Find and Fill Horizon Gaps
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))
x |
|
flag |
logical, flag empty horizons that have been added. default: |
to_top |
numeric, fill from shallowest top depth in each profile to specified depth? default: |
to_bottom |
numeric, fill from deepest bottom depth in each profile to specified depth? default: |
SoilProfileCollection object
A.G. Brown and D.E. Beaudette
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) # 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 # 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)
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