Skip to content

Fix 2 interactive compartmental diagrams #7

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
arnold-c merged 2 commits into from
Jul 6, 2026
Merged

Fix 2 interactive compartmental diagrams #7

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
2bd85d2
diagram: update links to r session 2 and code-fold diagram chunks
arnold-c Jul 6, 2026
08b199f
Merge branch 'main' into fix-2-interactive-compartmental-diagrams
arnold-c Jul 6, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
801 changes: 452 additions & 349 deletions _book/day-1-interactive-session.html
View file
Open in desktop

Large diffs are not rendered by default.

114 changes: 57 additions & 57 deletions _book/r-session-02.html
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1193,7 +1193,7 @@
<span id="cb27-11"><a href="#cb27-11"></a> <span class="at">z =</span> Freq</span>
<span id="cb27-12"><a href="#cb27-12"></a> )) <span class="sc">+</span></span>
<span id="cb27-13"><a href="#cb27-13"></a> <span class="fu">geom_tile</span>(<span class="at">colour =</span> <span class="st">"grey"</span>, <span class="at">size =</span> <span class="fl">0.4</span>, <span class="fu">aes</span>(<span class="at">fill =</span> Freq)) <span class="sc">+</span></span>
<span id="cb27-14"><a href="#cb27-14"></a><span class="fu">scale_fill_gradientn</span>(</span>
<span id="cb27-14"><a href="#cb27-14"></a> <span class="fu">scale_fill_gradientn</span>(</span>
<span id="cb27-15"><a href="#cb27-15"></a> <span class="at">colours =</span> <span class="fu">c</span>(<span class="st">"red"</span>, <span class="st">"white"</span>, <span class="st">"blue"</span>),</span>
<span id="cb27-16"><a href="#cb27-16"></a> <span class="at">breaks =</span> <span class="fu">c</span>(<span class="sc">-</span><span class="dv">1</span>, <span class="sc">-</span><span class="fl">0.2</span>, <span class="dv">0</span>, <span class="fl">0.2</span>, <span class="dv">1</span>),</span>
<span id="cb27-17"><a href="#cb27-17"></a> <span class="at">labels =</span> <span class="fu">c</span>(<span class="st">"-1"</span>, <span class="st">"-0.2"</span>, <span class="st">"0"</span>, <span class="st">"0.2"</span>, <span class="st">"1"</span>)</span>
Expand Down Expand Up @@ -2331,23 +2331,23 @@
<span id="cb72-17"><a href="#cb72-17"></a> <span class="fu">opt_horizontal_padding</span>(<span class="at">scale =</span> <span class="dv">3</span>) <span class="sc">%&gt;%</span></span>
<span id="cb72-18"><a href="#cb72-18"></a> <span class="fu">cols_align</span>(<span class="st">"center"</span>)</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
</details><div class="cell-output-display column-body">
<div id="agcadredgr" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
<style>#agcadredgr table {
<div id="lzxtlifxad" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
<style>#lzxtlifxad table {
font-family: system-ui, 'Segoe UI', Roboto, Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol', 'Noto Color Emoji';
-webkit-font-smoothing: antialiased;
-moz-osx-font-smoothing: grayscale;
}

#agcadredgr thead, #agcadredgr tbody, #agcadredgr tfoot, #agcadredgr tr, #agcadredgr td, #agcadredgr th {
#lzxtlifxad thead, #lzxtlifxad tbody, #lzxtlifxad tfoot, #lzxtlifxad tr, #lzxtlifxad td, #lzxtlifxad th {
border-style: none;
}

#agcadredgr p {
#lzxtlifxad p {
margin: 0;
padding: 0;
}

#agcadredgr .gt_table {
#lzxtlifxad .gt_table {
display: table;
border-collapse: collapse;
line-height: normal;
Expand All @@ -2373,12 +2373,12 @@
border-left-color: #D3D3D3;
}

#agcadredgr .gt_caption {
#lzxtlifxad .gt_caption {
padding-top: 4px;
padding-bottom: 4px;
}

#agcadredgr .gt_title {
#lzxtlifxad .gt_title {
color: #333333;
font-size: 125%;
font-weight: initial;
Expand All @@ -2390,7 +2390,7 @@
border-bottom-width: 0;
}

#agcadredgr .gt_subtitle {
#lzxtlifxad .gt_subtitle {
color: #333333;
font-size: 85%;
font-weight: initial;
Expand All @@ -2402,7 +2402,7 @@
border-top-width: 0;
}

