From 9e1ea744a2e9b9d2e245137dd22693d3fbbcf54a Mon Sep 17 00:00:00 2001
From: James Hollway <james.hollway@graduateinstitute.ch>
Date: Sat, 25 Apr 2026 15:10:43 +0200
Subject: [PATCH 1/3] Fixed object reference in position tutorial

---
 .Rbuildignore                          |   4 +-
 .gitignore                             |   1 +
 inst/tutorials/tutorial5/position.Rmd  |  10 +-
 inst/tutorials/tutorial5/position.html | 305 +++++++++++++------------
 4 files changed, 164 insertions(+), 156 deletions(-)

diff --git a/.Rbuildignore b/.Rbuildignore
index cf845c5..a9ac29a 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -18,4 +18,6 @@ vignettes/precompile\.R
 ^Meta$
 ^CRAN-SUBMISSION$
 ^README\.Rmd$
-^.mailmap$
\ No newline at end of file
+^.mailmap$
+^\.positai$
+^\.claude$
diff --git a/.gitignore b/.gitignore
index d1b11a3..655a2bb 100644
--- a/.gitignore
+++ b/.gitignore
@@ -20,3 +20,4 @@ inst/tutorials/tutorial5/equivalence_data/*
 toadd/*
 .data.csv
 cache/*
+.positai
diff --git a/inst/tutorials/tutorial5/position.Rmd b/inst/tutorials/tutorial5/position.Rmd
index 2d967fd..193bb22 100644
--- a/inst/tutorials/tutorial5/position.Rmd
+++ b/inst/tutorials/tutorial5/position.Rmd
@@ -48,6 +48,7 @@ learnr::random_phrases_add(language = "en",
 friends <- to_uniplex(ison_algebra, "friends")
 social <- to_uniplex(ison_algebra, "social")
 tasks <- to_uniplex(ison_algebra, "tasks")
+alge <- to_named(ison_algebra)
 ```
 
 
@@ -479,7 +480,7 @@ What we are saying here is that we want to partition the nodes
 into two clusters, no matter how dissimilar they are.
 
 ```{r k-discrete, exercise = TRUE, exercise.setup = "varyclust"}
-plot(node_in_structural(alge, k = 2))
+plot(node_in_structural(to_named(ison_algebra), k = 2))
 ```
 
 But we're really just guessing. Maybe 2 is not the best `k`?
@@ -523,8 +524,8 @@ can return a somewhat different result to the elbow method.
 See what we have here, with all other arguments held the same:
 
 ```{r elbowsil, exercise = TRUE, exercise.setup = "varyclust"}
-plot(node_in_structural(alge, k = "elbow"))
-plot(node_in_structural(alge, k = "silhouette"))
+plot(node_in_structural(to_named(ison_algebra), k = "elbow"))
+plot(node_in_structural(to_named(ison_algebra), k = "silhouette"))
 ```
 
 Ok, so it looks like the elbow method returns `k == 3` as a good trade-off
@@ -551,7 +552,7 @@ however oftentimes this misses the point in finding clusters of nodes that,
 despite some variation, can be considered as similar on some dimension.
 
 ```{r strict, exercise = TRUE, exercise.setup = "varyclust"}
-plot(node_in_structural(alge, k = "strict"))
+plot(node_in_structural(to_named(ison_algebra), k = "strict"))
 ```
 
 Here for example, no two nodes have precisely the same tie-profile,
@@ -573,6 +574,7 @@ structurally equivalent classes.
 We can graph this of course, as above:
 
 ```{r strplot, exercise = TRUE, exercise.setup = "varyclust"}
+alge <- to_named(ison_algebra)
 alge %>% 
   mutate(se = node_in_structural(alge)) %>% 
   graphr(node_color = "se")
diff --git a/inst/tutorials/tutorial5/position.html b/inst/tutorials/tutorial5/position.html
index 8426eef..ba9c0d8 100644
--- a/inst/tutorials/tutorial5/position.html
+++ b/inst/tutorials/tutorial5/position.html
@@ -533,7 +533,7 @@ <h3>Step three: identifying the number of clusters</h3>
 <div class="tutorial-exercise" data-label="k-discrete"
 data-completion="1" data-diagnostics="1" data-startover="1"
 data-lines="0" data-pipe="|&gt;">
-<pre class="text"><code>plot(node_in_structural(alge, k = 2))</code></pre>
+<pre class="text"><code>plot(node_in_structural(to_named(ison_algebra), k = 2))</code></pre>
 <script type="application/json" data-ui-opts="1">{"engine":"r","has_checker":false,"caption":"<span data-i18n=\"text.enginecap\" data-i18n-opts=\"{&quot;engine&quot;:&quot;R&quot;}\">R Code<\/span>"}</script>
 </div>
 <p>But we’re really just guessing. Maybe 2 is not the best
@@ -571,8 +571,8 @@ <h3>Step three: identifying the number of clusters</h3>
 <div class="tutorial-exercise" data-label="elbowsil" data-completion="1"
 data-diagnostics="1" data-startover="1" data-lines="0"
 data-pipe="|&gt;">
-<pre class="text"><code>plot(node_in_structural(alge, k = &quot;elbow&quot;))
-plot(node_in_structural(alge, k = &quot;silhouette&quot;))</code></pre>
+<pre class="text"><code>plot(node_in_structural(to_named(ison_algebra), k = &quot;elbow&quot;))
+plot(node_in_structural(to_named(ison_algebra), k = &quot;silhouette&quot;))</code></pre>
 <script type="application/json" data-ui-opts="1">{"engine":"r","has_checker":false,"caption":"<span data-i18n=\"text.enginecap\" data-i18n-opts=\"{&quot;engine&quot;:&quot;R&quot;}\">R Code<\/span>"}</script>
 </div>
 <p>Ok, so it looks like the elbow method returns <code>k == 3</code> as
@@ -597,7 +597,7 @@ <h3>Step three: identifying the number of clusters</h3>
 <div class="tutorial-exercise" data-label="strict" data-completion="1"
 data-diagnostics="1" data-startover="1" data-lines="0"
 data-pipe="|&gt;">
-<pre class="text"><code>plot(node_in_structural(alge, k = &quot;strict&quot;))</code></pre>
+<pre class="text"><code>plot(node_in_structural(to_named(ison_algebra), k = &quot;strict&quot;))</code></pre>
 <script type="application/json" data-ui-opts="1">{"engine":"r","has_checker":false,"caption":"<span data-i18n=\"text.enginecap\" data-i18n-opts=\"{&quot;engine&quot;:&quot;R&quot;}\">R Code<\/span>"}</script>
 </div>
 <p>Here for example, no two nodes have precisely the same tie-profile,
@@ -620,7 +620,8 @@ <h3>Summarising profiles</h3>
 <div class="tutorial-exercise" data-label="strplot" data-completion="1"
 data-diagnostics="1" data-startover="1" data-lines="0"
 data-pipe="|&gt;">
-<pre class="text"><code>alge %&gt;% 
+<pre class="text"><code>alge &lt;- to_named(ison_algebra)
+alge %&gt;% 
   mutate(se = node_in_structural(alge)) %&gt;% 
   graphr(node_color = &quot;se&quot;)</code></pre>
 <script type="application/json" data-ui-opts="1">{"engine":"r","has_checker":false,"caption":"<span data-i18n=\"text.enginecap\" data-i18n-opts=\"{&quot;engine&quot;:&quot;R&quot;}\">R Code<\/span>"}</script>
@@ -876,6 +877,7 @@ <h2>Glossary</h2>
 friends <- to_uniplex(ison_algebra, "friends")
 social <- to_uniplex(ison_algebra, "social")
 tasks <- to_uniplex(ison_algebra, "tasks")
+alge <- to_named(ison_algebra)
 </script>
  
