logical argument indicating whether to ordinate the interaction
matrix or not. See details.
allowEmpty
logical argument indicating whether to allow null
matrices to have empty rows or columns
binary
logical argument indicating whether to ordinate the community
matrix based on abundance or binary (default) data.
verbose
Logical. Prints a graphical progress bar that tracks the
creation of null matrices. Useful for conservative null models on large
and/or sparse data.
Details
If the 'community' perspective is desired, simply transpose the matrix
before analysis using the transpose function ('t()'), but make sure you
understand the implications of this action, as the interpretation of the
output changes dramatically.
'method' is an argument handed to functions in the 'vegan' package. Leibold
& Mikkelson advocated the use of equiprobable rows and columns (provided
that rows and columns had at least one entry). This method is called 'r00'.
Methods maintaining row (site) frequencies include 'r0','r1' & 'r2'. The
default method argument is 'r1', which maintains the species richness of a
site (row totals) and fills species ranges (columns) based on their marginal
probabilities. Arguably the most conservative null algorithm is the fixed
row - fixed column total null, which is implemented as 'fixedfixed'. See the
help file for 'commsimulator' or Wright et al. 1998 for more information.
If 'order' is FALSE, the interaction matrix is not ordinated, allowing the
user to order the matrix based on site characteristics or other biologically
relevant characteristics.
This function can either be used as a standalone, or can be used through the
'metacommunity()' function, which determines all 3 elements of metacommunity
structure (coherence, boundary clumping, & turnover) (Leibold & Mikkelson
2002). The turnover metric used here is equivalent to the number of checkerboard
units community with species ranges (range perspective) filled in
Value
A data.frame containing the test statistic (turnover), z-value (z), p-value (pval), mean (simulatedMean) and variance (simulatedVariance) of simulations, and randomization method (method)
Author(s)
Tad Dallas
References
Leibold, M.A. and G.M. Mikkelson. 2002. Coherence, species
turnover, and boundary clumping: elements of meta-community structure. Oikos
97: 237 - 250.
Wright, D.H., Patterson, B.D., Mikkelson, G.M., Cutler, A. & Atmar, W.
(1998). A comparative analysis of nested subset patterns of species
composition. Oecologia 113, 1-20.
Examples
#define an interaction matrix
data(TestMatrices)
intmat <- TestMatrices[[3]]
#determine species turnover
turnover.intmat <- Turnover(intmat, method='r1', sims=100, scores=1, binary=TRUE)