Sample soil spectroscopy data from Africa Sentinel Sites

Description

Sample data (113 samples) containing absorbances in the Mid infrared region (MIR) collected at 57 sites (Africa Sentinel Sites).

Usage

data(afspec)

Format

The afspec data set contains two data frames — "samples" and "ab". "samples" table contains the following columns:

SAMPLEID

factor; unique soil sample ID (duplicate IDs are possible as same soil sample can be measured twice)

Cluster

integer; Africa Sentinel Sites cluster number

Plot

integer; Africa Sentinel Sites plot number

Depth

factor; lower depth of the sampled horizon

Site

factor; site name

Country

factor; country name

Region

factor; region name

Longitude

numeric; longitude in decimal degrees on the WGS84 datum (Lat in the LDSF Field Database)

Latitude

numeric; latitude in decimal degrees on the WGS84 datum (Lat in the LDSF Field Database)

"ab" table contains the following columns:

SAMPLEID

factor; ...

m4003.5..m599.8

numeric; mid-infrared raw absorbance for denoted wavenumbers (Bruker-LTS instrument)

...

other raw absorbance values

Author(s)

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

References

• 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.

• World Agroforestry Centre (http://worldagroforestry.org)

Examples

library(sp)
library(rgdal)
data(afspec)
sp <- afspec$samples[,c("Longitude","Latitude")]
coordinates(sp) <- ~Longitude+Latitude
proj4string(sp) <- CRS("+proj=longlat +datum=WGS84")
## prepare 'samples' table
samples <- cbind(afspec$samples["SAMPLEID"], 
    MID="AfSIS-MIR", 
    DateTime=Sys.time())
## convert to "SpectraPoints"
afspec.sp <- SpectraPoints(Spectra=Spectra(samples, afspec$ab), sp=sp)
summary(afspec.sp)
get("attributes", spec.opts)
## predict soil pH:
data(m.PHIHOX)
PHIHOX <- predict(afspec.sp, model=m.PHIHOX)
data(m.ORCCNS)
ORCCNS <- predict(afspec.sp, model=m.ORCCNS)
## Not run: 
library(plotKML)
afspec.pnts <- SpatialPointsDataFrame(sp, cbind(PHIHOX, ORCCNS))
data(SAGA_pal)
plotKML(afspec.pnts["PHIHOX"], colour_scale=rev(SAGA_pal[[1]]))
plotKML(afspec.pnts["ORCCNS"], colour_scale=SAGA_pal[[1]])
## plot with global soil legends:
library(GSIF)
data(soil.legends)
brks = c(soil.legends[["PHIHOX"]]$MIN[1]/10, soil.legends[["PHIHOX"]]$MAX/10)
pH.range <- cbind(soil.legends[["PHIHOX"]]$MAX, soil.legends[["PHIHOX"]]$MIN)
levs = paste(signif(rowMeans(pH.range)/10, 2))
afspec.pnts$Col <- cut(afspec.pnts$PHIHOX, breaks=brks, labels=levs)
plotKML(afspec.pnts["Col"], colour_scale=soil.legends[["PHIHOX"]]$COLOR)

## End(Not run)