 <script type="application/shiny-prerendered" data-context="server">
@@ -928,11 +930,11 @@ <h2>Glossary</h2>
 "                                      \"Beau travail!\",", "                                      \"Bravo!\",", 
 "                                      \"Super!\"),", "                           encouragement = c(\"Bon effort\"))", 
 "friends <- to_uniplex(ison_algebra, \"friends\")", "social <- to_uniplex(ison_algebra, \"social\")", 
-"tasks <- to_uniplex(ison_algebra, \"tasks\")"), chunk_opts = list(
-    label = "setup", include = FALSE, purl = FALSE, eval = TRUE)), 
-    setup = NULL, chunks = list(list(label = "data", code = "", 
-        opts = list(label = "\"data\"", exercise = "TRUE", purl = "FALSE"), 
-        engine = "r")), code_check = NULL, error_check = NULL, 
+"tasks <- to_uniplex(ison_algebra, \"tasks\")", "alge <- to_named(ison_algebra)"
+), chunk_opts = list(label = "setup", include = FALSE, purl = FALSE, 
+    eval = TRUE)), setup = NULL, chunks = list(list(label = "data", 
+    code = "", opts = list(label = "\"data\"", exercise = "TRUE", 
+        purl = "FALSE"), engine = "r")), code_check = NULL, error_check = NULL, 
     check = NULL, solution = structure(c("data(\"ison_algebra\", package = \"manynet\")", 
     "?manynet::ison_algebra", "# If you want to see the network object, you can run the name of the object", 
     "# ison_algebra", "# or print the code with brackets at the front and end of the code", 
@@ -991,13 +993,13 @@ <h2>Glossary</h2>
 "                                      \"Beau travail!\",", "                                      \"Bravo!\",", 
 "                                      \"Super!\"),", "                           encouragement = c(\"Bon effort\"))", 
 "friends <- to_uniplex(ison_algebra, \"friends\")", "social <- to_uniplex(ison_algebra, \"social\")", 
-"tasks <- to_uniplex(ison_algebra, \"tasks\")"), chunk_opts = list(
-    label = "setup", include = FALSE, purl = FALSE, eval = TRUE)), 
-    setup = "", chunks = list(list(label = "data", code = "", 
-        opts = list(label = "\"data\"", exercise = "TRUE", purl = "FALSE"), 
-        engine = "r"), list(label = "separatingnets", code = "", 
-        opts = list(label = "\"separatingnets\"", exercise = "TRUE", 
-            exercise.setup = "\"data\"", purl = "FALSE"), engine = "r")), 
+"tasks <- to_uniplex(ison_algebra, \"tasks\")", "alge <- to_named(ison_algebra)"
+), chunk_opts = list(label = "setup", include = FALSE, purl = FALSE, 
+    eval = TRUE)), setup = "", chunks = list(list(label = "data", 
+    code = "", opts = list(label = "\"data\"", exercise = "TRUE", 
+        purl = "FALSE"), engine = "r"), list(label = "separatingnets", 
+    code = "", opts = list(label = "\"separatingnets\"", exercise = "TRUE", 
+        exercise.setup = "\"data\"", purl = "FALSE"), engine = "r")), 
     code_check = NULL, error_check = NULL, check = NULL, solution = structure(c("friends <- to_uniplex(ison_algebra, \"friends\")", 
     "graphr(friends) + ggtitle(\"Friendship\")", "", "social <- to_uniplex(ison_algebra, \"social\")", 
     "graphr(social) + ggtitle(\"Social\")", "", "tasks <- to_uniplex(ison_algebra, \"tasks\")", 
@@ -1029,22 +1031,22 @@ <h2>Glossary</h2>
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-    "character")), answers = list(structure(list(id = "lnr_ans_84a4d54", 
+    "character")), answers = list(structure(list(id = "lnr_ans_17f5052", 
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+        "character")), correct = TRUE, message = structure("Very good!", html = TRUE, class = c("html", 
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+        "character")), correct = FALSE, message = structure("Try it again. I have a good feeling about this.", html = TRUE, class = c("html", 
         "character")), type = "literal"), class = c("tutorial_question_answer", 
-    "tutorial_quiz_answer")), structure(list(id = "lnr_ans_3c849f9", 
+    "tutorial_quiz_answer")), structure(list(id = "lnr_ans_ec462c5", 
         option = "Highest degree nodes", value = "Highest degree nodes", 
         label = structure("Highest degree nodes", html = TRUE, class = c("html", 
-        "character")), correct = FALSE, message = structure("Try it again. I have a good feeling about this.", html = TRUE, class = c("html", 
+        "character")), correct = FALSE, message = structure("That’s okay: you learn more from mistakes than successes. Let’s do it one more time.", html = TRUE, class = c("html", 
         "character")), type = "literal"), class = c("tutorial_question_answer", 
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@@ -1054,7 +1056,7 @@ <h2>Glossary</h2>
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+    seed = 365485519.829808, options = list()), class = c("learnr_radio", 
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 </script>
 
@@ -1062,29 +1064,29 @@ <h2>Glossary</h2>
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-    "tutorial_quiz_answer")), structure(list(id = "lnr_ans_c5507bb", 
+    "tutorial_quiz_answer")), structure(list(id = "lnr_ans_3f6b9cc", 
         option = "Structuralism", value = "Structuralism", label = structure("Structuralism", html = TRUE, class = c("html", 
-        "character")), correct = FALSE, message = structure("Please try again.", html = TRUE, class = c("html", 
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@@ -1094,31 +1096,31 @@ <h2>Glossary</h2>
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 </script>
  
 <script type="application/shiny-prerendered" data-context="server">
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@@ -1129,7 +1131,7 @@ <h2>Glossary</h2>
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 </script>
 
