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<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):425438 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("devtools", "roxygen2"), repos = "http://cran.us.r-project.org")
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 'ghgvcr'
</code></pre>
<pre><code class="r">
options(warn = FALSE)
# test('../ghgvcR') example(ghgvcr)
## the following is equivalent to
config.xml <- system.file("config.xml", package = "ghgvcr")
config.list <- xmlToList(xmlParse(config.xml))
</code></pre>
<pre><code>Error: could not find function "xmlToList"
</code></pre>
<pre><code class="r">ecosystem_data <- config.list$ecosystem_data
</code></pre>
<pre><code>Error: object 'config.list' not found
</code></pre>
<pre><code class="r">
x <- ghgvcr::ghgvc(options = config.list$options, ecosystem_data = config.list$ecosystem_data)
</code></pre>
<pre><code>Error: there is no package called 'ghgvcr'
</code></pre>
<pre><code class="r">
writeLines(x, "inst/extdata/output.json")
</code></pre>
<pre><code>Error: object 'x' not found
</code></pre>
<pre><code class="r">write.csv(as.data.frame(fromJSON(x)), "inst/extdata/output.csv")
</code></pre>
<pre><code>Error: could not find function "fromJSON"
</code></pre>
<pre><code class="r">multisite_config.xml <- system.file("multisite_config.xml", package = "ghgvcr")
multipft_config.list <- xmlToList(xmlParse(multipft_config.xml))
</code></pre>
<pre><code>Error: could not find function "xmlToList"
</code></pre>
<pre><code class="r">
x2 <- ghgvcr::ghgvc2(multipft_config.list)
</code></pre>
<pre><code>Error: there is no package called 'ghgvcr'
</code></pre>
<pre><code class="r">
writeLines(x2, "inst/extdata/multipft_output.json")
</code></pre>
<pre><code>Error: object 'x2' not found
</code></pre>
<pre><code class="r">write.csv(as.data.frame(fromJSON(x2)), "inst/extdata/multipft_output.csv")
</code></pre>
<pre><code>Error: could not find function "fromJSON"
</code></pre>
<h3>Plots:</h3>
<pre><code class="r">library(ggplot2)
# number of ecosystems:
n.ecosystems <- length(names(ecosystem_data))
</code></pre>
<pre><code>Error: object 'ecosystem_data' not found
</code></pre>
<pre><code class="r">for (i in 1:n.ecosystems) {
result <- ecosystem_data[[i]]
ecosystem.name <- result$name
if (i == 1) {
result.df <- as.data.frame(result)
} else {
result.df <- rbind(result.df, as.data.frame(result))
}
rownames(result.df)[i] <- gsub(" ", "", ecosystem.name)
}
</code></pre>
<pre><code>Error: object 'n.ecosystems' not found
</code></pre>
<pre><code class="r">
# identify cols with numbers
result.num <- suppressWarnings(as.numeric(result))
</code></pre>
<pre><code>Error: object 'result' not found
</code></pre>
<pre><code class="r">num.logical <- !(is.na(result.num) | result.num == -9999)
</code></pre>
<pre><code>Error: object 'result.num' not found
</code></pre>
<pre><code class="r">result.df <- result.df[, !(result.num == -9999 | is.na(result.num))]
</code></pre>
<pre><code>Error: object 'result.df' not found
</code></pre>
<pre><code class="r">
# transpose data.frame for plotting:
result.tdf <- cbind(variable = names(result.df), as.data.frame(t(result.df)))
</code></pre>
<pre><code>Error: object 'result.df' not found
</code></pre>
<pre><code class="r">
forcings.index <- grepl("F", names(result.df))
</code></pre>
<pre><code>Error: object 'result.df' not found
</code></pre>
<pre><code class="r">forcings.names <- names(result.df)[forcings.index]
</code></pre>
<pre><code>Error: object 'result.df' not found
</code></pre>
<pre><code class="r">
forcings <- result.tdf[forcings.index, ]
</code></pre>
<pre><code>Error: object 'result.tdf' not found
</code></pre>
<pre><code class="r">forcings.long <- melt(forcings, id.vars = "variable")
</code></pre>
<pre><code>Error: could not find function "melt"
</code></pre>
<pre><code class="r">colnames(forcings.long) <- c("variable", "ecosystem", "value")
</code></pre>
<pre><code>Error: object 'forcings.long' 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 = "dodge", stat = "identity") + ggtitle(label = "Example plot: values of F for two ecosystems") +
xlab("Variable") + ylab("Units of F") + coord_flip()
</code></pre>
<pre><code>## Error: object 'forcings.long' not found
</code></pre>
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