aqp (version 1.6)

addBracket: Add Depth Brackets

Description

Add depth-wise brackets to an existing plot of a SoilProfileCollection object.

Usage

addBracket(idx, top, bottom, tick.length = 0.05, 
arrow.length = 0.05, offset = -0.3, missing.bottom.depth = 25, 
...)

Arguments

idx

vector of integers, related to profile order: see details

top

numeric vector of bracket top depths

bottom

numeric vector of bracket bottom depths

tick.length

length of bracket "tick" mark

arrow.length

length of arrowhead

offset

numeric, length of left-hand offset from each profile

missing.bottom.depth

distance (in depth units) to extend brackets that are missing a lower depth

...

further arguments passed on to segments or arrows

Details

The idx argument is an integer index linking depth bracket top/bottom depths to a sketch of profiles generated by plot.SoilProfileCollection. See examples below.

See Also

plotSPC

Examples

# sample data
data(sp1)

# add color vector
sp1$soil_color <- with(sp1, munsell2rgb(hue, value, chroma))

# promote to SoilProfileCollection
depths(sp1) <- id ~ top + bottom

# plot profiles
plot(sp1)

# manually add depth bracket with + bottom
addBracket(1, 5, 75)
# mannual add depth bracket with no bottom depth
addBracket(2, 40, col='red')

# extract top/bottom depths associated with all A horizons
f <- function(i) {
  h <- horizons(i)
  idx <- grep('^A', h$name)
  c(min(h$top[idx]), max(h$bottom[idx], na.rm=TRUE))
}

# apply function to sp1, result is a list
a <- profileApply(sp1, f, simplify=FALSE)
# convert list into matrix
a <- do.call('rbind', a)

# generate index linking our top/bottom depths with original ordering
key <- match(row.names(a), profile_id(sp1))

# plot
plot(sp1)
# annotate with brackets 
addBracket(key, a[, 1], a[, 2])

# more interesting example using diagnostic horizons
if(require(soilDB)) {
  # load some sample data with diagnostic horizons
  data(loafercreek)
  
  # extract first 15 profiles
  x <- loafercreek[1:15, ]
  s <- site(x)

  # plot
  par(mar=c(0,0,0,0))
  plot(x, name='hzname', id.style='top')
  
  # add bracket describing the particle size control section, 
  # from site-level data
  addBracket(match(s$pedon_id, profile_id(x)), 
  s$psctopdepth, s$pscbotdepth, offset=-0.4)
  
  # add brackets describing the argillic horizon
  addDiagnosticBracket(x, 'argillic horizon', col='red')
  # add brackets describing paralithic contact
  addDiagnosticBracket(x, 'paralithic contact', col='blue')
}