aqp: hasDarkColors – R documentation

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hasDarkColors

Find horizons with colors darker than a Munsell hue, value, chroma threshold

Description

hasDarkColors returns a boolean value by horizon representing whether darkness thresholds are met. The code is fully vectorized and deals with missing data and optional thresholds.

Default arguments are set up for "5-3-3 colors" – the basic criteria for Mollic/Umbric epipedon/mineral soil darkness. Any of the thresholds or column names can be altered. Any thresholds that are set equal to NA will be ignored.

Usage

hasDarkColors(
  p,
  d_hue = NA,
  m_hue = NA,
  d_value = 5,
  d_chroma = NA,
  m_value = 3,
  m_chroma = 3,
  dhuenm = "d_hue",
  dvalnm = "d_value",
  dchrnm = "d_chroma",
  mhuenm = "m_hue",
  mvalnm = "m_value",
  mchrnm = "m_chroma"
)

Arguments

`p`	A SoilProfileCollection.
`d_hue`	Optional: character vector of dry hues to match (default: NA)
`m_hue`	Optional: character vector of moist hues to match (default: NA)
`d_value`	Maximum value of dry value (default: 5)
`d_chroma`	Optional: Maximum value of dry chroma (default: NA)
`m_value`	Maximum value of moist value (default: 3)
`m_chroma`	Maximum value of moist chroma (default: 3)
`dhuenm`	Column name containing dry hue.
`dvalnm`	Column name containing dry value.
`dchrnm`	Column name containing dry chroma.
`mhuenm`	Column name containing moist hue.
`mvalnm`	Column name containing moist value.
`mchrnm`	Column name containing moist chroma.

Value

Boolean value (for each horizon in p) reflecting whether "darkness" criteria are met.

Author(s)

Andrew G. Brown

Examples

# construct a fake profile
spc <- data.frame(id=1, taxsubgrp = "Lithic Haploxeralfs",
                  hzdesgn  = c("A","AB","Bt","BCt","R"),
                  hzdept   = c(0, 20, 32, 42,  49),
                  hzdepb   = c(20, 32, 42, 49, 200),
                  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

# print results in table
data.frame(id = spc[[idname(spc)]],
           hz_desgn = spc$hzdesgn,
           has_dark_colors = hasDarkColors(spc))

aqp

Algorithms for Quantitative Pedology

v1.29

GPL (>= 3)

Authors

Dylan Beaudette [aut, cre], Pierre Roudier [aut, ctb], Andrew Brown [aut, ctb]

Initial release

2021-04-05