#agcadredgr .gt_heading {
#lzxtlifxad .gt_heading {
background-color: #FFFFFF;
text-align: center;
border-bottom-color: #FFFFFF;
Expand All @@ -2414,13 +2414,13 @@
border-right-color: #D3D3D3;
}

#agcadredgr .gt_bottom_border {
#lzxtlifxad .gt_bottom_border {
border-bottom-style: solid;
border-bottom-width: 2px;
border-bottom-color: #5F5F5F;
}

#agcadredgr .gt_col_headings {
#lzxtlifxad .gt_col_headings {
border-top-style: solid;
border-top-width: 2px;
border-top-color: #5F5F5F;
Expand All @@ -2435,7 +2435,7 @@
border-right-color: #D3D3D3;
}

#agcadredgr .gt_col_heading {
#lzxtlifxad .gt_col_heading {
color: #333333;
background-color: #FFFFFF;
font-size: 100%;
Expand All @@ -2455,7 +2455,7 @@
overflow-x: hidden;
}

#agcadredgr .gt_column_spanner_outer {
#lzxtlifxad .gt_column_spanner_outer {
color: #333333;
background-color: #FFFFFF;
font-size: 100%;
Expand All @@ -2467,15 +2467,15 @@
padding-right: 4px;
}

#agcadredgr .gt_column_spanner_outer:first-child {
#lzxtlifxad .gt_column_spanner_outer:first-child {
padding-left: 0;
}

#agcadredgr .gt_column_spanner_outer:last-child {
#lzxtlifxad .gt_column_spanner_outer:last-child {
padding-right: 0;
}

#agcadredgr .gt_column_spanner {
#lzxtlifxad .gt_column_spanner {
border-bottom-style: solid;
border-bottom-width: 2px;
border-bottom-color: #5F5F5F;
Expand All @@ -2487,11 +2487,11 @@
width: 100%;
}

#agcadredgr .gt_spanner_row {
#lzxtlifxad .gt_spanner_row {
border-bottom-style: hidden;
}

#agcadredgr .gt_group_heading {
#lzxtlifxad .gt_group_heading {
padding-top: 8px;
padding-bottom: 8px;
padding-left: 15px;
Expand All @@ -2517,7 +2517,7 @@
text-align: left;
}

#agcadredgr .gt_empty_group_heading {
#lzxtlifxad .gt_empty_group_heading {
padding: 0.5px;
color: #333333;
background-color: #FFFFFF;
Expand All @@ -2532,15 +2532,15 @@
vertical-align: middle;
}

#agcadredgr .gt_from_md > :first-child {
#lzxtlifxad .gt_from_md > :first-child {
margin-top: 0;
}

#agcadredgr .gt_from_md > :last-child {
#lzxtlifxad .gt_from_md > :last-child {
margin-bottom: 0;
}

#agcadredgr .gt_row {
#lzxtlifxad .gt_row {
padding-top: 8px;
padding-bottom: 8px;
padding-left: 15px;
Expand All @@ -2559,7 +2559,7 @@
overflow-x: hidden;
}

#agcadredgr .gt_stub {
#lzxtlifxad .gt_stub {
color: #FFFFFF;
background-color: #5F5F5F;
font-size: 100%;
Expand All @@ -2572,7 +2572,7 @@
padding-right: 15px;
}

#agcadredgr .gt_stub_row_group {
#lzxtlifxad .gt_stub_row_group {
color: #333333;
background-color: #FFFFFF;
font-size: 100%;
Expand All @@ -2586,15 +2586,15 @@
vertical-align: top;
}

#agcadredgr .gt_row_group_first td {
#lzxtlifxad .gt_row_group_first td {
border-top-width: 2px;
}

#agcadredgr .gt_row_group_first th {
#lzxtlifxad .gt_row_group_first th {
border-top-width: 2px;
}

#agcadredgr .gt_summary_row {
#lzxtlifxad .gt_summary_row {
color: #333333;
background-color: #FFFFFF;
text-transform: inherit;
Expand All @@ -2604,16 +2604,16 @@
padding-right: 15px;
}

#agcadredgr .gt_first_summary_row {
#lzxtlifxad .gt_first_summary_row {
border-top-style: solid;
border-top-color: #5F5F5F;
}

