From bb2d360f7458e307f115b76e4953b54045807296 Mon Sep 17 00:00:00 2001
From: realxinzhao <xin.zhao@pnnl.gov>
Date: Sat, 16 Mar 2024 11:25:08 -0400
Subject: [PATCH] Update site

---
 docs/articles/vignette_news.html          |   2 +-
 docs/articles/vignette_visualization.html | 606 +++++++++++-----------
 2 files changed, 304 insertions(+), 304 deletions(-)

diff --git a/docs/articles/vignette_news.html b/docs/articles/vignette_news.html
index f7c84dd0..b774a18f 100644
--- a/docs/articles/vignette_news.html
+++ b/docs/articles/vignette_news.html
@@ -112,7 +112,7 @@
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>News</h1>
             
-            <h4 data-toc-skip class="date">2024-02-12</h4>
+            <h4 data-toc-skip class="date">2024-03-16</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jgcri/gcamfaostat/blob/HEAD/vignettes/vignette_news.Rmd" class="external-link"><code>vignettes/vignette_news.Rmd</code></a></small>
       <div class="hidden name"><code>vignette_news.Rmd</code></div>
diff --git a/docs/articles/vignette_visualization.html b/docs/articles/vignette_visualization.html
index bc3369d3..fe26912b 100644
--- a/docs/articles/vignette_visualization.html
+++ b/docs/articles/vignette_visualization.html
@@ -112,7 +112,7 @@
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>Visualization</h1>
             
-            <h4 data-toc-skip class="date">2024-02-12</h4>
+            <h4 data-toc-skip class="date">2024-03-16</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jgcri/gcamfaostat/blob/HEAD/vignettes/vignette_visualization.Rmd" class="external-link"><code>vignettes/vignette_visualization.Rmd</code></a></small>
       <div class="hidden name"><code>vignette_visualization.Rmd</code></div>
@@ -208,25 +208,25 @@ <h3 id="load-package-data">0. Load package data<a class="anchor" aria-label="anc
 data can be loaded from cache.</li>
 </ul>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
-<code class="sourceCode R">
-<span class="fu">devtools</span><span class="fu">::</span><span class="fu"><a href="https://devtools.r-lib.org/reference/load_all.html" class="external-link">load_all</a></span><span class="op">(</span><span class="op">)</span> 
-<span class="co"># Load other libraries</span>
-<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span>
-<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span>
-<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">treemap</span><span class="op">)</span>
-<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">RColorBrewer</span><span class="op">)</span>
-
-<span class="co">## Define input data needed ----</span>
-<span class="va">MODULE_INPUTS</span> <span class="op">&lt;-</span>
-  <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>FILE <span class="op">=</span> <span class="st">"aglu/FAO/FAO_ag_items_PRODSTAT"</span>,
-    FILE <span class="op">=</span> <span class="st">"common/GCAM_region_names"</span>,
-    FILE <span class="op">=</span> <span class="st">"common/iso_GCAM_regID"</span>,
-    FILE <span class="op">=</span> <span class="st">"aglu/AGLU_ctry"</span>,
-    <span class="st">"FAO_Food_Macronutrient_All_2010_2019"</span>,
-    <span class="st">"QCL_CROP_PRIMARY"</span>,
-    <span class="st">"QCL_FODDERCROP"</span>,
-    <span class="st">"Bal_new_all"</span>,
-    <span class="st">"OA"</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span></span>
+<span><span class="fu">devtools</span><span class="fu">::</span><span class="fu"><a href="https://devtools.r-lib.org/reference/load_all.html" class="external-link">load_all</a></span><span class="op">(</span><span class="op">)</span> </span>
+<span><span class="co"># Load other libraries</span></span>
+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="http://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span></span>
+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span>
+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">treemap</span><span class="op">)</span></span>
+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">RColorBrewer</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co">## Define input data needed ----</span></span>
+<span><span class="va">MODULE_INPUTS</span> <span class="op">&lt;-</span></span>
+<span>  <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>FILE <span class="op">=</span> <span class="st">"aglu/FAO/FAO_ag_items_PRODSTAT"</span>,</span>
+<span>    FILE <span class="op">=</span> <span class="st">"common/GCAM_region_names"</span>,</span>
+<span>    FILE <span class="op">=</span> <span class="st">"common/iso_GCAM_regID"</span>,</span>
+<span>    FILE <span class="op">=</span> <span class="st">"aglu/AGLU_ctry"</span>,</span>
+<span>    <span class="st">"FAO_Food_Macronutrient_All_2010_2019"</span>,</span>
+<span>    <span class="st">"QCL_CROP_PRIMARY"</span>,</span>
+<span>    <span class="st">"QCL_FODDERCROP"</span>,</span>
+<span>    <span class="st">"Bal_new_all"</span>,</span>
+<span>    <span class="st">"OA"</span><span class="op">)</span></span></code></pre></div>
 <ul>
 <li>To get more information of the input data and trace their use in the
 package, use <code>info</code> or <code>dstrace</code> function. They
@@ -234,18 +234,18 @@ <h3 id="load-package-data">0. Load package data<a class="anchor" aria-label="anc
 processing flows.</li>
 </ul>
 <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="co"># For example</span>
-<span class="fu"><a href="../reference/info.html">info</a></span><span class="op">(</span><span class="st">"QCL_CROP_PRIMARY"</span><span class="op">)</span>
-<span class="fu"><a href="../reference/dstrace.html">dstrace</a></span><span class="op">(</span><span class="st">"common/iso_GCAM_regID"</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span><span class="co"># For example</span></span>
+<span><span class="fu"><a href="../reference/info.html">info</a></span><span class="op">(</span><span class="st">"QCL_CROP_PRIMARY"</span><span class="op">)</span></span>
+<span><span class="fu"><a href="../reference/dstrace.html">dstrace</a></span><span class="op">(</span><span class="st">"common/iso_GCAM_regID"</span><span class="op">)</span></span></code></pre></div>
 <ul>
 <li>Load the data defined in <code>MODULE_INPUTS</code> from drake
 cache</li>
 </ul>
 <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="co"># Load the data to all_data as a list</span>
-<span class="va">MODULE_INPUTS</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/load_from_cache.html">load_from_cache</a></span><span class="op">(</span><span class="op">)</span> <span class="op">-&gt;</span> <span class="va">all_data</span>
-<span class="co"># Assign the data items to their names as data frames</span>
-<span class="fu"><a href="../reference/get_data_list.html">get_data_list</a></span><span class="op">(</span><span class="va">all_data</span>, <span class="va">MODULE_INPUTS</span>, strip_attributes <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span><span class="co"># Load the data to all_data as a list</span></span>
+<span><span class="va">MODULE_INPUTS</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/load_from_cache.html">load_from_cache</a></span><span class="op">(</span><span class="op">)</span> <span class="op">-&gt;</span> <span class="va">all_data</span></span>
+<span><span class="co"># Assign the data items to their names as data frames</span></span>
+<span><span class="fu"><a href="../reference/get_data_list.html">get_data_list</a></span><span class="op">(</span><span class="va">all_data</span>, <span class="va">MODULE_INPUTS</span>, strip_attributes <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
 <ul>
 <li>Define a base year period for visualizing cross-sectional data. The
 mean value will be used. Note that 2013-2017 is used here since 2015 is
@@ -253,7 +253,7 @@ <h3 id="load-package-data">0. Load package data<a class="anchor" aria-label="anc
 year(s)</li>
 </ul>
 <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">BaseYear</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">2013</span><span class="op">:</span><span class="fl">2017</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span><span class="va">BaseYear</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">2013</span><span class="op">:</span><span class="fl">2017</span><span class="op">)</span></span></code></pre></div>
 </div>
 <div class="section level3">
 <h3 id="population-1">1. Population<a class="anchor" aria-label="anchor" href="#population-1"></a>
@@ -262,30 +262,30 @@ <h3 id="population-1">1. Population<a class="anchor" aria-label="anchor" href="#
 <li>Get data ready</li>
 </ul>
 <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="co"># simplify population data</span>
-<span class="va">OA</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">element_code</span> <span class="op">==</span> <span class="fl">511</span>, <span class="va">item_code</span> <span class="op">==</span> <span class="fl">3010</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">transmute</a></span><span class="op">(</span><span class="va">area</span>, <span class="va">area_code</span>, <span class="va">year</span>, value <span class="op">=</span> <span class="va">value</span> <span class="op">/</span> <span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">BaseYear</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">year</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="va">BaseYear</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="fu">gcamdata</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/gcamdata/man/left_join_error_no_match.html" class="external-link">left_join_error_no_match</a></span><span class="op">(</span><span class="va">AGLU_ctry</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span>area <span class="op">=</span> <span class="va">FAO_country</span>, <span class="va">iso</span><span class="op">)</span>, by <span class="op">=</span> <span class="st">"area"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
-  <span class="fu">gcamdata</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/gcamdata/man/left_join_error_no_match.html" class="external-link">left_join_error_no_match</a></span><span class="op">(</span><span class="va">iso_GCAM_regID</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">iso</span>, <span class="va">GCAM_region_ID</span><span class="op">)</span>, by <span class="op">=</span> <span class="st">"iso"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate-joins.html" class="external-link">left_join</a></span><span class="op">(</span><span class="va">GCAM_region_names</span>, by <span class="op">=</span> <span class="st">"GCAM_region_ID"</span><span class="op">)</span> <span class="op">-&gt;</span> 
-  <span class="va">POP</span> <span class="co">#1000 persons</span></code></pre></div>
+<code class="sourceCode R"><span><span class="co"># simplify population data</span></span>
+<span><span class="va">OA</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">element_code</span> <span class="op">==</span> <span class="fl">511</span>, <span class="va">item_code</span> <span class="op">==</span> <span class="fl">3010</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">transmute</a></span><span class="op">(</span><span class="va">area</span>, <span class="va">area_code</span>, <span class="va">year</span>, value <span class="op">=</span> <span class="va">value</span> <span class="op">/</span> <span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">BaseYear</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">year</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="va">BaseYear</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="fu">gcamdata</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/gcamdata/man/left_join_error_no_match.html" class="external-link">left_join_error_no_match</a></span><span class="op">(</span><span class="va">AGLU_ctry</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span>area <span class="op">=</span> <span class="va">FAO_country</span>, <span class="va">iso</span><span class="op">)</span>, by <span class="op">=</span> <span class="st">"area"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>  <span class="fu">gcamdata</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/gcamdata/man/left_join_error_no_match.html" class="external-link">left_join_error_no_match</a></span><span class="op">(</span><span class="va">iso_GCAM_regID</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">iso</span>, <span class="va">GCAM_region_ID</span><span class="op">)</span>, by <span class="op">=</span> <span class="st">"iso"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate-joins.html" class="external-link">left_join</a></span><span class="op">(</span><span class="va">GCAM_region_names</span>, by <span class="op">=</span> <span class="st">"GCAM_region_ID"</span><span class="op">)</span> <span class="op">-&gt;</span> </span>
+<span>  <span class="va">POP</span> <span class="co">#1000 persons</span></span></code></pre></div>
 <ul>
 <li>Plot and save</li>
 </ul>
 <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="co"># Figure title</span>
-<span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="st">"World population grouped by GCAM 32 regions, "</span>, <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">min</a></span><span class="op">(</span><span class="va">BaseYear</span><span class="op">)</span>, <span class="st">"-"</span>, <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="va">BaseYear</span><span class="op">)</span>, <span class="st">" mean ("</span>,
-       <span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">round</a></span><span class="op">(</span><span class="va">POP</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarize</a></span><span class="op">(</span>value <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="op">/</span> <span class="fl">1000000</span><span class="op">)</span>,<span class="fl">1</span><span class="op">)</span>, <span class="st">" Billion)"</span><span class="op">)</span> <span class="op">-&gt;</span> <span class="va">title</span>
-
-<span class="fu"><a href="../reference/treemap_wrapper.html">treemap_wrapper</a></span><span class="op">(</span>
-  .DF <span class="op">=</span> <span class="va">POP</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">region</span>, <span class="va">area</span>, <span class="va">value</span><span class="op">)</span>, 
-  .Depth <span class="op">=</span> <span class="fl">2</span>,
-  .Palette <span class="op">=</span> <span class="st">"YlOrRd"</span>, .LastLabelCol <span class="op">=</span> <span class="st">"blue"</span>,
-  .FigTitle <span class="op">=</span> <span class="va">title</span>, .FigTitleSize <span class="op">=</span> <span class="fl">16</span>, 
-  .SaveName <span class="op">=</span> <span class="st">"Fig_WorldPopulation"</span>, 
-  .SaveScaler <span class="op">=</span> <span class="fl">1.2</span>
