Slightly more readable syntax (#17)

* Slightly more readable syntax

* Specify R language in code chunk

* Incorporate a couple Copilot suggestions

* Render website

---------

Co-authored-by: jmwingenroth <jwing421@gmail.com>

Author: cullen-molitor

02-data.Rmd

@@ -96,20 +96,20 @@ This section will go over how to access data stored in the emLab data directorie
 
 2. Set the base data directory at the top of your code to the location directory lives. You should be able to use the following code snippet to do this, which should work on either your local machines, or on a GRIT server such as quebracho or sequoia. Note that this code will automatically generate the correct directory path if using a GRIT server or a local Mac or Windows machine. If using a local Linux machine, you will need to manually modify this to incorporate your unique user name so that it matches the directory entered in Step 9 above.
 
-```
-# First determine if system is quebracho or sequoia, our GRIT servers. If so, set directory appropriately
-data_directory_base <-  ifelse(Sys.info()["nodename"] == "quebracho" | Sys.info()["nodename"] == "sequoia",
-                               "/home/emlab",
-                               # Otherwise, set the directory for local machines based on the OS
-                               # If using Mac OS, the directory will be automatically set as follows
-                               ifelse(Sys.info()["sysname"]=="Darwin",
-                                      "/Users/Shared/nextcloud/emLab",
-                               # If using Windows, the directory will be automatically set as follows
-                               ifelse(Sys.info()["sysname"]=="Windows",
-                                      "G:/Shared\ drives/nextcloud/emLab",
-                                      # If using Linux, will need to manually modify the following directory path based on their user name
-                                      # Replace your_username with your local machine user name
-                                      "/home/your_username/Nextcloud")))
+```{r}
+# Setting the base data directory in R.
+# First determine if system is one of our GRIT servers (quebracho or sequoia). 
+# Otherwise, set the directory for local machines based on the OS (Darwin, Windows, or Linux).
+# Finally, if no conditions are met, set the directory to directly within the default home 
+# directory.
+
+data_directory_base <- dplyr::case_when(
+  Sys.info()["nodename"] %in% c("quebracho", "sequoia") ~ "/home/emlab",   # GRIT servers
+  Sys.info()["sysname"] == "Darwin" ~ "/Users/Shared/nextcloud/emLab",     # Mac OS
+  Sys.info()["sysname"] == "Windows" ~ "G:/Shared drives/nextcloud/emLab", # Windows OS
+  Sys.info()["sysname"] == "Linux" ~ "/home/your_username/Nextcloud",      # Linux OS (use your username)
+  TRUE ~ "~/Nextcloud"                                                     # Anything else
+)
 ```
 
 

docs/1-file-structure.html

@@ -6,7 +6,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
   <title>1 File Structure | emLab Standard Operating Procedures</title>
   <meta name="description" content="Standard operating procedures for emLab projects" />
-  <meta name="generator" content="bookdown 0.45 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.46 and GitBook 2.6.7" />
 
   <meta property="og:title" content="1 File Structure | emLab Standard Operating Procedures" />
   <meta property="og:type" content="book" />
@@ -23,7 +23,7 @@
 <meta name="author" content="Environmental Markets Lab (emLab)" />
 
 
-<meta name="date" content="2025-12-01" />
+<meta name="date" content="2026-04-09" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -54,6 +54,71 @@
 <script src="assets/anchor-sections-1.1.0/anchor-sections.js"></script>
 
 
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+pre > code.sourceCode > span:empty { height: 1.2em; }
+.sourceCode { overflow: visible; }
+code.sourceCode > span { color: inherit; text-decoration: inherit; }
+pre.sourceCode { margin: 0; }
+@media screen {
+div.sourceCode { overflow: auto; }
+}
+@media print {
+pre > code.sourceCode { white-space: pre-wrap; }
+pre > code.sourceCode > span { text-indent: -5em; padding-left: 5em; }
+}
+pre.numberSource code
+  { counter-reset: source-line 0; }
+pre.numberSource code > span
+  { position: relative; left: -4em; counter-increment: source-line; }
+pre.numberSource code > span > a:first-child::before
+  { content: counter(source-line);
+    position: relative; left: -1em; text-align: right; vertical-align: baseline;
+    border: none; display: inline-block;
+    -webkit-touch-callout: none; -webkit-user-select: none;
+    -khtml-user-select: none; -moz-user-select: none;
+    -ms-user-select: none; user-select: none;
+    padding: 0 4px; width: 4em;
+    color: #aaaaaa;
+  }
+pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa;  padding-left: 4px; }
+div.sourceCode
+  {   }
+@media screen {
+pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
+}
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+code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
+</style>
 
 <style type="text/css">
 

docs/1.1-folder-naming.html

@@ -6,7 +6,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
   <title>1.1 Folder Naming | emLab Standard Operating Procedures</title>
   <meta name="description" content="Standard operating procedures for emLab projects" />
-  <meta name="generator" content="bookdown 0.45 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.46 and GitBook 2.6.7" />
 
   <meta property="og:title" content="1.1 Folder Naming | emLab Standard Operating Procedures" />
   <meta property="og:type" content="book" />
@@ -23,7 +23,7 @@
 <meta name="author" content="Environmental Markets Lab (emLab)" />
 
 
-<meta name="date" content="2025-12-01" />
