niiw.post: Random draws from the posterior distribution with...

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

Description

Given iid d-dimensional niche indicators X = (X_1,…,X_N) with X_i \sim N(μ, Σ), this function generates random draws from p(μ,Σ | X) for the Normal-Independent-Inverse-Wishart (NIIW) prior.

Usage

niiw.post(nsamples, X, lambda, Omega, Psi, nu, mu0 = lambda, burn)

Arguments

nsamples	The number of posterior draws.
X	A data matrix with observations along the rows.
lambda	Mean of μ. See 'Details'.
Omega	Variance of μ. Defaults to Omega = 0. See 'Details'.
Psi	Scale matrix of Σ. Defaults to Psi = 0. See 'Details'.
nu	Degrees of freedom of Σ. Defaults to nu = ncol(X)+1. See 'Details'.
mu0	Initial value of μ to start the Gibbs sampler. See 'Details'.
burn	Burn-in for the MCMC sampling algorithm. Either an integer giving the number of initial samples to discard, or a fraction with 0 < burn < 1. Defaults to burn = floor(nsamples/10).

Details

The NIIW distribution p(μ, Σ | λ, κ, Ψ, ν) is defined as

Σ \sim W^{-1}(Ψ, ν), \quad μ | Σ \sim N(λ, Ω).

The default value Omega = 0 uses the Lebesque prior on μ: p(μ) \propto 1. In this case the NIW and NIIW priors produce identical resuls, but niw.post() is faster.

The default value Psi = 0 uses the scale-invariant prior on Σ: p(Σ) \propto |Σ|^{-(ν+d+1)/2}.

The default value nu = ncol(X)+1 for Omega = 0 and Psi = 0 makes E[μ|X]=`colMeans(X)` and E[Σ | X]=`var(X)`.

Random draws are obtained by a Markov chain Monte Carlo (MCMC) algorithm; specifically, a Gibbs sampler alternates between draws from p(μ | Σ, X) and p(Σ | μ, X), which are Normal and Inverse-Wishart distributions respectively.

Value

Returns a list with elements mu and Sigma of sizes c(nsamples, length(lambda)) and c(dim(Psi), nsamples).

See Also

niw.post(), rwish().

Examples

# simulate normal data with mean and variance (mu0, Sigma0)
d <- 4
mu0 <- rnorm(d)
Sigma0 <- matrix(rnorm(d^2), d, d)
Sigma0 <- Sigma0 %*% t(Sigma0)
N <- 1e2
X <- matrix(rnorm(N*d), N, d) # iid N(0,1)
X <- t(t(X %*% chol(Sigma0)) + mu0) # each row is N(mu0, Sigma)

# prior parameters
# flat prior on mu
lambda <- 0
Omega <- 0
# informative prior on Sigma
Psi <- crossprod(matrix(rnorm(d^2), d, d))
nu <- 5

# sample from NIIW posterior
nsamples <- 2e3
system.time({
  siiw <- niiw.post(nsamples, X, lambda, Omega, Psi, nu, burn = 100)
})

# sample from NIW posterior
kappa <- 0
system.time({
  siw <- niw.post(nsamples, X, lambda, kappa, Psi, nu)
})

# check that posteriors are the same

# p(mu | X)
clrs <- c("black", "red")
par(mar = c(4.2, 4.2, 2, 1)+.1)
niche.par.plot(list(siiw, siw), col = clrs, plot.mu = TRUE, plot.Sigma = FALSE)
legend(x = "topright", legend = c("NIIW Prior", "NIW Prior"), fill = clrs)

# p(Sigma | X)
par(mar = c(4.2, 4.2, 2, 1)+.1)
niche.par.plot(list(siiw, siw), col = clrs, plot.mu = FALSE, plot.Sigma = TRUE)
legend(x = "topright", legend = c("NIIW Prior", "NIW Prior"), fill = clrs)

nicheROVER documentation built on June 4, 2021, 1:09 a.m.