sp4: Soil Chemical Data from Serpentinitic Soils of California
In aqp: Algorithms for Quantitative Pedology
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.
idsite name
namehorizon designation
tophorizon top boundary in cm
bottomhorizon bottom boundary in cm
Kexchangeable K in c mol/kg
Mgexchangeable Mg in cmol/kg
Caexchangeable Ca in cmol/kg
CEC_7cation exchange capacity (NH4OAc at pH 7)
ex_Ca_to_Mgextractable Ca:Mg ratio
sandsand content by weight percentage
siltsilt content by weight percentage
clayclay 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.
Examples
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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 2, 2019, 4:51 p.m.
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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.
idsite name
namehorizon designation
tophorizon top boundary in cm
bottomhorizon bottom boundary in cm
Kexchangeable K in c mol/kg
Mgexchangeable Mg in cmol/kg
Caexchangeable Ca in cmol/kg
CEC_7cation exchange capacity (NH4OAc at pH 7)
ex_Ca_to_Mgextractable Ca:Mg ratio
sandsand content by weight percentage
siltsilt content by weight percentage
clayclay 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.
Examples
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 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 | # 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
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