MCMCStateVector: Construct a MCMC state vector.

In venelin/PCMBayes: Bayesian inference for multivariate Phylogenetic Comparative Models

Description

Construct a MCMC state vector.

Usage

MCMCStateVector(K, n, l, r, m, v)

Arguments

K	an integer (see Details).
n	an integer vector of length K denoting shift nodes (see Details).
l	a real vector of length K (see Details).
r	an integer vector of length K (see Details).
m	an integer vector of length R, where R denotes the total number of regimes (see Details).
v	a real vector of length P, where P denotes the total number of numeric parameters of the MCMC model represented by the state (see Details).

Details

The MCMCState of an MCMC is represented by a numerical vector:

\vec{s}=(K, n_2,...,n_{K+1}, l_2,...,l_{K+1}, r_2,...,r_{K+1}, m_1,...,m_R, v_1,...,v_P)^T

The element of this vector are described as follows:

K:

number of shifts;

(n_2,...,n_{K+1})^T:

shift nodes - the shifts in the model occur at points within the branches leading to the shift nodes in tip-ward direction. The corresponding locations of these points are specified by (l_2,...,l_{K+1})^T. The nodes (n_2,...,n_{K+1})^T should be ordered according to PCMTreePreorder(ctx$tree).

(l_2,...,l_{K+1})^T:

offset of the shift points measured as distances from the beginnings of the branches leading to shift nodes in tip-ward direction.

(r_2,...,r_{K+1})^T:

regime index vector. This is an integer vector with elements among (N+1,n_2,...,n_{K+1})^T, indicating the regime associated with each part in the tree. The regimes are named as the shift nodes, with N+1 corresponding to the part (and regime) originating at the root. It is possible to have lumped regimes, that is, different parts of the tree having the same regime. This regime-lumping must obey the following rules:

1. neighbor parts cannot have a lumped regime. Two parts originating at nodes n_i and n_j in the tree are called neighbor parts if they are separated solely by n_i or by n_j;

2. to resolve the conflict between the shift nodes of the different parts covered by a lumped regime, it is established that the name of a lumped regime must equal the shift-node that appears first, according to PCMTreePreorder(ctx$tree).

(m_1,...,m_R)^T:

model type assignment to the unique regimes. This is an integer vector with elements between 1 and M, M denoting the total number of model types possible. Each element corresponds to an element in unique(c(N+1,r_2,...,r_{K+1}))

(v_1,...,v_P)^T:

real numbers passed to PCMParamLoadOrStore. This is a vectorized form of all model parameters.

Value

a numerical vector representing the concatenation of K, n, l, r, m, v, with S3 class set to 'MCMCStateVector'.

See Also

MCMCState

venelin/PCMBayes documentation built on Dec. 23, 2019, 6:39 p.m.