add tidysdm start

_quarto.yml

@@ -11,6 +11,7 @@ project:
     - modeling-02.qmd
     - modeling-03.qmd
     - modeling-04.qmd
+    - tidysdm-01.qmd
     - about.qmd
 execute: 
   cache: true
@@ -19,7 +20,7 @@ website:
   title: "Species distribution modeling with R"
   page-navigation: true
   back-to-top-navigation: true
-  page-footer: "Copyright 2023, Bigelow Laboratory for Ocean Science" 
+  page-footer: "Copyright 2024, Bigelow Laboratory for Ocean Science" 
   sidebar:
     style: "docked"
     search: true
@@ -40,6 +41,8 @@ website:
         text: Modeling with split
       - href: modeling-04.qmd
         text: Background count
+      - href: tidysdm-01.qmd
+        text: Working with tidysdm 
       - href: about.qmd
         text: About
     tools:

covariates.qmd

@@ -109,7 +109,7 @@ unweightedH = hist(days_sample, breaks = 'month',
                    xlab = "Date")
 ```
 
-#### Weighted sampling in time
+#### Weighted sampling in time{#sec-timeweighting}
 
 Let's take a look at the same process but this time we'll use a weight to sample more when we tend to have more observations. We'll use the original histogram counts
 

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="./modeling-04.html" rel="prev">
+<link href="./tidysdm-01.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>
@@ -170,6 +170,12 @@
   <a href="./modeling-04.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Background count</span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./tidysdm-01.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Working with tidysdm</span></a>
+  </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
@@ -601,8 +607,8 @@ <h1 class="title">About</h1>
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="./modeling-04.html" class="pagination-link  aria-label=" background="" count"="">
-        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">Background count</span>
+      <a href="./tidysdm-01.html" class="pagination-link  aria-label=" working="" with="" tidysdm"="">
+        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">Working with tidysdm</span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">
@@ -615,7 +621,7 @@ <h1 class="title">About</h1>
       &nbsp;
     </div>   
     <div class="nav-footer-center">
-<p>Copyright 2023, Bigelow Laboratory for Ocean Science</p>
+<p>Copyright 2024, Bigelow Laboratory for Ocean Science</p>
 </div>
     <div class="nav-footer-right">
       &nbsp;

docs/covariates.html

@@ -205,6 +205,12 @@
   <a href="./modeling-04.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Background count</span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./tidysdm-01.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Working with tidysdm</span></a>
+  </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
@@ -412,8 +418,8 @@ <h4 data-number="3.1.1" class="anchored" data-anchor-id="unweighted-sampling-in-
 </div>
 </div>
 </section>
-<section id="weighted-sampling-in-time" class="level4" data-number="3.1.2">
-<h4 data-number="3.1.2" class="anchored" data-anchor-id="weighted-sampling-in-time"><span class="header-section-number">3.1.2</span> Weighted sampling in time</h4>
+<section id="sec-timeweighting" class="level4" data-number="3.1.2">
+<h4 data-number="3.1.2" class="anchored" data-anchor-id="sec-timeweighting"><span class="header-section-number">3.1.2</span> Weighted sampling in time</h4>
 <p>Let’s take a look at the same process but this time we’ll use a weight to sample more when we tend to have more observations. We’ll use the original histogram counts</p>
 <div class="cell">
 <div class="sourceCode cell-code" id="cb8"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a><span class="fu">set.seed</span>(<span class="dv">1234</span>)</span>
@@ -1046,7 +1052,7 @@ <h3 data-number="4.3" class="anchored" data-anchor-id="next-extract-observation-
       &nbsp;
     </div>   
     <div class="nav-footer-center">
-<p>Copyright 2023, Bigelow Laboratory for Ocean Science</p>
+<p>Copyright 2024, Bigelow Laboratory for Ocean Science</p>
 </div>
     <div class="nav-footer-right">
       &nbsp;

docs/index.html

@@ -204,6 +204,12 @@
   <a href="./modeling-04.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Background count</span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./tidysdm-01.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Working with tidysdm</span></a>
+  </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
@@ -397,33 +403,6 @@ <h3 data-number="3.4" class="anchored" data-anchor-id="data-storage"><span class
 │   ├── 2022
 │   ├── 2023
 │   └── database.csv.gz
-├── nbs2
-│   ├── 2000
-│   ├── 2001
-│   ├── 2002
-│   ├── 2003
-│   ├── 2004
-│   ├── 2005
-│   ├── 2006
-│   ├── 2007
-│   ├── 2008
-│   ├── 2009
-│   ├── 2010
-│   ├── 2011
-│   ├── 2012
-│   ├── 2013
-│   ├── 2014
-│   ├── 2015
-│   ├── 2016
-│   ├── 2017
-│   ├── 2018
-│   ├── 2019
-│   ├── 2020
-│   ├── 2021
-│   ├── 2022
-│   ├── 2023
-│   ├── 2024
-│   └── database.csv.gz
 ├── obis
 │   └── Mola_mola.gpkg
 ├── obs
