Render bookdown

docs/01-BioDIGS_project_overview.md

@@ -0,0 +1,39 @@
+:::: {.borrowed_chunk}
+
+# (PART\*) BioDIGS Overview {-}
+
+# Background
+
+One critical aspect of an undergraduate STEM education is hands-on research. Undergraduate research experiences enhance what students learn in the classroom as well as increase a student's interest in pursuing STEM careers [@Russell2007]. It can also lead to improved scientific reasoning and increased academic performance overall [@Buffalari2020]. However, many students at underresourced institutions like community colleges, Historically Black Colleges and Universities (HBCUs), tribal colleges and universities, and Hispanic-serving institutions have limited access to research opportunities compared to their cohorts at larger four-year colleges and R1 institutions. These students are also more likely to belong to groups that are already under-represented in STEM disciplines, particularly genomics and data science [@Canner2017; @GDSCN2022].
+
+The BioDIGS Project aims to be at the intersection of genomics, data science, cloud computing, and education.
+
+
+## What is genomics?
+
+Genomics broadly refers to the study of genomes, which are an organism's complete set of DNA. This includes both genes and non-coding regions of DNA. Traditional genomics involves sequencing and analyzing the genome of individual species.
+
+Metagenomics expands genomics to look at the collective genomes of entire communities of organisms in an environmental sample, like soil. It allows researchers to study not just the genes of culturable or isolated organisms, but the entirety of genetic material present in a given environment. By using genomic techniques to survey the soil microbes, we can identify everything in the soil, including microbes that no one has identified before.
+
+We are doing both traditional genomics and metagenomics as part of BioDIGS.
+
+## What is data science?
+
+Data science is an interdisciplinary field that uses scientific methods, processes, algorithms and systems to extract knowledge and insights from structured and unstructured data. It includes collecting, cleaning, and combining data from multiple databases, exploring data and developing statistical and machine learning models to identify patterns in complex datasets, and creating tools to efficiently store, process, and access large amounts of data.
+
+## What is cloud computing?
+
+Cloud computing just means using the internet to get access to powerful computer resources like storage, servers, databases, networking tools, and specialized software programs. Instead of having to buy and maintain their own powerful computers, storage servers, and other systems, users can pay to use them through an internet connection as needed. Users only pay for what they need, when they actually use it, and professionals update and maintain the systems in large data centers. It is a particularly useful tool for researchers and students at smaller institutions with limited computational services, especially when working with complex databases.
+
+The genome assembly and analyses for BioDIGS have been done using the NHGRI [AnVIL](https://anvilproject.org/) cloud computing platform, as well as [Galaxy](usegalaxy.org).
+
+## Why soil microbes?
+
+It can be challenging to include undergraduates in human genomic and health research, especially in a classroom context. Both human genetic data and human health data are protected data, which limits the sort of information students can access without undergoing specialized ethics training. However, the same sorts of data cleaning and analysis methods used for human genomic data are also used for microbial genomic data, which does not have the same sort of legal protections as human genetic data. This makes it ideal for training undergraduate students at the beginning of their careers and can be used to prepare students for future research in human genomics and health [@Jurkowski2017]. Additionally, the microbes in the soil can have big impacts on our health [@BrevikBurgess2014].
+
+## Heavy metals and human health
+
+Human activities that change the landscape can also change what sorts of inorganic and abiotic compounds we find in the soil, particularly increasing the amount of heavy metals [@Yan2020]. When cars drive on roads, compounds from the exhaust, oil, and other fluids might settle onto the roads and be washed into the soil. When we put salt on roads, parking lots, and sidewalks, the salts themselves will eventually be washed away and enter the ecosystem through both water and soil. Chemicals from factories and other businesses also leech into our environment. Previous research has demonstrated that in areas with more human activity, like cities, soils include greater concentrations of heavy metals than found in rural areas with limited human populations [@Khan2023; @Wang2022]. Increased heavy metal concentrations also disproportionately affect lower-income and predominantly minority areas [@Jones2022].
+
+Research suggests that increased heavy metal concentration in soils has major impacts on the soil microbial community. In particular, increased heavy metal concentration is associated with an increase in soil bacteria that have antibiotic resistance markers [@Gorovtsov2018; @Nguyen2019; @Sun2021].
+::::

docs/02-research_team.md

@@ -0,0 +1,50 @@
+:::: {.borrowed_chunk}
+
+# Research Team
+
+This project is coordinated by the Genomics Data Science Community Network (GDSCN). You can read more about the GDSCN and its mission at the network [website](https://www.gdscn.org/home).
+
+## Soil sampling 
+
+This map shows the current sampling locations for the BioDIGS project. The extensive network of the GDSCN has made this data collection possible. 
+
+<iframe src="https://www.google.com/maps/d/embed?mid=1j6lqxJuQ1ACOmtT14TKdZ2D127XYnok&ehbc=2E312F" width="640" height="480" title="BioDIGS current sampling locations"></iframe>
+
+Soil sampling for this project was done by both faculty and student volunteers from schools that aren't traditional R1 research institutions. Many of the faculty are also members of the GDSCN. This list of locations reflects GDSCN institutions and friends of GDSCN who have collected soil samples.
+
+- **Annandale, VA**: Northern Virginia Community College
+- **Atlanta, GA**: Spelman College
+- **Baltimore, MD**: College of Southern Maryland, Notre Dame College of Maryland, Towson University
+- **Bismark, ND**: United Tribes Technical College
+- **El Paso, TX**: El Paso Community College, The University of Texas at El Paso
+- **Fresno, CA**: Clovis Community College
+- **Greensboro, NC**: North Carolina A&T State University
+- **Harrisonburg, VA**: James Madison University
+- **Honolulu, Hawai'i**: University of Hawai'i at M&amacr;noa
+- **Las Cruces, NM**: Do&ntilde;a Ana Community College
+- **Montgomery County, MD**: Montgomery College, Towson University
+- **Nashville, TN**: Meharry Medical College
+- **New York, NY**: Guttman Community College CUNY
+- **Petersburg, VA**: Virginia State University
+- **Seattle, WA**: North Seattle College, Pierce College
+- **Tsaile, AZ**: Din&eacute; College  
+
+
+# Support
+
+This project would not be possible without financial and technical support from many organizations and people. 
+
+## Funding
+
+Funding for this project has been provided by the [National Human Genome Research Institute](https://www.genome.gov/) (Contract # 75N92022P00232 awarded to Johns Hopkins University). 
+
+## Sponsors
+
+[PacBio](https://www.pacb.com/) and [CosmosID](https://www.cosmosid.com/) have graciously donated supplies.
+
+[Advances in Genome Biology and Technology](https://www.agbt.org/) provided funding support for several team members to attend AGBT 2024.
+
+## Analytical and Computational Support
+
+Computational support has been provided by NHGRI's [AnVIL](https://anvilproject.org/) cloud computing platform and [Galaxy](usegalaxy.org).
+::::

docs/03-data_tour.md

@@ -0,0 +1,26 @@
+:::: {.borrowed_chunk}
+
+# Data
+
+There are currently three major kinds of data available from BioDIGS: sample metadata, soil testing data, and genomics and metagenomics data. All of these are available for use in your classroom.
+
+## Sample Metadata
+
+This dataset contains information about the samples themselves, including GPS coordinates for the sample location, date the sample was taken, and the site name. This dataset is also available from the [BioDIGS website](https://biodigs.org/#site_data)
+
+You can also see images of each sampling site and soil characteristics at the [sample map](https://biodigs.org/#sample_map).
+
+## Soil Testing Data
+
+This dataset includes basic information about the soil itself like pH, percentage of organic matter, variety of soil metal concentrations. The complete data dictionary is available [here](https://docs.google.com/spreadsheets/d/109xYUM48rjj33B76hZ3bNlrm8u-_S6uyoE_3wSCp0r0/edit#gid=188448677). The dataset is available at the [BioDIGS website](https://biodigs.org/#soil_data).
+
+This dataset was generated by the [Delaware Soil Testing Program](https://www.udel.edu/canr/cooperative-extension/environmental-stewardship/soil-testing/) at the University of Delaware.
+
+## Genomics and Metagenomics Data
+
+You can access this data in both raw and processed forms.
+
+The Illumina and Nanopore sequences were generated at the [Johns Hopkins University Genetic Resources Core Facility](https://grcf.jhmi.edu/). PacBio sequencing was done by [PacBio](https://www.pacb.com/) directly.
+
+More information coming soon!
+::::

