added missing ref

_common.R

@@ -24,7 +24,7 @@ options(
 status <- function(type) {
   status <- switch(type,
     restructuring = "undergoing heavy restructuring and may be confusing or incomplete",
-    drafting = "currently draft version, a peer-review publication is pending",
+    drafting = "draft version, a peer-review publication is pending",
     stop("Invalid `type`", call. = FALSE)
   )
 

docs/extending.md

@@ -1,7 +1,7 @@
 # Generating 2nd, 3rd round sampling
 
 ::: {.rmdnote}
-You are reading the work-in-progress Spatial Sampling and Resampling for Machine Learning. This chapter is currently currently draft version, a peer-review publication is pending. You can find the polished first edition at <https://opengeohub.github.io/spatial-sampling-ml/>.
+You are reading the work-in-progress Spatial Sampling and Resampling for Machine Learning. This chapter is currently draft version, a peer-review publication is pending. You can find the polished first edition at <https://opengeohub.github.io/spatial-sampling-ml/>.
 :::
 
 

docs/generating-2nd-3rd-round-sampling.html

@@ -56,7 +56,7 @@ <h1>
 <span class="header-section-number">4</span> Generating 2nd, 3rd round sampling<a class="anchor" aria-label="anchor" href="#generating-2nd-3rd-round-sampling"><i class="fas fa-link"></i></a>
 </h1>
 <div class="rmdnote">
-<p>You are reading the work-in-progress Spatial Sampling and Resampling for Machine Learning. This chapter is currently currently draft version, a peer-review publication is pending. You can find the polished first edition at <a href="https://opengeohub.github.io/spatial-sampling-ml/" class="uri">https://opengeohub.github.io/spatial-sampling-ml/</a>.</p>
+<p>You are reading the work-in-progress Spatial Sampling and Resampling for Machine Learning. This chapter is currently draft version, a peer-review publication is pending. You can find the polished first edition at <a href="https://opengeohub.github.io/spatial-sampling-ml/" class="uri">https://opengeohub.github.io/spatial-sampling-ml/</a>.</p>
 </div>
 <div id="uncertainty-guided-sampling" class="section level2" number="4.1">
 <h2>

