This function calculates the cumulative (method="cumulative", default) or maximum difference between (method="minmax") horizons within a profile that match a defined pattern (pattern) or, more generally, any set of horizon-level logical expressions encoded in a function (FUN).
Usage
thicknessOf(
x,
pattern = NULL,
hzdesgn = hzdesgnname(x, required = TRUE),
method = "cumulative",
prefix = "",
thickvar = "thickness",
depthvars = horizonDepths(x),
FUN = function(x, pattern, hzdesgn, ...) grepl(pattern, x[[hzdesgn]]),
na.rm = FALSE,
...
)Arguments
- x
A SoilProfileCollection
- pattern
character. A pattern to match in
hzdesgn; used with the defaultFUNdefinition for regular expression pattern matching on horizons.- hzdesgn
character. A column containing horizon designations or other horizon-level character label used to identify matches; used with the default
FUNdefinition.- method
character. Either
"cumulative"(default) or"minmax". See details.- prefix
character. Column prefix for calculated
thickvar(anddepthvarformethod="minmax") column results. Default:"".- thickvar
character Length
1. Column name to use for calculated thickness column. Default:"thickness"- depthvars
character. Length
2. Column names to use for calculated minimum top depth and maximum bottom depth inmethod="minmax". Default:horizonDepths(x)- FUN
function. A function that returns a logical vector equal in length to the number of horizons in
x. See details.- na.rm
logical. Omit
NAvalues in summaries of thickness and in matching? Default:FALSE- ...
Additional arguments passed to the matching function
FUN.
Value
A data.frame-like object (corresponding to the aqp_df_class() of x) with one row per profile in x. First column is always the profile ID which is followed by "thickness". In method="minmax" the upper and lower boundaries used to calculate "thickness" are also returned as "tmin" and "tmax" columns, respectively.
Details
The two thickness methods currently available are:
method="cumulative"(default): cumulative thickness of horizons whereFUNreturns truemethod="minmax": maximum bottom depth minus minimum top depth of horizons whereFUNreturns true
If a custom function (FUN) is used, it should accept arbitrary additional arguments via an ellipsis (...).
It is not necessary to do anything with arguments, but the result should match the number of horizons found in the input SoilProfileCollection x.
Examples
data("jacobs2000")
# cumulative thickness of horizon designations matching "Bt"
thicknessOf(jacobs2000, "Bt")
#> id thickness
#> 1 92-1 110
#> 2 92-2 99
#> 3 92-3 111
#> 4 92-4 0
#> 5 92-5 26
#> 6 92-6 64
#> 7 92-7 0
# maximum bottom depth minus minimum top depth of horizon designations matching "Bt"
thicknessOf(jacobs2000, "Bt", prefix = "Bt_", method = "minmax")
#> id Bt_top Bt_bottom Bt_thickness
#> 1 92-1 43 153 110
#> 2 92-2 46 145 99
#> 3 92-3 64 175 111
#> 4 92-4 Inf -Inf 0
#> 5 92-5 109 135 26
#> 6 92-6 104 168 64
#> 7 92-7 Inf -Inf 0
# cumulative thickness of horizon designations matching "A|B"
thicknessOf(jacobs2000, "A|B", prefix = "AorB_")
#> id AorB_thickness
#> 1 92-1 131
#> 2 92-2 117
#> 3 92-3 136
#> 4 92-4 20
#> 5 92-5 54
#> 6 92-6 110
#> 7 92-7 43
# maximum bottom depth minus minimum top depth of horizon designations matching "A|B"
thicknessOf(jacobs2000, "A|B", method = "minmax", prefix = "AorB_")
#> id AorB_top AorB_bottom AorB_thickness
#> 1 92-1 0 156 156
#> 2 92-2 0 145 145
#> 3 92-3 0 175 175
#> 4 92-4 0 20 20
#> 5 92-5 0 135 135
#> 6 92-6 0 168 168
#> 7 92-7 0 140 140
# note that the latter includes the thickness of E horizons between the A and the B
# when using a custom function (be sure to accept ... and consider the effect of NA values)
# calculate cumulative thickness of horizons containing >18% clay
thicknessOf(jacobs2000, prefix = "claygt18_",
FUN = function(x, ...) !is.na(x[["clay"]]) & x[["clay"]] > 18)
#> id claygt18_thickness
#> 1 92-1 170
#> 2 92-2 167
#> 3 92-3 81
#> 4 92-4 0
#> 5 92-5 0
#> 6 92-6 49
#> 7 92-7 0