afss: Africa Sentinel Site data (wet chemistry)
In soil.spec: Soil Spectroscopy Tools and Reference Models

Description Usage Format Note Author(s) References Examples

Africa soil sampled collected at AfSIS sentinel sites. Part of the African Land Degradation Surveillance Framework (LDSF) Field Database.

1	data(afss)

The afss data set contains two data frames — sites and horizons. Sites table contains the following columns:

SOURCEID: factor; study soil profile ID (SPID in the LDSF Field Database)
CNTISOC: factor; ISO country code (CC in the LDSF Field Database)
LOCNAME: factor; sentinel site name referring to the closest populated place (Site in the LDSF Field Database)
LONWGS84: numeric; longitude in decimal degrees on the WGS84 datum (Lon in the LDSF Field Database)
LATWGS84: numeric; latitude in decimal degrees on the WGS84 datum (Lat in the LDSF Field Database)

Horizons table contains the following columns:

SOURCEID: factor; study soil profile ID (SPID in the LDSF Field Database)
SAMPLEID: factor; soil sample ID (SSID in the LDSF Field Database)
UHDICM: numeric; upper sampling depth from the surface in cm
LHDICM: numeric; lower sampling depth from the surface in cm
ORCCNS: numeric; soil organic carbon content in permille (SOC in the LDSF Field Database)
PHIHOX: numeric; pH index measured in water solution (pH in the LDSF Field Database)
EXB: numeric; Exchangeable bases in ppm (ExBas in the LDSF Field Database)
ALUM3S: numeric; Aluminium concentration in ppm (m3.Al in the LDSF Field Database)
ECAM3S: numeric; Exchangeable Ca in cmolc/kg (ExCa in the LDSF Field Database)
EXKM3S: numeric; Exchangeable K in cmolc/kg (ExK in the LDSF Field Database)
EMGM3S: numeric; Exchangeable Mg in cmolc/kg (ExMg in the LDSF Field Database)
ENAM3S: numeric; Exchangeable Mg in cmolc/kg (ExNa in the LDSF Field Database)
NITCNS: numeric; Exchangeable N as volumetric percentage (Total.Nitrogen in the LDSF Field Database)
SNDLDF: numeric; weight percentage of the sand particles (0.05–2.0 mm; Sand in the LDSF Field Database)

afss.spec table contains the following columns:

SAMPLEID: factor; soil sample ID (SSID in the LDSF Field Database)
m4003.5: numeric; mid-infrared raw absorbance for denoted wavenumbers (Bruker-LTS instrument)
...: other raw absorbance values

The soil samples from the sentinel site network were collected using three stage sampling scheme: a number of sentinel sites (about 10 by 10 kilometers in size) have been first selected over the whole continent (60 sites in 2012). Each sentinel site is stratied into 16 grid cells (each 1 square kilometer), and sampling cluster centroids are randomly located within the grid cells. Around each centroid, 10 sampling plots are randomly located and soil samples taken (or 160 points per sentinel site). At each sampling plot, soil samples were taken at two depths: 0–20, and 20–50 cm. The block size of each sampling plot is 1000 square meters or 0.1 ha. All of the initial Mehlich-3 nutrient concentrations were in mg/kg (or ppm) units, and were converted to molar equivalent units in cmolc/kg (xCa = Ca/200, xK = K/391, xMg = Mg/121, xNa = Na/230).

Africa Soil Information Service (http://africasoils.net)

Vagen, T., Shepherd, K. D., Walsh, M. G., Winowiecki, L., Desta, L. T., & Tondoh, J. E. (2010) AfSIS technical specifications: soil health surveillance. World Agroforestry Centre, Nairobi, Kenya.

library(sp)
library(rgdal)

data(afss)
xy <- afss$sites
coordinates(xy) <- ~ LONWGS84 + LATWGS84
proj4string(xy) <- "+proj=longlat +datum=WGS84"
xy$PHIHOX_d1 <- merge(xy@data, afss$horizons[afss$horizons$UHDICM==0,], all.x=TRUE)$PHIHOX

## Not run: 
## plot points in Google Earth:
library(plotKML)
data(R_pal)
plotKML(xy["PHIHOX_d1"], colour_scale=R_pal[["pH_pal"]])

## obtain country borders:
con.admin <- url("http://gsif.isric.org/lib/exe/fetch.php?media=admin.af.rda")
load(con.admin)
proj4string(admin.af) <- get("ref_CRS", envir = plotKML.opts)
admin.af <- as(admin.af, "SpatialLines") 
## overlay and plot points and maps:
plot(admin.af, col="darkgrey", xlim=xy@bbox[1,], ylim=xy@bbox[2,])
points(xy, pch=21, bg="white", cex=.6, col="black")

## obtain MIR measurements for AfSS samples:
con <- url("http://gsif.isric.org/lib/exe/fetch.php?media=afss.spec.rda")
load(con)
str(afss.spec)

## End(Not run)