mantel.pertables {betaper}R Documentation

Function to assess the efects of taxonomic uncertainty on Mantel tests

Description

This function asses the effects of taxonomic uncertainty on the coefficient of correlation and the p-values of a Mantel test.

Usage

mantel.pertables(pertab, env, dist.method = "bray", binary = FALSE, cor.method = "pearson", permutations = 100)
## S3 method for class 'mantel.pertables':
plot (x, xlab = "Environmental distance", ylab = "Sorensen's similarity index", pch = 19, ...)

Arguments

pertab A pertables object (i.e. a list of simulated community data matrices obtained with pertables.
env Data frame with the environmental variables.
dist.method Method to compute the dissimilarity matrices from the biological and environmental data tables. One of the methods described in function vegdist of the package vegan.
binary Value for the argument binary in the function vegdist of the package vegan.
cor.method Correlation method, as accepted by cor: "pearson", "spearman" or "kendall".
permutations Number of permutations in assessing significance.
x mantel.pertables object to plot.
xlab Label to name x-axis
ylab Label to name y-axis
pch Plotting 'character', i.e., symbol to use in the distance decay plot. See points for examples of use of this graphical argument.
... Additional graphical parameters passed to plot.

Value

mantel.pertables returns an object of classmantel.pertables, basically a list with the following components:

mantel A list with two components: mantel.raw, an object of class 'mantel', i.e. the results of applying mantel to the original biological data table without the unidentified species, and ptax, a p-value showing the probability of obtaining the same mantel statistic under different scenarios of taxonomic uncertainty.
simulation A list with the results of the simulation: results, i.e. a data.frame with all the simulated mantel statistics and p-values; mantel.quant, i.e. a data.frame with the summary of results by quantiles; vegdist, i.e. a list with all the dissimilarity matrices employed.


The objects of class mantel.pertables have print and plot S3 methods for a simple access to results. See the examples.

Author(s)

Luis Cayuela and Marcelino de la Cruz

References

Cayuela, L., De la Cruz, M. and Ruokolainen, K. A method to incorporate the effect of taxonomic uncertainty on multivariate analyses of ecological data (Ecography, submitted)

See Also

pertables, mantel

Examples

  ## Not run: 
require(vegan)

data(Amazonia)
data(soils)

# Define a new index that includes the terms used in the Amazonia dataset to define undetermined taxa at different taxonomic levels
index.Amazon <- c(paste("sp.", rep(1:20), sep=""), "Indet.", "indet.")

#Generate a pertables object (i.e. a list of biological data tables simulated from taxonomic uncertainty)
Amazonia100 <- pertables(Amazonia, index=index.Amazon, nsim=100)

# Assess the effects of taxonomic uncertainty on a Mantel test of biological dissimilarity  correlated to soil dissimilarity among sites:

Amazonia.mantel <- mantel.pertables(pertab=Amazonia100, env=soils, dist.method = "bray")

Amazonia.mantel

plot(Amazonia.mantel)
 
## End(Not run)

[Package betaper version 1.1-0 Index]