docs/05-anvil_onboarding.md

@@ -0,0 +1,52 @@
+# (PART\*) Student Guide to AnVIL {-}
+
+:::: {.borrowed_chunk}
+
+# AnVIL Workspace
+
+
+
+You can easily access the data on AnVIL by cloning the dedicated workspace. These sections guide you through creating an AnVIL account and accessing the workspace.
+
+
+## Create Google Account
+
+
+If you do not already have a Google account that you would like to use for accessing Terra, [create one now](https://accounts.google.com/SignUp).
+
+If you would like to create a Google account that is associated with your non-Gmail, institutional email address, follow [these instructions](https://support.terra.bio/hc/en-us/articles/360029186611).
+
+## Clone the Workspace
+
+
+1. [Launch Terra](https://anvil.terra.bio/#workspaces)
+
+1. Locate the Workspace you want to clone. If a Workspace has been shared with you ahead of time, it will appear in "MY WORKSPACES". You can clone a Workspace that was shared with you to perform your own analyses. In the screenshot below, no Workspaces have been shared.
+
+    <img src="resources/images/05-anvil_onboarding_files/figure-html//1JvfOluHe543cUCyyH3zz0ew-1J1QjhdYGZufW9NrC_M_g117abafa453_0_0.png" title="Screenshot of Terra &quot;MY WORKSPACES&quot; menu. The &quot;MY WORKSPACES&quot; tab is highlighted. No Workspaces are visible because none have been shared with the user. There is an option to create a new Workspace." alt="Screenshot of Terra &quot;MY WORKSPACES&quot; menu. The &quot;MY WORKSPACES&quot; tab is highlighted. No Workspaces are visible because none have been shared with the user. There is an option to create a new Workspace." width="480" />
+
+1. If a Workspace hasn't been shared with you, navigate to the "FEATURED" or "PUBLIC" Workspace tabs.
+
+    <img src="resources/images/05-anvil_onboarding_files/figure-html//1JvfOluHe543cUCyyH3zz0ew-1J1QjhdYGZufW9NrC_M_g117abafa453_0_144.png" title="Screenshot of Terra &quot;My Workspaces&quot; menu. The &quot;FEATURED&quot; tab is highlighted." alt="Screenshot of Terra &quot;My Workspaces&quot; menu. The &quot;FEATURED&quot; tab is highlighted." width="480" />
+
+1. Use the search box to find the Workspace you want to clone.
+
+    <img src="resources/images/05-anvil_onboarding_files/figure-html//1JvfOluHe543cUCyyH3zz0ew-1J1QjhdYGZufW9NrC_M_g117abafa453_0_288.png" title="Screenshot of Terra &quot;My Workspaces&quot; menu. The search bar is highlighted and the user has typed in the term &quot;COVID-19&quot;. A Workspace related to COVID-19 appears in the results." alt="Screenshot of Terra &quot;My Workspaces&quot; menu. The search bar is highlighted and the user has typed in the term &quot;COVID-19&quot;. A Workspace related to COVID-19 appears in the results." width="480" />
+
+1. Click the teardrop button on the far right next to the Workspace you want to clone. Click "Clone". You can also clone the Workspace from the Workspace Dashboard instead of the search results.
+
+    <img src="resources/images/05-anvil_onboarding_files/figure-html//1JvfOluHe543cUCyyH3zz0ew-1J1QjhdYGZufW9NrC_M_g117abafa453_0_432.png" title="Screenshot of Terra &quot;My Workspaces&quot; menu with the Workspace that we want to clone. The teardrop button has been clicked to bring up the options. The &quot;Clone&quot; option from the list is highlighted." alt="Screenshot of Terra &quot;My Workspaces&quot; menu with the Workspace that we want to clone. The teardrop button has been clicked to bring up the options. The &quot;Clone&quot; option from the list is highlighted." width="480" />
+    <img src="resources/images/05-anvil_onboarding_files/figure-html//1JvfOluHe543cUCyyH3zz0ew-1J1QjhdYGZufW9NrC_M_g117abafa453_0_577.png" title="Screenshot of the Dashboard for the Workspace that we want to clone. The teardrop button has been clicked to bring up the options. The &quot;Clone&quot; option from the list is highlighted." alt="Screenshot of the Dashboard for the Workspace that we want to clone. The teardrop button has been clicked to bring up the options. The &quot;Clone&quot; option from the list is highlighted." width="480" />
+
+1. You will see a popup box appear. Name your Workspace and select the appropriate Terra Billing Project.  **All activity in the Workspace will be charged to this Billing Project** (regardless of who conducted it). Remember that each Workspace should have its own Billing Project.
+
+    <img src="resources/images/05-anvil_onboarding_files/figure-html//1JvfOluHe543cUCyyH3zz0ew-1J1QjhdYGZufW9NrC_M_g117abafa453_0_722.png" title="Screenshot of the &quot;clone workspace&quot; Terra popup dialog box. The Workspace name and Billing Project dropdown are highlighted. Text has been filled in for the Workspace name as &quot;Lab-member-1-workspace-2&quot;." alt="Screenshot of the &quot;clone workspace&quot; Terra popup dialog box. The Workspace name and Billing Project dropdown are highlighted. Text has been filled in for the Workspace name as &quot;Lab-member-1-workspace-2&quot;." width="480" />
+
+1. If you are working with protected data, you can set the **Authorization Domain** to limit who can be added to your Workspace.  Note that the Authorization Domain cannot be changed after the Workspace is created (i.e. there is no way to make this Workspace shareable with a larger audience in the future).  Workspaces by default are only visible to people you specifically share them with.  Authorization domains add an extra layer of enforcement over privacy, but by nature make sharing more complicated.  We recommend using Authorization Domains in cases where it is extremely important and/or legally required that the data be kept private (e.g. protected patient data, industry data).  For data you would merely prefer not be shared with the world, we recommend relying on standard Workspace sharing permissions rather than Authorization Domains, as Authorization Domains can make future collaborations, publications, or other sharing complicated.
+
+    <img src="resources/images/05-anvil_onboarding_files/figure-html//1JvfOluHe543cUCyyH3zz0ew-1J1QjhdYGZufW9NrC_M_g117abafa453_0_867.png" title="Screenshot of Terra popup dialog box for creating a new Workspace. The drop-down menu labeled &quot;Authorization domain&quot; is highlighted." alt="Screenshot of Terra popup dialog box for creating a new Workspace. The drop-down menu labeled &quot;Authorization domain&quot; is highlighted." width="480" />
+
+1. Click "CLONE WORKSPACE".  The new Workspace should now show up under your Workspaces.
+
+    <img src="resources/images/05-anvil_onboarding_files/figure-html//1JvfOluHe543cUCyyH3zz0ew-1J1QjhdYGZufW9NrC_M_g117abafa453_0_1012.png" title="Screenshot of Terra popup dialog box for creating a new Workspace. The &quot;Clone Workspace&quot; button is highlighted." alt="Screenshot of Terra popup dialog box for creating a new Workspace. The &quot;Clone Workspace&quot; button is highlighted." width="480" />
+::::

