From 20d26e8634d050bb34f9e5b5892580da5bf9f8de Mon Sep 17 00:00:00 2001
From: Louis <louis.lacoste@agroparistech.fr>
Date: Mon, 9 Feb 2026 17:50:07 +0100
Subject: [PATCH] Working on LBM seq analysis

---
 analysis_benchmark_lbm_seq.qmd | 40 +++++++++++++++++++++++++++++-----
 1 file changed, 34 insertions(+), 6 deletions(-)

diff --git a/analysis_benchmark_lbm_seq.qmd b/analysis_benchmark_lbm_seq.qmd
index fcf63b6..926c086 100644
--- a/analysis_benchmark_lbm_seq.qmd
+++ b/analysis_benchmark_lbm_seq.qmd
@@ -203,14 +203,42 @@ ggplot(seq_df_otu_lodes, aes(x = x, alluvium = alluvium, stratum = stratum, labe
 ```
 
 ```{r}
-ARI_ranks <- function(df_otu) {
-memb_mat <- df_otu |> select(starts_with("Z"))
-memb_list <- lapply(seq_len(ncol(memb_mat)), function(i) memb_mat[,i] |> unlist() |> as.vector())
-outer(memb_list,memb_list, FUN = Vectorize(ARI))}
-ARI_ranks(seq_df_otu)
-ARI_ranks(notrans_df_otu)
+list_memberships <- function(df_otu) {
+    memb_mat <- df_otu |> select(starts_with("Z"))
+    memb_list <- lapply(seq_len(ncol(memb_mat)), function(i) {
+        memb_mat[, i] |>
+            unlist() |>
+            as.vector()
+    })
+    return(memb_list)
+}
+seq_memb_list <- list_memberships(seq_df_otu)
+notrans_memb_list <- list_memberships(notrans_df_otu)
+outer(seq_memb_list, seq_memb_list, Vectorize(ARI))
+outer(notrans_memb_list, notrans_memb_list, Vectorize(ARI))
 ```
 
+### ARI phylogénie et clustering
+
+```{r}
+phylo_df <- data.frame(merged = rownames(tail(per_taxa_networks, 1)[[1]])) %>% separate(col = "merged", into = c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species"), sep = ";_;")
+
+phylo_df <- phylo_df %>% rename_all(~ str_c("Rank", which(colnames(phylo_df) == .)))
+
+phylo_df <- phylo_df %>% mutate_all(as.factor)
+
+phylo_memb_list <- lapply(seq_len(ncol(phylo_df)), function(i) {
+    phylo_df[, i] |>
+        unlist() |>
+        as.factor()
+})
+
+outer(phylo_memb_list, , Vectorize(ARI))
+```
+
+
+## ICL
+
 ```{r}
 # Extract ICL
 ICL_per_ranks <- function(model_results) {