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10 changes: 5 additions & 5 deletions docs/09-soil_exploration_module.md
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# (PART\*) Data Exploration {-}
# (PART\*) Student Activity {-}




# Exploring Soil Testing Data With R
# Introduction

In this activity, you'll have a chance to become familiar with the BioDIGS soil testing data. This dataset includes information on the inorganic components of each soil sample, particularly metal concentrations. Human activity can increase the concentration of inorganic compounds in the soil. 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. All of this means the concentration of heavy metals and other chemicals will vary among the soil samples collected for the BioDIGS project.

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1. Create and interpret histograms and boxplots for variables in the soil testing data


## Part 1. Examining the Data
# Part 1. Examining the Data

We will use the `BioDIGS` package to retrieve the data. We first need to install the package from where it is stored on GitHub.

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:::

## Part 2. Summarizing the Data with Statistics
# Part 2. Summarizing the Data with Statistics

Now that we have the dataset loaded, let's explore the data in more depth.

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:::

## Part 3. Visualizing the Data
# Part 3. Visualizing the Data

Often, it can be easier to immediately interpret data displayed as a plot than as a list of values. For example, we can more easily understand how the arsenic concentration of the soil samples are distributed if we create histograms compared to looking at point values like mean, standard deviation, minimum, and maximum.

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<meta http-equiv="X-UA-Compatible" content="IE=edge" />
<title>Page not found | BioDIGS: 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 name="generator" content="bookdown 0.40 and GitBook 2.6.7" />

<meta property="og:title" content="Page not found | BioDIGS: Exploring Soil Data" />
<meta property="og:type" content="book" />
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<meta name="date" content="2024-09-09" />
<meta name="date" content="2024-10-16" />

<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="apple-mobile-web-app-capable" content="yes" />
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<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>
<li class="part"><span><b>Student Activity</b></span></li>
<li class="chapter" data-level="13" data-path="introduction.html"><a href="introduction.html"><i class="fa fa-check"></i><b>13</b> Introduction</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.-examining-the-data"><i class="fa fa-check"></i><b>13.3</b> Part 1. Examining the Data</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.-summarizing-the-data-with-statistics"><i class="fa fa-check"></i><b>13.4</b> Part 2. Summarizing the Data with Statistics</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.-visualizing-the-data"><i class="fa fa-check"></i><b>13.5</b> Part 3. Visualizing the Data</a></li>
<li class="chapter" data-level="13.1" data-path="introduction.html"><a href="introduction.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="introduction.html"><a href="introduction.html#objectives-1"><i class="fa fa-check"></i><b>13.2</b> Objectives</a></li>
</ul></li>
<li class="chapter" data-level="14" data-path="activity-questions.html"><a href="activity-questions.html"><i class="fa fa-check"></i><b>14</b> Activity Questions</a>
<li class="chapter" data-level="14" data-path="part-1.-examining-the-data.html"><a href="part-1.-examining-the-data.html"><i class="fa fa-check"></i><b>14</b> Part 1. Examining the Data</a></li>
<li class="chapter" data-level="15" data-path="part-2.-summarizing-the-data-with-statistics.html"><a href="part-2.-summarizing-the-data-with-statistics.html"><i class="fa fa-check"></i><b>15</b> Part 2. Summarizing the Data with Statistics</a></li>
<li class="chapter" data-level="16" data-path="part-3.-visualizing-the-data.html"><a href="part-3.-visualizing-the-data.html"><i class="fa fa-check"></i><b>16</b> Part 3. Visualizing the Data</a></li>
<li class="chapter" data-level="17" data-path="activity-questions.html"><a href="activity-questions.html"><i class="fa fa-check"></i><b>17</b> Activity Questions</a>
<ul>
<li class="chapter" data-level="14.1" data-path="activity-questions.html"><a href="activity-questions.html#part-1.-examining-the-data-1"><i class="fa fa-check"></i><b>14.1</b> Part 1. Examining the Data</a></li>
<li class="chapter" data-level="14.2" data-path="activity-questions.html"><a href="activity-questions.html#part-2.-summarizing-the-data-with-statistics-1"><i class="fa fa-check"></i><b>14.2</b> Part 2. Summarizing the Data with Statistics</a></li>
<li class="chapter" data-level="14.3" data-path="activity-questions.html"><a href="activity-questions.html#part-3.-visualizing-the-data-1"><i class="fa fa-check"></i><b>14.3</b> Part 3. Visualizing the Data</a></li>
<li class="chapter" data-level="17.1" data-path="activity-questions.html"><a href="activity-questions.html#part-1.-examining-the-data-1"><i class="fa fa-check"></i><b>17.1</b> Part 1. Examining the Data</a></li>
<li class="chapter" data-level="17.2" data-path="activity-questions.html"><a href="activity-questions.html#part-2.-summarizing-the-data-with-statistics-1"><i class="fa fa-check"></i><b>17.2</b> Part 2. Summarizing the Data with Statistics</a></li>
<li class="chapter" data-level="17.3" data-path="activity-questions.html"><a href="activity-questions.html#part-3.-visualizing-the-data-1"><i class="fa fa-check"></i><b>17.3</b> Part 3. Visualizing the Data</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="15" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>15</b> References</a></li>
<li class="chapter" data-level="18" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>18</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>
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10 changes: 5 additions & 5 deletions docs/About.md
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## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz Etc/UTC
## date 2024-09-09
## date 2024-10-16
## 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)
## bookdown 0.40 2024-07-02 [1] CRAN (R 4.3.2)
## 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)
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## 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)
## knitr 1.48 2024-07-07 [1] CRAN (R 4.3.2)
## 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)
Expand All @@ -80,7 +80,7 @@ These credits are based on our [course contributors table guidelines](https://gi
## 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)
## rmarkdown 2.25 2023-09-18 [1] RSPM (R 4.3.0)
## 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)
Expand All @@ -89,7 +89,7 @@ These credits are based on our [course contributors table guidelines](https://gi
## 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)
## xfun 0.48 2024-10-03 [1] CRAN (R 4.3.2)
## 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)
##
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38 changes: 19 additions & 19 deletions docs/about-the-authors.html
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<meta http-equiv="X-UA-Compatible" content="IE=edge" />
<title>About the Authors | BioDIGS: 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 name="generator" content="bookdown 0.40 and GitBook 2.6.7" />

