A method for "slicing" of SoilProfileCollection objects into constant depth intervals. Now deprecated, see [dice()].

slice.fast(object, fm, top.down = TRUE, just.the.data = FALSE, strict = TRUE)

# S4 method for class 'SoilProfileCollection'
slice(object, fm, top.down = TRUE, just.the.data = FALSE, strict = TRUE)

get.slice(h, id, top, bottom, vars, z, include = "top", strict = TRUE)

Arguments

object

a SoilProfileCollection

fm

A formula: either integer.vector ~ var1 + var2 + var3 where named variables are sliced according to integer.vector OR where all variables are sliced according to integer.vector: integer.vector ~ ..

top.down

logical, slices are defined from the top-down: 0:10 implies 0-11 depth units.

just.the.data

Logical, return just the sliced data or a new SoilProfileCollection object.

strict

Check for logic errors? Default: TRUE

h

Horizon data.frame

id

Profile ID

top

Top Depth Column Name

bottom

Bottom Depth Column Name

vars

Variables of Interest

z

Slice Depth (index).

include

Either 'top' or 'bottom'. Boundary to include in slice. Default: 'top'

Value

Either a new SoilProfileCollection with data sliced according to fm, or a data.frame.

Details

By default, slices are defined from the top-down: 0:10 implies 0-11 depth units.

References

D.E. Beaudette, P. Roudier, A.T. O'Geen, Algorithms for quantitative pedology: A toolkit for soil scientists, Computers & Geosciences, Volume 52, March 2013, Pages 258-268, 10.1016/j.cageo.2012.10.020.

See also

Author

D.E. Beaudette

Examples


library(aqp)

# simulate some data, IDs are 1:20
d <- lapply(1:20, random_profile)
d <- do.call('rbind', d)

# init SoilProfileCollection object
depths(d) <- id ~ top + bottom
head(horizons(d))
#>   id top bottom name        p1        p2          p3        p4         p5 hzID
#> 1  1   0     28   H1  9.201405 -6.835655   0.8525996  4.824201  -7.994531    1
#> 2  1  28     37   H2 15.312323 -5.353120  -3.0780103 22.126603  -5.419231    2
#> 3  1  37     64   H3 24.106495 -6.386571   2.0878183 20.331013   0.581044    3
#> 4  1  64     91   H4 19.940854 -4.466280   1.4647572 17.199065 -13.806440    4
#> 5 10   0     13   H1 14.852170 -4.626349  -3.5354367  5.675210  -1.138095    5
#> 6 10  13     34   H2 17.246366 -2.943876 -23.2641706 11.316858   5.286298    6

# generate single slice at 10 cm
# output is a SoilProfileCollection object
s <- dice(d, fm = 10 ~ name + p1 + p2 + p3)

# generate single slice at 10 cm, output data.frame
s <- dice(d, 10 ~ name + p1 + p2 + p3, SPC = FALSE)

# generate integer slices from 0 - 26 cm
# note that slices are specified by default as "top-down"
# result is a SoilProfileCollection
# e.g. the lower depth will always by top + 1
s <- dice(d, fm = 0:25 ~ name + p1 + p2 + p3)
par(mar=c(0,1,0,1))
plotSPC(s)


# generate slices from 0 - 11 cm, for all variables
s <- dice(d, fm = 0:10 ~ .)
print(s)
#> SoilProfileCollection with 20 profiles and 220 horizons
#> profile ID: id  |  horizon ID: sliceID 
#> Depth range: 11 - 11 cm
#> 
#> ----- Horizons (6 / 220 rows  |  10 / 13 columns) -----
#>  id sliceID top bottom hzID name       p1        p2        p3       p4
#>   1       1   0      1    1   H1 9.201405 -6.835655 0.8525996 4.824201
#>   1       2   1      2    1   H1 9.201405 -6.835655 0.8525996 4.824201
#>   1       3   2      3    1   H1 9.201405 -6.835655 0.8525996 4.824201
#>   1       4   3      4    1   H1 9.201405 -6.835655 0.8525996 4.824201
#>   1       5   4      5    1   H1 9.201405 -6.835655 0.8525996 4.824201
#>   1       6   5      6    1   H1 9.201405 -6.835655 0.8525996 4.824201
#> [... more horizons ...]
#> 
#> ----- Sites (6 / 20 rows  |  1 / 1 columns) -----
#>  id
#>   1
#>  10
#>  11
#>  12
#>  13
#>  14
#> [... more sites ...]
#> 
#> Spatial Data:
#> [EMPTY]

# compute percent missing, for each slice,
# if all vars are missing, then NA is returned
d$p1[1:10] <- NA
s <- dice(d, 10 ~ ., SPC = FALSE, pctMissing = TRUE)
head(s)
#>   hzID id top bottom name        p1         p2          p3         p4
#> 1    1  1  10     11   H1        NA -6.8356554   0.8525996   4.824201
#> 2    5 10  10     11   H1        NA -4.6263494  -3.5354367   5.675210
#> 3   11 11  10     11   H1  6.009662  1.3820162 -12.1439838 -13.858707
#> 4   15 12  10     11   H2  6.511279 -4.4183782 -25.1033888  -1.818884
#> 5   20 13  10     11   H1 10.972373 -1.6643068  -6.6952467 -10.342752
#> 6   24 14  10     11   H1  3.773004 -0.5507985   1.1623836   9.395569
#>           p5 sliceID .oldTop .oldBottom .pctMissing
#> 1  -7.994531      11       0         28   0.1666667
#> 2  -1.138095     102       0         13   0.1666667
#> 3  -1.401404     208       0         27   0.0000000
#> 4  -4.632886     274       9         26   0.0000000
#> 5  -4.558176     367       0         28   0.0000000
#> 6 -14.160065     462       0         18   0.0000000

if (FALSE) { # \dontrun{
##
## check sliced data
##

# test that mean of 1 cm slices property is equal to the
# hz-thickness weighted mean value of that property
data(sp1)
depths(sp1) <- id ~ top + bottom

# get the first profile
sp1.sub <- sp1[which(profile_id(sp1) == 'P009'), ]

# compute hz-thickness wt. mean
hz.wt.mean <- with(
  horizons(sp1.sub),
  sum((bottom - top) * prop) / sum(bottom - top)
)

# hopefully the same value, calculated via slice()
s <- dice(sp1.sub, fm = 0:max(sp1.sub) ~ prop)
hz.slice.mean <- mean(s$prop, na.rm = TRUE)

# they are the same
all.equal(hz.slice.mean, hz.wt.mean)
} # }