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Generalize Horizon Names

Source: R/generalize.hz.R
generalize.hz.Rd

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)

Usage

generalize.hz(
  x,
  new,
  pattern,
  non.matching.code = "not-used",
  hzdepm = NULL,
  ordered = !missing(hzdepm),
  na.rm = TRUE,
  ...
)

# S4 method for class 'character'
generalizeHz(
  x,
  new,
  pattern,
  non.matching.code = "not-used",
  hzdepm = NULL,
  ordered = !missing(hzdepm),
  ...
)

# S4 method for class 'SoilProfileCollection'
generalizeHz(
  x,
  new,
  pattern,
  non.matching.code = "not-used",
  hzdepm = NULL,
  ordered = !missing(hzdepm),
  ghl = "genhz",
  ...
)

Arguments

x

character vector of horizon names or a SoilProfileCollection object

new

character vector of generalized horizon labels (GHL)

pattern

character vector of REGEX patterns, same length as new

non.matching.code

character, label used for any horizon not matched by pattern

hzdepm

numeric vector of horizon mid-points; NA values in hzdepm will result in non.matching.code (or NA if not defined) in result

ordered

logical, default TRUE when hzdepm argument is specified

na.rm

logical, default TRUE will ignore missing depths in calculating sort order when hzdepm is specified and ordered=TRUE

...

additional arguments passed to grep() such as perl = TRUE for advanced REGEX

ghl

Generalized Horizon Designation column name (to be created/updated when x is a SoilProfileCollection)

Value

factor (an ordered factor when ordered=TRUE) of the same length as x (if character) or as number of horizons in x (if SoilProfileCollection)

Details

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.

References

Beaudette, D.E., Roudier, P., Skovlin, J. (2016). Probabilistic Representation of Genetic Soil Horizons. In: Hartemink, A., Minasny, B. (eds) Digital Soil Morphometrics. Progress in Soil Science. Springer, Cham. https://doi.org/10.1007/978-3-319-28295-4_18

See also

hzdesgnname()

Author

D.E. Beaudette

Examples


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"