Description Usage Arguments Details Value Author(s) See Also Examples
AIC
1 |
seq |
List of sequence(s) |
E |
Vector of state space of length S |
mu |
Vector of initial distribution |
Ptrans |
Matrix of transition probabilities of the embedded Markov chain J=(J_m)_{m} |
distr |
- "NP" for nonparametric case, laws have to be used, param is useless - Matrix of distributions of size SxS if TypeSojournTime is equal to "fij"; - Vector of distributions of size S if TypeSojournTime is equal to "fi" or "fj"; - A distribution if TypeSojournTime is equal to "f". The distributions to be used in distr must be one of "uniform", "geom", "pois", "dweibull", "nbinom". |
param |
- Useless if distr = "NP" - Array of distribution parameters of size SxSx2 (2 corresponds to the maximal number of distribution parameters) if TypeSojournTime is equal to "fij"; - Matrix of distribution parameters of size Sx2 if TypeSojournTime is equal to "fi" or "fj"; - Vector of distribution parameters of length 2 if TypeSojournTime is equal to "f". |
laws |
- Useless if distr \neq "NP" - Array of size SxSxKmax if TypeSojournTime is equal to "fij"; - Matrix of size SxKmax if TypeSojournTime is equal to "fi" or "fj"; - Vector of length Kmax if the TypeSojournTime is equal to "f". Kmax is the maximum length of the sojourn times. |
TypeSojournTime |
Character: "fij", "fi", "fj", "f" |
AIC(M) = -2*log{L} + 2*M, where L is the log-likelihood, M is the number of parameters of the model.
AIC |
List: value of AIC for each sequence |
Vlad Stefan Barbu, barbu@univ-rouen.fr
Caroline Berard, caroline.berard@univ-rouen.fr
Dominique Cellier, dominique.cellier@laposte.net
Mathilde Sautreuil, mathilde.sautreuil@etu.univ-rouen.fr
Nicolas Vergne, nicolas.vergne@univ-rouen.fr
simulSM, estimMk, simulMk, estimSM, LoglikelihoodSM, LoglikelihoodMk, AIC_Mk
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 | alphabet = c("a","c","g","t")
S = length(alphabet)
## creation of the initial distribution
vect.init = c(1/4,1/4,1/4,1/4)
# creation of the transition matrix
Pij = matrix(c(0,0.2,0.3,0.5,0.4,0,0.2,0.4,0.1,0.2,0,0.7,0.8,0.1,0.1,0),
nrow = S, ncol = S, byrow = TRUE)
#Pij
# [,1] [,2] [,3] [,4]
#[1,] 0.0 0.2 0.3 0.5
#[2,] 0.4 0.0 0.2 0.4
#[3,] 0.1 0.2 0.0 0.7
#[4,] 0.8 0.1 0.1 0.0
################################
## Parametric simulation of several trajectories (3 trajectories of length 1000, 10 000
## and 2000 respectively)
## with sojourn times depending on the present state and on the next state
## the sojourn times are modelled by different distributions
################################
lengthSeq3 = c(1000, 10000, 2000)
## creation of the distribution matrix
distr.matrix = matrix(c("dweibull", "pois", "geom", "nbinom", "geom", "nbinom",
"pois", "dweibull", "pois", "pois", "dweibull", "geom", "pois","geom", "geom",
"nbinom"), nrow = S, ncol = S, byrow = TRUE)
## creation of an array containing the parameters
param1.matrix = matrix(c(0.6,2,0.4,4,0.7,2,5,0.6,2,3,0.6,0.6,4,0.3,0.4,4),
nrow = S, ncol = S, byrow = TRUE)
param2.matrix = matrix(c(0.8,0,0,2,0,5,0,0.8,0,0,0.8,0,4,0,0,4),
nrow = S, ncol = S, byrow = TRUE)
param.array = array(c(param1.matrix, param2.matrix), c(S,S,2))
### simulation of 3 sequences
seq3 = simulSM(E = alphabet, NbSeq = 3, lengthSeq = lengthSeq3,
TypeSojournTime = "fij", init = vect.init, Ptrans = Pij, distr = distr.matrix,
param = param.array, File.out = NULL)
#################################
## Computation of AIC
#################################
AIC_SM(seq = seq3, E = alphabet, mu = rep(1/4,4), Ptrans = Pij, distr = distr.matrix,
param = param.array, TypeSojournTime = "fij")
#[[1]]
#[1] 1566.418
#
#[[2]]
#[1] 15683.48
#
#[[3]]
#[1] 3146.728
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