rednering quarto lab report

Gulf-IEA · Feb 6, 2024 · bdb7d1a · bdb7d1a
1 parent 9ba1b43
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diff --git a/.Rhistory b/.Rhistory
@@ -0,0 +1,28 @@
+rm(list = ls())
+dat <- read.table("../indicator_data/surface_omega_series.txt", skip = 0, header = F)
+head(dat)
+tail(dat)
+dat$dates <- paste0(month.abb[dat$V2], dat$V1)
+datdata <- dat$dates
+inddata <- data.frame(dat$V3)
+labs <- c("Ocean acidification", "Surface aragonite saturation", "")
+indnames <- data.frame(matrix(labs, nrow = 3, byrow = F))
+s <- list(labels = indnames, indicators = inddata, datelist = datdata)
+class(s) <-"indicatordata"
+plotIndicatorTimeSeries(s)
+library(plotTimeSeries)
+library(spam)
+rm(list = ls())
+dat <- read.table("../indicator_data/surface_omega_series.txt", skip = 0, header = F)
+head(dat)
+tail(dat)
+dat$dates <- paste0(month.abb[dat$V2], dat$V1)
+datdata <- dat$dates
+inddata <- data.frame(dat$V3)
+labs <- c("Ocean acidification", "Surface aragonite saturation", "")
+indnames <- data.frame(matrix(labs, nrow = 3, byrow = F))
+s <- list(labels = indnames, indicators = inddata, datelist = datdata)
+class(s) <-"indicatordata"
+plotIndicatorTimeSeries(s)
+inddata <- s
+save(inddata, file = "OA_test.RData")
diff --git a/Lab report/OA.qmd b/Lab report/OA.qmd
@@ -1,4 +1,4 @@
-## Ocean acificiation indicator
+## Ocean acidification indicator
 
 Sent by F. Gomez on 02/19/2023
 

diff --git a/Lab report/_book/OA.html b/Lab report/_book/OA.html
@@ -7,7 +7,7 @@
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
 
-<title>Caribbean ESR Lab Report - Ocean acificiation indicator</title>
+<title>Caribbean ESR Lab Report - Ocean acidification indicator</title>
 <style>
 code{white-space: pre-wrap;}
 span.smallcaps{font-variant: small-caps;}
@@ -96,7 +96,6 @@
 }</script>
 
 
-<link rel="stylesheet" href="styles.css">
 </head>
 
 <body class="nav-sidebar floating">
@@ -108,7 +107,7 @@
       <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
         <i class="bi bi-layout-text-sidebar-reverse"></i>
       </button>
-      <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./OA.html">Part 2: Indicators</a></li><li class="breadcrumb-item"><a href="./OA.html"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Ocean acificiation indicator</span></a></li></ol></nav>
+      <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./OA.html">Part 2: Indicators</a></li><li class="breadcrumb-item"><a href="./OA.html"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Ocean acidification indicator</span></a></li></ol></nav>
       <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
       </a>
       <button type="button" class="btn quarto-search-button" aria-label="" onclick="window.quartoOpenSearch();">
@@ -160,7 +159,7 @@
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./OA.html" class="sidebar-item-text sidebar-link active"><span class="chapter-title">Ocean acificiation indicator</span></a>
+  <a href="./OA.html" class="sidebar-item-text sidebar-link active"><span class="chapter-title">Ocean acidification indicator</span></a>
   </div>
 </li>
       </ul>
@@ -178,7 +177,7 @@
 
 <header id="title-block-header" class="quarto-title-block default">
 <div class="quarto-title">
-<h1 class="title"><span class="chapter-title">Ocean acificiation indicator</span></h1>
+<h1 class="title"><span class="chapter-title">Ocean acidification indicator</span></h1>
 </div>
 
 

diff --git a/Lab report/_book/index.html b/Lab report/_book/index.html
@@ -64,7 +64,6 @@
 }</script>
 
 
-<link rel="stylesheet" href="styles.css">
 </head>
 
 <body class="nav-sidebar floating">
@@ -145,6 +144,7 @@ <h2 id="toc-title">Table of contents</h2>
   <ul>
   <li><a href="#esr-lab-reports" id="toc-esr-lab-reports" class="nav-link active" data-scroll-target="#esr-lab-reports">ESR Lab Reports</a></li>
   <li><a href="#caribbean-esr" id="toc-caribbean-esr" class="nav-link" data-scroll-target="#caribbean-esr">Caribbean ESR</a></li>
+  <li><a href="#some-notes" id="toc-some-notes" class="nav-link" data-scroll-target="#some-notes">Some notes</a></li>
   </ul>
 </nav>
     </div>
@@ -187,6 +187,18 @@ <h2 class="anchored" data-anchor-id="esr-lab-reports">ESR Lab Reports</h2>
 <section id="caribbean-esr" class="level2">
 <h2 class="anchored" data-anchor-id="caribbean-esr">Caribbean ESR</h2>
 <p>This lab report is for the Caribbean ESR that was compiled from 2023-2024. This is the first ESR for the Caribbean region. Here we can add more text about why this ESR is being compiled.</p>
+</section>
+<section id="some-notes" class="level2">
+<h2 class="anchored" data-anchor-id="some-notes">Some notes</h2>
+<p>This lab report was created the following way:</p>
+<ol type="1">
+<li>clone the Caribbean ESR repo into my R studio</li>
+<li>create a new folder in the repo called “Lab report”</li>
+<li>create 2 files, one called “index.qmd” and abother called “_quarto.txt” within the Lab report folder</li>
+<li>rename the “_quarto.txt” file to “_quarto.yml” in file explorer to change it into the book YAML</li>
+<li>populate the YAML document</li>
+</ol>
+<p>Note: this works great for rendering the quarto book as an html file. I can’t figure out how to render it as a pdf though. This is not really necessary for the lab report but something to keep in mind.</p>
 
