major reorganziation for tidysdm

BigelowLab · Oct 29, 2024 · 147cc04 · 147cc04
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diff --git a/.gitignore b/.gitignore
@@ -2,7 +2,6 @@
 data/oisst/*
 data/nbs/*
 data/nbs2/*
-*.tif
 .DS_Store
 
 # accidental cloud based transaction file?

diff --git a/_quarto.yml b/_quarto.yml
@@ -4,14 +4,17 @@ project:
   execute-dir: project
   render:
     - index.qmd
-    - observations.qmd
-    - predictors.qmd
-    - covariates.qmd
-    - modeling-01.qmd
-    - modeling-02.qmd
-    - modeling-03.qmd
-    - modeling-04.qmd
+    - trad00-observations.qmd
+    - trad01-predictors.qmd
+    - trad02-covariates.qmd
+    - trad03-basic_modeling.qmd
+    - trad04-month_models.qmd
+    - trad05-model_splits.qmd
+    - trad06-background_count.qmd
     - tidysdm-01.qmd
+    - tidysdm-02-thinning.qmd
+    - tidysdm-03-background.qmd
+    - tidysdm-04-modeling.qmd
     - about.qmd
 execute: 
   cache: true
@@ -25,26 +28,25 @@ website:
     style: "docked"
     search: true
     contents:
-      - href: index.qmd
-        text: Home
-      - href: observations.qmd
-        text: Observations
-      - href: predictors.qmd
-        text: Predictors
-      - href: covariates.qmd
-        text: Extracting covariates
-      - href: modeling-01.qmd
-        text: Basic modeling
-      - href: modeling-02.qmd
-        text: Modeling by month
-      - href: modeling-03.qmd
-        text: Modeling with split
-      - href: modeling-04.qmd
-        text: Background count
-      - href: tidysdm-01.qmd
-        text: Working with tidysdm 
-      - href: about.qmd
-        text: About
+      - text: Home
+        href: index.qmd
+      - section: "Traditional modeling"
+        href: trad00-observations.qmd
+        contents:
+          - trad01-predictors.qmd
+          - trad02-covariates.qmd
+          - trad03-basic_modeling.qmd
+          - trad04-month_models.qmd
+          - trad05-model_splits.qmd
+          - trad06-background_count.qmd
+      - section: Working with tidysdm 
+        href: tidysdm-01.qmd
+        contents:
+          - tidysdm-02-thinning.qmd
+          - tidysdm-03-background.qmd
+          - tidysdm-04-modeling.qmd
+      - text: About
+        href: about.qmd
     tools:
       - icon: github
         menu:

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/mask/mask_factor.tif b/data/mask/mask_factor.tif
diff --git a/data/mask/mask_factor.tif.aux.xml b/data/mask/mask_factor.tif.aux.xml
@@ -0,0 +1,8 @@
+<PAMDataset>
+  <PAMRasterBand band="1">
+    <CategoryNames>
+      <Category></Category>
+      <Category>mask</Category>
+    </CategoryNames>
+  </PAMRasterBand>
+</PAMDataset>
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-01.html" rel="prev">
+<link href="./tidysdm-04-modeling.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>
@@ -129,54 +129,82 @@
  <span class="menu-text">Home</span></a>
   </div>
 </li>
-        <li class="sidebar-item">
-  <div class="sidebar-item-container"> 
-  <a href="./observations.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text">Observations</span></a>
-  </div>
-</li>
-        <li class="sidebar-item">
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a href="./trad00-observations.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Traditional modeling</span></a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-1" aria-expanded="true" aria-label="Toggle section">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-1" class="collapse list-unstyled sidebar-section depth1 show">  
+          <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./predictors.html" class="sidebar-item-text sidebar-link">
+  <a href="./trad01-predictors.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Predictors</span></a>
   </div>
 </li>
-        <li class="sidebar-item">
+          <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./covariates.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text">Extracting covariates</span></a>
+  <a href="./trad02-covariates.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Covariates for observations and background</span></a>
   </div>
 </li>
-        <li class="sidebar-item">
+          <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./modeling-01.html" class="sidebar-item-text sidebar-link">
+  <a href="./trad03-basic_modeling.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Basic modeling</span></a>
   </div>
 </li>
-        <li class="sidebar-item">
+          <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./modeling-02.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text">Modeling by month</span></a>
+  <a href="./trad04-month_models.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Modeling each month</span></a>
   </div>
 </li>
-        <li class="sidebar-item">
+          <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./modeling-03.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text">Modeling with split</span></a>
+  <a href="./trad05-model_splits.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Modeling with splits</span></a>
   </div>
 </li>
-        <li class="sidebar-item">
+          <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./modeling-04.html" class="sidebar-item-text sidebar-link">
+  <a href="./trad06-background_count.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">
+      </ul>
+  </li>
+        <li class="sidebar-item sidebar-item-section">
+      <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>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-2" aria-expanded="true" aria-label="Toggle section">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 show">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./tidysdm-02-thinning.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Data thinning</span></a>
   </div>
 </li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./tidysdm-03-background.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Background sampling</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./tidysdm-04-modeling.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Modeling</span></a>
+  </div>
+</li>
+      </ul>
+  </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./about.html" class="sidebar-item-text sidebar-link active">
@@ -607,8 +635,8 @@ <h1 class="title">About</h1>
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <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 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>          
   </div>
   <div class="nav-page nav-page-next">

