adonis.pertables {betaper} | R Documentation |
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.
adonis.pertables(formula = X ~ ., data, permutations = 5, method = "bray") ## S3 method for class 'adonis.pertables': plot(x, ...)
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. |
x |
adonis.pertables object to plot. |
... |
Additional graphical parameters passed to plot. |
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.
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
, adonis
## 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.adonis <- adonis.pertables(Amazonia100 ~ Ca + K + Mg + Na, data=soils)
Amazonia.adonis
plot(Amazonia.adonis)
## End(Not run)