@@ -1163,9 +1165,9 @@ <h2>Glossary</h2>
 "                                      \"Beau travail!\",", "                                      \"Bravo!\",", 
 "                                      \"Super!\"),", "                           encouragement = c(\"Bon effort\"))", 
 "friends <- to_uniplex(ison_algebra, \"friends\")", "social <- to_uniplex(ison_algebra, \"social\")", 
-"tasks <- to_uniplex(ison_algebra, \"tasks\")"), chunk_opts = list(
-    label = "setup", include = FALSE, purl = FALSE, eval = TRUE)), 
-    setup = "alge <- to_named(ison_algebra)\nfriends <- to_uniplex(alge, \"friends\")\nsocial <- to_uniplex(alge, \"social\")\ntasks <- to_uniplex(alge, \"tasks\")", 
+"tasks <- to_uniplex(ison_algebra, \"tasks\")", "alge <- to_named(ison_algebra)"
+), chunk_opts = list(label = "setup", include = FALSE, purl = FALSE, 
+    eval = TRUE)), setup = "alge <- to_named(ison_algebra)\nfriends <- to_uniplex(alge, \"friends\")\nsocial <- to_uniplex(alge, \"social\")\ntasks <- to_uniplex(alge, \"tasks\")", 
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         opts = list(label = "\"objects-setup\"", purl = "FALSE"), 
         engine = "r"), list(label = "bridges", code = "sum(tie_is_bridge(friends))\nany(node_by_bridges(friends)>0)", 
@@ -1227,9 +1229,9 @@ <h2>Glossary</h2>
 "                                      \"Beau travail!\",", "                                      \"Bravo!\",", 
 "                                      \"Super!\"),", "                           encouragement = c(\"Bon effort\"))", 
 "friends <- to_uniplex(ison_algebra, \"friends\")", "social <- to_uniplex(ison_algebra, \"social\")", 
-"tasks <- to_uniplex(ison_algebra, \"tasks\")"), chunk_opts = list(
-    label = "setup", include = FALSE, purl = FALSE, eval = TRUE)), 
-    setup = "alge <- to_named(ison_algebra)\nfriends <- to_uniplex(alge, \"friends\")\nsocial <- to_uniplex(alge, \"social\")\ntasks <- to_uniplex(alge, \"tasks\")", 
+"tasks <- to_uniplex(ison_algebra, \"tasks\")", "alge <- to_named(ison_algebra)"
+), chunk_opts = list(label = "setup", include = FALSE, purl = FALSE, 
+    eval = TRUE)), setup = "alge <- to_named(ison_algebra)\nfriends <- to_uniplex(alge, \"friends\")\nsocial <- to_uniplex(alge, \"social\")\ntasks <- to_uniplex(alge, \"tasks\")", 
     chunks = list(list(label = "objects-setup", code = "alge <- to_named(ison_algebra)\nfriends <- to_uniplex(alge, \"friends\")\nsocial <- to_uniplex(alge, \"social\")\ntasks <- to_uniplex(alge, \"tasks\")", 
         opts = list(label = "\"objects-setup\"", purl = "FALSE"), 
         engine = "r"), list(label = "constraint", code = "", 
@@ -1291,9 +1293,9 @@ <h2>Glossary</h2>
 "                                      \"Beau travail!\",", "                                      \"Bravo!\",", 
 "                                      \"Super!\"),", "                           encouragement = c(\"Bon effort\"))", 
 "friends <- to_uniplex(ison_algebra, \"friends\")", "social <- to_uniplex(ison_algebra, \"social\")", 
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+"tasks <- to_uniplex(ison_algebra, \"tasks\")", "alge <- to_named(ison_algebra)"
+), chunk_opts = list(label = "setup", include = FALSE, purl = FALSE, 
+    eval = TRUE)), setup = "alge <- to_named(ison_algebra)\nfriends <- to_uniplex(alge, \"friends\")\nsocial <- to_uniplex(alge, \"social\")\ntasks <- to_uniplex(alge, \"tasks\")", 
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         opts = list(label = "\"objects-setup\"", purl = "FALSE"), 
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@@ -1332,11 +1334,11 @@ <h2>Glossary</h2>
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     question = structure("Do bridges innovate?", html = TRUE, class = c("html", 
-    "character")), answers = list(structure(list(id = "lnr_ans_600e324", 
+    "character")), answers = list(structure(list(id = "lnr_ans_bafb4bf", 
         option = "No", value = "No", label = structure("No", html = TRUE, class = c("html", 
-        "character")), correct = TRUE, message = structure("What first-rate work!", html = TRUE, class = c("html", 
+        "character")), correct = TRUE, message = structure("Delightful!", html = TRUE, class = c("html", 
         "character")), type = "literal"), class = c("tutorial_question_answer", 
-    "tutorial_quiz_answer")), structure(list(id = "lnr_ans_a6b4531", 
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@@ -1348,23 +1350,23 @@ <h2>Glossary</h2>
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     loading = NULL, random_answer_order = TRUE, allow_retry = TRUE, 
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 </script>
  
