Description Usage Arguments Details Value Author(s) References See Also Examples
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.
1 2 3 |
fml |
Model formula, where the left hand side gives a pertables object (i.e. a list of simulated community data matrices obtained with |
data |
Data frame containing the variables on the right hand side of the model formula. |
scale |
Scale species to unit variance (like correlations). |
x |
|
pch |
Plotting 'character', i.e., symbol to use in the CCA plot. See |
... |
Additional graphical parameters passed to plot. |
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.
cca_pertables
returns an object of class cca_pertables
, basically a list with the following components:
raw |
An object of class class |
simulation |
A list with the results of the simulation: |
The objects of class cca_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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 | 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)
## 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.cca <- cca_pertables(Amazonia4.p2 ~., data=soils)
Amazonia.cca
plot(Amazonia.cca)
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