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Computes pairwise associations between every row (species) in a species x site matrix. Note that usage of this function is advantageous when non-symmetric association metrics are desired, but the pairwise computation will prevent accounting for indirect effects between species. As such this function should be considered preliminary, and its use experimental.
● Data Source:
CranContrib
● Keywords:
● Alias: pairwise_association
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Infers species associations from community matrices. Uses local and (optional) regional-scale co-occurrence data by comparing observed partial correlation coefficients between species to those estimated from regional species distributions. Extends Gaussian graphical models to a null modeling framework. Provides interface to a variety of inverse covariance matrix estimation methods.
● Data Source:
CranContrib
● Keywords: package
● Alias: netassoc, netassoc-package
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Draws a network of species associations. By default edge widths are proportional to association strength and edge color reflects association type (blue, positive; red, negative).
● Data Source:
CranContrib
● Keywords:
● Alias: plot_netassoc_network
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Plots species x species or species x site matrix with color map
● Data Source:
CranContrib
● Keywords:
● Alias: plot_netassoc_matrix
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Estimates the inverse covariance matrix then uses this matrix to calculate partial correlation coefficents.
● Data Source:
CranContrib
● Keywords:
● Alias: partial_correlation
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Infers a species association network by determining which co-occurrence patterns between species are more or less likely than expected under a null model of community assembly. Defaults to estimation of association using a robust shrinkage estimator for inverse covariance matrices.
● Data Source:
CranContrib
● Keywords:
● Alias: make_netassoc_network
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providing 
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