Objectives

Using the concepts (and code) from the Numerical Taxonomy and Ordination chapter, compute pair-wise distances between soil series concepts from a suite of 8 physical and climatic variables. These 8 variables (characteristics) will be used to develop a climate signature for each soil series (individual). Present and interpret the results using both a dendrogram and ordination.

Key steps:

Brief Description of the Data Source

Annual and monthly climate summaries have been estimated from the SSR2 standard stack of 1981–2010 PRISM data. Weighted percentiles were estimated from a single sample from within each map unit delineation, weighted by


log(polygon area * component percentage)

We will be using the annual climate summaries. See this document for more information on how summaries like these have been developed and how to access them via fetchOSD.

Setup

First, you will need to load some packages. If you have completed the pre-class assignment then all of these packages should be in place.

library(soilDB)
library(sharpshootR)
library(latticeExtra)
library(reshape2)
library(RColorBrewer)
library(cluster)
library(ape)
library(vegan)
library(MASS)

An Example

The fetchOSD function from the soilDB package is a simple interface data that have been extracted from the text OSDs and summarized from the current SSURGO snapshot. The extended=TRUE argument is used to access the climate data we will be using in this assignment.

soils <- c('Ava', 'Drummer', 'Cisne', 'Pierre', 'Cecil', 'Appling', 'San Joaquin', 'Redding', 'Corning')
s <- fetchOSD(soils, extended = TRUE)
Select percentiles are provided for 7 annual climate summaries and elevation. Note that “q50” is the median value and “n” is the number of samples (i.e. number of delineations) used to estimate the percentiles.
series climate_var minimum q01 q05 q25 q50 q75 q95 q99 maximum n
APPLING Elevation (m) 1.00 55.00 74.00 115.00 178.00 245.00 311.00 353.00 486.00 95707
APPLING Effective Precipitation (mm) 156.63 238.02 270.79 333.11 358.18 407.95 491.55 551.45 903.67 95707
APPLING Frost-Free Days 177.00 188.00 193.00 200.00 212.00 225.00 233.00 236.00 251.00 95707
APPLING Mean Annual Air Temperature (degrees C) 11.52 12.98 13.30 13.88 15.33 16.24 16.76 17.30 18.01 95707
APPLING Mean Annual Precipitation (mm) 1031.00 1068.00 1082.00 1113.00 1146.00 1241.00 1315.00 1347.00 1695.00 95707
APPLING Growing Degree Days (degrees C) 1976.00 2290.00 2362.00 2475.00 2723.00 2928.00 3056.00 3176.00 3333.00 95707
APPLING Fraction of Annual PPT as Rain 95.00 95.00 96.00 96.00 98.00 99.00 99.00 99.00 100.00 95707
APPLING Design Freeze Index (degrees C) 25.00 30.00 34.00 49.00 76.00 135.00 166.00 182.00 259.00 95707

The data look something like this. Your assignment is to compute pair-wise distances between series concepts, using median values (filled circles in the figure) from these data.