New S4 Classes and Methods added to AQP (Algorithms for Quantitative Pedology) Package

Submitted by dylan on Thu, 2011-10-20 21:52.

Thanks to some major help from Pierre Roudier, the aqp package now has some new S4-style classes and methods-- custom tailored to the complexities of soil profile data. These new classes/methods are available in the aqp development package, found on our R-Forge repository. An update to CRAN is pending. A couple of examples are presented below. Note that methods may change at any time, so consider these examples preliminary.

Soil Property Data ModelSoil Property Data Model

 
Examples

library(aqp) # need at least version 0.99-8.42

# init some sample data:
data(sp1)

# add some fake coordinates
sp1$x <- rnorm(nrow(sp1))
sp1$y <- rnorm(nrow(sp1))

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

# init SoilProfileCollection
depths(sp1) <- id ~ top + bottom

# move 'group' to site data slot
site(sp1) <- ~ group

# plot the data, ordered by 'group'
plot(sp1, plot.order=order(sp1$group))

# test a more realistic data set
data(ca630)

# combine into single DF
ca <- join(ca630$lab, ca630$site)

# throw-out data missing MLRA
ca <- subset(ca, subset=ca$mlra != '')

# init SPC
depths(ca) <- pedon_key ~ hzn_top + hzn_bot

# extract site data
site(ca) <- ~ mlra + county + ssa + lon + lat + cntrl_depth_to_top + cntrl_depth_to_bot + sampled_taxon_name

# extract spatial data as SpatialPoints
coordinates(ca) <- ~ lon + lat
# assign CRS
proj4string(ca) <- '+proj=latlong +datum=WGS84'


# simple map: syntax isn't as nice as it could be
f <- factor(site(ca)$mlra, levels=c('18','22A','22'))
plot(ca@sp, pch=16, col=f, axes=TRUE)
legend('topright', legend=levels(f), col=1:3, pch=16)


# convert to SpatialPointsDataFrame by subsetting horizon data (first horizon)
ca.SPDF <- ca[, 1]
spplot(ca.SPDF, 'bs_7', col.regions=bpy.colors(10))

# coerce to SpatialPointsDataFrame (only site data are retained!)
ca.SPDF <- as(ca, 'SpatialPointsDataFrame')
ca.SPDF$mlra <- factor(ca.SPDF$mlra, levels=c('18','22A','22'))

# do some aggregation:
# using groups defined in @site, to aggregate properties stored in @horizons
a <- slab(ca, fm=mlra ~ bs_7)
a$mlra <- factor(a$mlra, levels=c('18','22A','22'))

# plot aggregate data
xyplot(
top ~ p.q50 | mlra, data=a, lower=a$p.q25, upper=a$p.q75,
ylim=c(160,-5), alpha=0.5, scales=list(alternating=1, y=list(tick.num=7)),
panel=panel.depth_function, prepanel=prepanel.depth_function,
strip=strip.custom(bg='Yellow'), layout=c(3,1),
ylab='Depth (cm)', xlab='% Base Saturation', par.settings=list(superpose.line=list(col='black'))
)

 
More examples to follow soon!