Soil Chemical Data from Serpentinitic Soils of California

Format

A data frame with 30 observations on the following 13 variables.

id

site name

name

horizon designation

top

horizon top boundary in cm

bottom

horizon bottom boundary in cm

K

exchangeable K in c mol/kg

Mg

exchangeable Mg in cmol/kg

Ca

exchangeable Ca in cmol/kg

CEC_7

cation exchange capacity (NH4OAc at pH 7)

ex_Ca_to_Mg

extractable Ca:Mg ratio

sand

sand content by weight percentage

silt

silt content by weight percentage

clay

clay content by weight percentage

CF

>2mm fraction by volume percentage

Source

https://www.soils.org/publications/sssaj/articles/73/6/2087

Details

Selected soil physical and chemical data from (McGahan et al., 2009).

References

McGahan, D.G., Southard, R.J, Claassen, V.P. 2009. Plant-Available Calcium Varies Widely in Soils on Serpentinite Landscapes. Soil Sci. Soc. Am. J. 73: 2087-2095.

Examples


# load sample data set, a simple data.frame object with horizon-level data from 10 profiles
library(aqp)
data(sp4)
str(sp4)
#> 'data.frame':	30 obs. of  13 variables:
#>  $ id         : chr  "colusa" "colusa" "colusa" "colusa" ...
#>  $ name       : chr  "A" "ABt" "Bt1" "Bt2" ...
#>  $ top        : int  0 3 8 30 0 9 0 4 13 0 ...
#>  $ bottom     : int  3 8 30 42 9 34 4 13 40 6 ...
#>  $ K          : num  0.3 0.2 0.1 0.1 0.2 0.3 0.2 0.6 0.8 0.4 ...
#>  $ Mg         : num  25.7 23.7 23.2 44.3 21.9 18.9 12.1 12.1 17.7 16.4 ...
#>  $ Ca         : num  9 5.6 1.9 0.3 4.4 4.5 1.4 7 4.4 24.1 ...
#>  $ CEC_7      : num  23 21.4 23.7 43 18.8 27.5 23.7 18 20 31.1 ...
#>  $ ex_Ca_to_Mg: num  0.35 0.23 0.08 0.01 0.2 0.2 0.58 0.51 0.25 1.47 ...
#>  $ sand       : int  46 42 40 27 54 49 43 36 27 43 ...
#>  $ silt       : int  33 31 28 18 20 18 55 49 45 42 ...
#>  $ clay       : int  21 27 32 55 25 34 3 15 27 15 ...
#>  $ CF         : num  0.12 0.27 0.27 0.16 0.55 0.84 0.5 0.75 0.67 0.02 ...
sp4$idbak <- sp4$id
#sp4 <- sp4[order(match(sp4$id, aqp:::.coalesce.idx(sort(sp4$id))), sp4$top),]


# upgrade to SoilProfileCollection
# 'id' is the name of the column containing the profile ID
# 'top' is the name of the column containing horizon upper boundaries
# 'bottom' is the name of the column containing horizon lower boundaries
depths(sp4) <- id ~ top + bottom

