sp4: Soil Chemical Data from Serpentinitic Soils of California

Description Usage Format Details Source References Examples

Description

Soil Chemical Data from Serpentinitic Soils of California

Usage

1

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

Details

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

Source

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

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.

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# setup environment
library(aqp)

# load sample data set, a simple data.frame object with horizon-level data from 10 profiles
data(sp4)
str(sp4)

# optionally read about it...
# ?sp4

# 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
str(sp4) # internal structure

# inspect object properties
idname(sp4) # self-explanitory
horizonDepths(sp4) # self-explanitory

# you can change these:
depth_units(sp4) # defaults to 'cm'
metadata(sp4) # not much to start with

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

# more generic interface for adjusting metadata
md <- metadata(sp4) # save original metadata

# add columns
md$describer <- 'DGM'
md$date <- as.Date('2009-01-01')
md$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.'

# re-assign
metadata(sp4) <- md
depth_units(sp4) <- 'cm' # fix depth units, back to 'cm'

# further inspection with common function overloads
length(sp4) # number of profiles in the collection
nrow(sp4) # number of horizons in the collection
names(sp4) # column names
min(sp4) # shallowest profile depth in collection
max(sp4) # deepest profile depth in collection

# extraction of soil profile components
profile_id(sp4) # vector of profile IDs
horizons(sp4) # horizon data

# extraction of specific horizon attributes
sp4$clay # vector of clay content

# subsetting SoilProfileCollection objects
sp4[1, ] # first profile in the collection
sp4[, 1] # first horizon from each profile

# 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))

# 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]

# extract site-level data 
site(sp4) # as a data.frame
sp4$depth # specific columns as a vector

# 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')

Example output

This is aqp 1.10
'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 ...
[1] "SoilProfileCollection"
attr(,"package")
[1] "aqp"
Formal class 'SoilProfileCollection' [package "aqp"] with 7 slots
  ..@ idcol     : chr "id"
  ..@ depthcols : chr [1:2] "top" "bottom"
  ..@ metadata  :'data.frame':	1 obs. of  1 variable:
  .. ..$ depth_units: chr "cm"
  ..@ horizons  :'data.frame':	30 obs. of  13 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 ...
  ..@ 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
[1] "id"
[1] "top"    "bottom"
[1] "cm"
  depth_units
1          cm
[1] 10
[1] 30
    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 
       "silt"        "clay"          "CF" 
[1] 16
[1] 49
 [1] "colusa"         "glenn"          "kings"          "mariposa"      
 [5] "mendocino"      "napa"           "san benito"     "shasta"        
 [9] "shasta-trinity" "tehama"        
               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
19       mariposa    A   0      3 0.6 28.3  5.8  29.3        0.20   42   26
20       mariposa  Bt1   3     14 0.4 33.7  6.2  27.9        0.18   41   34
21       mariposa  Bt2  14     34 0.3 44.3  6.2  34.1        0.14   36   33
22       mariposa  Bt3  34     49 0.1 78.2  4.4  43.6        0.06   36   31
23      mendocino    A   0      2 0.5 12.8  2.2  19.3        0.18   57   30
24      mendocino  Bt1   2      8 0.2 27.1  3.4  19.8        0.13   51   28
25      mendocino  Bt2   8     30 0.2 30.5  3.7  22.9        0.12   51   26
10           napa    A   0      6 0.4 16.4 24.1  31.1        1.47   43   42
11           napa   Bt   6     20 0.1 16.2 21.5  27.9        1.32   54   29
12     san benito    A   0      8  NA  3.0  0.7   3.1        0.24   80    8
13     san benito   Bt   8     20 0.0  0.1  5.6   5.6        0.11   74    7
14         shasta    A   0      3 0.3  9.7  3.5  13.2        0.36   37   49
15         shasta   Bt   3     40 0.2 10.1  2.0  12.2        0.20   39   46
26 shasta-trinity   A1   0      2 0.2 18.8  6.6  23.0        0.35   34   44
27 shasta-trinity   A2   2      5 0.2 25.5  4.1  21.5        0.16   33   42
28 shasta-trinity   AB   5     12 0.3 29.3  3.5  29.6        0.12   24   36
29 shasta-trinity  Bt1  12     23 0.2 30.3  1.5  26.5        0.05   20   29
30 shasta-trinity  Bt2  23     40 0.1 64.9  0.8  48.7        0.01   11   22
16         tehama    A   0      3 0.4 12.4 16.3  40.2        1.31   57   19
17         tehama  Bt1   3      7 0.5 20.2 16.5  32.7        0.82   55   20
18         tehama  Bt2   7     16 0.2 27.7 13.7  30.0        0.50   51   17
   clay   CF
1    21 0.12
2    27 0.27
3    32 0.27
4    55 0.16
5    25 0.55
6    34 0.84
7     3 0.50
8    15 0.75
9    27 0.67
19   32 0.25
20   25 0.38
21   31 0.71
22   33 0.67
23   13 0.16
24   21 0.14
25   23 0.80
10   15 0.02
11   17 0.07
12   12 0.43
13   19 0.60
14   14 0.78
15   14 0.88
26   22 0.17
27   25 0.13
28   40 0.09
29   51 0.05
30   67 0.05
16   24 0.43
17   25 0.10
18   32 0.34
 [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
Object of class SoilProfileCollection
Number of profiles: 1

