niche.par.plot: Plot for niche parameters.

In mlysy/nicheROVER: Niche Region and Niche Overlap Metrics for Multidimensional Ecological Niches

Plot for niche parameters.

Description

For one or more species, plots some or all of the niche parameters \mu and \Sigma.

Usage

niche.par.plot(
  niche.par,
  plot.mu = TRUE,
  plot.Sigma = TRUE,
  plot.index,
  col,
  ndens = 512,
  ylab
)

Arguments

niche.par	List with nspecies = length(niche.par), each element of which is a list with parameters mu and Sigma. See 'Details'.
plot.mu	Logical. If TRUE, plot the distribution of \mu for each niche indicator (e.g., stable isotope). See 'Details'.
plot.Sigma	Logical. If TRUE, plot the distribution of \Sigma for each niche indicator. See 'Details'.
plot.index	Either a scalar of a numeric vector of length 2. If plot.index = i then plot the distribution of \mu_i. If plot.index = c(i,j) then plot the distribution of \Sigma_{ij}.
col	Vector of colors in which to plot each species.
ndens	Number of points at which to evaluate density estimates.
ylab	Optional label for y-axis. If missing, defaults to p(\mu_i | X) and p(\Sigma_{ij} | X).

Details

Each element of the list niche.par is a distribution of niche parameters. That is, names(niche.par[[1]]) = c("mu", "Sigma"), and if niso is the number of niche indicators (e.g., stable isotopes), then dim(niche.par[[1]]$mu) = c(nsamples, niso) and dim(niche.par[[1]]$Sigma) = c(niso, niso, nsamples).

Value

Returns a plot of the distribution of some or all niche parameters.

See Also

niw.post(), niiw.post() for niche parameter output, stats::density() for density estimation from sample data.

Examples

# fish data
data(fish)

# generate parameter draws from the "default" posteriors of each fish
nsamples <- 1e3
system.time({
  fish.par <- tapply(1:nrow(fish), fish$species,
                     function(ii) niw.post(nsamples = nsamples, X = fish[ii,2:4]))
})

# various parameter plots
clrs <- c("black", "red", "blue", "orange") # colors for each species

# mu1, mu2, and Sigma12
par(mar = c(4, 4, .5, .1)+.1, mfrow = c(1,3))
niche.par.plot(fish.par, col = clrs, plot.index = 1)
niche.par.plot(fish.par, col = clrs, plot.index = 2)
niche.par.plot(fish.par, col = clrs, plot.index = 1:2)
legend("topright", legend = names(fish.par), fill = clrs)

# all mu
niche.par.plot(fish.par, col = clrs, plot.mu = TRUE, plot.Sigma = FALSE)
legend("topright", legend = names(fish.par), fill = clrs)

# all mu and Sigma
par(mar = c(4.2, 4.2, 2, 1)+.1)
niche.par.plot(fish.par, col = clrs, plot.mu = TRUE, plot.Sigma = TRUE)
legend("topright", legend = names(fish.par), fill = clrs)

mlysy/nicheROVER documentation built on Oct. 17, 2023, 2:21 p.m.