# check it out
class(sp4) # class name
#> [1] "SoilProfileCollection"
#> attr(,"package")
#> [1] "aqp"
str(sp4) # internal structure
#> Formal class 'SoilProfileCollection' [package "aqp"] with 9 slots
#>   ..@ idcol       : chr "id"
#>   ..@ hzidcol     : chr "hzID"
#>   ..@ depthcols   : chr [1:2] "top" "bottom"
#>   ..@ metadata    :List of 7
#>   .. ..$ aqp_df_class    : chr "data.frame"
#>   .. ..$ aqp_group_by    : chr ""
#>   .. ..$ aqp_hzdesgn     : chr ""
#>   .. ..$ aqp_hztexcl     : chr ""
#>   .. ..$ depth_units     : chr "cm"
#>   .. ..$ stringsAsFactors: logi FALSE
#>   .. ..$ original.order  : int [1:30] 1 2 3 4 5 6 7 8 9 10 ...
#>   ..@ horizons    :'data.frame':	30 obs. of  15 variables:
#>   .. ..$ id         : chr [1:30] "colusa" "colusa" "colusa" "colusa" ...
#>   .. ..$ name       : chr [1:30] "A" "ABt" "Bt1" "Bt2" ...
#>   .. ..$ top        : int [1:30] 0 3 8 30 0 9 0 4 13 0 ...
#>   .. ..$ bottom     : int [1:30] 3 8 30 42 9 34 4 13 40 3 ...
#>   .. ..$ K          : num [1:30] 0.3 0.2 0.1 0.1 0.2 0.3 0.2 0.6 0.8 0.6 ...
#>   .. ..$ Mg         : num [1:30] 25.7 23.7 23.2 44.3 21.9 18.9 12.1 12.1 17.7 28.3 ...
#>   .. ..$ Ca         : num [1:30] 9 5.6 1.9 0.3 4.4 4.5 1.4 7 4.4 5.8 ...
#>   .. ..$ CEC_7      : num [1:30] 23 21.4 23.7 43 18.8 27.5 23.7 18 20 29.3 ...
#>   .. ..$ ex_Ca_to_Mg: num [1:30] 0.35 0.23 0.08 0.01 0.2 0.2 0.58 0.51 0.25 0.2 ...
#>   .. ..$ sand       : int [1:30] 46 42 40 27 54 49 43 36 27 42 ...
#>   .. ..$ silt       : int [1:30] 33 31 28 18 20 18 55 49 45 26 ...
#>   .. ..$ clay       : int [1:30] 21 27 32 55 25 34 3 15 27 32 ...
#>   .. ..$ CF         : num [1:30] 0.12 0.27 0.27 0.16 0.55 0.84 0.5 0.75 0.67 0.25 ...
#>   .. ..$ idbak      : chr [1:30] "colusa" "colusa" "colusa" "colusa" ...
#>   .. ..$ hzID       : chr [1:30] "1" "2" "3" "4" ...
#>   ..@ site        :'data.frame':	10 obs. of  1 variable:
#>   .. ..$ id: chr [1:10] "colusa" "glenn" "kings" "mariposa" ...
#>   ..@ sp          :Formal class 'SpatialPoints' [package "sp"] with 3 slots
#>   .. .. ..@ coords     : num [1, 1] 0
#>   .. .. ..@ bbox       : logi [1, 1] NA
#>   .. .. ..@ proj4string:Formal class 'CRS' [package "sp"] with 1 slot
#>   .. .. .. .. ..@ projargs: chr NA
#>   ..@ diagnostic  :'data.frame':	0 obs. of  0 variables
#>   ..@ restrictions:'data.frame':	0 obs. of  0 variables

# check integrity of site:horizon linkage
spc_in_sync(sp4)
#>   nSites relativeOrder valid
#> 1   TRUE          TRUE  TRUE

# check horizon depth logic
checkHzDepthLogic(sp4)
#>                id valid depthLogic sameDepth missingDepth overlapOrGap
#> 1          colusa  TRUE      FALSE     FALSE        FALSE        FALSE
#> 2           glenn  TRUE      FALSE     FALSE        FALSE        FALSE
#> 3           kings  TRUE      FALSE     FALSE        FALSE        FALSE
#> 4        mariposa  TRUE      FALSE     FALSE        FALSE        FALSE
#> 5       mendocino  TRUE      FALSE     FALSE        FALSE        FALSE
#> 6            napa  TRUE      FALSE     FALSE        FALSE        FALSE
#> 7      san benito  TRUE      FALSE     FALSE        FALSE        FALSE
#> 8          shasta  TRUE      FALSE     FALSE        FALSE        FALSE
#> 9  shasta-trinity  TRUE      FALSE     FALSE        FALSE        FALSE
#> 10         tehama  TRUE      FALSE     FALSE        FALSE        FALSE

# inspect object properties
idname(sp4) # self-explanitory
#> [1] "id"
horizonDepths(sp4) # self-explanitory
#> [1] "top"    "bottom"

