aqp: sp2 – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

sp2

Honcut Creek Soil Profile Data

Description

A collection of 18 soil profiles, consisting of select soil morphologic attributes, associated with a stratigraphic study conducted near Honcut Creek, California.

Format

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

Author(s)

Dylan E. Beaudette

Source

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.

References

http://casoilresource.lawr.ucdavis.edu/

Examples

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)
}

aqp

Algorithms for Quantitative Pedology

v1.29

GPL (>= 3)

Authors

Dylan Beaudette [aut, cre], Pierre Roudier [aut, ctb], Andrew Brown [aut, ctb]

Initial release

2021-04-05

sp2