Table of transitions — statetable • cfda

Calculates a frequency table counting the number of times each pair of states were observed in successive observation times.

statetable(data, removeDiagonal = FALSE)

Arguments

data: data.frame containing id, id of the trajectory, time, time at which a change occurs and state, associated state.
removeDiagonal: if TRUE, does not count transition from a state i to i

Value

a matrix of size K*K containing the number of transition for each pair

See also

Other Descriptive statistics: boxplot.timeSpent(), compute_duration(), compute_number_jumps(), compute_time_spent(), estimate_pt(), hist.duration(), hist.njump(), plot.pt(), plotData(), summary_cfd()

Author

Quentin Grimonprez

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 = 10, K = K, P = PJK, lambda = lambda_PJK, Tmax = 10)

# table of transitions
statetable(d_JK)
#>    1  2  3  4
#> 1  0  9 11 12
#> 2  6  0  6 10
#> 3  7 10  0  4
#> 4 10  6  7  0