-<span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span><span class="co"># Figure title</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="st">"World population grouped by GCAM 32 regions, "</span>, <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">min</a></span><span class="op">(</span><span class="va">BaseYear</span><span class="op">)</span>, <span class="st">"-"</span>, <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="va">BaseYear</span><span class="op">)</span>, <span class="st">" mean ("</span>,</span>
+<span>       <span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">round</a></span><span class="op">(</span><span class="va">POP</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarize</a></span><span class="op">(</span>value <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="op">/</span> <span class="fl">1000000</span><span class="op">)</span>,<span class="fl">1</span><span class="op">)</span>, <span class="st">" Billion)"</span><span class="op">)</span> <span class="op">-&gt;</span> <span class="va">title</span></span>
+<span></span>
+<span><span class="fu"><a href="../reference/treemap_wrapper.html">treemap_wrapper</a></span><span class="op">(</span></span>
+<span>  .DF <span class="op">=</span> <span class="va">POP</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">region</span>, <span class="va">area</span>, <span class="va">value</span><span class="op">)</span>, </span>
+<span>  .Depth <span class="op">=</span> <span class="fl">2</span>,</span>
+<span>  .Palette <span class="op">=</span> <span class="st">"YlOrRd"</span>, .LastLabelCol <span class="op">=</span> <span class="st">"blue"</span>,</span>
+<span>  .FigTitle <span class="op">=</span> <span class="va">title</span>, .FigTitleSize <span class="op">=</span> <span class="fl">16</span>, </span>
+<span>  .SaveName <span class="op">=</span> <span class="st">"Fig_WorldPopulation"</span>, </span>
+<span>  .SaveScaler <span class="op">=</span> <span class="fl">1.2</span></span>
+<span><span class="op">)</span></span></code></pre></div>
 <ul>
 <li>Preview<br><img src="../reference/figures/Fig_WorldPopulation.png" style="width:20.0%" alt="Population">
 </li>
@@ -298,52 +298,52 @@ <h3 id="harvested-area-1">2. Harvested area<a class="anchor" aria-label="anchor"
 <li>Get data ready</li>
 </ul>
 <div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">QCL_CROP_PRIMARY</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/bind.html" class="external-link">bind_rows</a></span><span class="op">(</span><span class="va">QCL_FODDERCROP</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">year</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="va">BaseYear</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">element</span> <span class="op">==</span> <span class="st">"Area harvested"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="co"># Change to Mha</span>
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>value <span class="op">=</span> <span class="va">value</span> <span class="op">/</span> <span class="fl">1000000</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="op">-</span><span class="va">unit</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
-  <span class="co"># the iso mapping in AGLU_ctry works good now</span>
-  <span class="fu">gcamdata</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/gcamdata/man/left_join_error_no_match.html" class="external-link">left_join_error_no_match</a></span><span class="op">(</span><span class="va">AGLU_ctry</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span>area <span class="op">=</span> <span class="va">FAO_country</span>, <span class="va">iso</span><span class="op">)</span>, by <span class="op">=</span> <span class="st">"area"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
-  <span class="fu">gcamdata</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/gcamdata/man/left_join_error_no_match.html" class="external-link">left_join_error_no_match</a></span><span class="op">(</span><span class="va">iso_GCAM_regID</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">iso</span>, <span class="va">GCAM_region_ID</span><span class="op">)</span>, by <span class="op">=</span> <span class="st">"iso"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate-joins.html" class="external-link">left_join</a></span><span class="op">(</span><span class="va">GCAM_region_names</span>, by <span class="op">=</span> <span class="st">"GCAM_region_ID"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">region</span>, <span class="va">item_code</span>, <span class="va">item</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="co"># 5-year average</span>
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarize</a></span><span class="op">(</span>value <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="op">/</span> <span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">BaseYear</span><span class="op">)</span>, .groups <span class="op">=</span> <span class="st">"drop"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">ungroup</a></span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate-joins.html" class="external-link">inner_join</a></span><span class="op">(</span>
-    <span class="va">FAO_ag_items_PRODSTAT</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
-      <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">item</span><span class="op">)</span>, <span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">GCAM_commodity</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
-      <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">item_code</span>, <span class="va">GCAM_subsector</span><span class="op">)</span>, by <span class="op">=</span> <span class="st">"item_code"</span><span class="op">)</span> <span class="op">-&gt;</span>
-  <span class="va">Tree_Area_Reg_Sector</span></code></pre></div>
+<code class="sourceCode R"><span><span class="va">QCL_CROP_PRIMARY</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/bind.html" class="external-link">bind_rows</a></span><span class="op">(</span><span class="va">QCL_FODDERCROP</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">year</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="va">BaseYear</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">element</span> <span class="op">==</span> <span class="st">"Area harvested"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="co"># Change to Mha</span></span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>value <span class="op">=</span> <span class="va">value</span> <span class="op">/</span> <span class="fl">1000000</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="op">-</span><span class="va">unit</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>  <span class="co"># the iso mapping in AGLU_ctry works good now</span></span>
+<span>  <span class="fu">gcamdata</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/gcamdata/man/left_join_error_no_match.html" class="external-link">left_join_error_no_match</a></span><span class="op">(</span><span class="va">AGLU_ctry</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span>area <span class="op">=</span> <span class="va">FAO_country</span>, <span class="va">iso</span><span class="op">)</span>, by <span class="op">=</span> <span class="st">"area"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>  <span class="fu">gcamdata</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/gcamdata/man/left_join_error_no_match.html" class="external-link">left_join_error_no_match</a></span><span class="op">(</span><span class="va">iso_GCAM_regID</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">iso</span>, <span class="va">GCAM_region_ID</span><span class="op">)</span>, by <span class="op">=</span> <span class="st">"iso"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate-joins.html" class="external-link">left_join</a></span><span class="op">(</span><span class="va">GCAM_region_names</span>, by <span class="op">=</span> <span class="st">"GCAM_region_ID"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">region</span>, <span class="va">item_code</span>, <span class="va">item</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="co"># 5-year average</span></span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarize</a></span><span class="op">(</span>value <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="op">/</span> <span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">BaseYear</span><span class="op">)</span>, .groups <span class="op">=</span> <span class="st">"drop"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">ungroup</a></span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate-joins.html" class="external-link">inner_join</a></span><span class="op">(</span></span>
+<span>    <span class="va">FAO_ag_items_PRODSTAT</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>      <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">item</span><span class="op">)</span>, <span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">GCAM_commodity</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>      <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">item_code</span>, <span class="va">GCAM_subsector</span><span class="op">)</span>, by <span class="op">=</span> <span class="st">"item_code"</span><span class="op">)</span> <span class="op">-&gt;</span></span>
+<span>  <span class="va">Tree_Area_Reg_Sector</span></span></code></pre></div>
 <ul>
 <li>Plot and save</li>
 </ul>
 <div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="st">"World area harvested grouped by GCAM crops, "</span>, <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">min</a></span><span class="op">(</span><span class="va">BaseYear</span><span class="op">)</span>, <span class="st">"-"</span>, <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="va">BaseYear</span><span class="op">)</span>, <span class="st">" mean ("</span>,
-       <span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">round</a></span><span class="op">(</span><span class="va">Tree_Area_Reg_Sector</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarize</a></span><span class="op">(</span>value <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="op">)</span>,<span class="fl">0</span><span class="op">)</span>, <span class="st">" Mha)"</span><span class="op">)</span> <span class="op">-&gt;</span> <span class="va">title</span>
-
-<span class="fu"><a href="../reference/treemap_wrapper.html">treemap_wrapper</a></span><span class="op">(</span>
-  .DF <span class="op">=</span> <span class="va">Tree_Area_Reg_Sector</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">GCAM_subsector</span>, <span class="va">item</span>, <span class="va">value</span><span class="op">)</span>, 
-  .Depth <span class="op">=</span> <span class="fl">2</span>,
-  .Palette <span class="op">=</span> <span class="st">"Set2"</span>,
-  .FigTitle <span class="op">=</span> <span class="va">title</span>, .FigTitleSize <span class="op">=</span> <span class="fl">16</span>, 
-  .SaveName <span class="op">=</span> <span class="st">"Fig_WorldAreaHarvested"</span>, 
-  .SaveScaler <span class="op">=</span> <span class="fl">1.1</span>
-<span class="op">)</span>
-
-<span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="st">"World area harvested grouped by GCAM crops and regions, "</span>, <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">min</a></span><span class="op">(</span><span class="va">BaseYear</span><span class="op">)</span>, <span class="st">"-"</span>, <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="va">BaseYear</span><span class="op">)</span>, <span class="st">" mean ("</span>,
-       <span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">round</a></span><span class="op">(</span><span class="va">Tree_Area_Reg_Sector</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarize</a></span><span class="op">(</span>value <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="op">)</span>,<span class="fl">0</span><span class="op">)</span>, <span class="st">" Mha)"</span><span class="op">)</span> <span class="op">-&gt;</span> <span class="va">title</span>
-
-<span class="fu"><a href="../reference/treemap_wrapper.html">treemap_wrapper</a></span><span class="op">(</span>
-  .DF <span class="op">=</span> <span class="va">Tree_Area_Reg_Sector</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">region</span>, <span class="va">GCAM_subsector</span>, <span class="va">item</span>, <span class="va">value</span><span class="op">)</span>, 
-  .Depth <span class="op">=</span> <span class="fl">3</span>,
-  .Palette <span class="op">=</span> <span class="st">"Set2"</span>,
-  .FigTitle <span class="op">=</span> <span class="va">title</span>, .FigTitleSize <span class="op">=</span> <span class="fl">20</span>,
-  .SaveName <span class="op">=</span> <span class="st">"Fig_WorldAreaHarvestedReg"</span>, 
-  .SaveScaler <span class="op">=</span> <span class="fl">1.6</span>
-<span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="st">"World area harvested grouped by GCAM crops, "</span>, <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">min</a></span><span class="op">(</span><span class="va">BaseYear</span><span class="op">)</span>, <span class="st">"-"</span>, <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="va">BaseYear</span><span class="op">)</span>, <span class="st">" mean ("</span>,</span>
+<span>       <span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">round</a></span><span class="op">(</span><span class="va">Tree_Area_Reg_Sector</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarize</a></span><span class="op">(</span>value <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="op">)</span>,<span class="fl">0</span><span class="op">)</span>, <span class="st">" Mha)"</span><span class="op">)</span> <span class="op">-&gt;</span> <span class="va">title</span></span>
+<span></span>
+<span><span class="fu"><a href="../reference/treemap_wrapper.html">treemap_wrapper</a></span><span class="op">(</span></span>
+<span>  .DF <span class="op">=</span> <span class="va">Tree_Area_Reg_Sector</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">GCAM_subsector</span>, <span class="va">item</span>, <span class="va">value</span><span class="op">)</span>, </span>
+<span>  .Depth <span class="op">=</span> <span class="fl">2</span>,</span>
+<span>  .Palette <span class="op">=</span> <span class="st">"Set2"</span>,</span>
+<span>  .FigTitle <span class="op">=</span> <span class="va">title</span>, .FigTitleSize <span class="op">=</span> <span class="fl">16</span>, </span>
+<span>  .SaveName <span class="op">=</span> <span class="st">"Fig_WorldAreaHarvested"</span>, </span>
+<span>  .SaveScaler <span class="op">=</span> <span class="fl">1.1</span></span>
+<span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="st">"World area harvested grouped by GCAM crops and regions, "</span>, <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">min</a></span><span class="op">(</span><span class="va">BaseYear</span><span class="op">)</span>, <span class="st">"-"</span>, <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="va">BaseYear</span><span class="op">)</span>, <span class="st">" mean ("</span>,</span>
