construct.rates.setup: Get a rate matrix design setup object

In cthmm: Latent Continuous Time Markov Chains

Description

Rates are defined as log(theta_ij)=W^T Beta, where W are predictors for rate entry i,j

Usage

  construct.rates.setup(num.states = NULL,
    transition.codes = NULL, fixed.rates = NULL,
    design.matrix = NULL, covariate.array = NULL,
    deriv.array = NULL, param.values = NULL,
    param.types = NULL, variable.predictors = NULL)

Arguments

num.states	number of hidden states
transition.codes	matrix with columns "ni" and "nj" for each non-zero i,j transition intensity
fixed.rates	optional rate matrix with fixed entries (same for all individuals)
design.matrix	array of dim(num beta parameters, num.non.zero.transitions) that encodes the variables/constants used in linear predictors of log(rates). Variables are named, and constants are entered as constants. The rows correspond to the transitions in the transition.codes entry.
covariate.array	(dim=c(num.betas,num.thetas, num.subjects)) with covariates values for all subjects
deriv.array
param.values	inital or fixed values of beta parameters
param.types	a vector of length(num.beta.parameters), with entries=0 if parameter is free, 1 if fixed at param.value.
variable.predictors	matrix with columns "i" and "j" that encode the variable predictors in the design.matrix

Value

rate.setup object

Author(s)

Jane Lange

cthmm documentation built on May 2, 2019, 5:46 p.m.