mantel.pertables {betaper} | R Documentation |
This function asses the effects of taxonomic uncertainty on the coefficient of correlation and the p-values of a Mantel test.
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, ...)
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. |
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.
Luis Cayuela and Marcelino de la Cruz
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)
pertables
, mantel
## 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)