rda.pertables {betaper} | R Documentation |
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' .
rda.pertables(formula, data, scale=FALSE,...) ## S3 method for class 'rda.pertables': plot (x, pch = 18, ...)
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. |
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.
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.
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
, rda
## 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)