Skip to content

Commit

Permalink
updating vignettes
Browse files Browse the repository at this point in the history
  • Loading branch information
@mrke
mrke committed Jun 7, 2024
1 parent aae93f2 commit 15a737b
Show file tree
Hide file tree
Showing 3 changed files with 13 additions and 13 deletions.
4 changes: 2 additions & 2 deletions inst/doc/endotherm-model-tutorial.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -800,7 +800,7 @@ <h2>Metabolic chamber example</h2>
<span id="cb3-66"><a href="#cb3-66" tabindex="-1"></a>}) <span class="co"># run endoR across environments</span></span>
<span id="cb3-67"><a href="#cb3-67" tabindex="-1"></a><span class="fu">proc.time</span>() <span class="sc">-</span> ptm <span class="co"># stop timing</span></span></code></pre></div>
<pre><code>## user system elapsed
## 0.1 0.0 0.1</code></pre>
## 0.24 0.02 0.25</code></pre>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a><span class="co"># extract the output</span></span>
<span id="cb5-2"><a href="#cb5-2" tabindex="-1"></a>endo.out1 <span class="ot">&lt;-</span> <span class="fu">do.call</span>(<span class="st">&quot;rbind&quot;</span>, <span class="fu">lapply</span>(endo.out, data.frame))</span>
<span id="cb5-3"><a href="#cb5-3" tabindex="-1"></a></span>
Expand Down Expand Up @@ -959,7 +959,7 @@ <h2>Microclimate model integration example</h2>
<span id="cb6-76"><a href="#cb6-76" tabindex="-1"></a>})</span>
<span id="cb6-77"><a href="#cb6-77" tabindex="-1"></a><span class="fu">proc.time</span>() <span class="sc">-</span> ptm <span class="co"># end timing</span></span></code></pre></div>
<pre><code>## user system elapsed
## 0.47 0.00 0.47</code></pre>
## 1.05 0.00 1.05</code></pre>
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb8-1"><a href="#cb8-1" tabindex="-1"></a><span class="co"># extract the output</span></span>
<span id="cb8-2"><a href="#cb8-2" tabindex="-1"></a>endo.out1 <span class="ot">&lt;-</span> <span class="fu">do.call</span>(<span class="st">&quot;rbind&quot;</span>, <span class="fu">lapply</span>(endo.out, data.frame))</span>
<span id="cb8-3"><a href="#cb8-3" tabindex="-1"></a></span>
Expand Down
2 changes: 1 addition & 1 deletion inst/doc/leaf-temperature-tutorial.Rmd
View file
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ author: "Michael Kearney"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{Leaf Temperature Tutorial}
%\VignetteIndexEntry{Leaf Temperature Simulations}
%\VignetteEncoding{UTF-8}
%\VignetteEngine{knitr::rmarkdown}
urlcolor: blue
Expand Down
20 changes: 10 additions & 10 deletions inst/doc/leaf-temperature-tutorial.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -507,7 +507,7 @@ <h3>Run the NicheMapR ectotherm model</h3>
<span id="cb9-8"><a href="#cb9-8" tabindex="-1"></a> <span class="at">postur =</span> postur, <span class="at">preshr =</span> P_a, <span class="at">PDIF =</span> PDIFs)</span>
<span id="cb9-9"><a href="#cb9-9" tabindex="-1"></a><span class="fu">print</span>(<span class="fu">proc.time</span>() <span class="sc">-</span> ptm) <span class="co"># Stop the clock</span></span></code></pre></div>
<pre><code>## user system elapsed
## 0.01 0.00 0.02</code></pre>
## 0.03 0.00 0.03</code></pre>
<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb11-1"><a href="#cb11-1" tabindex="-1"></a>environ <span class="ot">&lt;-</span> <span class="fu">as.data.frame</span>(ecto<span class="sc">$</span>environ)</span>
<span id="cb11-2"><a href="#cb11-2" tabindex="-1"></a>T_leaf_NMR <span class="ot">&lt;-</span> environ<span class="sc">$</span>TC</span></code></pre></div>
<p>Now plot the results against air temperature at leaf height and at
Expand Down Expand Up @@ -575,7 +575,7 @@ <h3>Run NicheMapR ectoR_devel model</h3>
<span id="cb13-43"><a href="#cb13-43" tabindex="-1"></a>}</span>
<span id="cb13-44"><a href="#cb13-44" tabindex="-1"></a><span class="fu">print</span>(<span class="fu">proc.time</span>() <span class="sc">-</span> ptm) <span class="co"># Stop the clock</span></span></code></pre></div>