 <script type="application/shiny-prerendered" data-context="server">
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     label = structure("same/similar tie partners.", html = TRUE, class = c("html", 
-    "character")), correct = TRUE, message = structure("Amazing!", html = TRUE, class = c("html", 
+    "character")), correct = TRUE, message = structure("Well done!", html = TRUE, class = c("html", 
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-"tutorial_quiz_answer")), structure(list(id = "lnr_ans_7837804", 
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@@ -1376,7 +1378,7 @@ <h2>Glossary</h2>
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 )), session = session)
 </script>
@@ -1411,19 +1413,19 @@ <h2>Glossary</h2>
 "                                      \"Beau travail!\",", "                                      \"Bravo!\",", 
 "                                      \"Super!\"),", "                           encouragement = c(\"Bon effort\"))", 
 "friends <- to_uniplex(ison_algebra, \"friends\")", "social <- to_uniplex(ison_algebra, \"social\")", 
-"tasks <- to_uniplex(ison_algebra, \"tasks\")"), chunk_opts = list(
-    label = "setup", include = FALSE, purl = FALSE, eval = TRUE)), 
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-        opts = list(label = "\"data\"", exercise = "TRUE", purl = "FALSE"), 
-        engine = "r"), list(label = "find-se", code = "node_in_structural(ison_algebra)\n\nison_algebra %>% \n  mutate(se = node_in_structural(ison_algebra)) %>% \n  graphr(node_color = \"se\")", 
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-            exercise.setup = "\"data\""), engine = "r")), code_check = NULL, 
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-        background = "#F7F7F7", strip.white = TRUE, cache = 0, 
-        cache.path = "position_cache/html/", cache.vars = NULL, 
+"tasks <- to_uniplex(ison_algebra, \"tasks\")", "alge <- to_named(ison_algebra)"
+), chunk_opts = list(label = "setup", include = FALSE, purl = FALSE, 
+    eval = TRUE)), setup = "", chunks = list(list(label = "data", 
+    code = "", opts = list(label = "\"data\"", exercise = "TRUE", 
+        purl = "FALSE"), engine = "r"), list(label = "find-se", 
+    code = "node_in_structural(ison_algebra)\n\nison_algebra %>% \n  mutate(se = node_in_structural(ison_algebra)) %>% \n  graphr(node_color = \"se\")", 
+    opts = list(label = "\"find-se\"", exercise = "TRUE", exercise.setup = "\"data\""), 
+    engine = "r")), code_check = NULL, error_check = NULL, check = NULL, 
+    solution = NULL, tests = NULL, options = list(eval = FALSE, 
+        echo = TRUE, results = "markup", tidy = FALSE, tidy.opts = NULL, 
+        collapse = FALSE, prompt = FALSE, comment = NA, highlight = FALSE, 
+        size = "normalsize", background = "#F7F7F7", strip.white = TRUE, 
+        cache = 0, cache.path = "position_cache/html/", cache.vars = NULL, 
         cache.lazy = TRUE, dependson = NULL, autodep = FALSE, 
         cache.rebuild = FALSE, fig.keep = "high", fig.show = "asis", 
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@@ -1475,13 +1477,13 @@ <h2>Glossary</h2>
 "                                      \"Beau travail!\",", "                                      \"Bravo!\",", 
 "                                      \"Super!\"),", "                           encouragement = c(\"Bon effort\"))", 
 "friends <- to_uniplex(ison_algebra, \"friends\")", "social <- to_uniplex(ison_algebra, \"social\")", 
-"tasks <- to_uniplex(ison_algebra, \"tasks\")"), chunk_opts = list(
-    label = "setup", include = FALSE, purl = FALSE, eval = TRUE)), 
-    setup = "", chunks = list(list(label = "data", code = "", 
-        opts = list(label = "\"data\"", exercise = "TRUE", purl = "FALSE"), 
-        engine = "r"), list(label = "construct-cor", code = "", 
-        opts = list(label = "\"construct-cor\"", exercise = "TRUE", 
-            exercise.setup = "\"data\"", purl = "FALSE"), engine = "r")), 
+"tasks <- to_uniplex(ison_algebra, \"tasks\")", "alge <- to_named(ison_algebra)"
+), chunk_opts = list(label = "setup", include = FALSE, purl = FALSE, 
+    eval = TRUE)), setup = "", chunks = list(list(label = "data", 
+    code = "", opts = list(label = "\"data\"", exercise = "TRUE", 
+        purl = "FALSE"), engine = "r"), list(label = "construct-cor", 
+    code = "", opts = list(label = "\"construct-cor\"", exercise = "TRUE", 
+        exercise.setup = "\"data\"", purl = "FALSE"), engine = "r")), 
     code_check = NULL, error_check = NULL, check = NULL, solution = structure(c("node_x_tie(ison_algebra)", 
     "dim(node_x_tie(ison_algebra))"), chunk_opts = list(label = "construct-cor-solution")), 
     tests = NULL, options = list(eval = FALSE, echo = TRUE, results = "markup", 
@@ -1538,13 +1540,13 @@ <h2>Glossary</h2>
 "                                      \"Beau travail!\",", "                                      \"Bravo!\",", 
 "                                      \"Super!\"),", "                           encouragement = c(\"Bon effort\"))", 
 "friends <- to_uniplex(ison_algebra, \"friends\")", "social <- to_uniplex(ison_algebra, \"social\")", 
-"tasks <- to_uniplex(ison_algebra, \"tasks\")"), chunk_opts = list(
-    label = "setup", include = FALSE, purl = FALSE, eval = TRUE)), 
-    setup = "", chunks = list(list(label = "data", code = "", 
-        opts = list(label = "\"data\"", exercise = "TRUE", purl = "FALSE"), 
-        engine = "r"), list(label = "construct-binary", code = "", 
-        opts = list(label = "\"construct-binary\"", exercise = "TRUE", 
-            exercise.setup = "\"data\"", purl = "FALSE"), engine = "r")), 
+"tasks <- to_uniplex(ison_algebra, \"tasks\")", "alge <- to_named(ison_algebra)"
+), chunk_opts = list(label = "setup", include = FALSE, purl = FALSE, 
+    eval = TRUE)), setup = "", chunks = list(list(label = "data", 
+    code = "", opts = list(label = "\"data\"", exercise = "TRUE", 
+        purl = "FALSE"), engine = "r"), list(label = "construct-binary", 
+    code = "", opts = list(label = "\"construct-binary\"", exercise = "TRUE", 
+        exercise.setup = "\"data\"", purl = "FALSE"), engine = "r")), 
     code_check = NULL, error_check = NULL, check = NULL, solution = structure(c("# But it's easier to simplify the network by removing the classification into different types of ties.", 
     "# Note that this also reduces the total number of possible paths between nodes", 
     "ison_algebra %>%", "  select_ties(-type) %>%", "  node_x_tie()"
@@ -1603,19 +1605,19 @@ <h2>Glossary</h2>
 "                                      \"Beau travail!\",", "                                      \"Bravo!\",", 
 "                                      \"Super!\"),", "                           encouragement = c(\"Bon effort\"))", 
 "friends <- to_uniplex(ison_algebra, \"friends\")", "social <- to_uniplex(ison_algebra, \"social\")", 
-"tasks <- to_uniplex(ison_algebra, \"tasks\")"), chunk_opts = list(
-    label = "setup", include = FALSE, purl = FALSE, eval = TRUE)), 
-    setup = "", chunks = list(list(label = "data", code = "", 
-        opts = list(label = "\"data\"", exercise = "TRUE", purl = "FALSE"), 
-        engine = "r"), list(label = "varyclust", code = "alge <- to_named(ison_algebra) # fake names to make comparison clearer\nplot(node_in_structural(alge, cluster = \"hier\", distance = \"euclidean\"))\n\n# changing the type of distance used\nplot(node_in_structural(alge, cluster = \"hier\", distance = \"manhattan\"))\n\n# changing the clustering algorithm\nplot(node_in_structural(alge, cluster = \"concor\", distance = \"euclidean\"))", 
-        opts = list(label = "\"varyclust\"", exercise = "TRUE", 
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-        background = "#F7F7F7", strip.white = TRUE, cache = 0, 
-        cache.path = "position_cache/html/", cache.vars = NULL, 
+"tasks <- to_uniplex(ison_algebra, \"tasks\")", "alge <- to_named(ison_algebra)"
+), chunk_opts = list(label = "setup", include = FALSE, purl = FALSE, 
+    eval = TRUE)), setup = "", chunks = list(list(label = "data", 
+    code = "", opts = list(label = "\"data\"", exercise = "TRUE", 
+        purl = "FALSE"), engine = "r"), list(label = "varyclust", 
+    code = "alge <- to_named(ison_algebra) # fake names to make comparison clearer\nplot(node_in_structural(alge, cluster = \"hier\", distance = \"euclidean\"))\n\n# changing the type of distance used\nplot(node_in_structural(alge, cluster = \"hier\", distance = \"manhattan\"))\n\n# changing the clustering algorithm\nplot(node_in_structural(alge, cluster = \"concor\", distance = \"euclidean\"))", 
+    opts = list(label = "\"varyclust\"", exercise = "TRUE", exercise.setup = "\"data\""), 
+    engine = "r")), code_check = NULL, error_check = NULL, check = NULL, 
+    solution = NULL, tests = NULL, options = list(eval = FALSE, 
+        echo = TRUE, results = "markup", tidy = FALSE, tidy.opts = NULL, 
