From eeda1cc53e8e74448f48277c120a477aba497020 Mon Sep 17 00:00:00 2001
From: GitHub Actions <actions@github.com>
Date: Tue, 1 Oct 2024 00:27:34 +0000
Subject: [PATCH] site deploy

Auto-generated via {sandpaper}
Source  : c99afe3a88da8407daf2a78ea5eec03d1d2a67e6
Branch  : md-outputs
Author  : GitHub Actions <actions@github.com>
Time    : 2024-09-24 00:24:32 +0000
Message : markdown source builds

Auto-generated via {sandpaper}
Source  : 626ca5d063735e2147837d90cffa96f3bc9ac2ea
Branch  : main
Author  : Naupaka Zimmerman <naupaka@gmail.com>
Time    : 2024-09-20 22:07:11 +0000
Message : Merge pull request #277 from datacarpentry/update/workflows

Update Workflows to Version 0.16.5
---
 00-introduction.html                         |  8 +++---
 01-r-basics.html                             |  2 +-
 02-data-prelude.html                         |  2 +-
 03-basics-factors-dataframes.html            | 12 ++++-----
 04-bioconductor-vcfr.html                    |  2 +-
 05-dplyr.html                                |  2 +-
 06-data-visualization.html                   | 10 +++----
 07-r-help.html                               |  2 +-
 404.html                                     |  4 +--
 CODE_OF_CONDUCT.html                         |  2 +-
 LICENSE.html                                 |  2 +-
 aio.html                                     | 28 ++++++++++----------
 discuss.html                                 |  2 +-
 images.html                                  |  4 +--
 index.html                                   | 10 +++----
 instructor-notes.html                        |  4 +--
 instructor/00-introduction.html              |  8 +++---
 instructor/01-r-basics.html                  |  2 +-
 instructor/02-data-prelude.html              |  2 +-
 instructor/03-basics-factors-dataframes.html | 12 ++++-----
 instructor/04-bioconductor-vcfr.html         |  2 +-
 instructor/05-dplyr.html                     |  2 +-
 instructor/06-data-visualization.html        | 10 +++----
 instructor/07-r-help.html                    |  2 +-
 instructor/404.html                          |  4 +--
 instructor/CODE_OF_CONDUCT.html              |  2 +-
 instructor/LICENSE.html                      |  2 +-
 instructor/aio.html                          | 28 ++++++++++----------
 instructor/discuss.html                      |  2 +-
 instructor/images.html                       |  4 +--
 instructor/index.html                        | 10 +++----
 instructor/instructor-notes.html             |  4 +--
 instructor/key-points.html                   |  4 +--
 instructor/profiles.html                     |  4 +--
 instructor/reference.html                    |  2 +-
 key-points.html                              |  4 +--
 pkgdown.yml                                  |  2 +-
 profiles.html                                |  4 +--
 reference.html                               |  2 +-
 39 files changed, 107 insertions(+), 107 deletions(-)

diff --git a/00-introduction.html b/00-introduction.html
index 1a599388..a66faada 100644
--- a/00-introduction.html
+++ b/00-introduction.html
@@ -704,7 +704,7 @@ <h3 class="callout-title">Exercise: Work interactively in R</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>You will get the same output you did as when you ran
 <code>getwd()</code> from the source. You can run any command in the
@@ -796,7 +796,7 @@ <h3 class="callout-title">Exercise: What do these functions do?</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <ul><li>
 <code>dir()</code> # Lists files in the working directory</li>
@@ -941,7 +941,7 @@ <h3 class="callout-title">Exercise: Searching for R functions</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <p>While your search results may return several tests, we list a few you
 might find:</p>
@@ -1043,7 +1043,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/00-introduction.html",
   "dateCreated": "2018-03-12",
   "dateModified": "2024-09-20",
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diff --git a/01-r-basics.html b/01-r-basics.html
index 80cac366..4f520def 100644
--- a/01-r-basics.html
+++ b/01-r-basics.html
@@ -1825,7 +1825,7 @@ <h3 class="callout-title">Key Points</h3>
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diff --git a/02-data-prelude.html b/02-data-prelude.html
index 2da8cd80..71ddbd9d 100644
--- a/02-data-prelude.html
+++ b/02-data-prelude.html
@@ -654,7 +654,7 @@ <h3 class="callout-title">Key Points</h3>
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   "dateCreated": "2018-03-12",
   "dateModified": "2024-09-20",
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diff --git a/03-basics-factors-dataframes.html b/03-basics-factors-dataframes.html
index bd6dfab9..b00ec8c3 100644
--- a/03-basics-factors-dataframes.html
+++ b/03-basics-factors-dataframes.html
@@ -491,7 +491,7 @@ <h3 class="callout-title">Exercise: Review the arguments of the
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <ol style="list-style-type: upper-alpha"><li><p>The <code>read.csv()</code> function has the argument ‘header’
 set to TRUE by default, this means the function always assumes the first
@@ -699,7 +699,7 @@ <h3 class="callout-title">Exercise: Revisiting modes and classess</h3>
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 </button>
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@@ -1005,7 +1005,7 @@ <h3 class="callout-title">Exercise: Subsetting a data frame</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
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   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
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@@ -1836,7 +1836,7 @@ <h3 class="callout-title">Exercise: Putting it all together - data frames</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
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 <div class="codewrapper sourceCode" id="cb91">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1987,7 +1987,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/03-basics-factors-dataframes.html",
   "dateCreated": "2018-03-12",
   "dateModified": "2024-09-20",
-  "datePublished": "2024-09-24"
+  "datePublished": "2024-10-01"
 }
 
