adonis_pertables: Function to assess the efects of taxonomic uncertainty on permutational multivariate analysis of variance using distance matrices

Description

This function asses the effects of taxonomic uncertainty on the R2 coefficients and the p-values of a permutational multivariate analysis of variance using distance matrices.

Usage

adonis_pertables(formula = X ~ ., data, permutations = 5, method = "bray")
# S3 method for adonis_pertables
plot(x, …)

Arguments

formula

A typical model formula such as 'Y ~ A + B*C', but where 'Y' is a pertables object (i.e. a list of simulated community data matrices obtained with pertables; 'A', 'B', and 'C' may be factors or continuous variables.

data

The data frame from which 'A', 'B', and 'C' would be drawn.

permutations

Number of replicate permutations used for the hypothesis tests (F tests) for each simulated community data matrices obtained with pertables.

method

The name of any method used in 'vegdist' to calculate pairwise distances.

adonis_pertables object to plot.

…

Additional graphical parameters passed to plot.

Value

adonis_pertables returns an object of classadonis_pertables, basically a list with the following components:

raw

An object of class adonis, i.e. the results of applying mantel to the original biological data table without the unidentified species. This includes p-values for each explanatory variable showing the probability of obtaining the same F statistic under different scenarios of taxonomic uncertainty.

simulation

A list with the results of the simulation: F, i.e. a data.frame with all the simulated pseudo-F (columns) for each explanatory variable (rows); R2, i.e. a data.frame with all the simulated R2 coefficients (columns) for each explanatory variable (rows); pvalue, i.e. a data.frame with all the simulated p-values (columns) for each explanatory variable (rows); R2.quant, i.e. a data.frame with the summary of R2 by quantiles; p.quant,, i.e. a data.frame with the summary of pvalue by quantiles.

The objects of class adonis_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.")

# Generate a pertables object (i.e. a list of biological data tables simulated from taxonomic
# uncertainty)
 
# }
# NOT RUN {
Amazonia100 <- pertables(Amazonia, index=index.Amazon, nsim=100)

# Assess the effects of taxonomic uncertainty on a PERMANOVA (i.e., adonis) test:

Amazonia.adonis <- adonis_pertables(Amazonia100 ~ Ca + K + Mg + Na, data=soils)

Amazonia.adonis

plot(Amazonia.adonis)
# }
# 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.adonis <- adonis_pertables(Amazonia4.p2  ~ Ca + K + Mg + Na, data=soils)

Amazonia.adonis

plot(Amazonia.adonis)

# }