+<span>       <span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">round</a></span><span class="op">(</span><span class="va">Tree_Area_Reg_Sector</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarize</a></span><span class="op">(</span>value <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="op">)</span>,<span class="fl">0</span><span class="op">)</span>, <span class="st">" Mha)"</span><span class="op">)</span> <span class="op">-&gt;</span> <span class="va">title</span></span>
+<span></span>
+<span><span class="fu"><a href="../reference/treemap_wrapper.html">treemap_wrapper</a></span><span class="op">(</span></span>
+<span>  .DF <span class="op">=</span> <span class="va">Tree_Area_Reg_Sector</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">region</span>, <span class="va">GCAM_subsector</span>, <span class="va">item</span>, <span class="va">value</span><span class="op">)</span>, </span>
+<span>  .Depth <span class="op">=</span> <span class="fl">3</span>,</span>
+<span>  .Palette <span class="op">=</span> <span class="st">"Set2"</span>,</span>
+<span>  .FigTitle <span class="op">=</span> <span class="va">title</span>, .FigTitleSize <span class="op">=</span> <span class="fl">20</span>,</span>
+<span>  .SaveName <span class="op">=</span> <span class="st">"Fig_WorldAreaHarvestedReg"</span>, </span>
+<span>  .SaveScaler <span class="op">=</span> <span class="fl">1.6</span></span>
+<span><span class="op">)</span></span></code></pre></div>
 <ul>
 <li>Preview<br><img src="../reference/figures/Fig_WorldAreaHarvested.png" style="width:20.0%"><img src="../reference/figures/Fig_WorldAreaHarvestedReg.png" style="width:20.0%">
 </li>
@@ -356,92 +356,92 @@ <h3 id="yield">3. Yield<a class="anchor" aria-label="anchor" href="#yield"></a>
 <li>Get data ready</li>
 </ul>
 <div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
-<code class="sourceCode R">
-<span class="va">YieldBaseYear</span> <span class="op">=</span> <span class="fl">1990</span>
-<span class="va">QCL_CROP_PRIMARY</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="co"># disaggregate dissolved regions in history</span>
-  <span class="fu"><a href="../reference/FAO_AREA_DISAGGREGATE_HIST_DISSOLUTION_ALL.html">FAO_AREA_DISAGGREGATE_HIST_DISSOLUTION_ALL</a></span><span class="op">(</span>SUDAN2012_MERGE <span class="op">=</span> <span class="cn">T</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="co"># the iso mapping in AGLU_ctry works good now</span>
-  <span class="fu"><a href="../reference/left_join_error_no_match.html">left_join_error_no_match</a></span><span class="op">(</span><span class="va">AGLU_ctry</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span>area <span class="op">=</span> <span class="va">FAO_country</span>, <span class="va">iso</span><span class="op">)</span>, by <span class="op">=</span> <span class="st">"area"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
-  <span class="fu"><a href="../reference/left_join_error_no_match.html">left_join_error_no_match</a></span><span class="op">(</span><span class="va">iso_GCAM_regID</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">iso</span>, <span class="va">GCAM_region_ID</span><span class="op">)</span>, by <span class="op">=</span> <span class="st">"iso"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate-joins.html" class="external-link">left_join</a></span><span class="op">(</span><span class="va">GCAM_region_names</span>, by <span class="op">=</span> <span class="st">"GCAM_region_ID"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">GCAM_region_ID</span>, <span class="va">region</span>, <span class="va">element</span>, <span class="va">unit</span>, <span class="va">year</span>, <span class="va">item_code</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="co"># aggregate to 32 GCAM regions</span>
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarize</a></span><span class="op">(</span>value <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">value</span><span class="op">)</span>, .groups <span class="op">=</span> <span class="st">"drop"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate-joins.html" class="external-link">inner_join</a></span><span class="op">(</span>
-    <span class="va">FAO_ag_items_PRODSTAT</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
-      <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">item</span><span class="op">)</span>, <span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">GCAM_commodity</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
-      <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">item_code</span>, <span class="va">GCAM_subsector</span><span class="op">)</span>, by <span class="op">=</span> <span class="st">"item_code"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by_all.html" class="external-link">group_by_at</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">GCAM_region_ID</span>, <span class="va">region</span>, <span class="va">GCAM_subsector</span>, <span class="va">year</span>, <span class="va">element</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="co"># Aggregate to GCAM sectors</span>
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarize</a></span><span class="op">(</span>value <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">value</span><span class="op">)</span>, .groups <span class="op">=</span> <span class="st">"drop"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">year</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="va">YieldBaseYear</span>, <span class="fl">2020</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="fu">spread</span><span class="op">(</span><span class="va">element</span>, <span class="va">value</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">`Area harvested`</span> <span class="op">&gt;</span> <span class="fl">0</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
-  <span class="co"># Calculate regio-sector yield</span>
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>Yield <span class="op">=</span> <span class="va">Production</span> <span class="op">/</span> <span class="va">`Area harvested`</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
-  <span class="fu">gather</span><span class="op">(</span><span class="va">element</span>, <span class="va">value</span>, <span class="va">`Area harvested`</span>, <span class="va">Production</span>,  <span class="va">Yield</span><span class="op">)</span> <span class="op">-&gt;</span>
-  <span class="va">Yield_1990_2020_GCAMRegSector</span>
-
-<span class="va">Yield_1990_2020_GCAMRegSector</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">element</span> <span class="op">==</span> <span class="st">"Yield"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by_all.html" class="external-link">group_by_at</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="op">-</span><span class="va">year</span>, <span class="op">-</span><span class="va">value</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
-  <span class="co"># Calculate growth rate</span>
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>value <span class="op">=</span> <span class="va">value</span> <span class="op">/</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/nth.html" class="external-link">first</a></span><span class="op">(</span><span class="va">value</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">value</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">year</span> <span class="op">!=</span> <span class="va">YieldBaseYear</span><span class="op">)</span> <span class="op">-&gt;</span>
-  <span class="va">Yield_1990_2020_GCAMRegSector_Growth</span>
-
-<span class="va">Yield_1990_2020_GCAMRegSector_Growth</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="co"># Join area to get weight</span>
-  <span class="fu"><a href="../reference/left_join_error_no_match.html">left_join_error_no_match</a></span><span class="op">(</span><span class="va">Yield_1990_2020_GCAMRegSector</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-                             <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">element</span> <span class="op">==</span> <span class="st">"Area harvested"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu">spread</span><span class="op">(</span><span class="va">element</span>, <span class="va">value</span><span class="op">)</span>, 
-                           by <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"GCAM_region_ID"</span>, <span class="st">"region"</span>, <span class="st">"GCAM_subsector"</span>, <span class="st">"year"</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by_all.html" class="external-link">group_by_at</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">GCAM_subsector</span>, <span class="va">year</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarize</a></span><span class="op">(</span>value <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/weighted.mean.html" class="external-link">weighted.mean</a></span><span class="op">(</span><span class="va">value</span>, w <span class="op">=</span> <span class="va">`Area harvested`</span><span class="op">)</span>, .groups <span class="op">=</span> <span class="st">"drop"</span><span class="op">)</span><span class="op">-&gt;</span> 
-  <span class="va">Yield_1990_2020_WorldGCAMSector_Growth_FixdArea</span>
-
-<span class="va">Yield_1990_2020_GCAMRegSector</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="fu">spread</span><span class="op">(</span><span class="va">element</span>, <span class="va">value</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by_all.html" class="external-link">group_by_at</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">GCAM_subsector</span>, <span class="va">year</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarize</a></span><span class="op">(</span>Production <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">Production</span><span class="op">)</span>,
-         `Area harvested` <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">`Area harvested`</span><span class="op">)</span>, .groups <span class="op">=</span> <span class="st">"drop"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>Yield <span class="op">=</span> <span class="va">Production</span> <span class="op">/</span> <span class="va">`Area harvested`</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
-  <span class="fu">gather</span><span class="op">(</span><span class="va">element</span>, <span class="va">value</span>, <span class="va">`Area harvested`</span>, <span class="va">Production</span>,  <span class="va">Yield</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">element</span> <span class="op">==</span> <span class="st">"Yield"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by_all.html" class="external-link">group_by_at</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="op">-</span><span class="va">year</span>, <span class="op">-</span><span class="va">value</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>value <span class="op">=</span> <span class="va">value</span> <span class="op">/</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/nth.html" class="external-link">first</a></span><span class="op">(</span><span class="va">value</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">value</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">year</span> <span class="op">!=</span> <span class="va">YieldBaseYear</span><span class="op">)</span> <span class="op">-&gt;</span>
-  <span class="va">Yield_1990_2020_WorldGCAMSector_Growth_ChangingArea</span>
-
-<span class="co"># Order sectors</span>
-<span class="va">Yield_1990_2020_WorldGCAMSector_Growth_ChangingArea</span><span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="op">-</span><span class="va">value</span><span class="op">)</span>  <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/pull.html" class="external-link">pull</a></span><span class="op">(</span><span class="va">GCAM_subsector</span><span class="op">)</span> <span class="op">-&gt;</span> <span class="va">SectorRank</span></code></pre></div>
+<code class="sourceCode R"><span></span>
+<span><span class="va">YieldBaseYear</span> <span class="op">=</span> <span class="fl">1990</span></span>
+<span><span class="va">QCL_CROP_PRIMARY</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="co"># disaggregate dissolved regions in history</span></span>
+<span>  <span class="fu"><a href="../reference/FAO_AREA_DISAGGREGATE_HIST_DISSOLUTION_ALL.html">FAO_AREA_DISAGGREGATE_HIST_DISSOLUTION_ALL</a></span><span class="op">(</span>SUDAN2012_MERGE <span class="op">=</span> <span class="cn">T</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="co"># the iso mapping in AGLU_ctry works good now</span></span>
+<span>  <span class="fu"><a href="../reference/left_join_error_no_match.html">left_join_error_no_match</a></span><span class="op">(</span><span class="va">AGLU_ctry</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span>area <span class="op">=</span> <span class="va">FAO_country</span>, <span class="va">iso</span><span class="op">)</span>, by <span class="op">=</span> <span class="st">"area"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>  <span class="fu"><a href="../reference/left_join_error_no_match.html">left_join_error_no_match</a></span><span class="op">(</span><span class="va">iso_GCAM_regID</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">iso</span>, <span class="va">GCAM_region_ID</span><span class="op">)</span>, by <span class="op">=</span> <span class="st">"iso"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate-joins.html" class="external-link">left_join</a></span><span class="op">(</span><span class="va">GCAM_region_names</span>, by <span class="op">=</span> <span class="st">"GCAM_region_ID"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">GCAM_region_ID</span>, <span class="va">region</span>, <span class="va">element</span>, <span class="va">unit</span>, <span class="va">year</span>, <span class="va">item_code</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="co"># aggregate to 32 GCAM regions</span></span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarize</a></span><span class="op">(</span>value <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">value</span><span class="op">)</span>, .groups <span class="op">=</span> <span class="st">"drop"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate-joins.html" class="external-link">inner_join</a></span><span class="op">(</span></span>