+        collapse = FALSE, prompt = FALSE, comment = NA, highlight = FALSE, 
+        size = "normalsize", background = "#F7F7F7", strip.white = TRUE, 
+        cache = 0, cache.path = "position_cache/html/", cache.vars = NULL, 
         cache.lazy = TRUE, dependson = NULL, autodep = FALSE, 
         cache.rebuild = FALSE, fig.keep = "high", fig.show = "asis", 
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@@ -1642,11 +1644,11 @@ <h2>Glossary</h2>
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-    "character")), answers = list(structure(list(id = "lnr_ans_6736b39", 
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         option = "Yes", value = "Yes", label = structure("Yes", html = TRUE, class = c("html", 
-        "character")), correct = TRUE, message = structure("Smashing!", html = TRUE, class = c("html", 
+        "character")), correct = TRUE, message = structure("Fantastic!", html = TRUE, class = c("html", 
         "character")), type = "literal"), class = c("tutorial_question_answer", 
-    "tutorial_quiz_answer")), structure(list(id = "lnr_ans_7d36710", 
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@@ -1657,7 +1659,7 @@ <h2>Glossary</h2>
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     loading = NULL, random_answer_order = FALSE, allow_retry = TRUE, 
-    seed = 762560801.144905, options = list()), class = c("learnr_radio", 
+    seed = 988924257.539496, options = list()), class = c("learnr_radio", 
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@@ -1691,15 +1693,15 @@ <h2>Glossary</h2>
 "                                      \"Beau travail!\",", "                                      \"Bravo!\",", 
 "                                      \"Super!\"),", "                           encouragement = c(\"Bon effort\"))", 
 "friends <- to_uniplex(ison_algebra, \"friends\")", "social <- to_uniplex(ison_algebra, \"social\")", 
-"tasks <- to_uniplex(ison_algebra, \"tasks\")"), chunk_opts = list(
-    label = "setup", include = FALSE, purl = FALSE, eval = TRUE)), 
-    setup = "\nalge <- to_named(ison_algebra) # fake names to make comparison clearer\nplot(node_in_structural(alge, cluster = \"hier\", distance = \"euclidean\"))\n\n# changing the type of distance used\nplot(node_in_structural(alge, cluster = \"hier\", distance = \"manhattan\"))\n\n# changing the clustering algorithm\nplot(node_in_structural(alge, cluster = \"concor\", distance = \"euclidean\"))", 
+"tasks <- to_uniplex(ison_algebra, \"tasks\")", "alge <- to_named(ison_algebra)"
+), chunk_opts = list(label = "setup", include = FALSE, purl = FALSE, 
+    eval = TRUE)), setup = "\nalge <- to_named(ison_algebra) # fake names to make comparison clearer\nplot(node_in_structural(alge, cluster = \"hier\", distance = \"euclidean\"))\n\n# changing the type of distance used\nplot(node_in_structural(alge, cluster = \"hier\", distance = \"manhattan\"))\n\n# changing the clustering algorithm\nplot(node_in_structural(alge, cluster = \"concor\", distance = \"euclidean\"))", 
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         opts = list(label = "\"varyclust\"", exercise = "TRUE", 
             exercise.setup = "\"data\""), engine = "r"), list(
-        label = "k-discrete", code = "plot(node_in_structural(alge, k = 2))", 
+        label = "k-discrete", code = "plot(node_in_structural(to_named(ison_algebra), k = 2))", 
         opts = list(label = "\"k-discrete\"", exercise = "TRUE", 
             exercise.setup = "\"varyclust\""), engine = "r")), 
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@@ -1720,7 +1722,7 @@ <h2>Glossary</h2>
         message = TRUE, render = NULL, ref.label = NULL, child = NULL, 
         engine = "r", split = FALSE, include = TRUE, purl = TRUE, 
         max.print = 1000, label = "k-discrete", exercise = TRUE, 
-        exercise.setup = "varyclust", code = "plot(node_in_structural(alge, k = 2))", 
+        exercise.setup = "varyclust", code = "plot(node_in_structural(to_named(ison_algebra), k = 2))", 
         out.width.px = 624, out.height.px = 384, params.src = "k-discrete, exercise = TRUE, exercise.setup = \"varyclust\"", 
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     engine = "r", version = "4"), class = c("r", "tutorial_exercise"
@@ -1757,15 +1759,15 @@ <h2>Glossary</h2>
 "                                      \"Beau travail!\",", "                                      \"Bravo!\",", 
 "                                      \"Super!\"),", "                           encouragement = c(\"Bon effort\"))", 
 "friends <- to_uniplex(ison_algebra, \"friends\")", "social <- to_uniplex(ison_algebra, \"social\")", 
-"tasks <- to_uniplex(ison_algebra, \"tasks\")"), chunk_opts = list(
-    label = "setup", include = FALSE, purl = FALSE, eval = TRUE)), 
-    setup = "\nalge <- to_named(ison_algebra) # fake names to make comparison clearer\nplot(node_in_structural(alge, cluster = \"hier\", distance = \"euclidean\"))\n\n# changing the type of distance used\nplot(node_in_structural(alge, cluster = \"hier\", distance = \"manhattan\"))\n\n# changing the clustering algorithm\nplot(node_in_structural(alge, cluster = \"concor\", distance = \"euclidean\"))", 
+"tasks <- to_uniplex(ison_algebra, \"tasks\")", "alge <- to_named(ison_algebra)"
+), chunk_opts = list(label = "setup", include = FALSE, purl = FALSE, 
+    eval = TRUE)), setup = "\nalge <- to_named(ison_algebra) # fake names to make comparison clearer\nplot(node_in_structural(alge, cluster = \"hier\", distance = \"euclidean\"))\n\n# changing the type of distance used\nplot(node_in_structural(alge, cluster = \"hier\", distance = \"manhattan\"))\n\n# changing the clustering algorithm\nplot(node_in_structural(alge, cluster = \"concor\", distance = \"euclidean\"))", 
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         opts = list(label = "\"varyclust\"", exercise = "TRUE", 
             exercise.setup = "\"data\""), engine = "r"), list(
-        label = "elbowsil", code = "plot(node_in_structural(alge, k = \"elbow\"))\nplot(node_in_structural(alge, k = \"silhouette\"))", 
+        label = "elbowsil", code = "plot(node_in_structural(to_named(ison_algebra), k = \"elbow\"))\nplot(node_in_structural(to_named(ison_algebra), k = \"silhouette\"))", 
         opts = list(label = "\"elbowsil\"", exercise = "TRUE", 
             exercise.setup = "\"varyclust\""), engine = "r")), 
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@@ -1786,9 +1788,9 @@ <h2>Glossary</h2>
         message = TRUE, render = NULL, ref.label = NULL, child = NULL, 
         engine = "r", split = FALSE, include = TRUE, purl = TRUE, 
         max.print = 1000, label = "elbowsil", exercise = TRUE, 
-        exercise.setup = "varyclust", code = c("plot(node_in_structural(alge, k = \"elbow\"))", 
-        "plot(node_in_structural(alge, k = \"silhouette\"))"), 
-        out.width.px = 624, out.height.px = 384, params.src = "elbowsil, exercise = TRUE, exercise.setup = \"varyclust\"", 
+        exercise.setup = "varyclust", code = c("plot(node_in_structural(to_named(ison_algebra), k = \"elbow\"))", 
+        "plot(node_in_structural(to_named(ison_algebra), k = \"silhouette\"))"
+        ), out.width.px = 624, out.height.px = 384, params.src = "elbowsil, exercise = TRUE, exercise.setup = \"varyclust\"", 
         fig.num = 0, exercise.df_print = "paged", exercise.checker = "NULL"), 
     engine = "r", version = "4"), class = c("r", "tutorial_exercise"
 )))
@@ -1824,15 +1826,15 @@ <h2>Glossary</h2>
 "                                      \"Beau travail!\",", "                                      \"Bravo!\",", 
 "                                      \"Super!\"),", "                           encouragement = c(\"Bon effort\"))", 
 "friends <- to_uniplex(ison_algebra, \"friends\")", "social <- to_uniplex(ison_algebra, \"social\")", 
-"tasks <- to_uniplex(ison_algebra, \"tasks\")"), chunk_opts = list(
-    label = "setup", include = FALSE, purl = FALSE, eval = TRUE)), 
-    setup = "\nalge <- to_named(ison_algebra) # fake names to make comparison clearer\nplot(node_in_structural(alge, cluster = \"hier\", distance = \"euclidean\"))\n\n# changing the type of distance used\nplot(node_in_structural(alge, cluster = \"hier\", distance = \"manhattan\"))\n\n# changing the clustering algorithm\nplot(node_in_structural(alge, cluster = \"concor\", distance = \"euclidean\"))", 
+"tasks <- to_uniplex(ison_algebra, \"tasks\")", "alge <- to_named(ison_algebra)"
+), chunk_opts = list(label = "setup", include = FALSE, purl = FALSE, 
+    eval = TRUE)), setup = "\nalge <- to_named(ison_algebra) # fake names to make comparison clearer\nplot(node_in_structural(alge, cluster = \"hier\", distance = \"euclidean\"))\n\n# changing the type of distance used\nplot(node_in_structural(alge, cluster = \"hier\", distance = \"manhattan\"))\n\n# changing the clustering algorithm\nplot(node_in_structural(alge, cluster = \"concor\", distance = \"euclidean\"))", 
