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$matrix_color_munsell, convertColors = FALSE))
#' # calculate a mixed 150-200cm color ~"parent material"
jacobs2000$surface_color <- profileApply(jacobs2000, function(p) {
print(profile_id(p))
# and derive the parent material from the 150-200cm interval
p2 <- glom(p, 0, 25, truncate = TRUE)
p2$thickness <- p2$bottom - p2$top
# mix colors
clrs <- na.omit(horizons(p2)[,c('matrix_color_munsell','thickness')])
mixMunsell(clrs$matrix_color_munsell, w = clrs$thickness)$munsell
})
jacobs2000$b_horizon_color <- profileApply(jacobs2000, function(p) {
# and derive the parent material from the 150-200cm interval
p2 <- glom(p, 25, 100, truncate = TRUE)
p2$thickness <- p2$bottom - p2$top
# mix colors
clrs <- na.omit(horizons(p2)[,c('matrix_color_munsell','thickness')])
mixMunsell(clrs$matrix_color_munsell, w = clrs$thickness)$munsell
})
jacobs2000$c_horizon_color <- profileApply(jacobs2000, function(p) {
# and derive the parent material from the 150-200cm interval
p2 <- glom(p, 150, 200, truncate = TRUE)
p2$thickness <- p2$bottom - p2$top
# mix colors
clrs <- na.omit(horizons(p2)[,c('matrix_color_munsell','thickness')])
mixMunsell(clrs$matrix_color_munsell, w = clrs$thickness)$munsell
})
# segment profile into 1cm slices (for proper depth weighting)
jacobs2000$rubif <- profileApply(jacobs2000, function(p) {
# sum the melanization index over the 0-100cm interval
p2 <- segment(p, 25:100)
ccol <- parseMunsell(p$c_horizon_color, convertColors = FALSE)
sum(harden.rubification(
hue = p2$hue,
chroma = as.numeric(p2$chroma),
hue_ref = ccol$hue,
chroma_ref = as.numeric(ccol$chroma)
), na.rm = TRUE)
})
jacobs2000$rubiforder <- order(jacobs2000$rubif)
# segment profile into 1cm slices (for proper depth weighting)
jacobs2000$melan <- profileApply(jacobs2000, function(p) {
# sum the melanization index over the 0-100cm interval
p2 <- segment(p, 0:25)
ccol <- parseMunsell(p$c_horizon_color, convertColors = FALSE)
sum(harden.melanization(
value = as.numeric(p2$value),
value_ref = as.numeric(ccol$value)), na.rm = TRUE)
})
jacobs2000$melanorder <- order(jacobs2000$melan)
# Plot in order of increasing Rubification index
par(mar=c(1,0,1,0))
plotSPC(jacobs2000, axis.line.offset = -1,
color = "matrix_color",
label = "rubif",
plot.order = jacobs2000$rubiforder)
title("Modified Harden Rubification Index")
# Add [estimated] parent material color swatches
.trash <- lapply(seq_along(jacobs2000$c_horizon_color), function(i) {
rect(i - 0.15, 230, i + 0.15, 220,
col = parseMunsell(jacobs2000$surface_color[jacobs2000$rubiforder[i]]))
rect(i - 0.15, 245, i + 0.15, 235,
col = parseMunsell(jacobs2000$b_horizon_color[jacobs2000$rubiforder[i]]))
rect(i - 0.15, 260, i + 0.15, 250,
col = parseMunsell(jacobs2000$c_horizon_color[jacobs2000$rubiforder[i]]))
})
# Plot in order of increasing Melanization index
par(mar=c(1,0,1,0))
plotSPC(jacobs2000, axis.line.offset = -1,
color = "matrix_color",
label = "melan",
plot.order = jacobs2000$melanorder)
title("Modified Harden Melanization Index")
# Add [estimated] parent material color swatches
.trash <- lapply(seq_along(jacobs2000$c_horizon_color), function(i) {
rect(i - 0.15, 230, i + 0.15, 220,
col = parseMunsell(jacobs2000$surface_color[jacobs2000$melanorder[i]]))
rect(i - 0.15, 245, i + 0.15, 235,
col = parseMunsell(jacobs2000$b_horizon_color[jacobs2000$melanorder[i]]))
rect(i - 0.15, 260, i + 0.15, 250,
col = parseMunsell(jacobs2000$c_horizon_color[jacobs2000$melanorder[i]]))
})
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