Horizon attributes:
      id name top bottom   K   Mg  Ca CEC_7 ex_Ca_to_Mg sand silt clay   CF
1 colusa    A   0      3 0.3 25.7 9.0  23.0        0.35   46   33   21 0.12
2 colusa  ABt   3      8 0.2 23.7 5.6  21.4        0.23   42   31   27 0.27
3 colusa  Bt1   8     30 0.1 23.2 1.9  23.7        0.08   40   28   32 0.27
4 colusa  Bt2  30     42 0.1 44.3 0.3  43.0        0.01   27   18   55 0.16

Sampling site attributes:
      id
1 colusa

Spatial Data:
     [,1]
[1,]   NA
[1] NA
Object of class SoilProfileCollection
Number of profiles: 10
Depth range: 2-9 cm

Horizon attributes:
         id name top bottom   K   Mg   Ca CEC_7 ex_Ca_to_Mg sand silt clay   CF
1    colusa    A   0      3 0.3 25.7  9.0  23.0        0.35   46   33   21 0.12
2     glenn    A   0      9 0.2 21.9  4.4  18.8        0.20   54   20   25 0.55
3     kings    A   0      4 0.2 12.1  1.4  23.7        0.58   43   55    3 0.50
4  mariposa    A   0      3 0.6 28.3  5.8  29.3        0.20   42   26   32 0.25
5 mendocino    A   0      2 0.5 12.8  2.2  19.3        0.18   57   30   13 0.16
6      napa    A   0      6 0.4 16.4 24.1  31.1        1.47   43   42   15 0.02

Sampling site attributes:
         id
1    colusa
2     glenn
3     kings
4  mariposa
5 mendocino
6      napa
guessing horizon designations are stored in `name`
guessing horizon designations are stored in `name`
guessing horizon designations are stored in `name`
[1] TRUE
[1] TRUE
               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
 [1] 42 34 40 49 30 20 20 40 40 16
guessing horizon designations are stored in `name`
               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 depth
1    21 0.12    42
2    27 0.27    42
3    32 0.27    42
4    55 0.16    42
5    25 0.55    34
6    34 0.84    34
7     3 0.50    40
8    15 0.75    40
9    27 0.67    40
10   32 0.25    49
11   25 0.38    49
12   31 0.71    49
13   33 0.67    49
14   13 0.16    30
15   21 0.14    30
16   23 0.80    30
17   15 0.02    20
18   17 0.07    20
19   12 0.43    20
20   19 0.60    20
21   14 0.78    40
22   14 0.88    40
23   22 0.17    40
24   25 0.13    40
25   40 0.09    40
26   51 0.05    40
27   67 0.05    40
28   24 0.43    16
29   25 0.10    16
30   32 0.34    16

aqp documentation built on May 31, 2017, 2:24 a.m.