From a382f612330ad3f9a2b249d0ca0814915156ff2b Mon Sep 17 00:00:00 2001
From: Louis <louis.lacoste@agroparistech.fr>
Date: Tue, 24 Feb 2026 14:51:46 +0100
Subject: [PATCH] Extracting folder

---
 analysis_benchmark_lbm_seq.qmd | 23 +++++++++++++++--------
 1 file changed, 15 insertions(+), 8 deletions(-)

diff --git a/analysis_benchmark_lbm_seq.qmd b/analysis_benchmark_lbm_seq.qmd
index 926c086..f0c84d8 100644
--- a/analysis_benchmark_lbm_seq.qmd
+++ b/analysis_benchmark_lbm_seq.qmd
@@ -19,8 +19,9 @@ otu_df <- sapply(per_taxa_networks, nrow) %>%
     rownames_to_column() %>%
     rename(Nb_OTU = ".", Rank = "rowname")
 
+result_folder <- here("results", "lbm-seq", "chaillou")
 
-flist <- list.files(here("results", "lbm-seq", "chaillou"), full.names = TRUE, pattern = ".Rds")
+flist <- list.files(result_folder, full.names = TRUE, pattern = ".Rds")
 
 para_flist <- grepv(pattern = "para.Rds", flist)
 seq_flist <- grepv(pattern = "seq.Rds", flist)
@@ -118,7 +119,7 @@ extract_memberships <- function(model) {
     rownames(memberships[["Z1"]]) <- rownames(model$adj)
     rownames(memberships[["Z2"]]) <- colnames(model$adj)
     memberships
-    map_memberships <- list(Z1 = apply(memberships[["Z1"]], 1, which.max), Z2 = apply(memberships[["Z2"]], 1, which.max)) 
+    map_memberships <- list(Z1 = apply(memberships[["Z1"]], 1, which.max), Z2 = apply(memberships[["Z2"]], 1, which.max))
     map_memberships
 }
 ```
@@ -132,13 +133,15 @@ notrans_memberships <- lapply(notrans_model, extract_memberships)
 ```
 
 ```{r}
-tibble("Para v No transfer" = map2_dbl(purrr::transpose(para_memberships)[["Z1"]], purrr::transpose(notrans_memberships)[["Z1"]], .f = ARI), "Sequential v No transfer" = map2_dbl(purrr::transpose(seq_memberships)[["Z1"]], purrr::transpose(notrans_memberships)[["Z1"]], .f = ARI), "Para v Sequential" = map2_dbl(purrr::transpose(para_memberships)[["Z1"]], purrr::transpose(seq_memberships)[["Z1"]], .f = ARI)) %>% t() %>%
-knitr::kable(col.names = paste0("Rank", seq(2,5)), caption = "ARI for the methods for OTU memberships")
+tibble("Para v No transfer" = map2_dbl(purrr::transpose(para_memberships)[["Z1"]], purrr::transpose(notrans_memberships)[["Z1"]], .f = ARI), "Sequential v No transfer" = map2_dbl(purrr::transpose(seq_memberships)[["Z1"]], purrr::transpose(notrans_memberships)[["Z1"]], .f = ARI), "Para v Sequential" = map2_dbl(purrr::transpose(para_memberships)[["Z1"]], purrr::transpose(seq_memberships)[["Z1"]], .f = ARI)) %>%
+    t() %>%
+    knitr::kable(col.names = paste0("Rank", seq(2, 5)), caption = "ARI for the methods for OTU memberships")
 ```
 
 ```{r}
-tibble("Para v No transfer" = map2_dbl(purrr::transpose(para_memberships)[["Z2"]], purrr::transpose(notrans_memberships)[["Z2"]], .f = ARI), "Sequential v No transfer" = map2_dbl(purrr::transpose(seq_memberships)[["Z2"]], purrr::transpose(notrans_memberships)[["Z2"]], .f = ARI), "Para v Sequential" = map2_dbl(purrr::transpose(para_memberships)[["Z2"]], purrr::transpose(seq_memberships)[["Z2"]], .f = ARI)) %>% t() %>%
-knitr::kable(col.names = paste0("Rank", seq(2,5)), caption = "ARI for the methods for sample memberships")
+tibble("Para v No transfer" = map2_dbl(purrr::transpose(para_memberships)[["Z2"]], purrr::transpose(notrans_memberships)[["Z2"]], .f = ARI), "Sequential v No transfer" = map2_dbl(purrr::transpose(seq_memberships)[["Z2"]], purrr::transpose(notrans_memberships)[["Z2"]], .f = ARI), "Para v Sequential" = map2_dbl(purrr::transpose(para_memberships)[["Z2"]], purrr::transpose(seq_memberships)[["Z2"]], .f = ARI)) %>%
+    t() %>%
+    knitr::kable(col.names = paste0("Rank", seq(2, 5)), caption = "ARI for the methods for sample memberships")
 ```
 
 ```{r}
@@ -245,8 +248,12 @@ ICL_per_ranks <- function(model_results) {
     model_rank_list <- lapply(model_results, function(model_per_rank) model_per_rank[[1]]) # Extract first rep per rank
     return(sapply(model_rank_list, function(model) max(model$ICL, na.rm = TRUE)))
 }
-ICL_df <- data.frame("No trans" = ICL_per_ranks(notrans_results), "Seq" =
-ICL_per_ranks(seq_results)) %>% t() %>% as.data.frame()
+ICL_df <- data.frame(
+    "No trans" = ICL_per_ranks(notrans_results), "Seq" =
+        ICL_per_ranks(seq_results)
+) %>%
+    t() %>%
+    as.data.frame()
 ```
 
 ```{r}