<pre><code>## user system elapsed
## 0.49 0.00 0.50</code></pre>
## 0.59 0.02 0.61</code></pre>
<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb15-1"><a href="#cb15-1" tabindex="-1"></a><span class="co"># plot</span></span>
<span id="cb15-2"><a href="#cb15-2" tabindex="-1"></a><span class="fu">plot</span>(<span class="fu">seq</span>(<span class="dv">0</span>, <span class="dv">23</span>), T_air_1cm[sub], <span class="at">type =</span> <span class="st">&#39;l&#39;</span>, <span class="at">col =</span> <span class="st">&#39;blue&#39;</span>, <span class="at">ylab =</span> <span class="st">&#39;temperature, deg C&#39;</span>, <span class="at">xlab =</span> <span class="st">&#39;hour of day&#39;</span>, <span class="at">ylim =</span> <span class="fu">c</span>(<span class="dv">15</span>, <span class="dv">50</span>))</span>
<span id="cb15-3"><a href="#cb15-3" tabindex="-1"></a><span class="fu">points</span>(<span class="fu">seq</span>(<span class="dv">0</span>, <span class="dv">23</span>), T_air_1<span class="fl">.2</span>m[sub], <span class="at">type =</span> <span class="st">&#39;l&#39;</span>, <span class="at">col =</span> <span class="st">&#39;blue&#39;</span>, <span class="at">lty =</span> <span class="dv">2</span>)</span>
Expand Down Expand Up @@ -644,7 +644,7 @@ <h3>Run the Campbell and Norman model</h3>
<span id="cb17-25"><a href="#cb17-25" tabindex="-1"></a>)})) <span class="co"># run leaf_temperature across environments</span></span>
<span id="cb17-26"><a href="#cb17-26" tabindex="-1"></a><span class="fu">print</span>(<span class="fu">proc.time</span>() <span class="sc">-</span> ptm) <span class="co"># Stop the clock</span></span></code></pre></div>
<pre><code>## user system elapsed
## 0.63 0.11 0.81</code></pre>
## 0.79 0.21 1.06</code></pre>
<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb19-1"><a href="#cb19-1" tabindex="-1"></a><span class="co"># plot</span></span>
<span id="cb19-2"><a href="#cb19-2" tabindex="-1"></a><span class="fu">plot</span>(<span class="fu">seq</span>(<span class="dv">0</span>, <span class="dv">23</span>), T_air_1cm[sub], <span class="at">type =</span> <span class="st">&#39;l&#39;</span>, <span class="at">col =</span> <span class="st">&#39;blue&#39;</span>, <span class="at">ylab =</span> <span class="st">&#39;temperature, deg C&#39;</span>, <span class="at">xlab =</span> <span class="st">&#39;hour of day&#39;</span>, <span class="at">ylim =</span> <span class="fu">c</span>(<span class="dv">15</span>, <span class="dv">50</span>))</span>
<span id="cb19-3"><a href="#cb19-3" tabindex="-1"></a><span class="fu">points</span>(<span class="fu">seq</span>(<span class="dv">0</span>, <span class="dv">23</span>), T_air_1<span class="fl">.2</span>m[sub], <span class="at">type =</span> <span class="st">&#39;l&#39;</span>, <span class="at">col =</span> <span class="st">&#39;blue&#39;</span>, <span class="at">lty =</span> <span class="dv">2</span>)</span>
Expand Down Expand Up @@ -681,7 +681,7 @@ <h3>Run the plantecophys leaf temperature model</h3>
<span id="cb20-15"><a href="#cb20-15" tabindex="-1"></a> <span class="at">LeafAbs =</span> alpha_L)})) <span class="co"># run FindTleaf across environments</span></span>
<span id="cb20-16"><a href="#cb20-16" tabindex="-1"></a><span class="fu">print</span>(<span class="fu">proc.time</span>() <span class="sc">-</span> ptm) <span class="co"># Stop the clock</span></span></code></pre></div>
<pre><code>## user system elapsed
## 0.72 0.17 1.00</code></pre>
## 0.92 0.33 1.31</code></pre>
<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb22-1"><a href="#cb22-1" tabindex="-1"></a><span class="co"># plot</span></span>
