Results from any of the varyX (e.g., varyAbundance) functions.
exclude
Results columns to exclude from correlation. For instance, with alpha
metrics, one would want to, at the minimum, exclude the plot name column.
return.raw
Default is FALSE. Whether to return the raw correlation coefficients
between the metrics for each element from vary.results, or whether to summarize the
correlations by their mean per parameter set from vary.results.
cor.method
Default is "spearman", but takes any of the other options from the
base cor function.
Details
Not a well tested function.
Value
If return.raw is set to FALSE, returns a list of matrices, one for each set
of parameters in vary.results, summarizing the mean correlation coefficients between
each pairwise metric correlation. If return.raw is set to TRUE, returns a list of
lists, one for each set of parameters. Each of these lists is the length of the number
of iterations in vary.results. Each element in the list is a matrix of pairwise metric
correlations.
References
Miller, E. T., D. R. Farine, and C. H. Trisos. 2015. Phylogenetic community
structure metrics and null models: a review with new methods and software.
bioRxiv 025726.
Examples
#below not run for timing issues on CRAN
#system.time(vSize <- varyX(alpha=TRUE, tree.size=c(40, 50), richness=20:30, delta=1,
#abundances=round(rlnorm(5000, meanlog=2, sdlog=1)) + 1, iterations=2, cores="seq"))
#test <- summCorrs(vSize, exclude=c("plot", "richness"))