+<span>    <span class="va">FAO_ag_items_PRODSTAT</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>      <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">item</span><span class="op">)</span>, <span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">GCAM_commodity</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>      <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">item_code</span>, <span class="va">GCAM_subsector</span><span class="op">)</span>, by <span class="op">=</span> <span class="st">"item_code"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by_all.html" class="external-link">group_by_at</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">GCAM_region_ID</span>, <span class="va">region</span>, <span class="va">GCAM_subsector</span>, <span class="va">year</span>, <span class="va">element</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="co"># Aggregate to GCAM sectors</span></span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarize</a></span><span class="op">(</span>value <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">value</span><span class="op">)</span>, .groups <span class="op">=</span> <span class="st">"drop"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">year</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="va">YieldBaseYear</span>, <span class="fl">2020</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="fu">spread</span><span class="op">(</span><span class="va">element</span>, <span class="va">value</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">`Area harvested`</span> <span class="op">&gt;</span> <span class="fl">0</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>  <span class="co"># Calculate regio-sector yield</span></span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>Yield <span class="op">=</span> <span class="va">Production</span> <span class="op">/</span> <span class="va">`Area harvested`</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>  <span class="fu">gather</span><span class="op">(</span><span class="va">element</span>, <span class="va">value</span>, <span class="va">`Area harvested`</span>, <span class="va">Production</span>,  <span class="va">Yield</span><span class="op">)</span> <span class="op">-&gt;</span></span>
+<span>  <span class="va">Yield_1990_2020_GCAMRegSector</span></span>
+<span></span>
+<span><span class="va">Yield_1990_2020_GCAMRegSector</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">element</span> <span class="op">==</span> <span class="st">"Yield"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by_all.html" class="external-link">group_by_at</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="op">-</span><span class="va">year</span>, <span class="op">-</span><span class="va">value</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>  <span class="co"># Calculate growth rate</span></span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>value <span class="op">=</span> <span class="va">value</span> <span class="op">/</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/nth.html" class="external-link">first</a></span><span class="op">(</span><span class="va">value</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">value</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">year</span> <span class="op">!=</span> <span class="va">YieldBaseYear</span><span class="op">)</span> <span class="op">-&gt;</span></span>
+<span>  <span class="va">Yield_1990_2020_GCAMRegSector_Growth</span></span>
+<span></span>
+<span><span class="va">Yield_1990_2020_GCAMRegSector_Growth</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="co"># Join area to get weight</span></span>
+<span>  <span class="fu"><a href="../reference/left_join_error_no_match.html">left_join_error_no_match</a></span><span class="op">(</span><span class="va">Yield_1990_2020_GCAMRegSector</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>                             <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">element</span> <span class="op">==</span> <span class="st">"Area harvested"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu">spread</span><span class="op">(</span><span class="va">element</span>, <span class="va">value</span><span class="op">)</span>, </span>
+<span>                           by <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"GCAM_region_ID"</span>, <span class="st">"region"</span>, <span class="st">"GCAM_subsector"</span>, <span class="st">"year"</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by_all.html" class="external-link">group_by_at</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">GCAM_subsector</span>, <span class="va">year</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarize</a></span><span class="op">(</span>value <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/weighted.mean.html" class="external-link">weighted.mean</a></span><span class="op">(</span><span class="va">value</span>, w <span class="op">=</span> <span class="va">`Area harvested`</span><span class="op">)</span>, .groups <span class="op">=</span> <span class="st">"drop"</span><span class="op">)</span><span class="op">-&gt;</span> </span>
+<span>  <span class="va">Yield_1990_2020_WorldGCAMSector_Growth_FixdArea</span></span>
+<span></span>
+<span><span class="va">Yield_1990_2020_GCAMRegSector</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="fu">spread</span><span class="op">(</span><span class="va">element</span>, <span class="va">value</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by_all.html" class="external-link">group_by_at</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">GCAM_subsector</span>, <span class="va">year</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarize</a></span><span class="op">(</span>Production <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">Production</span><span class="op">)</span>,</span>
+<span>         `Area harvested` <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">`Area harvested`</span><span class="op">)</span>, .groups <span class="op">=</span> <span class="st">"drop"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>Yield <span class="op">=</span> <span class="va">Production</span> <span class="op">/</span> <span class="va">`Area harvested`</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>  <span class="fu">gather</span><span class="op">(</span><span class="va">element</span>, <span class="va">value</span>, <span class="va">`Area harvested`</span>, <span class="va">Production</span>,  <span class="va">Yield</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">element</span> <span class="op">==</span> <span class="st">"Yield"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by_all.html" class="external-link">group_by_at</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="op">-</span><span class="va">year</span>, <span class="op">-</span><span class="va">value</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>value <span class="op">=</span> <span class="va">value</span> <span class="op">/</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/nth.html" class="external-link">first</a></span><span class="op">(</span><span class="va">value</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">value</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">year</span> <span class="op">!=</span> <span class="va">YieldBaseYear</span><span class="op">)</span> <span class="op">-&gt;</span></span>
+<span>  <span class="va">Yield_1990_2020_WorldGCAMSector_Growth_ChangingArea</span></span>
+<span></span>
+<span><span class="co"># Order sectors</span></span>
+<span><span class="va">Yield_1990_2020_WorldGCAMSector_Growth_ChangingArea</span><span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="op">-</span><span class="va">value</span><span class="op">)</span>  <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/pull.html" class="external-link">pull</a></span><span class="op">(</span><span class="va">GCAM_subsector</span><span class="op">)</span> <span class="op">-&gt;</span> <span class="va">SectorRank</span></span></code></pre></div>
 <ul>
 <li>Plot and save</li>
 </ul>
 <div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">Yield_1990_2020_GCAMRegSector_Growth</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>GCAM_subsector <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a></span><span class="op">(</span><span class="va">GCAM_subsector</span>, levels <span class="op">=</span> <span class="va">SectorRank</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>  
-  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span> 
-  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_boxplot.html" class="external-link">geom_boxplot</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span>x <span class="op">=</span> <span class="va">GCAM_subsector</span>, y <span class="op">=</span> <span class="va">value</span>, fill <span class="op">=</span> <span class="va">GCAM_subsector</span><span class="op">)</span>, outlier.size <span class="op">=</span> <span class="op">-</span><span class="fl">1</span><span class="op">)</span> <span class="op">+</span>
-  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_path.html" class="external-link">geom_line</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">Yield_1990_2020_WorldGCAMSector_Growth_ChangingArea</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-              <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>GCAM_subsector <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a></span><span class="op">(</span><span class="va">GCAM_subsector</span>, levels <span class="op">=</span> <span class="va">SectorRank</span><span class="op">)</span><span class="op">)</span>,
-             <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span>x <span class="op">=</span> <span class="va">GCAM_subsector</span>, y <span class="op">=</span> <span class="va">value</span>, group <span class="op">=</span> <span class="va">year</span><span class="op">)</span>, color <span class="op">=</span> <span class="st">"blue"</span>, size <span class="op">=</span> <span class="fl">1.6</span>, alpha <span class="op">=</span> <span class="fl">0.9</span> <span class="op">)</span> <span class="op">+</span>
-  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_point.html" class="external-link">geom_point</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">Yield_1990_2020_WorldGCAMSector_Growth_FixdArea</span>,
-             <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span>x <span class="op">=</span> <span class="va">GCAM_subsector</span>, y <span class="op">=</span> <span class="va">value</span><span class="op">)</span>, fill <span class="op">=</span> <span class="st">"red"</span>, size <span class="op">=</span> <span class="fl">2.5</span>, shape <span class="op">=</span> <span class="fl">21</span>, color <span class="op">=</span> <span class="st">"black"</span> <span class="op">)</span> <span class="op">+</span>
-  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/scale_continuous.html" class="external-link">scale_y_continuous</a></span><span class="op">(</span>limits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">3.3</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span>
-  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span>y <span class="op">=</span> <span class="st">"1990 = 1"</span>, x <span class="op">=</span> <span class="st">"GCAM Crop Sector"</span>,
-       title <span class="op">=</span> <span class="st">"Yield change in 1990 - 2020, distribution (Tukey style) across GCAM regions."</span>, 
-       subtitle <span class="op">=</span> <span class="st">"World mean growth (blue line) vs. weighted mean of regional growth (red dots)"</span>,
-       caption <span class="op">=</span> <span class="st">"Data: FAOSTAT \n Package: JGCRI/gcamfaostat"</span><span class="op">)</span> <span class="op">+</span>
-  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggtheme.html" class="external-link">theme_bw</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span> 
-  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/theme.html" class="external-link">theme</a></span><span class="op">(</span>text <span class="op">=</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/element.html" class="external-link">element_text</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">16</span><span class="op">)</span>,
-        axis.text <span class="op">=</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/element.html" class="external-link">element_text</a></span><span class="op">(</span>colour <span class="op">=</span> <span class="st">"black"</span>, size <span class="op">=</span> <span class="fl">16</span><span class="op">)</span>,
-        axis.text.x <span class="op">=</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/element.html" class="external-link">element_text</a></span><span class="op">(</span>angle <span class="op">=</span> <span class="fl">40</span>, hjust <span class="op">=</span> <span class="fl">1</span>, vjust <span class="op">=</span> <span class="fl">1</span><span class="op">)</span>,
-        strip.background <span class="op">=</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/element.html" class="external-link">element_rect</a></span><span class="op">(</span>fill <span class="op">=</span> <span class="st">"grey90"</span><span class="op">)</span>,
-        legend.position <span class="op">=</span> <span class="st">"none"</span><span class="op">)</span> <span class="op">-&gt;</span> <span class="va">p</span>
-
-<span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggsave.html" class="external-link">ggsave</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/file.path.html" class="external-link">file.path</a></span><span class="op">(</span><span class="st">"../man/figures"</span>, <span class="st">"WorldYield.png"</span><span class="op">)</span>, <span class="va">p</span>, width <span class="op">=</span> <span class="fl">15</span>, height <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span><span class="va">Yield_1990_2020_GCAMRegSector_Growth</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>GCAM_subsector <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a></span><span class="op">(</span><span class="va">GCAM_subsector</span>, levels <span class="op">=</span> <span class="va">SectorRank</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>  </span>
+<span>  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span> </span>
+<span>  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_boxplot.html" class="external-link">geom_boxplot</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span>x <span class="op">=</span> <span class="va">GCAM_subsector</span>, y <span class="op">=</span> <span class="va">value</span>, fill <span class="op">=</span> <span class="va">GCAM_subsector</span><span class="op">)</span>, outlier.size <span class="op">=</span> <span class="op">-</span><span class="fl">1</span><span class="op">)</span> <span class="op">+</span></span>
+<span>  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_path.html" class="external-link">geom_line</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">Yield_1990_2020_WorldGCAMSector_Growth_ChangingArea</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>              <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>GCAM_subsector <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a></span><span class="op">(</span><span class="va">GCAM_subsector</span>, levels <span class="op">=</span> <span class="va">SectorRank</span><span class="op">)</span><span class="op">)</span>,</span>