     chunks = list(list(label = "data", code = "", opts = list(
         label = "\"data\"", exercise = "TRUE", purl = "FALSE"), 
         engine = "r"), list(label = "varyclust", code = "alge <- to_named(ison_algebra) # fake names to make comparison clearer\nplot(node_in_structural(alge, cluster = \"hier\", distance = \"euclidean\"))\n\n# changing the type of distance used\nplot(node_in_structural(alge, cluster = \"hier\", distance = \"manhattan\"))\n\n# changing the clustering algorithm\nplot(node_in_structural(alge, cluster = \"concor\", distance = \"euclidean\"))", 
         opts = list(label = "\"varyclust\"", exercise = "TRUE", 
             exercise.setup = "\"data\""), engine = "r"), list(
-        label = "strict", code = "plot(node_in_structural(alge, k = \"strict\"))", 
+        label = "strict", code = "plot(node_in_structural(to_named(ison_algebra), k = \"strict\"))", 
         opts = list(label = "\"strict\"", exercise = "TRUE", 
             exercise.setup = "\"varyclust\""), engine = "r")), 
     code_check = NULL, error_check = NULL, check = NULL, solution = NULL, 
@@ -1853,7 +1855,7 @@ <h2>Glossary</h2>
         message = TRUE, render = NULL, ref.label = NULL, child = NULL, 
         engine = "r", split = FALSE, include = TRUE, purl = TRUE, 
         max.print = 1000, label = "strict", exercise = TRUE, 
-        exercise.setup = "varyclust", code = "plot(node_in_structural(alge, k = \"strict\"))", 
+        exercise.setup = "varyclust", code = "plot(node_in_structural(to_named(ison_algebra), k = \"strict\"))", 
         out.width.px = 624, out.height.px = 384, params.src = "strict, exercise = TRUE, exercise.setup = \"varyclust\"", 
         fig.num = 0, exercise.df_print = "paged", exercise.checker = "NULL"), 
     engine = "r", version = "4"), class = c("r", "tutorial_exercise"
@@ -1890,15 +1892,15 @@ <h2>Glossary</h2>
 "                                      \"Beau travail!\",", "                                      \"Bravo!\",", 
 "                                      \"Super!\"),", "                           encouragement = c(\"Bon effort\"))", 
 "friends <- to_uniplex(ison_algebra, \"friends\")", "social <- to_uniplex(ison_algebra, \"social\")", 
-"tasks <- to_uniplex(ison_algebra, \"tasks\")"), chunk_opts = list(
-    label = "setup", include = FALSE, purl = FALSE, eval = TRUE)), 
-    setup = "\nalge <- to_named(ison_algebra) # fake names to make comparison clearer\nplot(node_in_structural(alge, cluster = \"hier\", distance = \"euclidean\"))\n\n# changing the type of distance used\nplot(node_in_structural(alge, cluster = \"hier\", distance = \"manhattan\"))\n\n# changing the clustering algorithm\nplot(node_in_structural(alge, cluster = \"concor\", distance = \"euclidean\"))", 
+"tasks <- to_uniplex(ison_algebra, \"tasks\")", "alge <- to_named(ison_algebra)"
+), chunk_opts = list(label = "setup", include = FALSE, purl = FALSE, 
+    eval = TRUE)), setup = "\nalge <- to_named(ison_algebra) # fake names to make comparison clearer\nplot(node_in_structural(alge, cluster = \"hier\", distance = \"euclidean\"))\n\n# changing the type of distance used\nplot(node_in_structural(alge, cluster = \"hier\", distance = \"manhattan\"))\n\n# changing the clustering algorithm\nplot(node_in_structural(alge, cluster = \"concor\", distance = \"euclidean\"))", 
     chunks = list(list(label = "data", code = "", opts = list(
         label = "\"data\"", exercise = "TRUE", purl = "FALSE"), 
         engine = "r"), list(label = "varyclust", code = "alge <- to_named(ison_algebra) # fake names to make comparison clearer\nplot(node_in_structural(alge, cluster = \"hier\", distance = \"euclidean\"))\n\n# changing the type of distance used\nplot(node_in_structural(alge, cluster = \"hier\", distance = \"manhattan\"))\n\n# changing the clustering algorithm\nplot(node_in_structural(alge, cluster = \"concor\", distance = \"euclidean\"))", 
         opts = list(label = "\"varyclust\"", exercise = "TRUE", 
             exercise.setup = "\"data\""), engine = "r"), list(
-        label = "strplot", code = "alge %>% \n  mutate(se = node_in_structural(alge)) %>% \n  graphr(node_color = \"se\")", 
+        label = "strplot", code = "alge <- to_named(ison_algebra)\nalge %>% \n  mutate(se = node_in_structural(alge)) %>% \n  graphr(node_color = \"se\")", 
         opts = list(label = "\"strplot\"", exercise = "TRUE", 
             exercise.setup = "\"varyclust\""), engine = "r")), 
     code_check = NULL, error_check = NULL, check = NULL, solution = NULL, 
@@ -1919,7 +1921,8 @@ <h2>Glossary</h2>
         message = TRUE, render = NULL, ref.label = NULL, child = NULL, 
         engine = "r", split = FALSE, include = TRUE, purl = TRUE, 
         max.print = 1000, label = "strplot", exercise = TRUE, 
-        exercise.setup = "varyclust", code = c("alge %>% ", "  mutate(se = node_in_structural(alge)) %>% ", 
+        exercise.setup = "varyclust", code = c("alge <- to_named(ison_algebra)", 
+        "alge %>% ", "  mutate(se = node_in_structural(alge)) %>% ", 
         "  graphr(node_color = \"se\")"), out.width.px = 624, 
         out.height.px = 384, params.src = "strplot, exercise = TRUE, exercise.setup = \"varyclust\"", 
         fig.num = 0, exercise.df_print = "paged", exercise.checker = "NULL"), 
@@ -1957,15 +1960,15 @@ <h2>Glossary</h2>
 "                                      \"Beau travail!\",", "                                      \"Bravo!\",", 
 "                                      \"Super!\"),", "                           encouragement = c(\"Bon effort\"))", 
 "friends <- to_uniplex(ison_algebra, \"friends\")", "social <- to_uniplex(ison_algebra, \"social\")", 
-"tasks <- to_uniplex(ison_algebra, \"tasks\")"), chunk_opts = list(
-    label = "setup", include = FALSE, purl = FALSE, eval = TRUE)), 
-    setup = "\nalge <- to_named(ison_algebra) # fake names to make comparison clearer\nplot(node_in_structural(alge, cluster = \"hier\", distance = \"euclidean\"))\n\n# changing the type of distance used\nplot(node_in_structural(alge, cluster = \"hier\", distance = \"manhattan\"))\n\n# changing the clustering algorithm\nplot(node_in_structural(alge, cluster = \"concor\", distance = \"euclidean\"))\nalge %>% \n  mutate(se = node_in_structural(alge)) %>% \n  graphr(node_color = \"se\")", 
+"tasks <- to_uniplex(ison_algebra, \"tasks\")", "alge <- to_named(ison_algebra)"
+), chunk_opts = list(label = "setup", include = FALSE, purl = FALSE, 
+    eval = TRUE)), setup = "\nalge <- to_named(ison_algebra) # fake names to make comparison clearer\nplot(node_in_structural(alge, cluster = \"hier\", distance = \"euclidean\"))\n\n# changing the type of distance used\nplot(node_in_structural(alge, cluster = \"hier\", distance = \"manhattan\"))\n\n# changing the clustering algorithm\nplot(node_in_structural(alge, cluster = \"concor\", distance = \"euclidean\"))\nalge <- to_named(ison_algebra)\nalge %>% \n  mutate(se = node_in_structural(alge)) %>% \n  graphr(node_color = \"se\")", 
     chunks = list(list(label = "data", code = "", opts = list(
         label = "\"data\"", exercise = "TRUE", purl = "FALSE"), 
         engine = "r"), list(label = "varyclust", code = "alge <- to_named(ison_algebra) # fake names to make comparison clearer\nplot(node_in_structural(alge, cluster = \"hier\", distance = \"euclidean\"))\n\n# changing the type of distance used\nplot(node_in_structural(alge, cluster = \"hier\", distance = \"manhattan\"))\n\n# changing the clustering algorithm\nplot(node_in_structural(alge, cluster = \"concor\", distance = \"euclidean\"))", 
         opts = list(label = "\"varyclust\"", exercise = "TRUE", 
             exercise.setup = "\"data\""), engine = "r"), list(
-        label = "strplot", code = "alge %>% \n  mutate(se = node_in_structural(alge)) %>% \n  graphr(node_color = \"se\")", 
+        label = "strplot", code = "alge <- to_named(ison_algebra)\nalge %>% \n  mutate(se = node_in_structural(alge)) %>% \n  graphr(node_color = \"se\")", 
         opts = list(label = "\"strplot\"", exercise = "TRUE", 
             exercise.setup = "\"varyclust\""), engine = "r"), 
         list(label = "summ", code = "", opts = list(label = "\"summ\"", 
@@ -2026,15 +2029,15 @@ <h2>Glossary</h2>
 "                                      \"Beau travail!\",", "                                      \"Bravo!\",", 
 "                                      \"Super!\"),", "                           encouragement = c(\"Bon effort\"))", 
 "friends <- to_uniplex(ison_algebra, \"friends\")", "social <- to_uniplex(ison_algebra, \"social\")", 
-"tasks <- to_uniplex(ison_algebra, \"tasks\")"), chunk_opts = list(
-    label = "setup", include = FALSE, purl = FALSE, eval = TRUE)), 
-    setup = "\nalge <- to_named(ison_algebra) # fake names to make comparison clearer\nplot(node_in_structural(alge, cluster = \"hier\", distance = \"euclidean\"))\n\n# changing the type of distance used\nplot(node_in_structural(alge, cluster = \"hier\", distance = \"manhattan\"))\n\n# changing the clustering algorithm\nplot(node_in_structural(alge, cluster = \"concor\", distance = \"euclidean\"))\nalge %>% \n  mutate(se = node_in_structural(alge)) %>% \n  graphr(node_color = \"se\")", 
