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```
#######################################################################
# rEMM - Extensible Markov Model (EMM) for Data Stream Clustering in R
# Copyright (C) 2011 Michael Hahsler
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License along
# with this program; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
## Simple Markov Chain for EMM
## to make it fast we don't use generics but use a smc_prefix
## Creator
SimpleMC <- function(size = 10L) {
size <- as.integer(size)
new(
"SimpleMC",
unused = size:1,
top = size,
counts = matrix(0, ncol = size, nrow = size),
initial_counts = structure(rep(0, size),
names = rep(NA, size))
)
}
smc_size <- function(x) {
length(x@unused) - x@top
}
## state names are stored as names of the initial counts!!!
smc_states <- function(x, ...) {
names(x@initial_counts)[!is.na(names(x@initial_counts))]
}
smc_names2index <- function(x, state) {
match(state, names(x@initial_counts))
}
smc_expand <- function(x) {
old_size <- length(x@initial_counts)
new_x <- SimpleMC(old_size * 2L)
new_x@counts[1:old_size, 1:old_size] <- x@counts
new_x@initial_counts[1:old_size] <- x@initial_counts
names(new_x@initial_counts)[1:old_size] <-
names(x@initial_counts)
new_x@top <- old_size + x@top
new_x@unused[(old_size + 1):length(new_x@unused)] <- x@unused
new_x
}
smc_compact <- function(x) {
keep <- !is.na(names(x@initial_counts))
x@counts <- x@counts[keep, keep, drop = FALSE]
x@initial_counts <- x@initial_counts[keep]
x@top <- 0L
x@unused <- rep(NA_integer_, length(x@initial_counts))
x
}
smc_addState <- function(x, state) {
state <- unique(state)
if (any(smc_containsState(x, state))) {
cont <- smc_containsState(x, state)
warning("State ", state[cont], " already exists! (not added)")
state <- state[-cont]
}
## expand if necessary (we double the size)
## Note: it would make sense to implements shrink
while (x@top < length(state))
x <- smc_expand(x)
pos <- x@unused[(x@top - length(state) + 1L):x@top]
x@unused[(x@top - length(state) + 1L):x@top] <- NA
x@top <- x@top - length(state)
names(x@initial_counts)[pos] <- state
## we don't need to clean up counts. removeState does it!
## we don't need to initialize x@initial_counts[pos] <- 0
x
}
smc_removeState <- function(x, state) {
pos <- smc_names2index(x, state)
if (any(is.na(pos))) {
missing <- is.na(pos)
warning("State ", state[missing], " does not exist!")
pos <- pos[!missing]
state <- state[!missing]
if (length(pos) < 1)
return(x)
}
## clean matrix
x@counts[pos, ] <- 0
x@counts[, pos] <- 0
old_top <- x@top
x@initial_counts[pos] <- 0
names(x@initial_counts)[pos] <- NA
x@top <- x@top + length(pos)
x@unused[(old_top + 1):x@top] <- pos
x
}
smc_addTransition <- function(x, from, to, w = 1) {
pos_f <- smc_names2index(x, from)
pos_t <- smc_names2index(x, to)
if (length(pos_f) != length(pos_t))
stop("Lengths do not match!")
if (length(pos_f) != length(w))
w <- rep.int(w[1], length(pos_f))
missing <- is.na(pos_f) | is.na(pos_t)
if (any(missing)) {
warning("Some states do not exist (edge not added)!")
}
for (i in 1:length(pos_f))
x@counts[pos_f[i], pos_t[i]] <- x@counts[pos_f[i], pos_t[i]] + w[i]
x
}
smc_setTransitions <- function(x, from, to, value = 0) {
pos_f <- smc_names2index(x, from)
pos_t <- smc_names2index(x, to)
if (length(pos_f) != length(pos_t))
stop("Lengths do not match!")
if (length(pos_f) != length(value))
value <- rep.int(value[1], length(pos_f))
missing <- is.na(pos_f) | is.na(pos_t)
if (any(missing)) {
warning("Some states do not exist (edge not added)!")
}
for (i in 1:length(pos_f))
x@counts[pos_f[i], pos_t[i]] <- value[i]
x
}
smc_removeSelfTransition <- function(x) {
diag(x@counts) <- 0
x
}
smc_removeTransition <- function(x, from, to) {
pos_f <- smc_names2index(x, from)
pos_t <- smc_names2index(x, to)
x@counts[cbind(pos_f, pos_t)] <- 0
x
}
smc_mergeStates <- function(x, state) {
pos <- smc_names2index(x, state)
if (any(is.na(pos))) {
missing <- is.na(pos)
warning("Some states do not exist (merge might fail)!")
state <- state[!missing]
pos <- pos[!missing]
}
if (length(pos) < 2) {
warning("Need at least 2 states to merge!")
return(x)
}
to <- pos[1]
## initial counts
x@initial_counts[to] <- sum(x@initial_counts[pos])
## update matrix
x@counts[to, ] <- colSums(x@counts[pos, ])
x@counts[, to] <- rowSums(x@counts[, pos])
## remove additional states
x <- smc_removeState(x, state[-1])
x
}
smc_fade <- function(x, f) {
x@counts <- x@counts * f
x@initial_counts <- x@initial_counts * f
x
}
smc_countMatrix <- function(x) {
used <- !is.na(names(x@initial_counts))
if (length(used) < 1)
return(matrix(ncol = 0, nrow = 0))
m <- x@counts[used, used, drop = FALSE]
dimnames(m) <- list(names(x@initial_counts)[used],
names(x@initial_counts)[used])
m
}
smc_initialCounts <- function(x) {
x@initial_counts[!is.na(names(x@initial_counts))]
}
smc_containsState <- function(x, state) {
!is.na(match(state, names(x@initial_counts)))
}
smc_as.igraph <- function(x) {
graph.adjacency(smc_countMatrix(x), weighted = TRUE)
}
## convert to graph (needs package graph!)
smc_as.graph <- function(x) {
if (!.installed("graph"))
stop ("Package graph needed! Please install from Bioconductor.")
graph::graphAM(
adjMat = smc_countMatrix(x),
edgemode = "directed",
values = list(weight = 1)
)
}
```

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