+<span>             <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span>x <span class="op">=</span> <span class="va">GCAM_subsector</span>, y <span class="op">=</span> <span class="va">value</span>, group <span class="op">=</span> <span class="va">year</span><span class="op">)</span>, color <span class="op">=</span> <span class="st">"blue"</span>, size <span class="op">=</span> <span class="fl">1.6</span>, alpha <span class="op">=</span> <span class="fl">0.9</span> <span class="op">)</span> <span class="op">+</span></span>
+<span>  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_point.html" class="external-link">geom_point</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">Yield_1990_2020_WorldGCAMSector_Growth_FixdArea</span>,</span>
+<span>             <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span>x <span class="op">=</span> <span class="va">GCAM_subsector</span>, y <span class="op">=</span> <span class="va">value</span><span class="op">)</span>, fill <span class="op">=</span> <span class="st">"red"</span>, size <span class="op">=</span> <span class="fl">2.5</span>, shape <span class="op">=</span> <span class="fl">21</span>, color <span class="op">=</span> <span class="st">"black"</span> <span class="op">)</span> <span class="op">+</span></span>
+<span>  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/scale_continuous.html" class="external-link">scale_y_continuous</a></span><span class="op">(</span>limits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">3.3</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span>
+<span>  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span>y <span class="op">=</span> <span class="st">"1990 = 1"</span>, x <span class="op">=</span> <span class="st">"GCAM Crop Sector"</span>,</span>
+<span>       title <span class="op">=</span> <span class="st">"Yield change in 1990 - 2020, distribution (Tukey style) across GCAM regions."</span>, </span>
+<span>       subtitle <span class="op">=</span> <span class="st">"World mean growth (blue line) vs. weighted mean of regional growth (red dots)"</span>,</span>
+<span>       caption <span class="op">=</span> <span class="st">"Data: FAOSTAT \n Package: JGCRI/gcamfaostat"</span><span class="op">)</span> <span class="op">+</span></span>
+<span>  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggtheme.html" class="external-link">theme_bw</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span> </span>
+<span>  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/theme.html" class="external-link">theme</a></span><span class="op">(</span>text <span class="op">=</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/element.html" class="external-link">element_text</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">16</span><span class="op">)</span>,</span>
+<span>        axis.text <span class="op">=</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/element.html" class="external-link">element_text</a></span><span class="op">(</span>colour <span class="op">=</span> <span class="st">"black"</span>, size <span class="op">=</span> <span class="fl">16</span><span class="op">)</span>,</span>
+<span>        axis.text.x <span class="op">=</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/element.html" class="external-link">element_text</a></span><span class="op">(</span>angle <span class="op">=</span> <span class="fl">40</span>, hjust <span class="op">=</span> <span class="fl">1</span>, vjust <span class="op">=</span> <span class="fl">1</span><span class="op">)</span>,</span>
+<span>        strip.background <span class="op">=</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/element.html" class="external-link">element_rect</a></span><span class="op">(</span>fill <span class="op">=</span> <span class="st">"grey90"</span><span class="op">)</span>,</span>
+<span>        legend.position <span class="op">=</span> <span class="st">"none"</span><span class="op">)</span> <span class="op">-&gt;</span> <span class="va">p</span></span>
+<span></span>
+<span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggsave.html" class="external-link">ggsave</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/file.path.html" class="external-link">file.path</a></span><span class="op">(</span><span class="st">"../man/figures"</span>, <span class="st">"WorldYield.png"</span><span class="op">)</span>, <span class="va">p</span>, width <span class="op">=</span> <span class="fl">15</span>, height <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></span></code></pre></div>
 <ul>
 <li>Preview<br><img src="../reference/figures/Fig_WorldYield.png" style="width:20.0%">
 </li>
@@ -454,73 +454,73 @@ <h3 id="supply-utilization-1">4. Supply-utilization<a class="anchor" aria-label=
 <li>Get data ready</li>
 </ul>
 <div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="co"># Define elements and items</span>
-<span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Opening stocks"</span>, <span class="st">"Import"</span>, <span class="st">"Production"</span><span class="op">)</span> <span class="op">-&gt;</span> <span class="va">ElEMSupply</span>
-<span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Food"</span>, <span class="st">"Feed"</span>,  <span class="st">"Processed"</span>, <span class="st">"Other uses"</span>, <span class="st">"Export"</span>, <span class="st">"Closing stocks"</span>, <span class="st">"Residuals"</span><span class="op">)</span> <span class="op">-&gt;</span> <span class="va">ELEMDemand</span>
-<span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="va">ElEMSupply</span>, <span class="va">ELEMDemand</span><span class="op">)</span> <span class="op">-&gt;</span> <span class="va">ELEMAll</span>
-
-<span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="va">ElEMSupply</span>, <span class="va">ELEMDemand</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="va">rev</span><span class="op">)</span> <span class="op">-&gt;</span> <span class="va">ELEMLevel</span>
-<span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="st">"Supply: "</span>, <span class="va">ElEMSupply</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="st">"Demand: "</span>, <span class="va">ELEMDemand</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="va">rev</span> <span class="op">)</span> <span class="op">-&gt;</span> <span class="va">ELEMLabel</span>
-<span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Maize"</span>, <span class="st">"Wheat"</span>, <span class="st">"Rice, paddy"</span>, <span class="st">"Soybeans"</span>, <span class="st">"Potatoes"</span>, <span class="st">"Oil palm fruit"</span>, <span class="st">"Bananas"</span>, <span class="st">"Avocados"</span><span class="op">)</span> <span class="op">-&gt;</span> <span class="va">KeySectorCrops</span>
-
-<span class="co"># These are items from FAO </span>
-<span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Meat, pig"</span>, <span class="st">"Meat, chicken"</span>, <span class="st">"Eggs, hen, in shell"</span>, <span class="st">"Meat, cattle"</span>, 
-  <span class="st">"Pelagic Fish"</span>, <span class="st">"Freshwater Fish"</span> , <span class="st">"Meat, sheep"</span>, <span class="st">"Meat, goat"</span><span class="op">)</span> <span class="op">-&gt;</span> <span class="va">KeySectorMeat</span>
-<span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="va">KeySectorCrops</span>, <span class="va">KeySectorMeat</span><span class="op">)</span> <span class="op">-&gt;</span> <span class="va">SECLevel</span>
-
-<span class="co"># Define color pal.</span>
-<span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/pkg/RColorBrewer/man/ColorBrewer.html" class="external-link">brewer.pal</a></span><span class="op">(</span>n <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">ELEMAll</span><span class="op">)</span>, name <span class="op">=</span> <span class="st">"Spectral"</span><span class="op">)</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">ElEMSupply</span><span class="op">)</span><span class="op">]</span>,
-  <span class="fu"><a href="https://rdrr.io/pkg/RColorBrewer/man/ColorBrewer.html" class="external-link">brewer.pal</a></span><span class="op">(</span>n <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">ELEMAll</span><span class="op">)</span>, name <span class="op">=</span> <span class="st">"Spectral"</span><span class="op">)</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">ElEMSupply</span><span class="op">)</span><span class="op">+</span><span class="fl">1</span><span class="op">:</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">ELEMDemand</span><span class="op">)</span><span class="op">]</span>
-<span class="op">)</span> <span class="op">-&gt;</span> <span class="va">ColUpdate</span>
-
-
-<span class="va">Bal_new_all</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">year</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="va">BaseYear</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
-  <span class="co"># Aggregate seed and loss into others</span>
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>element <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/replace.html" class="external-link">replace</a></span><span class="op">(</span><span class="va">element</span>, <span class="va">element</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Seed"</span>, <span class="st">"Loss"</span><span class="op">)</span>, <span class="st">"Other uses"</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by_all.html" class="external-link">group_by_at</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="op">-</span><span class="va">value</span>, <span class="op">-</span><span class="va">area_code</span>, <span class="op">-</span><span class="va">area</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarize</a></span><span class="op">(</span>value <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="op">/</span> <span class="fl">1000</span>, .groups <span class="op">=</span> <span class="st">"drop"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">element</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="va">ELEMAll</span>, <span class="va">item</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="va">SECLevel</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="co"># year-average</span>
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by_all.html" class="external-link">group_by_at</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="op">-</span><span class="va">value</span>, <span class="op">-</span><span class="va">year</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarize</a></span><span class="op">(</span>value <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="va">value</span><span class="op">)</span>, .groups <span class="op">=</span> <span class="st">"drop"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>value <span class="op">=</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/if_else.html" class="external-link">if_else</a></span><span class="op">(</span><span class="op">!</span><span class="va">element</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="va">ElEMSupply</span>, <span class="op">-</span><span class="va">value</span>, <span class="va">value</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>element <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a></span><span class="op">(</span><span class="va">element</span>, levels <span class="op">=</span> <span class="va">ELEMLevel</span>, labels <span class="op">=</span> <span class="va">ELEMLabel</span><span class="op">)</span>,
-         item <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a></span><span class="op">(</span><span class="va">item</span>, levels <span class="op">=</span> <span class="va">SECLevel</span>, labels <span class="op">=</span> <span class="va">SECLevel</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>CropMeat <span class="op">=</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/if_else.html" class="external-link">if_else</a></span><span class="op">(</span><span class="va">item</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="va">KeySectorCrops</span>, <span class="st">"Crop"</span>, <span class="st">"Meat"</span><span class="op">)</span><span class="op">)</span> <span class="op">-&gt;</span>
-  <span class="va">DF_SUA</span></code></pre></div>
+<code class="sourceCode R"><span><span class="co"># Define elements and items</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Opening stocks"</span>, <span class="st">"Import"</span>, <span class="st">"Production"</span><span class="op">)</span> <span class="op">-&gt;</span> <span class="va">ElEMSupply</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Food"</span>, <span class="st">"Feed"</span>,  <span class="st">"Processed"</span>, <span class="st">"Other uses"</span>, <span class="st">"Export"</span>, <span class="st">"Closing stocks"</span>, <span class="st">"Residuals"</span><span class="op">)</span> <span class="op">-&gt;</span> <span class="va">ELEMDemand</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="va">ElEMSupply</span>, <span class="va">ELEMDemand</span><span class="op">)</span> <span class="op">-&gt;</span> <span class="va">ELEMAll</span></span>
+<span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="va">ElEMSupply</span>, <span class="va">ELEMDemand</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="va">rev</span><span class="op">)</span> <span class="op">-&gt;</span> <span class="va">ELEMLevel</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="st">"Supply: "</span>, <span class="va">ElEMSupply</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="st">"Demand: "</span>, <span class="va">ELEMDemand</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="va">rev</span> <span class="op">)</span> <span class="op">-&gt;</span> <span class="va">ELEMLabel</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Maize"</span>, <span class="st">"Wheat"</span>, <span class="st">"Rice, paddy"</span>, <span class="st">"Soybeans"</span>, <span class="st">"Potatoes"</span>, <span class="st">"Oil palm fruit"</span>, <span class="st">"Bananas"</span>, <span class="st">"Avocados"</span><span class="op">)</span> <span class="op">-&gt;</span> <span class="va">KeySectorCrops</span></span>
+<span></span>
+<span><span class="co"># These are items from FAO </span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Meat, pig"</span>, <span class="st">"Meat, chicken"</span>, <span class="st">"Eggs, hen, in shell"</span>, <span class="st">"Meat, cattle"</span>, </span>
+<span>  <span class="st">"Pelagic Fish"</span>, <span class="st">"Freshwater Fish"</span> , <span class="st">"Meat, sheep"</span>, <span class="st">"Meat, goat"</span><span class="op">)</span> <span class="op">-&gt;</span> <span class="va">KeySectorMeat</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="va">KeySectorCrops</span>, <span class="va">KeySectorMeat</span><span class="op">)</span> <span class="op">-&gt;</span> <span class="va">SECLevel</span></span>
+<span></span>
+<span><span class="co"># Define color pal.</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/pkg/RColorBrewer/man/ColorBrewer.html" class="external-link">brewer.pal</a></span><span class="op">(</span>n <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">ELEMAll</span><span class="op">)</span>, name <span class="op">=</span> <span class="st">"Spectral"</span><span class="op">)</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">ElEMSupply</span><span class="op">)</span><span class="op">]</span>,</span>