docs/generating-spatial-sampling.html

@@ -56,7 +56,7 @@ <h1>
 <span class="header-section-number">1</span> Generating spatial sampling<a class="anchor" aria-label="anchor" href="#generating-spatial-sampling"><i class="fas fa-link"></i></a>
 </h1>
 <div class="rmdnote">
-<p>You are reading the work-in-progress Spatial Sampling and Resampling for Machine Learning. This chapter is currently currently draft version, a peer-review publication is pending. You can find the polished first edition at <a href="https://opengeohub.github.io/spatial-sampling-ml/" class="uri">https://opengeohub.github.io/spatial-sampling-ml/</a>.</p>
+<p>You are reading the work-in-progress Spatial Sampling and Resampling for Machine Learning. This chapter is currently draft version, a peer-review publication is pending. You can find the polished first edition at <a href="https://opengeohub.github.io/spatial-sampling-ml/" class="uri">https://opengeohub.github.io/spatial-sampling-ml/</a>.</p>
 </div>
 <div id="spatial-sampling" class="section level2" number="1.1">
 <h2>
@@ -497,14 +497,14 @@ <h2>
 <span id="cb19-4"><a href="generating-spatial-sampling.html#cb19-4" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; H2O is not running yet, starting it now...</span></span>
 <span id="cb19-5"><a href="generating-spatial-sampling.html#cb19-5" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; </span></span>
 <span id="cb19-6"><a href="generating-spatial-sampling.html#cb19-6" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; Note:  In case of errors look at the following log files:</span></span>
-<span id="cb19-7"><a href="generating-spatial-sampling.html#cb19-7" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;     /tmp/RtmpJi5Csw/file52ef4b12809c/h2o_tomislav_started_from_r.out</span></span>
-<span id="cb19-8"><a href="generating-spatial-sampling.html#cb19-8" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;     /tmp/RtmpJi5Csw/file52ef3589a9d5/h2o_tomislav_started_from_r.err</span></span>
+<span id="cb19-7"><a href="generating-spatial-sampling.html#cb19-7" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;     /tmp/RtmpMfyNVN/file525216bad313/h2o_tomislav_started_from_r.out</span></span>
+<span id="cb19-8"><a href="generating-spatial-sampling.html#cb19-8" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;     /tmp/RtmpMfyNVN/file525218152b27/h2o_tomislav_started_from_r.err</span></span>
 <span id="cb19-9"><a href="generating-spatial-sampling.html#cb19-9" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; </span></span>
 <span id="cb19-10"><a href="generating-spatial-sampling.html#cb19-10" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; </span></span>
 <span id="cb19-11"><a href="generating-spatial-sampling.html#cb19-11" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; Starting H2O JVM and connecting: .. Connection successful!</span></span>
 <span id="cb19-12"><a href="generating-spatial-sampling.html#cb19-12" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; </span></span>
 <span id="cb19-13"><a href="generating-spatial-sampling.html#cb19-13" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; R is connected to the H2O cluster: </span></span>
-<span id="cb19-14"><a href="generating-spatial-sampling.html#cb19-14" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;     H2O cluster uptime:         2 seconds 68 milliseconds </span></span>
+<span id="cb19-14"><a href="generating-spatial-sampling.html#cb19-14" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;     H2O cluster uptime:         1 seconds 957 milliseconds </span></span>
 <span id="cb19-15"><a href="generating-spatial-sampling.html#cb19-15" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;     H2O cluster timezone:       Europe/Amsterdam </span></span>
 <span id="cb19-16"><a href="generating-spatial-sampling.html#cb19-16" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;     H2O data parsing timezone:  UTC </span></span>
 <span id="cb19-17"><a href="generating-spatial-sampling.html#cb19-17" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;     H2O cluster version:        3.30.0.1 </span></span>
@@ -535,7 +535,7 @@ <h2>
 <span id="cb19-42"><a href="generating-spatial-sampling.html#cb19-42" aria-hidden="true" tabindex="-1"></a>  <span class="sc">|</span>                                                                            </span>
 <span id="cb19-43"><a href="generating-spatial-sampling.html#cb19-43" aria-hidden="true" tabindex="-1"></a>  <span class="er">|</span>                                                                      <span class="er">|</span>   <span class="dv">0</span>%</span>
 <span id="cb19-44"><a href="generating-spatial-sampling.html#cb19-44" aria-hidden="true" tabindex="-1"></a>  <span class="sc">|</span>                                                                            </span>
-<span id="cb19-45"><a href="generating-spatial-sampling.html#cb19-45" aria-hidden="true" tabindex="-1"></a>  <span class="er">|=================================================</span>                     <span class="er">|</span>  <span class="dv">70</span>%</span>
+<span id="cb19-45"><a href="generating-spatial-sampling.html#cb19-45" aria-hidden="true" tabindex="-1"></a>  <span class="er">|=======</span>                                                               <span class="er">|</span>  <span class="dv">10</span>%</span>
 <span id="cb19-46"><a href="generating-spatial-sampling.html#cb19-46" aria-hidden="true" tabindex="-1"></a>  <span class="sc">|</span>                                                                            </span>
 <span id="cb19-47"><a href="generating-spatial-sampling.html#cb19-47" aria-hidden="true" tabindex="-1"></a>  <span class="er">|======================================================================|</span> <span class="dv">100</span>%</span>
 <span id="cb19-48"><a href="generating-spatial-sampling.html#cb19-48" aria-hidden="true" tabindex="-1"></a><span class="co">#km.nut</span></span></code></pre></div>
@@ -554,10 +554,10 @@ <h2>
 <span class="fu"><a href="https://rdrr.io/pkg/raster/man/names.html">names</a></span><span class="op">(</span><span class="va">class_df.c</span><span class="op">)</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/pkg/raster/man/names.html">names</a></span><span class="op">(</span><span class="va">eberg_spc</span><span class="op">@</span><span class="va">predicted</span><span class="op">@</span><span class="va">data</span><span class="op">[</span>,<span class="fl">1</span><span class="op">:</span><span class="fl">4</span><span class="op">]</span><span class="op">)</span>
 <span class="fu"><a href="https://rdrr.io/r/utils/str.html">str</a></span><span class="op">(</span><span class="va">class_df.c</span><span class="op">)</span>
 <span class="co">#&gt; 'data.frame':    100 obs. of  4 variables:</span>
-<span class="co">#&gt;  $ PC1: num  1.77 -1.88 -2.16 1.48 -6.14 ...</span>
-<span class="co">#&gt;  $ PC2: num  -0.0139 2.5271 -4.9895 2.2981 0.6775 ...</span>
-<span class="co">#&gt;  $ PC3: num  -1.332 5.526 -3.361 3.143 -0.605 ...</span>
-<span class="co">#&gt;  $ PC4: num  0.0427 4.5728 -2.9965 -2.2581 1.5728 ...</span>
+<span class="co">#&gt;  $ PC1: num  -0.272 -1.22 -2.455 -3.951 1.636 ...</span>
+<span class="co">#&gt;  $ PC2: num  -3.25 -1.47 2.33 2.03 2.25 ...</span>
+<span class="co">#&gt;  $ PC3: num  1.56 -3.6 5.25 -2.12 3.38 ...</span>
+<span class="co">#&gt;  $ PC4: num  0.16 -1.49 4.58 1.22 -2.16 ...</span>
 <span class="co">#write.csv(class_df.c, "NCluster_100_class_centers.csv")</span></code></pre></div>
 <p>To select sampling points we use the minimum distance to class centers <span class="citation">(<a href="references.html#ref-Brus2021sampling" role="doc-biblioref">D. J. Brus, 2021</a>)</span>:</p>
 <div class="sourceCode" id="cb22"><pre class="downlit sourceCode r">

