| diagnosticPropertyPlot {sharpshootR} | R Documentation |
Generate a graphical description of the presence/absence of soil diagnostic properties.
diagnosticPropertyPlot(f, v, k, grid.label='pedon_id', dend.label='pedon_id') diagnosticPropertyPlot2(f, v, k, grid.label='pedon_id')
f |
a |
v |
a character vector of site-level attribute names that are boolean (e.g. TRUE/FALSE) data |
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 |
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.
a list is silently returned by this function, containing:
rda data.frame containing IDs and grouping code
profile.ordera vector containing the order of soil profiles (row-order in figure), according to diagnostic property values
var.ordera vector containing the order of variables (column-order in figure), according to their distribution among profiles
D.E. Beaudette and J.M. Skovlin
## Not run:
##D # sample data, an SPC
##D data(gopheridge, package='soilDB')
##D
##D # get depth class
##D sdc <- getSoilDepthClass(gopheridge)
##D site(gopheridge) <- sdc
##D
##D # diagnostic properties to consider, no need to convert to factors
##D v <- c('lithic.contact', 'paralithic.contact', 'argillic.horizon',
##D 'cambic.horizon', 'ochric.epipedon', 'mollic.epipedon', 'very.shallow',
##D 'shallow', 'mod.deep', 'deep', 'very.deep')
##D
##D # base graphics
##D x <- diagnosticPropertyPlot(gopheridge, v, k=5)
##D
##D # lattice graphics
##D x <- diagnosticPropertyPlot2(gopheridge, v, k=3)
##D
##D # check output
##D str(x)
## End(Not run)