docs/08-student_using_rstudio.md

@@ -0,0 +1,175 @@
+:::: {.borrowed_chunk}
+
+# Using RStudio on AnVIL
+
+In the next few steps, you will walk through how to get set up to use RStudio on the AnVIL platform. AnVIL is centered around different “Workspaces”. Each Workspace functions almost like a mini code laboratory - it is a place where data can be examined, stored, and analyzed. The first thing we want to do is to copy or “clone” a Workspace to create a space for you to experiment.
+
+Use a web browser to go to the AnVIL website. In the browser type:
+
+```
+anvil.terra.bio
+```
+
+:::{.notice}
+**Tip**
+At this point, it might make things easier to open up a new window in your browser and split your screen. That way, you can follow along with this guide on one side and execute the steps on the other.
+:::
+
+Your instructor will give you information on which workspace you should clone.
+
+## Video overview of RStudio on AnVIL
+
+
+Here is a video tutorial that describes the basics of using RStudio on AnVIL.
+
+<iframe src="https://drive.google.com/file/d/1v72ZG8JIRDUaewFQgGfcCO_qoM4eYmYX/preview" width="640" height="360" allow="autoplay"></iframe>
+
+### Objectives
+
+- Start compute for your RStudio environment
+- Tour RStudio on AnVIL
+- Stop compute to minimize expenses
+
+### Slides
+
+The slides for this tutorial are are located [here](https://docs.google.com/presentation/d/1eypYLLqD11-NwHLs4adGpcuSB07dYEJfAaALSMvgzqw).
+
+## Launching RStudio
+
+
+:::{.warning}
+AnVIL is very versatile and can scale up to use very powerful cloud computers. It's very important that you select a cloud computing environment appropriate to your needs to avoid runaway costs.  If you are uncertain, start with the default settings; it is fairly easy to increase your compute resources later, if needed, but harder to scale down.
+:::
+
+Note that, in order to use RStudio, you must have access to a Terra Workspace with permission to compute (i.e. you must be a "Writer" or "Owner" of the Workspace).
+
+1. Open Terra - use a web browser to go to [`anvil.terra.bio`](https://anvil.terra.bio/)
+
+1. In the drop-down menu on the left, navigate to "Workspaces". Click the triple bar in the top left corner to access the menu. Click "Workspaces".
+
+    <img src="resources/images/08-student_using_rstudio_files/figure-html//1a35Mb8f0M-bQkBcHa1cyQc6YxXoBLtExCz96nv08vkA_g117989bd49c_0_150.png" title="Screenshot of Terra drop-down menu.  The &quot;hamburger&quot; button to extend the drop-down menu is highlighted, and the menu item &quot;Workspaces&quot; is highlighted." alt="Screenshot of Terra drop-down menu.  The &quot;hamburger&quot; button to extend the drop-down menu is highlighted, and the menu item &quot;Workspaces&quot; is highlighted." width="100%" />
+
+1. Click on the name of your Workspace. You should be routed to a link that looks like: `https://anvil.terra.bio/#workspaces/<billing-project>/<workspace-name>`.
+
+1. Click on the cloud icon on the far right to access your Cloud Environment options.
+
+    <img src="resources/images/08-student_using_rstudio_files/figure-html//1a35Mb8f0M-bQkBcHa1cyQc6YxXoBLtExCz96nv08vkA_g14ea2db115d_0_22.png" title="Screenshot of a Terra Workspace. The cloud icon to create a new cloud environment is highlighted." alt="Screenshot of a Terra Workspace. The cloud icon to create a new cloud environment is highlighted." width="100%" />
+
+1. In the dialogue box, click the "Settings" button under RStudio.
+
+    <img src="resources/images/08-student_using_rstudio_files/figure-html//1a35Mb8f0M-bQkBcHa1cyQc6YxXoBLtExCz96nv08vkA_g14ea2db115d_0_18.png" title="Screenshot of the Cloud Environment Details dialogue box. The Settings button under RStudio is highlighted." alt="Screenshot of the Cloud Environment Details dialogue box. The Settings button under RStudio is highlighted." width="100%" />
+
+1. You will see some details about the default RStudio cloud environment, and a list of costs because it costs a small amount of money to use cloud computing.
+
+    <img src="resources/images/08-student_using_rstudio_files/figure-html//1a35Mb8f0M-bQkBcHa1cyQc6YxXoBLtExCz96nv08vkA_g14ea2db115d_0_35.png" title="Screenshot of the RStudio Cloud Environment dialogue box. The cost to run the environment is highlighted." alt="Screenshot of the RStudio Cloud Environment dialogue box. The cost to run the environment is highlighted." width="100%" />
+
+
+
+1. If you are uncertain about what you need, the default configuration is a reasonable, cost-conservative choice.  It is fairly easy to increase your compute resources later, if needed, but harder to scale down. Click the “Create” button.
+
+    <img src="resources/images/08-student_using_rstudio_files/figure-html//1a35Mb8f0M-bQkBcHa1cyQc6YxXoBLtExCz96nv08vkA_g14ea2db115d_0_41.png" title="Screenshot of the RStudio Cloud Environment dialogue box. The &quot;CREATE&quot; button is highlighted." alt="Screenshot of the RStudio Cloud Environment dialogue box. The &quot;CREATE&quot; button is highlighted." width="100%" />
+
+
+
+1. Otherwise, click “CUSTOMIZE” to modify the environment for your needs.
+
+    <img src="resources/images/08-student_using_rstudio_files/figure-html//1a35Mb8f0M-bQkBcHa1cyQc6YxXoBLtExCz96nv08vkA_g14ea2db115d_0_48.png" title="Screenshot of the RStudio Cloud Environment dialogue box. The &quot;CUSTOMIZE&quot; button is highlighted." alt="Screenshot of the RStudio Cloud Environment dialogue box. The &quot;CUSTOMIZE&quot; button is highlighted." width="100%" />
+
+
+
+
+
+
+
+
+
+
+
+1. The dialogue box will close and you will be returned to your Workspace.  You can see the status of your cloud environment by hovering over the RStudio logo.  It will take a few minutes for Terra to request computers and install software.
+
+    <img src="resources/images/08-student_using_rstudio_files/figure-html//1a35Mb8f0M-bQkBcHa1cyQc6YxXoBLtExCz96nv08vkA_g14ea2db115d_0_91.png" title="Screenshot of a Terra Workspace. The hovertext for the RStudio icon is highlighted, and indicates that the status of the environment is &quot;Creating&quot;." alt="Screenshot of a Terra Workspace. The hovertext for the RStudio icon is highlighted, and indicates that the status of the environment is &quot;Creating&quot;." width="100%" />
+
+1. When your environment is ready, its status will change to “Running”.  Click on the RStudio logo to open a new dialogue box that will let you launch RStudio.
+
+    <img src="resources/images/08-student_using_rstudio_files/figure-html//1a35Mb8f0M-bQkBcHa1cyQc6YxXoBLtExCz96nv08vkA_g14ea2db115d_0_95.png" title="Screenshot of a Terra Workspace. The hovertext for the RStudio icon is highlighted, and indicates that the status of the environment is &quot;Running&quot;." alt="Screenshot of a Terra Workspace. The hovertext for the RStudio icon is highlighted, and indicates that the status of the environment is &quot;Running&quot;." width="100%" />
+
+1. Click the launch icon to open RStudio.  This is also where you can pause, modify, or delete your environment when needed.
+
+    <img src="resources/images/08-student_using_rstudio_files/figure-html//1a35Mb8f0M-bQkBcHa1cyQc6YxXoBLtExCz96nv08vkA_g14ea2db115d_0_99.png" title="Screenshot of the RStudio Environment Details dialogue box. The &quot;Open&quot; button is highlighted." alt="Screenshot of the RStudio Environment Details dialogue box. The &quot;Open&quot; button is highlighted." width="100%" />
+
+1. You should now see the RStudio interface with information about the version printed to the console.
+
+    <img src="resources/images/08-student_using_rstudio_files/figure-html//1a35Mb8f0M-bQkBcHa1cyQc6YxXoBLtExCz96nv08vkA_g14ea2db115d_0_103.png" title="Screenshot of the RStudio environment interface." alt="Screenshot of the RStudio environment interface." width="100%" />
+
+## Touring RStudio
+
+
