plotIndicatorsReconstruction: Plot reconstructed indicators

In cfda: Categorical Functional Data Analysis

Plot reconstructed indicators

Description

Plot reconstructed indicators

Usage

plotIndicatorsReconstruction(reconstruction, id, states = NULL)

Arguments

reconstruction	output of reconstructIndicators
id	id of the individual to plot. id must be in reconstruction$id
states	states to plot, by default all states are plotted

Value

ggplot

Author(s)

Quentin Grimonprez

See Also

reconstructIndicators

Examples

set.seed(42)
# Simulate the Jukes-Cantor model of nucleotide replacement
K <- 3
Tmax <- 1
d_JK <- generate_Markov(n = 100, K = K, Tmax = Tmax)
d_JK2 <- cut_data(d_JK, Tmax)

# create basis object
m <- 20
b <- create.bspline.basis(c(0, Tmax), nbasis = m, norder = 4)

# compute encoding
encoding <- compute_optimal_encoding(d_JK2, b, computeCI = FALSE, nCores = 1)

indicators <- reconstructIndicators(encoding)

# we plot the first path and its reconstructed indicators
iInd <- 3
plotData(d_JK2[d_JK2$id == iInd, ])

plotIndicatorsReconstruction(indicators, id = iInd)

# the column state contains the state associated with the greatest indicator.
# So, the output can be used with plotData function
plotData(remove_duplicated_states(indicators[indicators$id == iInd, ]))

cfda documentation built on April 3, 2025, 9:21 p.m.