PottsUtils (version 0.3-3)

rPotts1: Generate One Random Sample from a Potts Model

Description

Generate one random sample from a Potts model with external field by Gibbs Sampling that takes advantage of conditional independence, or the partial decoupling method.

Usage

rPotts1(nvertex, ncolor, neighbors, blocks, edges=NULL, weights=1,
          spatialMat=NULL, beta, external, colors,
          algorithm=c("Gibbs", "PartialDecoupling"))

Arguments

nvertex

number of vertices in a graph.

ncolor

number of colors each vertex can take.

neighbors

all neighbors in a graph. It is not required when using the partial decoupling method.

blocks

the blocks of vertices in a graph. It is not required when using the partial decoupling method.

edges

all edges in a graph. The default value is NULL. It is not required when using Gibbs sampling.

weights

weights between neighbors or \(\delta_{ij}\)s in the partial decoupling method. When using Gibbs sampling, there is one for each corresponding component in neighbors. When using partial decoupling, there is one for each corresponding component in edges. The default values are 1s for all.

spatialMat

a matrix that describes the relationship among vertices in neighbor. It is not required when using the partial decoupling method. The default value is NULL corresponding to the simple or compound Potts model.

beta

the parameter inverse temperature of the Potts model.

external

a matrix giving values of external field. The number of rows equal to nvertex and number of columns equal to ncolor.

colors

the current colors of vertices.

algorithm

a character string specifying the algorithm used to generate samples. It must be either "Gibbs", or "PartialDecoupling", and may be abbreviated. The default is "Gibbs".

Value

The output is a vector with the kth component being the new color of vertex k.

Details

This function generates random samples from a Potts model as follows: $$ p({\bf z})=C(\beta)^{-1} \exp\{\sum_i \alpha_i(z_i) + \beta \sum_{i \sim j} w_{ij} f(z_{i},z_{j})\} $$

where \(C(\beta)\) is a normalizing constant and \(i \sim j\) indicates neighboring vertices. The parameter \(\beta\) is called the "inverse temperature", which determines the level of spatial homogeneity between neighboring vertices in the graph. We assume \(\beta > 0\). The set \({\bf z}=\{z_{1}, z_{2},\ldots,\}\) comprises the indices to the colors of all vertices. Function \(f(z_{i}, z_{j})\) determines the relationship among vertices in neighbor. Parameter \(w_{ij}\) is the weight between vertex \(i\) and \(j\). The term \(\sum_i \alpha_i(z_i)\) is called the "external field".

For the simple, the compound, and the simple repulsion Potts models, the external field is equal to 0. For the simple and the compound Potts model \(f(z_{i}, z_{j}) = I(z_{i}=z_{j})\). Parameters \(w_{ij}\) are all equal for the simple Potts model but not so for the compound model.

For the repulsion Potts model \(f(z_i , z_j) = \beta_1\) if \(z_i = z_j\); \(f(z_i , z_j) = \beta_2\) if \(|z_i - z_j| = 1\); \(f(z_i , z_j) = \beta_3\) otherwise.

The argument spatialMat is used to specify the relationship among vertices in neighbor. The default value is NULL corresponding to the simple or the compound Potts model. The component at the \(i\)th row and \(j\)th column defining the relationship when the color of a vertex is \(i\) and the color of its neighbors is \(j\). Besides the default setup, for the simple and the compound Potts models spatailMat could be an identity matrix also. For the repulsion Potts model, it is $$\left(\begin{array}{ccccc} a_1 & a_2 & a_3 & \ldots & a_3 \\ a_2 & a_1 & a_2 & \ldots & a_3 \\ \vdots & \vdots & \vdots & \ddots & \vdots \\ a_3 & a_3 & a_3 & \ldots & a_1 \end{array}\right)$$ Other relationships among neighboring vertices can be specified through it as well.

Gibbs sampling can be used to generate samples from all kinds of Potts models. We use the method that takes advantage of conditional independence to speed up the simulation. See BlocksGibbs for details.

The partial decoupling method could be used to generate samples from the simple Potts model plus the external field. The \(\delta_{ij}\)s are specified through the argument weights.

References

Dai Feng (2008) Bayesian Hidden Markov Normal Mixture Models with Application to MRI Tissue Classification Ph. D. Dissertation, The University of Iowa

David M. Higdon (1998) Auxiliary variable methods for Markov Chain Monte Carlo with applications Journal of the American Statistical Association vol. 93 585-595

See Also

BlocksGibbs, Wolff SW

Examples

# NOT RUN {
  
# }
# NOT RUN {
  neighbors <- getNeighbors(matrix(1, 16, 16), c(2,2,0,0))
  blocks <- getBlocks(matrix(1, 16, 16), 2)
  spatialMat <- matrix(c(2, 0, -1, 0, 2, 0, -1, 0, 2), ncol=3)
  mu <- c(22, 70 ,102)
  sigma <- c(17, 16, 19)
  count <- c(40, 140, 76)
  y <- unlist(lapply(1:3, function(i) rnorm(count[i], mu[i], sigma[i])))
  external <- do.call(cbind,
                      lapply(1:3, function(i) dnorm(y, mu[i],sigma[i])))
  current.colors <- rep(1:3, count)
  rPotts1(nvertex=16^2, ncolor=3, neighbors=neighbors, blocks=blocks,  
          spatialMat=spatialMat, beta=0.3, external=external,
          colors=current.colors, algorithm="G")
  edges <- getEdges(matrix(1, 16, 16), c(2,2,0,0))
  rPotts1(nvertex=16^2, ncolor=3, edges=edges, beta=0.3,
          external=external, colors=current.colors, algorithm="P")
 
# }