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R implementation of the Greenhouse Gas Value Calculator
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data		data
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tests		tests
vignettes		vignettes
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.dockerignore		.dockerignore
.gitattributes		.gitattributes
.gitignore		.gitignore
.travis.yml		.travis.yml
DESCRIPTION		DESCRIPTION
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LICENSE		LICENSE
NAMESPACE		NAMESPACE
README.Rmd		README.Rmd
README.html		README.html
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docker-entrypoint.sh		docker-entrypoint.sh
docker-push.sh		docker-push.sh
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<body>
<h1>ghgvcr</h1>

<p>R implementation of the Greenhouse Gas Value Calculator</p>

<p>Citation: Kristina J. Teixeira and Evan H. Delucia 2011. The greenhouse gas value of ecosystems. Global Change Biology. 17(1):425�438 doi: 10.1111/j.1365-2486.2010.02220.x</p>

<hr/>

<h3>Inputs</h3>

<ul>
<li><code>inst/config.xml</code> example input file</li>
<li><code>inst/extdata/ghgvc1.Rdata</code> all objects used and provided by ghgvc 1.0</li>
<li><code>inputs.Rdata</code> example of inputs as R objects for ghgvcr example (below)</li>
<li><code>inst/extdata/multipft_input.xml</code></li>
</ul>

<h3>Outputs</h3>

<p>produced by example below:</p>

<ul>
<li><code>inst/extdata/output.csv</code></li>
<li><code>inst/extdata/output.json</code></li>
</ul>

<h3>Installing the ghgvcr package on the PEcAn 1.2.6 VM</h3>

<p>The bash and R code snippets below install dependencies, and only need to be run once. </p>

<pre><code class="r">sudo apt-get install git
sudo apt-get install libcurl4-openssl-dev # dependency of Rcurl, 

git clone https://github.com/dlebauer/pecan.git pecan
git clone https://github.com/dlebauer/ghgvcR.git ghgvcR
R 
</code></pre>

<pre><code class="r">install.packages(c(&quot;devtools&quot;, &quot;roxygen2&quot;), repos = &quot;http://cran.us.r-project.org&quot;)
library(devtools)
install(ghgvcr)
install(pecan/utils)
</code></pre>

<h3>Example of how to run the calculator</h3>

<ul>
<li>This can be run at the command line: <code>./src/ghgvc_script.R</code></li>
</ul>

<pre><code>## Error: there is no package called &#39;ghgvcr&#39;
</code></pre>

<pre><code class="r">
options(warn = FALSE)
# test(&#39;../ghgvcR&#39;) example(ghgvcr)


## the following is equivalent to
config.xml &lt;- system.file(&quot;config.xml&quot;, package = &quot;ghgvcr&quot;)
config.list &lt;- xmlToList(xmlParse(config.xml))
</code></pre>

<pre><code>Error: could not find function &quot;xmlToList&quot;
</code></pre>

<pre><code class="r">ecosystem_data &lt;- config.list$ecosystem_data
</code></pre>

<pre><code>Error: object &#39;config.list&#39; not found
</code></pre>

<pre><code class="r">
x &lt;- ghgvcr::ghgvc(options = config.list$options, ecosystem_data = config.list$ecosystem_data)
</code></pre>

<pre><code>Error: there is no package called &#39;ghgvcr&#39;
</code></pre>

<pre><code class="r">

writeLines(x, &quot;inst/extdata/output.json&quot;)
</code></pre>

<pre><code>Error: object &#39;x&#39; not found
</code></pre>

<pre><code class="r">write.csv(as.data.frame(fromJSON(x)), &quot;inst/extdata/output.csv&quot;)
</code></pre>

<pre><code>Error: could not find function &quot;fromJSON&quot;
</code></pre>

<pre><code class="r">multisite_config.xml &lt;- system.file(&quot;multisite_config.xml&quot;, package = &quot;ghgvcr&quot;)
multipft_config.list &lt;- xmlToList(xmlParse(multipft_config.xml))
</code></pre>

