Chapter 14 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.

devtools::install_github("fhdsl/BioDIGSData")

Once you’ve installed the package, we can load the library and assign the soil testing data to an object. This command follows the code structure:

dataset_object_name <- stored_BioDIGS_dataset

library(BioDIGSData)

soil.values <- BioDIGS_soil_data()

It seems like the dataset loaded, but it’s always a good idea to verify. There are many ways to check, but the easiest approach (if you’re using RStudio) is to look at the Environment tab on the upper right-hand side of the screen. You should now have an object called soil.values that includes some number of observations for 28 variables. The observations refer to the number of rows in the dataset, while the variables tell you the number of columns. As long as neither the observations or variables are 0, you can be confident that your dataset loaded.

Let’s take a quick look at the dataset. We can do this by clicking on soil.values object in the Environment tab. (Note: this is equivalent to typing View(soil.values) in the R console.)

This will open a new window for us to scroll through the dataset.

Well, the data definitely loaded, but those column names aren’t immediately understandable. What could As_EPA3051 possibly mean? In addition to the dataset, we need to load the data dictionary as well.

Data dictionary: a file containing the names, definitions, and attributes about data in a database or dataset.

In this case, the data dictionary can help us make sense of what sort of values each column represents. The data dictionary for the BioDIGS soil testing data is available in the R package (see code below), but we have also reproduced it here.

?BioDIGS_soil_data()

• site_id Unique letter and number site name
• full_name Full site name
• As_EPA3051 Arsenic (mg/kg), EPA Method 3051A. Quantities < 3.0 are not detectable.
• Cd_EPA3051 Cadmium (mg/kg), EPA Method 3051A. Quantities < 0.2 are not detectable.
• Cr_EPA3051 Chromium (mg/kg), EPA Method 3051A
• Cu_EPA3051 Copper (mg/kg), EPA Method 3051A
• Ni_EPA3051 Nickel (mg/kg), EPA Method 3051A
• Pb_EPA3051 Lead (mg/kg), EPA Method 3051A
• Zn_EPA3051 Zinc (mg/kg), EPA Method 3051A
• water_pH
• A-E_Buffer_pH
• OM_by_LOI_pct Organic Matter by Loss on Ignition
• P_Mehlich3 Phosphorus (mg/kg), using the Mehlich 3 soil test extractant
• K_Mehlich3 Potassium (mg/kg), using the Mehlich 3 soil test extractant
• Ca_Mehlich3 Calcium (mg/kg), using the Mehlich 3 soil test extractant
• Mg_Mehlich3 Magnesium (mg/kg), using the Mehlich 3 soil test extractant
• Mn_Mehlich3 Manganese (mg/kg), using the Mehlich 3 soil test extractant
• Zn_Mehlich3 Zinc (mg/kg), using the Mehlich 3 soil test extractant
• Cu_Mehlich3 Copper (mg/kg), using the Mehlich 3 soil test extractant
• Fe_Mehlich3 Iron (mg/kg), using the Mehlich 3 soil test extractant
• B_Mehlich3 Boron (mg/kg), using the Mehlich 3 soil test extractant
• S_Mehlich3 Sulfur (mg/kg), using the Mehlich 3 soil test extractant
• Na_Mehlich3 Sodium (mg/kg), using the Mehlich 3 soil test extractant
• Al_Mehlich3 Aluminum (mg/kg), using the Mehlich 3 soil test extractant
• Est_CEC Cation Exchange Capacity (meq/100g) at pH 7.0 (CEC)
• Base_Sat_pct Base saturation (BS). This represents the percentage of CEC occupied by bases (Ca2+, Mg2+, K+, and Na+). The %BS increases with increasing soil pH. The availability of Ca2+, Mg2+, and K+ increases with increasing %BS.
• P_Sat_ratio Phosphorus saturation ratio. This is the ratio between the amount of phosphorus present in the soil and the total capacity of that soil to retain phosphorus. The ability of phosphorus to be bound in the soil is primary a function of iron (Fe) and aluminum (Al) content in that soil.

Using the data dictionary, we find that the values in column As_EPA3051 give us the arsenic concentration in mg/kg of each soil sample, as determined by EPA Method 3051A. This method uses a combination of heat and acid to extract specific elements (like arsenic, cadmium, chromium, copper, nickel, lead, and zinc) from soil samples.

While arsenic can occur naturally in soils, higher levels suggest the soil may have been contaminated by mining, hazardous waste, or pesticide application. Arsenic is toxic to humans.

QUESTIONS:

1. What data is found in the column labeled “Fe_Mehlich3”? Why would we be interested how much of this is in the soil? (You may have to search the internet for this answer.)

2. What data is found in the column labeled “Base_Sat_pct”? What does this variable tell us about the soil?

We can also look at just the names of all the columns using the R console using the colnames() command.

colnames(soil.values)

##  [1] "site_id"       "site_name"     "type"          "As_EPA3051"   
##  [5] "Cd_EPA3051"    "Cr_EPA3051"    "Cu_EPA3051"    "Ni_EPA3051"   
##  [9] "Pb_EPA3051"    "Zn_EPA3051"    "water_pH"      "OM_by_LOI_pct"
## [13] "P_Mehlich3"    "K_Mehlich3"    "Ca_Mehlich3"   "Mg_Mehlich3"  
## [17] "Mn_Mehlich3"   "Zn_Mehlich3"   "Cu_Mehlich3"   "Fe_Mehlich3"  
## [21] "B_Mehlich3"    "S_Mehlich3"    "Na_Mehlich3"   "Al_Mehlich3"  
## [25] "Est_CEC"       "Base_Sat_pct"  "P_Sat_ratio"   "region"

Most of the column names are found in the data dictionary, but the very last column (“region”) isn’t. How peculiar! Let’s look at what sort of values this particular column contains. The tab with the table of the soil.views object should still be open in the upper left pane of the RStudio window. If not, you can open it again by clicking on soils.view in the Environment pane, or by using the View() command.

View(soil.values)

If you scroll to the end of the table, we can see that “region” seems to refer to the city or area where the samples were collected. For example, the first 6 samples all come from Baltimore City.

You may notice that some cells in the soil.values table contain NA. This just means that the soil testing data for that sample isn’t available yet. We’ll take care of those values in the next part.

QUESTIONS:

3. How many observations are in the soil testing values dataset that you loaded? What do each of these observations refer to?

4. How many different regions are represented in the soil testing dataset? How many of them have soil testing data available?

---

All illustrations CC-BY.
All other materials CC-BY unless noted otherwise.