# R-Mode vs Q-Mode Two-Way Cluster Analyses and Abundance Plot for Community Ecology Data This mode plots both R-mode (across sites) and Q-mode (across taxa) dendrograms for a community ecology data set, with branches aligned with a grid of dots representing the relative abundance of taxa at each site in the dataset. ```r twoWayEcologyCluster( xDist, yDist, propAbund, clustMethod = "average", marginBetween = 0.1, abundExpansion = 3, cex.axisLabels = 1, trimChar = 5, 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. - `cex.axisLabels`: Character expansion parameter for controlling the plotting of axis labels on the abundance dot-grid only. - `trimChar`: How many characters should the axis labels be trimmed to? Default is 5, which means only the first five letters of each taxon/site label will be shown on the dot-abundance plot. - `xAxisLabel`: The label placed on the horizontal axis of the plot. - `yAxisLabel`: The label placed on the vertical axis of the plot. ## Returns 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 or even predict what will happen. ## Examples ```r set.seed(1) # generate random community ecology data # using a Poisson distribution data<-matrix(rpois(5*7,1),5,7) # get relative abundance, distance matrices propAbundMat<-t(apply(data,1,function(x) x/sum(x))) rownames(propAbundMat)<-paste0("site ", 1:nrow(propAbundMat)) colnames(propAbundMat)<-paste0("taxon ", 1:ncol(propAbundMat)) # for simplicity, let's calculate # the pairwise square chord distance # between sites and taxa squareChordDist<-function(mat){ res<-apply(mat,1,function(x) apply(mat,1,function(y) sum((sqrt(x)-sqrt(y))^2) ) ) # res<-as.dist(res) return(res) } # its not a very popular distance metric # but it will do # quite popular in palynology siteDist<-squareChordDist(propAbundMat) taxaDist<-squareChordDist(t(propAbundMat)) dev.new(width=10) twoWayEcologyCluster( xDist = siteDist, yDist = taxaDist, propAbund = propAbundMat ) ## Not run: # now let's try an example with the example kanto dataset # and use bray-curtis distance from vegan library(vegan) data(kanto) # get distance matrices for sites and taxa # based on bray-curtis dist # standardized to total abundance # standardize site matrix to relative abundance siteStandKanto <- decostand(kanto, method = "total") # calculate site distance matrix (Bray-Curtis) siteDistKanto <- vegdist(siteStandKanto, "bray") # calculate taxa distance matrix (Bray-Curtis) # from transposed standardized site matrix taxaDistKanto <- vegdist(t(siteStandKanto), "bray") dev.new(width=10) twoWayEcologyCluster( xDist = siteDistKanto, yDist = taxaDistKanto, propAbund = siteStandKanto, cex.axisLabels = 0.8 ) ## End(Not run) ``` ## 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`. ## Author(s) David W. Bapst

twoWayEcologyCluster function