Generalize Horizon Names

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",
  ...
)

Arguments

x

a character vector of horizon names or a SoilProfileCollection

new

a character vector of new horizon classes

pattern

a character vector of REGEX patterns, same length as new

non.matching.code

label used for any horizon not matching any pattern

hzdepm

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

ordered

by default, the result is an ordered factor when hzdepm is defined.

...

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

(ordered) factor 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.

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 

# generalize
sp1$genhz <- generalize.hz(sp1$name,
                           new=c('O','A','B','C','R'),
                           pattern=c('O', '^A','^B','C','R'))

# 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 <- generalize.hz(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