aqp (version 1.18)

aggregateColor: Summarize Soil Colors

Description

Summarize soil color data, weighted by occurrence and horizon thickness.

Usage

aggregateColor(x, groups = "genhz", col = "soil_color", k=NULL, profile_wt=NULL)

Arguments

x

a SoilProfileCollection object

groups

the name of a horizon or site attribute used to group horizons, see examples

col

the name of a horizon-level attribute with soil color specified in hexadecimal (i.e. "#rrggbb")

k

single integer specifiying the number of colors discretized via PAM, see details

profile_wt

the name of a site-level attribute used to modify weighting, e.g. area

Value

A list with the following components:

scaled.data

a list of colors and associated weights, one item for each generalized horizon label with at least one color specified in the source data

aggregate.data

a data.frame of weighted-mean colors, one row for each generalized horizon label with at least one color specified in the source data

Details

Weights are computed by: w_i = sqrt(sum(thickness_i)) * n_i where w_i is the weight associated with color i, thickness_i is the total thickness of all horizons associated with the color i, and n_i is the number of horizons associated with color i. Weights are computed within groups specified by groups.

See Also

generalize.hz

Examples

# NOT RUN {
# load some example data
data(sp1, package='aqp')

# upgrade to SoilProfileCollection and convert Munsell colors
sp1$soil_color <- with(sp1, munsell2rgb(hue, value, chroma))
depths(sp1) <- id ~ top + bottom
site(sp1) <- ~ group

# generalize horizon names
n <- c('O', 'A', 'B', 'C')
p <- c('O', 'A', 'B', 'C')
sp1$genhz <- generalize.hz(sp1$name, n, p)

# aggregate colors over horizon-level attribute: 'genhz'
a <- aggregateColor(sp1, groups = 'genhz', col = 'soil_color')

# aggregate colors over site-level attribute: 'group'
a <- aggregateColor(sp1, groups = 'group', col = 'soil_color')

# aggregate colors over site-level attribute: 'group'
# discretize colors to 4 per group
a <- aggregateColor(sp1, groups = 'group', col = 'soil_color', k = 4)

# aggregate colors over depth-slices
s <- slice(sp1, c(5, 10, 15, 25, 50, 100, 150) ~ soil_color)
s$slice <- paste0(s$top, ' cm')
s$slice <- factor(s$slice, levels=guessGenHzLevels(s, 'slice')$levels)
a <- aggregateColor(s, groups = 'slice', col = 'soil_color')

# }
# NOT RUN {
# optionally plot with helper function
if(require(sharpshootR))
  aggregateColorPlot(a)
# }
# NOT RUN {
# a more interesting example
# }
# NOT RUN {
data(loafercreek, package = 'soilDB')

# generalize horizon names using REGEX rules
n <- c('Oi', 'A', 'BA','Bt1','Bt2','Bt3','Cr','R')
p <- c('O', '^A$|Ad|Ap|AB','BA$|Bw', 
'Bt1$|^B$','^Bt$|^Bt2$','^Bt3|^Bt4|CBt$|BCt$|2Bt|2CB$|^C$','Cr','R')
loafercreek$genhz <- generalize.hz(loafercreek$hzname, n, p)

# remove non-matching generalized horizon names
loafercreek$genhz[loafercreek$genhz == 'not-used'] <- NA
loafercreek$genhz <- factor(loafercreek$genhz)

a <- aggregateColor(loafercreek, 'genhz')

# plot results with helper function
par(mar=c(1,4,4,1))
aggregateColorPlot(a, print.n.hz = TRUE)

# inspect aggregate data
a$aggregate.data
# }