docs/resampling-for-spatiotemporal-machine-learning.html

@@ -56,7 +56,7 @@ <h1>
 <span class="header-section-number">3</span> Resampling for spatiotemporal Machine Learning<a class="anchor" aria-label="anchor" href="#resampling-for-spatiotemporal-machine-learning"><i class="fas fa-link"></i></a>
 </h1>
 <div class="rmdnote">
-<p>You are reading the work-in-progress Spatial Sampling and Resampling for Machine Learning. This chapter is currently currently draft version, a peer-review publication is pending. You can find the polished first edition at <a href="https://opengeohub.github.io/spatial-sampling-ml/" class="uri">https://opengeohub.github.io/spatial-sampling-ml/</a>.</p>
+<p>You are reading the work-in-progress Spatial Sampling and Resampling for Machine Learning. This chapter is currently draft version, a peer-review publication is pending. You can find the polished first edition at <a href="https://opengeohub.github.io/spatial-sampling-ml/" class="uri">https://opengeohub.github.io/spatial-sampling-ml/</a>.</p>
 </div>
 <div id="case-study-cookfarm-dataset" class="section level2" number="3.1">
 <h2>

docs/resampling-methods-for-machine-learning.html

@@ -56,7 +56,7 @@ <h1>
 <span class="header-section-number">2</span> Resampling methods for Machine Learning<a class="anchor" aria-label="anchor" href="#resampling-methods-for-machine-learning"><i class="fas fa-link"></i></a>
 </h1>
 <div class="rmdnote">
-<p>You are reading the work-in-progress Spatial Sampling and Resampling for Machine Learning. This chapter is currently currently draft version, a peer-review publication is pending. You can find the polished first edition at <a href="https://opengeohub.github.io/spatial-sampling-ml/" class="uri">https://opengeohub.github.io/spatial-sampling-ml/</a>.</p>
+<p>You are reading the work-in-progress Spatial Sampling and Resampling for Machine Learning. This chapter is currently draft version, a peer-review publication is pending. You can find the polished first edition at <a href="https://opengeohub.github.io/spatial-sampling-ml/" class="uri">https://opengeohub.github.io/spatial-sampling-ml/</a>.</p>
 </div>
 <div id="resampling-and-cross-validation" class="section level2" number="2.1">
 <h2>

docs/resampling.md

@@ -1,7 +1,7 @@
 # Resampling methods for Machine Learning
 
 ::: {.rmdnote}
-You are reading the work-in-progress Spatial Sampling and Resampling for Machine Learning. This chapter is currently currently draft version, a peer-review publication is pending. You can find the polished first edition at <https://opengeohub.github.io/spatial-sampling-ml/>.
+You are reading the work-in-progress Spatial Sampling and Resampling for Machine Learning. This chapter is currently draft version, a peer-review publication is pending. You can find the polished first edition at <https://opengeohub.github.io/spatial-sampling-ml/>.
 :::
 
 

docs/resampling_st.md

@@ -1,7 +1,7 @@
 # Resampling for spatiotemporal Machine Learning
 
 ::: {.rmdnote}
-You are reading the work-in-progress Spatial Sampling and Resampling for Machine Learning. This chapter is currently currently draft version, a peer-review publication is pending. You can find the polished first edition at <https://opengeohub.github.io/spatial-sampling-ml/>.
+You are reading the work-in-progress Spatial Sampling and Resampling for Machine Learning. This chapter is currently draft version, a peer-review publication is pending. You can find the polished first edition at <https://opengeohub.github.io/spatial-sampling-ml/>.
 :::
 
 

docs/sampling.md

@@ -1,7 +1,7 @@
 # Generating spatial sampling
 
 ::: {.rmdnote}
-You are reading the work-in-progress Spatial Sampling and Resampling for Machine Learning. This chapter is currently currently draft version, a peer-review publication is pending. You can find the polished first edition at <https://opengeohub.github.io/spatial-sampling-ml/>.
+You are reading the work-in-progress Spatial Sampling and Resampling for Machine Learning. This chapter is currently draft version, a peer-review publication is pending. You can find the polished first edition at <https://opengeohub.github.io/spatial-sampling-ml/>.
 :::
 
