unlist(lapply(seq_along(best_partitions), function(col_idx) {
-        epsilon = eps,
+        setNames(
-        repetitions = repetitions,
+            rep(col_idx, best_partitions[[col_idx]]$M),
-        list_of_clusterings = list_collection,
+            best_partitions[[col_idx]]$net_id
-        real_block_memberships = list(
-            row = real_row_clustering,
-            col = real_col_clustering
         )
-    ))
+    }))
-},
+    # ARI computation
-mc.cores = parallel::detectCores() - 1,
+    clustering <- clustering[order(names(clustering))]
-mc.progress = TRUE,
+    ari <- aricode::ARI(rep(c(1, 2, 3), each = 3), clustering)
-mc.retry = -1
+
+    toc()
+    cat(paste("Finished", s))
+    return(
+        data.frame(epsilon = eps, model = model_to_test, ARI = ari)
+    )
+}
+# ,
+# mc.cores = parallel::detectCores() - 1,
+# mc.progress = TRUE,
+# mc.retry = -1
 )
 
-saveRDS(results, file = paste0(
+data_frame_result <- do.call("rbind", results)
+
+saveRDS(data_frame_result, file = paste0(
     "simulation/data/",
-    "simulated_collection_clustering_",
+    "simulated_collection_data_clustering_",
     model_to_test, "_",
     format(Sys.time(), "%d-%m-%y-%X"),
     ".Rds"

rapport.tex

@@ -32,6 +32,9 @@
   \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
 \usepackage{booktabs}
 
+% Figure placement
+\floatplacement{figure}{H}
+
 %% Tikz Related
 \usetikzlibrary{calc,shapes,backgrounds,arrows,automata,shadows,positioning}
 \usetikzlibrary{arrows,shapes,positioning,shadows,trees,calc,backgrounds,automata,positioning}
@@ -1060,6 +1063,15 @@ We illustrate our capacity to perform a partition of a collection for all
 colBiSBM models in \ref{sec:network-clustering-of-simulated-networks}.
 
 \chapter{Simulation studies}\label{chap:simulation-studies}
+
+The below simulations are meant to test the capacities of our models.
+We assess the inference capacities of the algorithm and method, the model
+selection performances and the clustering capacities.
+
+\paragraph{Reproducibility} All the codes used to obtain data and to perform the
+analysis can be found on the report repository at
+\url{https://gitea.polarolouis.fr/polarolouis/rapport-CEI-MIA-2023}.
+
 \include{Rcodes/simulation/inference_analyze}
 \include{Rcodes/simulation/model_selection_analyze}
 \include{Rcodes/simulation/netclustering_analyze}