rda.pertables {betaper}R Documentation

Function to assess the efects of taxonomic uncertainty on [Partial] Redundance Analysis

Description

This function asses the effects of taxonomic uncertainty on two widely used parameters of a [Partial] Redundance Analysis, i.e. the 'percentage explained variance' (sometimes referred to as R-squared) and the 'pseudo-F' .

Usage

rda.pertables(formula, data, scale=FALSE,...)
## S3 method for class 'rda.pertables':
plot (x, pch = 18, ...)

Arguments

formula Model formula, where the left hand side gives a pertables object (i.e. a list of simulated community data matrices obtained with pertables, right hand side gives the constraining variables, and conditioning variables can be given within a special function Condition.
data Data frame containing the variables on the right hand side of the model formula.
scale Scale species to unit variance (like correlations).
x rda.pertables object to plot.
pch Plotting 'character', i.e., symbol to use in the RDA plot. See points for examples of use of this graphical argument.
... Additional graphical parameters passed to plot.

Details

This function is a wrapper to submit a pertables object to rda function of the vegan package. See the documentation of rda for details about formula and Condition use.

Value

rda.pertables returns an object of class'rda.pertables', basically a list with the following components:

raw An object of class class'rda'. The results of applying rda to the original biological data table without the unidentified species.
simulation A list with the results of the simulation: 'results', i.e. a data.frame with all the simulated R-squared and pseudo-F values; 'rda.quant', i.e. a data.frame with the summary of 'results' by quantiles; 'sites' i.e. a list with the scores of the sites of all the simulated data tables and 'biplot', i.e. a list with the scores of the environmental data in all the analyses


The objects of class 'rda.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, rda

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 RDA analysis of biological data explained by all the environmental variables of the soil data:

Amazonia.rda <- rda.pertables(Amazonia100 ~., data=soils)

Amazonia.rda

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

[Package betaper version 1.1-0 Index]