Algorithms for quantitative pedology: A toolkit for soil scientists

Soils are routinely sampled and characterized according to genetic horizons (layers), resulting in data that are associated with principal dimensions: location (x,y), depth (z), and property space (p). The high dimensionality and grouped nature of this type of data can complicate standard analysis, summarization, and visualization. The aqp package was developed to address some of these issues, as well as provide a useful framework for the advancement of quantitative studies in soil genesis, geography, and classification. 1 Background The soils of the world support a wide range of natural ecosystems, agricultural production, industrial processes, and the largest surficial carbon pool (Schlesinger, 1997). The rise and fall of past civilizations can be directly linked to the use and misuse of the soil resource (Hillel, 1998). A staggering quantity of soils information has been collected over the last 100 years, yet these data are often underutilized due to the sheer volume and complex structure. We have developed an R package that supports the interpretation of massive soils databases through numerical extensions to traditional methods of visualizing, aggregating, and classifying soils information. Further development of these numerical analogues will provide a new set of quantitative tools that soil scientists and surveyors can use in conjunction with well-established, qualitative methods. Soil science is an integrative approach to understanding surficial processes that includes concepts from several disciplines (Buol et al., 2003). Pedology, one of several branches of soil science, is the study of the genesis, morphology, classification, and geography of soils. Soil profiles are usually described, sampled, and characterized by genetic horizons (“layers” defined by morphology and usually associated with an inferred process), extending from the surface to a lower boundary determined by bedrock contact or to a depth of 150-200 cm (Soil Survey Division Staff, 1993). The stratigraphy and morphology of soil horizons are usually the first data that the soil scientist uses to qualitatively classify a soil: i.e. degree of alteration relative to the parent material (Figure 1(a)), expression of oxidized or reduced forms of iron (Figure 1(b)), accumulation of organic matter, or evidence of cyclical deposition of new material (Figure 1(c)). Hans Jenny was one of the first researchers to advocate a semi-quantitative theory of soil genesis; in which he described the “factors of soil formation” concept (Jenny, 1941). This novel approach is based on the expression: S = f(cl, o, r, p, t) (1) where S represents a branch within a soil classification system, a collection of soil properties associated with a soil profile or a single layer (horizon). The parameters within the “clorpt” framework are: cl