fillHzGaps: Find and Fill Horizon Gaps

In aqp: Algorithms for Quantitative Pedology

Find and Fill Horizon Gaps

Description

This function attempts to find "gaps" in the horizon records of a SoilProfileCollection object and fill with placeholder horizons (profile ID, horizon ID, to/bottom depths, all else NA). Missing horizon records between the top of each profile and to_top, or the bottom of each profile and to_bottom are treated as gaps when those arguments are not NULL. You can use this function to prepare a potentially messy SoilProfileCollection for subsequent analyses that are sensitive to horizon sequence inconsistencies or require a conformal "rectangle" of data spanning known depths.

Gaps are defined as:

• within each profile, for horizons i to n_hz:

• ⁠bottom_i != top_i+1 (but only to i = 1:(n_hz - 1)⁠

Usage

fillHzGaps(x, flag = TRUE, to_top = 0, to_bottom = max(x))

Arguments

x	SoilProfileCollection object
flag	logical, flag empty horizons that have been added. default: TRUE
to_top	numeric, fill from shallowest top depth in each profile to specified depth? default: 0
to_bottom	numeric, fill from deepest bottom depth in each profile to specified depth? default: aqp::max(x)

Value

a possibly modified SoilProfileCollection object

Author(s)

A.G. Brown and D.E. Beaudette

Examples

data(sp4)
depths(sp4) <- id ~ top + bottom

# introduce depth logic errors
idx <- c(2, 6:7, 8, 12)
sp4$top[idx] <- NA

# check
horizons(sp4)[idx, ]

# create gaps by removing logic errors
x <- HzDepthLogicSubset(sp4, byhz = TRUE)

# check on removed horizons (hzID values)
metadata(x)$removed.horizons

# inspect
par(mar = c(0, 0, 0, 2))
plotSPC(x, width = 0.3, default.color = 'royalblue', 
name = 'hzID', name.style = 'center-center', cex.names = 0.8,
cex.id = 0.66)

# fill gaps left by HzDepthLogicSubset()
z <- fillHzGaps(x, flag = TRUE)

# graphical check
plotSPC(z, width = 0.3, color = '.filledGap', name = 'hzID', 
show.legend = FALSE, name.style = 'center-center', cex.names = 0.8,
cex.id = 0.66)

# fill top to 0 cm
z2 <- fillHzGaps(x, flag = TRUE, to_top = 0)
plotSPC(z2, width = 0.3, color = '.filledGap', name = 'hzID', show.legend = FALSE)

# fill bottom to max(SPC)
z3 <- fillHzGaps(x, flag = TRUE, to_top = 0, to_bottom = max(x))
plotSPC(z3, width = 0.3, color = '.filledGap', name = 'hzID', show.legend = FALSE)

## another example
data(sp4)
depths(sp4) <- id ~ top + bottom

# remove 1st horizons from profiles 1:4
idx <- sp4[,, .FIRST, .HZID]
replaceHorizons(sp4) <- horizons(sp4)[-idx[1:4], ]

# prepare for dice()
z <- fillHzGaps(sp4, to_top = 0, to_bottom = 50, flag = TRUE) 

# empty-horizon padding is in place for formula interface to dice()
d <- dice(z, fm = 0:50 ~ .)
plotSPC(d, color = 'Ca', show.legend = FALSE)
plotSPC(d, color = '.filledGap', show.legend = FALSE)

aqp documentation built on Sept. 8, 2023, 5:45 p.m.