diagnosticPropertyPlot: Diagnostic Property Plot (base graphics)

In sharpshootR: A Soil Survey Toolkit

Diagnostic Property Plot (base graphics)

Description

Generate a graphical description of the presence/absence of soil diagnostic properties.

Usage

diagnosticPropertyPlot(
  f,
  v,
  k,
  grid.label = "pedon_id",
  dend.label = "pedon_id",
  sort.vars = TRUE
)

Arguments

f	SoilProfileCollection object
v	character vector of site-level attribute names of logical type
k	an integer, number of groups to highlight
grid.label	the name of a site-level attribute (usually unique) annotating the y-axis of the grid
dend.label	the name of a site-level attribute (usually unique) annotating dendrogram terminal leaves
sort.vars	sort variables according to natural clustering (TRUE), or use supplied ordering in v

Details

This function attempts to display several pieces of information within a single figure. First, soil profiles are sorted according to the presence/absence of diagnostic features named in v. Second, these diagnostic features are sorted according to their distribution among soil profiles. Third, a binary grid is established with row-ordering of profiles based on step 1 and column-ordering based on step 2. Blue cells represent the presence of a diagnostic feature. Soils with similar diagnostic features should 'clump' together. See examples below.

Value

a list is silently returned by this function, containing:

rd

a data.frame containing IDs and grouping code

profile.order

a vector containing the order of soil profiles (row-order in figure), according to diagnostic property values

var.order

a vector containing the order of variables (column-order in figure), according to their distribution among profiles

Author(s)

D.E. Beaudette and J.M. Skovlin

See Also

multinominal2logical

Examples

if(require(aqp) &
   require(soilDB) &
   require(latticeExtra)
) {
  
  # sample data, an SPC
  data(gopheridge, package='soilDB')
  
  # get depth class
  sdc <- getSoilDepthClass(gopheridge, name = 'hzname')
  site(gopheridge) <- sdc
  
  # diagnostic properties to consider, no need to convert to factors
  v <- c('lithic.contact', 'paralithic.contact', 'argillic.horizon', 
         'cambic.horizon', 'ochric.epipedon', 'mollic.epipedon', 'very.shallow',
         'shallow', 'mod.deep', 'deep', 'very.deep')
  
  # base graphics
  x <- diagnosticPropertyPlot(gopheridge, v, k=5)
  
  # lattice graphics
  x <- diagnosticPropertyPlot2(gopheridge, v, k=3)
  
  # check output
  str(x)
  
}

sharpshootR documentation built on Oct. 23, 2024, 1:06 a.m.