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Soil Profile Color Signatures

Source: R/soilColorSignature.R
soilColorSignature.Rd

Generate a color signature for each soil profile in a collection.

Usage

soilColorSignature(
  spc,
  color,
  space = c("sRGB", "CIELAB"),
  method = c("colorBucket", "depthSlices", "pam"),
  perceptualDistMat = FALSE,
  pam.k = 3,
  prob = c(0.1, 0.5, 0.9),
  useProportions = TRUE,
  pigmentNames = c(".white.pigment", ".red.pigment", ".green.pigment", ".yellow.pigment",
    ".blue.pigment"),
  apply.fun = lapply,
  r = NULL,
  g = NULL,
  b = NULL,
  RescaleLightnessBy = NULL
)

Arguments

spc

a SoilProfileCollection object

color

horizon-level attributes, either character of length 1 specifying a column containing Munsell or sRGB in hex notation, or character vector of three column names containing either sRGB or CIELAB color coordinates. sRGB color coordinates should be within the range of 0 to 1.

space

character, either 'sRGB' or 'LAB', specifying color space

method

algorithm used to compute color signature, colorBucket, depthSlices, or pam

perceptualDistMat

logical, optionally return a distance matrix based on perceptual color distances, when “method` is one of 'depthSlices' or 'pam', see Details

pam.k

number of color classes for method = 'pam'

prob

numeric vector, requested percentiles for method = 'depthSlices'

useProportions

use proportions or quantities, see details

pigmentNames

names for resulting pigment proportions or quantities

apply.fun

function passed to aqp::profileApply(APPLY.FUN) argument, can be used to add progress bars via pbapply::pblapply(), or parallel processing with furrr::future_map()

r

deprecated, use color argument

g

deprecated, use color argument

b

deprecated, use color argument

RescaleLightnessBy

deprecated, scaling factor for CIELAB L-coordinate

Value

For the colorBucket method, a data.frame:

  • id column: set according to idname(spc)

  • .white.pigment: proportion or quantity of CIELAB L-values

  • .red.pigment: proportion or quantity of CIELAB positive A-values

  • .green.pigment: proportion or quantity of CIELAB negative A-values

  • .yellow.pigment: proportion or quantity of CIELAB positive B-values

  • .blue.pigment: proportion or quantity of CIELAB negative B-values

Column names can be adjusted with the pigmentNames argument.

For the depthSlices method, a data.frame:

  • id column: set according to idname(spc)

  • L.1, A.1, B.1: CIELAB color coordinates associated with the first depth slice, at depth percentile given in prob[1]

  • ...

  • L.n, A.n, B.n: CIELAB color coordinates associated with the n depth slice, at depth percentile given in prob[n]

For the pam method, a data.frame:

  • id column: set according to idname(spc)

  • L.1, A.1, B.1: CIELAB color coordinates associated with the first color cluster, after sorting all clusters in ascending order along L, A, B axes.

  • ...

  • L.n, A.n, B.n: CIELAB color coordinates associated with the nth color cluster, after sorting all clusters in ascending order along L, A, B axes.

When perceptualDistMat = TRUE and method is one of 'depthSlices' or 'pam', a distance matrix is returned.

Details

Interpreation of color signature.

Choices related to weighting, scaling, and distance metric.

Perceptual distances (dE00), summed over color groups.

See the related tutorial.

References

https://en.wikipedia.org/wiki/Lab_color_space

See also

plotProfileDendrogram()

Author

D.E. Beaudette

Examples


# trivial example, not very interesting
data(sp1)
depths(sp1) <- id ~ top + bottom

# Munsell notation
sp1$m <- sprintf("%s %s/%s", sp1$hue, sp1$value, sp1$chroma)

# extract color signature
pig <- soilColorSignature(sp1, color = 'm')