sharpshootR (version 1.8)

SoilTaxonomyDendrogram: Soil Taxonomy Dendrogram

Description

Plot a dendrogram based on the first 4 levels of Soil Taxonomy, with soil profiles hanging below. A dissimilarity matrix is computed using Gower's distance metric for nominal-scale variables, based on order, sub order, great group, and subgroup level taxa. See the Details and Examples sections below for more information.

Usage

SoilTaxonomyDendrogram(
  spc,
  name = "hzname",
  name.style = "right-center",
  rotationOrder = NULL,
  max.depth = 150,
  n.depth.ticks = 6,
  scaling.factor = 0.015,
  cex.names = 0.75,
  cex.id = 0.75,
  axis.line.offset = -4,
  width = 0.1,
  y.offset = 0.5,
  shrink = FALSE,
  font.id = 2,
  cex.taxon.labels = 0.66,
  dend.color = par("fg"),
  dend.width = 1,
  ...
)

Arguments

spc

a SoilProfileCollection object, typically returned by soilDB::fetchOSD

name

column name containing horizon names

name.style

passed to aqp::plotSPC (default: "right-center")

rotationOrder

numeric vector with desired ordering of leaves in the dendrogram from left to right, or character vector matching profile IDs

max.depth

depth at which profiles are truncated for plotting

n.depth.ticks

suggested number of ticks on the depth axis

scaling.factor

scaling factor used to convert depth units into plotting units

cex.names

character scaling for horizon names

cex.id

character scaling for profile IDs

axis.line.offset

horizontal offset for depth axis

width

width of profiles

y.offset

vertical offset between dendrogram and profiles

shrink

logical, should long horizon names be shrunk by 80% ?

font.id

font style applied to profile id, default is 2 (bold)

cex.taxon.labels

character scaling for taxonomic information

dend.color

dendrogram line color

dend.width

dendrogram line width

...

additional arguments to aqp::plotSPC

Value

An invisibly-returned list containing:

• dist: pair-wise dissimilarity matrix

• order: final ordering of hclust leaves

Details

This function looks for specific site-level attributes named: soilorder, suborder, greatgroup, and subgroup.

The rotationOrder argument uses (requires) the dendextend::rotate() function to re-order leaves within the hclust representation of the ST hierarchy. Perfect sorting is not always possible.

Examples

# NOT RUN {
# }
# NOT RUN {
if(requireNamespace("curl") &
   curl::has_internet() &
   require(aqp) &
   require(soilDB)
) {
  
  
  
  # soils of interest
  s.list <- c('musick', 'cecil', 'drummer', 'amador', 'pentz', 'reiff', 
              'san joaquin','montpellier','grangeville','pollasky','ramona')
  
  # fetch and convert data into an SPC
  h <- fetchOSD(s.list)
  
  # plot dendrogram + profiles
  SoilTaxonomyDendrogram(h)
  
  # again, this time save the pair-wise dissimilarity matrix
  # note that there isn't a lot of discrimination between soils
  (d <- SoilTaxonomyDendrogram(h))
  
  
  # a different set
  soils <- c('cecil', 'altavista', 'lloyd', 'wickham', 'wilkes',
             'chewacla', 'congaree')
  
  # get morphology + extended summaries for sorting of dendrogram
  s <- fetchOSD(soils, extended = TRUE)
  
  # get summary and ignore the figure
  res <- vizHillslopePosition(s$hillpos)
  
  # compare default sorting to soils sorting according to catenary, e.g.
  # hillslope position
  par(mar=c(0,0,1,1), mfrow=c(2,1))
  
  SoilTaxonomyDendrogram(s$SPC, width=0.25)
  mtext('default sorting', side = 2, line=-1, font=3, cex=1.25)
  
  SoilTaxonomyDendrogram(s$SPC, rotationOrder = res$order, width=0.25)
  mtext('approx. catenary sorting', side = 2, line=-1, font=3, cex=1.25)
 
  
# classic chronosequence from the San Joaquin Valley, CA
library(aqp)
library(soilDB)
library(sharpshootR)

s <- c('tujunga', 'hanford', 'greenfield', 'snelling', 'san joaquin')
osds <- fetchOSD(s)

idx <- match(toupper(s), profile_id(osds))

# encode horizon boundarydistinctness via vertical offset
osds$hd <- hzDistinctnessCodeToOffset(
  osds$distinctness, 
  codes=c('very abrupt', 'abrupt', 'clear', 'gradual', 'diffuse')
)

# encode horizon boundary topography via vertical offset
osds$hzto <- hzTopographyCodeToOffset(
  osds$topography, 
  codes = c('smooth', 'wavy', 'irregular', 'broken')
)

# also encode horizon boundary topography las line type
osds$hzto.lty <- hzTopographyCodeToLineType(
  osds$topography,
  codes = c('smooth', 'wavy', 'irregular', 'broken')
)

# label data source, used later 
site(osds)$source <- 'OSD'

# concise representation of hz bnd distinctness and topography
# similar to field notes
osds$bnd.code <- sprintf(
  "%s%s",
  substr(osds$distinctness, 1, 1),
  substr(osds$topography, 1, 1)
)

# remove NA
osds$bnd.code <- gsub('NANA', '', osds$bnd.code)

par(mar = c(0, 0, 0, 1), bg = 'black', fg = 'white')

plotSPC(
osds, 
plot.order = idx, 
width = 0.3, 
name.style = 'center-center', 
cex.names = 0.66, 
plot.depth.axis = FALSE, 
hz.depths = TRUE, 
shrink = TRUE, 
hz.distinctness.offset = 'hd', 
hz.topography.offset = 'hzto', 
hz.boundary.lty = 'hzto.lty'
)

legend(
'bottomright', 
horiz = TRUE, 
legend = c('Smooth', 'Wavy', 'Irregular', 'Broken'), 
lty = 1:4, 
inset = 0.05, 
bty = 'n', 
cex = 0.85
)

# note that `rotationOrder` uses the ordering of series names (uppercase to match profile IDs)
# to re-order the terminal branches of the dendrogram
SoilTaxonomyDendrogram(
osds, 
rotationOrder = toupper(s), 
cex.taxon.labels = 0.85, 
width = 0.3, 
name.style = 'center-center', 
cex.names = 0.66, 
plot.depth.axis = FALSE, 
hz.depths = TRUE, 
shrink = TRUE, 
hz.distinctness.offset = 'hd', 
hz.topography.offset = 'hzto', 
hz.boundary.lty = 'hzto.lty'
)

legend(
'bottomright', 
horiz = TRUE, 
legend = c('Smooth', 'Wavy', 'Irregular', 'Broken'), 
lty = 1:4, 
inset = 0.05, 
bty = 'n', 
cex = 0.85
)
     
}

# }
# NOT RUN {
# }