296 Soil Profiles from the La Rochelle region of France (F. Carre and Girard, 2002)
SoilProfileCollection object
296 Soil Profiles from the La Rochelle region of France (F. Carre and Girard, 2002). These data can be found on the OSACA project page (http://eusoils.jrc.ec.europa.eu/projects/OSACA/).
These data are c/o F. Carre (Florence.CARRE@ineris.fr).
F. Carre, M.C. Girard. 2002. Quantitative mapping of soil types based on regression kriging of taxonomic distances with landform and land cover attributes. Geoderma. 110: 241–263.
if (FALSE) { # \dontrun{
library(scales)
data(sp5)
par(mar=c(1,1,1,1))
# plot a random sampling of profiles
s <- sample(1:length(sp5), size=25)
plot(sp5[s, ], divide.hz=FALSE)
# plot the first 100 profiles, as 4 rows of 25, hard-coding the max depth
layout(matrix(c(1,2,3,4), ncol=1), height=c(0.25,0.25,0.25,0.25))
plot(sp5[1:25, ], max.depth=300)
plot(sp5[26:50, ], max.depth=300)
plot(sp5[51:75, ], max.depth=300)
plot(sp5[76:100, ], max.depth=300)
# 4x1 matrix of plotting areas
layout(matrix(c(1,2,3,4), ncol=1), height=c(0.25,0.25,0.25,0.25))
# plot profiles, with points added to the mid-points of randomly selected horizons
sub <- sp5[1:25, ]
plot(sub, max.depth=300) ; mtext('Set 1', 2, line=-0.5, font=2)
y.p <- profileApply(sub, function(x) {
s <- sample(1:nrow(x), 1)
h <- horizons(x); with(h[s,], (top+bottom)/2)
})
points(1:25, y.p, bg='white', pch=21)
# plot profiles, with arrows pointing to profile bottoms
sub <- sp5[26:50, ]
plot(sub, max.depth=300); mtext('Set 2', 2, line=-0.5, font=2)
y.a <- profileApply(sub, function(x) max(x))
arrows(1:25, y.a-50, 1:25, y.a, len=0.1, col='white')
# plot profiles, with points connected by lines: ideally reflecting some kind of measured data
sub <- sp5[51:75, ]
plot(sub, max.depth=300); mtext('Set 3', 2, line=-0.5, font=2)
y.p <- 20*(sin(1:25) + 2*cos(1:25) + 5)
points(1:25, y.p, bg='white', pch=21)
lines(1:25, y.p, lty=2)
# plot profiles, with polygons connecting horizons with max clay content (+/-) 10 cm
sub <- sp5[76:100, ]
y.clay.max <- profileApply(sub, function(x) {
i <- which.max(x$clay)
h <- horizons(x)
with(h[i, ], (top+bottom)/2)
} )
plot(sub, max.depth=300); mtext('Set 4', 2, line=-0.5, font=2)
polygon(c(1:25, 25:1), c(y.clay.max-10, rev(y.clay.max+10)),
border='black', col=rgb(0,0,0.8, alpha=0.25))
points(1:25, y.clay.max, pch=21, bg='white')
# close plot
dev.off()
# plotting parameters
yo <- 100 # y-offset
sf <- 0.65 # scaling factor
# plot profile sketches
par(mar=c(0,0,0,0))
plot(sp5[1:25, ], max.depth=300, y.offset=yo, scaling.factor=sf)
# optionally add describe plotting area above profiles with lines
# abline(h=c(0,90,100, (300*sf)+yo), lty=2)
# simulate an environmental variable associated with profiles (elevation, etc.)
r <- vector(mode='numeric', length=25)
r[1] <- -50 ; for(i in 2:25) {r[i] <- r[i-1] + rnorm(mean=-1, sd=25, n=1)}
# rescale
r <- rescale(r, to=c(80, 0))
# illustrate gradient with points/lines/arrows
lines(1:25, r)
points(1:25, r, pch=16)
arrows(1:25, r, 1:25, 95, len=0.1)
# add scale for simulated gradient
axis(2, at=pretty(0:80), labels=rev(pretty(0:80)), line=-1, cex.axis=0.75, las=2)
# depict a secondary environmental gradient with polygons (water table depth, etc.)
polygon(c(1:25, 25:1), c((100-r)+150, rep((300*sf)+yo, times=25)),
border='black', col=rgb(0,0,0.8, alpha=0.25))
} # }