Chapter 3 Soil Data
3.1 Soil organic carbon (SOC) ground measurements
SOC concentration samples (g kg-1) were acquired from the Rapid Carbon Assessment Project (RCAP) using the SoilWeb RaCA Query API and the SoilDB package. This database contains standardized soil data of 38 RACA sites, 188 profiles and 846 horizons, and a Depth range of 26 - 203 cm.
3.2 Some Libraries
library(soilDB)
require(aqp)
library(plyr)
library(maps)
library(lattice)
library(reshape2)
library(cluster)
library(GSIF)
library(tidyverse)
library(rgdal)
library(sp)
3.3 Input data in R
## SoilProfileCollection with 6 profiles and 25 horizons
## profile ID: rcapid | horizon ID: phiid
## Depth range: 95 - 100 cm
##
## ----- Horizons (6 / 25 rows | 10 / 23 columns) -----
## hzname rcapid phiid hzdept hzdepb clay silt sand texture_class phfield
## Ap1 C1201C061 2944764 0 5 NA NA NA l NA
## Ap2 C1201C061 2944765 5 28 NA NA NA l NA
## Bt C1201C061 2944766 28 54 NA NA NA sl NA
## C C1201C061 2944767 54 100 NA NA NA lcos NA
## Ap1 C1201C062 2944760 0 5 NA NA NA l NA
## Ap2 C1201C062 2944761 5 30 NA NA NA l NA
## [... more horizons ...]
##
## ----- Sites (6 / 6 rows | 10 / 54 columns) -----
## rcapid peiid siteiid pedon_id rcasiteid rcapointnumber plotconfig
## C1201C061 636193 642286 C1201C06-1 C1201C06 1 Standard cluster
## C1201C062 636192 642286 C1201C06-2 C1201C06 2 Standard cluster
## C1201C063 636194 642286 C1201C06-3 C1201C06 3 Standard cluster
## C1201C064 636195 642286 C1201C06-4 C1201C06 4 Standard cluster
## C1201C065 636196 642286 C1201C06-5 C1201C06 5 Standard cluster
## C1201F291 636197 642287 C1201F29-1 C1201F29 1 Standard cluster
## exposedsoilpct azimuthfromplotcenter distancefromplotcenter
## 10 0 1
## 10 360 30
## 10 90 30
## 10 180 30
## 10 270 30
## 0 30 180
##
## Spatial Data:
## [EMPTY]# Extract and add carbon data to the SPC
site(rData) <- r.state$stock
# convert taxonname to a factor
rData$taxonname <- factor(rData$taxonname)
# Create a dataframe with site/horizon and cstock
nData <- merge(rData@horizons,rData@site)
# Check the data type
class(nData)## [1] "data.frame"3.4 Create the SOC data
# Select Soil and Site Data
mSoil <- nData %>% dplyr::select(rcapid, phiid, hzdept, hzdepb, value_30cm, clay, silt, sand, total_frags_pct)
mSites <- nData %>% dplyr::select(rcapid, tax_subgroup, x, y)
# Rename the Columns
names(mSoil)[c(1,2,3,4,5,9)] <- c("ProfID", "HorID", "top", "bottom", "SOC", "CRFVOL")
names(mSites)[c(1,2,3,4)] <- c("ProfID", "soiltype", "X", "Y") # X== -Ve n Y = +Ve
# Add index number to data
X.1 = row.names(mSites)
mSites <- cbind(X.1, mSites)
mSites$X.1 = as.integer(mSites$X.1)# Promote to SoilProfileCollection
# The SoilProfileCollection is a object class in R designed to handle soil profile data
depths(mSoil) <- ProfID ~ top + bottom
class(mSoil)## [1] "SoilProfileCollection"
## attr(,"package")
## [1] "aqp"