betaper (version 1.1-2)

cca_pertables: Function to assess the efects of taxonomic uncertainty on [Partial] Constrained Correspondence Analysis

Description

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

Usage

cca_pertables(fml, data,  scale = FALSE,...)
# S3 method for cca_pertables
plot (x, pch = 18, …)

Arguments

fml

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

cca_pertables object to plot.

pch

Plotting 'character', i.e., symbol to use in the CCA plot. See points for examples of use of this graphical argument.

…

Additional graphical parameters passed to plot.

Value

cca_pertables returns an object of class cca_pertables, basically a list with the following components:

raw

An object of class classcca. The results of applying cca 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; cca.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 cca_pertables have print and plot S3 methods for a simple access to results. See the examples.

Details

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

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.

See Also

pertables, cca

Examples

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

Amazonia.cca <- cca_pertables(Amazonia100 ~., data=soils)

Amazonia.cca

plot(Amazonia.cca)
# }
# 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.cca <- cca_pertables(Amazonia4.p2 ~., data=soils)
Amazonia.cca

plot(Amazonia.cca)

# }