Generalize a vector of horizon names, based on new classes, and REGEX
patterns. Or create a new column ghl in a SoilProfileCollection (requires a horizon designation name to be defined for the collection, see details)
generalize.hz(
x,
new,
pattern,
non.matching.code = "not-used",
hzdepm = NULL,
ordered = !missing(hzdepm),
...
)
# S4 method for character
generalizeHz(
x,
new,
pattern,
non.matching.code = "not-used",
hzdepm = NULL,
ordered = !missing(hzdepm),
...
)
# S4 method for SoilProfileCollection
generalizeHz(
x,
new,
pattern,
non.matching.code = "not-used",
hzdepm = NULL,
ordered = !missing(hzdepm),
ghl = "genhz",
...
)character vector of horizon names or a SoilProfileCollection object
character vector of generalized horizon labels (GHL)
character vector of REGEX patterns, same length as new
character, label used for any horizon not matched by pattern
numeric vector of horizon mid-points; NA values in hzdepm will result in non.matching.code (or NA if not defined) in result
logical, TRUE when hzdepm argument is specified
additional arguments passed to grep() such as perl = TRUE for advanced REGEX
Generalized Horizon Designation column name (to be created/updated when x is a SoilProfileCollection)
factor (possibly an ordered factor) of the same length as x (if character) or as number of horizons in x (if SoilProfileCollection)
When x is a SoilProfileCollection the ghl column will be updated with the factor results. This requires that the "horizon designation name" metadata be defined for the collection to set the column for input designations.
Beaudette, D. E., Roudier, P., & Skovlin, J. (2016). Probabilistic representation of genetic soil horizons. Digital soil morphometrics, 281-293.
data(sp1)
# check original distribution of hz designations
table(sp1$name)
#>
#> 2C 2C1 2C2 3Ab 3Bwb 3C 3Cb A A1 A2 A3 AB AB1 AB2 AB3 BA
#> 2 2 2 1 2 2 1 4 4 4 1 5 1 1 1 2
#> Bt Bt1 Bt2 Bw1 Bw2 Bw3 C C1 C2 Oa/A Oe Oi Rt
#> 1 3 3 3 3 1 1 2 2 1 1 3 1
# generalized horizon labels
# character vector input
sp1$genhz <- generalizeHz(
sp1$name,
new = c('O','A','B','C','R'),
pattern = c('O', '^A','^B','C','R'),
ordered = TRUE
)
# see how we did / what we missed
table(sp1$genhz, sp1$name)
#>
#> 2C 2C1 2C2 3Ab 3Bwb 3C 3Cb A A1 A2 A3 AB AB1 AB2 AB3 BA Bt Bt1 Bt2
#> O 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> A 0 0 0 0 0 0 0 4 4 4 1 5 1 1 1 0 0 0 0
#> B 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 1 3 3
#> C 2 2 2 0 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0
#> R 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> not-used 0 0 0 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#>
#> Bw1 Bw2 Bw3 C C1 C2 Oa/A Oe Oi Rt
#> O 0 0 0 0 0 0 1 1 3 0
#> A 0 0 0 0 0 0 0 0 0 0
#> B 3 3 1 0 0 0 0 0 0 0
#> C 0 0 0 1 2 2 0 0 0 0
#> R 0 0 0 0 0 0 0 0 0 1
#> not-used 0 0 0 0 0 0 0 0 0 0
## a more advanced example, requries `perl = TRUE`
# example data
x <- c('A', 'AC', 'Bt1', '^AC', 'C', 'BC', 'CB')
# new labels
n <- c('A', '^AC', 'C')
# patterns:
# "A anywhere in the name"
# "literal '^A' anywhere in the name"
# "C anywhere in name, but without preceding A"
p <- c('A', '^A', '(?<!A)C')
# note additional argument
res <- generalizeHz(
x,
new = n,
pattern = p,
perl = TRUE
)
# double-check: OK
table(res, x)
#> x
#> res A AC BC Bt1 C CB ^AC
#> A 0 0 0 0 0 0 1
#> ^AC 1 1 0 0 0 0 0
#> C 0 0 1 0 1 1 0
#> not-used 0 0 0 1 0 0 0
## apply to a SoilProfileCollection
data(sp1)
depths(sp1) <- id ~ top + bottom
# must set horizon designation metadata
hzdesgnname(sp1) <- 'name'
# result is a SoilProfileCollection
x <- generalizeHz(
sp1,
new = c('O','A','B','C','R'),
pattern = c('O', '^A','^B','C','R'),
ordered = TRUE
)
# GHL stored in 'genhz' column
x$genhz
#> [1] A A A B B R O A
#> [9] C C O A B B B A
#> [17] A A B B A A B B
#> [25] O A A A A C C C
#> [33] C C A A B B B C
#> [41] C not-used C O A A B B
#> [49] C C C O A A A B
#> [57] B C not-used not-used
#> Levels: O < A < B < C < R < not-used
# GHL metadata is set
GHL(x)
#> [1] "genhz"