# you can change these:
depth_units(sp4) # defaults to 'cm'
#> [1] "cm"
metadata(sp4) # not much to start with
#> $aqp_df_class
#> [1] "data.frame"
#> 
#> $aqp_group_by
#> [1] ""
#> 
#> $aqp_hzdesgn
#> [1] ""
#> 
#> $aqp_hztexcl
#> [1] ""
#> 
#> $depth_units
#> [1] "cm"
#> 
#> $stringsAsFactors
#> [1] FALSE
#> 
#> $original.order
#>  [1]  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
#> [26] 26 27 28 29 30
#> 

# alter the depth unit metadata
depth_units(sp4) <- 'inches' # units are really 'cm'

# more generic interface for adjusting metadata

# add attributes to metadata list
metadata(sp4)$describer <- 'DGM'
metadata(sp4)$date <- as.Date('2009-01-01')
metadata(sp4)$citation <- 'McGahan, D.G., Southard, R.J, Claassen, V.P.
2009. Plant-Available Calcium Varies Widely in Soils
on Serpentinite Landscapes. Soil Sci. Soc. Am. J. 73: 2087-2095.'

depth_units(sp4) <- 'cm' # fix depth units, back to 'cm'

# further inspection with common function overloads
length(sp4) # number of profiles in the collection
#> [1] 10
nrow(sp4) # number of horizons in the collection
#> [1] 30
names(sp4) # column names
#>     horizons1     horizons2     horizons3     horizons4     horizons5 
#>          "id"        "name"         "top"      "bottom"           "K" 
#>     horizons6     horizons7     horizons8     horizons9    horizons10 
#>          "Mg"          "Ca"       "CEC_7" "ex_Ca_to_Mg"        "sand" 
#>    horizons11    horizons12    horizons13    horizons14    horizons15 
#>        "silt"        "clay"          "CF"       "idbak"        "hzID" 
min(sp4) # shallowest profile depth in collection
#> [1] 16
max(sp4) # deepest profile depth in collection
#> [1] 49

