| sp4 {aqp} | R Documentation |
Soil Chemical Data from Serpentinitic Soils of California
data(sp4)
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
Selected soil physical and chemical data from (McGahan et al., 2009).
https://www.soils.org/publications/sssaj/articles/73/6/2087
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.
# setup environment
library(aqp)
# load sample data set, a simple data.frame object with horizon-level data from 10 profiles
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 ...
# 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
## [1] "SoilProfileCollection"
## attr(,"package")
## [1] "aqp"
str(sp4) # internal structure
## 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
# 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
## Error in metadata(sp4): no slot of name "history" for this object of class "SoilProfileCollection"
# 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
## Error in metadata(sp4): no slot of name "history" for this object of class "SoilProfileCollection"
# add columns
md$describer <- 'DGM'
## Error in md$describer <- "DGM": object 'md' not found
md$date <- as.Date('2009-01-01')
## Error in md$date <- as.Date("2009-01-01"): object 'md' not found
md$citation <- 'McGahan, D.G., Southard, R.J, Claassen, V.P.
2009. Plant-Available Calcium Varies Widely in Soils
on Serpentinite Landscapes. Soil Sci. Soc. Am. J. 73: 2087-2095.'
## Error in md$citation <- "McGahan, D.G., Southard, R.J, Claassen, V.P. \n2009. Plant-Available Calcium Varies Widely in Soils \non Serpentinite Landscapes. Soil Sci. Soc. Am. J. 73: 2087-2095.": object 'md' not found
# re-assign
metadata(sp4) <- md
## Error in eval(expr, envir, enclos): object 'md' not found
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
## "silt" "clay" "CF"
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
## 1 colusa A 0 3 0.3 25.7 9.0 23.0 0.35 46
## 2 colusa ABt 3 8 0.2 23.7 5.6 21.4 0.23 42
## 3 colusa Bt1 8 30 0.1 23.2 1.9 23.7 0.08 40
## 4 colusa Bt2 30 42 0.1 44.3 0.3 43.0 0.01 27
## 5 glenn A 0 9 0.2 21.9 4.4 18.8 0.20 54
## 6 glenn Bt 9 34 0.3 18.9 4.5 27.5 0.20 49
## 7 kings A 0 4 0.2 12.1 1.4 23.7 0.58 43
## 8 kings Bt1 4 13 0.6 12.1 7.0 18.0 0.51 36
## 9 kings Bt2 13 40 0.8 17.7 4.4 20.0 0.25 27
## 19 mariposa A 0 3 0.6 28.3 5.8 29.3 0.20 42
## 20 mariposa Bt1 3 14 0.4 33.7 6.2 27.9 0.18 41
## 21 mariposa Bt2 14 34 0.3 44.3 6.2 34.1 0.14 36
## 22 mariposa Bt3 34 49 0.1 78.2 4.4 43.6 0.06 36
## 23 mendocino A 0 2 0.5 12.8 2.2 19.3 0.18 57
## 24 mendocino Bt1 2 8 0.2 27.1 3.4 19.8 0.13 51
## 25 mendocino Bt2 8 30 0.2 30.5 3.7 22.9 0.12 51
## 10 napa A 0 6 0.4 16.4 24.1 31.1 1.47 43
## 11 napa Bt 6 20 0.1 16.2 21.5 27.9 1.32 54
## 12 san benito A 0 8 NA 3.0 0.7 3.1 0.24 80
## 13 san benito Bt 8 20 0.0 0.1 5.6 5.6 0.11 74
## 14 shasta A 0 3 0.3 9.7 3.5 13.2 0.36 37
## 15 shasta Bt 3 40 0.2 10.1 2.0 12.2 0.20 39
## 26 shasta-trinity A1 0 2 0.2 18.8 6.6 23.0 0.35 34
## 27 shasta-trinity A2 2 5 0.2 25.5 4.1 21.5 0.16 33
## 28 shasta-trinity AB 5 12 0.3 29.3 3.5 29.6 0.12 24
## 29 shasta-trinity Bt1 12 23 0.2 30.3 1.5 26.5 0.05 20
## 30 shasta-trinity Bt2 23 40 0.1 64.9 0.8 48.7 0.01 11
## 16 tehama A 0 3 0.4 12.4 16.3 40.2 1.31 57
## 17 tehama Bt1 3 7 0.5 20.2 16.5 32.7 0.82 55
## 18 tehama Bt2 7 16 0.2 27.7 13.7 30.0 0.50 51
## silt clay CF
## 1 33 21 0.12
## 2 31 27 0.27
## 3 28 32 0.27
## 4 18 55 0.16
## 5 20 25 0.55
## 6 18 34 0.84
## 7 55 3 0.50
## 8 49 15 0.75
## 9 45 27 0.67
## 19 26 32 0.25
## 20 34 25 0.38
## 21 33 31 0.71
## 22 31 33 0.67
## 23 30 13 0.16
## 24 28 21 0.14
## 25 26 23 0.80
## 10 42 15 0.02
## 11 29 17 0.07
## 12 8 12 0.43
## 13 7 19 0.60
## 14 49 14 0.78
## 15 46 14 0.88
## 26 44 22 0.17
## 27 42 25 0.13
## 28 36 40 0.09
## 29 29 51 0.05
## 30 22 67 0.05
## 16 19 24 0.43
## 17 20 25 0.10
## 18 17 32 0.34
# 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
## [24] 25 40 51 67 24 25 32
# subsetting SoilProfileCollection objects
sp4[1, ] # first profile in the collection