 
@@ -494,14 +494,14 @@ h2o.init(nthreads = -1)
 #> H2O is not running yet, starting it now...
 #> 
 #> Note:  In case of errors look at the following log files:
-#>     /tmp/RtmpJi5Csw/file52ef4b12809c/h2o_tomislav_started_from_r.out
-#>     /tmp/RtmpJi5Csw/file52ef3589a9d5/h2o_tomislav_started_from_r.err
+#>     /tmp/RtmpMfyNVN/file525216bad313/h2o_tomislav_started_from_r.out
+#>     /tmp/RtmpMfyNVN/file525218152b27/h2o_tomislav_started_from_r.err
 #> 
 #> 
 #> Starting H2O JVM and connecting: .. Connection successful!
 #> 
 #> R is connected to the H2O cluster: 
-#>     H2O cluster uptime:         2 seconds 68 milliseconds 
+#>     H2O cluster uptime:         1 seconds 957 milliseconds 
 #>     H2O cluster timezone:       Europe/Amsterdam 
 #>     H2O data parsing timezone:  UTC 
 #>     H2O cluster version:        3.30.0.1 
@@ -524,7 +524,7 @@ h2o.init(nthreads = -1)
 df.hex <- as.h2o(eberg_spc@predicted@data[,1:4], destination_frame = "df")
 #>   |                                                                              |                                                                      |   0%  |                                                                              |======================================================================| 100%
 km.nut <- h2o.kmeans(training_frame=df.hex, k=100, keep_cross_validation_predictions = TRUE)
-#>   |                                                                              |                                                                      |   0%  |                                                                              |=================================================                     |  70%  |                                                                              |======================================================================| 100%
+#>   |                                                                              |                                                                      |   0%  |                                                                              |=======                                                               |  10%  |                                                                              |======================================================================| 100%
 #km.nut
 ```
 
@@ -546,10 +546,10 @@ class_df.c = as.data.frame(h2o.centers(km.nut))
 names(class_df.c) = names(eberg_spc@predicted@data[,1:4])
 str(class_df.c)
 #> 'data.frame':	100 obs. of  4 variables:
-#>  $ PC1: num  1.77 -1.88 -2.16 1.48 -6.14 ...
-#>  $ PC2: num  -0.0139 2.5271 -4.9895 2.2981 0.6775 ...
-#>  $ PC3: num  -1.332 5.526 -3.361 3.143 -0.605 ...
-#>  $ PC4: num  0.0427 4.5728 -2.9965 -2.2581 1.5728 ...
+#>  $ PC1: num  -0.272 -1.22 -2.455 -3.951 1.636 ...
+#>  $ PC2: num  -3.25 -1.47 2.33 2.03 2.25 ...
+#>  $ PC3: num  1.56 -3.6 5.25 -2.12 3.38 ...
+#>  $ PC4: num  0.16 -1.49 4.58 1.22 -2.16 ...
 #write.csv(class_df.c, "NCluster_100_class_centers.csv")
 ```
 

docs/summary-notes.html

@@ -56,7 +56,7 @@ <h1>
 <span class="header-section-number">5</span> Summary notes<a class="anchor" aria-label="anchor" href="#summary-notes"><i class="fas fa-link"></i></a>
 </h1>
 <div class="rmdnote">
-<p>You are reading the work-in-progress Spatial Sampling and Resampling for Machine Learning. This chapter is currently currently draft version, a peer-review publication is pending. You can find the polished first edition at <a href="https://opengeohub.github.io/spatial-sampling-ml/" class="uri">https://opengeohub.github.io/spatial-sampling-ml/</a>.</p>
+<p>You are reading the work-in-progress Spatial Sampling and Resampling for Machine Learning. This chapter is currently draft version, a peer-review publication is pending. You can find the polished first edition at <a href="https://opengeohub.github.io/spatial-sampling-ml/" class="uri">https://opengeohub.github.io/spatial-sampling-ml/</a>.</p>
 </div>
 <div id="which-sampling-algorithm-to-choose" class="section level2" number="5.1">
 <h2>

docs/summary.md

@@ -1,7 +1,7 @@
 # Summary notes
 
 ::: {.rmdnote}
-You are reading the work-in-progress Spatial Sampling and Resampling for Machine Learning. This chapter is currently currently draft version, a peer-review publication is pending. You can find the polished first edition at <https://opengeohub.github.io/spatial-sampling-ml/>.
+You are reading the work-in-progress Spatial Sampling and Resampling for Machine Learning. This chapter is currently draft version, a peer-review publication is pending. You can find the polished first edition at <https://opengeohub.github.io/spatial-sampling-ml/>.
 :::
 
 ## Which sampling algorithm to choose?