boxplot.timeSpent {cfda}

Boxplot of time spent in each state

Description

Boxplot of time spent in each state

Usage

## S3 method for class 'timeSpent'
boxplot(x, col = NULL, ...)

Arguments

x

output of compute_time_spent function

col

a vector containing color for each state

...

extra parameters for geom_boxplot

Value

a ggplot object that can be modified using ggplot2 package.

Author(s)

Quentin Grimonprez

See Also

compute_time_spent

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

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

# compute time spent by each id in each state
timeSpent <- compute_time_spent(d_JK2)

# plot the result
boxplot(timeSpent, col = c("#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F"))

# modify the plot using ggplot2
library(ggplot2)
boxplot(timeSpent, notch = TRUE, outlier.colour = "black") +
  coord_flip() +
  labs(title = "Time spent in each state")