aqp (version 2.1.0)

estimatePSCS: Estimate boundaries of the U.S Soil Taxonomy Particle Size Control Section

Description

Estimates the upper and lower boundary of the particle size control section for Mineral or Organic soilsby applying a programmatic version of the particle size control section key from the Keys to Soil Taxonomy (13th edition). See details for assumptions and required data elements.

Usage

estimatePSCS(
  p,
  hzdesgn = hzdesgnname(p, required = TRUE),
  clay.attr = hzmetaname(p, "clay", required = TRUE),
  texcl.attr = hztexclname(p, required = TRUE),
  lieutex = hzmetaname(p, "lieutex"),
  tax_order_field = "tax_order",
  bottom.pattern = "Cr|R|Cd|m",
  simplify = TRUE,
  ...
)

Value

A numeric vector (when simplify=TRUE) containing the top and bottom depth of the particle size control section. First value is top, second value is bottom. If p contains more than one profile, the result is a data.frame with profile ID plus PSCS top and bottom depths.

Arguments

p

A SoilProfileCollection

hzdesgn

Name of the horizon attribute containing the horizon designation. Default hzdesgnname(p, required = TRUE)

clay.attr

Name of the horizon attribute containing clay contents. Default hzmetaname(p, "clay", required = TRUE)

texcl.attr

Name of the horizon attribute containing textural class (used for finding sandy textures). Default hztexclname(p, required = TRUE)

lieutex

Optional data element used in addition to the horizon designation to identify kinds of organic soil material for soils with organic surfaces. Default: hzmetaname(p, "lieutex")

tax_order_field

Name of the site attribute containing taxonomic order; for handling PSCS rules for Andisols in lieu of lab data. May be NA or column missing altogether, in which case Andisol PSC possibility is ignored.

bottom.pattern

Regular expression pattern to match a root-restrictive contact. Default matches Cr, R, Cd or m. This argument is passed to both minDepthOf() and getArgillicBounds().

simplify

Return a length 2 vector with upper and lower boundary when p has length 1? Default TRUE.

...

additional arguments are passed to getArgillicBounds()

Author

Andrew Gene Brown

Details

Requires information to identify argillic horizons (clay contents, horizon designations) with getArgillicBounds() as well as the presence of plow layers and surface organic soil material. Any getArgillicBounds() arguments may be passed to estimatePSCS.

Also, requires information on taxonomic order to handle Andisols.

In aqp 2.1, particle size control sections of organic soils Histosols and Histels are supported. This requires setting the "lieutex" horizon metadata column using hzmetaname<-() Horizon designations containing "f" or "W" are recognized as permafrost and water layers, respectively, for application of the organic soils key to control sections. In lieu textures "SPM" and "PEAT" are used to identify low density organic materials used for surface tier thickness. To avoid using the 160 cm surface tier, set the "lieutex" column to any column that does not contain "SPM" or "PEAT" values.

WARNING: Soils in arenic or grossarenic subgroups, with fragipans, or with strongly contrasting PSCs may not be classified correctly. The author would welcome a dataset to develop this functionality for.

References

Soil Survey Staff. 2014. Keys to Soil Taxonomy, 12th ed. USDA-Natural Resources Conservation Service, Washington, DC.

See Also

getArgillicBounds(), getSurfaceHorizonDepth()

Examples

data(sp1, package = 'aqp')
depths(sp1) <- id ~ top + bottom
site(sp1) <- ~ group

# set required metadata
hzdesgnname(sp1) <- 'name'
hztexclname(sp1) <- 'texture'
hzmetaname(sp1, 'clay') <- 'prop'

x <- estimatePSCS(sp1)
x

# change horizon texture and set inlieu texture column to turn
# first profile into an organic soil
sp1$name[1:6] <- c("Oi1", "Oi2", "Oi3", "Oaf", "Cf1", "Cf2")
sp1$texture <- as.character(sp1$texture)
sp1$texture[1:6] <- c("PEAT", "PEAT", "PEAT", "MUCK", "GRVLS", "GRVLS")
sp1$bottom[6] <- 200
hzmetaname(sp1, 'lieutex') <- 'texture'

y <- estimatePSCS(sp1[1, ], simplify = FALSE)

# 74cm lower boundary is 25cm past the upper boundary of permafrost (49cm)
# but minimum depth is 100cm unless there is a root-limiting layer
y