aqp (version 0.99-8.56)

sp1: Soil Profile Data Example 1

Description

Soil profile data from Pinnacles National Monument, CA.

Usage

data(sp1)

References

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

Examples

data(sp1)
# convert colors
sp1$soil_color <- with(sp1, munsell2rgb(hue, value, chroma))

## promote to SoilProfileCollection
depths(sp1) <- id ~ top + bottom
site(sp1) <- ~ group

# extract 1-unit thick slices of 'prop' at defined depths
s <- slice(sp1, 0:25 ~ prop)
plot(s, name='prop')

# try again, this time with the horizon name and color
s <- slice(sp1, 0:25 ~ name + soil_color)
plot(s)


# aggregate all profiles into 1cm depth slices, 
# using data from column 'prop'
s1 <- soil.slot.multiple(sp1, fm= ~ prop)

# check mean +/- 1SD
xyplot(top ~ p.mean + I(p.mean + p.sd) + I(p.mean - p.sd), 
data=s1, type='S', horizontal=TRUE, col=1, lty=c(1,2,2), 
panel=panel.superpose, ylim=c(110,-5))

# check median & IQR
xyplot(top ~ p.q50 + p.q25 + p.q75, 
data=s1, type='S', horizontal=TRUE, col=1, lty=c(1,2,2), 
panel=panel.superpose, ylim=c(110,-5))

# other segment sizes
# 5cm
s5 <- soil.slot.multiple(sp1, fm= ~ prop, seg_size=5)

# 10cm segments:
s10 <- soil.slot.multiple(sp1, fm= ~ prop, seg_size=10)

# 20cm
s20 <- soil.slot.multiple(sp1, fm= ~ prop, seg_size=20)

# variation in segment-weighted mean property: very little
sapply(
list(s1,s5,s10,s20), 
function(i) {
	with(i, sum((bottom - top) * p.mean) / sum(bottom - top)) 
	}
)

# combined viz
g2 <- make.groups("1cm interval"=s1, "5cm interval"=s5, 
"10cm interval"=s10, "20cm interval"=s20)

# note special syntax for plotting step function
xyplot(cbind(top,bottom) ~ p.mean, groups=which, data=g2, id=g2$which,
panel=panel.depth_function, ylim=c(250,-10), 
scales=list(y=list(tick.number=10)), xlab='Property', 
ylab='Depth (cm)', main='Soil Profile Averaging by Slotting',
auto.key=list(columns=4, points=FALSE, lines=TRUE)
)