plotPlotter: Plot simulated plots in arena
In metricTester: Test Metric and Null Model Statistical Performance

Description Usage Arguments Details Value References Examples

Given a matrix of plot bounds, plots the plots in an already plotted, simulated arena.

1	plotPlotter(plot.bounds)

plot.bounds

Matrix of plot bounds

Plots plots as defined by the supplied matrix, e.g. a call to plotPlacer. An active plot with the simulated arena needs to already be open, see example.

Plotted plots

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

tree <- geiger::sim.bdtree(b=0.1, d=0, stop="taxa", n=50)

temp <- evolveTraits(tree)

phydistmatrix <- ape::cophenetic.phylo(temp[[1]])

#define a color for each species
cols <- plotrix::color.scale(x=1:nrow(phydistmatrix),
cs1=c(0.2,0.4,0.8), cs2=c(0,0.5,0.8), cs3=c(1,0.5,0))

#prep the data for the simulation
prepped <- prepSimulations(tree, arena.length=300, mean.log.individuals=2, 
length.parameter=5000, sd.parameter=50, max.distance=20, proportion.killed=0.2,
competition.iterations=3)

positions <- filteringArena(prepped)

#plot the arena. don't close the window
plot(positions$arena$X, positions$arena$Y, pch=20, cex=1, xlim=c(0,300), ylim=c(0,300), 
col=cols[positions$arena$individuals])

bounds <- plotPlacer(no.plots=10, arena.length=300,
plot.length=50)$plot.bounds

plotPlotter(bounds)