cfda (version 0.12.1)

plot.pt: Plot probabilities

Description

Plot the probabilities of each state at each given time

Usage

# S3 method for pt
plot(x, col = NULL, ribbon = FALSE, ...)

Value

a ggplot object that can be modified using ggplot2 package.

Arguments

x

output of estimate_pt

col

a vector containing color for each state

ribbon

if TRUE, use ribbon to plot probabilities

...

only if ribbon = TRUE, parameter addBorder, if TRUE, add black border to the ribbons.

Author

Quentin Grimonprez

See Also

estimate_pt

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

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)

d_JK2 <- cut_data(d_JK, 10)

pt <- estimate_pt(d_JK2)

plot(pt, ribbon = TRUE)