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

Source: R/mollicEpipedon.R

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.

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

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))
#>   id hz_desgn has_dark_colors
#> 1  1        A            TRUE
#> 2  1       AB            TRUE
#> 3  1       Bt           FALSE
#> 4  1      BCt           FALSE
#> 5  1        R              NA