guessHzAttrName: Guess Horizon Slot Column Names

In aqp: Algorithms for Quantitative Pedology

Guess Horizon Slot Column Names

Description

guessHzAttrName(): Guess the horizon column name where possible/preferred formative elements are known. There is a preference for records where more optional requirements are met to handle cases where there will be many matches. For example, working with soil data one might have "low, RV and high" total clay, as well as clay fractions. One could distinguish between these different measurements using standard formative elements for column names from the database of interest. Result is the first match in horizonNames(x) with the most required plus optional patterns matched.

e.g. guessHzAttrName(x, attr="clay", optional=c("total", "_r")) matches (claytotal_r == totalclay_r) over (clay_r == claytotal == totalclay) over clay.

guessHzDesgnName(): This follows the historic convention used by aqp::plotSPC() looking for "hzname" or other column names containing the regular expression "name". If the pattern "name" is not found, the pattern "desgn" is searched as a fallback, as "hzdesgn" or "hz_desgn" are other common column naming schemes for horizon designation name.

guessHzTexClName(): This function is used to provide a texture class attribute column name to functions. It will use regular expressions to match "texcl" which is typically the texture of the fine earth fraction, without modifiers or in-lieu textures. Alternately, it will match "texture" for cases where "texcl" is absent (e.g. in NASIS Component Horizon).

Usage

guessHzAttrName(x, attr, optional = NULL, verbose = TRUE, required = FALSE)

guessHzDesgnName(x, required = FALSE)

guessHzTexClName(x, required = FALSE)

Arguments

x	A SoilProfileCollection
attr	A regular expression containing required formative element of attribute name.
optional	A character vector of regular expression(s) containing optional formative elements of attribute name.
verbose	A boolean value for whether to produce message output about guesses.
required	logical Default: FALSE. Is this attribute required? If it is, set to TRUE to trigger error on invalid value.

Value

Character containing horizon attribute column name. Result is the first match in horizonNames(x) with the most required plus optional patterns matched.

Author(s)

Andrew G. Brown

Examples

# a has the required attr pattern, but none of the optional
a <- data.frame(id = 1, top = c(0,10), bottom=c(10,40),
                clay=c(18,19))
depths(a) <- id ~ top + bottom

guessHzAttrName(a, attr="clay", optional=c("total", "_r"))

# b has requried attr pattern, and one of the opional patterns
#   notice that it also contains "clay" but preferentially matches more optional patterns
b <- data.frame(id = 1, top = c(0,10), bottom=c(10,40),
                clay=c(0.18,0.19), clay_r=c(18,19))
depths(b) <- id ~ top + bottom

guessHzAttrName(b, attr="clay", optional=c("total", "_r"))

# c has total and _r (both optional) on either side of clay
# having all of the optional patterns plus required is best evidence, and first
# column containing that combination will be returned
c <- data.frame(id = 1, top = c(0,10), bottom=c(10,40),
                totalclay_r=c(18,19), claytotal_r=c(0.18,0.19))
depths(c) <- id ~ top + bottom

guessHzAttrName(c, attr="clay", optional=c("total", "_r"))


a <- data.frame(id = 1, top = c(0,10), bottom=c(10,40), horizonname=c("A","Bw"))
depths(a) <- id ~ top + bottom

# store guess in metadata
hzdesgnname(a) <- guessHzDesgnName(a)

# inspect result
hzdesgnname(a)


a <- data.frame(id = 1, top = c(0,10), bottom=c(10,40), texture=c("A","Bw"))
depths(a) <- id ~ top + bottom

# store guess in metadata
hztexclname(a) <- guessHzTexClName(a)

# inspect result
hztexclname(a)

aqp documentation built on Sept. 8, 2023, 5:45 p.m.