Calculate Melanization component of Profile Development Index after Harden (1982) "A quantitative index of soil development from field descriptions: Examples from a chronosequence in central California". Accepts vectorized inputs for value and reference value to produce vector output. A convenient use case would be to apply this on a profile-specific basis, where the value_ref has a single value, and value is a vector of length equal to the number of horizons within the upper 100 cm.

harden.melanization(value, value_ref)

## Arguments

value

numeric vector containing Munsell values

value_ref

A numeric vector containingMunsell value(s) for reference material

## Value

A numeric vector reflecting horizon darkening relative to a reference (e.g. parent) material.

## Details

In Harden (1982), melanization is calculated relative to a reference parent material for all horizons within 100cm of the soil surface. In addition, several other non-color components are normalized relative to a maximum value and summed to obtain the overall Profile Development Index.

Andrew G. Brown

## Examples

library(aqp)
data("jacobs2000", package="aqp")

# LEFT JOIN hue, value, chroma matrix color columns
horizons(jacobs2000) <- cbind(horizons(jacobs2000)[,c(idname(jacobs2000), hzidname(jacobs2000))],
parseMunsell(jacobs2000$matrix_color_munsell, convertColors = FALSE)) # calculate a mixed 150-200cm color ~"parent material" jacobs2000$c_horizon_color <- profileApply(jacobs2000, function(p) {

# and derive the parent material from the 150-200cm interval
p150_200 <- glom(p, 150, 200, truncate = TRUE)
p150_200$thickness <- p150_200$bottom - p150_200$top # mix colors clrs <- na.omit(horizons(p150_200)[,c('matrix_color_munsell','thickness')]) mixMunsell(clrs$matrix_color_munsell, w = clrs$thickness)$munsell

})
#> closest match has a spectral distance that is large, results may be unreliable
#> closest match has a spectral distance that is large, results may be unreliable

# segment profile into 1cm slices (for proper depth weighting)
jacobs2000$melan <- profileApply(jacobs2000, function(p) { # sum the melanization index over the 0-100cm interval p0_100 <- segment(p, 0:100) ccol <- parseMunsell(p$c_horizon_color, convertColors = FALSE)

sum(harden.melanization(
value = as.numeric(p0_100$value), value_ref = as.numeric(ccol$value)), na.rm = TRUE)

})

jacobs2000$melanorder <- order(jacobs2000$melan)

# Plot in order of increasing Melanization index

plotSPC(jacobs2000, axis.line.offset = -1,
color = "matrix_color",
label = "melan",
plot.order = jacobs2000$melanorder) abline(h = c(0,100,150,200), lty = 2) # Add [estimated] parent material color swatches lapply(seq_along(jacobs2000$c_horizon_color), function(i) {
rect(i - 0.15, 250, i + 0.15, 225,
col = parseMunsell(jacobs2000$c_horizon_color[jacobs2000$melanorder[i]]))
}) #> []
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