The AQP family of R packages has seen a lot of development over the last 3 months. Some of the highlights include:

1. HTML manual pages with syntax-highlighting and figures, c/o knitr
2. new vignettes: "dealing with bad data", gridded SSURGO (gSSURGO) demo, and "aggregating properties by bedrock kind"
3. a new package called sharpshootR containing misc. functions to support soil survey
4. slab() has been re-written and is now much more efficient (with memory), transparent (10x fewer lines of code), and "slab functions" are much simpler to write.

Something fun to play with before the new year: experimental code in aqp for simulating soil profile data from a single "template" profile. The basic idea: simulate horizon thickness data using a family of Gaussian functions with mean defined by horizon thickness values found in the template and standard deviation defined by the user. Larger hz.sd values will yield more drastic variation in the simulated results. Note that only "horizonation" (e.g. the sequence of horizons and their respective thickness) is simulated; horizon attributes (e.g. texture, pH, etc.) are copied from the "template" profile.

Basic usage is demonstrated below, see package manual page for details. This function is only available in the version of aqp hosted by R-Forge. It should be on CRAN by the new year.

Simulated Profiles

Automated OSD lookup and display

 
UPDATED 2013-04-08


This functionality it now available in the soilDB and sharpshootR packages. All code on this page is now superseded by the fetchOSD() and SoilTaxonomyDendrogram() functions.

 
UPDATED 2012-11-07

I have been thinking about a URL-based interface to basic Official Soil Series Description (OSD) data for a while now... something that when fed a URL, would return CSV-formatted records to the calling process. These type of interfaces can later be used to support more complicated systems, such as our smartphone interface to SoilWeb. URLs can be accessed like files in R, making it possible to do something like this:

The orientation of terrain surface (aspect) can have dramatic effects on landscape-scale variation in soil temperature and moisture. Summarizing aspect angle is complicated by the fact that sampled values are measured on a circular scale. The circular package for R can be used to summarize, model, and visualize this type of data.

An example function is presented below that demonstrates several components of the circular package: special data structures, summary functions, plotting functions and their application to circular data derived from measurements collected by compass. Spread and central tendency are depicted with a combination of circular histogram and kernel density estimate. The circular mean, and relative confidence in that mean are depicted with an arrow: longer arrow lengths correspond to greater confidence in the mean.

Circular Histogram

Here is a quick demonstration of how functionality from the AQP package can be used to answer complex soils-related questions. In these examples the profileApply() function is used to iterate over a collection of soil profiles, and compute several metrics of soil development:

• depth of maximum clay content
• clay/RF content within the PCS
• clay content within the argillic horizon
• thickness of argillic horizon
• depth to argillic horizon

 
UPDATE 2013-04-08: This functionality is now available in the sharpshootR package.

Previously, soil profile comparison methods from the aqp package only took into account horizon-level attributes. As of last week the profile_compare() function can now accommodate horizon and site-level attributes. In other words, it is now possible to compute pair-wise dissimilarity between soil profiles using a combination of horizon-level properties (soil texture, pH, color, etc.) and site-level properties (surface slope, vegetation, soil taxonomy, etc.)-- continuous, categorical, or boolean.

An example is presented below which is based on the loafercreek sample data set included with the soilDB package. Be sure to use the latest version of soilDB, 0.5-5 or later. Dissimilarity matrices created from horizon and site+horizon data are compared by placing their respective dendrograms back-to-back. Code from the ape package is used to facilitate dendrogram plotting, manipulation, and indexing. Blue line segments connect matching nodes from each dendrogram. Soil profiles with paralithic contact are marked with orange squares for clarity.

Dueling Dendrograms