<span id="cb22-2"><a href="#cb22-2" tabindex="-1"></a><span class="fu">plot</span>(<span class="fu">seq</span>(<span class="dv">0</span>, <span class="dv">23</span>), T_air_1cm[sub], <span class="at">type =</span> <span class="st">&#39;l&#39;</span>, <span class="at">col =</span> <span class="st">&#39;blue&#39;</span>, <span class="at">ylab =</span> <span class="st">&#39;temperature, deg C&#39;</span>, <span class="at">xlab =</span> <span class="st">&#39;hour of day&#39;</span>, <span class="at">ylim =</span> <span class="fu">c</span>(<span class="dv">15</span>, <span class="dv">50</span>))</span>
<span id="cb22-3"><a href="#cb22-3" tabindex="-1"></a><span class="fu">points</span>(<span class="fu">seq</span>(<span class="dv">0</span>, <span class="dv">23</span>), T_air_1<span class="fl">.2</span>m[sub], <span class="at">type =</span> <span class="st">&#39;l&#39;</span>, <span class="at">col =</span> <span class="st">&#39;blue&#39;</span>, <span class="at">lty =</span> <span class="dv">2</span>)</span>
Expand Down Expand Up @@ -726,7 +726,7 @@ <h3>Run the tealeaves model</h3>
<span id="cb23-29"><a href="#cb23-29" tabindex="-1"></a>}</span>
<span id="cb23-30"><a href="#cb23-30" tabindex="-1"></a><span class="fu">print</span>(<span class="fu">proc.time</span>() <span class="sc">-</span> ptm) <span class="co"># Stop the clock</span></span></code></pre></div>
<pre><code>## user system elapsed
## 40.22 0.99 41.99</code></pre>
## 37.59 0.90 39.64</code></pre>
<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb25-1"><a href="#cb25-1" tabindex="-1"></a><span class="fu">colnames</span>(T_leaf_tealeaves) <span class="ot">&lt;-</span> <span class="fu">colnames</span>(T_leaf)</span>
<span id="cb25-2"><a href="#cb25-2" tabindex="-1"></a>T_leaf_tealeaves <span class="ot">&lt;-</span> <span class="fu">as.data.frame</span>(T_leaf_tealeaves)<span class="sc">$</span>T_leaf <span class="sc">-</span></span>
<span id="cb25-3"><a href="#cb25-3" tabindex="-1"></a> <span class="fl">273.15</span></span>
Expand Down Expand Up @@ -824,7 +824,7 @@ <h2>Incorporating stomatal dynamics with the plantecophys package</h2>
<span id="cb30-8"><a href="#cb30-8" tabindex="-1"></a> <span class="at">postur =</span> postur, <span class="at">preshr =</span> P_a, <span class="at">PDIF =</span> PDIFs)</span>
<span id="cb30-9"><a href="#cb30-9" tabindex="-1"></a><span class="fu">print</span>(<span class="fu">proc.time</span>() <span class="sc">-</span> ptm) <span class="co"># Stop the clock</span></span></code></pre></div>
<pre><code>## user system elapsed
## 0.02 0.00 0.01</code></pre>
## 0.02 0.00 0.02</code></pre>
<div class="sourceCode" id="cb32"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb32-1"><a href="#cb32-1" tabindex="-1"></a>environ <span class="ot">&lt;-</span> <span class="fu">as.data.frame</span>(ecto<span class="sc">$</span>environ)</span>
<span id="cb32-2"><a href="#cb32-2" tabindex="-1"></a>T_leaf_NMR_plantecophys <span class="ot">&lt;-</span> environ<span class="sc">$</span>TC</span></code></pre></div>
<p>Compare the two calculations of leaf temperature. Stomatal closure in
Expand Down Expand Up @@ -983,7 +983,7 @@ <h3>Simulate microclimate in the Mojave Desert</h3>
## running micro_global to get clear sky solar
## running microclimate model for 731 days from 01/01/2016 to 31/12/2017 at site long -116.53 lat 33.83
## user system elapsed
## 36.57 0.20 36.88</code></pre>
## 38.55 0.16 38.72</code></pre>
<div class="sourceCode" id="cb40"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb40-1"><a href="#cb40-1" tabindex="-1"></a><span class="co"># define time zone</span></span>
<span id="cb40-2"><a href="#cb40-2" tabindex="-1"></a>tz <span class="ot">&lt;-</span> <span class="fu">paste0</span>(<span class="st">&quot;Etc/GMT-&quot;</span>, <span class="fu">floor</span>(micro<span class="sc">$</span>longlat[<span class="dv">1</span>]<span class="sc">/</span><span class="dv">15</span> <span class="sc">*</span> <span class="sc">-</span><span class="dv">1</span>))</span>
<span id="cb40-3"><a href="#cb40-3" tabindex="-1"></a>dates <span class="ot">&lt;-</span> micro<span class="sc">$</span>dates</span>
