estimate_Markov {cfda}

Estimate transition matrix and spent time

Description

Calculates crude initial values for transition intensities by assuming that the data represent the exact transition times of the Markov process.

Usage

estimate_Markov(data)

Arguments

data

data.frame containing id, id of the trajectory, time, time at which a change occurs and state, associated state.

Value

list of two elements: Q, the estimated transition matrix, and lambda, the estimated time spent in each state

Author(s)

Cristian Preda

See Also

plot.Markov

Examples

# Simulate the Jukes-Cantor model of nucleotide replacement
K <- 4
PJK <- matrix(1 / 3, nrow = K, ncol = K) - diag(rep(1 / 3, K))
lambda_PJK <- c(1, 1, 1, 1)
d_JK <- generate_Markov(n = 100, K = K, P = PJK, lambda = lambda_PJK, Tmax = 10)

# estimation
mark <- estimate_Markov(d_JK)
mark$P
mark$lambda