+Next, we will be using RStudio and the package `Glimma` to create interactive plots. See [this vignette](https://bioconductor.org/packages/release/bioc/vignettes/Glimma/inst/doc/limma_edger.html) for more information.
+
+1. The Bioconductor team has created a very useful package to programmatically interact with Terra and Google Cloud. Install the `AnVIL` package. It will make some steps easier as we go along.
+
+
+
+    <img src="resources/images/08-student_using_rstudio_files/figure-html//1BLTCaogA04bbeSD1tR1Wt-mVceQA6FHXa8FmFzIARrg_g11f12bc99af_0_49.png" title="Screenshot of the RStudio environment interface. Code has been typed in the console and is highlighted." alt="Screenshot of the RStudio environment interface. Code has been typed in the console and is highlighted." width="480" />
+
+1. You can now quickly install precompiled binaries using the AnVIL package’s `install()` function. We will use it to install the `Glimma` package and the `airway` package. The `airway` package contains a `SummarizedExperiment` data class. This data describes an RNA-Seq experiment on four human airway smooth muscle cell lines treated with dexamethasone. 
+
+{Note: for some of the packages, you will have to install packaged from the CRAN repository, using the install.packages() function. The examples will show you which install method to use.}
+
+
+
+    <img src="resources/images/08-student_using_rstudio_files/figure-html//1BLTCaogA04bbeSD1tR1Wt-mVceQA6FHXa8FmFzIARrg_g11f12bc99af_0_56.png" title="Screenshot of the RStudio environment interface. Code has been typed in the console and is highlighted." alt="Screenshot of the RStudio environment interface. Code has been typed in the console and is highlighted." width="480" />
+
+1. Load the example data.
+
+
+
+    <img src="resources/images/08-student_using_rstudio_files/figure-html//1BLTCaogA04bbeSD1tR1Wt-mVceQA6FHXa8FmFzIARrg_g11f12bc99af_0_56.png" title="Screenshot of the RStudio environment interface. Code has been typed in the console and is highlighted." alt="Screenshot of the RStudio environment interface. Code has been typed in the console and is highlighted." width="480" />
+
+1. The multidimensional scaling (MDS) plot is frequently used to explore differences in samples. When this data is MDS transformed, the first two dimensions explain the greatest variance between samples, and the amount of variance decreases monotonically with increasing dimension. The following code will launch a new window where you can interact with the MDS plot.
+
+
+
+    <img src="resources/images/08-student_using_rstudio_files/figure-html//1BLTCaogA04bbeSD1tR1Wt-mVceQA6FHXa8FmFzIARrg_g11f12bc99af_0_70.png" title="Screenshot of the Glimma popout showing the data in an MDS plot. All data points are blue." alt="Screenshot of the Glimma popout showing the data in an MDS plot. All data points are blue." width="480" />
+
+1. Change the `colour_by` setting to "groups" so you can easily distinguish between groups. In this data, the "group" is the treatment.
+
+    <img src="resources/images/08-student_using_rstudio_files/figure-html//1BLTCaogA04bbeSD1tR1Wt-mVceQA6FHXa8FmFzIARrg_g11f12bc99af_0_77.png" title="Screenshot of the Glimma popout showing the data in an MDS plot. Data points are colored blue and orange by group. The colour by dropdown menu on the interactive plot is hightlighted." alt="Screenshot of the Glimma popout showing the data in an MDS plot. Data points are colored blue and orange by group. The colour by dropdown menu on the interactive plot is hightlighted." width="480" />
+
+1. You can download the interactive html file by clicking on "Save As".
+
+    <img src="resources/images/08-student_using_rstudio_files/figure-html//1BLTCaogA04bbeSD1tR1Wt-mVceQA6FHXa8FmFzIARrg_g1204ed6da7f_0_0.png" title="Screenshot of the Glimma popout showing the data in an MDS plot. The Save As menu is highlighted." alt="Screenshot of the Glimma popout showing the data in an MDS plot. The Save As menu is highlighted." width="480" />
+
+1. You can also download plots and other files created directly in RStudio. To download the following plot, click on "Export" and save in your preferred format to the default directory. This saves the file in your cloud environment.
+
+
+
+    <img src="resources/images/08-student_using_rstudio_files/figure-html//1BLTCaogA04bbeSD1tR1Wt-mVceQA6FHXa8FmFzIARrg_g1204ed6da7f_0_12.png" title="Screenshot of the RStudio interface. A plot has been created. The Export menu has been highlighted." alt="Screenshot of the RStudio interface. A plot has been created. The Export menu has been highlighted." width="480" />
+
+1. You should see the plot in the "Files" pane.
+
+    <img src="resources/images/08-student_using_rstudio_files/figure-html//1BLTCaogA04bbeSD1tR1Wt-mVceQA6FHXa8FmFzIARrg_g1204ed6da7f_0_19.png" title="Screenshot of the RStudio interface. A plot has been created. The saved pdf file is now visible under the &quot;Files&quot; pane." alt="Screenshot of the RStudio interface. A plot has been created. The saved pdf file is now visible under the &quot;Files&quot; pane." width="480" />
+
+1. Select this file and click "More" > "Export"
+
+    <img src="resources/images/08-student_using_rstudio_files/figure-html//1BLTCaogA04bbeSD1tR1Wt-mVceQA6FHXa8FmFzIARrg_g1204ed6db6a_0_0.png" title="Screenshot of the RStudio interface. A plot has been created. The saved pdf file is now visible under the &quot;Files&quot; pane. The &quot;More&quot; and &quot;Export&quot; menus have been highlighted." alt="Screenshot of the RStudio interface. A plot has been created. The saved pdf file is now visible under the &quot;Files&quot; pane. The &quot;More&quot; and &quot;Export&quot; menus have been highlighted." width="480" />
+
+1. Select "Download" to save the file to your local machine.
+
+    <img src="resources/images/08-student_using_rstudio_files/figure-html//1BLTCaogA04bbeSD1tR1Wt-mVceQA6FHXa8FmFzIARrg_g1204ed6db6a_0_8.png" title="Screenshot of the RStudio interface. The popup to download the selected file has been highlighted," alt="Screenshot of the RStudio interface. The popup to download the selected file has been highlighted," width="480" />
+
+## Pausing RStudio
+
+
+1. The right-hand side icon reminds you that you are accruing cloud computing costs. If you don’t see this icon, you may need to scroll to the right.
+
+    <img src="resources/images/08-student_using_rstudio_files/figure-html//1BLTCaogA04bbeSD1tR1Wt-mVceQA6FHXa8FmFzIARrg_g11f12bc99af_0_84.png" title="Screenshot of the RStudio interface. The icon on the right showing that the cloud environment is running is highlighted." alt="Screenshot of the RStudio interface. The icon on the right showing that the cloud environment is running is highlighted." width="100%" />
+
+1. You should minimize charges when you are not performing an analysis. You can do this by clicking on the RStudio icon and selecting “Pause”. This will release the CPU and memory resources for other people to use. Note that your work will be saved in the environment and continue to accrue a very small cost.  This work will be lost if the cloud environment gets deleted.  If there is anything you would like to save permanently, it's a good idea to copy it from your compute environment to another location, such as the Workspace bucket, GitHub, or your local machine, depending on your needs.
+
+    <img src="resources/images/08-student_using_rstudio_files/figure-html//1BLTCaogA04bbeSD1tR1Wt-mVceQA6FHXa8FmFzIARrg_g11f12bc99af_0_91.png" title="Screenshot of the RStudio menu. The pause button which stops the cloud environment is highlighted." alt="Screenshot of the RStudio menu. The pause button which stops the cloud environment is highlighted." width="100%" />
+
+:::{.notice}
+You can also pause your cloud environment(s) at https://anvil.terra.bio/#clusters.
+:::
+::::

