1 Loafercreek - Context

The Loafercreek series (fine-loamy, mixed, superactive, thermic Ultic Haploxeralfs) is comprised of soils on foothills underlain by vertically-bedded metavolcanic rock. They are moderately deep (50 to 100cm) to a paralithic contact.

The Loafercreek series was established in Butte county (CA612) and now is mapped in Calaveras and Tuolumne (CA630) as well as small portions of Mariposa and Stanislaus Counties (CA630 join with CA649 and CA644).

The metamorphic belt is comprised of Mesozoic and Paleozoic age metamorphic rocks. The metavolcanic rocks, dominantly what is called greenstone, are derived from metamorphosed intermediate to mafic igneous rocks such as andesite, basalt or gabbro. The metavolcanic rocks in this area were recognized by miners during the gold rush to form distinctive tombstone-like outcrops.

Areas of soils conceptually related to Loafercreek have been mapped primarily as Auburn in the Sierra Nevada Foothills.

Many areas of Auburn soils, and related soils on similar landforms, are outside the range of the family (12th edition taxonomy) of the series. Auburn soils were historically mapped as Ruptic-Lithic Xerochrepts. Reading soil survey manuscript descriptions of map units modeled after the old series concepts shows that their definition spans, at a minimum, shallow to moderately deep depth classes, likely with deeper inclusions.

The Loafercreek series concept might fit the range in characteristics of the deeper (moderately deep) areas within Auburn mapunits. We will study some of the soils similar to Loafercreek to understand its range in characteristics.


1.1 Loafercreek’s siblings

Loafercreek’s siblings are the soils that geographically occupy the same landscapes and parent materials, and often are components in the same mapunits. In some mapunits sibling soils are explicitly part of a component range due to inclusion of “similar soils” to the named component, or implied by bracketing of strongly contrasting components. In many other cases, mapping assoccated with a particular soil name does not necessarily reflect modern series concepts for that same name.

Auburn, by definition, does not have an argillic horizon and classifies with the Lithic Haploxerepts. In CA630, the shallow metavolcanic soils with argillic horizons (Ultic Haploxeralfs) are the Bonanza and Dunstone series. Fine PSC soils are similar to the Argonaut concept. Skeletal PSC soils are Jasperpeak (shallow, Lithic Haploxeralfs) and Gopheridge (moderately deep, Ultic Haploxeralfs). Soils with a deep bedrock restriction are called Motherlode.

1.2 This demo

In this series of demos, we are going to use R-based pedon summaries to explore properties of the Loafercreek soils found during the soil survey inventory in CA630.

This demo has three worked “examples” involving the use of profileApply() for summarizing pedon data.

You can use this R script version of the demo document to avoid having to copy and paste all the code. This will allow you to focus on interpreting the output. This version has all of the text as comments.

Readers are encouraged to run all of the code in their own IDE/text editor/console. Also, you are encouraged to use ?function.name to view R manual pages whenever you encounter a function() you do not recognize.

You can get the latest development versions of aqp, soilDB and sharpshootR using devtools package:

# install devtools if needed
# install.packages("devtools")
devtools::install_github('ncss-tech/aqp', dependencies = FALSE, build = FALSE)
devtools::install_github('ncss-tech/soilDB', dependencies = FALSE, build = FALSE)
devtools::install_github('ncss-tech/sharpshootR', dependencies = FALSE, build = FALSE)

1.3 For reference

NCSS-Tech Stats for Soil Survey - Chapter 2 - Lessons on Data Types

2 SoilProfileCollection

2.1 Loading loafercreek

To get soil data out of the database, and into an R object, we typically will use the library soilDB.

When loading soilDB we also load the dependency aqp.

aqp gives us the basic data structure we use to hold pedon data: the SoilProfileCollection object.

One of the built-in datasets provided by soilDB is loafercreek.

The sharpshootR library has some great functions for summarizing pedon data. We will load that too so we can use it later.

Let’s load loafercreek which is a SoilProfileCollection (SPC) object from soilDB.

library(soilDB)
library(sharpshootR)

data("loafercreek")

2.2 SoilProfileCollection

A SoilProfileCollection (SPC) is an S4 object contains site (spc@site) and horizon (spc@horizon) slots, which are each comprised of a single data.frame.

The contents of a SPC should be accessed/edited-by-replacement by using horizons(spc) and site(spc).

For instance:

# access the cly attribute from the horizons data frame
horizons(spc)$clay

#add new site data by merging a data frame on site ID
site(spc) <- merge(site(spc), new.site.data, by="uniquesiteid")

SPC data (sites, horizons) can also be accessed in ways similar to a base R data.frame via square bracket notation: spc[your.site.index, your.horizon.index].

In practice, you are usually indexing either a site-level OR a horizon-level attribute. You want to be aware of the length of any index you are using, and ensure you are getting what you expect, due to the flexibility built into the SPC data access methods.

We use the data.frame-like bracket notation to get a few profiles (by specifying a site-index) and plot them.

my.sub.set <- loafercreek[3:6, ]

# number of rows (sites or profiles)
nrow(site(my.sub.set))
## [1] 4
plotSPC(my.sub.set, alt.label = 'pedon_id', alt.label.col = "#ffff00")
## guessing horizon designations are stored in `hzname`