mutate_profile: Transform a SPC (by profile) with a set of expressions

In aqp: Algorithms for Quantitative Pedology

Transform a SPC (by profile) with a set of expressions

Description

mutate_profile() is a function used for transforming SoilProfileCollections. Each expression is applied to site or horizon level attributes of individual profiles. This distinguishes this function from transform, which is applied to all values in a collection, regardless of which profile they came from.

Usage

mutate_profile(object, ..., col_names = NULL, horizon_level = NULL)

mutate_profile_raw(object, expr, col_names = NULL, horizon_level = NULL)

Arguments

object	A SoilProfileCollection
...	A set of comma-delimited R expressions that resolve to a transformation to be applied to a single profile e.g mutate_profile(hzdept = max(hzdept) - hzdept)
col_names	character. Optional column names. Should match the number of expressions in ....
horizon_level	logical. If TRUE results of expressions are added to the SoilProfileCollection's horizon slot, if FALSE the results are added to the site slot. If NULL (default) the results are stored in the site or horizon slot based on the number of rows in each slot compared to the length of the result calculated from the first and last profile in the collection.
expr	A list of expressions in terms of column names in site or horizon table of object

Details

If the length an expression's result matches the number of horizons, the result is stored as a horizon-level variable. If the result has length 1, it is stored as a site-level variable. In the ambiguous case where the first and last profile have only one horizon, the results are stored in the horizon slot by default. To force results into site slot use horizon_level = FALSE.

Value

A SoilProfileCollection.

Author(s)

Andrew G. Brown.

Examples

data(sp4)
depths(sp4) <- id ~ top + bottom

mutate_profile(sp4, clay_wtd_average = weighted.mean(clay, bottom - top))

data(jacobs2000)

set.seed(123)

## col_names allows for column names to be calculated
x <- mutate_profile(jacobs2000, bottom - top / sum(bottom - top),
                    col_names = paste0("relthk", floor(runif(1, 0, 100))))
x$relthk28

# mutate_profile_raw allows for lists of expressions to be evaluated
master_desgn <- c("O", "A", "E", "B", "C", "R", "L", "M")
thk_names <- paste0("thk_", master_desgn)

# calculate thickness for each horizon
x$thk <- x$bottom - x$top

## construct an arbitrary number of expressions using variable inputs
ops <- lapply(master_desgn, function(x) {
  substitute(sum(thk[grepl(PATTERN, name)], na.rm = TRUE), list(PATTERN = x))
})
names(ops) <- thk_names

# do mutation
y <- mutate_profile_raw(x, ops)

site(y)[c(idname(y), thk_names)]

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