<meta property="og:title" content="About the Authors | BioDIGS: Exploring Soil Data" />
<meta property="og:type" content="book" />
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<meta name="date" content="2024-09-09" />
<meta name="date" content="2024-10-16" />

<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="apple-mobile-web-app-capable" content="yes" />
Expand Down Expand Up @@ -169,23 +169,23 @@
<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>
<li class="part"><span><b>Student Activity</b></span></li>
<li class="chapter" data-level="13" data-path="introduction.html"><a href="introduction.html"><i class="fa fa-check"></i><b>13</b> Introduction</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.-examining-the-data"><i class="fa fa-check"></i><b>13.3</b> Part 1. Examining the Data</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.-summarizing-the-data-with-statistics"><i class="fa fa-check"></i><b>13.4</b> Part 2. Summarizing the Data with Statistics</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.-visualizing-the-data"><i class="fa fa-check"></i><b>13.5</b> Part 3. Visualizing the Data</a></li>
<li class="chapter" data-level="13.1" data-path="introduction.html"><a href="introduction.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="introduction.html"><a href="introduction.html#objectives-1"><i class="fa fa-check"></i><b>13.2</b> Objectives</a></li>
</ul></li>
<li class="chapter" data-level="14" data-path="activity-questions.html"><a href="activity-questions.html"><i class="fa fa-check"></i><b>14</b> Activity Questions</a>
<li class="chapter" data-level="14" data-path="part-1.-examining-the-data.html"><a href="part-1.-examining-the-data.html"><i class="fa fa-check"></i><b>14</b> Part 1. Examining the Data</a></li>
<li class="chapter" data-level="15" data-path="part-2.-summarizing-the-data-with-statistics.html"><a href="part-2.-summarizing-the-data-with-statistics.html"><i class="fa fa-check"></i><b>15</b> Part 2. Summarizing the Data with Statistics</a></li>
<li class="chapter" data-level="16" data-path="part-3.-visualizing-the-data.html"><a href="part-3.-visualizing-the-data.html"><i class="fa fa-check"></i><b>16</b> Part 3. Visualizing the Data</a></li>
<li class="chapter" data-level="17" data-path="activity-questions.html"><a href="activity-questions.html"><i class="fa fa-check"></i><b>17</b> Activity Questions</a>
<ul>
<li class="chapter" data-level="14.1" data-path="activity-questions.html"><a href="activity-questions.html#part-1.-examining-the-data-1"><i class="fa fa-check"></i><b>14.1</b> Part 1. Examining the Data</a></li>
<li class="chapter" data-level="14.2" data-path="activity-questions.html"><a href="activity-questions.html#part-2.-summarizing-the-data-with-statistics-1"><i class="fa fa-check"></i><b>14.2</b> Part 2. Summarizing the Data with Statistics</a></li>
<li class="chapter" data-level="14.3" data-path="activity-questions.html"><a href="activity-questions.html#part-3.-visualizing-the-data-1"><i class="fa fa-check"></i><b>14.3</b> Part 3. Visualizing the Data</a></li>
<li class="chapter" data-level="17.1" data-path="activity-questions.html"><a href="activity-questions.html#part-1.-examining-the-data-1"><i class="fa fa-check"></i><b>17.1</b> Part 1. Examining the Data</a></li>
<li class="chapter" data-level="17.2" data-path="activity-questions.html"><a href="activity-questions.html#part-2.-summarizing-the-data-with-statistics-1"><i class="fa fa-check"></i><b>17.2</b> Part 2. Summarizing the Data with Statistics</a></li>
<li class="chapter" data-level="17.3" data-path="activity-questions.html"><a href="activity-questions.html#part-3.-visualizing-the-data-1"><i class="fa fa-check"></i><b>17.3</b> Part 3. Visualizing the Data</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="15" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>15</b> References</a></li>
<li class="chapter" data-level="18" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>18</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>
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## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz Etc/UTC
## date 2024-09-09
## date 2024-10-16
## 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)
## bookdown 0.40 2024-07-02 [1] CRAN (R 4.3.2)
## 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)
Expand All @@ -336,7 +336,7 @@ <h1>About the Authors<a href="about-the-authors.html#about-the-authors" class="a
## 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)
## knitr 1.48 2024-07-07 [1] CRAN (R 4.3.2)
## 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)
Expand All @@ -352,7 +352,7 @@ <h1>About the Authors<a href="about-the-authors.html#about-the-authors" class="a
## 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)
## rmarkdown 2.25 2023-09-18 [1] RSPM (R 4.3.0)
## 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)
Expand All @@ -361,7 +361,7 @@ <h1>About the Authors<a href="about-the-authors.html#about-the-authors" class="a
## 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)
## xfun 0.48 2024-10-03 [1] CRAN (R 4.3.2)
## 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)
##
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