R/getSurfaceHorizonDepth.R
getSurfaceHorizonDepth.RdFind the thickness of horizon designations, or any other character patterns, that are continuous from the soil surface (depth = 0 or shallowest depth in profile).
getSurfaceHorizonDepth(
p,
pattern,
hzdesgn = hzdesgnname(p, required = TRUE),
simplify = TRUE
)
getMineralSoilSurfaceDepth(
p,
hzdesgn = hzdesgnname(p, required = TRUE),
pattern = "O",
simplify = TRUE
)
getPlowLayerDepth(
p,
hzdesgn = hzdesgnname(p, required = TRUE),
pattern = "^Ap[^b]*",
simplify = TRUE
)a SoilProfileCollection
a regular expression pattern to match for all horizons to be considered part of the "surface".
column name containing horizon designation. Default: hzdesgnname(p, required = TRUE).
logical. Return single profile results as vector (default: TRUE) or data.frame (FALSE)
a numeric value corresponding to the bottom depth of the last horizon matching 'pattern' that is contiguous with other matching horizons up to the soil surface. If length(p) > 1 then a data.frame containing profile ID, horizon ID, top or bottom depths, horizon designation and pattern.
The horizon designation to match is specified with the regular expression pattern 'pattern'. All horizons matching that pattern, that are continuous from the soil surface, count towards the depth / thickness value that is ultimately returned. For instance: horizon designations: A1-A2-A3-C-Ab , would return A3 bottom depth given pattern = "^A[1-9]*$".
getSurfaceHorizonDepth is used by getPlowLayerDepth for matching Ap horizons; and, it is used by getMineralSoilSurfaceDepth to find the thickness of O horizons in lieu of lab data.
library(aqp)
data(sp1, package = 'aqp')
depths(sp1) <- id ~ top + bottom
site(sp1) <- ~ group
p <- sp1[1]
q <- sp1[2]
# look at horizon designations in p and q
p$name
#> [1] "A1" "A2" "AB" "BA" "Bt" "Rt"
q$name
#> [1] "Oi" "A" "C1" "C2"
# thickness of all surface horizons containing A
getSurfaceHorizonDepth(p, pattern = 'A', hzdesgn = 'name')
#> [1] 57
# thickness of all surface horizons that start with A
getSurfaceHorizonDepth(p, pattern = '^A', hzdesgn = 'name')
#> [1] 49
# thickness of all surface horizons that start with A, and the A is not followed by B
getSurfaceHorizonDepth(p, pattern = '^A[^B]*', hzdesgn = 'name')
#> [1] 49
# thickness of all surface horizons that start with A
# followed by a number from _2_ to 9 (returns ZERO)
getSurfaceHorizonDepth(p, pattern = '^A[2-9]*', hzdesgn = 'name')
#> [1] 49
# getPlowLayerDepth matches first two horizons in fake Ap horizon data with "buried Ap"
p$aphorizons <- c("Ap1","Ap2","AB", rep('C', nrow(p) - 4), "Apb")
getPlowLayerDepth(p, hzdesgn = 'aphorizons')
#> [1] 14
# getMineralSoilSurfaceDepthmatches first 3 horizons in fake O horizon data
p$ohorizons <- c("Oi1","Oi2","Oe", rep('C', nrow(p) - 4), "2C")
getMineralSoilSurfaceDepth(p, hzdesgn='ohorizons')
#> [1] 49
# matches first Oi horizon with original horizon designations of pedon 2
getMineralSoilSurfaceDepth(q, hzdesgn='name')
#> [1] 5