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)

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

SoilProfileCollection object

Author

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, ]
#>          id name top bottom   K   Mg  Ca CEC_7 ex_Ca_to_Mg sand silt clay   CF
#> 2    colusa  ABt  NA      8 0.2 23.7 5.6  21.4        0.23   42   31   27 0.27
#> 6     glenn   Bt  NA     34 0.3 18.9 4.5  27.5        0.20   49   18   34 0.84
#> 7     kings    A  NA      4 0.2 12.1 1.4  23.7        0.58   43   55    3 0.50
#> 8     kings  Bt1  NA     13 0.6 12.1 7.0  18.0        0.51   36   49   15 0.75
#> 12 mariposa  Bt2  NA     34 0.3 44.3 6.2  34.1        0.14   36   33   31 0.71
#>    hzID
#> 2     2
#> 6     6
#> 7     7
#> 8     8
#> 12   12

# create gaps by removing logic errors
x <- HzDepthLogicSubset(sp4, byhz = TRUE)
#> dropping horizons with invalid depth logic, see `metadata(x)$removed.horizons`

# inspect
par(mar = c(0, 0, 0, 1))
plotSPC(x, width = 0.3, default.color = 'royalblue', name = 'hzID')


z <- fillHzGaps(x, flag = TRUE)

plotSPC(z, width = 0.3, color = '.filledGap', name = 'hzID', show.legend = FALSE)


# 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
#> This is already a SoilProfileCollection-class object, doing nothing.

# 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 ~ .)
#> dropping profiles with invalid depth logic, see `metadata(x)$removed.profiles`
#> OBF: 4.5
plotSPC(d, color = 'Ca', show.legend = FALSE)

plotSPC(d, color = '.filledGap', show.legend = FALSE)