Find all intervals that are potentially part of a Cambic horizon

Source: R/getCambicBounds.R

Find all intervals that are potentially part of a Cambic horizon excluding those that are part of an argillic horizon (defined either by depth interval or getArgillicBounds()).

There may be multiple cambic horizons (indexes) in a profile. Each cambic index has a top and bottom depth associated: cambic_top and cambic_bottom. This result is designed to be used for single profiles, or with profileApply(..., frameify = TRUE)

getCambicBounds(
  p,
  hzdesgn = hzdesgnname(p, required = TRUE),
  texcl.attr = hztexclname(p, required = TRUE),
  clay.attr = hzmetaname(p, "clay", required = TRUE),
  argi_bounds = NULL,
  d_value = "d_value",
  m_value = "m_value",
  m_chroma = "m_chroma",
  sandy.texture.pattern = "-S$|^S$|COS$|L[^V]FS$|[^L]VFS$|LS$|LFS$",
  ...
)

Arguments

p

A single-profile SoilProfileCollection

hzdesgn

Column name containing horizon designations.

texcl.attr

Arguments to getArgillicBounds()

clay.attr

Arguments to getArgillicBounds()

argi_bounds

Optional: numeric vector of length 2 with top and bottom of argillic; (Default: NULL)

d_value

Column name containing dry value. Default: d_value

m_value

Column name containing moist value. Default: m_value

m_chroma

Column name containing moist chroma Default: m_chroma

sandy.texture.pattern

this is a pattern for matching sandy textural classes: -S$|^S$|COS$|L[^V]FS$|[^L]VFS$|LS$|LFS$

...

Arguments to getArgillicBounds()

Value

A data.frame containing profile, cambic indexes, along with top and bottom depths.

Author

Andrew G. Brown

Examples

# construct a fake profile
spc <- data.frame(id=1, taxsubgrp = "Lithic Haploxerepts",
                  hzname   = c("A","AB","Bw","BC","R"),
                  hzdept   = c(0,  20, 32, 42,  49),
                  hzdepb   = c(20, 32, 42, 49, 200),
                  clay     = c(19, 22, 22, 21,  NA),
                  texcl    = c("l","l","l", "l","br"),
                  d_value  = c(5,   5,  5,  6,  NA),
                  m_value  = c(2.5, 3,  3,  4,  NA),
                  m_chroma = c(2,   3,  4,  4,  NA))

# promote to SoilProfileCollection
depths(spc) <- id ~ hzdept + hzdepb

# set required metadata
hzdesgnname(spc) <- 'hzname'
hztexclname(spc) <- 'texcl'
hzmetaname(spc, 'clay') <- 'clay'

# print results in table
getCambicBounds(spc)
#>   id cambic_top cambic_bottom cambic_index
#> 1  1         32            49            1