paleotree (version 3.1.3)

twoWayEcologyCluster: R-Mode vs Q-Mode Two-Way Cluster Analyses and Abundance Plot for Community Ecology Data

Description

This mode plots both R-mode (across sites) and Q-mode (across taxa) dendrograms for a community ecology dataset, with branches aligned with a grid of dots representing the relative abundance of taxa at each site in the dataset.

Usage

twoWayEcologyCluster(xDist, yDist, propAbund, clustMethod = "average",
  marginBetween = 0.1, abundExpansion = 4, xAxisLabel = "Across Sites",
  yAxisLabel = "Across Taxa")

Arguments

xDist

The pair-wise distance matrix for the cluster diagram drawn along the horizontal axis of the graphic. Should be a distance matrix, or a matrix that can be coerced to a distance matrix, for the same number of units as rows in propAbund.

yDist

The pair-wise distance matrix for the cluster diagram drawn along the vertical axis of the graphic. Should be a distance matrix, or a matrix that can be coerced to a distance matrix, for the same number of units as columns in propAbund.

propAbund

A matrix of abundance data, preferably relative abundance scaled as proportions of the total number of individuals at each site. This data determines the size scale of the taxon/site dots.

clustMethod

The agglomerative clustering method used, as with argument method with function hclust. clustMethod must be one of "average" (the default method for this function, also known as average-linkage or as UPGMA), "ward.D", "ward.D2", "single", "complete", "mcquitty" (also known as WPGMA), "median" (also known as WPGMC) or "centroid" (also known as UPGMC).

marginBetween

Argument controlling space placed between the cluster diagrams and the abundance plot. Default is 0.1.

abundExpansion

An argument that is a multiplier controlling the size of dots plotted for reflecting relative abundance.

xAxisLabel

The label placed on the horizontal axis of the plot.

yAxisLabel

The label placed on the vertical axis of the plot.

Value

This function creates a plot, and returns nothing, not even invisible output.

Details

You might be able to apply this to datasets that aren't community ecology datasets of proportional abundance, but I can't guarantee pr even predict what will happen.

References

The function here was designed to emulate previous published 'two-way' cluster diagrams, particularly the one in Miller, 1988:

Miller, A. I. 1988. Spatial Resolution in Subfossil Molluscan Remains: Implications for Paleobiological Analyses. Paleobiology 14(1):91-103.

See Also

Several other functions for community ecology data in paleotree are described at the communityEcology help file. Also see the example dataset, kanto.

Examples

# NOT RUN {
library(vegan)

# generate random community ecology data
	# using a Poisson distribution
data<-matrix(rpois(5*7,1),5,7)

# relative abundance, distance matrices
propAbundMat<-t(apply(data,1,function(x) x/sum(x)))
rownames(propAbundMat)<-paste0("x", 1:nrow(propAbundMat))
colnames(propAbundMat)<-paste0("y", 1:ncol(propAbundMat))

siteDist<-vegdist(propAbundMat, "bray")
taxaDist<-vegdist(t(propAbundMat), "bray")

dev.new(width=10)	

twoWayEcologyCluster(
	xDist = siteDist, 
	yDist = taxaDist,
	propAbund = propAbundMat
	)

##############################################	

# now let's try an example with some pokemon data
data(kanto)

# get distance matrices for sites and taxa
	# based on bray-curtis dist
	# standardized to total abundance

# standardize site matrix to relative abundance
siteStand <- decostand(kanto, method = "total")

# calculate site distance matrix (Bray-Curtis)
siteDist <- vegdist(siteStand, "bray")

# calculate taxa distance matrix (Bray-Curtis)
	# from transposed standardized site matrix 
taxaDist <- vegdist(t(siteStand), "bray")

dev.new(width=10)	

twoWayEcologyCluster(
    xDist = siteDist,
    yDist = taxaDist,
    propAbund = siteStand
    )
# }