+<meta name="date" content="2026-04-09" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -54,6 +54,71 @@
 <script src="assets/anchor-sections-1.1.0/anchor-sections.js"></script>
 
 
+<style type="text/css">
+html { -webkit-text-size-adjust: 100%; }
+pre > code.sourceCode { white-space: pre; position: relative; }
+pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
+pre > code.sourceCode > span:empty { height: 1.2em; }
+.sourceCode { overflow: visible; }
+code.sourceCode > span { color: inherit; text-decoration: inherit; }
+pre.sourceCode { margin: 0; }
+@media screen {
+div.sourceCode { overflow: auto; }
+}
+@media print {
+pre > code.sourceCode { white-space: pre-wrap; }
+pre > code.sourceCode > span { text-indent: -5em; padding-left: 5em; }
+}
+pre.numberSource code
+  { counter-reset: source-line 0; }
+pre.numberSource code > span
+  { position: relative; left: -4em; counter-increment: source-line; }
+pre.numberSource code > span > a:first-child::before
+  { content: counter(source-line);
+    position: relative; left: -1em; text-align: right; vertical-align: baseline;
+    border: none; display: inline-block;
+    -webkit-touch-callout: none; -webkit-user-select: none;
+    -khtml-user-select: none; -moz-user-select: none;
+    -ms-user-select: none; user-select: none;
+    padding: 0 4px; width: 4em;
+    color: #aaaaaa;
+  }
+pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa;  padding-left: 4px; }
+div.sourceCode
+  {   }
+@media screen {
+pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
+}
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+code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
+</style>
 
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docs/1.2-google-shared-drive.html

@@ -6,7 +6,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
   <title>1.2 Google Shared Drive | emLab Standard Operating Procedures</title>
   <meta name="description" content="Standard operating procedures for emLab projects" />
-  <meta name="generator" content="bookdown 0.45 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.46 and GitBook 2.6.7" />
 
   <meta property="og:title" content="1.2 Google Shared Drive | emLab Standard Operating Procedures" />
   <meta property="og:type" content="book" />
@@ -23,7 +23,7 @@
 <meta name="author" content="Environmental Markets Lab (emLab)" />
 
 
-<meta name="date" content="2025-12-01" />
+<meta name="date" content="2026-04-09" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -54,6 +54,71 @@
 <script src="assets/anchor-sections-1.1.0/anchor-sections.js"></script>
 
 
+<style type="text/css">
+html { -webkit-text-size-adjust: 100%; }
+pre > code.sourceCode { white-space: pre; position: relative; }
+pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
+pre > code.sourceCode > span:empty { height: 1.2em; }
+.sourceCode { overflow: visible; }
+code.sourceCode > span { color: inherit; text-decoration: inherit; }
+pre.sourceCode { margin: 0; }
+@media screen {
+div.sourceCode { overflow: auto; }
+}
+@media print {
+pre > code.sourceCode { white-space: pre-wrap; }
+pre > code.sourceCode > span { text-indent: -5em; padding-left: 5em; }
+}
+pre.numberSource code
+  { counter-reset: source-line 0; }
+pre.numberSource code > span
+  { position: relative; left: -4em; counter-increment: source-line; }
+pre.numberSource code > span > a:first-child::before
+  { content: counter(source-line);
+    position: relative; left: -1em; text-align: right; vertical-align: baseline;
+    border: none; display: inline-block;
+    -webkit-touch-callout: none; -webkit-user-select: none;
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+    -ms-user-select: none; user-select: none;
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+pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa;  padding-left: 4px; }
+div.sourceCode
+  {   }
+@media screen {
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+}
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docs/1.3-grit-data-storage-space.html

@@ -6,7 +6,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
   <title>1.3 GRIT data storage space | emLab Standard Operating Procedures</title>
   <meta name="description" content="Standard operating procedures for emLab projects" />
-  <meta name="generator" content="bookdown 0.45 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.46 and GitBook 2.6.7" />
 
   <meta property="og:title" content="1.3 GRIT data storage space | emLab Standard Operating Procedures" />
   <meta property="og:type" content="book" />
@@ -23,7 +23,7 @@
 <meta name="author" content="Environmental Markets Lab (emLab)" />
 
 
-<meta name="date" content="2025-12-01" />
+<meta name="date" content="2026-04-09" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -54,6 +54,71 @@
 <script src="assets/anchor-sections-1.1.0/anchor-sections.js"></script>
 
 
+<style type="text/css">
+html { -webkit-text-size-adjust: 100%; }
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+pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
+pre > code.sourceCode > span:empty { height: 1.2em; }
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+pre.sourceCode { margin: 0; }
+@media screen {
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+}
+@media print {
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+  { position: relative; left: -4em; counter-increment: source-line; }
+pre.numberSource code > span > a:first-child::before
+  { content: counter(source-line);
+    position: relative; left: -1em; text-align: right; vertical-align: baseline;
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+    -webkit-touch-callout: none; -webkit-user-select: none;
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+div.sourceCode
+  {   }
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+}
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+</style>
 
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