+<span>  <span class="fu"><a href="https://rdrr.io/pkg/RColorBrewer/man/ColorBrewer.html" class="external-link">brewer.pal</a></span><span class="op">(</span>n <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">ELEMAll</span><span class="op">)</span>, name <span class="op">=</span> <span class="st">"Spectral"</span><span class="op">)</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">ElEMSupply</span><span class="op">)</span><span class="op">+</span><span class="fl">1</span><span class="op">:</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">ELEMDemand</span><span class="op">)</span><span class="op">]</span></span>
+<span><span class="op">)</span> <span class="op">-&gt;</span> <span class="va">ColUpdate</span></span>
+<span></span>
+<span></span>
+<span><span class="va">Bal_new_all</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">year</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="va">BaseYear</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>  <span class="co"># Aggregate seed and loss into others</span></span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>element <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/replace.html" class="external-link">replace</a></span><span class="op">(</span><span class="va">element</span>, <span class="va">element</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Seed"</span>, <span class="st">"Loss"</span><span class="op">)</span>, <span class="st">"Other uses"</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by_all.html" class="external-link">group_by_at</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="op">-</span><span class="va">value</span>, <span class="op">-</span><span class="va">area_code</span>, <span class="op">-</span><span class="va">area</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarize</a></span><span class="op">(</span>value <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="op">/</span> <span class="fl">1000</span>, .groups <span class="op">=</span> <span class="st">"drop"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">element</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="va">ELEMAll</span>, <span class="va">item</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="va">SECLevel</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="co"># year-average</span></span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by_all.html" class="external-link">group_by_at</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="op">-</span><span class="va">value</span>, <span class="op">-</span><span class="va">year</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarize</a></span><span class="op">(</span>value <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="va">value</span><span class="op">)</span>, .groups <span class="op">=</span> <span class="st">"drop"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>value <span class="op">=</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/if_else.html" class="external-link">if_else</a></span><span class="op">(</span><span class="op">!</span><span class="va">element</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="va">ElEMSupply</span>, <span class="op">-</span><span class="va">value</span>, <span class="va">value</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>element <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a></span><span class="op">(</span><span class="va">element</span>, levels <span class="op">=</span> <span class="va">ELEMLevel</span>, labels <span class="op">=</span> <span class="va">ELEMLabel</span><span class="op">)</span>,</span>
+<span>         item <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a></span><span class="op">(</span><span class="va">item</span>, levels <span class="op">=</span> <span class="va">SECLevel</span>, labels <span class="op">=</span> <span class="va">SECLevel</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>CropMeat <span class="op">=</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/if_else.html" class="external-link">if_else</a></span><span class="op">(</span><span class="va">item</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="va">KeySectorCrops</span>, <span class="st">"Crop"</span>, <span class="st">"Meat"</span><span class="op">)</span><span class="op">)</span> <span class="op">-&gt;</span></span>
+<span>  <span class="va">DF_SUA</span></span></code></pre></div>
 <ul>
 <li>Plot and save</li>
 </ul>
 <div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">DF_SUA</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/facet_wrap.html" class="external-link">facet_wrap</a></span><span class="op">(</span><span class="op">~</span><span class="va">CropMeat</span>, scales <span class="op">=</span> <span class="st">"free"</span><span class="op">)</span> <span class="op">+</span>
-    <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_bar.html" class="external-link">geom_bar</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span>x <span class="op">=</span> <span class="va">item</span>, y <span class="op">=</span> <span class="va">value</span>, fill <span class="op">=</span> <span class="va">element</span><span class="op">)</span>,
-             stat <span class="op">=</span> <span class="st">"identity"</span>, color <span class="op">=</span> <span class="st">"black"</span>, position<span class="op">=</span><span class="st">"stack"</span><span class="op">)</span> <span class="op">+</span>
-  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_abline.html" class="external-link">geom_hline</a></span><span class="op">(</span>yintercept <span class="op">=</span> <span class="fl">0</span><span class="op">)</span><span class="op">+</span>
-  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/scale_manual.html" class="external-link">scale_fill_manual</a></span><span class="op">(</span>values <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Supply: Opening stocks"</span> <span class="op">=</span> <span class="va">ColUpdate</span><span class="op">[</span><span class="fl">1</span><span class="op">]</span>, 
-                               <span class="st">"Supply: Import"</span> <span class="op">=</span> <span class="va">ColUpdate</span><span class="op">[</span><span class="fl">2</span><span class="op">]</span>, 
-                               <span class="st">"Supply: Production"</span> <span class="op">=</span> <span class="va">ColUpdate</span><span class="op">[</span><span class="fl">3</span><span class="op">]</span>,
-                               <span class="st">"Demand: Food"</span> <span class="op">=</span> <span class="va">ColUpdate</span><span class="op">[</span><span class="fl">4</span><span class="op">]</span>,
-                               <span class="st">"Demand: Feed"</span> <span class="op">=</span> <span class="va">ColUpdate</span><span class="op">[</span><span class="fl">5</span><span class="op">]</span>, 
-                               <span class="st">"Demand: Processed"</span> <span class="op">=</span> <span class="va">ColUpdate</span><span class="op">[</span><span class="fl">6</span><span class="op">]</span>,
-                               <span class="st">"Demand: Other uses"</span> <span class="op">=</span> <span class="va">ColUpdate</span><span class="op">[</span><span class="fl">7</span><span class="op">]</span>,
-                               <span class="st">"Demand: Residuals"</span> <span class="op">=</span> <span class="va">ColUpdate</span><span class="op">[</span><span class="fl">8</span><span class="op">]</span>,
-                               <span class="st">"Demand: Export"</span> <span class="op">=</span> <span class="va">ColUpdate</span><span class="op">[</span><span class="fl">9</span><span class="op">]</span>,
-                               <span class="st">"Demand: Closing stocks"</span> <span class="op">=</span> <span class="va">ColUpdate</span><span class="op">[</span><span class="fl">10</span><span class="op">]</span> <span class="op">)</span> <span class="op">)</span> <span class="op">+</span>
-  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span>x <span class="op">=</span> <span class="st">"Key agriculture Commodities"</span>,
-       y <span class="op">=</span> <span class="st">"Million tonnes"</span>, fill <span class="op">=</span> <span class="st">"Element"</span>,
-       title <span class="op">=</span> <span class="st">"World supply utilization for key commodities, 2013 - 2017 mean"</span>,
-       subtitle <span class="op">=</span> <span class="st">"Other uses include seed use, losses, and industrial use"</span>,
-       caption <span class="op">=</span> <span class="st">"Data: FAOSTAT \n Package: JGCRI/gcamfaostat"</span><span class="op">)</span> <span class="op">+</span>
-  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggtheme.html" class="external-link">theme_bw</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span> 
-  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/theme.html" class="external-link">theme</a></span><span class="op">(</span>text <span class="op">=</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/element.html" class="external-link">element_text</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">16</span><span class="op">)</span>,
-        axis.text <span class="op">=</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/element.html" class="external-link">element_text</a></span><span class="op">(</span>colour <span class="op">=</span> <span class="st">"black"</span>, size <span class="op">=</span> <span class="fl">16</span><span class="op">)</span>,
-        axis.text.x <span class="op">=</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/element.html" class="external-link">element_text</a></span><span class="op">(</span>angle <span class="op">=</span> <span class="fl">35</span>, hjust <span class="op">=</span> <span class="fl">1</span>, vjust <span class="op">=</span> <span class="fl">1</span><span class="op">)</span>,
-        strip.background <span class="op">=</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/element.html" class="external-link">element_rect</a></span><span class="op">(</span>fill <span class="op">=</span> <span class="st">"grey100"</span><span class="op">)</span>,
-        strip.text <span class="op">=</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/element.html" class="external-link">element_text</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">16</span><span class="op">)</span><span class="op">)</span> <span class="op">-&gt;</span> <span class="va">p</span>;<span class="va">p</span>
-
-<span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggsave.html" class="external-link">ggsave</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/file.path.html" class="external-link">file.path</a></span><span class="op">(</span><span class="st">"../man/figures"</span>, <span class="st">"Fig_WorldSUA.png"</span><span class="op">)</span>, <span class="va">p</span>, width <span class="op">=</span> <span class="fl">16</span>, height <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span><span class="va">DF_SUA</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<span>  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/facet_wrap.html" class="external-link">facet_wrap</a></span><span class="op">(</span><span class="op">~</span><span class="va">CropMeat</span>, scales <span class="op">=</span> <span class="st">"free"</span><span class="op">)</span> <span class="op">+</span></span>
+<span>    <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_bar.html" class="external-link">geom_bar</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span>x <span class="op">=</span> <span class="va">item</span>, y <span class="op">=</span> <span class="va">value</span>, fill <span class="op">=</span> <span class="va">element</span><span class="op">)</span>,</span>
+<span>             stat <span class="op">=</span> <span class="st">"identity"</span>, color <span class="op">=</span> <span class="st">"black"</span>, position<span class="op">=</span><span class="st">"stack"</span><span class="op">)</span> <span class="op">+</span></span>
+<span>  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_abline.html" class="external-link">geom_hline</a></span><span class="op">(</span>yintercept <span class="op">=</span> <span class="fl">0</span><span class="op">)</span><span class="op">+</span></span>
+<span>  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/scale_manual.html" class="external-link">scale_fill_manual</a></span><span class="op">(</span>values <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Supply: Opening stocks"</span> <span class="op">=</span> <span class="va">ColUpdate</span><span class="op">[</span><span class="fl">1</span><span class="op">]</span>, </span>
+<span>                               <span class="st">"Supply: Import"</span> <span class="op">=</span> <span class="va">ColUpdate</span><span class="op">[</span><span class="fl">2</span><span class="op">]</span>, </span>
+<span>                               <span class="st">"Supply: Production"</span> <span class="op">=</span> <span class="va">ColUpdate</span><span class="op">[</span><span class="fl">3</span><span class="op">]</span>,</span>
+<span>                               <span class="st">"Demand: Food"</span> <span class="op">=</span> <span class="va">ColUpdate</span><span class="op">[</span><span class="fl">4</span><span class="op">]</span>,</span>
+<span>                               <span class="st">"Demand: Feed"</span> <span class="op">=</span> <span class="va">ColUpdate</span><span class="op">[</span><span class="fl">5</span><span class="op">]</span>, </span>
+<span>                               <span class="st">"Demand: Processed"</span> <span class="op">=</span> <span class="va">ColUpdate</span><span class="op">[</span><span class="fl">6</span><span class="op">]</span>,</span>
+<span>                               <span class="st">"Demand: Other uses"</span> <span class="op">=</span> <span class="va">ColUpdate</span><span class="op">[</span><span class="fl">7</span><span class="op">]</span>,</span>
+<span>                               <span class="st">"Demand: Residuals"</span> <span class="op">=</span> <span class="va">ColUpdate</span><span class="op">[</span><span class="fl">8</span><span class="op">]</span>,</span>
+<span>                               <span class="st">"Demand: Export"</span> <span class="op">=</span> <span class="va">ColUpdate</span><span class="op">[</span><span class="fl">9</span><span class="op">]</span>,</span>
+<span>                               <span class="st">"Demand: Closing stocks"</span> <span class="op">=</span> <span class="va">ColUpdate</span><span class="op">[</span><span class="fl">10</span><span class="op">]</span> <span class="op">)</span> <span class="op">)</span> <span class="op">+</span></span>
