cut_data {cfda}

Cut data to a maximal given time

Description

Cut data to a maximal given time

Usage

cut_data(
  data,
  Tmax,
  prolongLastState = "all",
  NAstate = "Not observed",
  warning = FALSE
)

Arguments

data

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

Tmax

max time considered

prolongLastState

list of states to prolong (can be "all"). In the case where the last state of a trajectory is lesser than Tmax, we can assume that this trajectory will be in the same state at time Tmax only if it is an absorbing state. Otherwise it will add NAstate and throw a warning. Set 'prolongLastState = c()' to indicate there is no absorbing state.

NAstate

state value used when the last state is not prolonged.

warning

if TRUE, the function raises warnings when it has prolonged a trajectory with NAstate

Value

a data.frame with the same format as data where each individual has Tmax as last time entry.

Author(s)

Cristian Preda

See Also

Other format: convertToCfd(), matrixToCfd(), remove_duplicated_states()

Examples

# Simulate the Jukes-Cantor model of nucleotide replacement
set.seed(42)
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)
tail(d_JK)

# cut at Tmax = 8
d_JK2 <- cut_data(d_JK, Tmax = 8)
tail(d_JK2)

# do not prolong any state
try(d_JK2 <- cut_data(d_JK, Tmax = 12, prolongLastState = c()))