Boxplot of time spent in each state
# S3 method for class 'timeSpent'
boxplot(x, col = NULL, ...)Arguments
- x
output of
compute_time_spentfunction- col
a vector containing color for each state
- ...
extra parameters for
geom_boxplot
Value
a ggplot object that can be modified using ggplot2 package.
See also
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")
#> Notch went outside hinges
#> ℹ Do you want `notch = FALSE`?
#> Notch went outside hinges
#> ℹ Do you want `notch = FALSE`?
#> Notch went outside hinges
#> ℹ Do you want `notch = FALSE`?
#> Notch went outside hinges
#> ℹ Do you want `notch = FALSE`?