+<span>  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span>x <span class="op">=</span> <span class="st">"Key agriculture Commodities"</span>,</span>
+<span>       y <span class="op">=</span> <span class="st">"Million tonnes"</span>, fill <span class="op">=</span> <span class="st">"Element"</span>,</span>
+<span>       title <span class="op">=</span> <span class="st">"World supply utilization for key commodities, 2013 - 2017 mean"</span>,</span>
+<span>       subtitle <span class="op">=</span> <span class="st">"Other uses include seed use, losses, and industrial use"</span>,</span>
+<span>       caption <span class="op">=</span> <span class="st">"Data: FAOSTAT \n Package: JGCRI/gcamfaostat"</span><span class="op">)</span> <span class="op">+</span></span>
+<span>  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggtheme.html" class="external-link">theme_bw</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span> </span>
+<span>  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/theme.html" class="external-link">theme</a></span><span class="op">(</span>text <span class="op">=</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/element.html" class="external-link">element_text</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">16</span><span class="op">)</span>,</span>
+<span>        axis.text <span class="op">=</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/element.html" class="external-link">element_text</a></span><span class="op">(</span>colour <span class="op">=</span> <span class="st">"black"</span>, size <span class="op">=</span> <span class="fl">16</span><span class="op">)</span>,</span>
+<span>        axis.text.x <span class="op">=</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/element.html" class="external-link">element_text</a></span><span class="op">(</span>angle <span class="op">=</span> <span class="fl">35</span>, hjust <span class="op">=</span> <span class="fl">1</span>, vjust <span class="op">=</span> <span class="fl">1</span><span class="op">)</span>,</span>
+<span>        strip.background <span class="op">=</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/element.html" class="external-link">element_rect</a></span><span class="op">(</span>fill <span class="op">=</span> <span class="st">"grey100"</span><span class="op">)</span>,</span>
+<span>        strip.text <span class="op">=</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/element.html" class="external-link">element_text</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">16</span><span class="op">)</span><span class="op">)</span> <span class="op">-&gt;</span> <span class="va">p</span>;<span class="va">p</span></span>
+<span></span>
+<span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggsave.html" class="external-link">ggsave</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/file.path.html" class="external-link">file.path</a></span><span class="op">(</span><span class="st">"../man/figures"</span>, <span class="st">"Fig_WorldSUA.png"</span><span class="op">)</span>, <span class="va">p</span>, width <span class="op">=</span> <span class="fl">16</span>, height <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></span></code></pre></div>
 <ul>
 <li>Preview<br><img src="../reference/figures/Fig_WorldSUA.png" style="width:20.0%">
 </li>
@@ -533,78 +533,78 @@ <h3 id="food-calories-1">5. Food calories<a class="anchor" aria-label="anchor" h
 <li>Get data ready</li>
 </ul>
 <div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">FAO_Food_Macronutrient_All_2010_2019</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">year</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="va">BaseYear</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
-  <span class="co"># Aggregate to region and GCAM commodity</span>
-  <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by_all.html" class="external-link">group_by_at</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">GCAM_region_ID</span>, <span class="va">GCAM_commodity</span>, <span class="va">year</span>, <span class="va">macronutrient</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span>value <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">value</span><span class="op">)</span>, .groups <span class="op">=</span> <span class="st">"drop"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
-  <span class="co"># Mean over aglu.MODEL_MACRONUTRIENT_YEARS</span>
-  <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by_all.html" class="external-link">group_by_at</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="op">-</span><span class="va">year</span>, <span class="op">-</span><span class="va">value</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span>value <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="va">value</span><span class="op">)</span>, .groups <span class="op">=</span> <span class="st">"drop"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
-  <span class="fu">spread</span><span class="op">(</span><span class="va">macronutrient</span>, <span class="va">value</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
-  <span class="fu"><a href="../reference/left_join_error_no_match.html">left_join_error_no_match</a></span><span class="op">(</span>
-    <span class="va">POP</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">GCAM_region_ID</span>, <span class="va">region</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
-      <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarize</a></span><span class="op">(</span>POP <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">value</span><span class="op">)</span><span class="op">/</span><span class="fl">1000</span>, .groups <span class="op">=</span> <span class="st">"drop"</span><span class="op">)</span>, <span class="co"># Million</span>
-    by <span class="op">=</span> <span class="st">"GCAM_region_ID"</span>
-  <span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
-  <span class="co"># Grouping</span>
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>MeatCrop <span class="op">=</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/if_else.html" class="external-link">if_else</a></span><span class="op">(</span><span class="va">GCAM_commodity</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span>
-                              <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Beef"</span>, <span class="st">"SheepGoat"</span>, <span class="st">"Dairy"</span>, <span class="st">"OtherMeat_Fish"</span>, <span class="st">"Pork"</span>, <span class="st">"Poultry"</span><span class="op">)</span>, <span class="st">"Meat"</span>, <span class="st">"Crop"</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>Food <span class="op">=</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/if_else.html" class="external-link">if_else</a></span><span class="op">(</span><span class="va">GCAM_commodity</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span>
-                          <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Beef"</span>, <span class="st">"SheepGoat"</span><span class="op">)</span>, <span class="st">"Ruminant"</span>, <span class="st">"Crops"</span><span class="op">)</span>,
-         Food <span class="op">=</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/if_else.html" class="external-link">if_else</a></span><span class="op">(</span><span class="va">GCAM_commodity</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span>  <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"OtherMeat_Fish"</span>, <span class="st">"Pork"</span>, <span class="st">"Poultry"</span><span class="op">)</span>,
-                        <span class="st">"Non-ruminant"</span>, <span class="va">Food</span><span class="op">)</span>,
-         Food <span class="op">=</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/if_else.html" class="external-link">if_else</a></span><span class="op">(</span><span class="va">GCAM_commodity</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span>  <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Dairy"</span><span class="op">)</span>,
-                        <span class="st">"Dairy"</span>, <span class="va">Food</span><span class="op">)</span>,
-         Food <span class="op">=</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/if_else.html" class="external-link">if_else</a></span><span class="op">(</span><span class="va">GCAM_commodity</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="st">"NEC"</span>, <span class="st">"Other processed"</span>, <span class="va">Food</span><span class="op">)</span>,
-         Food <span class="op">=</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/if_else.html" class="external-link">if_else</a></span><span class="op">(</span><span class="va">GCAM_commodity</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"OilCrop"</span>, <span class="st">"Soybean"</span>, <span class="st">"OilPalm"</span>,  <span class="st">"FiberCrop"</span><span class="op">)</span>, <span class="st">"Oilseed"</span>, <span class="va">Food</span><span class="op">)</span>,
-         Food <span class="op">=</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/if_else.html" class="external-link">if_else</a></span><span class="op">(</span><span class="va">GCAM_commodity</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Corn"</span>, <span class="st">"Wheat"</span>, <span class="st">"Rice"</span>, <span class="st">"OtherGrain"</span><span class="op">)</span>, <span class="st">"Cereal grains"</span>, <span class="va">Food</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>PcPdKcal <span class="op">=</span> <span class="va">MKcal</span> <span class="op">/</span> <span class="va">POP</span> <span class="op">/</span> <span class="fl">365</span><span class="op">)</span> <span class="op">-&gt;</span>
-  <span class="va">DF_Macronutrient_FoodItem</span></code></pre></div>
+<code class="sourceCode R"><span><span class="va">FAO_Food_Macronutrient_All_2010_2019</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">year</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="va">BaseYear</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>  <span class="co"># Aggregate to region and GCAM commodity</span></span>
+<span>  <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by_all.html" class="external-link">group_by_at</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">GCAM_region_ID</span>, <span class="va">GCAM_commodity</span>, <span class="va">year</span>, <span class="va">macronutrient</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span>value <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">value</span><span class="op">)</span>, .groups <span class="op">=</span> <span class="st">"drop"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>  <span class="co"># Mean over aglu.MODEL_MACRONUTRIENT_YEARS</span></span>
+<span>  <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by_all.html" class="external-link">group_by_at</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="op">-</span><span class="va">year</span>, <span class="op">-</span><span class="va">value</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span>value <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="va">value</span><span class="op">)</span>, .groups <span class="op">=</span> <span class="st">"drop"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>  <span class="fu">spread</span><span class="op">(</span><span class="va">macronutrient</span>, <span class="va">value</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>  <span class="fu"><a href="../reference/left_join_error_no_match.html">left_join_error_no_match</a></span><span class="op">(</span></span>
+<span>    <span class="va">POP</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">GCAM_region_ID</span>, <span class="va">region</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>      <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarize</a></span><span class="op">(</span>POP <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">value</span><span class="op">)</span><span class="op">/</span><span class="fl">1000</span>, .groups <span class="op">=</span> <span class="st">"drop"</span><span class="op">)</span>, <span class="co"># Million</span></span>
+<span>    by <span class="op">=</span> <span class="st">"GCAM_region_ID"</span></span>
+<span>  <span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>  <span class="co"># Grouping</span></span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>MeatCrop <span class="op">=</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/if_else.html" class="external-link">if_else</a></span><span class="op">(</span><span class="va">GCAM_commodity</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span></span>
+<span>                              <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Beef"</span>, <span class="st">"SheepGoat"</span>, <span class="st">"Dairy"</span>, <span class="st">"OtherMeat_Fish"</span>, <span class="st">"Pork"</span>, <span class="st">"Poultry"</span><span class="op">)</span>, <span class="st">"Meat"</span>, <span class="st">"Crop"</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>Food <span class="op">=</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/if_else.html" class="external-link">if_else</a></span><span class="op">(</span><span class="va">GCAM_commodity</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span></span>
+<span>                          <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Beef"</span>, <span class="st">"SheepGoat"</span><span class="op">)</span>, <span class="st">"Ruminant"</span>, <span class="st">"Crops"</span><span class="op">)</span>,</span>
+<span>         Food <span class="op">=</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/if_else.html" class="external-link">if_else</a></span><span class="op">(</span><span class="va">GCAM_commodity</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span>  <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"OtherMeat_Fish"</span>, <span class="st">"Pork"</span>, <span class="st">"Poultry"</span><span class="op">)</span>,</span>
+<span>                        <span class="st">"Non-ruminant"</span>, <span class="va">Food</span><span class="op">)</span>,</span>
+<span>         Food <span class="op">=</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/if_else.html" class="external-link">if_else</a></span><span class="op">(</span><span class="va">GCAM_commodity</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span>  <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Dairy"</span><span class="op">)</span>,</span>
+<span>                        <span class="st">"Dairy"</span>, <span class="va">Food</span><span class="op">)</span>,</span>
+<span>         Food <span class="op">=</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/if_else.html" class="external-link">if_else</a></span><span class="op">(</span><span class="va">GCAM_commodity</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="st">"NEC"</span>, <span class="st">"Other processed"</span>, <span class="va">Food</span><span class="op">)</span>,</span>