# extraction of soil profile components
profile_id(sp4) # vector of profile IDs
#>  [1] "colusa"         "glenn"          "kings"          "mariposa"      
#>  [5] "mendocino"      "napa"           "san benito"     "shasta"        
#>  [9] "shasta-trinity" "tehama"        
horizons(sp4) # horizon data
#>                id name top bottom   K   Mg   Ca CEC_7 ex_Ca_to_Mg sand silt
#> 1          colusa    A   0      3 0.3 25.7  9.0  23.0        0.35   46   33
#> 2          colusa  ABt   3      8 0.2 23.7  5.6  21.4        0.23   42   31
#> 3          colusa  Bt1   8     30 0.1 23.2  1.9  23.7        0.08   40   28
#> 4          colusa  Bt2  30     42 0.1 44.3  0.3  43.0        0.01   27   18
#> 5           glenn    A   0      9 0.2 21.9  4.4  18.8        0.20   54   20
#> 6           glenn   Bt   9     34 0.3 18.9  4.5  27.5        0.20   49   18
#> 7           kings    A   0      4 0.2 12.1  1.4  23.7        0.58   43   55
#> 8           kings  Bt1   4     13 0.6 12.1  7.0  18.0        0.51   36   49
#> 9           kings  Bt2  13     40 0.8 17.7  4.4  20.0        0.25   27   45
#> 10       mariposa    A   0      3 0.6 28.3  5.8  29.3        0.20   42   26
#> 11       mariposa  Bt1   3     14 0.4 33.7  6.2  27.9        0.18   41   34
#> 12       mariposa  Bt2  14     34 0.3 44.3  6.2  34.1        0.14   36   33
#> 13       mariposa  Bt3  34     49 0.1 78.2  4.4  43.6        0.06   36   31
#> 14      mendocino    A   0      2 0.5 12.8  2.2  19.3        0.18   57   30
#> 15      mendocino  Bt1   2      8 0.2 27.1  3.4  19.8        0.13   51   28
#> 16      mendocino  Bt2   8     30 0.2 30.5  3.7  22.9        0.12   51   26
#> 17           napa    A   0      6 0.4 16.4 24.1  31.1        1.47   43   42
#> 18           napa   Bt   6     20 0.1 16.2 21.5  27.9        1.32   54   29
#> 19     san benito    A   0      8  NA  3.0  0.7   3.1        0.24   80    8
#> 20     san benito   Bt   8     20 0.0  0.1  5.6   5.6        0.11   74    7
#> 21         shasta    A   0      3 0.3  9.7  3.5  13.2        0.36   37   49
#> 22         shasta   Bt   3     40 0.2 10.1  2.0  12.2        0.20   39   46
#> 23 shasta-trinity   A1   0      2 0.2 18.8  6.6  23.0        0.35   34   44
#> 24 shasta-trinity   A2   2      5 0.2 25.5  4.1  21.5        0.16   33   42
#> 25 shasta-trinity   AB   5     12 0.3 29.3  3.5  29.6        0.12   24   36
#> 26 shasta-trinity  Bt1  12     23 0.2 30.3  1.5  26.5        0.05   20   29
#> 27 shasta-trinity  Bt2  23     40 0.1 64.9  0.8  48.7        0.01   11   22
#> 28         tehama    A   0      3 0.4 12.4 16.3  40.2        1.31   57   19
#> 29         tehama  Bt1   3      7 0.5 20.2 16.5  32.7        0.82   55   20
#> 30         tehama  Bt2   7     16 0.2 27.7 13.7  30.0        0.50   51   17
#>    clay   CF          idbak hzID
#> 1    21 0.12         colusa    1
#> 2    27 0.27         colusa    2
#> 3    32 0.27         colusa    3
#> 4    55 0.16         colusa    4
#> 5    25 0.55          glenn    5
#> 6    34 0.84          glenn    6
#> 7     3 0.50          kings    7
#> 8    15 0.75          kings    8
#> 9    27 0.67          kings    9
#> 10   32 0.25       mariposa   10
#> 11   25 0.38       mariposa   11
#> 12   31 0.71       mariposa   12
#> 13   33 0.67       mariposa   13
#> 14   13 0.16      mendocino   14
#> 15   21 0.14      mendocino   15
#> 16   23 0.80      mendocino   16
#> 17   15 0.02           napa   17
#> 18   17 0.07           napa   18
#> 19   12 0.43     san benito   19
#> 20   19 0.60     san benito   20
#> 21   14 0.78         shasta   21
#> 22   14 0.88         shasta   22
#> 23   22 0.17 shasta-trinity   23
#> 24   25 0.13 shasta-trinity   24
#> 25   40 0.09 shasta-trinity   25
#> 26   51 0.05 shasta-trinity   26
#> 27   67 0.05 shasta-trinity   27
#> 28   24 0.43         tehama   28
#> 29   25 0.10         tehama   29
#> 30   32 0.34         tehama   30

# extraction of specific horizon attributes
sp4$clay # vector of clay content
#>  [1] 21 27 32 55 25 34  3 15 27 32 25 31 33 13 21 23 15 17 12 19 14 14 22 25 40
#> [26] 51 67 24 25 32

