thicknessOf: Calculate Thickness of Horizons Matching Logical Criteria

In aqp: Algorithms for Quantitative Pedology

Calculate Thickness of Horizons Matching Logical Criteria

Description

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 default FUN definition 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 FUN definition.
method	character. Either "cumulative" (default) or "minmax". See details.
prefix	character. Column prefix for calculated thickvar (and depthvar for method="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 in method="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 NA values in summaries of thickness and in matching? Default: FALSE
...	Additional arguments passed to the matching function FUN.

Details

The two thickness methods currently available are:

• method="cumulative" (default): cumulative thickness of horizons where FUN returns true

• method="minmax": maximum bottom depth minus minimum top depth of horizons where FUN returns 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.

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.

Examples

data("jacobs2000")

# cumulative thickness of horizon designations matching "Bt"
thicknessOf(jacobs2000, "Bt")

# maximum bottom depth minus minimum top depth of horizon designations matching "Bt"
thicknessOf(jacobs2000, "Bt", prefix = "Bt_", method = "minmax")

# cumulative thickness of horizon designations matching "A|B"
thicknessOf(jacobs2000, "A|B", prefix = "AorB_")

# maximum bottom depth minus minimum top depth of horizon designations matching "A|B"
thicknessOf(jacobs2000, "A|B", method = "minmax", prefix = "AorB_")
# 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)

aqp documentation built on Oct. 19, 2024, 5:06 p.m.