niche.par.plot: 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 $p(\Sigma_{ij} | X)$.

Value

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

Details

niche.par is a list, each element of which 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).

Examples

Run this code

# NOT RUN {
# 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)
# }