aqp (version 1.4)

SoilProfileCollection-class: SoilProfileCollection Class

Description

Basic class for storing soil profile collections, associated site data, and metadata.

Objects from the Class

Objects can be created by calls of the form new("SoilProfileCollection", ...).

Examples

## 1. test validity methods

# this should work fine
data(sp1)
depths(sp1) <- id ~ top + bottom

# horizon logic can be tested via data.frame and 
# test_hz_logic(i, topcol, bottomcol, test.NA=TRUE, strict=FALSE)

## 2. use the digest library to detect duplicate data
data(sp1)

# make a copy, make new IDs, and stack
s.1 <- sp1 
s.2 <- sp1
s.2$id <- paste(s.2$id, '-copy', sep='')
s <- rbind(s.1, s.2)
depths(s) <- id ~ top + bottom

# digests are computed from horizon-level data only
# horizon boundaries and 'prop'
# result is an index of unqique profiles
if(require(digest)) {
	u <- unique(s, vars=c('top', 'bottom', 'prop'))
}

# compare with and without dupes:
# note subsetting of SoilProfileCollection
cbind(dupes=length(s), no.dupes=length(s[u, ]))

## 3. concatonate SoilProfileCollection objects
require(plyr)
d <- ldply(1:10, random_profile)

# promote to SoilProfileCollection and plot
depths(d) <- id ~ top + bottom
plot(d)

# split into new SoilProfileCollection objects by index
d.1 <- d[1, ]
d.2 <- d[2, ]
d.345 <- d[3:5, ]

# recombine
d.new <- rbind(d.345, d.1, d.2)
plot(d.new)


# these next examples should throw an error
# insert a missing horizon boundary
data(sp1)
sp1$top[1] <- NA
depths(sp1) <- id ~ top + bottom

# insert a bogus horizon boundary
## NOTE: this is currently valid, as this check breaks slice(SPC, ...)
data(sp1)
sp1$top[2] <- 30
depths(sp1) <- id ~ top + bottom