<pre><code>Error: could not find function &quot;xmlToList&quot;
</code></pre>

<pre><code class="r">
x2 &lt;- ghgvcr::ghgvc2(multipft_config.list)
</code></pre>

<pre><code>Error: there is no package called &#39;ghgvcr&#39;
</code></pre>

<pre><code class="r">
writeLines(x2, &quot;inst/extdata/multipft_output.json&quot;)
</code></pre>

<pre><code>Error: object &#39;x2&#39; not found
</code></pre>

<pre><code class="r">write.csv(as.data.frame(fromJSON(x2)), &quot;inst/extdata/multipft_output.csv&quot;)
</code></pre>

<pre><code>Error: could not find function &quot;fromJSON&quot;
</code></pre>

<h3>Plots:</h3>

<pre><code class="r">library(ggplot2)
# number of ecosystems:
n.ecosystems &lt;- length(names(ecosystem_data))
</code></pre>

<pre><code>Error: object &#39;ecosystem_data&#39; not found
</code></pre>

<pre><code class="r">for (i in 1:n.ecosystems) {
    result &lt;- ecosystem_data[[i]]
    ecosystem.name &lt;- result$name
    if (i == 1) {
        result.df &lt;- as.data.frame(result)

    } else {
        result.df &lt;- rbind(result.df, as.data.frame(result))
    }
    rownames(result.df)[i] &lt;- gsub(&quot; &quot;, &quot;&quot;, ecosystem.name)
}
</code></pre>

<pre><code>Error: object &#39;n.ecosystems&#39; not found
</code></pre>

<pre><code class="r">
# identify cols with numbers
result.num &lt;- suppressWarnings(as.numeric(result))
</code></pre>

<pre><code>Error: object &#39;result&#39; not found
</code></pre>

<pre><code class="r">num.logical &lt;- !(is.na(result.num) | result.num == -9999)
</code></pre>

<pre><code>Error: object &#39;result.num&#39; not found
</code></pre>

<pre><code class="r">result.df &lt;- result.df[, !(result.num == -9999 | is.na(result.num))]
</code></pre>

<pre><code>Error: object &#39;result.df&#39; not found
</code></pre>

<pre><code class="r">
# transpose data.frame for plotting:
result.tdf &lt;- cbind(variable = names(result.df), as.data.frame(t(result.df)))
</code></pre>

<pre><code>Error: object &#39;result.df&#39; not found
</code></pre>

<pre><code class="r">
forcings.index &lt;- grepl(&quot;F&quot;, names(result.df))
</code></pre>

<pre><code>Error: object &#39;result.df&#39; not found
</code></pre>

<pre><code class="r">forcings.names &lt;- names(result.df)[forcings.index]
</code></pre>

<pre><code>Error: object &#39;result.df&#39; not found
</code></pre>

<pre><code class="r">

forcings &lt;- result.tdf[forcings.index, ]
</code></pre>

<pre><code>Error: object &#39;result.tdf&#39; not found
</code></pre>

<pre><code class="r">forcings.long &lt;- melt(forcings, id.vars = &quot;variable&quot;)
</code></pre>

<pre><code>Error: could not find function &quot;melt&quot;
</code></pre>

<pre><code class="r">colnames(forcings.long) &lt;- c(&quot;variable&quot;, &quot;ecosystem&quot;, &quot;value&quot;)
</code></pre>

<pre><code>Error: object &#39;forcings.long&#39; not found
</code></pre>

<pre><code class="r">
</code></pre>

<pre><code class="r">ggplot(data = forcings.long, aes(x = variable, y = value, fill = ecosystem)) + 
    geom_bar(position = &quot;dodge&quot;, stat = &quot;identity&quot;) + ggtitle(label = &quot;Example plot: values of F for two ecosystems&quot;) + 
    xlab(&quot;Variable&quot;) + ylab(&quot;Units of F&quot;) + coord_flip()
</code></pre>

<pre><code>## Error: object &#39;forcings.long&#39; not found
</code></pre>

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