+"tasks <- to_uniplex(ison_algebra, \"tasks\")", "alge <- to_named(ison_algebra)"
+), chunk_opts = list(label = "setup", include = FALSE, purl = FALSE, 
+    eval = TRUE)), setup = "\nalge <- to_named(ison_algebra) # fake names to make comparison clearer\nplot(node_in_structural(alge, cluster = \"hier\", distance = \"euclidean\"))\n\n# changing the type of distance used\nplot(node_in_structural(alge, cluster = \"hier\", distance = \"manhattan\"))\n\n# changing the clustering algorithm\nplot(node_in_structural(alge, cluster = \"concor\", distance = \"euclidean\"))\nalge <- to_named(ison_algebra)\nalge %>% \n  mutate(se = node_in_structural(alge)) %>% \n  graphr(node_color = \"se\")", 
     chunks = list(list(label = "data", code = "", opts = list(
         label = "\"data\"", exercise = "TRUE", purl = "FALSE"), 
         engine = "r"), list(label = "varyclust", code = "alge <- to_named(ison_algebra) # fake names to make comparison clearer\nplot(node_in_structural(alge, cluster = \"hier\", distance = \"euclidean\"))\n\n# changing the type of distance used\nplot(node_in_structural(alge, cluster = \"hier\", distance = \"manhattan\"))\n\n# changing the clustering algorithm\nplot(node_in_structural(alge, cluster = \"concor\", distance = \"euclidean\"))", 
         opts = list(label = "\"varyclust\"", exercise = "TRUE", 
             exercise.setup = "\"data\""), engine = "r"), list(
-        label = "strplot", code = "alge %>% \n  mutate(se = node_in_structural(alge)) %>% \n  graphr(node_color = \"se\")", 
+        label = "strplot", code = "alge <- to_named(ison_algebra)\nalge %>% \n  mutate(se = node_in_structural(alge)) %>% \n  graphr(node_color = \"se\")", 
         opts = list(label = "\"strplot\"", exercise = "TRUE", 
             exercise.setup = "\"varyclust\""), engine = "r"), 
         list(label = "block", code = "", opts = list(label = "\"block\"", 
@@ -2100,9 +2103,9 @@ <h2>Glossary</h2>
 "                                      \"Beau travail!\",", "                                      \"Bravo!\",", 
 "                                      \"Super!\"),", "                           encouragement = c(\"Bon effort\"))", 
 "friends <- to_uniplex(ison_algebra, \"friends\")", "social <- to_uniplex(ison_algebra, \"social\")", 
-"tasks <- to_uniplex(ison_algebra, \"tasks\")"), chunk_opts = list(
-    label = "setup", include = FALSE, purl = FALSE, eval = TRUE)), 
-    setup = "\nalge <- to_named(ison_algebra) # fake names to make comparison clearer\nplot(node_in_structural(alge, cluster = \"hier\", distance = \"euclidean\"))\n\n# changing the type of distance used\nplot(node_in_structural(alge, cluster = \"hier\", distance = \"manhattan\"))\n\n# changing the clustering algorithm\nplot(node_in_structural(alge, cluster = \"concor\", distance = \"euclidean\"))", 
+"tasks <- to_uniplex(ison_algebra, \"tasks\")", "alge <- to_named(ison_algebra)"
+), chunk_opts = list(label = "setup", include = FALSE, purl = FALSE, 
+    eval = TRUE)), setup = "\nalge <- to_named(ison_algebra) # fake names to make comparison clearer\nplot(node_in_structural(alge, cluster = \"hier\", distance = \"euclidean\"))\n\n# changing the type of distance used\nplot(node_in_structural(alge, cluster = \"hier\", distance = \"manhattan\"))\n\n# changing the clustering algorithm\nplot(node_in_structural(alge, cluster = \"concor\", distance = \"euclidean\"))", 
     chunks = list(list(label = "data", code = "", opts = list(
         label = "\"data\"", exercise = "TRUE", purl = "FALSE"), 
         engine = "r"), list(label = "varyclust", code = "alge <- to_named(ison_algebra) # fake names to make comparison clearer\nplot(node_in_structural(alge, cluster = \"hier\", distance = \"euclidean\"))\n\n# changing the type of distance used\nplot(node_in_structural(alge, cluster = \"hier\", distance = \"manhattan\"))\n\n# changing the clustering algorithm\nplot(node_in_structural(alge, cluster = \"concor\", distance = \"euclidean\"))", 
@@ -2168,19 +2171,19 @@ <h2>Glossary</h2>
 "                                      \"Beau travail!\",", "                                      \"Bravo!\",", 
 "                                      \"Super!\"),", "                           encouragement = c(\"Bon effort\"))", 
 "friends <- to_uniplex(ison_algebra, \"friends\")", "social <- to_uniplex(ison_algebra, \"social\")", 
-"tasks <- to_uniplex(ison_algebra, \"tasks\")"), chunk_opts = list(
-    label = "setup", include = FALSE, purl = FALSE, eval = TRUE)), 
-    setup = NULL, chunks = list(list(label = "freeplay", code = "", 
-        opts = list(label = "\"freeplay\"", exercise = "TRUE"), 
-        engine = "r")), code_check = NULL, error_check = NULL, 
-    check = NULL, solution = NULL, tests = NULL, options = list(
-        eval = FALSE, echo = TRUE, results = "markup", tidy = FALSE, 
-        tidy.opts = NULL, collapse = FALSE, prompt = FALSE, comment = NA, 
-        highlight = FALSE, size = "normalsize", background = "#F7F7F7", 
-        strip.white = TRUE, cache = 0, cache.path = "position_cache/html/", 
-        cache.vars = NULL, cache.lazy = TRUE, dependson = NULL, 
-        autodep = FALSE, cache.rebuild = FALSE, fig.keep = "high", 
-        fig.show = "asis", fig.align = "default", fig.path = "position_files/figure-html/", 
+"tasks <- to_uniplex(ison_algebra, \"tasks\")", "alge <- to_named(ison_algebra)"
+), chunk_opts = list(label = "setup", include = FALSE, purl = FALSE, 
+    eval = TRUE)), setup = NULL, chunks = list(list(label = "freeplay", 
+    code = "", opts = list(label = "\"freeplay\"", exercise = "TRUE"), 
+    engine = "r")), code_check = NULL, error_check = NULL, check = NULL, 
+    solution = NULL, tests = NULL, options = list(eval = FALSE, 
+        echo = TRUE, results = "markup", tidy = FALSE, tidy.opts = NULL, 
+        collapse = FALSE, prompt = FALSE, comment = NA, highlight = FALSE, 
+        size = "normalsize", background = "#F7F7F7", strip.white = TRUE, 
+        cache = 0, cache.path = "position_cache/html/", cache.vars = NULL, 
+        cache.lazy = TRUE, dependson = NULL, autodep = FALSE, 
+        cache.rebuild = FALSE, fig.keep = "high", fig.show = "asis", 
+        fig.align = "default", fig.path = "position_files/figure-html/", 
         dev = "png", dev.args = NULL, dpi = 192, fig.ext = "png", 
         fig.width = 6.5, fig.height = 4, fig.env = "figure", 
         fig.cap = NULL, fig.scap = NULL, fig.lp = "fig:", fig.subcap = NULL, 
@@ -2203,7 +2206,7 @@ <h2>Glossary</h2>
 <!--/html_preserve-->
 <!--html_preserve-->
 <script type="application/shiny-prerendered" data-context="execution_dependencies">
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+{"type":"list","attributes":{"names":{"type":"character","attributes":{},"value":["packages"]}},"value":[{"type":"list","attributes":{"names":{"type":"character","attributes":{},"value":["packages","version"]},"class":{"type":"character","attributes":{},"value":["data.frame"]},"row.names":{"type":"integer","attributes":{},"value":[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84]}},"value":[{"type":"character","attributes":{},"value":["autograph","backports","base","bslib","cachem","checkmate","cli","coda","commonmark","compiler","datasets","digest","dplyr","evaluate","farver","fastmap","fontawesome","generics","ggdendro","ggforce","ggplot2","ggraph","ggrepel","glue","graphics","graphlayouts","grDevices","grid","gridExtra","gtable","htmltools","htmlwidgets","httpuv","igraph","jquerylib","jsonlite","knitr","later","lattice","learnr","lifecycle","litedown","magrittr","manynet","markdown","MASS","memoise","methods","mime","network","otel","patchwork","pillar","pkgconfig","polyclip","promises","purrr","R6","RColorBrewer","Rcpp","rlang","rmarkdown","rprojroot","rstudioapi","S7","sass","scales","shiny","statnet.common","stats","tibble","tidygraph","tidyr","tidyselect","tools","tweenr","utils","vctrs","viridis","viridisLite","withr","xfun","xtable","yaml"]},{"type":"character","attributes":{},"value":["1.0.1","1.5.0","4.5.2","0.10.0","1.1.0","2.3.4","3.6.5","0.19-4.1","2.0.0","4.5.2","4.5.2","0.6.39","1.2.0","1.0.5","2.1.2","1.2.0","0.5.3","0.1.4","0.2.0","0.5.0","4.0.2","2.2.2","0.9.7","1.8.0","4.5.2","1.2.3","4.5.2","4.5.2","2.3","0.3.6","0.5.9","1.6.4","1.6.16","2.2.2","0.1.4","2.0.0","1.51","1.4.8","0.22-9","0.11.6","1.0.5","0.9","2.0.4","2.0.2","2.0","7.3-65","2.0.1","4.5.2","0.13","1.20.0","0.2.0","1.3.2","1.11.1","2.0.3","1.10-7","1.5.0","1.2.1","2.6.1","1.1-3","1.1.1","1.1.7","2.30","2.1.1","0.18.0","0.2.1","0.4.10","1.4.0","1.13.0","4.13.0","4.5.2","3.3.1","1.3.1","1.3.2","1.2.1","4.5.2","2.0.3","4.5.2","0.7.1","0.6.5","0.4.3","3.0.2","0.56","1.8-8","2.3.12"]}]}]}
 </script>
 <!--/html_preserve-->
 </div>

