collapseHz: Collapse Horizons within Profiles Based on Pattern Matching

In aqp: Algorithms for Quantitative Pedology

Collapse Horizons within Profiles Based on Pattern Matching

Description

Combines layers and aggregates data by grouping adjacent horizons which match pattern in hzdesgn or, alternately, share a common value in by argument. Numeric properties are combined using the weighted average, and other properties are derived from the dominant condition based on thickness of layers and values in each group.

Usage

collapseHz(
  x,
  pattern = NULL,
  by = NULL,
  hzdesgn = hzdesgnname(x, required = TRUE),
  FUN = function(x, pattern, hzdesgn, ...) grepl(pattern, x[[hzdesgn]], ignore.case =
    FALSE),
  ...,
  AGGFUN = NULL,
  ignore_numerics = NULL,
  na.rm = FALSE
)

Arguments

x	A SoilProfileCollection
pattern	character. A regular expression pattern to match in hzdesgn column. Default: NULL.
by	character. A column name specifying horizons that should be combined. Aggregation will be applied to adjacent groups of layers within profiles that have the same value in by. Used in lieu of pattern and hzdesgn. Default: NULL.
hzdesgn	character. Any character column containing horizon-level identifiers. Default: hzdesgnname(x, required = TRUE).
FUN	function. A function that returns a logical vector equal in length to the number of horizons in x. Used only when pattern is specified. See details.
...	Additional arguments passed to the matching function FUN.
AGGFUN	list. A named list containing custom aggregation functions. List element names should match the column name that they transform. The functions defined should take three arguments: x (a vector of horizon property values), top (a vector of top depths), and bottom (a vector of bottom depths). Default: NULL applies weighted.mean() to all numeric columns not listed in ignore_numerics and takes the dominant condition (value with greatest aggregate thickness sum) for all other columns. See details.
ignore_numerics	character. Vector of column names that contain numeric values which should not be aggregated using weighted.mean(). For example, soil color "value" and "chroma".
na.rm	logical. If TRUE NA values are ignored when calculating min/max boundaries for each group and in weighted averages. If FALSE NA values are propagated to the result. Default: FALSE.

Details

If a custom matching 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.

Custom aggregation functions defined in the AGGFUN argument should either return a single vector value for each group*column combination, or should return a data.frame object with named columns. If the input column name is used as a column name in the result data.frame, then the values of that column name in the result SoilProfileCollection will be replaced by the output of the aggregation function. See examples.

Value

A SoilProfileCollection

Author(s)

Andrew G. Brown

See Also

hz_dissolve()

Examples

data(jacobs2000)

# calculate a new SPC with genhz column based on patterns
new_labels <- c("A", "E", "Bt", "Bh", "C")
patterns <- c("A", "E", "B.*t", "B.*h", "C")
jacobs2000_gen <- generalizeHz(jacobs2000, new = new_labels, pattern = patterns)

# use existing generalized horizon labels
i <- collapseHz(jacobs2000_gen, by = "genhz")

profile_id(i) <- paste0(profile_id(i), "_collapse")

plot(
  c(i, jacobs2000),
  color = "genhz",
  name = "name",
  name.style = "center-center",
  cex.names = 1
)
 
# custom pattern argument  
j <- collapseHz(jacobs2000,
                c(
                  `A` = "^A",
                  `E` = "E",
                  `Bt` = "[ABC]+t",
                  `C` = "^C",
                  `foo` = "bar"
                ))
profile_id(j) <- paste0(profile_id(j), "_collapse")
plot(c(j, jacobs2000), color = "clay")

# custom aggregation function for matrix_color_munsell
k <- collapseHz(jacobs2000,
                pattern = c(
                  `A` = "^A",
                  `E` = "E",
                  `Bt` = "[ABC]+t",
                  `C` = "^C",
                  `foo` = "bar"
                ),
                AGGFUN = list(
                  matrix_color_munsell = function(x, top, bottom) {
                    thk <- bottom - top
                    if (length(x) > 1) {
                      xord <- order(thk, decreasing = TRUE)
                      paste0(paste0(x[xord], " (t=", thk[xord], ")"), collapse = ", ")
                    } else
                      x
                  }
                )
              )
profile_id(k) <- paste0(profile_id(k), "_collapse_custom")

unique(k$matrix_color_munsell)

# custom aggregation function for matrix_color_munsell (returns data.frame)
m <- collapseHz(jacobs2000,
                pattern = c(
                  `A` = "^A",
                  `E` = "E",
                  `Bt` = "[ABC]+t",
                  `C` = "^C",
                  `foo` = "bar"
                ),
                AGGFUN = list(
                  matrix_color_munsell = function(x, top, bottom) {
                    thk <- bottom - top
                    if (length(x) > 1) {
                      xord <- order(thk, decreasing = TRUE)
                      data.frame(matrix_color_munsell = paste0(x, collapse = ";"),
                                 n_matrix_color = length(x))
                    } else {
                      data.frame(matrix_color_munsell = x, 
                                 n_matrix_color = length(x))
                    }
                  }
                )
              )
profile_id(m) <- paste0(profile_id(m), "_collapse_custom")

m$matrix_color_munsell.n_matrix_color

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