docs/404.html

@@ -0,0 +1,304 @@
+<!DOCTYPE html>
+<html lang="" xml:lang="">
+<head>
+
+  <meta charset="utf-8" />
+  <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+  <title>Page not found | BioDIGS in the Classroom: Exploring Soil Data</title>
+  <meta name="description" content="This activity guides students through exploration of the BioDIGS soil data using the tidyverse in R." />
+  <meta name="generator" content="bookdown 0.39.1 and GitBook 2.6.7" />
+
+  <meta property="og:title" content="Page not found | BioDIGS in the Classroom: Exploring Soil Data" />
+  <meta property="og:type" content="book" />
+
+  <meta property="og:description" content="This activity guides students through exploration of the BioDIGS soil data using the tidyverse in R." />
+
+
+  <meta name="twitter:card" content="summary" />
+  <meta name="twitter:title" content="Page not found | BioDIGS in the Classroom: Exploring Soil Data" />
+
+  <meta name="twitter:description" content="This activity guides students through exploration of the BioDIGS soil data using the tidyverse in R." />
+
+
+
+
+<meta name="date" content="2024-08-05" />
+
+  <meta name="viewport" content="width=device-width, initial-scale=1" />
+  <meta name="apple-mobile-web-app-capable" content="yes" />
+  <meta name="apple-mobile-web-app-status-bar-style" content="black" />
+
+  <link rel="shortcut icon" href="assets/GDSCN_style/gdscn_favicon.ico" type="image/x-icon" />
+
+
+<script src="libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
+<script src="https://cdn.jsdelivr.net/npm/fuse.js@6.4.6/dist/fuse.min.js"></script>
+<link href="libs/gitbook-2.6.7/css/style.css" rel="stylesheet" />
+<link href="libs/gitbook-2.6.7/css/plugin-table.css" rel="stylesheet" />
+<link href="libs/gitbook-2.6.7/css/plugin-bookdown.css" rel="stylesheet" />
+<link href="libs/gitbook-2.6.7/css/plugin-highlight.css" rel="stylesheet" />
+<link href="libs/gitbook-2.6.7/css/plugin-search.css" rel="stylesheet" />
+<link href="libs/gitbook-2.6.7/css/plugin-fontsettings.css" rel="stylesheet" />
+<link href="libs/gitbook-2.6.7/css/plugin-clipboard.css" rel="stylesheet" />
+
+
+
+
+
+
+
+
+<link href="libs/anchor-sections-1.1.0/anchor-sections.css" rel="stylesheet" />
+<link href="libs/anchor-sections-1.1.0/anchor-sections-hash.css" rel="stylesheet" />
+<script src="libs/anchor-sections-1.1.0/anchor-sections.js"></script>
+
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id={MeasurementID}"></script>
+<script>
+  window.dataLayer = window.dataLayer || [];
+  function gtag(){dataLayer.push(arguments);}
+  gtag('js', new Date());
+
+  gtag('config', '{MeasurementID}');
+</script>
+
+
+<style type="text/css">
+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
+  {  background-color: #f8f8f8; }
+@media screen {
+pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
+}
+code span.al { color: #ef2929; } /* Alert */
+code span.an { color: #8f5902; font-weight: bold; font-style: italic; } /* Annotation */
+code span.at { color: #204a87; } /* Attribute */
+code span.bn { color: #0000cf; } /* BaseN */
+code span.cf { color: #204a87; font-weight: bold; } /* ControlFlow */
+code span.ch { color: #4e9a06; } /* Char */
+code span.cn { color: #8f5902; } /* Constant */
+code span.co { color: #8f5902; font-style: italic; } /* Comment */
+code span.cv { color: #8f5902; font-weight: bold; font-style: italic; } /* CommentVar */
+code span.do { color: #8f5902; font-weight: bold; font-style: italic; } /* Documentation */
+code span.dt { color: #204a87; } /* DataType */
+code span.dv { color: #0000cf; } /* DecVal */
+code span.er { color: #a40000; font-weight: bold; } /* Error */
+code span.ex { } /* Extension */
+code span.fl { color: #0000cf; } /* Float */
+code span.fu { color: #204a87; font-weight: bold; } /* Function */
+code span.im { } /* Import */
+code span.in { color: #8f5902; font-weight: bold; font-style: italic; } /* Information */
+code span.kw { color: #204a87; font-weight: bold; } /* Keyword */
+code span.op { color: #ce5c00; font-weight: bold; } /* Operator */
+code span.ot { color: #8f5902; } /* Other */
+code span.pp { color: #8f5902; font-style: italic; } /* Preprocessor */
+code span.sc { color: #ce5c00; font-weight: bold; } /* SpecialChar */
+code span.ss { color: #4e9a06; } /* SpecialString */
+code span.st { color: #4e9a06; } /* String */
+code span.va { color: #000000; } /* Variable */
+code span.vs { color: #4e9a06; } /* VerbatimString */
+code span.wa { color: #8f5902; font-weight: bold; font-style: italic; } /* Warning */
+</style>
+
+<style type="text/css">
+
+  div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
+</style>
+
+<link rel="stylesheet" href="assets/style.css" type="text/css" />
+<link rel="stylesheet" href="assets/AnVIL_style/anvil.css" type="text/css" />
+</head>
+
+<body>
+
+
+
+  <div class="book without-animation with-summary font-size-2 font-family-1" data-basepath=".">
+
+    <div class="book-summary">
+      <nav role="navigation">
+
+<ul class="summary">
+<a href="https://anvilproject.org/" target="_blank"><img src="assets/AnVIL_style/logo-anvil.png" style="width: 80%; padding-left: 15px; padding-top: 8px;"</a>
+
+<li class="divider"></li>
+<li class="chapter" data-level="" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i>About this Book</a>
+<ul>
+<li class="chapter" data-level="0.1" data-path="index.html"><a href="index.html#target-audience"><i class="fa fa-check"></i><b>0.1</b> Target Audience</a></li>
+<li class="chapter" data-level="0.2" data-path="index.html"><a href="index.html#platform"><i class="fa fa-check"></i><b>0.2</b> Platform</a></li>
+<li class="chapter" data-level="0.3" data-path="index.html"><a href="index.html#data"><i class="fa fa-check"></i><b>0.3</b> Data</a></li>
+</ul></li>
+<li class="chapter" data-level="4" data-path="data-1.html"><a href="data-1.html"><i class="fa fa-check"></i><b>4</b> Data</a>
+<ul>
+<li class="chapter" data-level="4.1" data-path="data-1.html"><a href="data-1.html#sample-metadata"><i class="fa fa-check"></i><b>4.1</b> Sample Metadata</a></li>
+<li class="chapter" data-level="4.2" data-path="data-1.html"><a href="data-1.html#soil-testing-data"><i class="fa fa-check"></i><b>4.2</b> Soil Testing Data</a></li>
+<li class="chapter" data-level="4.3" data-path="data-1.html"><a href="data-1.html#genomics-and-metagenomics-data"><i class="fa fa-check"></i><b>4.3</b> Genomics and Metagenomics Data</a></li>
+</ul></li>
+<li class="part"><span><b>Instructor Checklist for AnVIL</b></span></li>
+<li class="part"><span><b>Student Guide to AnVIL</b></span></li>
+<li class="chapter" data-level="11" data-path="anvil-workspace.html"><a href="anvil-workspace.html"><i class="fa fa-check"></i><b>11</b> AnVIL Workspace</a>
+<ul>
+<li class="chapter" data-level="11.1" data-path="anvil-workspace.html"><a href="anvil-workspace.html#create-google-account"><i class="fa fa-check"></i><b>11.1</b> Create Google Account</a></li>
+<li class="chapter" data-level="11.2" data-path="anvil-workspace.html"><a href="anvil-workspace.html#clone-the-workspace"><i class="fa fa-check"></i><b>11.2</b> Clone the Workspace</a></li>
+</ul></li>
+<li class="chapter" data-level="12" data-path="using-rstudio-on-anvil.html"><a href="using-rstudio-on-anvil.html"><i class="fa fa-check"></i><b>12</b> Using RStudio on AnVIL</a>
+<ul>
+<li class="chapter" data-level="12.1" data-path="using-rstudio-on-anvil.html"><a href="using-rstudio-on-anvil.html#video-overview-of-rstudio-on-anvil"><i class="fa fa-check"></i><b>12.1</b> Video overview of RStudio on AnVIL</a>
+<ul>
+<li class="chapter" data-level="12.1.1" data-path="using-rstudio-on-anvil.html"><a href="using-rstudio-on-anvil.html#objectives"><i class="fa fa-check"></i><b>12.1.1</b> Objectives</a></li>
+<li class="chapter" data-level="12.1.2" data-path="using-rstudio-on-anvil.html"><a href="using-rstudio-on-anvil.html#slides"><i class="fa fa-check"></i><b>12.1.2</b> Slides</a></li>
+</ul></li>
+<li class="chapter" data-level="12.2" data-path="using-rstudio-on-anvil.html"><a href="using-rstudio-on-anvil.html#launching-rstudio"><i class="fa fa-check"></i><b>12.2</b> Launching RStudio</a></li>
+<li class="chapter" data-level="12.3" data-path="using-rstudio-on-anvil.html"><a href="using-rstudio-on-anvil.html#touring-rstudio"><i class="fa fa-check"></i><b>12.3</b> Touring RStudio</a></li>
+<li class="chapter" data-level="12.4" data-path="using-rstudio-on-anvil.html"><a href="using-rstudio-on-anvil.html#pausing-rstudio"><i class="fa fa-check"></i><b>12.4</b> Pausing RStudio</a></li>
+</ul></li>
+<li class="part"><span><b>Data Exploration</b></span></li>
+<li class="chapter" data-level="13" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html"><i class="fa fa-check"></i><b>13</b> Exploring Soil Testing Data With R</a>
+<ul>
+<li class="chapter" data-level="13.1" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#before-you-start"><i class="fa fa-check"></i><b>13.1</b> Before You Start</a></li>
+<li class="chapter" data-level="13.2" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#objectives-1"><i class="fa fa-check"></i><b>13.2</b> Objectives</a></li>
+<li class="chapter" data-level="13.3" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#part-1.-data-import"><i class="fa fa-check"></i><b>13.3</b> Part 1. Data Import</a></li>
+<li class="chapter" data-level="13.4" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#part-2.-data-summarization"><i class="fa fa-check"></i><b>13.4</b> Part 2. Data Summarization</a></li>
+<li class="chapter" data-level="13.5" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#part-3.-data-visualization"><i class="fa fa-check"></i><b>13.5</b> Part 3. Data Visualization</a></li>
+</ul></li>
+<li class="chapter" data-level="" data-path="about-the-authors.html"><a href="about-the-authors.html"><i class="fa fa-check"></i>About the Authors</a></li>
+<li class="chapter" data-level="14" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>14</b> References</a></li>
+<li class="divider"></li>
+<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by: </a> </p>
+<p style="text-align:center;"> <a href="https://hutchdatascience.org/"> The Fred Hutch Data Science Lab </a></p>
+<a href="https://hutchdatascience.org/" target="_blank"><img src="https://raw.githubusercontent.com/jhudsl/OTTR_Template/main/style-sets/fhdasl/copy_to_assets/big-dasl-stacked.png" style="width: 80%; padding-left: 34px; padding-top: 8px;"</a>
+<p style="text-align:center; font-size: 12px;"> <a href="https://github.com/rstudio4edu/rstudio4edu-book/"> Style adapted from: rstudio4edu-book </a> <a href ="https://creativecommons.org/licenses/by/2.0/"> (CC-BY 2.0) </a></p>
+<p style="padding-left: 40px;"><div class="trapezoid" style = "padding-left: 40px;"><span><a href="https://docs.google.com/forms/d/e/1FAIpQLScrDVb_utm55pmb_SHx-RgELTEbCCWdLea0T3IzS0Oj00GE4w/viewform?usp=pp_url&entry.1565230805=BioDIGS+in+the+Classroom:+Exploring+Soil+Data"> Click here to provide feedback</a> <img src="assets/itcr_arrow.png" style=" width: 10%" ></span></div></p>
+
+</ul>
+
+      </nav>
+    </div>
+
+    <div class="book-body">
+      <div class="body-inner">
+        <div class="book-header" role="navigation">
+          <h1>
+            <i class="fa fa-circle-o-notch fa-spin"></i><a href="./">BioDIGS in the Classroom: Exploring Soil Data</a>
+          </h1>
+        </div>
+
+        <div class="page-wrapper" tabindex="-1" role="main">
+          <div class="page-inner">
+
+            <section class="normal" id="section-">
+<head>
+  <meta name="viewport" content="width=device-width,minimum-scale=1.0,maximum-scale=10.0,initial-scale=1.0">
+  <!--script src="https://kit.fontawesome.com/6a26f47516.js"></script-->
+  <!--<script src="assets/hideOutput.js"></script>-->
+</head>
+
+
+
+<div class="hero-image-container"> 
+  <img class= "hero-image" src="assets/AnVIL_style/dasl_thin_main_image.png">
+</div>
+<div id="page-not-found" class="section level1">
+<h1>Page not found</h1>
+<p>The page you requested cannot be found (perhaps it was moved or renamed).</p>
+<p>You may want to try searching to find the page's new location, or use
+the table of contents to find the page you are looking for.</p>
+</div>
+<hr>
+<center> 
+  <div class="footer">
+      All illustrations <a href="https://creativecommons.org/licenses/by/4.0/">CC-BY. </a>
+      <br>
+      All other materials <a href= "https://creativecommons.org/licenses/by/4.0/"> CC-BY </a> unless noted otherwise.
+  </div>
+</center>
+            </section>
+
+          </div>
+        </div>
+      </div>
+
+
+    </div>
+  </div>
+<script src="libs/gitbook-2.6.7/js/app.min.js"></script>
+<script src="libs/gitbook-2.6.7/js/clipboard.min.js"></script>
+<script src="libs/gitbook-2.6.7/js/plugin-search.js"></script>
+<script src="libs/gitbook-2.6.7/js/plugin-sharing.js"></script>
+<script src="libs/gitbook-2.6.7/js/plugin-fontsettings.js"></script>
+<script src="libs/gitbook-2.6.7/js/plugin-bookdown.js"></script>
+<script src="libs/gitbook-2.6.7/js/jquery.highlight.js"></script>
+<script src="libs/gitbook-2.6.7/js/plugin-clipboard.js"></script>
+<script>
+gitbook.require(["gitbook"], function(gitbook) {
+gitbook.start({
+"sharing": {
+"github": false,
+"facebook": true,
+"twitter": true,
+"linkedin": false,
+"weibo": false,
+"instapaper": false,
+"vk": false,
+"whatsapp": false,
+"all": ["facebook", "twitter", "linkedin", "weibo", "instapaper"]
+},
+"fontsettings": {
+"theme": "white",
+"family": "sans",
+"size": 2
+},
+"edit": {
+"link": null,
+"text": null
+},
+"history": {
+"link": null,
+"text": null
+},
+"view": {
+"link": null,
+"text": null
+},
+"download": null,
+"search": {
+"engine": "fuse",
+"options": null
+},
+"toc": {
+"collapse": "section"
+}
+});
+});
+</script>
+
+</body>
+
+</html>

