SoilTaxonomyDendrogram: Soil Taxonomy Dendrogram

In sharpshootR: A Soil Survey Toolkit

Description

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.

Usage

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)

Arguments

spc	a SoilProfileCollection object, see details
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

Details

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

Value

An invisibly-returned list containing:

dist

pair-wise dissimilarity matrix

Author(s)

D.E. Beaudette

References

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/

Examples

## Not run: 
library(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))

## End(Not run)

sharpshootR documentation built on May 2, 2019, 4:46 p.m.