getArgillicBounds() estimates upper and lower boundary of argillic diagnostic subsurface horizon for a profile in a single-profile SoilProfileCollection object (`p`). The upper boundary is where the clay increase threshold is met. Uses crit.clay.argillic() as the threshold function for determining whether a clay increase occurs and get.increase.matrix to determine whether the increase is met, whether vertical distance of increase is sufficiently short, and in which horizon.
The lower boundary is first approximated as the depth to a lithic/paralithic/densic contact, or some other horizon matchable by a custom regular expression pattern. Subsequently, that boundary is extended upwards to the end of "evidence of illuviation."
The depth to contact is estimated using `bottom.pattern` "Cr|R|Cd" by default. It matches anything containing Cr, R or Cd.
The lower gradational horizon regular expression `lower.grad.pattern` default is '"^[2-9]*CB*[^rt]*$"'. It matches anything that starts with a lithologic discontinuity (or none) and a C master horizon designation. May contain B as second horizon designation in transitional horizon. May not contain 'r' or 't' subscript.
There also is an option `require_t` to omit the requirement for evidence of eluviation in form of 't' subscript in `hzdesgn`.
Even if "t" subscript is not required for positive identification, the presence of lower gradational C horizons lacking 't' will still be used to modify the lower boundary upward from a detected contact, if needed. If this behavior is not desired, just set `lower.grad.pattern` to something that will not match any horizons in your data.
getArgillicBounds(p, hzdesgn = "hzname", attr = "clay", require_t = TRUE,
bottom.pattern = "Cr|R|Cd",
lower.grad.pattern = "^[2-9]*B*CB*[^rtd]*[1-9]*$",
as.list = FALSE)a single-profile SoilProfileCllection
the name of the column/attribute containing the horizon designation; default="hzname"
the name of the column/attribute containing the clay content; default="clay"
require a "t" subscript for positive identification of upper and lower bound of argillic? default:
regular expression passed to estimateSoilDepth() to match the lower boundary of the soil. default is "Cr|R|Cd" which approximately matches paralithic, lithic and densic contacts.
this is a pattern for adjusting the bottom depth of the argillic horizon upwards from the bottom depth of the soil. The absence of illuviation is used as a final control on horizon pattern matching.
return result as a 'list'?
Returns a numeric vector; first value is top depth, second value is bottom depth. If as.list is TRUE, returns a list with top depth named "ubound" and bottom depth named "lbound"
get.increase.matrix, get.argillic.increase.depth, crit.clay.argillic
# NOT RUN {
data(sp1, package = 'aqp')
depths(sp1) <- id ~ top + bottom
site(sp1) <- ~ group
p <- sp1[1]
attr <- 'prop' # clay contents
foo <- getArgillicBounds(p, hzdesgn='name', attr = attr)
foo
# }
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