| SoilTaxonomyDendrogram {sharpshootR} | R Documentation |
Plot a dendrogram based on the first 4 levels of Soil Taxonomy, with soil profiles hanging below. A dissimmilarity 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.
SoilTaxonomyDendrogram(spc, name = "hzname", 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, cex.taxon.labels = 0.66)
spc |
a |
name |
column name containing horizon names |
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 |
cex.taxon.labels |
character scaling for taxonomic information |
This function looks for specific site-level attributes named: soilorder, suborder, greatgroup, and subgroup.
An invisibly-returned list containing:
distpair-wise dissimilarity matrix
D.E. Beaudette
D.E. Beaudette, P. Roudier and A.T. O'Geen. 2012. Algorithms for Quantitative Pedology, a Toolkit for Soil Scientists. Computers & Geosciences: 52: 258–268. (doi: 10.1016/j.cageo.2012.10.020)
http://aqp.r-forge.r-project.org/
## Not run:
##D library(soilDB)
##D
##D # soils of interest
##D s.list <- c('musick', 'cecil', 'drummer', 'amador', 'pentz', 'reiff',
##D 'san joaquin','montpellier','grangeville','pollasky','ramona')
##D
##D # fetch and convert data into an SPC
##D h <- fetchOSD(s.list)
##D
##D # plot dendrogram + profiles
##D SoilTaxonomyDendrogram(h)
##D
##D # again, this time save the pair-wise dissimilarity matrix
##D # note that there isn't a lot of discrimination between soils
##D (d <- SoilTaxonomyDendrogram(h))
## End(Not run)