calcField: Calculate phylogenetic and trait fields
In eliotmiller/metricTester: Test Metric and Null Model Statistical Performance

Description Usage Arguments Details Value References Examples

Given a prepped field.input object, calculate all fields of interest.

1	calcField(field.input, metrics)

field.input

Prepped field.input object.

metrics

Optional. If not provided, defines the metrics as all of those in defineMetrics. If only a subset of those is desired, then metrics should take the form of a character vector corresponding to named functions from defineMetrics. The available metrics can be determined by running names(defineMetrics()). Otherwise, if the user would like to define a new metric on the fly, the argument can take the form of a named list of new functions (metrics).

Currently we are calculating 19 phylogenetic community structure metrics. This function first confirms that the input is of class metrics.input and, if so, then confirms that the metrics to be calculated are in a named list (via checkMetrics), then lapplies all metric functions to the input metrics.input object.

A data frame with the calculated metrics and the associated species richness of all input "communities".

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

#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)

#in this example, occasionally some species are not in the CDM, so prune the tree
#accordingly so as not to throw any errors
tree <- drop.tip(tree, setdiff(tree$tip.label, colnames(cdm)))

prepped <- prepFieldData(tree=tree, picante.cdm=cdm)

results <- calcField(prepped)