R: Pattern-based analysis of metacommunity structure
metacom-package
R Documentation
Pattern-based analysis of metacommunity structure
Description
'metacom' provides functions for the analysis of the elements of
metacommunity structure (coherence, boundary clumping, & turnover),
following the pattern-based metacommunity framework of Leibold & Mikkelson
2002 and Presley et al. 2010. This package is designed to allow the user to
distinguish between several idealized patterns of metacommunity structure
(Presley et al. 2010) utilizing any number of null model algorithms for the
randomization procedure. However, these metrics can also be used in
isolation, and without ordination via reciprocal averaging, and instead,
ordering along some biological gradient.
A metacommunity is a set of sites (e.g. plants in plant-pollinator networks)
associated through interactions (e.g. insect species (columns) interact with
plant species (rows) in plant-pollinator networks). The pattern-based
metacommunity concept, proposed by Leibold & Mikkelson 2002 and expounded on
by Presley et al. 2010, allows for the evaluation of metacommunity structure
by using randomization techniques to discern between 10 patterns of
metacommunity structure. This is performed by ordinating site-by-species
interaction matrices and calculating three metrics; coherence, boundary
clumping & turnover.
The metacom package calculates these three metrics; coherence is calculated
using the function Coherence(), boundary clumping with BoundaryClump(), and
turnover (from either species or range perspective) using the Turnover()
function. These functions are consolidated in the Metacommunity() function,
which can be used to calculate all three metrics. In order to interpret the
output of these functions, it will be helpful to read Leibold & Mikkelson
2002 and Presley et al. 2010, but to also read Ulrich and Gotelli 2013, as
this paper outlines the difficulty seemingly inherent with investigating
community structure. Also, these functions do not have to be used strictly
in the Leibold and Mikkelson 2002 framework.
I caution the user to be aware that the creation of null matrices can be
performed to allow (or not allow) sites to be empty, or species to not exist
at any site (i.e. column sums and/or row sums are allowed to be zero). This
is controlled by the logical argument 'allow.empty' in the Metacommunity(),
NullMaker(), Coherence(), and Turnover() functions. Restricting nulls to not
allow empty rows or columns may be biologically realistic, but it also
reduces the number of unique null matrices that can be built, which will
impact computation time, making it infeasible or impossible in some
situations. These situations occur when you have a very sparse interaction
matrix, and is also influenced by null model algorithm ('method') that you
choose.
The 'metacom' package is partially adapted from previous Matlab code written
by Christopher Higgins (available at
http://www.tarleton.edu/Faculty/higgins/EMS.htm) and relies on many
functions in the 'vegan' package (Oksanen et al. 2012)
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. & Mikkelson, G. (2002) Coherence, species turnover, and boundary
clumping: elements of metacommunity structure. Oikos, 97, 237-250.
Leibold, M., Holyoak, M., Mouquet, N., Amarasekare, P., Chase, J., Hoopes,
M., Holt, R., Shurin, J., Law, R., Tilman, D. et al. (2004) The
metacommunity concept: a framework for multi-scale community ecology.
Ecology letters, 7, 601-613.
Oksanen, J., F.G. Blanchet, R. Kindt, P. Legendre, P.R. Minchin, R.B.
O'Hara, G.L. Simpson, P. Solymos, M.H.H. Stevens and H. Wagner (2012).
vegan: Community Ecology Package. R package version 2.0-4.
http://CRAN.R-project.org/package=vegan
Presley, S., Higgins, C. & Willig, M. (2010) A comprehensive framework for
the evaluation of metacommunity structure. Oikos, 119, 908-917.
Ulrich, W. and Gotelli, N. J. (2013) Pattern detection in null model
analysis. Oikos, 122: 2-18. doi: 10.1111/j.1600-0706.2012.20325.x
Willig, M., Presley, S., Bloch, C., Castro-Arellano, I., Cisneros, L.,
Higgins, C. & Klingbeil, B. (2011) Tropical metacommunities along
elevational gradients: effects of forest type and other environmental
factors. Oikos, 120, 1497-1508.