@@ -866,7 +845,7 @@ <h3 data-number="3.4" class="anchored" data-anchor-id="data-storage"><span class
       &nbsp;
     </div>   
     <div class="nav-footer-center">
-<p>Copyright 2023, Bigelow Laboratory for Ocean Science</p>
+<p>Copyright 2024, Bigelow Laboratory for Ocean Science</p>
 </div>
     <div class="nav-footer-right">
       &nbsp;

docs/modeling-01.html

@@ -205,6 +205,12 @@
   <a href="./modeling-04.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Background count</span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./tidysdm-01.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Working with tidysdm</span></a>
+  </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
@@ -1051,7 +1057,7 @@ <h2 data-number="7" class="anchored" data-anchor-id="thinking-about-auc"><span c
       &nbsp;
     </div>   
     <div class="nav-footer-center">
-<p>Copyright 2023, Bigelow Laboratory for Ocean Science</p>
+<p>Copyright 2024, Bigelow Laboratory for Ocean Science</p>
 </div>
     <div class="nav-footer-right">
       &nbsp;

docs/modeling-02.html

@@ -205,6 +205,12 @@
   <a href="./modeling-04.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Background count</span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./tidysdm-01.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Working with tidysdm</span></a>
+  </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
@@ -890,7 +896,7 @@ <h3 data-number="3.2" class="anchored" data-anchor-id="iterate-through-the-month
       &nbsp;
     </div>   
     <div class="nav-footer-center">
-<p>Copyright 2023, Bigelow Laboratory for Ocean Science</p>
+<p>Copyright 2024, Bigelow Laboratory for Ocean Science</p>
 </div>
     <div class="nav-footer-right">
       &nbsp;

docs/modeling-03.html

@@ -205,6 +205,12 @@
   <a href="./modeling-04.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Background count</span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./tidysdm-01.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Working with tidysdm</span></a>
+  </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
@@ -843,7 +849,7 @@ <h1 data-number="2"><span class="header-section-number">2</span> Model with trai
       &nbsp;
     </div>   
     <div class="nav-footer-center">
-<p>Copyright 2023, Bigelow Laboratory for Ocean Science</p>
+<p>Copyright 2024, Bigelow Laboratory for Ocean Science</p>
 </div>
     <div class="nav-footer-right">
       &nbsp;

docs/modeling-04.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-01.html" rel="next">
 <link href="./modeling-03.html" rel="prev">
 <script src="site_libs/quarto-html/quarto.js"></script>
 <script src="site_libs/quarto-html/popper.min.js"></script>
@@ -205,6 +205,12 @@
   <a href="./modeling-04.html" class="sidebar-item-text sidebar-link active">
  <span class="menu-text">Background count</span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./tidysdm-01.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Working with tidysdm</span></a>
+  </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
@@ -771,8 +777,8 @@ <h1 class="title">Background count</h1>
       </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-01.html" class="pagination-link" aria-label="Working with tidysdm">
+        <span class="nav-page-text">Working with tidysdm</span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
 </nav>
@@ -783,7 +789,7 @@ <h1 class="title">Background count</h1>
       &nbsp;
     </div>   
     <div class="nav-footer-center">
-<p>Copyright 2023, Bigelow Laboratory for Ocean Science</p>
+<p>Copyright 2024, Bigelow Laboratory for Ocean Science</p>
 </div>
     <div class="nav-footer-right">
       &nbsp;

docs/observations.html

@@ -205,6 +205,12 @@
   <a href="./modeling-04.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Background count</span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./tidysdm-01.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Working with tidysdm</span></a>
+  </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
@@ -750,7 +756,7 @@ <h2 data-number="2" class="anchored" data-anchor-id="observations-through-time">
       &nbsp;
     </div>   
     <div class="nav-footer-center">
-<p>Copyright 2023, Bigelow Laboratory for Ocean Science</p>
+<p>Copyright 2024, Bigelow Laboratory for Ocean Science</p>
 </div>
     <div class="nav-footer-right">
       &nbsp;

docs/predictors.html

@@ -205,6 +205,12 @@
   <a href="./modeling-04.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Background count</span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./tidysdm-01.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Working with tidysdm</span></a>
+  </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
@@ -807,7 +813,7 @@ <h3 data-number="4.2" class="anchored" data-anchor-id="nbs-wind-data"><span clas
       &nbsp;
     </div>   
     <div class="nav-footer-center">
-<p>Copyright 2023, Bigelow Laboratory for Ocean Science</p>
+<p>Copyright 2024, Bigelow Laboratory for Ocean Science</p>
 </div>
     <div class="nav-footer-right">
       &nbsp;