From 5c66b70792ede47963cfb6c5d89d7a118e5a9e5f Mon Sep 17 00:00:00 2001
From: James Hollway <james.hollway@graduateinstitute.ch>
Date: Sat, 25 Apr 2026 15:11:44 +0200
Subject: [PATCH 2/3] #patch bump

---
 DESCRIPTION | 4 ++--
 NEWS.md     | 6 ++++++
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index f36cf78..9748ca1 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: netrics
 Title: Many Ways to Measure and Classify Membership for Networks, Nodes, and Ties
-Version: 0.2.2
-Date: 2026-04-24
+Version: 0.2.3
+Date: 2026-04-25
 Description: Many tools for calculating network, node, or tie
    marks, measures, motifs and memberships of many different types of networks.
    Marks identify structural positions, measures quantify network properties,
diff --git a/NEWS.md b/NEWS.md
index 00a7dc4..55cc3a1 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,9 @@
+# netrics 0.2.3
+
+## Tutorials
+
+- Fixed object reference in position tutorial
+
 # netrics 0.2.2
 
 ## Package

From 5f1542a6449e5ce8989dd502ded13c63a60eb6da Mon Sep 17 00:00:00 2001
From: James Hollway <james.hollway@graduateinstitute.ch>
Date: Sat, 25 Apr 2026 15:13:52 +0200
Subject: [PATCH 3/3] Updated cran comments

---
 cran-comments.md | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/cran-comments.md b/cran-comments.md
index b55f507..064df7a 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -9,6 +9,4 @@
 
 0 errors | 0 warnings | 0 notes
 
-- While last package submission was only 9 days ago:
-  - Updates to bring netrics into line with latest version of manynet (> v2.0.0)
-  - Fixes a reverse dependency issue in cross-package documentation referencing
+- Fixed reverse dependency issue