From 46e0b06eec063978212ec559897643a9119e5c0a Mon Sep 17 00:00:00 2001
From: Liang Zhang <psychelzh@outlook.com>
Date: Tue, 24 Sep 2024 02:49:47 +0800
Subject: [PATCH] Add gss dynamic

---
 R/mantel.R | 27 +++++++++++++++++++++++++++
 R/sync.R   |  7 -------
 R/utils.R  |  8 --------
 _targets.R | 53 +++++++++++++++++++++++++++++++----------------------
 4 files changed, 58 insertions(+), 37 deletions(-)
 create mode 100644 R/mantel.R
 delete mode 100644 R/sync.R

diff --git a/R/mantel.R b/R/mantel.R
new file mode 100644
index 0000000..a92b7b8
--- /dev/null
+++ b/R/mantel.R
@@ -0,0 +1,27 @@
+calc_mantel <- function(data, ydis, col_xdis = last_col()) {
+  data |>
+    mutate(
+      mantel = map(
+        pick({{ col_xdis }})[[1]],
+        \(xdis) vegan::mantel(xdis, ydis)
+      ),
+      .keep = "unused"
+    )
+}
+
+extract_stats_mantel <- function(data_mantel) {
+  data_mantel |>
+    mutate(
+      map(mantel, tidy_mantel) |>
+        list_rbind(),
+      .keep = "unused"
+    )
+}
+
+tidy_mantel <- function(mantel) {
+  tibble(
+    statistic = mantel$statistic,
+    p.value = mantel$signif,
+    method = mantel$method
+  )
+}
diff --git a/R/sync.R b/R/sync.R
deleted file mode 100644
index e5561b0..0000000
--- a/R/sync.R
+++ /dev/null
@@ -1,7 +0,0 @@
-calc_sync_smc <- function(sync_whole_trials, smc) {
-  sync_whole_trials |>
-    mutate(
-      mantel = map(neu_sync, ~ vegan::mantel(.x, smc)),
-      .keep = "unused"
-    )
-}
diff --git a/R/utils.R b/R/utils.R
index 43ffe84..2a2ba5e 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -8,14 +8,6 @@ convert_p2_p1 <- function(statistic, p.value,
   )
 }
 
-tidy_mantel <- function(mantel) {
-  tibble(
-    statistic = mantel$statistic,
-    p.value = mantel$signif,
-    method = mantel$method
-  )
-}
-
 get_resid <- function(y, x) {
   resid(lm(y ~ x, na.action = na.exclude))
 }
diff --git a/_targets.R b/_targets.R
index d716b4d..b6f1629 100644
--- a/_targets.R
+++ b/_targets.R
@@ -174,6 +174,31 @@ list(
       collect() |>
       calc_group_pattern()
   ),
+  tar_target(
+    patterns_group_dynamic,
+    arrow::read_parquet(file_cca_y) |>
+      calc_group_pattern_dynamic()
+  ),
+  tar_target(data_gss_dynamic, calc_mantel(patterns_group_dynamic, pattern_semantics)),
+  tar_target(stats_gss_dynamic, extract_stats_mantel(data_gss_dynamic)),
+  tarchetypes::tar_rep(
+    data_gss_dynamic_permuted,
+    calc_mantel(
+      patterns_group_dynamic,
+      seriation::permute(pattern_semantics, sample.int(150L))
+    ),
+    reps = 10,
+    batches = 100
+  ),
+  tarchetypes::tar_rep2(
+    stats_gss_dynamic_permuted,
+    extract_stats_mantel(data_gss_dynamic_permuted),
+    data_gss_dynamic_permuted
+  ),
+  tar_target(
+    clusters_stats_gss_dynamic,
+    calc_clusters_stats(stats_gss_dynamic, stats_gss_dynamic_permuted)
+  ),
   tar_target(
     # leave one out
     patterns_group_whole_loo,
@@ -349,10 +374,7 @@ list(
         .by = cca_id
       )
   ),
-  tar_target(
-    sync_smc,
-    calc_sync_smc(sync_whole_trials, smc)
-  ),
+  tar_target(sync_smc, calc_mantel(sync_whole_trials, smc)),
   tar_target(
     sync_dynamic,
     whole_erps |>
@@ -367,13 +389,14 @@ list(
         .by = cca_id
       )
   ),
+  tar_target(sync_smc_dynamic, calc_mantel(sync_dynamic, smc)),
   tar_target(
-    sync_smc_dynamic,
-    calc_sync_smc(sync_dynamic, smc)
+    stats_sync_smc_dynamic,
+    extract_stats_mantel(sync_smc_dynamic)
   ),
   tarchetypes::tar_rep(
     sync_smc_dynamic_permuted,
-    calc_sync_smc(
+    calc_mantel(
       sync_dynamic,
       seriation::permute(smc, sample.int(206L))
     ),
@@ -382,23 +405,9 @@ list(
   ),
   tarchetypes::tar_rep2(
     stats_sync_smc_dynamic_permuted,
-    sync_smc_dynamic_permuted |>
-      mutate(
-        map(mantel, tidy_mantel) |>
-          list_rbind(),
-        .keep = "unused"
-      ),
+    extract_stats_mantel(sync_smc_dynamic_permuted),
     sync_smc_dynamic_permuted
   ),
-  tar_target(
-    stats_sync_smc_dynamic,
-    sync_smc_dynamic |>
-      mutate(
-        map(mantel, tidy_mantel) |>
-          list_rbind(),
-        .keep = "unused"
-      )
-  ),
   tar_target(
     clusters_stats_sync_smc_dynamic,
     stats_sync_smc_dynamic |>