docs/About.md

@@ -0,0 +1,129 @@
+# About the Authors {-}
+
+These credits are based on our [course contributors table guidelines](https://github.com/jhudsl/OTTR_Template/wiki/How-to-give-credits).
+
+ 
+ 
+
+|Credits|Names|
+|-------|-----|
+|**Pedagogy**||
+|Content Developer|Elizabeth Humphries|
+|Content Editors|[Ava Hoffman], [Kate Isaac]|
+|Project Directors|[Ava Hoffman], [Michael Schatz], [Jeff Leek], [Frederick Tan]|
+|**Production**||
+|Content Publisher|[Ira Gooding]|
+|**Technical**||
+|Template Publishing Engineers|[Candace Savonen], [Carrie Wright], [Ava Hoffman]|
+|Publishing Maintenance Engineer|[Candace Savonen]|
+|Technical Publishing Stylists|[Carrie Wright], [Candace Savonen]|
+|Package Developers ([ottrpal])|[John Muschelli], [Candace Savonen], [Carrie Wright]|
+|Package Developer ([BioDIGSData])| [Ava Hoffman]|
+|**Funding**||
+|Funder| [National Human Genome Research Institute (NHGRI)] |
+|Funding Staff| Fallon Bachman, Jennifer Vessio, Emily Voeglein|
+
+ 
+
+
+<!-- |Content Contributor | [Jeff Leek], [Michael Schatz], [Frederick Tan]| -->
+<!-- |Content Editors| [Katherine Cox], Natalie Kucher, [Frederick Tan]| -->
+<!-- |Content Directors | Kasper Hansen, [Jeff Leek], [Frederick Tan]| -->
+<!-- |Content Consultants (General) | [Jeff Leek], [Frederick Tan], [Carrie Wright] | -->
+
+
+```
+## ─ Session info ───────────────────────────────────────────────────────────────
+##  setting  value
+##  version  R version 4.3.2 (2023-10-31)
+##  os       Ubuntu 22.04.4 LTS
+##  system   x86_64, linux-gnu
+##  ui       X11
+##  language (EN)
+##  collate  en_US.UTF-8
+##  ctype    en_US.UTF-8
+##  tz       Etc/UTC
+##  date     2024-08-05
+##  pandoc   3.1.1 @ /usr/local/bin/ (via rmarkdown)
+## 
+## ─ Packages ───────────────────────────────────────────────────────────────────
+##  package     * version date (UTC) lib source
+##  bookdown      0.39.1  2024-06-11 [1] Github (rstudio/bookdown@f244cf1)
+##  bslib         0.6.1   2023-11-28 [1] RSPM (R 4.3.0)
+##  cachem        1.0.8   2023-05-01 [1] RSPM (R 4.3.0)
+##  cli           3.6.2   2023-12-11 [1] RSPM (R 4.3.0)
+##  devtools      2.4.5   2022-10-11 [1] RSPM (R 4.3.0)
+##  digest        0.6.34  2024-01-11 [1] RSPM (R 4.3.0)
+##  ellipsis      0.3.2   2021-04-29 [1] RSPM (R 4.3.0)
+##  evaluate      0.23    2023-11-01 [1] RSPM (R 4.3.0)
+##  fastmap       1.1.1   2023-02-24 [1] RSPM (R 4.3.0)
+##  fs            1.6.3   2023-07-20 [1] RSPM (R 4.3.0)
+##  glue          1.7.0   2024-01-09 [1] RSPM (R 4.3.0)
+##  htmltools     0.5.7   2023-11-03 [1] RSPM (R 4.3.0)
+##  htmlwidgets   1.6.4   2023-12-06 [1] RSPM (R 4.3.0)
+##  httpuv        1.6.14  2024-01-26 [1] RSPM (R 4.3.0)
+##  jquerylib     0.1.4   2021-04-26 [1] RSPM (R 4.3.0)
+##  jsonlite      1.8.8   2023-12-04 [1] RSPM (R 4.3.0)
+##  knitr         1.47.3  2024-06-11 [1] Github (yihui/knitr@e1edd34)
+##  later         1.3.2   2023-12-06 [1] RSPM (R 4.3.0)
+##  lifecycle     1.0.4   2023-11-07 [1] RSPM (R 4.3.0)
+##  magrittr      2.0.3   2022-03-30 [1] RSPM (R 4.3.0)
+##  memoise       2.0.1   2021-11-26 [1] RSPM (R 4.3.0)
+##  mime          0.12    2021-09-28 [1] RSPM (R 4.3.0)
+##  miniUI        0.1.1.1 2018-05-18 [1] RSPM (R 4.3.0)
+##  pkgbuild      1.4.3   2023-12-10 [1] RSPM (R 4.3.0)
+##  pkgload       1.3.4   2024-01-16 [1] RSPM (R 4.3.0)
+##  profvis       0.3.8   2023-05-02 [1] RSPM (R 4.3.0)
+##  promises      1.2.1   2023-08-10 [1] RSPM (R 4.3.0)
+##  purrr         1.0.2   2023-08-10 [1] RSPM (R 4.3.0)
+##  R6            2.5.1   2021-08-19 [1] RSPM (R 4.3.0)
+##  Rcpp          1.0.12  2024-01-09 [1] RSPM (R 4.3.0)
+##  remotes       2.4.2.1 2023-07-18 [1] RSPM (R 4.3.0)
+##  rlang         1.1.4   2024-06-04 [1] CRAN (R 4.3.2)
+##  rmarkdown     2.27.1  2024-06-11 [1] Github (rstudio/rmarkdown@e1c93a9)
+##  sass          0.4.8   2023-12-06 [1] RSPM (R 4.3.0)
+##  sessioninfo   1.2.2   2021-12-06 [1] RSPM (R 4.3.0)
+##  shiny         1.8.0   2023-11-17 [1] RSPM (R 4.3.0)
+##  stringi       1.8.3   2023-12-11 [1] RSPM (R 4.3.0)
+##  stringr       1.5.1   2023-11-14 [1] RSPM (R 4.3.0)
+##  urlchecker    1.0.1   2021-11-30 [1] RSPM (R 4.3.0)
+##  usethis       2.2.3   2024-02-19 [1] RSPM (R 4.3.0)
+##  vctrs         0.6.5   2023-12-01 [1] RSPM (R 4.3.0)
+##  xfun          0.44.4  2024-06-11 [1] Github (yihui/xfun@9da62cc)
+##  xtable        1.8-4   2019-04-21 [1] RSPM (R 4.3.0)
+##  yaml          2.3.8   2023-12-11 [1] RSPM (R 4.3.0)
+## 
+##  [1] /usr/local/lib/R/site-library
+##  [2] /usr/local/lib/R/library
+## 
+## ──────────────────────────────────────────────────────────────────────────────
+```
+
+<!-- Author information -->
+
+
+[Katherine Cox]: https://publichealth.jhu.edu/faculty/4170/katherine-cox
+[Ira Gooding]: https://publichealth.jhu.edu/faculty/4130/ira-gooding
+[Ava Hoffman]: https://www.avahoffman.com/
+[Kate Isaac]: https://kweav.github.io/
+[Jeff Leek]: https://jtleek.com/
+[John Muschelli]: https://johnmuschelli.com/
+[National Human Genome Research Institute (NHGRI)]: https://www.genome.gov/
+[Candace Savonen]: https://www.cansavvy.com/
+[Michael Schatz]: http://schatz-lab.org/
+[Frederick Tan]: https://carnegiescience.edu/frederick-tan
+[Carrie Wright]: https://carriewright11.github.io/
+
+<!-- Links -->
+
+[Ottrpal]: https://github.com/jhudsl/ottrpal
+[BioDIGSData]: https://github.com/fhdsl/BioDIGSData
+
+<!-- Fill out this table using these instructions: https://github.com/jhudsl/DaSL_Course_Template_Bookdown/wiki/How-to-give-credits
+
+For JHU courses, You will need to add Ira as a credit:
+
+|Content Publisher|[Ira Gooding]|
+...
+[Ira Gooding]: https://publichealth.jhu.edu/faculty/4130/ira-gooding
+-->

docs/References.md

@@ -0,0 +1,2 @@
+
+# References 

docs/assets/style.css

@@ -313,7 +313,6 @@ div.wip{
   background-image: url("../assets/box_images/under_construction.png");
 }
 
-
 /* .book .book-body .page-wrapper .page-inner section.normal is needed
    to override the styles produced by gitbook, which are ridiculously
    overspecified. Goal of the selectors is to ensure internal "margins"

docs/index.md

@@ -0,0 +1,34 @@
+---
+title: "BioDIGS in the Classroom: Exploring Soil Data"
+date: "August 05, 2024"
+site: bookdown::bookdown_site
+documentclass: book
+bibliography: book.bib
+biblio-style: apalike
+link-citations: yes
+description: "This activity guides students through exploration of the BioDIGS soil data using the tidyverse in R."
+favicon: assets/GDSCN_style/gdscn_favicon.ico
+---
+
+
+# About this Book {-}
+
+This is a companion training guide for BioDIGS, a GDSCN project that brings a research experience into the classroom. This activity guides students through exploration of the BioDIGS soil data using the tidyverse in R. Students will learn basic data summarization, visualization, and mapping skills. Visit the BioDIGS (BioDiversity and Informatics for Genomics Scholars) website [here](https://biodigs.org/) for more information about this collaborative, distributed research project, including how you can get involved!
+
+The GDSCN (Genomics Data Science Community Network) is a consortium of educators who aim to create a world where researchers, educators, and students from diverse backgrounds are able to fully participate in genomic data science research. You can find more information about its mission and initiatives [here](https://www.gdscn.org/home).
+
+![BioDIGS logo](https://raw.githubusercontent.com/fhdsl/AnVIL_BioDIGS_Book/main/assets/GDSCN_style/logo_BioDIGS_final.png){width=300px}
+
+## Target Audience
+
+The activities in this guide are written for undergraduate students and beginning graduate students. Some sections require basic understanding of the R programming language, which is indicated at the beginning of the chapter.
+
+## Platform
+
+The activities in this guide are demonstrated on NHGRI's [AnVIL](https://anvilproject.org/) cloud computing platform. AnVIL is the preferred computing platform for the GDSCN. However, all of these activities can be done using your personal installation of R or using the online [Galaxy](usegalaxy.org) portal.
+
+## Data
+
+The data generated by the BioDIGS project is available through the [BioDIGS website](biodigs.org), as well as through an [AnVIL workspace](https://anvilproject.org).
+
+Data about the soil itself as well as soil metal content was generated by the [Delaware Soil Testing Program](https://www.udel.edu/canr/cooperative-extension/environmental-stewardship/soil-testing/) at the University of Delaware. Sequences were generated by the [Johns Hopkins University Genetic Resources Core Facility](https://grcf.jhmi.edu/) and by [PacBio](https://www.pacb.com/).

docs/libs/anchor-sections-1.1.0/anchor-sections-hash.css

@@ -0,0 +1,2 @@
+/* Styles for section anchors */
+a.anchor-section::before {content: '#';font-size: 80%;}

docs/libs/anchor-sections-1.0.1/anchor-sections.css → docs/libs/anchor-sections-1.1.0/anchor-sections.css

@@ -1,5 +1,4 @@
 /* Styles for section anchors */
 a.anchor-section {margin-left: 10px; visibility: hidden; color: inherit;}
-a.anchor-section::before {content: '#';}
 .hasAnchor:hover a.anchor-section {visibility: visible;}
 ul > li > .anchor-section {display: none;}

docs/libs/anchor-sections-1.1.0/anchor-sections.js

@@ -0,0 +1,11 @@
+document.addEventListener('DOMContentLoaded', function () {
+  // If section divs is used, we need to put the anchor in the child header
+  const headers = document.querySelectorAll("div.hasAnchor.section[class*='level'] > :first-child")
+
+  headers.forEach(function (x) {
+    // Add to the header node
+    if (!x.classList.contains('hasAnchor')) x.classList.add('hasAnchor')
+    // Remove from the section or div created by Pandoc
+    x.parentElement.classList.remove('hasAnchor')
+  })
+})

docs/libs/gitbook-2.6.7/css/plugin-highlight.css

@@ -133,7 +133,7 @@
 .book.color-theme-1 .book-body .page-wrapper .page-inner section.normal code {
   /*
 
