really add tidysdm05...

BigelowLab · Nov 5, 2024 · 0b2871f · 0b2871f
1 parent 9c7b454
commit 0b2871f
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Showing 34 changed files with 1,049 additions and 205 deletions.
diff --git a/_quarto.yml b/_quarto.yml
@@ -15,6 +15,7 @@ project:
     - tidysdm-02-thinning.qmd
     - tidysdm-03-background.qmd
     - tidysdm-04-modeling.qmd
+    - tidysdm-05-prediction.qmd
     - about.qmd
 execute: 
   cache: false
@@ -45,6 +46,7 @@ website:
           - tidysdm-02-thinning.qmd
           - tidysdm-03-background.qmd
           - tidysdm-04-modeling.qmd
+          - tidysdm-05-prediction.qmd
       - text: About
         href: about.qmd
     tools:

diff --git a/data/bkg/bkg-covariates.gpkg b/data/bkg/bkg-covariates.gpkg
diff --git a/data/bkg/buffered-polygon.gpkg b/data/bkg/buffered-polygon.gpkg
diff --git a/data/obs/model_input.gpkg b/data/obs/model_input.gpkg
diff --git a/data/obs/obs-covariates.gpkg b/data/obs/obs-covariates.gpkg
diff --git a/data/obs/thinned_obs.gpkg b/data/obs/thinned_obs.gpkg
diff --git a/docs/about.html b/docs/about.html
@@ -30,7 +30,7 @@
 <script src="site_libs/quarto-search/fuse.min.js"></script>
 <script src="site_libs/quarto-search/quarto-search.js"></script>
 <meta name="quarto:offset" content="./">
-<link href="./tidysdm-04-modeling.html" rel="prev">
+<link href="./tidysdm-05-prediction.html" rel="prev">
 <script src="site_libs/quarto-html/quarto.js"></script>
 <script src="site_libs/quarto-html/popper.min.js"></script>
 <script src="site_libs/quarto-html/tippy.umd.min.js"></script>
@@ -202,6 +202,12 @@
   <a href="./tidysdm-04-modeling.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Modeling</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./tidysdm-05-prediction.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">tidysdm-05-prediction</span></a>
+  </div>
 </li>
       </ul>
   </li>
@@ -635,8 +641,8 @@ <h1 class="title">About</h1>
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="./tidysdm-04-modeling.html" class="pagination-link  aria-label=" modeling"="">
-        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">Modeling</span>
+      <a href="./tidysdm-05-prediction.html" class="pagination-link  aria-label=" tidysdm-05-prediction"="">
+        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">tidysdm-05-prediction</span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">

diff --git a/docs/index.html b/docs/index.html
@@ -236,6 +236,12 @@
   <a href="./tidysdm-04-modeling.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Modeling</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./tidysdm-05-prediction.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">tidysdm-05-prediction</span></a>
+  </div>
 </li>
       </ul>
   </li>
@@ -399,6 +405,7 @@ <h3 data-number="3.4" class="anchored" data-anchor-id="data-storage"><span class
 <pre><code>data
 ├── bkg
 │   ├── bkg-covariates.gpkg
+│   ├── bkg-covariates.gpkg-journal
 │   ├── buffered-polygon.gpkg
 │   └── obs-covariates.gpkg
 ├── mask

diff --git a/docs/search.json b/docs/search.json
diff --git a/docs/tidysdm-01.html b/docs/tidysdm-01.html
@@ -203,6 +203,12 @@
   <a href="./tidysdm-04-modeling.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Modeling</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./tidysdm-05-prediction.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">tidysdm-05-prediction</span></a>
+  </div>
 </li>
       </ul>
   </li>

diff --git a/docs/tidysdm-02-thinning.html b/docs/tidysdm-02-thinning.html
@@ -237,6 +237,12 @@
   <a href="./tidysdm-04-modeling.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Modeling</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./tidysdm-05-prediction.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">tidysdm-05-prediction</span></a>
+  </div>
 </li>
       </ul>
   </li>

diff --git a/docs/tidysdm-03-background.html b/docs/tidysdm-03-background.html
@@ -237,6 +237,12 @@
   <a href="./tidysdm-04-modeling.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Modeling</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./tidysdm-05-prediction.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">tidysdm-05-prediction</span></a>
+  </div>
 </li>
       </ul>
   </li>

diff --git a/docs/tidysdm-04-modeling.html b/docs/tidysdm-04-modeling.html
@@ -64,7 +64,7 @@
 <script src="site_libs/quarto-search/fuse.min.js"></script>
 <script src="site_libs/quarto-search/quarto-search.js"></script>
 <meta name="quarto:offset" content="./">
-<link href="./about.html" rel="next">
+<link href="./tidysdm-05-prediction.html" rel="next">
 <link href="./tidysdm-03-background.html" rel="prev">
 <script src="site_libs/quarto-html/quarto.js"></script>
 <script src="site_libs/quarto-html/popper.min.js"></script>
@@ -237,6 +237,12 @@
   <a href="./tidysdm-04-modeling.html" class="sidebar-item-text sidebar-link active">
  <span class="menu-text">Modeling</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./tidysdm-05-prediction.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">tidysdm-05-prediction</span></a>
+  </div>
 </li>
       </ul>
   </li>
@@ -394,7 +400,7 @@ <h1 data-number="4"><span class="header-section-number">4</span> Tuning</h1>
 <pre><code>i 1 of 4 resampling: default_glm</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>✔ 1 of 4 resampling: default_glm (305ms)</code></pre>
+<pre><code>✔ 1 of 4 resampling: default_glm (365ms)</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
 <pre><code>i 2 of 4 tuning:     default_rf</code></pre>
@@ -403,7 +409,7 @@ <h1 data-number="4"><span class="header-section-number">4</span> Tuning</h1>
 <pre><code>i Creating pre-processing data to finalize unknown parameter: mtry</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>✔ 2 of 4 tuning:     default_rf (2.2s)</code></pre>
+<pre><code>✔ 2 of 4 tuning:     default_rf (2.4s)</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
 <pre><code>i 3 of 4 tuning:     default_gbm</code></pre>
@@ -412,13 +418,13 @@ <h1 data-number="4"><span class="header-section-number">4</span> Tuning</h1>
 <pre><code>i Creating pre-processing data to finalize unknown parameter: mtry</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>✔ 3 of 4 tuning:     default_gbm (6s)</code></pre>
+<pre><code>✔ 3 of 4 tuning:     default_gbm (6.6s)</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
 <pre><code>i 4 of 4 tuning:     default_maxent</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>✔ 4 of 4 tuning:     default_maxent (1.9s)</code></pre>
+<pre><code>✔ 4 of 4 tuning:     default_maxent (2s)</code></pre>
 </div>
 <div class="sourceCode cell-code" id="cb24"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb24-1"><a href="#cb24-1" aria-hidden="true" tabindex="-1"></a>models</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-stdout">
@@ -911,8 +917,8 @@ <h1 data-number="6"><span class="header-section-number">6</span> Saving models a
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="./about.html" class="pagination-link" aria-label="About">
-        <span class="nav-page-text">About</span> <i class="bi bi-arrow-right-short"></i>
+      <a href="./tidysdm-05-prediction.html" class="pagination-link" aria-label="tidysdm-05-prediction">
+        <span class="nav-page-text">tidysdm-05-prediction</span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
 </nav>