metricTester (version 1.3.6)

killSomeBig: Remove most closely related individuals for large arenas

Description

Given a phylogenetic tree, a large spatial arena of individuals with species identities, and arguments for the desired distance and percent removed, removes some of the most closely related individuals in the arena.

Usage

killSomeBig(tree, arena.output, max.distance, proportion.killed)

Arguments

tree

Phylo object

arena.output

A spatial arena with three columns: individuals (the species ID), X (the x axis location of that individual), and Y (the y axis location). The arena.output actually needs a number of other elements in order for later functions to work properly, so any modifications to the code should take note of this.

max.distance

The geographic distance within which geographically neighboring individuals should be considered to influence the individual in question.

proportion.killed

The percent of individuals in the total arena that should be considered (as a proportion, e.g. 0.5 = half).

Value

A list of 5 elements: the average relatedness in the geographic neighbordhood of consideration (appended to any previous values that were fed into the function), the number of individuals killed, the original input regional abundance vector, the new spatial arena, and the dimensions of that arena.

Details

This function identifies individuals in the most genetically clustered geographic neighborhoods, continues on to identify the most closely related individual to a focal individual, and randomly chooses whether to remove that individual or the focal individual. It expects a list with a number of additional elements beyond the arena (currently, the mean genetic relatedness of geographic neighborhoods, a vector of regional abundance [where each element is a species name, repeated as many times as is present in pool], and the dimensions of the arena). This function is invoked if the number of individuals in the arena exceeds 50,000. It was originally intended only for arenas with large numbers of individuals, but it ends up being faster than the original version of the function for all but the smallest arenas. That said, if the local area within the arena that the function considers does not contain any individuals, then it will fail. To overcome this, either a larger max.distance would need to be set, or more individuals should be settled in the arena, or the original version of the function should be invoked by modifying the code in competitionArena(). Note, however, that if there are more than e.g. 50,000 individuals total in the arena, the original version of the function should never be used, or all memory in the computer will be used and it will crash.

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

Examples

# NOT RUN {
#simulate tree with birth-death process
tree <- geiger::sim.bdtree(b=0.1, d=0, stop="taxa", n=50)

#prep the data for the simulation
prepped <- prepSimulations(tree, arena.length=300, mean.log.individuals=1, 
length.parameter=5000, sd.parameter=50, max.distance=20, proportion.killed=0.2,
competition.iterations=5)

#use the random simulation to generate a starting arena
random <- randomArena(prepped)

#in normal use, these parameters will be carried down from the simulations.input object
new.arena <- killSomeBig(tree, arena.output=random, max.distance=50, 
proportion.killed=0.2)

#look at how number of individuals in arena changes
dim(random$arena)
dim(new.arena$arena)
# }