Description Usage Format Author(s) Source References Examples
A collection of 18 soil profiles, consisting of select soil morphologic attributes, associated with a stratigraphic study conducted near Honcut Creek, California.
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A data frame with 154 observations on the following 21 variables.
id
profile id
surface
dated surface
top
horizon top in cm
bottom
horizon bottom in cm
bound_distinct
horizon lower boundary distinctness class
bound_topography
horizon lower boundary topography class
name
horizon name
texture
USDA soil texture class
prop
field-estimated clay content
structure_grade
soil structure grade
structure_size
soil structure size
structure_type
soil structure type
stickiness
stickiness
plasticity
plasticity
field_ph
field-measured pH
hue
Munsell hue
value
Munsell value
chroma
Munsell chroma
r
RGB red component
g
RGB green component
b
RGB blue component
soil_color
R-friendly encoding of soil color
Dylan E. Beaudette
Busacca, Alan J.; Singer, Michael J.; Verosub, Kenneth L. 1989. Late Cenozoic stratigraphy of the Feather and Yuba rivers area, California, with a section on soil development in mixed alluvium at Honcut Creek. USGS Bulletin 1590-G.
http://casoilresource.lawr.ucdavis.edu/
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 | data(sp2)
# convert into SoilProfileCollection object
depths(sp2) <- id ~ top + bottom
# transfer site-level data
site(sp2) <- ~ surface
# generate a new plotting order, based on the dated surface each soil was described on
p.order <- order(sp2$surface)
# plot
par(mar=c(1,0,3,0))
plot(sp2, plot.order=p.order)
# setup multi-figure output
par(mfrow=c(2,1), mar=c(0,0,1,0))
# truncate plot to 200 cm depth
plot(sp2, plot.order=p.order, max.depth=200)
abline(h=200, lty=2, lwd=2)
# compute numerical distances between profiles
# based on select horizon-level properties, to a depth of 200 cm
d <- profile_compare(sp2, vars=c('prop','field_ph','hue'),
max_d=200, k=0, sample_interval=5, rescale.result=TRUE)
# plot dendrogram with ape package:
if(require(ape) & require(cluster)) {
h <- diana(d)
p <- as.phylo(as.hclust(h))
plot(p, cex=0.75, label.offset=0.01, font=1, direct='down', srt=90, adj=0.5, y.lim=c(-0.125, 0.5))
# add in the dated surface type via color
tiplabels(col=as.numeric(sp2$surface), pch=15)
# based on distance matrix values, YMMV
legend('topleft', legend=levels(sp2$surface), col=1:6, pch=15, bty='n', bg='white', cex=0.75)
}
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