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<h1 class="title toc-ignore">Notes</h1>
</div>
<div id="thursday" class="section level1">
<h1>Thursday</h1>
<p>For building a package with roxygen documentation (the part that makes the help files for you), you need to tell RStudio to build that documentation when you click ‘Build and Reload’.</p>
<p>Go to Tools > Project Options > Build Tools Then click the box that says the build documentation with roxygen. A pop-up window should appear. Click the box at the bottom that says to remake documentation when you click ‘Build and Reload’.</p>
<hr />
<p>Seasonal data. If you have seasonal data that you would like to analyze, please put in this format:</p>
<pre><code> Year Month metric.tons
2018 1 1
2018 2 2
2018 3 3
...
2019 1 4
2019 2 6
2019 3 NA</code></pre>
<p>Read in with this code:</p>
<pre><code>test <- read.csv("Data/test.csv", stringsAsFactors = FALSE)
save(test, file="test.RData")</code></pre>
</div>
<div id="wednesday" class="section level1">
<h1>Wednesday</h1>
<p>To save data in R to a .csv file use the following:</p>
<pre><code>write.csv(landings, file="test.csv", row.names=FALSE, quote=FALSE)</code></pre>
<p>This works for data.frames, like landings, and also matrices:</p>
<pre><code>mat <- matrix(rnorm(10),5,2)
colnames(mat) <- c("number 1", "number 2")
write.csv(landings, file="test.csv", row.names=FALSE, quote=FALSE)</code></pre>
</div>
<div id="tuesday" class="section level1">
<h1>Tuesday</h1>
<p>The bookdown-demo repository has been edited so that it does not try to make a PDF. If you want that, there are instructions in the README.md file.</p>
<hr />
<p>Read in simple csv file named <code>test.csv</code> that looks like this</p>
<pre><code> Year Species metric.tons
1 2018 Fish1 1
2 2019 Fish1 2
3 2018 Fish2 3
4 2019 Fish2 4
5 2018 Fish3 6
6 2019 Fish4 NA</code></pre>
<p>with this code:</p>
<pre><code>test <- read.csv("Data/test.csv", stringsAsFactors = FALSE)
save(test, file="test.RData")</code></pre>
<hr />
<p>Read in a file where the data are in columns. If your data (test.csv) look like this with each species (or site) across the columns:</p>
<pre><code>Year,Anchovy,Sardine,Chub mackerel,Horse mackerel,Mackerel,Jack Mackerel
1964,5449.2,12984.4,1720.7,4022.4,NA,NA
1965,4263.5,10611.1,1278.5,4158.3,NA,NA
1966,5146.4,11437.8,802.6,3012.1,NA,NA</code></pre>
<p>Use this code:</p>
<pre><code>library(reshape2)
test <- read.csv("Data/test.csv", stringsAsFactors = FALSE)
melt(test, id="Year", value.name="metric.tons", variable.name="Species")
save(test, file="test.RData")</code></pre>
<p>If your data also have, say, a month (or qtr) column, use this code:</p>
<pre><code>library(reshape2)
test <- read.csv("Data/test.csv", stringsAsFactors = FALSE)
melt(test, id=c("Year","Month"), value.name="metric.tons", variable.name="Species")
save(test, file="test.RData")</code></pre>
<hr />
<p>If you have a response variable and multiple explanatory variables:</p>
<pre><code>Year, Anchovy, SST, Mackerel
1964, 5449.2, 24.4, 1720.7
1965, 4263.5, 30.1, 1278.5
1966, 5146.4, 23.8, 802.6</code></pre>
<p>Use this code:</p>
<pre><code>test <- read.csv("Data/test.csv", stringsAsFactors = FALSE)
save(test, file="test.RData")</code></pre>
<p>Use this <code>lm()</code> model (or gam() etc):</p>
<pre><code>fit <- lm(Anchovy ~ SST + Mackerel, data=test)</code></pre>
<hr />
<p>What is a list? It is a object with multiple other types of objects ‘tied’ together.</p>
<pre class="r"><code>a <- list(ar=c(.8,.3), name="model", years=1:10)
a</code></pre>
<pre><code>## $ar
## [1] 0.8 0.3
##
## $name
## [1] "model"
##
## $years
## [1] 1 2 3 4 5 6 7 8 9 10</code></pre>
<p>You can now reference the different objects in <code>a</code>.</p>
<pre class="r"><code>a$ar</code></pre>
<pre><code>## [1] 0.8 0.3</code></pre>
<pre class="r"><code>a$name</code></pre>
<pre><code>## [1] "model"</code></pre>
<hr />
<p>Why is the <code>arima.sim</code> throwing an error sometimes? You must specify a stationary model and if you just randomly chose the <span class="math inline">\(\beta\)</span>’s (AR parameters) and <span class="math inline">\(\theta\)</span>’s (MA parameters) then you might be specifying a non-stationary model.</p>
</div>
<div id="monday" class="section level1">
<h1>Monday</h1>
<p>Please install the rmarkdown package. I forgot to include that.</p>
<pre><code>install.packages("rmarkdown")</code></pre>
<hr />
<p>If you do not have LaTeX installed, you can install the tinytex package. Run these commands. This will allow you to make PDF files from R Markdown files. Some of you installed tinytex, but you need to run the 2nd command also to install LiveTeX.</p>
<pre><code>install.packages('tinytex')
tinytex::install_tinytex()</code></pre>
<hr />
<p>If your get an error saying package or repository unavailable when you are trying to install packages, try the following:</p>
<ul>
<li>Make sure you are online.</li>
<li>Run <code>chooseCRANmirror()</code> from the command line. Pick any mirror.</li>
<li>Try installing package again. Repeat with a different mirror if it doesn’t work.</li>
</ul>
<hr />
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