remove seed from background testing

docs/index.html

@@ -348,7 +348,6 @@ <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
 ├── model
 │   ├── v1
@@ -1511,6 +1510,7 @@ <h3 data-number="3.4" class="anchored" data-anchor-id="data-storage"><span class
 │   └── Mola_mola.gpkg
 ├── obs
 │   ├── obs-covariates.gpkg
+│   ├── obs-covariates.gpkg-journal
 │   └── obs.gpkg
 └── oisst
     ├── 2000

docs/modeling-04.html

@@ -64,6 +64,8 @@
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 <script src="site_libs/quarto-search/quarto-search.js"></script>
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-      Species distribution modeling with R
-      </li></ol></nav>
+      <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./modeling-04.html">Background count</a></li></ol></nav>
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@@ -192,6 +192,12 @@
   <a href="./modeling-03.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Modeling with split</span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./modeling-04.html" class="sidebar-item-text sidebar-link active">
+ <span class="menu-text">Background count</span></a>
+  </div>
 </li>
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   <div class="sidebar-item-container"> 
@@ -328,7 +334,7 @@ <h1 class="title">Background count</h1>
 y    1 46  46.12 -0.25 WGS 84 FALSE [y]</code></pre>
 </div>
 </div>
-<p>Now we can make the models for those months, but we need to establish the number of background points for each model. Let’s do a simple progression… from 100 to 10000.</p>
+<p>Now we can make the models for those months, but we need to establish the number of background points for each model. Let’s do a simple progression… from 10 to 10000. We’ll build a model for each number of background points, make a predictive map and then compute AUC.</p>
 <p>Comments in the code block below help explain the steps taken.</p>
 <div class="cell">
 <div class="sourceCode cell-code" id="cb12"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb12-1"><a href="#cb12-1" aria-hidden="true" tabindex="-1"></a><span class="co"># choose a sequence of background counts</span></span>
@@ -345,7 +351,7 @@ <h1 class="title">Background count</h1>
 <span id="cb12-12"><a href="#cb12-12" aria-hidden="true" tabindex="-1"></a>    <span class="co"># prepare all of the observations</span></span>
 <span id="cb12-13"><a href="#cb12-13" aria-hidden="true" tabindex="-1"></a>    obn <span class="ot">=</span> dplyr<span class="sc">::</span><span class="fu">select</span>(ob, dplyr<span class="sc">::</span><span class="fu">all_of</span>(<span class="fu">c</span>(<span class="st">"sst"</span>, <span class="st">"u_wind"</span>, <span class="st">"v_wind"</span>))) <span class="sc">|&gt;</span></span>
 <span id="cb12-14"><a href="#cb12-14" aria-hidden="true" tabindex="-1"></a>      sf<span class="sc">::</span><span class="fu">st_drop_geometry</span>()</span>
-<span id="cb12-15"><a href="#cb12-15" aria-hidden="true" tabindex="-1"></a>    <span class="co"># prepare and sample the background</span></span>
+<span id="cb12-15"><a href="#cb12-15" aria-hidden="true" tabindex="-1"></a>    <span class="co"># prepare and then sample the background</span></span>
 <span id="cb12-16"><a href="#cb12-16" aria-hidden="true" tabindex="-1"></a>    bkn <span class="ot">=</span> dplyr<span class="sc">::</span><span class="fu">select</span>(bk, dplyr<span class="sc">::</span><span class="fu">all_of</span>(<span class="fu">c</span>(<span class="st">"sst"</span>, <span class="st">"u_wind"</span>, <span class="st">"v_wind"</span>))) <span class="sc">|&gt;</span></span>
 <span id="cb12-17"><a href="#cb12-17" aria-hidden="true" tabindex="-1"></a>      sf<span class="sc">::</span><span class="fu">st_drop_geometry</span>() <span class="sc">|&gt;</span> </span>
 <span id="cb12-18"><a href="#cb12-18" aria-hidden="true" tabindex="-1"></a>      dplyr<span class="sc">::</span><span class="fu">slice_sample</span>(<span class="at">n=</span>nbk)</span>
@@ -363,15 +369,27 @@ <h1 class="title">Background count</h1>
 <span id="cb12-30"><a href="#cb12-30" aria-hidden="true" tabindex="-1"></a>    dplyr<span class="sc">::</span><span class="fu">tibble</span>(<span class="at">nbkg =</span> nbk, <span class="at">AUC =</span> pauc<span class="sc">$</span>area)</span>
 <span id="cb12-31"><a href="#cb12-31" aria-hidden="true" tabindex="-1"></a>  }, <span class="at">ob =</span> obs, <span class="at">bk =</span> bkg, <span class="at">preds =</span> predictors) <span class="sc">|&gt;</span></span>
 <span id="cb12-32"><a href="#cb12-32" aria-hidden="true" tabindex="-1"></a>  <span class="co"># bind all of the individual tibbles into one data frame (still a tibble)</span></span>
-<span id="cb12-33"><a href="#cb12-33" aria-hidden="true" tabindex="-1"></a>  dplyr<span class="sc">::</span><span class="fu">bind_rows</span>() </span>
-<span id="cb12-34"><a href="#cb12-34" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb12-35"><a href="#cb12-35" aria-hidden="true" tabindex="-1"></a>ggplot2<span class="sc">::</span><span class="fu">ggplot</span>(<span class="at">data =</span> x, ggplot2<span class="sc">::</span><span class="fu">aes</span>(<span class="at">x =</span> nbkg, <span class="at">y =</span> AUC)) <span class="sc">+</span></span>
-<span id="cb12-36"><a href="#cb12-36" aria-hidden="true" tabindex="-1"></a>  ggplot2<span class="sc">::</span><span class="fu">geom_point</span>() <span class="sc">+</span> </span>
-<span id="cb12-37"><a href="#cb12-37" aria-hidden="true" tabindex="-1"></a>  ggplot2<span class="sc">::</span><span class="fu">geom_smooth</span>(<span class="at">method =</span> <span class="st">"loess"</span>, <span class="at">se =</span> <span class="cn">TRUE</span>, <span class="at">formula =</span> y <span class="sc">~</span> x) <span class="sc">+</span> </span>
-<span id="cb12-38"><a href="#cb12-38" aria-hidden="true" tabindex="-1"></a>  ggplot2<span class="sc">::</span><span class="fu">labs</span>(<span class="at">x =</span> <span class="st">"Number of Background Points"</span>,</span>
-<span id="cb12-39"><a href="#cb12-39" aria-hidden="true" tabindex="-1"></a>                <span class="at">title =</span> <span class="st">"Choosing the number of background points"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<span id="cb12-33"><a href="#cb12-33" aria-hidden="true" tabindex="-1"></a>  dplyr<span class="sc">::</span><span class="fu">bind_rows</span>() <span class="sc">|&gt;</span></span>
+<span id="cb12-34"><a href="#cb12-34" aria-hidden="true" tabindex="-1"></a>  dplyr<span class="sc">::</span><span class="fu">glimpse</span>()</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">
+<pre><code>Rows: 25
+Columns: 2
+$ nbkg &lt;dbl&gt; 10, 20, 50, 100, 250, 500, 1000, 1500, 2000, 2500, 3000, 3500, 40…
+$ AUC  &lt;dbl&gt; 0.8124647, 0.8078305, 0.8071452, 0.8101962, 0.8229343, 0.8267463,…</code></pre>
+</div>
+</div>
+<p>Now we can show these with a simple plot.</p>
+<div class="cell">
+<details>
+<summary>Code</summary>
+<div class="sourceCode cell-code" id="cb14"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb14-1"><a href="#cb14-1" aria-hidden="true" tabindex="-1"></a>ggplot2<span class="sc">::</span><span class="fu">ggplot</span>(<span class="at">data =</span> x, ggplot2<span class="sc">::</span><span class="fu">aes</span>(<span class="at">x =</span> nbkg, <span class="at">y =</span> AUC)) <span class="sc">+</span></span>
+<span id="cb14-2"><a href="#cb14-2" aria-hidden="true" tabindex="-1"></a>  ggplot2<span class="sc">::</span><span class="fu">geom_point</span>() <span class="sc">+</span> </span>
+<span id="cb14-3"><a href="#cb14-3" aria-hidden="true" tabindex="-1"></a>  ggplot2<span class="sc">::</span><span class="fu">geom_smooth</span>(<span class="at">method =</span> <span class="st">"loess"</span>, <span class="at">se =</span> <span class="cn">TRUE</span>, <span class="at">formula =</span> y <span class="sc">~</span> x) <span class="sc">+</span> </span>
+<span id="cb14-4"><a href="#cb14-4" aria-hidden="true" tabindex="-1"></a>  ggplot2<span class="sc">::</span><span class="fu">labs</span>(<span class="at">x =</span> <span class="st">"Number of Background Points"</span>,</span>
+<span id="cb14-5"><a href="#cb14-5" aria-hidden="true" tabindex="-1"></a>                <span class="at">title =</span> <span class="st">"Choosing the number of background points"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+</details>
 <div class="cell-output-display">
-<p><img src="modeling-04_files/figure-html/unnamed-chunk-8-1.png" class="img-fluid" width="672"></p>
+<p><img src="modeling-04_files/figure-html/unnamed-chunk-9-1.png" class="img-fluid" width="672"></p>
 </div>
 </div>
 <p>This workflow reveals to us that for the seasonal May-Oct model that we get no improvement in AUC once we get to 2500 background points.</p>
@@ -612,6 +630,18 @@ <h1 class="title">Background count</h1>
   }
 });
 </script>
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modeling-04.qmd

