aqp (version 1.19)

estimateSoilDepth: Estimate Soil Depth

Description

Estimate the soil depth of a single profile within a SoilProfileCollection object. This function would typically be called by profileApply.

Usage

estimateSoilDepth(f, name = "hzname", top = "hzdept", bottom = "hzdepb", p = 'Cr|R|Cd', 
no.contact.depth = NULL, no.contact.assigned = NULL)

Arguments

f

A SoilProfileCollection object of length 1, e.g. a single profile

name

the name of the column that contains horizon designations

top

the name of the column that contains horizon top depths

bottom

the name of the column that contains horizon bottom depths

p

a REGEX pattern for determining contact with bedrock

no.contact.depth

in the absense of contact with bedrock, a depth at which we can assume a standard depth

no.contact.assigned

assumed standard depth

Value

a single integer, the soil depth

See Also

getSoilDepthClass, profileApply

Examples

# NOT RUN {
data(sp1)
depths(sp1) <- id ~ top + bottom

# apply to each profile in a collection, and save as site-level attribute
sp1$depth <- profileApply(sp1, estimateSoilDepth, name='name', top='top', bottom='bottom')

# this function can be used to "find" depth to any feature 
# that can be defined via REGEX pattern matching on the horizon name
# for example, locate the depth to the top "Bt" horizon
# returning NA when there is no match
sp1$top_Bt <- profileApply(sp1, estimateSoilDepth, name='name', top='top', 
                           bottom='bottom', p='Bt', no.contact.depth=0, no.contact.assigned=NA)

# reduced margins
par(mar=c(1,1,1,2))
# adjust default y-offset and depth scaling for following examples
plot(sp1, y.offset=10, scaling.factor=0.5)

# get plotting parameters for profile widths and depth scaling factors
lsp <- get("last_spc_plot", envir = aqp.env)

# positions on x-axis, same for both depth and top "Bt" horizon
x.positions <- (1:length(sp1)) - lsp$width

# annotate contact with unicode right-arrow
# y-position is adjusted based on plot y-offset and scaling factor
y.positions <- lsp$y.offset + (sp1$depth * lsp$scaling.factor)
text(x.positions, y.positions, '\u2192', col='red', adj=1, cex=1.25, lwd=2)

# annotate top "Bt" depth with unicode right-arrow
# y-position is adjusted based on plot y-offset and scaling factor
y.positions <- lsp$y.offset + (sp1$top_Bt * lsp$scaling.factor)
text(x.positions, y.positions, '\u2192', col='blue', adj=1, cex=1.25, lwd=2)


# }
# NOT RUN {
# sample data
data(gopheridge, package='soilDB')

# run on a single profile
estimateSoilDepth(gopheridge[1, ])

# apply to an entire collection
profileApply(gopheridge, estimateSoilDepth)
# }