# subsetting SoilProfileCollection objects
sp4[1, ] # first profile in the collection
#> SoilProfileCollection with 1 profiles and 4 horizons
#> profile ID: id  |  horizon ID: hzID 
#> Depth range: 42 - 42 cm
#> 
#> ----- Horizons (4 / 4 rows  |  10 / 15 columns) -----
#>      id hzID top bottom name   K   Mg  Ca CEC_7 ex_Ca_to_Mg
#>  colusa    1   0      3    A 0.3 25.7 9.0  23.0        0.35
#>  colusa    2   3      8  ABt 0.2 23.7 5.6  21.4        0.23
#>  colusa    3   8     30  Bt1 0.1 23.2 1.9  23.7        0.08
#>  colusa    4  30     42  Bt2 0.1 44.3 0.3  43.0        0.01
#> 
#> ----- Sites (1 / 1 rows  |  1 / 1 columns) -----
#>      id
#>  colusa
#> 
#> Spatial Data:
#>      [,1]
#> [1,]   NA
#> CRS:  NA
sp4[, 1] # first horizon from each profile
#> SoilProfileCollection with 10 profiles and 10 horizons
#> profile ID: id  |  horizon ID: hzID 
#> Depth range: 2 - 9 cm
#> 
#> ----- Horizons (6 / 10 rows  |  10 / 15 columns) -----
#>         id hzID top bottom name   K   Mg   Ca CEC_7 ex_Ca_to_Mg
#>     colusa    1   0      3    A 0.3 25.7  9.0  23.0        0.35
#>      glenn    5   0      9    A 0.2 21.9  4.4  18.8        0.20
#>      kings    7   0      4    A 0.2 12.1  1.4  23.7        0.58
#>   mariposa   10   0      3    A 0.6 28.3  5.8  29.3        0.20
#>  mendocino   14   0      2    A 0.5 12.8  2.2  19.3        0.18
#>       napa   17   0      6    A 0.4 16.4 24.1  31.1        1.47
#> [... more horizons ...]
#> 
#> ----- Sites (6 / 10 rows  |  1 / 1 columns) -----
#>         id
#>     colusa
#>      glenn
#>      kings
#>   mariposa
#>  mendocino
#>       napa
#> [... more sites ...]
#> 
#> Spatial Data:
#> [EMPTY]

# basic plot method, highly customizable: see manual page ?plotSPC
plot(sp4)
# inspect plotting area, very simple to overlay graphical elements
abline(v=1:length(sp4), lty=3, col='blue')
# profiles are centered at integers, from 1 to length(obj)
axis(1, line=-1.5, at=1:10, cex.axis=0.75, font=4, col='blue', lwd=2)
# y-axis is based on profile depths
axis(2, line=-1, at=pretty(1:max(sp4)), cex.axis=0.75, font=4, las=1, col='blue', lwd=2)



# symbolize soil properties via color
par(mar=c(0,0,4,0))
plot(sp4, color='clay')

plot(sp4, color='CF')


# apply a function to each profile, returning a single value per profile,
# in the same order as profile_id(sp4)
soil.depths <- profileApply(sp4, max) # recall that max() gives the depth of a soil profile

# check that the order is correct
all.equal(names(soil.depths), profile_id(sp4))
#> [1] TRUE

# a vector of values that is the same length as the number of profiles
# can be stored into site-level data
sp4$depth <- soil.depths
# check: looks good
max(sp4[1, ]) == sp4$depth[1]
#> [1] TRUE

# extract site-level data
site(sp4) # as a data.frame
#>                id depth
#> 1          colusa    42
#> 2           glenn    34
#> 3           kings    40
#> 4        mariposa    49
#> 5       mendocino    30
#> 6            napa    20
#> 7      san benito    20
#> 8          shasta    40
#> 9  shasta-trinity    40
#> 10         tehama    16
sp4$depth # specific columns as a vector
#>  [1] 42 34 40 49 30 20 20 40 40 16

# use site-level data to alter plotting order
new.order <- order(sp4$depth) # the result is an index of rank
par(mar=c(0,0,0,0))
plot(sp4, plot.order=new.order)