+<span>         Food <span class="op">=</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/if_else.html" class="external-link">if_else</a></span><span class="op">(</span><span class="va">GCAM_commodity</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"OilCrop"</span>, <span class="st">"Soybean"</span>, <span class="st">"OilPalm"</span>,  <span class="st">"FiberCrop"</span><span class="op">)</span>, <span class="st">"Oilseed"</span>, <span class="va">Food</span><span class="op">)</span>,</span>
+<span>         Food <span class="op">=</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/if_else.html" class="external-link">if_else</a></span><span class="op">(</span><span class="va">GCAM_commodity</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Corn"</span>, <span class="st">"Wheat"</span>, <span class="st">"Rice"</span>, <span class="st">"OtherGrain"</span><span class="op">)</span>, <span class="st">"Cereal grains"</span>, <span class="va">Food</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>PcPdKcal <span class="op">=</span> <span class="va">MKcal</span> <span class="op">/</span> <span class="va">POP</span> <span class="op">/</span> <span class="fl">365</span><span class="op">)</span> <span class="op">-&gt;</span></span>
+<span>  <span class="va">DF_Macronutrient_FoodItem</span></span></code></pre></div>
 <ul>
 <li>Plot and save</li>
 </ul>
 <div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">DF_Macronutrient_FoodItem</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarize</a></span><span class="op">(</span>PKcal <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">MKcal</span><span class="op">)</span><span class="op">/</span><span class="fl">10</span><span class="op">^</span><span class="fl">9</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate-joins.html" class="external-link">left_join</a></span><span class="op">(</span><span class="va">POP</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarize</a></span><span class="op">(</span>BPOP <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="op">/</span> <span class="fl">1000000</span><span class="op">)</span>, by <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/character.html" class="external-link">character</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>PcPdKcal <span class="op">=</span> <span class="va">PKcal</span> <span class="op">/</span> <span class="va">BPOP</span> <span class="op">/</span> <span class="fl">365</span> <span class="op">*</span> <span class="fl">1000000</span><span class="op">)</span> <span class="op">-&gt;</span> <span class="va">WorldSTAT</span>
-
-<span class="co"># World level by commodity</span>
-<span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="st">"World food calories availability, "</span>, <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">min</a></span><span class="op">(</span><span class="va">BaseYear</span><span class="op">)</span>, <span class="st">"-"</span>, <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="va">BaseYear</span><span class="op">)</span>, <span class="st">" mean ("</span>,
-       <span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">round</a></span><span class="op">(</span><span class="va">WorldSTAT</span><span class="op">$</span><span class="va">PKcal</span>,<span class="fl">2</span><span class="op">)</span>, <span class="st">" Peta-Kcal or "</span>, <span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">round</a></span><span class="op">(</span><span class="va">WorldSTAT</span><span class="op">$</span><span class="va">PcPdKcal</span>, <span class="fl">0</span><span class="op">)</span>,<span class="st">" Kcal/ca/d)"</span><span class="op">)</span> <span class="op">-&gt;</span>
-  <span class="va">title</span>
-<span class="fu"><a href="../reference/treemap_wrapper.html">treemap_wrapper</a></span><span class="op">(</span>
-  .DF <span class="op">=</span> <span class="va">DF_Macronutrient_FoodItem</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">Food</span>, <span class="va">GCAM_commodity</span>, value <span class="op">=</span> <span class="va">MKcal</span><span class="op">)</span>,
-  .Depth <span class="op">=</span> <span class="fl">2</span>,
-  .FigTitle <span class="op">=</span> <span class="va">title</span>, .FigTitleSize <span class="op">=</span> <span class="fl">14</span>,
-  .SaveName <span class="op">=</span> <span class="st">"Fig_WorldFoodCalories"</span>,
-  .SaveScaler <span class="op">=</span> <span class="fl">1</span>
-<span class="op">)</span>
-
-<span class="co"># By commodity and region</span>
-<span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="st">"World food calories availability by region and commodity, "</span>, <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">min</a></span><span class="op">(</span><span class="va">BaseYear</span><span class="op">)</span>, <span class="st">"-"</span>, <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="va">BaseYear</span><span class="op">)</span>, <span class="st">" mean ("</span>,
-       <span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">round</a></span><span class="op">(</span><span class="va">WorldSTAT</span><span class="op">$</span><span class="va">PKcal</span>,<span class="fl">2</span><span class="op">)</span>, <span class="st">" Peta-Kcal)"</span><span class="op">)</span> <span class="op">-&gt;</span>
-  <span class="va">title</span>
-<span class="fu"><a href="../reference/treemap_wrapper.html">treemap_wrapper</a></span><span class="op">(</span>
-  .DF <span class="op">=</span> <span class="va">DF_Macronutrient_FoodItem</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">region</span>, <span class="va">Food</span>, <span class="va">GCAM_commodity</span>, value <span class="op">=</span> <span class="va">MKcal</span><span class="op">)</span>,
-  .Depth <span class="op">=</span> <span class="fl">3</span>,
-  .FigTitle <span class="op">=</span> <span class="va">title</span>, .FigTitleSize <span class="op">=</span> <span class="fl">18</span>,
-  .SaveName <span class="op">=</span> <span class="st">"Fig_WorldFoodCaloriesReg"</span>,
-  .SaveScaler <span class="op">=</span> <span class="fl">1.6</span>
-<span class="op">)</span>
-
-<span class="co"># By commodity and region per ca per day</span>
-<span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="st">"Per ca. per day food calories availability by region and commodity, "</span>,
-       <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">min</a></span><span class="op">(</span><span class="va">BaseYear</span><span class="op">)</span>, <span class="st">"-"</span>, <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="va">BaseYear</span><span class="op">)</span>, <span class="st">" mean (world: "</span>, <span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">round</a></span><span class="op">(</span><span class="va">WorldSTAT</span><span class="op">$</span><span class="va">PcPdKcal</span>, <span class="fl">0</span><span class="op">)</span>,<span class="st">" Kcal/ca/d)"</span><span class="op">)</span> <span class="op">-&gt;</span>
-  <span class="va">title</span>
-<span class="fu"><a href="../reference/treemap_wrapper.html">treemap_wrapper</a></span><span class="op">(</span>
-  .DF <span class="op">=</span> <span class="va">DF_Macronutrient_FoodItem</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">region</span>, <span class="va">Food</span>, <span class="va">GCAM_commodity</span>, value <span class="op">=</span> <span class="va">PcPdKcal</span><span class="op">)</span>,
-  .Depth <span class="op">=</span> <span class="fl">3</span>,
-  .FigTitle <span class="op">=</span> <span class="va">title</span>, .FigTitleSize <span class="op">=</span> <span class="fl">20</span>,
-  .SaveName <span class="op">=</span> <span class="st">"Fig_WorldFoodCaloriesRegPcPerDay"</span>,
-  .SaveScaler <span class="op">=</span> <span class="fl">1.8</span>
-<span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span><span class="va">DF_Macronutrient_FoodItem</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarize</a></span><span class="op">(</span>PKcal <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">MKcal</span><span class="op">)</span><span class="op">/</span><span class="fl">10</span><span class="op">^</span><span class="fl">9</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate-joins.html" class="external-link">left_join</a></span><span class="op">(</span><span class="va">POP</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarize</a></span><span class="op">(</span>BPOP <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="op">/</span> <span class="fl">1000000</span><span class="op">)</span>, by <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/character.html" class="external-link">character</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>PcPdKcal <span class="op">=</span> <span class="va">PKcal</span> <span class="op">/</span> <span class="va">BPOP</span> <span class="op">/</span> <span class="fl">365</span> <span class="op">*</span> <span class="fl">1000000</span><span class="op">)</span> <span class="op">-&gt;</span> <span class="va">WorldSTAT</span></span>
+<span></span>
+<span><span class="co"># World level by commodity</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="st">"World food calories availability, "</span>, <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">min</a></span><span class="op">(</span><span class="va">BaseYear</span><span class="op">)</span>, <span class="st">"-"</span>, <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="va">BaseYear</span><span class="op">)</span>, <span class="st">" mean ("</span>,</span>
+<span>       <span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">round</a></span><span class="op">(</span><span class="va">WorldSTAT</span><span class="op">$</span><span class="va">PKcal</span>,<span class="fl">2</span><span class="op">)</span>, <span class="st">" Peta-Kcal or "</span>, <span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">round</a></span><span class="op">(</span><span class="va">WorldSTAT</span><span class="op">$</span><span class="va">PcPdKcal</span>, <span class="fl">0</span><span class="op">)</span>,<span class="st">" Kcal/ca/d)"</span><span class="op">)</span> <span class="op">-&gt;</span></span>
+<span>  <span class="va">title</span></span>
+<span><span class="fu"><a href="../reference/treemap_wrapper.html">treemap_wrapper</a></span><span class="op">(</span></span>
+<span>  .DF <span class="op">=</span> <span class="va">DF_Macronutrient_FoodItem</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">Food</span>, <span class="va">GCAM_commodity</span>, value <span class="op">=</span> <span class="va">MKcal</span><span class="op">)</span>,</span>
+<span>  .Depth <span class="op">=</span> <span class="fl">2</span>,</span>
+<span>  .FigTitle <span class="op">=</span> <span class="va">title</span>, .FigTitleSize <span class="op">=</span> <span class="fl">14</span>,</span>
+<span>  .SaveName <span class="op">=</span> <span class="st">"Fig_WorldFoodCalories"</span>,</span>
+<span>  .SaveScaler <span class="op">=</span> <span class="fl">1</span></span>
+<span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># By commodity and region</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="st">"World food calories availability by region and commodity, "</span>, <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">min</a></span><span class="op">(</span><span class="va">BaseYear</span><span class="op">)</span>, <span class="st">"-"</span>, <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="va">BaseYear</span><span class="op">)</span>, <span class="st">" mean ("</span>,</span>
+<span>       <span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">round</a></span><span class="op">(</span><span class="va">WorldSTAT</span><span class="op">$</span><span class="va">PKcal</span>,<span class="fl">2</span><span class="op">)</span>, <span class="st">" Peta-Kcal)"</span><span class="op">)</span> <span class="op">-&gt;</span></span>
+<span>  <span class="va">title</span></span>
+<span><span class="fu"><a href="../reference/treemap_wrapper.html">treemap_wrapper</a></span><span class="op">(</span></span>
+<span>  .DF <span class="op">=</span> <span class="va">DF_Macronutrient_FoodItem</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">region</span>, <span class="va">Food</span>, <span class="va">GCAM_commodity</span>, value <span class="op">=</span> <span class="va">MKcal</span><span class="op">)</span>,</span>
+<span>  .Depth <span class="op">=</span> <span class="fl">3</span>,</span>
+<span>  .FigTitle <span class="op">=</span> <span class="va">title</span>, .FigTitleSize <span class="op">=</span> <span class="fl">18</span>,</span>
+<span>  .SaveName <span class="op">=</span> <span class="st">"Fig_WorldFoodCaloriesReg"</span>,</span>
+<span>  .SaveScaler <span class="op">=</span> <span class="fl">1.6</span></span>
+<span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># By commodity and region per ca per day</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="st">"Per ca. per day food calories availability by region and commodity, "</span>,</span>
+<span>       <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">min</a></span><span class="op">(</span><span class="va">BaseYear</span><span class="op">)</span>, <span class="st">"-"</span>, <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="va">BaseYear</span><span class="op">)</span>, <span class="st">" mean (world: "</span>, <span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">round</a></span><span class="op">(</span><span class="va">WorldSTAT</span><span class="op">$</span><span class="va">PcPdKcal</span>, <span class="fl">0</span><span class="op">)</span>,<span class="st">" Kcal/ca/d)"</span><span class="op">)</span> <span class="op">-&gt;</span></span>
+<span>  <span class="va">title</span></span>
+<span><span class="fu"><a href="../reference/treemap_wrapper.html">treemap_wrapper</a></span><span class="op">(</span></span>
+<span>  .DF <span class="op">=</span> <span class="va">DF_Macronutrient_FoodItem</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">region</span>, <span class="va">Food</span>, <span class="va">GCAM_commodity</span>, value <span class="op">=</span> <span class="va">PcPdKcal</span><span class="op">)</span>,</span>
+<span>  .Depth <span class="op">=</span> <span class="fl">3</span>,</span>
+<span>  .FigTitle <span class="op">=</span> <span class="va">title</span>, .FigTitleSize <span class="op">=</span> <span class="fl">20</span>,</span>
+<span>  .SaveName <span class="op">=</span> <span class="st">"Fig_WorldFoodCaloriesRegPcPerDay"</span>,</span>
+<span>  .SaveScaler <span class="op">=</span> <span class="fl">1.8</span></span>
+<span><span class="op">)</span></span></code></pre></div>
 <ul>
 <li>Preview<br><img src="../reference/figures/Fig_WorldFoodCalories.png" style="width:20.0%"><img src="../reference/figures/Fig_WorldFoodCaloriesReg.png" style="width:20.0%"><img src="../reference/figures/Fig_WorldFoodCaloriesRegPcPerDay.png" style="width:20.0%">
 </li>