mantel_pertables: 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 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.

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.

References

Cayuela, L., De la Cruz, M. and Ruokolainen, K. (2011). A method to incorporate the effect of taxonomic uncertainty on multivariate analyses of ecological data. Ecography, 34: 94-102. http://dx.doi.org/10.1111/j.1600-0587.2009.05899.x.

Examples

Run this code

# NOT RUN {


data(Amazonia)
data(soils)

# Define a new index that includes the terms used in the \code{Amazonia} dataset to define
# undetermined taxa at different taxonomic levels

index.Amazon <- c(paste("sp.", rep(1:20), sep=""), "Indet.", "indet.")

# }
# NOT RUN {
# 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)
# }
# NOT RUN {
# Fast example for Rcheck

Amazonia4.p2 <- pertables.p2(Amazonia[1:50,], index=index.Amazon, nsim=4, ncl=2, iseed=4)
set.seed(2)
Amazonia.mantel <- mantel_pertables(pertab=Amazonia4.p2, env=soils, dist.method = "bray")

Amazonia.mantel

plot(Amazonia.mantel)

# }