diff --git a/docs/index.html b/docs/index.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="./observations.html" rel="next">
+<link href="./trad00-observations.html" rel="next">
 <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>
@@ -163,54 +163,82 @@
  <span class="menu-text">Home</span></a>
   </div>
 </li>
-        <li class="sidebar-item">
-  <div class="sidebar-item-container"> 
-  <a href="./observations.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text">Observations</span></a>
-  </div>
-</li>
-        <li class="sidebar-item">
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a href="./trad00-observations.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Traditional modeling</span></a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-1" aria-expanded="true" aria-label="Toggle section">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-1" class="collapse list-unstyled sidebar-section depth1 show">  
+          <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./predictors.html" class="sidebar-item-text sidebar-link">
+  <a href="./trad01-predictors.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Predictors</span></a>
   </div>
 </li>
-        <li class="sidebar-item">
+          <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./covariates.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text">Extracting covariates</span></a>
+  <a href="./trad02-covariates.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Covariates for observations and background</span></a>
   </div>
 </li>
-        <li class="sidebar-item">
+          <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./modeling-01.html" class="sidebar-item-text sidebar-link">
+  <a href="./trad03-basic_modeling.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Basic modeling</span></a>
   </div>
 </li>
-        <li class="sidebar-item">
+          <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./modeling-02.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text">Modeling by month</span></a>
+  <a href="./trad04-month_models.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Modeling each month</span></a>
   </div>
 </li>
-        <li class="sidebar-item">
+          <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./modeling-03.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text">Modeling with split</span></a>
+  <a href="./trad05-model_splits.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Modeling with splits</span></a>
   </div>
 </li>
-        <li class="sidebar-item">
+          <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./modeling-04.html" class="sidebar-item-text sidebar-link">
+  <a href="./trad06-background_count.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">
+      </ul>
+  </li>
+        <li class="sidebar-item sidebar-item-section">
+      <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>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-2" aria-expanded="true" aria-label="Toggle section">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 show">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./tidysdm-02-thinning.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Data thinning</span></a>
   </div>
 </li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./tidysdm-03-background.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Background sampling</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./tidysdm-04-modeling.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Modeling</span></a>
+  </div>
+</li>
+      </ul>
+  </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./about.html" class="sidebar-item-text sidebar-link">
@@ -373,6 +401,9 @@ <h3 data-number="3.4" class="anchored" data-anchor-id="data-storage"><span class
 │   ├── bkg-covariates.gpkg
 │   ├── buffered-polygon.gpkg
 │   └── obs-covariates.gpkg
+├── mask
+│   ├── mask_factor.tif
+│   └── mask_factor.tif.aux.xml
 ├── model
 │   ├── v1
 │   ├── v2
@@ -406,8 +437,10 @@ <h3 data-number="3.4" class="anchored" data-anchor-id="data-storage"><span class
 ├── obis
 │   └── Mola_mola.gpkg
 ├── obs
+│   ├── model_input.gpkg
 │   ├── obs-covariates.gpkg
-│   └── obs.gpkg
+│   ├── obs.gpkg
+│   └── thinned_obs.gpkg
 └── oisst
     ├── 2000
     ├── 2001
@@ -833,8 +866,8 @@ <h3 data-number="3.4" class="anchored" data-anchor-id="data-storage"><span class
   <div class="nav-page nav-page-previous">
   </div>
   <div class="nav-page nav-page-next">
-      <a href="./observations.html" class="pagination-link" aria-label="Observations">
-        <span class="nav-page-text">Observations</span> <i class="bi bi-arrow-right-short"></i>
+      <a href="./trad00-observations.html" class="pagination-link" aria-label="Traditional modeling">
+        <span class="nav-page-text">Traditional modeling</span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
 </nav>

diff --git a/docs/observations_files/figure-html/space-time-1.png b/docs/observations_files/figure-html/space-time-1.png