## 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
## 1 colusa A 0 3 0.3 25.7 9.0 23.0 0.35 46 33 21
## 2 colusa ABt 3 8 0.2 23.7 5.6 21.4 0.23 42 31 27
## 3 colusa Bt1 8 30 0.1 23.2 1.9 23.7 0.08 40 28 32
## 4 colusa Bt2 30 42 0.1 44.3 0.3 43.0 0.01 27 18 55
## CF
## 1 0.12
## 2 0.27
## 3 0.27
## 4 0.16
##
## Sampling site attributes:
## id
## 1 colusa
##
## Spatial Data:
## [,1]
## [1,] NA
## [1] NA
sp4[, 1] # first horizon from each profile
## 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
## 1 colusa A 0 3 0.3 25.7 9.0 23.0 0.35 46 33 21
## 2 glenn A 0 9 0.2 21.9 4.4 18.8 0.20 54 20 25
## 3 kings A 0 4 0.2 12.1 1.4 23.7 0.58 43 55 3
## 4 mariposa A 0 3 0.6 28.3 5.8 29.3 0.20 42 26 32
## 5 mendocino A 0 2 0.5 12.8 2.2 19.3 0.18 57 30 13
## 6 napa A 0 6 0.4 16.4 24.1 31.1 1.47 43 42 15
## CF
## 1 0.12
## 2 0.55
## 3 0.50
## 4 0.25
## 5 0.16
## 6 0.02
##
## Sampling site attributes:
## id
## 1 colusa
## 2 glenn
## 3 kings
## 4 mariposa
## 5 mendocino
## 6 napa
# 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
## 1 colusa A 0 3 0.3 25.7 9.0 23.0 0.35 46
## 2 colusa ABt 3 8 0.2 23.7 5.6 21.4 0.23 42
## 3 colusa Bt1 8 30 0.1 23.2 1.9 23.7 0.08 40
## 4 colusa Bt2 30 42 0.1 44.3 0.3 43.0 0.01 27
## 5 glenn A 0 9 0.2 21.9 4.4 18.8 0.20 54
## 6 glenn Bt 9 34 0.3 18.9 4.5 27.5 0.20 49
## 7 kings A 0 4 0.2 12.1 1.4 23.7 0.58 43
## 8 kings Bt1 4 13 0.6 12.1 7.0 18.0 0.51 36
## 9 kings Bt2 13 40 0.8 17.7 4.4 20.0 0.25 27
## 10 mariposa A 0 3 0.6 28.3 5.8 29.3 0.20 42
## 11 mariposa Bt1 3 14 0.4 33.7 6.2 27.9 0.18 41
## 12 mariposa Bt2 14 34 0.3 44.3 6.2 34.1 0.14 36
## 13 mariposa Bt3 34 49 0.1 78.2 4.4 43.6 0.06 36
## 14 mendocino A 0 2 0.5 12.8 2.2 19.3 0.18 57
## 15 mendocino Bt1 2 8 0.2 27.1 3.4 19.8 0.13 51
## 16 mendocino Bt2 8 30 0.2 30.5 3.7 22.9 0.12 51
## 17 napa A 0 6 0.4 16.4 24.1 31.1 1.47 43
## 18 napa Bt 6 20 0.1 16.2 21.5 27.9 1.32 54
## 19 san benito A 0 8 NA 3.0 0.7 3.1 0.24 80
## 20 san benito Bt 8 20 0.0 0.1 5.6 5.6 0.11 74
## 21 shasta A 0 3 0.3 9.7 3.5 13.2 0.36 37
## 22 shasta Bt 3 40 0.2 10.1 2.0 12.2 0.20 39
## 23 shasta-trinity A1 0 2 0.2 18.8 6.6 23.0 0.35 34
## 24 shasta-trinity A2 2 5 0.2 25.5 4.1 21.5 0.16 33
## 25 shasta-trinity AB 5 12 0.3 29.3 3.5 29.6 0.12 24
## 26 shasta-trinity Bt1 12 23 0.2 30.3 1.5 26.5 0.05 20
## 27 shasta-trinity Bt2 23 40 0.1 64.9 0.8 48.7 0.01 11
## 28 tehama A 0 3 0.4 12.4 16.3 40.2 1.31 57
## 29 tehama Bt1 3 7 0.5 20.2 16.5 32.7 0.82 55
## 30 tehama Bt2 7 16 0.2 27.7 13.7 30.0 0.50 51
## silt clay CF depth
## 1 33 21 0.12 42
## 2 31 27 0.27 42
## 3 28 32 0.27 42
## 4 18 55 0.16 42
## 5 20 25 0.55 34
## 6 18 34 0.84 34
## 7 55 3 0.50 40
## 8 49 15 0.75 40
## 9 45 27 0.67 40
## 10 26 32 0.25 49
## 11 34 25 0.38 49
## 12 33 31 0.71 49
## 13 31 33 0.67 49
## 14 30 13 0.16 30
## 15 28 21 0.14 30
## 16 26 23 0.80 30
## 17 42 15 0.02 20
## 18 29 17 0.07 20
## 19 8 12 0.43 20
## 20 7 19 0.60 20
## 21 49 14 0.78 40
## 22 46 14 0.88 40
## 23 44 22 0.17 40
## 24 42 25 0.13 40
## 25 36 40 0.09 40
## 26 29 51 0.05 40
## 27 22 67 0.05 40
## 28 19 24 0.43 16
## 29 20 25 0.10 16
## 30 17 32 0.34 16