estimateSoilDepth {aqp} R Documentation

## 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 = hzdesgnname(f),
p = "Cr|R|Cd",
selection = min,
no.contact.depth = NULL,
no.contact.assigned = NULL
)
```

### Arguments

 `f` SoilProfileCollection object of length 1, e.g. a single profile `name` name of the column that contains horizon designations `p` REGEX pattern for determining "contact", or depth to some morphologic feature (e.g. `Bt`) `selection` an R function applied in the presence of multiple matching horizons: `min` (default), `max`, `mean`, etc. `no.contact.depth` in the absence of contact matching `p`, a depth at which we can assume a standard depth-to-contact `no.contact.assigned` value assigned when no contact is encountered at or below `no.contact.depth`

### Details

The choice of a `selection` function usually follows:

`min`: the top of the first matching horizon, `max`: the top bot the last matching horizon, or possibly `mean`: somewhere in-between.

### Value

single value representing the depth to `contact` or `no.contact.assigned`

### Author(s)

D.E. Beaudette and J.M. Skovlin

`getSoilDepthClass`, `profileApply`

### Examples

```

## consider a situation where there were multiple candidate
## "contacts": 2 Cd horizons over an R

# init hypothetical profile
d <- data.frame(
id = '1',
top = c(0, 10, 20, 30, 40, 50, 60),
bottom = c(10, 20, 30, 40, 50, 60, 80),
name = c('A', 'Bt1', 'Bt2', 'BC', 'Cd1', 'Cd2', 'R'),
stringsAsFactors = FALSE
)

depths(d) <- id ~ top + bottom

# init horizon designation
hzdesgnname(d) <- 'name'

# visual check
par(mar = c(0, 0, 0, 1))
plotSPC(d, hz.depths = TRUE, name.style = 'center-center', cex.names = 1, width = 0.1)

# top of the first Cd
estimateSoilDepth(d, name = 'name')

# top of the first Cd
estimateSoilDepth(d, name = 'name', selection = min)

# top of the R
estimateSoilDepth(d, name = 'name', selection = max)

# top of the second Cd
estimateSoilDepth(d, name = 'name', selection = max, p = 'Cd')

## another example

data(sp1)
depths(sp1) <- id ~ top + bottom

# init horizon designation
hzdesgnname(d) <- 'name'

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

# 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',
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
plotSPC(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, ], name = 'hzname')

# apply to an entire collection
profileApply(gopheridge, estimateSoilDepth, name = 'hzname')

## End(Not run)
```

[Package aqp version 1.40 Index]