#agcadredgr .gt_first_summary_row.thick {
#lzxtlifxad .gt_first_summary_row.thick {
border-top-width: 2px;
}

#agcadredgr .gt_last_summary_row {
#lzxtlifxad .gt_last_summary_row {
padding-top: 8px;
padding-bottom: 8px;
padding-left: 15px;
Expand All @@ -2623,7 +2623,7 @@
border-bottom-color: #5F5F5F;
}

#agcadredgr .gt_grand_summary_row {
#lzxtlifxad .gt_grand_summary_row {
color: #333333;
background-color: #D5D5D5;
text-transform: inherit;
Expand All @@ -2633,7 +2633,7 @@
padding-right: 15px;
}

#agcadredgr .gt_first_grand_summary_row {
#lzxtlifxad .gt_first_grand_summary_row {
padding-top: 8px;
padding-bottom: 8px;
padding-left: 15px;
Expand All @@ -2643,7 +2643,7 @@
border-top-color: #5F5F5F;
}

#agcadredgr .gt_last_grand_summary_row_top {
#lzxtlifxad .gt_last_grand_summary_row_top {
padding-top: 8px;
padding-bottom: 8px;
padding-left: 15px;
Expand All @@ -2653,11 +2653,11 @@
border-bottom-color: #5F5F5F;
}

#agcadredgr .gt_striped {
#lzxtlifxad .gt_striped {
background-color: #F4F4F4;
}

#agcadredgr .gt_table_body {
#lzxtlifxad .gt_table_body {
border-top-style: solid;
border-top-width: 2px;
border-top-color: #5F5F5F;
Expand All @@ -2666,7 +2666,7 @@
border-bottom-color: #5F5F5F;
}

#agcadredgr .gt_footnotes {
#lzxtlifxad .gt_footnotes {
color: #333333;
background-color: #FFFFFF;
border-bottom-style: none;
Expand All @@ -2680,7 +2680,7 @@
border-right-color: #D3D3D3;
}

#agcadredgr .gt_footnote {
#lzxtlifxad .gt_footnote {
margin: 0px;
font-size: 90%;
padding-top: 4px;
Expand All @@ -2689,7 +2689,7 @@
padding-right: 15px;
}

#agcadredgr .gt_sourcenotes {
#lzxtlifxad .gt_sourcenotes {
color: #333333;
background-color: #FFFFFF;
border-bottom-style: none;
Expand All @@ -2703,80 +2703,80 @@
border-right-color: #D3D3D3;
}

#agcadredgr .gt_sourcenote {
#lzxtlifxad .gt_sourcenote {
font-size: 90%;
padding-top: 4px;
padding-bottom: 4px;
padding-left: 15px;
padding-right: 15px;
}

#agcadredgr .gt_left {
#lzxtlifxad .gt_left {
text-align: left;
}

#agcadredgr .gt_center {
#lzxtlifxad .gt_center {
text-align: center;
}

#agcadredgr .gt_right {
#lzxtlifxad .gt_right {
text-align: right;
font-variant-numeric: tabular-nums;
}

#agcadredgr .gt_font_normal {
#lzxtlifxad .gt_font_normal {
font-weight: normal;
}

#agcadredgr .gt_font_bold {
#lzxtlifxad .gt_font_bold {
font-weight: bold;
}

#agcadredgr .gt_font_italic {
#lzxtlifxad .gt_font_italic {
font-style: italic;
}

#agcadredgr .gt_super {
#lzxtlifxad .gt_super {
font-size: 65%;
}

#agcadredgr .gt_footnote_marks {
#lzxtlifxad .gt_footnote_marks {
font-size: 75%;
vertical-align: 0.4em;
position: initial;
}

#agcadredgr .gt_asterisk {
#lzxtlifxad .gt_asterisk {
font-size: 100%;
vertical-align: 0;
}

#agcadredgr .gt_indent_1 {
#lzxtlifxad .gt_indent_1 {
text-indent: 5px;
}

#agcadredgr .gt_indent_2 {
#lzxtlifxad .gt_indent_2 {
text-indent: 10px;
}

#agcadredgr .gt_indent_3 {
#lzxtlifxad .gt_indent_3 {
text-indent: 15px;
}

#agcadredgr .gt_indent_4 {
#lzxtlifxad .gt_indent_4 {
text-indent: 20px;
}

#agcadredgr .gt_indent_5 {
#lzxtlifxad .gt_indent_5 {
text-indent: 25px;
}

#agcadredgr .katex-display {
#lzxtlifxad .katex-display {
display: inline-flex !important;
margin-bottom: 0.75em !important;
}

