Metacommunity {metacom}

Analysis of the Elements of Metacommunity Structure

Description

'Metacommunity' is a wrapper for the analysis of the three elements of metacommunity structure (coherence, boundary clumping, & turnover) following the framework of Leibold & Mikkelson 2002. It is important to note here that the results of boundary clumping and turnover are only relevant if the matrix is significantly positively coherent (i.e. empirical matrix has fewer embedded absences than null matrices).

Usage

Metacommunity(comm, scores = 1, method = "r1",
  turnoverMethod = "EMS", sims = 1000, order = TRUE,
  orderNulls = FALSE, allowEmpty = FALSE, binary = TRUE,
  verbose = FALSE, seed = 1)

Arguments

comm

community data in the form of a presence absence matrix

scores

Axis scores to ordinate matrix. 1: primary axis scores (default) 2: secondary axis scores. See Details.

method

null model randomization method used by 'nullmaker'. See details.

turnoverMethod

(default='EMS') 'EMS' option generates null matrices as in Leibold and Mikkelson's original framework. However, null models that randomize occurrences – introducing embedded absences (bad), but in a far less constrained null space (good) – can also be used

sims

number of simulated null matrices to use in analysis

order

logical argument indicating whether to ordinate the interaction matrix or not. Default is TRUE. See details.

orderNulls

logical argument indicating whether to ordinate the null matrices. Default is FALSE.

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.

seed

seed for simulating the null model. Null matrices should be repeatable.

Details

'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 can be attained using many of swap algorithms described in the vegan package (sequential methods like 'tswap', 'swap', and non-sequential 'quasiswap' and 'backtracking'). See the help file for 'commsim' 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. The 'orderNulls' argument allows the user to ordinate the null matrices. While creating a more conservative test, this may negate the null model implemented (fixed row and column sums will not be maintained)

Value

A list of length 4, containing; Comm – ordinated matrix used to calculate coherence, boundary clumping & turnover

Coherence –output of the Coherence() function, giving information on the number of embedded absences and the significance relative to simulated null matrices

Turnover – output of the Turnover() function, testing the number of species replacements relative to simulated null matrices

Boundary – output of the BoundaryClump() function, which calculates the Morisita's index, assessing significance using a chi-squared test

Note

This function may take awhile to finish as a result of the creation of null matrices. If you are running multiple interaction matrices, the code can be parallelized using the 'snow' package.

Author(s)

Tad Dallas

References

Dallas,T. 2014. metacom: an R package for the analysis of metacommunity structure. Ecography. DOI:10.1111/j.1600-0587.2013.00695.x

Leibold, M.A. and G.M. Mikkelson. 2002. Coherence, species turnover, and boundary clumping: elements of meta-community structure. Oikos 97: 237 - 250.

Presley, S. J., C. L. Higgins, and M. R. Willig. 2010. A comprehensive framework for the evaluation of metacommunity structure. Oikos 119:908-917

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[[7]]

#determines the elements of metacommunity structure
ems.test <- Metacommunity(intmat, method='r1', sims=100, scores=1)