Expand Down Expand Up @@ -1054,7 +1054,7 @@ <h3>Compute stomatal dynamics with Photosyn</h3>
<span id="cb44-8"><a href="#cb44-8" tabindex="-1"></a> <span class="at">postur =</span> postur, <span class="at">preshr =</span> P_a, <span class="at">PDIF =</span> PDIFs)</span>
<span id="cb44-9"><a href="#cb44-9" tabindex="-1"></a><span class="fu">print</span>(<span class="fu">proc.time</span>() <span class="sc">-</span> ptm) <span class="co"># Stop the clock</span></span></code></pre></div>
<pre><code>## user system elapsed
## 1.38 0.08 1.46</code></pre>
## 1.05 0.08 1.12</code></pre>
<div class="sourceCode" id="cb46"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb46-1"><a href="#cb46-1" tabindex="-1"></a>environ <span class="ot">&lt;-</span> <span class="fu">as.data.frame</span>(ecto<span class="sc">$</span>environ)</span>
<span id="cb46-2"><a href="#cb46-2" tabindex="-1"></a>T_leaf_photosyn <span class="ot">&lt;-</span> environ<span class="sc">$</span>TC</span>
<span id="cb46-3"><a href="#cb46-3" tabindex="-1"></a><span class="fu">plot</span>(dates[sub], T_leaf_photosyn[sub], <span class="at">type =</span> <span class="st">&quot;l&quot;</span>, <span class="at">ylim =</span> <span class="fu">c</span>(<span class="sc">-</span><span class="dv">5</span>,</span>
Expand Down Expand Up @@ -1088,7 +1088,7 @@ <h3>Impose effects of water stress on stomatal dynamics</h3>
<span id="cb48-8"><a href="#cb48-8" tabindex="-1"></a> <span class="at">postur =</span> postur, <span class="at">preshr =</span> P_a, <span class="at">PDIF =</span> PDIFs)</span>
<span id="cb48-9"><a href="#cb48-9" tabindex="-1"></a><span class="fu">print</span>(<span class="fu">proc.time</span>() <span class="sc">-</span> ptm) <span class="co"># Stop the clock</span></span></code></pre></div>
<pre><code>## user system elapsed
## 1.34 0.05 1.39</code></pre>
## 0.98 0.08 1.09</code></pre>
<div class="sourceCode" id="cb50"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb50-1"><a href="#cb50-1" tabindex="-1"></a>environ <span class="ot">&lt;-</span> <span class="fu">as.data.frame</span>(ecto<span class="sc">$</span>environ)</span>
<span id="cb50-2"><a href="#cb50-2" tabindex="-1"></a>T_leaf <span class="ot">&lt;-</span> environ<span class="sc">$</span>TC</span>
<span id="cb50-3"><a href="#cb50-3" tabindex="-1"></a><span class="co"># plot(dates[sub], T_leaf[sub], type = &#39;l&#39;, ylim = c(-5,</span></span>
Expand Down Expand Up @@ -1124,7 +1124,7 @@ <h3>Impose effects of water stress on stomatal dynamics</h3>
<span id="cb51-25"><a href="#cb51-25" tabindex="-1"></a> <span class="at">postur =</span> postur, <span class="at">preshr =</span> P_a, <span class="at">PDIF =</span> PDIFs)</span>
<span id="cb51-26"><a href="#cb51-26" tabindex="-1"></a><span class="fu">print</span>(<span class="fu">proc.time</span>() <span class="sc">-</span> ptm) <span class="co"># Stop the clock</span></span></code></pre></div>
<pre><code>## user system elapsed
## 1.66 0.10 1.75</code></pre>
## 1.33 0.04 1.38</code></pre>
<div class="sourceCode" id="cb53"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb53-1"><a href="#cb53-1" tabindex="-1"></a>environ <span class="ot">&lt;-</span> <span class="fu">as.data.frame</span>(ecto<span class="sc">$</span>environ)</span>
<span id="cb53-2"><a href="#cb53-2" tabindex="-1"></a>T_leaf <span class="ot">&lt;-</span> environ<span class="sc">$</span>TC</span>
<span id="cb53-3"><a href="#cb53-3" tabindex="-1"></a><span class="fu">plot</span>(dates[sub], T_leaf[sub], <span class="at">type =</span> <span class="st">&quot;l&quot;</span>, <span class="at">ylim =</span> <span class="fu">c</span>(<span class="sc">-</span><span class="dv">5</span>, <span class="dv">70</span>), <span class="at">ylab =</span> <span class="st">&quot;leaf temperature, deg C&quot;</span>,</span>
Expand Down

0 comments on commit 15a737b

Please sign in to comment.