#agcadredgr div.Reactable > div.rt-table > div.rt-thead > div.rt-tr.rt-tr-group-header > div.rt-th-group:after {
#lzxtlifxad div.Reactable > div.rt-table > div.rt-thead > div.rt-tr.rt-tr-group-header > div.rt-th-group:after {
height: 0px !important;
}
</style>
Expand Down Expand Up @@ -4508,7 +4508,7 @@
<span id="cb88-894"><a href="#cb88-894"></a> <span class="at">z =</span> Freq</span>
<span id="cb88-895"><a href="#cb88-895"></a> )) <span class="sc">+</span></span>
<span id="cb88-896"><a href="#cb88-896"></a> <span class="fu">geom_tile</span>(<span class="at">colour =</span> <span class="st">"grey"</span>, <span class="at">size =</span> <span class="fl">0.4</span>, <span class="fu">aes</span>(<span class="at">fill =</span> Freq)) <span class="sc">+</span></span>
<span id="cb88-897"><a href="#cb88-897"></a><span class="fu">scale_fill_gradientn</span>(</span>
<span id="cb88-897"><a href="#cb88-897"></a> <span class="fu">scale_fill_gradientn</span>(</span>
<span id="cb88-898"><a href="#cb88-898"></a> <span class="at">colours =</span> <span class="fu">c</span>(<span class="st">"red"</span>, <span class="st">"white"</span>, <span class="st">"blue"</span>),</span>
<span id="cb88-899"><a href="#cb88-899"></a> <span class="at">breaks =</span> <span class="fu">c</span>(<span class="sc">-</span><span class="dv">1</span>, <span class="sc">-</span><span class="fl">0.2</span>, <span class="dv">0</span>, <span class="fl">0.2</span>, <span class="dv">1</span>),</span>
<span id="cb88-900"><a href="#cb88-900"></a> <span class="at">labels =</span> <span class="fu">c</span>(<span class="st">"-1"</span>, <span class="st">"-0.2"</span>, <span class="st">"0"</span>, <span class="st">"0.2"</span>, <span class="st">"1"</span>)</span>
Expand Down
Binary file modified _book/r-session-02_files/figure-html/unnamed-chunk-10-1.png
View file
Open in desktop
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified _book/r-session-02_files/figure-html/unnamed-chunk-11-1.png
View file
Open in desktop
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified _book/r-session-02_files/figure-html/unnamed-chunk-15-1.png
View file
Open in desktop
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified _book/r-session-02_files/figure-html/unnamed-chunk-17-1.png
View file
Open in desktop
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified _book/r-session-02_files/figure-html/unnamed-chunk-19-1.png
View file
Open in desktop
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified _book/r-session-02_files/figure-html/unnamed-chunk-22-1.png
View file
Open in desktop
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified _book/r-session-02_files/figure-html/unnamed-chunk-29-1.png
View file
Open in desktop
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified _book/r-session-02_files/figure-html/unnamed-chunk-3-1.png
View file
Open in desktop
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified _book/r-session-02_files/figure-html/unnamed-chunk-33-1.png
View file
Open in desktop
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified _book/r-session-02_files/figure-html/unnamed-chunk-35-1.png
View file
Open in desktop
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified _book/r-session-02_files/figure-html/unnamed-chunk-62-1.png
View file
Open in desktop
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified _book/r-session-02_files/figure-html/unnamed-chunk-68-1.png
View file
Open in desktop
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified _book/r-session-02_files/figure-html/unnamed-chunk-71-1.png
View file
Open in desktop
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified _book/r-session-02_files/figure-html/unnamed-chunk-72-1.png
View file
Open in desktop
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified _book/r-session-02_files/figure-html/unnamed-chunk-74-1.png
View file
Open in desktop
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified _book/r-session-02_files/figure-html/unnamed-chunk-76-1.png
View file
Open in desktop
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified _book/r-session-02_files/figure-html/unnamed-chunk-78-1.png
View file
Open in desktop
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified _book/r-session-02_files/figure-html/unnamed-chunk-8-1.png
View file
Open in desktop
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified _book/r-session-02_files/figure-html/unnamed-chunk-80-1.png
View file
Open in desktop
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Loading