metricTester (version 1.2.2)

reduceRandomizations: Reduce randomized results to a manageable list of dataframes

Description

The metricsNnulls function creates lists of lists of dataframes. This function will combine the dataframes from each null model into a single data frame. The output is a more manageable list of dataframes.

Usage

reduceRandomizations(randomizations.list)

Arguments

randomizations.list

The results of a call to metricsNnulls()

Details

Given a list of lists of dataframes, such as those that come from a call to metricsNnulls, where the first level of the list relates to a given randomization, and each second level is a data frame containing the calculated metrics after randomization according to a given null model, reduces the results to a simpler list of data frames, where each data frame contains all the results from a given null model from the input randomizations.list.

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

#simulate tree with birth-death process
tree <- geiger::sim.bdtree(b=0.1, d=0, stop="taxa", n=50)

sim.abundances <- round(rlnorm(5000, meanlog=2, sdlog=1)) + 1

cdm <- simulateComm(tree, richness.vector=10:25, abundances=sim.abundances)

#below not run for timing issues on CRAN
#rawResults <- metricsNnulls(tree, cdm)

#results <- reduceRandomizations(rawResults)