-Orginal Style from ethanschoonover.com/solarized (c) Jeremy Hull <sourdrums@gmail.com>
+Original Style from ethanschoonover.com/solarized (c) Jeremy Hull <sourdrums@gmail.com>
 
 */
   /* Solarized Green */

docs/libs/gitbook-2.6.7/js/plugin-clipboard.js

@@ -9,7 +9,9 @@ gitbook.require(["gitbook", "jQuery"], function(gitbook, $) {
 
     // the page.change event is thrown twice: before and after the page changes
     if (clipboard) {
-      // clipboard is already defined
+      // clipboard is already defined but we are on the same page
+      if (clipboard._prevPage === window.location.pathname) return;
+      // clipboard is already defined and url path change
       // we can deduct that we are before page changes
       clipboard.destroy(); // destroy the previous events listeners
       clipboard = undefined; // reset the clipboard object
@@ -24,6 +26,8 @@ gitbook.require(["gitbook", "jQuery"], function(gitbook, $) {
       }
     });
 
+    clipboard._prevPage = window.location.pathname
+
   });
 
 });

docs/reference-keys.txt

@@ -1,28 +1,22 @@
-introduction
-motivation
 target-audience
-curriculum
-a-new-chapter
-learning-objectives-1
-libraries
-subtopic
-code-examples
-image-example
-video-examples
-links-to-files
-links-to-websites
-citation-examples
-callout-boxes
-dropdown-summaries
-print-out-session-info
-anvil-module-library
-include-using-cowborrow_chapter
-background-highlighting-for-borrowed-chapters
-workspaces
-clone-a-workspace
-create-a-workspace
-open-a-workspace
-share-a-workspace
+platform
+data
+background
+what-is-genomics
+what-is-data-science
+what-is-cloud-computing
+why-soil-microbes
+heavy-metals-and-human-health
+research-team
+soil-sampling
+support
+funding
+sponsors
+analytical-and-computational-support
+data-1
+sample-metadata
+soil-testing-data
+genomics-and-metagenomics-data
 billing
 create-google-billing-account
 add-terra-to-google-billing-account
@@ -32,49 +26,37 @@ view-spend-for-google-billing
 create-terra-billing-project
 add-member-to-terra-billing-project
 disable-terra-billing-project
-onboarding
+notes-for-instructors
+checklist-for-running-activities-on-anvil
+setting-up-billing-on-anvil
+billing-project
+adding-instructors-as-owner
+adding-students-as-user
+understanding-the-various-billing-costs
+estimating-costs-before-the-class-begins
+how-much-does-a-class-cost
+setting-up-the-class-activity
+overview-of-class-setup
+collect-google-ids
+set-up-groups
+set-up-billing-projects
+set-permissions-on-the-workspace
+notify-terra
+getting-credit-for-professional-development
+anvil-workspace
 create-google-account
-using-programming-platforms-on-anvil
-video-overview-on-using-jupyter-notebooks
+clone-the-workspace
+using-rstudio-on-anvil
+video-overview-of-rstudio-on-anvil
 objectives
 slides
-launching-jupyter
-video-overview-on-using-galaxy
-objectives-1
-slides-1
-starting-galaxy
-navigating-galaxy
-deleting-galaxy
-video-overview-on-using-rstudio
-objectives-2
-slides-2
 launching-rstudio
 touring-rstudio
 pausing-rstudio
-deleting-rstudio
-student-instructions
-student-account-setup
-create-google-account-1
-log-in-to-terra
-share-username
-student-instructions-for-cloning-a-workspace
-with-no-variables-set
-with-variables-set
-student-instructions-for-launching-jupyter
-using-default-jupyter-environment
-using-custom-jupyter-environment
-student-instructions-for-launching-rstudio
-using-default-rstudio-environment
-using-custom-rstudio-environment
-user-management
-create-terra-group
-add-member-to-terra-group
-find-group-email
-why-anvil
-why-anvil-for-instructors
-instructor-modules
-why-anvil-for-instructors-1
-checklist-link
-checklist-timeline-premade-content
-recommendation-to-use-strides
+exploring-soil-testing-data-with-r
+before-you-start
+objectives-1
+part-1.-data-import
+part-2.-data-summarization
+part-3.-data-visualization
 references