 
 </section>

diff --git a/Lab report/_book/search.json b/Lab report/_book/search.json
@@ -16,8 +16,15 @@
   {
     "objectID": "OA.html",
     "href": "OA.html",
-    "title": "Ocean acificiation indicator",
+    "title": "Ocean acidification indicator",
     "section": "",
     "text": "Sent by F. Gomez on 02/19/2023\nNotes from Fabian:\nderived surface omega series from the MOM-Topaz hindcast 0.10deg resolution model *txt files have this structure: column1: year, column2=month, and column3=carbon system variable The mean magnitude of the simulated omega trends, around 9e-3 year-1, is consistent with observed trends in the Subtropical North Atlantic\nQuestion: What is causing the acceleration after 2008?\nAnswer: made a Taylor decomposition to figure out what was driving that acceleration in the simulated ??Ar anomaly. Interannual ??Ar changes were mostly driven by the balance between dic and alkalinity. There was a positive trend from the 1980s until mid 2000s, which contributed to moderate the ??Ar decline. But that trend vanished in the last 15 years or so, which probably has to do with this accelerated decline in ??Ar in the last decade.\n\nlibrary(plotTimeSeries)\nlibrary(spam)\n\n\nrm(list = ls())\n\ndat &lt;- read.table(\"../indicator_data/surface_omega_series.txt\", skip = 0, header = F)\nhead(dat)\ntail(dat)\ndat$dates &lt;- paste0(month.abb[dat$V2], dat$V1)\n\nFormat indicator object\n\ndatdata &lt;- dat$dates \ninddata &lt;- data.frame(dat$V3) \nlabs &lt;- c(\"Ocean acidification\", \"Surface aragonite saturation\", \"\") \nindnames &lt;- data.frame(matrix(labs, nrow = 3, byrow = F)) \ns &lt;- list(labels = indnames, indicators = inddata, datelist = datdata)\nclass(s) &lt;-\"indicatordata\"\n\nSave and plot\n\nplotIndicatorTimeSeries(s)\n\n\n\ninddata &lt;- s \nsave(inddata, file = \"OA_test.RData\")"
+  },
+  {
+    "objectID": "index.html#some-notes",
+    "href": "index.html#some-notes",
+    "title": "Caribbean ESR Lab Report",
+    "section": "Some notes",
+    "text": "Some notes\nThis lab report was created the following way:\n\nclone the Caribbean ESR repo into my R studio\ncreate a new folder in the repo called “Lab report”\ncreate 2 files, one called “index.qmd” and abother called “_quarto.txt” within the Lab report folder\nrename the “_quarto.txt” file to “_quarto.yml” in file explorer to change it into the book YAML\npopulate the YAML document\n\nNote: this works great for rendering the quarto book as an html file. I can’t figure out how to render it as a pdf though. This is not really necessary for the lab report but something to keep in mind."
   }
 ]
diff --git a/Lab report/_book/site_libs/bootstrap/bootstrap.min.css b/Lab report/_book/site_libs/bootstrap/bootstrap.min.css
diff --git a/Lab report/_quarto.yml b/Lab report/_quarto.yml
@@ -16,7 +16,13 @@ book:
 
 format:
   html:
-    theme: cosmo
-    css: styles.css
+    theme: flatly
     number-sections: false
-    output: false
+    output: false
+  pdf:
+    documentclass: scrreprt
+    toc: true
+    number-sections: false
+    output: false
+
+editor: visual
diff --git a/Lab report/index.qmd b/Lab report/index.qmd
@@ -1,7 +1,19 @@
 ## ESR Lab Reports
 
-ESR lab reports are quarto books that compile the R scripts for each indicator as well as any other descriptions of how the ESR will be put together. 
+ESR lab reports are quarto books that compile the R scripts for each indicator as well as any other descriptions of how the ESR will be put together.
 
 ## Caribbean ESR
 
 This lab report is for the Caribbean ESR that was compiled from 2023-2024. This is the first ESR for the Caribbean region. Here we can add more text about why this ESR is being compiled.
+
+## Some notes
+
+This lab report was created the following way:
+
+1.  clone the Caribbean ESR repo into my R studio
+2.  create a new folder in the repo called "Lab report"
+3.  create 2 files, one called "index.qmd" and abother called "_quarto.txt" within the Lab report folder
+4.  rename the "_quarto.txt" file to "_quarto.yml" in file explorer to change it into the book YAML
+5.  populate the YAML document 
+
+Note: this works great for rendering the quarto book as an html file. I can't figure out how to render it as a pdf though. This is not really necessary for the lab report but something to keep in mind.