@@ -91,7 +91,7 @@ predicitors = stars::st_apply(predictors, c("x", "y"), mean,
   print()
 ```
 
-Now we can make the models for those months, but we need to establish the number of background points for each model. Let's do a simple progression... from 100 to 10000. 
+Now we can make the models for those months, but we need to establish the number of background points for each model. Let's do a simple progression... from 10 to 10000.  We'll build a model for each number of background points, make a predictive map and then compute AUC.
 
 Comments in the code block below help explain the steps taken.
 
@@ -110,7 +110,7 @@ x = lapply(nback,
     # prepare all of the observations
     obn = dplyr::select(ob, dplyr::all_of(c("sst", "u_wind", "v_wind"))) |>
       sf::st_drop_geometry()
-    # prepare and sample the background
+    # prepare and then sample the background
     bkn = dplyr::select(bk, dplyr::all_of(c("sst", "u_wind", "v_wind"))) |>
       sf::st_drop_geometry() |> 
       dplyr::slice_sample(n=nbk)
@@ -128,8 +128,14 @@ x = lapply(nback,
     dplyr::tibble(nbkg = nbk, AUC = pauc$area)
   }, ob = obs, bk = bkg, preds = predictors) |>
   # bind all of the individual tibbles into one data frame (still a tibble)
-  dplyr::bind_rows() 
+  dplyr::bind_rows() |>
+  dplyr::glimpse()
+```
+
+Now we can show these with a simple plot.
 
+```{r}
+#| code-fold: true
 ggplot2::ggplot(data = x, ggplot2::aes(x = nbkg, y = AUC)) +
   ggplot2::geom_point() + 
   ggplot2::geom_smooth(method = "loess", se = TRUE, formula = y ~ x) +