get_encoding {cfda} | R Documentation |
Extract the computed encoding
Description
Extract the encoding as an fd
object or as a matrix
Usage
get_encoding(x, harm = 1, fdObject = FALSE, nx = NULL)
Arguments
x |
Output of |
harm |
harmonic to use for the encoding |
fdObject |
If TRUE returns a |
nx |
(Only if |
Details
The encoding is a_{x} \approx \sum_{i=1}^m \alpha_{x,i}\phi_i
.
Value
a fd
object or a list of two elements y
, a matrix with nx
rows containing
the encoding of the state and x
, the vector with time values.
Author(s)
Cristian Preda
See Also
Other encoding functions:
compute_optimal_encoding()
,
plot.fmca()
,
plotComponent()
,
plotEigenvalues()
,
predict.fmca()
,
print.fmca()
,
summary.fmca()
Examples
# Simulate the Jukes-Cantor model of nucleotide replacement
K <- 4
Tmax <- 6
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 = Tmax)
d_JK2 <- cut_data(d_JK, Tmax)
# create basis object
m <- 6
b <- create.bspline.basis(c(0, Tmax), nbasis = m, norder = 4)
# compute encoding
encoding <- compute_optimal_encoding(d_JK2, b, computeCI = FALSE, nCores = 1)
# extract the encoding using 1 harmonic
encodFd <- get_encoding(encoding, fdObject = TRUE)
encodMat <- get_encoding(encoding, nx = 200)
[Package cfda version 0.11.0 Index]