alphaMetricSims: Calculate alpha metrics under specified tree and community parameters
Description
Takes a specified set of tree size, shape, community richness and abundance parameters,
and calculates the alpha-level phylogenetic community structure metrics.
Number of species to be placed in each plot. See details.
delta
A value for the delta transformation (Pagel 1999). Values greater than 1
push the branching events towards the root, while values less than 1 push the branching
events closer to the tips. See details for particularly low delta values.
abundances
Vector of abundances, e.g. a repeated series of 1s for a
presence/absence community data matrix, a log-normal distribution, etc. See examples.
Value
A data frame of calculated alpha metrics, and the associated species richness
of each plot.
Details
The richness.vector (number of species to be placed into each plot) is
flexible. For instance, one might want give it 10:19, which would create 10 plots
of species richness 10, 11, ... 19. But one could also provide rep(10, 10) to create 10
plots of 10 species each. If given a small value, e.g. 0.1, the delta parameter
(tree shape) can occasionally result in oddly formatted trees that would cause errors.
To deal with this, there is an internal check that will recreate a new tree and
re-scale it with the desired delta. This has not been tested at delta < 0.1, and is
currently programmed with a while loop. Care should be taken not to get R stuck in an
indefinite loop at delta values even lower than 0.1
References
Miller, E. T., D. R. Farine, and C. H. Trisos. 2016. Phylogenetic community
structure metrics and null models: a review with new methods and software.
Ecography DOI: 10.1111/ecog.02070