From 2d933728e54861590b4fa19455946e1b4de64dac Mon Sep 17 00:00:00 2001
From: Beni Stocker <benjamin.stocker@gmail.com>
Date: Fri, 1 Mar 2024 18:23:47 +0100
Subject: [PATCH] added evaluation by index (among the 10 best)

---
 renv.lock                         | 1352 +++++------------------------
 vignettes/model_evaluation_VI.Rmd |   31 +-
 2 files changed, 239 insertions(+), 1144 deletions(-)

diff --git a/renv.lock b/renv.lock
index 031f771..84b651b 100644
--- a/renv.lock
+++ b/renv.lock
@@ -9,26 +9,15 @@
     ]
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-      "Version": "1.1.3",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "methods"
-      ],
-      "Hash": "b2866e62bab9378c3cc9476a1954226b"
-    },
     "DiceDesign": {
       "Package": "DiceDesign",
-      "Version": "1.9",
+      "Version": "1.10",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R"
       ],
-      "Hash": "b7b812ae4484d4bbf0a0baac72e8fc01"
+      "Hash": "ac8b12951882c375d1a14f64c93e78f1"
     },
     "GPfit": {
       "Package": "GPfit",
@@ -69,7 +58,7 @@
     },
     "Matrix": {
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-      "Version": "1.6-0",
+      "Version": "1.6-1.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -82,7 +71,7 @@
         "stats",
         "utils"
       ],
-      "Hash": "31262fd18481fab05c5e7258dac163ca"
+      "Hash": "1a00d4828f33a9d690806e98bd17150c"
     },
     "ModelMetrics": {
       "Package": "ModelMetrics",
@@ -118,28 +107,27 @@
     },
     "Rcpp": {
       "Package": "Rcpp",
-      "Version": "1.0.11",
+      "Version": "1.0.12",
       "Source": "Repository",
-      "Repository": "CRAN",
+      "Repository": "RSPM",
       "Requirements": [
         "methods",
         "utils"
       ],
-      "Hash": "ae6cbbe1492f4de79c45fce06f967ce8"
+      "Hash": "5ea2700d21e038ace58269ecdbeb9ec0"
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       "Package": "RcppEigen",
-      "Version": "0.3.3.9.3",
+      "Version": "0.3.4.0.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
-        "Matrix",
         "R",
         "Rcpp",
         "stats",
         "utils"
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-      "Hash": "1e035db628cefb315c571202d70202fe"
+      "Hash": "df49e3306f232ec28f1604e36a202847"
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       "Package": "SQUAREM",
@@ -151,58 +139,6 @@
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-        "geojsonio",
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-        "httr",
-        "jsonlite",
-        "keyring",
-        "memoise",
-        "rstudioapi",
-        "sf"
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@@ -247,25 +183,6 @@
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@@ -289,7 +206,7 @@
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@@ -300,36 +217,24 @@
         "htmltools",
         "jquerylib",
         "jsonlite",
+        "lifecycle",
         "memoise",
         "mime",
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+      "Hash": "c0d8599494bc7fb408cd206bbdd9cab0"
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+      "Hash": "c35768291560ce302c0a6589f92e837d"
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@@ -357,18 +262,6 @@
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@@ -382,32 +275,16 @@
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+      "Hash": "1216ac65ac55ec0058a6f75d7ca0fd52"
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@@ -474,10 +351,13 @@
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@@ -491,83 +371,16 @@
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-        "cli",
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@@ -584,7 +397,7 @@
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@@ -604,42 +417,22 @@
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@@ -658,32 +451,13 @@
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@@ -693,7 +467,7 @@
         "stats",
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@@ -708,18 +482,18 @@
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@@ -727,7 +501,7 @@
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@@ -743,16 +517,9 @@
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@@ -760,23 +527,7 @@
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@@ -793,14 +544,14 @@
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@@ -820,7 +571,7 @@
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@@ -831,11 +582,11 @@
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@@ -845,29 +596,7 @@
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@@ -880,84 +609,9 @@
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@@ -978,7 +632,7 @@
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@@ -993,93 +647,40 @@
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 }
diff --git a/vignettes/model_evaluation_VI.Rmd b/vignettes/model_evaluation_VI.Rmd
index 4ab1233..933b2cc 100644
--- a/vignettes/model_evaluation_VI.Rmd
+++ b/vignettes/model_evaluation_VI.Rmd
@@ -17,6 +17,8 @@ library(xgboost)
 library(ranger)
 library(caret)
 library(reactable)
+library(readr)
+library(forcats)
 source(here::here("R/calc_VI.R"))
 source(here::here("R/index_flue.R"))
 set.seed(0)
@@ -108,12 +110,35 @@ p <- ggplot(rsq) +
     aes(
       cluster,
       rsq,
-      colour = flue
+      fill = flue
     )
   ) +
-  theme_bw()
+  theme_classic()
 
 print(p)
 ```
 
-
+Which one performs best?
+```{r}
+best_ind <- rsq |> 
+  filter(cluster != "cNA") |> 
+  group_by(index) |> 
+  summarise(rsq = median(rsq)) |> 
+  arrange(desc(rsq)) |> 
+  dplyr::slice(1:10) |> 
+  pull(index)
+
+rsq |> 
+  filter(index %in% best_ind, cluster != "cNA") |> 
+  mutate(index = fct_reorder(index, rsq, .fun = "mean")) |> 
+  ggplot() +
+  geom_boxplot(
+    aes(
+      reorder(index, desc(rsq)),
+      rsq
+    ),
+    fill = "grey"
+  ) +
+  facet_wrap(~cluster, nrow = 3) +
+  theme_classic()
+```