docs/references.html

@@ -0,0 +1,302 @@
+<!DOCTYPE html>
+<html lang="" xml:lang="">
+<head>
+
+  <meta charset="utf-8" />
+  <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+  <title>Chapter 14 References | BioDIGS in the Classroom: Exploring Soil Data</title>
+  <meta name="description" content="This activity guides students through exploration of the BioDIGS soil data using the tidyverse in R." />
+  <meta name="generator" content="bookdown 0.39.1 and GitBook 2.6.7" />
+
+  <meta property="og:title" content="Chapter 14 References | BioDIGS in the Classroom: Exploring Soil Data" />
+  <meta property="og:type" content="book" />
+
+  <meta property="og:description" content="This activity guides students through exploration of the BioDIGS soil data using the tidyverse in R." />
+
+
+  <meta name="twitter:card" content="summary" />
+  <meta name="twitter:title" content="Chapter 14 References | BioDIGS in the Classroom: Exploring Soil Data" />
+
+  <meta name="twitter:description" content="This activity guides students through exploration of the BioDIGS soil data using the tidyverse in R." />
+
+
+
+
+<meta name="date" content="2024-08-05" />
+
+  <meta name="viewport" content="width=device-width, initial-scale=1" />
+  <meta name="apple-mobile-web-app-capable" content="yes" />
+  <meta name="apple-mobile-web-app-status-bar-style" content="black" />
+
+  <link rel="shortcut icon" href="assets/GDSCN_style/gdscn_favicon.ico" type="image/x-icon" />
+<link rel="prev" href="about-the-authors.html"/>
+
+<script src="libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
+<script src="https://cdn.jsdelivr.net/npm/fuse.js@6.4.6/dist/fuse.min.js"></script>
+<link href="libs/gitbook-2.6.7/css/style.css" rel="stylesheet" />
+<link href="libs/gitbook-2.6.7/css/plugin-table.css" rel="stylesheet" />
+<link href="libs/gitbook-2.6.7/css/plugin-bookdown.css" rel="stylesheet" />
+<link href="libs/gitbook-2.6.7/css/plugin-highlight.css" rel="stylesheet" />
+<link href="libs/gitbook-2.6.7/css/plugin-search.css" rel="stylesheet" />
+<link href="libs/gitbook-2.6.7/css/plugin-fontsettings.css" rel="stylesheet" />
+<link href="libs/gitbook-2.6.7/css/plugin-clipboard.css" rel="stylesheet" />
+
+
+
+
+
+
+
+
+<link href="libs/anchor-sections-1.1.0/anchor-sections.css" rel="stylesheet" />
+<link href="libs/anchor-sections-1.1.0/anchor-sections-hash.css" rel="stylesheet" />
+<script src="libs/anchor-sections-1.1.0/anchor-sections.js"></script>
+
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id={MeasurementID}"></script>
+<script>
+  window.dataLayer = window.dataLayer || [];
+  function gtag(){dataLayer.push(arguments);}
+  gtag('js', new Date());
+
+  gtag('config', '{MeasurementID}');
+</script>
+
+
+<style type="text/css">
+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
+  {  background-color: #f8f8f8; }
+@media screen {
+pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
+}
+code span.al { color: #ef2929; } /* Alert */
+code span.an { color: #8f5902; font-weight: bold; font-style: italic; } /* Annotation */
+code span.at { color: #204a87; } /* Attribute */
+code span.bn { color: #0000cf; } /* BaseN */
+code span.cf { color: #204a87; font-weight: bold; } /* ControlFlow */
+code span.ch { color: #4e9a06; } /* Char */
+code span.cn { color: #8f5902; } /* Constant */
+code span.co { color: #8f5902; font-style: italic; } /* Comment */
+code span.cv { color: #8f5902; font-weight: bold; font-style: italic; } /* CommentVar */
+code span.do { color: #8f5902; font-weight: bold; font-style: italic; } /* Documentation */
+code span.dt { color: #204a87; } /* DataType */
+code span.dv { color: #0000cf; } /* DecVal */
+code span.er { color: #a40000; font-weight: bold; } /* Error */
+code span.ex { } /* Extension */
+code span.fl { color: #0000cf; } /* Float */
+code span.fu { color: #204a87; font-weight: bold; } /* Function */
+code span.im { } /* Import */
+code span.in { color: #8f5902; font-weight: bold; font-style: italic; } /* Information */
+code span.kw { color: #204a87; font-weight: bold; } /* Keyword */
+code span.op { color: #ce5c00; font-weight: bold; } /* Operator */
+code span.ot { color: #8f5902; } /* Other */
+code span.pp { color: #8f5902; font-style: italic; } /* Preprocessor */
+code span.sc { color: #ce5c00; font-weight: bold; } /* SpecialChar */
+code span.ss { color: #4e9a06; } /* SpecialString */
+code span.st { color: #4e9a06; } /* String */
+code span.va { color: #000000; } /* Variable */
+code span.vs { color: #4e9a06; } /* VerbatimString */
+code span.wa { color: #8f5902; font-weight: bold; font-style: italic; } /* Warning */
+</style>
+
+<style type="text/css">
+
+  div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
+</style>
+
+<link rel="stylesheet" href="assets/style.css" type="text/css" />
+<link rel="stylesheet" href="assets/AnVIL_style/anvil.css" type="text/css" />
+</head>
+
+<body>
+
+
+
+  <div class="book without-animation with-summary font-size-2 font-family-1" data-basepath=".">
+
+    <div class="book-summary">
+      <nav role="navigation">
+
+<ul class="summary">
+<a href="https://anvilproject.org/" target="_blank"><img src="assets/AnVIL_style/logo-anvil.png" style="width: 80%; padding-left: 15px; padding-top: 8px;"</a>
+
+<li class="divider"></li>
+<li class="chapter" data-level="" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i>About this Book</a>
+<ul>
+<li class="chapter" data-level="0.1" data-path="index.html"><a href="index.html#target-audience"><i class="fa fa-check"></i><b>0.1</b> Target Audience</a></li>
+<li class="chapter" data-level="0.2" data-path="index.html"><a href="index.html#platform"><i class="fa fa-check"></i><b>0.2</b> Platform</a></li>
+<li class="chapter" data-level="0.3" data-path="index.html"><a href="index.html#data"><i class="fa fa-check"></i><b>0.3</b> Data</a></li>
+</ul></li>
+<li class="chapter" data-level="4" data-path="data-1.html"><a href="data-1.html"><i class="fa fa-check"></i><b>4</b> Data</a>
+<ul>
+<li class="chapter" data-level="4.1" data-path="data-1.html"><a href="data-1.html#sample-metadata"><i class="fa fa-check"></i><b>4.1</b> Sample Metadata</a></li>
+<li class="chapter" data-level="4.2" data-path="data-1.html"><a href="data-1.html#soil-testing-data"><i class="fa fa-check"></i><b>4.2</b> Soil Testing Data</a></li>
+<li class="chapter" data-level="4.3" data-path="data-1.html"><a href="data-1.html#genomics-and-metagenomics-data"><i class="fa fa-check"></i><b>4.3</b> Genomics and Metagenomics Data</a></li>
+</ul></li>
+<li class="part"><span><b>Instructor Checklist for AnVIL</b></span></li>
+<li class="part"><span><b>Student Guide to AnVIL</b></span></li>
+<li class="chapter" data-level="11" data-path="anvil-workspace.html"><a href="anvil-workspace.html"><i class="fa fa-check"></i><b>11</b> AnVIL Workspace</a>
+<ul>
+<li class="chapter" data-level="11.1" data-path="anvil-workspace.html"><a href="anvil-workspace.html#create-google-account"><i class="fa fa-check"></i><b>11.1</b> Create Google Account</a></li>
+<li class="chapter" data-level="11.2" data-path="anvil-workspace.html"><a href="anvil-workspace.html#clone-the-workspace"><i class="fa fa-check"></i><b>11.2</b> Clone the Workspace</a></li>
+</ul></li>
+<li class="chapter" data-level="12" data-path="using-rstudio-on-anvil.html"><a href="using-rstudio-on-anvil.html"><i class="fa fa-check"></i><b>12</b> Using RStudio on AnVIL</a>
+<ul>
+<li class="chapter" data-level="12.1" data-path="using-rstudio-on-anvil.html"><a href="using-rstudio-on-anvil.html#video-overview-of-rstudio-on-anvil"><i class="fa fa-check"></i><b>12.1</b> Video overview of RStudio on AnVIL</a>
+<ul>
+<li class="chapter" data-level="12.1.1" data-path="using-rstudio-on-anvil.html"><a href="using-rstudio-on-anvil.html#objectives"><i class="fa fa-check"></i><b>12.1.1</b> Objectives</a></li>
+<li class="chapter" data-level="12.1.2" data-path="using-rstudio-on-anvil.html"><a href="using-rstudio-on-anvil.html#slides"><i class="fa fa-check"></i><b>12.1.2</b> Slides</a></li>
+</ul></li>
+<li class="chapter" data-level="12.2" data-path="using-rstudio-on-anvil.html"><a href="using-rstudio-on-anvil.html#launching-rstudio"><i class="fa fa-check"></i><b>12.2</b> Launching RStudio</a></li>
+<li class="chapter" data-level="12.3" data-path="using-rstudio-on-anvil.html"><a href="using-rstudio-on-anvil.html#touring-rstudio"><i class="fa fa-check"></i><b>12.3</b> Touring RStudio</a></li>
+<li class="chapter" data-level="12.4" data-path="using-rstudio-on-anvil.html"><a href="using-rstudio-on-anvil.html#pausing-rstudio"><i class="fa fa-check"></i><b>12.4</b> Pausing RStudio</a></li>
+</ul></li>
+<li class="part"><span><b>Data Exploration</b></span></li>
+<li class="chapter" data-level="13" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html"><i class="fa fa-check"></i><b>13</b> Exploring Soil Testing Data With R</a>
+<ul>
+<li class="chapter" data-level="13.1" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#before-you-start"><i class="fa fa-check"></i><b>13.1</b> Before You Start</a></li>
+<li class="chapter" data-level="13.2" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#objectives-1"><i class="fa fa-check"></i><b>13.2</b> Objectives</a></li>
+<li class="chapter" data-level="13.3" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#part-1.-data-import"><i class="fa fa-check"></i><b>13.3</b> Part 1. Data Import</a></li>
+<li class="chapter" data-level="13.4" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#part-2.-data-summarization"><i class="fa fa-check"></i><b>13.4</b> Part 2. Data Summarization</a></li>
+<li class="chapter" data-level="13.5" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#part-3.-data-visualization"><i class="fa fa-check"></i><b>13.5</b> Part 3. Data Visualization</a></li>
+</ul></li>
+<li class="chapter" data-level="" data-path="about-the-authors.html"><a href="about-the-authors.html"><i class="fa fa-check"></i>About the Authors</a></li>
+<li class="chapter" data-level="14" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>14</b> References</a></li>
+<li class="divider"></li>
+<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by: </a> </p>
+<p style="text-align:center;"> <a href="https://hutchdatascience.org/"> The Fred Hutch Data Science Lab </a></p>
+<a href="https://hutchdatascience.org/" target="_blank"><img src="https://raw.githubusercontent.com/jhudsl/OTTR_Template/main/style-sets/fhdasl/copy_to_assets/big-dasl-stacked.png" style="width: 80%; padding-left: 34px; padding-top: 8px;"</a>
+<p style="text-align:center; font-size: 12px;"> <a href="https://github.com/rstudio4edu/rstudio4edu-book/"> Style adapted from: rstudio4edu-book </a> <a href ="https://creativecommons.org/licenses/by/2.0/"> (CC-BY 2.0) </a></p>
+<p style="padding-left: 40px;"><div class="trapezoid" style = "padding-left: 40px;"><span><a href="https://docs.google.com/forms/d/e/1FAIpQLScrDVb_utm55pmb_SHx-RgELTEbCCWdLea0T3IzS0Oj00GE4w/viewform?usp=pp_url&entry.1565230805=BioDIGS+in+the+Classroom:+Exploring+Soil+Data"> Click here to provide feedback</a> <img src="assets/itcr_arrow.png" style=" width: 10%" ></span></div></p>
+
+</ul>
+
+      </nav>
+    </div>
+
+    <div class="book-body">
+      <div class="body-inner">
+        <div class="book-header" role="navigation">
+          <h1>
+            <i class="fa fa-circle-o-notch fa-spin"></i><a href="./">BioDIGS in the Classroom: Exploring Soil Data</a>
+          </h1>
+        </div>
+
+        <div class="page-wrapper" tabindex="-1" role="main">
+          <div class="page-inner">
+
+            <section class="normal" id="section-">
+<head>
+  <meta name="viewport" content="width=device-width,minimum-scale=1.0,maximum-scale=10.0,initial-scale=1.0">
+  <!--script src="https://kit.fontawesome.com/6a26f47516.js"></script-->
+  <!--<script src="assets/hideOutput.js"></script>-->
+</head>
+
+
+
+<div class="hero-image-container"> 
+  <img class= "hero-image" src="assets/AnVIL_style/dasl_thin_main_image.png">
+</div>
+<div id="references" class="section level1 hasAnchor" number="14">
+<h1><span class="header-section-number">Chapter 14</span> References<a href="references.html#references" class="anchor-section" aria-label="Anchor link to header"></a></h1>
+
+</div>
+<hr>
+<center> 
+  <div class="footer">
+      All illustrations <a href="https://creativecommons.org/licenses/by/4.0/">CC-BY. </a>
+      <br>
+      All other materials <a href= "https://creativecommons.org/licenses/by/4.0/"> CC-BY </a> unless noted otherwise.
+  </div>
+</center>
+            </section>
+
+          </div>
+        </div>
+      </div>
+<a href="about-the-authors.html" class="navigation navigation-prev navigation-unique" aria-label="Previous page"><i class="fa fa-angle-left"></i></a>
+
+    </div>
+  </div>
+<script src="libs/gitbook-2.6.7/js/app.min.js"></script>
+<script src="libs/gitbook-2.6.7/js/clipboard.min.js"></script>
+<script src="libs/gitbook-2.6.7/js/plugin-search.js"></script>
+<script src="libs/gitbook-2.6.7/js/plugin-sharing.js"></script>
+<script src="libs/gitbook-2.6.7/js/plugin-fontsettings.js"></script>
+<script src="libs/gitbook-2.6.7/js/plugin-bookdown.js"></script>
+<script src="libs/gitbook-2.6.7/js/jquery.highlight.js"></script>
+<script src="libs/gitbook-2.6.7/js/plugin-clipboard.js"></script>
+<script>
+gitbook.require(["gitbook"], function(gitbook) {
+gitbook.start({
+"sharing": {
+"github": false,
+"facebook": true,
+"twitter": true,
+"linkedin": false,
+"weibo": false,
+"instapaper": false,
+"vk": false,
+"whatsapp": false,
+"all": ["facebook", "twitter", "linkedin", "weibo", "instapaper"]
+},
+"fontsettings": {
+"theme": "white",
+"family": "sans",
+"size": 2
+},
+"edit": {
+"link": null,
+"text": null
+},
+"history": {
+"link": null,
+"text": null
+},
+"view": {
+"link": null,
+"text": null
+},
+"download": null,
+"search": {
+"engine": "fuse",
+"options": null
+},
+"toc": {
+"collapse": "section"
+}
+});
+});
+</script>
+
+</body>
+
+</html>