Turnover
(Package: metacom) :
Determines species turnover
'Turnover' is a function that assesses species turnover from the range perspective (traditional method).
● Data Source:
CranContrib
● Keywords:
● Alias: Turnover
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Metacommunity
(Package: metacom) :
Analysis of the Elements of Metacommunity Structure
'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).
● Data Source:
CranContrib
● Keywords:
● Alias: Metacommunity
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Modularity
(Package: metacom) :
Calculates Barber's Bipartite Modularity
Modularity, community formation, boundary clumping. Call it what you want, there is a fair amount of overlap in definition here. As such, we posit that modularity statistics may be able to detect boundary clumping better than Morisita's index. We offer a function here to calculate modularity. Specifically, this function calculates Barber's Q statistic, and compares it relative to null model randomizations.
● Data Source:
CranContrib
● Keywords:
● Alias: Modularity
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Imagine
(Package: metacom) :
Plotting of site-by-species interaction matrices
'Imagine' produces an image plot, grid of small rectangles representing species occurrences in sites, of a given interaction matrix.
● Data Source:
CranContrib
● Keywords: ordination, plotting
● Alias: Imagine
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OrderMatrix
(Package: metacom) :
Ordinates interaction matrix
'OrderMatrix' ordinates an interaction matrix scores derived from reciprocal averaging (Gauch et al. 1977). These scores represent a latent environmental gradient along which species distributions are structured.
● Data Source:
CranContrib
● Keywords: ordination
● Alias: OrderMatrix
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metacom-package
(Package: metacom) :
Pattern-based analysis of metacommunity structure
'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.
● Data Source:
CranContrib
● Keywords:
● Alias: metacom, metacom-package
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Identifies structure (or quasi-structure) and outputs a classification.
● Data Source:
CranContrib
● Keywords:
● Alias: IdentifyStructure
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Coherence
(Package: metacom) :
Determines coherence
This function determines the number of embedded absences in an interaction matrix, and compares this value against null simulated matrices. Species ranges should be coherent along the ordination axis, as this axis represents a latent environmental gradient. A negative value of coherence (empirical matrix has more embedded absences than null matrices) indicates a 'checkerboard' pattern (Leibold & Mikkelson 2002). Nonsignificance has been historically interpreted as being indicative of a 'random' pattern, though this may be seen as accepting the null hypothesis, as nonsignificance cannot be used to infer a process.
● Data Source:
CranContrib
● Keywords:
● Alias: Coherence
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NullMaker
(Package: metacom) :
Null matrix creator
Creates null matrices based on the constraints of the null model algorithm ('method'). Also allows for null matrices with a species that occurs at no sites, or a site without any species to be removed from the suite of simulated null matrices. This function borrows heavily from the commsimulator() function in the 'vegan' package, but also allows for the fixed-fixed null model.
● Data Source:
CranContrib
● Keywords: ordination
● Alias: NullMaker
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BoundaryClump
(Package: metacom) :
Determines boundary clumping
'BoundaryClump' calculates the Morisita's Index (Morisita 1962) for presence-absence interaction matrices, using a chi-squared test to assess significance.
● Data Source:
CranContrib
● Keywords:
● Alias: BoundaryClump
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providing 
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