ppmSuite (version 0.3.4)

ccp_ppm: Function that fits a multivariate correlated product partition change point model

Description

ccp_ppm is a function that fits a Bayesian product partition change point model, where the set of change point indicators between time series are correlated.

Usage

ccp_ppm(ydata, model=1,
         nu0, mu0, sigma0,
         mltypes, thetas,
         devs,
         nburn, nskip, nsave,
         verbose = FALSE)

Value

The function returns a list containing arrays filled with MCMC iterates corresponding to model parameters. In order to provide more detail, in what follows let \(M\) be the number of MCMC iterates collected. The output list contains the following:

• C. An \(M \times \{L(n - 1)\}\) matrix containing MCMC iterates associated with each series indicators of a change point. The \(m\)th row in C is divided into \(L\) blocks; the first \((n - 1)\) change point indicators for time series 1, the next \((n - 1)\) change point indicators for time series 2, and so on.

• P. An \(M \times \{L(n - 1)\}\) matrix containing MCMC iterates associated with each series probability of a change point. The \(m\)th row in P is divided into \(L\) blocks; the first \((n - 1)\) change point probabilities for time series 1, the next \((n - 1)\) change point probabilities for time series 2, and so on.

Arguments

ydata

An \(L \times n\) data matrix, where \(L\) is the number of time series and \(n\), the number of time points.

model

Determines of model fit is such that there are p_its (model=1) or only p_t (model=2)

nu0

Degrees of freedom of the multivariate Student's t-distribution (see section Details).

mu0

Location vector of dimension \(L\) (see section Details).

sigma0

Positive definite scale matrix of order \(L \times L\) (see section Details).

mltypes

Type of marginal likelihood. Currently only available is:

• mltypes = 1. Observations within a block are conditionally independent \(Normal(\mu, \sigma^2)\) variates with mean \(\mu\) and variance \(\sigma^2\). The desired marginal likelihood is obtained after integrating \((\mu, \sigma^2)\) with respect to a \(Normal-Inverse-Gamma(\mu_{0}, \kappa_{0}, \alpha_{0}, \beta_{0})\) prior.

thetas

An \(L \times q\) matrix containing hyperparameters associated with the marginal likelihood. The number of rows \((L)\) corresponds to the number of series. The number of columns \((q)\) depend on the marginal likelihood:

• If mltypes = 1, then \(q = 4\) and thetas equals the hyperparameter \((\mu_{0}, \kappa_{0}, \alpha_{0}, \beta_{0})\) of the Normal-Inverse-Gamma prior.

devs

An \(L \times (n - 1)\) matrix containing the standard deviations of the candidate density associated with the random walk Metropolis-Hastings steps for updating change point probabilities.

nburn

The number of initial MCMC iterates to be discarded as burn-in.

nskip

The amount to thinning that should be applied to the MCMC chain.

nsave

Then number of MCMC iterates to be stored.

verbose

Logical indicating whether to print to screen the MCMC progression. The default value is verbose = FALSE.

Details

As described in Quinlan et al. (add cite), for each time series \(\boldsymbol{y}_{i} = (y_{i,1}, \ldots , y_{i,n})'\):

$$\boldsymbol{y}_{i} \mid \rho_{i} \sim \prod_{j = 1}^{b_{i}}\mathcal{F}(\boldsymbol{y}_{i,j} \mid \boldsymbol{\theta}_{i})$$

$$\rho_{i} \mid (p_{i,1}, \ldots , p_{i,n-1})' \sim \prod_{t \in T_{i}}p_{i,t} \prod_{t \notin T_{i}}(1 - p_{i,t}) : T_{i} = \{\tau_{i,1}, \ldots, \tau_{i,b_{i} - 1}\}$$

$$(p_{1,t}, \ldots , p_{L,t})' \sim logit-t(\nu_{0}, \boldsymbol{\mu}_{0}, \boldsymbol{\Sigma}_{0}).$$

Here, \(\rho_{i} = \{S_{i,1}, \ldots , S_{i,b_{i}}\}\) is a partition of the set \(\{1, \ldots , n\}\) into \(b_{i}\) contiguous blocks, and \(\boldsymbol{y}_{i,j} = (y_{i,t} : t \in S_{i,j})'\). Also, \(\tau_{i,j} = \max(S_{i,j})\) and \(\mathcal{F}( \cdot \mid \boldsymbol{\theta}_{i})\) is a marginal likelihood function which depends on the nature of \(\boldsymbol{y}_{i}\), indexed by a hyperparameter \(\boldsymbol{\theta}_{i}\). In addition, \(logit-t(\nu_{0}, \boldsymbol{\mu}_{0}, \boldsymbol{\Sigma}_{0})\) is the logit of a multivariate Student's t-distribution with degrees of freedom \(\nu_{0}\), location vector \(\boldsymbol{\mu}_{0}\) and scale matrix \(\boldsymbol{\Sigma}_{0}\).

Examples

# \donttest{
# Generate data that has two series, each with 100 observations
y1 <- replicate(25, rnorm(4, c(-1, 0, 1, 2), c(0.1, 0.25, 0.5, 0.75)))
y2 <- replicate(25, rnorm(4, c(2, 1, 0, -2), c(0.1, 0.25, 0.5, 0.75)))
y <- rbind(c(t(y1)), c(t(y2)))

# Marginal likelihood parameters
thetas <- matrix(1, nrow = 2,ncol = 4)
thetas[1,] <- c(0, 1, 2, 1)
thetas[2,] <- c(0, 1, 2, 1)

# M-H candidate density standard deviations
devs = matrix(0.1, nrow = 2, ncol = (dim(y)[2] - 1))

# Prior parameters for logit-t distribution
L <- nrow(y)
pivar <- 10
picorr <- 0.9
pimu <- rep(-6, L) # mean associated with logit of p_i
piSigma <- pivar*picorr*(rep(1, L) %*% t(rep(1, L))) +
           pivar*(1 - picorr)*diag(L)
nu0 = 3
mu0 = pimu
sigma0 = piSigma

# Fit the bayesian ppm change point model
fit <- ccp_ppm(nburn = 1000, nskip = 1, nsave = 1000, ydata = y, nu0 = nu0,
               mu0 = mu0, sigma0 = sigma0, mltypes = c(1, 1), thetas = thetas,
               devs = devs)
# }