metricTester (version 1.3.6)

plotPlotter: Plot simulated plots in arena

Description

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

Usage

plotPlotter(plot.bounds)

Arguments

plot.bounds

Matrix of plot bounds

Value

Plotted plots

Details

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.

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 {
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)
# }