# deconstruct SoilProfileCollection into a data.frame, with horizon+site data
as(sp4, 'data.frame')
#>                id name top bottom   K   Mg   Ca CEC_7 ex_Ca_to_Mg sand silt
#> 1          colusa    A   0      3 0.3 25.7  9.0  23.0        0.35   46   33
#> 2          colusa  ABt   3      8 0.2 23.7  5.6  21.4        0.23   42   31
#> 3          colusa  Bt1   8     30 0.1 23.2  1.9  23.7        0.08   40   28
#> 4          colusa  Bt2  30     42 0.1 44.3  0.3  43.0        0.01   27   18
#> 5           glenn    A   0      9 0.2 21.9  4.4  18.8        0.20   54   20
#> 6           glenn   Bt   9     34 0.3 18.9  4.5  27.5        0.20   49   18
#> 7           kings    A   0      4 0.2 12.1  1.4  23.7        0.58   43   55
#> 8           kings  Bt1   4     13 0.6 12.1  7.0  18.0        0.51   36   49
#> 9           kings  Bt2  13     40 0.8 17.7  4.4  20.0        0.25   27   45
#> 10       mariposa    A   0      3 0.6 28.3  5.8  29.3        0.20   42   26
#> 11       mariposa  Bt1   3     14 0.4 33.7  6.2  27.9        0.18   41   34
#> 12       mariposa  Bt2  14     34 0.3 44.3  6.2  34.1        0.14   36   33
#> 13       mariposa  Bt3  34     49 0.1 78.2  4.4  43.6        0.06   36   31
#> 14      mendocino    A   0      2 0.5 12.8  2.2  19.3        0.18   57   30
#> 15      mendocino  Bt1   2      8 0.2 27.1  3.4  19.8        0.13   51   28
#> 16      mendocino  Bt2   8     30 0.2 30.5  3.7  22.9        0.12   51   26
#> 17           napa    A   0      6 0.4 16.4 24.1  31.1        1.47   43   42
#> 18           napa   Bt   6     20 0.1 16.2 21.5  27.9        1.32   54   29
#> 19     san benito    A   0      8  NA  3.0  0.7   3.1        0.24   80    8
#> 20     san benito   Bt   8     20 0.0  0.1  5.6   5.6        0.11   74    7
#> 21         shasta    A   0      3 0.3  9.7  3.5  13.2        0.36   37   49
#> 22         shasta   Bt   3     40 0.2 10.1  2.0  12.2        0.20   39   46
#> 23 shasta-trinity   A1   0      2 0.2 18.8  6.6  23.0        0.35   34   44
#> 24 shasta-trinity   A2   2      5 0.2 25.5  4.1  21.5        0.16   33   42
#> 25 shasta-trinity   AB   5     12 0.3 29.3  3.5  29.6        0.12   24   36
#> 26 shasta-trinity  Bt1  12     23 0.2 30.3  1.5  26.5        0.05   20   29
#> 27 shasta-trinity  Bt2  23     40 0.1 64.9  0.8  48.7        0.01   11   22
#> 28         tehama    A   0      3 0.4 12.4 16.3  40.2        1.31   57   19
#> 29         tehama  Bt1   3      7 0.5 20.2 16.5  32.7        0.82   55   20
#> 30         tehama  Bt2   7     16 0.2 27.7 13.7  30.0        0.50   51   17
#>    clay   CF          idbak hzID depth
#> 1    21 0.12         colusa    1    42
#> 2    27 0.27         colusa    2    42
#> 3    32 0.27         colusa    3    42
#> 4    55 0.16         colusa    4    42
#> 5    25 0.55          glenn    5    34
#> 6    34 0.84          glenn    6    34
#> 7     3 0.50          kings    7    40
#> 8    15 0.75          kings    8    40
#> 9    27 0.67          kings    9    40
#> 10   32 0.25       mariposa   10    49
#> 11   25 0.38       mariposa   11    49
#> 12   31 0.71       mariposa   12    49
#> 13   33 0.67       mariposa   13    49
#> 14   13 0.16      mendocino   14    30
#> 15   21 0.14      mendocino   15    30
#> 16   23 0.80      mendocino   16    30
#> 17   15 0.02           napa   17    20
#> 18   17 0.07           napa   18    20
#> 19   12 0.43     san benito   19    20
#> 20   19 0.60     san benito   20    20
#> 21   14 0.78         shasta   21    40
#> 22   14 0.88         shasta   22    40
#> 23   22 0.17 shasta-trinity   23    40
#> 24   25 0.13 shasta-trinity   24    40
#> 25   40 0.09 shasta-trinity   25    40
#> 26   51 0.05 shasta-trinity   26    40
#> 27   67 0.05 shasta-trinity   27    40
#> 28   24 0.43         tehama   28    16
#> 29   25 0.10         tehama   29    16
#> 30   32 0.34         tehama   30    16