   </script><script>
diff --git a/04-bioconductor-vcfr.html b/04-bioconductor-vcfr.html
index b431b732..976a9c63 100644
--- a/04-bioconductor-vcfr.html
+++ b/04-bioconductor-vcfr.html
@@ -619,7 +619,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/04-bioconductor-vcfr.html",
   "dateCreated": "2018-03-12",
   "dateModified": "2024-09-20",
-  "datePublished": "2024-09-24"
+  "datePublished": "2024-10-01"
 }
 
   </script><script>
diff --git a/05-dplyr.html b/05-dplyr.html
index b70135f9..652e039b 100644
--- a/05-dplyr.html
+++ b/05-dplyr.html
@@ -1587,7 +1587,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/05-dplyr.html",
   "dateCreated": "2018-03-12",
   "dateModified": "2024-09-20",
-  "datePublished": "2024-09-24"
+  "datePublished": "2024-10-01"
 }
 
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diff --git a/06-data-visualization.html b/06-data-visualization.html
index 69f3084d..d89d705b 100644
--- a/06-data-visualization.html
+++ b/06-data-visualization.html
@@ -953,7 +953,7 @@ <h3 class="callout-title">Challenge</h3>
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   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
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 <div class="codewrapper sourceCode" id="cb25">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1048,7 +1048,7 @@ <h3 class="callout-title">Challenge</h3>
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 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
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-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
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@@ -1140,7 +1140,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
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@@ -1288,7 +1288,7 @@ <h3 class="callout-title">Key Points</h3>
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   "dateCreated": "2018-03-12",
   "dateModified": "2024-09-20",
-  "datePublished": "2024-09-24"
+  "datePublished": "2024-10-01"
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diff --git a/07-r-help.html b/07-r-help.html
index 24e68695..8b1b97ca 100644
--- a/07-r-help.html
+++ b/07-r-help.html
@@ -600,7 +600,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/07-r-help.html",
   "dateCreated": "2018-03-12",
   "dateModified": "2024-09-20",
-  "datePublished": "2024-09-24"
+  "datePublished": "2024-10-01"
 }
 
   </script><script>
diff --git a/404.html b/404.html
index 643ea6b2..e3552de2 100644
--- a/404.html
+++ b/404.html
@@ -396,8 +396,8 @@ <h1>Page not found</h1>
   "url": "https://datacarpentry.github.io/genomics-r-intro/404.html",
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/404.html",
   "dateCreated": "2018-03-12",
-  "dateModified": "2024-09-24",
-  "datePublished": "2024-09-24"
+  "dateModified": "2024-10-01",
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 }
 
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diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index 11abb247..fc14a0bd 100644
--- a/CODE_OF_CONDUCT.html
+++ b/CODE_OF_CONDUCT.html
@@ -413,7 +413,7 @@ <h1>Contributor Code of Conduct</h1>
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   "dateCreated": "2018-03-12",
   "dateModified": "2024-09-20",
-  "datePublished": "2024-09-24"
+  "datePublished": "2024-10-01"
 }
 
   </script><script>
diff --git a/LICENSE.html b/LICENSE.html
index ce86ac75..8859db97 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -461,7 +461,7 @@ <h1>Licenses</h1>
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/LICENSE.html",
   "dateCreated": "2018-03-12",
   "dateModified": "2024-09-20",
-  "datePublished": "2024-09-24"
+  "datePublished": "2024-10-01"
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diff --git a/aio.html b/aio.html
index 44fdc51d..9a457450 100644
--- a/aio.html
+++ b/aio.html
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 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>You will get the same output you did as when you ran
 <code>getwd()</code> from the source. You can run any command in the
@@ -865,7 +865,7 @@ <h3 class="callout-title">Exercise: What do these functions do?</h3>
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   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
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@@ -1018,7 +1018,7 @@ <h3 class="callout-title">Exercise: Searching for R functions</h3>
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   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
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 <div class="accordion-body">
 <p>While your search results may return several tests, we list a few you
 might find:</p>
@@ -3094,7 +3094,7 @@ <h3 class="callout-title">Exercise: Review the arguments of the
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   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
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-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
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 <div class="accordion-body">
 <ol style="list-style-type: upper-alpha">
 <li><p>The <code>read.csv()</code> function has the argument ‘header’
@@ -3309,7 +3309,7 @@ <h3 class="callout-title">Exercise: Revisiting modes and classess</h3>
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   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
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 <div class="codewrapper sourceCode" id="cb7">
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@@ -3625,7 +3625,7 @@ <h3 class="callout-title">Exercise: Subsetting a data frame</h3>
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   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <ol style="list-style-type: lower-alpha"><li>
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@@ -4332,7 +4332,7 @@ <h3 class="callout-title">Exercise</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
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 <div class="codewrapper sourceCode" id="cb84">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -4484,7 +4484,7 @@ <h3 class="callout-title">Exercise: Putting it all together - data frames</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
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