hz_segment: Segmenting of Soil Horizon Data by Depth Interval

In aqp: Algorithms for Quantitative Pedology

Segmenting of Soil Horizon Data by Depth Interval

Description

This function segments or subdivides horizon data from a SoilProfileCollection or data.frame by depth interval (e.g. c(0, 10), c(0, 50), or 25:100). This results in horizon records being split at the specified depth intervals, which duplicates the original horizon data but also adds new horizon depths. In addition, labels (i.e. "segment_id") are added to each horizon record that correspond with their depth interval (e.g. 025-100). This function is intended to harmonize horizons to a common support (i.e. depth interval) for further aggregation or summary. See the examples.

Usage

hz_segment(object, intervals, trim = TRUE, depthcols = c("top", "bottom"))

segment(object, intervals, trim = TRUE, hzdepcols = c("top", "bottom"))

Arguments

object	either a SoilProfileCollection or data.frame
intervals	a vector of integers over which to slice the horizon data (e.g. c(25, 100) or 25:100)
trim	logical, when TRUE horizons in object are truncated to the min/max specified in intervals. When FALSE, those horizons overlapping an interval are marked as such. Care should be taken when specifying more than one depth interval and trim = FALSE.
depthcols	a character vector of length 2 specifying the names of the horizon depths (e.g. c("top", "bottom")), only necessary if object is a
hzdepcols	deprecated being replaced by depthcols.

Details

hz_segment() performs no aggregation or resampling of the source data, rather, labels are added to horizon records for subsequent aggregation or summary. This makes it possible to process a very large number of records outside of the constraints associated with e.g. slice() or slab().

Value

Either a SoilProfileCollection or data.frame with the original horizon data segmented by depth intervals. There are usually more records in the resulting object, one for each time a segment interval partially overlaps with a horizon. A new column called segment_id identifying the depth interval is added.

Author(s)

Stephen Roecker

See Also

dice(), glom(), hz_dissolve(), hz_lag(), hz_intersect()

Examples

# example data
data(sp1)

# upgrade to SPC
depths(sp1) <- id ~ top + bottom

# segment and trim
z <- hz_segment(sp1, intervals = c(0, 10, 20, 30), trim = TRUE)

# display segment labels
# note that there are new horizon boundaries at segments
par(mar = c(0, 0, 3, 1))
plotSPC(z, color = 'segment_id', width = 0.3)

# highlight new horizon records
par(mar = c(0, 0, 2, 1))
plotSPC(z, color = NA, default.color = NA, width = 0.3, lwd = 1)
plotSPC(sp1, color = NA, default.color = NA, 
width = 0.3, lwd = 3, add = TRUE, name = NA, print.id = FALSE)
legend('top', horiz = TRUE, 
legend = c('original', 'segmented'), 
lwd = c(1, 3), cex = 0.85, bty = 'n')


# same results as slab()
# 10 random profiles
s <- lapply(1:10, random_profile, n_prop = 1, SPC = TRUE, method = 'random_walk')
s <- combine(s)

a.slab <- slab(s, fm = ~ p1, slab.structure = c(0, 10, 20, 30), slab.fun = mean, na.rm = TRUE)

z <- hz_segment(s, intervals = c(0, 10, 20, 30), trim = TRUE)
z <- horizons(z)
z$thick <- z$bottom - z$top

a.segment <- sapply(split(z, z$segment_id), function(i) {
  weighted.mean(i$p1, i$thick)
})


res <- data.frame(
  slab = a.slab$value,
  segment = a.segment,
  diff = a.slab$value - a.segment
)

print(res)
res$diff < 0.001



data(sp5)

# segment by upper 25-cm
test1 <- hz_segment(sp5, intervals = c(0, 100))
print(test1)
nrow(test1)
print(object.size(test1), units = "Mb")

# segment by 1-cm increments
test2 <- hz_segment(sp5, intervals = 0:100)
print(test2)
nrow(test2)
print(object.size(test2), units = "Mb")


# segment and aggregate
test3 <- hz_segment(horizons(sp5), 
                 intervals = c(0, 5, 15, 30, 60, 100, 200), 
                 depthcols = c("top", "bottom")
)
test3$hzthk <- test3$bottom - test3$top
test3_agg <- by(test3, test3$segment_id, function(x) {
  data.frame(
    hzID = x$hzID[1],
    segment_id = x$segment_id[1],
    average = weighted.mean(x$clay, w = x$hzthk)
  )
})
test3_agg <- do.call("rbind", test3_agg)

head(test3_agg)

aqp documentation built on Oct. 19, 2024, 5:06 p.m.