\name{sp2}
\alias{sp2}
\docType{data}
\title{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.}
\usage{data(sp2)}
\format{
  A data frame with 154 observations on the following 21 variables.
  \describe{
    \item{\code{id}}{profile id}
    \item{\code{surface}}{dated surface}
    \item{\code{top}}{horizon top in cm}
    \item{\code{bottom}}{horizon bottom in cm}
    \item{\code{bound_distinct}}{horizon lower boundary distinctness class}
    \item{\code{bound_topography}}{horizon lower boundary topography class}
    \item{\code{name}}{horizon name}
    \item{\code{texture}}{USDA soil texture class}
    \item{\code{prop}}{field-estimated clay content}
    \item{\code{structure_grade}}{soil structure grade}
    \item{\code{structure_size}}{soil structure size}
    \item{\code{structure_type}}{soil structure type}
    \item{\code{stickiness}}{stickiness}
    \item{\code{plasticity}}{plasticity}
    \item{\code{field_ph}}{field-measured pH}
    \item{\code{hue}}{Munsell hue}
    \item{\code{value}}{Munsell value}
    \item{\code{chroma}}{Munsell chroma}
    \item{\code{r}}{RGB red component}
    \item{\code{g}}{RGB green component}
    \item{\code{b}}{RGB blue component}
    \item{\code{soil_color}}{R-friendly encoding of soil color}
  }
}

\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/}
\author{Dylan E. Beaudette}

\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)
}

}
\keyword{datasets}