Description Usage Arguments Value Author(s) References See Also Examples
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.
1 2 3 | 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 |
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 |
method |
The name of any method used in 'vegdist' to calculate pairwise distances. |
x |
|
... |
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 |
simulation |
A list with the results of the simulation: |
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. (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.
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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)
## End(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)
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